From 9d08999413908008a7f275b6bbc95ff56c1fc4f5 Mon Sep 17 00:00:00 2001
From: yanzihan <yanzihan@westlake.edu.cn>
Date: Sat, 6 Jun 2026 11:21:11 +0800
Subject: [PATCH 01/24] update

---
 src/f3_workflows.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/f3_workflows.sh b/src/f3_workflows.sh
index 581668e..5794c27 100644
--- a/src/f3_workflows.sh
+++ b/src/f3_workflows.sh
@@ -39,7 +39,7 @@ echo " ---------------------------------------------------"
 # SCF batch pretreatment (main function)
 function f301_scf_batch_pretreatment(){ 
     echo " +-------------------------------------------------------------+"
-    echo " |                 SCF BATCH PRETREATMENT TOOLS               |"
+    echo " |                 SCF BATCH PRETREATMENT TOOLS                |"
     echo " +-------------------------------------------------------------+"
     echo " | 1) VASP SCF batch pretreatment                              |"
     echo " | 2) CP2K SCF batch pretreatment                              |"

From 906510e2b0fd0a800ecb70092225a8560ba9adf7 Mon Sep 17 00:00:00 2001
From: Xin Wu <xinwu@iis.u-tokyo.ac.jp>
Date: Thu, 11 Jun 2026 22:57:49 +0900
Subject: [PATCH 02/24] Fix the bug in EMD-plot

---
 Scripts/plt_scripts/plt_emd.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Scripts/plt_scripts/plt_emd.py b/Scripts/plt_scripts/plt_emd.py
index 0514d11..2450ebe 100644
--- a/Scripts/plt_scripts/plt_emd.py
+++ b/Scripts/plt_scripts/plt_emd.py
@@ -59,7 +59,7 @@ def process(self):
         with open(self.path['run'], 'r') as file:
             for line in file:
                 if 'time_step' in line:
-                    time_step = int(line.split()[1])
+                    time_step = float(line.split()[1])
                 if 'compute_hac' in line:
                     N_hac_data = int(int(line.split()[2]) / int(line.split()[3]))
                     Max_cor_time = int(int(line.split()[1]) * int(line.split()[2]))
@@ -67,7 +67,7 @@ def process(self):
         N_repeat = len(raw_data) // N_hac_data
         if len(raw_data) % N_hac_data != 0:
             raise ValueError(f"The MD calculation seems to be not completed, please check it!")
-        Time_upper = Max_cor_time * 1e-6  # ns
+        Time_upper = Max_cor_time * time_step * 1e-6  # ns
 
         # Classify and process data initially
         for col in raw_data.columns:

From c5665b904fffe59472588717394a40704f4f2f7a Mon Sep 17 00:00:00 2001
From: Xin Wu <xinwu@iis.u-tokyo.ac.jp>
Date: Fri, 12 Jun 2026 11:10:46 +0900
Subject: [PATCH 03/24] Fix the bug in NEMD-plot without SHC

---
 Scripts/plt_scripts/plt_nemd.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/Scripts/plt_scripts/plt_nemd.py b/Scripts/plt_scripts/plt_nemd.py
index f40ea82..2a9aa37 100644
--- a/Scripts/plt_scripts/plt_nemd.py
+++ b/Scripts/plt_scripts/plt_nemd.py
@@ -35,7 +35,7 @@ def print_usage():
     print("                     - S_eff: real or effective area of the system")
     print("  cutoff_freq   : Optional, Cutoff frequency for SHC calculation in THz (default: 60)")
     print("  save          : Optional, save the plot as 'nemd.png'")
-    print("  !!! Note !!!  : If no SHC data, set [scale_eff_size] and [cutoff_freq] to any number as placeholders when using 'save'.")
+    print("  !!! Note !!!  : If no SHC data, set [scale_eff_size] and [cutoff_freq] to any non-zero number as placeholders when using 'save'.")
 
 class NEMD_Processor:
     def __init__(self, _directory, _real_length=None, _scale_eff_size=1, _cutoff_freq=60, _scale_vacuum=1):
@@ -164,6 +164,7 @@ def process(self):
         Reformed_NEMD_data = {}
 
         # Get parameters from run.in
+        direction = None  # heat transfer axis; set by compute_shc, else auto-detected below
         with open(self.path['run'], 'r') as file:
             found_nemd = False
             for line in file:
@@ -210,6 +211,14 @@ def process(self):
             group = group_arr
         else:
             group = group_arr[:, 0]
+
+        if direction is None:
+            # No compute_shc in run.in: infer the heat transfer axis as the
+            # Cartesian direction where the source/sink groups are most separated
+            heat_pos = model.positions[(group == 1)].mean(axis=0)
+            cold_pos = model.positions[(group == N_temp_group - 1)].mean(axis=0)
+            direction = int(np.argmax(np.abs(heat_pos - cold_pos)))
+
         coords_heat = model.positions[(group == 1), direction].mean()
         coords_cold = model.positions[(group == N_temp_group - 1), direction].mean()
         xticks_length = np.linspace(coords_heat, coords_cold, N_temp_group - 1) * 0.1

From e2ddddbcc5284f690b9ad116adf4c6784caaee69 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Tue, 16 Jun 2026 21:12:51 +0800
Subject: [PATCH 04/24] fix: remove unnecessary chmod in update function to
 avoid git tracking permission changes

---
 Scripts/utils/update_gpumdkit.sh | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/Scripts/utils/update_gpumdkit.sh b/Scripts/utils/update_gpumdkit.sh
index da7e1ee..aefb60d 100644
--- a/Scripts/utils/update_gpumdkit.sh
+++ b/Scripts/utils/update_gpumdkit.sh
@@ -45,21 +45,10 @@ if [ "$local_commit" = "$remote_commit" ]; then
     echo "No updates available: Local $current_branch branch is up to date."
 else
     echo "Updates detected, pulling latest code for branch $current_branch..."
-    # Update permissions and pull code
-    if [ -f "gpumdkit.sh" ]; then
-        chmod -x gpumdkit.sh
-    else
-        echo "Warning: gpumdkit.sh not found, skipping permission change."
-    fi
 
     # Pull latest code
     if git pull origin "$current_branch"; then
         echo "Code successfully updated."
-        # Restore executable permission for gpumdkit.sh
-        if [ -f "gpumdkit.sh" ]; then
-            chmod +x gpumdkit.sh
-            echo "Restored executable permission for gpumdkit.sh."
-        fi
     else
         echo "Error: Failed to pull code. Check Git configuration or network connection."
         exit 1

From 05488a3f9408a2889279aecd27d93929c28291d4 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Tue, 16 Jun 2026 21:41:02 +0800
Subject: [PATCH 05/24] refactor: standardize argument checks and CLI usage in
 format_conversion scripts

- Add sys.argv parameter validation to all Python scripts
- Add dual usage hints (python xx.py / gpumdkit.sh -xx)
- Convert xdatcar2exyz.py from argparse to sys.argv for consistency
- Fix traj2exyz.py to exit on invalid arguments instead of continuing
- All prompts and comments in English
---
 Scripts/format_conversion/abacus2xyz_scf.py   |  1 +
 Scripts/format_conversion/add_groups.py       |  6 +++++
 Scripts/format_conversion/add_weight.py       |  3 ++-
 Scripts/format_conversion/cif2exyz.py         |  3 ++-
 Scripts/format_conversion/cif2pos.py          |  3 ++-
 Scripts/format_conversion/clean_xyz.py        |  6 +++++
 Scripts/format_conversion/exyz2pos.py         |  8 +++++-
 Scripts/format_conversion/get_frame.py        |  6 +++++
 Scripts/format_conversion/lmp2exyz.py         |  3 ++-
 Scripts/format_conversion/mtp2xyz.py          |  5 ++++
 Scripts/format_conversion/out2exyz.py         |  6 +++++
 Scripts/format_conversion/pos2exyz.py         |  5 ++--
 Scripts/format_conversion/pos2lmp.py          |  1 +
 Scripts/format_conversion/replicate.py        |  6 +++--
 Scripts/format_conversion/split_single_xyz.py |  2 +-
 Scripts/format_conversion/traj2exyz.py        | 13 ++++-----
 Scripts/format_conversion/xdatcar2exyz.py     | 27 +++++++++----------
 17 files changed, 73 insertions(+), 31 deletions(-)

diff --git a/Scripts/format_conversion/abacus2xyz_scf.py b/Scripts/format_conversion/abacus2xyz_scf.py
index 07b8051..906c495 100644
--- a/Scripts/format_conversion/abacus2xyz_scf.py
+++ b/Scripts/format_conversion/abacus2xyz_scf.py
@@ -26,6 +26,7 @@
 def main():
     if len(sys.argv) != 3:
         print("Usage: python abacus2xyz_scf.py <dir> <extxyz>")
+        print("   or: gpumdkit.sh -abacus2xyz <dir> <extxyz>")
         sys.exit(1)
 if __name__ == "__main__":
     main()
diff --git a/Scripts/format_conversion/add_groups.py b/Scripts/format_conversion/add_groups.py
index c0bcd2f..afbe12c 100644
--- a/Scripts/format_conversion/add_groups.py
+++ b/Scripts/format_conversion/add_groups.py
@@ -24,6 +24,12 @@
 from ase.io import read, write
 import numpy as np
 
+# Check arguments
+if len(sys.argv) < 3:
+    print("Usage: python add_groups.py <input.xyz> <element1> <element2> ...")
+    print("   or: gpumdkit.sh -addgroup <input.xyz> <element1> <element2> ...")
+    sys.exit(1)
+
 # Read the file name from command line arguments
 file_name = sys.argv[1]
 
diff --git a/Scripts/format_conversion/add_weight.py b/Scripts/format_conversion/add_weight.py
index ff3841b..4011e0f 100644
--- a/Scripts/format_conversion/add_weight.py
+++ b/Scripts/format_conversion/add_weight.py
@@ -28,7 +28,8 @@
 def main():
     # Check if the correct number of arguments are provided
     if len(sys.argv) != 4:
-        print("Usage: python script.py <input_file> <output_file> <new_weight>")
+        print("Usage: python add_weight.py <input.xyz> <output.xyz> <weight>")
+        print("   or: gpumdkit.sh -addweight <input.xyz> <output.xyz> <weight>")
         sys.exit(1)
 
     # Parse command line arguments
diff --git a/Scripts/format_conversion/cif2exyz.py b/Scripts/format_conversion/cif2exyz.py
index 6b0ac7c..0f56b72 100644
--- a/Scripts/format_conversion/cif2exyz.py
+++ b/Scripts/format_conversion/cif2exyz.py
@@ -24,7 +24,8 @@
 
 # Check command line arguments
 if len(sys.argv) != 3:
-    print(" Usage: python cif2exyz.py input.cif output.xyz")
+    print("Usage: python cif2exyz.py <input.cif> <output.xyz>")
+    print("   or: gpumdkit.sh -cif2exyz <input.cif> <output.xyz>")
     sys.exit(1)
 
 # Read input and output file paths
diff --git a/Scripts/format_conversion/cif2pos.py b/Scripts/format_conversion/cif2pos.py
index 8657fc6..8624acc 100644
--- a/Scripts/format_conversion/cif2pos.py
+++ b/Scripts/format_conversion/cif2pos.py
@@ -24,7 +24,8 @@
 
 # Check command line arguments
 if len(sys.argv) != 3:
-    print(" Usage: python cif2poscar.py input.cif output.vasp")
+    print("Usage: python cif2pos.py <input.cif> <output.vasp>")
+    print("   or: gpumdkit.sh -cif2pos <input.cif> <output.vasp>")
     sys.exit(1)
 
 # Read input and output file paths
diff --git a/Scripts/format_conversion/clean_xyz.py b/Scripts/format_conversion/clean_xyz.py
index 2ae4e97..c9767d2 100644
--- a/Scripts/format_conversion/clean_xyz.py
+++ b/Scripts/format_conversion/clean_xyz.py
@@ -23,6 +23,12 @@
 from ase.io import read, write
 import sys
 
+# Check arguments
+if len(sys.argv) < 3:
+    print("Usage: python clean_xyz.py <input.xyz> <output.xyz>")
+    print("   or: gpumdkit.sh -clean_xyz <input.xyz> <output.xyz>")
+    sys.exit(1)
+
 # Read all frames from the input train.xyz file
 frames = read(sys.argv[1], index=':')
 
diff --git a/Scripts/format_conversion/exyz2pos.py b/Scripts/format_conversion/exyz2pos.py
index 092f680..3f1b19b 100644
--- a/Scripts/format_conversion/exyz2pos.py
+++ b/Scripts/format_conversion/exyz2pos.py
@@ -30,7 +30,13 @@ def print_progress_bar(iteration, total, length=50):
     if iteration == total:
         print()
 
-input_file = sys.argv[1] if len(sys.argv) > 1 else 'train.xyz'
+# Check arguments
+if len(sys.argv) < 2:
+    print("Usage: python exyz2pos.py <input.xyz>")
+    print("   or: gpumdkit.sh -exyz2pos <input.xyz>")
+    sys.exit(1)
+
+input_file = sys.argv[1]
 
 # Read all frames
 frames = read(input_file, index=':')
diff --git a/Scripts/format_conversion/get_frame.py b/Scripts/format_conversion/get_frame.py
index 23e9971..10ead91 100644
--- a/Scripts/format_conversion/get_frame.py
+++ b/Scripts/format_conversion/get_frame.py
@@ -22,6 +22,12 @@
 import sys
 from ase.io import read, write
 
+# Check arguments
+if len(sys.argv) < 3:
+    print("Usage: python get_frame.py <input.xyz> <frame_number>")
+    print("   or: gpumdkit.sh -get_frame <input.xyz> <frame_number>")
+    sys.exit(1)
+
 def get_frame():
     input_file = sys.argv[1]
     frame_number = int(sys.argv[2])
diff --git a/Scripts/format_conversion/lmp2exyz.py b/Scripts/format_conversion/lmp2exyz.py
index 4533a91..08f9ad4 100644
--- a/Scripts/format_conversion/lmp2exyz.py
+++ b/Scripts/format_conversion/lmp2exyz.py
@@ -48,7 +48,8 @@ def lmp2exyz(dump_file, elements):
 
 if __name__ == '__main__':
     if len(sys.argv) < 3:
-        print(" Usage: python lmp2exyz.py <dump_file> <element1> <element2> ...")
+        print("Usage: python lmp2exyz.py <dump_file> <element1> <element2> ...")
+        print("   or: gpumdkit.sh -lmp2exyz <dump_file> <element1> <element2> ...")
         sys.exit(1)
     
     dump_file = sys.argv[1]
diff --git a/Scripts/format_conversion/mtp2xyz.py b/Scripts/format_conversion/mtp2xyz.py
index dd2d840..aca1e12 100644
--- a/Scripts/format_conversion/mtp2xyz.py
+++ b/Scripts/format_conversion/mtp2xyz.py
@@ -132,6 +132,11 @@ def dump_xyz(frames):
 
 
 if __name__ == "__main__":
+    # Check arguments
+    if len(sys.argv) < 3:
+        print("Usage: python mtp2xyz.py <train.cfg> <Symbol1> <Symbol2> ...")
+        sys.exit(1)
+    
     type_to_symbol = {i: s for i, s in enumerate(sys.argv[2:])}
     frames = load_cfg(sys.argv[1], type_to_symbol)
     #dump_nep(frames)
diff --git a/Scripts/format_conversion/out2exyz.py b/Scripts/format_conversion/out2exyz.py
index a46cf4f..c634115 100644
--- a/Scripts/format_conversion/out2exyz.py
+++ b/Scripts/format_conversion/out2exyz.py
@@ -23,6 +23,12 @@
 from ase import Atoms, Atom
 from tqdm import tqdm
 
+# Check arguments
+if len(sys.argv) < 2:
+    print("Usage: python out2exyz.py <directory>")
+    print("   or: gpumdkit.sh -out2exyz <directory>")
+    sys.exit(1)
+
 def Convert_atoms(atom):
     xx,yy,zz,yz,xz,xy = -atom.calc.results['stress']*atom.get_volume() 
     atom.info['virial'] = np.array([(xx, xy, xz), (xy, yy, yz), (xz, yz, zz)])
diff --git a/Scripts/format_conversion/pos2exyz.py b/Scripts/format_conversion/pos2exyz.py
index 8316016..211d450 100644
--- a/Scripts/format_conversion/pos2exyz.py
+++ b/Scripts/format_conversion/pos2exyz.py
@@ -44,9 +44,8 @@ def convert_poscar_to_extxyz(poscar_filenames, extxyz_filename):
 if __name__ == '__main__':
     # Check if the number of arguments is correct
     if len(sys.argv) < 3:
-        print("Usage: python pos2exyz.py <POSCAR> <extxyz_filename>")
-        print("Example 1: python pos2exyz.py POSCAR model.xyz")
-        # print("Example 2: python pos2exyz.py 'POSCAR*' train.xyz")
+        print("Usage: python pos2exyz.py <POSCAR> <output.xyz>")
+        print("   or: gpumdkit.sh -pos2exyz <POSCAR> <output.xyz>")
         sys.exit(1)
 
     poscar_filename_pattern = sys.argv[1]
diff --git a/Scripts/format_conversion/pos2lmp.py b/Scripts/format_conversion/pos2lmp.py
index b2cf10f..83122ae 100644
--- a/Scripts/format_conversion/pos2lmp.py
+++ b/Scripts/format_conversion/pos2lmp.py
@@ -30,6 +30,7 @@ def convert_poscar_to_lammps(poscar_path, lammps_data_path):
 if __name__ == "__main__":
     if len(sys.argv) != 3:
         print("Usage: python pos2lmp.py <poscar_file> <lammps_data_file>")
+        print("   or: gpumdkit.sh -pos2lmp <poscar_file> <lammps_data_file>")
         sys.exit(1)
     
     poscar_file = sys.argv[1]
diff --git a/Scripts/format_conversion/replicate.py b/Scripts/format_conversion/replicate.py
index 36a70f4..cb574ad 100644
--- a/Scripts/format_conversion/replicate.py
+++ b/Scripts/format_conversion/replicate.py
@@ -106,8 +106,10 @@ def reorder_atoms_by_input_species_order(atoms, original_atoms):
 
 def main():
     if len(sys.argv) < 4:
-        print(" Usage 1: python replicate.py input.vasp output.vasp a b c")
-        print(" Usage 2: python replicate.py input.vasp output.vasp target_num")
+        print("Usage 1: python replicate.py input.vasp output.vasp a b c")
+        print("Usage 2: python replicate.py input.vasp output.vasp target_num")
+        print("   or: gpumdkit.sh -replicate input.vasp output.vasp a b c")
+        print("   or: gpumdkit.sh -replicate input.vasp output.vasp target_num")
         sys.exit(1)
 
     infile = sys.argv[1]
diff --git a/Scripts/format_conversion/split_single_xyz.py b/Scripts/format_conversion/split_single_xyz.py
index 904cdb3..b862765 100644
--- a/Scripts/format_conversion/split_single_xyz.py
+++ b/Scripts/format_conversion/split_single_xyz.py
@@ -45,7 +45,7 @@ def split_xyz_to_individual_models(input_xyz_filename):
 if __name__ == '__main__':
     # Check if the number of arguments is correct
     if len(sys.argv) < 2:
-        print(" Usage: python script_name.py <input_xyz_filename>")
+        print("Usage: python split_single_xyz.py <input.xyz>")
         sys.exit(1)
 
     # Get input XYZ filename from command line argument
diff --git a/Scripts/format_conversion/traj2exyz.py b/Scripts/format_conversion/traj2exyz.py
index 9eb592b..7466b7d 100644
--- a/Scripts/format_conversion/traj2exyz.py
+++ b/Scripts/format_conversion/traj2exyz.py
@@ -47,9 +47,10 @@ def convert_traj_to_extxyz(input_file, output_file):
 if __name__ == "__main__":
     # Check if correct number of arguments are provided
     if len(sys.argv) != 3:
-        print(" Usage: python traj2exyz.py <input.traj> <output.xyz>")
-        sys.stdout.flush()
-    else:
-        input_path = sys.argv[1]
-        output_path = sys.argv[2]
-        convert_traj_to_extxyz(input_path, output_path)
\ No newline at end of file
+        print("Usage: python traj2exyz.py <input.traj> <output.xyz>")
+        print("   or: gpumdkit.sh -traj2exyz <input.traj> <output.xyz>")
+        sys.exit(1)
+    
+    input_path = sys.argv[1]
+    output_path = sys.argv[2]
+    convert_traj_to_extxyz(input_path, output_path)
\ No newline at end of file
diff --git a/Scripts/format_conversion/xdatcar2exyz.py b/Scripts/format_conversion/xdatcar2exyz.py
index 8b0b2a6..e910238 100644
--- a/Scripts/format_conversion/xdatcar2exyz.py
+++ b/Scripts/format_conversion/xdatcar2exyz.py
@@ -19,39 +19,38 @@
 =============================================================================
 """
 
-import argparse
 import sys
 from ase.io import read, write
 
-# 1. Setup Argument Parser for positional arguments
-parser = argparse.ArgumentParser(
-    description=" Convert VASP XDATCAR to extxyz format."
-)
-parser.add_argument("input", help=" Path to the input XDATCAR file")
-parser.add_argument("output", help=" Path to the output .xyz file")
+# Check arguments
+if len(sys.argv) < 3:
+    print("Usage: python xdatcar2exyz.py <XDATCAR> <output.xyz>")
+    print("   or: gpumdkit.sh -xdat2exyz <XDATCAR> <output.xyz>")
+    sys.exit(1)
 
-args = parser.parse_args()
+input_file = sys.argv[1]
+output_file = sys.argv[2]
 
-# 2. Execute conversion logic
+# Execute conversion logic
 try:
-    print(f" Reading XDATCAR: {args.input} ...")
+    print(f" Reading XDATCAR: {input_file} ...")
     
     # Read all frames from the trajectory (index=":")
     # ASE automatically parses scaling, lattice, and species
-    trajectory = read(args.input, index=":", format="vasp-xdatcar")
+    trajectory = read(input_file, index=":", format="vasp-xdatcar")
     
     num_frames = len(trajectory)
     print(f" Detected {num_frames} frames.")
     
-    print(f" Writing to extxyz: {args.output} ...")
+    print(f" Writing to extxyz: {output_file} ...")
     
     # Writing in extxyz format preserves the Lattice matrix in the header
-    write(args.output, trajectory, format="extxyz")
+    write(output_file, trajectory, format="extxyz")
     
     print(" Conversion complete.")
 
 except FileNotFoundError:
-    print(f" Error: Could not find '{args.input}'. Please check the path.")
+    print(f" Error: Could not find '{input_file}'. Please check the path.")
     sys.exit(1)
 except Exception as e:
     print(f" An unexpected error occurred: {e}")

From f61433d04112c8481f4e71a81ef3baa4afb980cd Mon Sep 17 00:00:00 2001
From: yanzihan <yanzihan@westlake.edu.cn>
Date: Wed, 17 Jun 2026 16:49:40 +0800
Subject: [PATCH 06/24] add -nep_modifier

---
 Scripts/utils/completion.sh                |   2 +-
 Scripts/utils/nep_modifier/README.md       | 298 ++++++++++++++++++
 Scripts/utils/nep_modifier/README_zh-CN.md | 298 ++++++++++++++++++
 Scripts/utils/nep_modifier/nep_modifier.py | 337 +++++++++++++++++++++
 docs/updates.info                          |   7 +-
 gpumdkit.sh                                |   5 +-
 6 files changed, 941 insertions(+), 6 deletions(-)
 create mode 100644 Scripts/utils/nep_modifier/README.md
 create mode 100644 Scripts/utils/nep_modifier/README_zh-CN.md
 create mode 100644 Scripts/utils/nep_modifier/nep_modifier.py

diff --git a/Scripts/utils/completion.sh b/Scripts/utils/completion.sh
index b1f8ff5..2f4b4e4 100644
--- a/Scripts/utils/completion.sh
+++ b/Scripts/utils/completion.sh
@@ -13,7 +13,7 @@ _gpumdkit_completions() {
     prev="${COMP_WORDS[COMP_CWORD-1]}" # Previous word
 
     # List of primary options (extracted from gpumdkit.sh)
-    local opts="-h -update -help -clean -time -plt -calc -cbc -range -out2xyz -xml2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -pos2lmp -lmp2exyz -traj2exyz -cp2k2xyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -get_frame -clean_xyz -get_volume -analyze_comp -replicate -hbond -pda -pynep -frame_range -chem_species -xdat2exyz"
+    local opts="-h -update -help -clean -time -plt -calc -cbc -range -out2xyz -xml2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -pos2lmp -lmp2exyz -traj2exyz -cp2k2xyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -get_frame -clean_xyz -get_volume -analyze_comp -replicate -hbond -pda -pynep -frame_range -chem_species -xdat2exyz -nep_modifier"
 
     # Provide secondary completion based on the previous word
     case "$prev" in
diff --git a/Scripts/utils/nep_modifier/README.md b/Scripts/utils/nep_modifier/README.md
new file mode 100644
index 0000000..c3bcca7
--- /dev/null
+++ b/Scripts/utils/nep_modifier/README.md
@@ -0,0 +1,298 @@
+# NEP Model Modifier
+
+> **English** | [简体中文](./README_zh-CN.md)
+
+> **WARNING**: This feature is currently in **testing**. The documentation was generated by AI and may contain errors. If you encounter any issues, please report them or join the QQ group: [825696376](https://qun.qq.com/universal-share/share?ac=1&authKey=buBNi1ADDzIFF2oZ1yA5FywG3LA9EL9yKZmb%2BN2MMz7nNuuxTas54wH7BgPEqP0s&busi_data=eyJncm91cENvZGUiOiI4MjU2OTYzNzYiLCJ0b2tlbiI6IlRxL1RLTDlOK3U2ekRSUXJ1TkNTUWd3ODNVV3BrdG9HN2lWWmJKMHAraGlDNzBZWFFyRUY2dUlSaW8rbUd4MisiLCJ1aW4iOiIxNDg5NjQ3MTc5In0%3D&data=fa4zSsT_IdI4ftCT_wwpytYHf--TaTB35lH0Jac5JHVpYoyXw3_3bZ1l1NZejsOZnGJku5u3BCbf5_bgrCkhZg&svctype=4&tempid=h5_group_info).
+
+An interactive CLI tool for modifying NEP (neuroevolution potential) models, powered by the [calorine](https://gitlab.com/materials-modeling/calorine) Python package (Lindgren et al., [JOSS, 2024, 9(95), 6264](https://doi.org/10.21105/joss.06264)). 
+
+A trained NEP model can serve as the starting point for further development rather than as a final product. Common workflows include:
+
+- **Increasing capacity**: expand the number of neurons or add higher-body descriptor terms when the initial architecture turns out to be too small.
+- **Adding a charge output**: promote a plain potential model to a charge-aware qNEP model by attaching a charge output head, then continue training with charge targets.
+- **Species manipulation**: prune a multi-element model down to a subset of elements, or extend an existing model with a new species without discarding the learned potential surface.
+- **Reducing capacity**: remove neurons or descriptor terms that contribute little to accuracy, for faster inference or as a starting point for fine-tuning on a narrower dataset.
+
+## Features
+
+| Operation | Description | Retraining Required? |
+|-----------|-------------|---------------------|
+| `augment()` | Expand neurons, descriptors, or add a charge head | Yes |
+| `prune()` | Reduce neurons, remove descriptor terms, or drop the charge head | Yes |
+| `remove_species()` | Remove one or more species | No (optional) |
+| `keep_species()` | Retain a subset of species, dropping all others | No (optional) |
+| `add_species()` | Add one or more species | Yes |
+
+All operations return a new Model instance; the source model is never modified in place.
+
+## Dependencies
+
+This tool requires the `calorine` Python package (>= 3.4).
+
+```bash
+# Option 1: Install from PyPI
+pip install 'calorine>=3.4'
+
+# Option 2: Install the latest version from GitLab
+pip install git+https://gitlab.com/materials-modeling/calorine.git@master
+```
+
+## Input Files
+
+| File | Description | Required |
+|------|-------------|----------|
+| `nep.txt` | NEP model file | Yes |
+| `nep.restart` | SNES restart file (stores optimizer state for fine-tuning) | No |
+
+The restart file stores a mean `mu` and a standard deviation `sigma` for every parameter; these are the current estimate of the SNES optimizer of the optimal value and exploration width, respectively. Loading the restart file is required for `augment`, `prune`, and `add_species` operations to properly initialize new and existing parameters.
+
+## Usage
+
+#### Interactive Mode
+
+1. Open your terminal and navigate to the directory containing your NEP model files.
+
+2. Run the tool:
+
+    ```
+    python nep_modifier.py
+    ```
+
+3. At startup, the tool displays a header with citation information, then prompts for input files. Press **Enter** to use defaults (`nep.txt nep.restart` in the current directory):
+
+    ```
+    +----------------------------------------------------+
+    |         NEP Model Modifier (calorine)              |
+    +----------------------------------------------------+
+    |  Powered by calorine package. If you use this tool,|
+    |  please cite the following papers:                 |
+    |                                                    |
+    |   Calorine: A Python package for constructing and  |
+    |      sampling neuroevolution potential models.     |
+    |   Journal of Open Source Software, 2024, 9, 6264.  |
+    |      https://doi.org/10.21105/joss.06264           |
+    +----------------------------------------------------+
+    [!] WARNING: This feature is currently in TESTING.
+    [!] The tutorial/docs were generated by AI and may contain errors.
+    [!] Report issues or join the QQ group: 825696376
+    +----------------------------------------------------+
+
+     Input <nep.txt> <nep.restart> (Enter to use defaults):
+     ------------>>
+    ```
+
+4. After loading, the tool displays model information and a menu:
+
+    ```
+     -----------------------------------------------------
+     Version          : 4
+     Model type       : potential
+     Types            : ('H', 'Li', 'B', 'N', 'O', ...)
+     Radial cutoff    : 6.0
+     Angular cutoff   : 5.0
+     n_max (rad/ang)  : 6 / 6
+     basis_size       : 6 / 6
+     l_max (3b/4b/5b) : 4 / 2 / 1
+     n_neuron         : 50
+     n_parameters     : 218858
+     -----------------------------------------------------
+
+     Choose an operation:
+     1) augment          (expand neurons/descriptors/charge)
+     2) prune            (shrink neurons/descriptors)
+     3) add_species      (add element)
+     4) remove_species   (remove element)
+     5) keep_species     (keep selected elements only)
+     6) Show model info
+     7) Export model
+     0) Exit
+     ------------>>
+    ```
+
+#### Command-Line Mode
+
+You can also launch the tool directly from `gpumdkit.sh`:
+
+```
+gpumdkit.sh -nep_modifier
+```
+
+## Operations
+
+### 1) augment - Expand Model
+
+`augment()` applies one or more structural changes atomically and returns a new model. Options:
+
+- **Increase n_neuron**: Add more neurons to the hidden layer. The existing trained weights are preserved; new neurons are initialized with `mu=0` and `sigma=sigma_new`.
+- **Increase l_max_5b**: Enable 5-body descriptor terms. This adds `n_max_angular + 1` new descriptor dimensions.
+- **Add charge_head**: Promote a plain NEP model (`potential`) to a charge-aware qNEP model (`potential_with_charges`). A second output node is added per species.
+
+After augmentation, remember to update your `nep.in` file to match the new architecture before resuming training.
+
+### 2) prune - Shrink Model
+
+`prune()` returns a new model with a smaller architecture. Options:
+
+- **Reduce n_neuron**: Neurons are ranked by importance score and the least important ones are removed.
+- **Reduce l_max_4b**: Remove 4-body descriptor terms (set to 0 to remove entirely).
+
+Surviving parameters receive adaptive SNES sigma values, re-opening the search distribution for the next training run.
+
+### 3) add_species - Add Elements
+
+Extends the model with:
+- A new per-species ANN sub-network (for each added element)
+- All new `(species_1, species_2)` descriptor weight pairs involving the new elements
+
+New parameters are initialized with `mu` drawn uniformly from [-1, 1] and `sigma = sigma_new`. The model must be trained further before the new element is meaningful.
+
+### 4) remove_species - Remove Elements
+
+Prunes all parameters associated with the listed elements: the ANN sub-networks, descriptor weight pairs, and their SNES statistics. A common use case is extracting a single-element model from a multi-element potential.
+
+### 5) keep_species - Keep Elements Only
+
+When isolating a small subset from a large foundation model, listing every species to drop via `remove_species()` is impractical. `keep_species()` accepts the elements to retain and derives the removal list automatically.
+
+## Examples
+
+#### Example 1: Extract a Sub-Model
+
+Extract Li, La, Zr, O from a 36-element foundation model:
+
+```
+ Input <nep.txt> <nep.restart> (Enter to use defaults):
+ ------------>>
+
+ Choose an operation:
+ 5) keep_species     (keep selected elements only)
+ ------------>>
+ 5
+
+ Input elements to keep (space-separated): (Li La Zr O)
+ ------------>>
+ Li La Zr O
+
+ Will keep: ['Li', 'La', 'Zr', 'O']
+ Confirm? (y/n)
+ ------------>>
+ y
+
+ Done: ('H', 'Li', ..., 'W') -> ('Li', 'O', 'Zr', 'La')
+ Params: 218858 -> 11818
+
+ Choose an operation:
+ 7) Export model
+ ------------>>
+ 7
+
+ Output directory: (.)
+ ------------>>
+ .
+
+ Written: nep_modified.txt
+ Written: nep_modified.restart
+```
+
+#### Example 2: Expand Model Capacity
+
+Increase neurons from 50 to 80 and enable 5-body descriptors:
+
+```
+ Choose an operation:
+ 1) augment          (expand neurons/descriptors/charge)
+ ------------>>
+ 1
+
+ Choose what to augment:
+ 1) Increase n_neuron
+ 2) Increase l_max_5b
+ 3) Add charge_head
+ 0) Cancel
+ ------------>>
+ 1
+
+ Input new n_neuron: (60)
+ ------------>>
+ 80
+
+ Confirm augment? (y/n)
+ ------------>>
+ y
+
+ Done: 218858 -> 345258 parameters
+```
+
+#### Example 3: Swap Elements
+
+Remove Pb and add Bi (chain operations):
+
+```
+ Choose an operation:
+ 4) remove_species   (remove element)
+ ------------>>
+ 4
+
+ Input elements to remove (space-separated):
+ ------------>>
+ Pb
+
+ Confirm? (y/n)
+ ------------>>
+ y
+
+ Done: ('Te', 'Pb') -> ('Te',)
+ Params: 2311 -> 1081
+
+ Choose an operation:
+ 3) add_species      (add element)
+ ------------>>
+ 3
+
+ Input elements to add (space-separated): (Bi Sn)
+ ------------>>
+ Bi
+
+ Confirm? (y/n)
+ ------------>>
+ y
+
+ Done: ('Te',) -> ('Te', 'Bi')
+ Params: 1081 -> 2491
+```
+
+## Output Files
+
+| File | Description |
+|------|-------------|
+| `nep_modified.txt` | Modified NEP model file |
+| `nep_modified.restart` | Updated SNES restart file (if restart was loaded) |
+| `nep_modified.in` | Training input file with updated architecture |
+
+Output files are named with a `_modified` suffix to avoid overwriting the originals. If a file with that name already exists, a numeric suffix (`_1`, `_2`, ...) is added automatically.
+
+To continue training with the modified model, place `nep_modified.txt` and `nep_modified.restart` in your GPUMD working directory and update `nep.in` accordingly.
+
+## Notes
+
+- All operations return a **new** Model instance; the source model is never modified in place.
+- Loading the restart file is essential for proper parameter initialization during `augment`, `prune`, and `add_species`.
+- When `augment()` adds new parameters, existing parameters retain their trained values (`mu` copied verbatim); `sigma` is re-opened to allow adaptation.
+- After `prune()`, surviving parameters receive adaptive sigma: `max(sigma_floor, sigma_factor * |mu|)`.
+- The `training_parameters` property returns architecture fields compatible with `write_nepfile()` for updating `nep.in`.
+
+## Citation
+
+If you use this tool in your research, please cite both calorine and GPUMDkit:
+
+**calorine:**
+
+> Lindgren, E., Rahm, M., Fransson, E., Eriksson, F., Österbacka, N., Fan, Z., & Erhart, P. calorine: A Python package for constructing and sampling neuroevolution potential models. [Journal of Open Source Software, 2024, 9, 6264](https://doi.org/10.21105/joss.06264).
+
+**GPUMDkit:**
+
+> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, e70074](https://doi.org/10.1002/mgea.70074).
+
+## Join Us
+
+Welcome to join our QQ group ([825696376](https://qun.qq.com/universal-share/share?ac=1&authKey=buBNi1ADDzIFF2oZ1yA5FywG3LA9EL9yKZmb%2BN2MMz7nNuuxTas54wH7BgPEqP0s&busi_data=eyJncm91cENvZGUiOiI4MjU2OTYzNzYiLCJ0b2tlbiI6IlRxL1RLTDlOK3U2ekRSUXJ1TkNTUWd3ODNVV3BrdG9HN2lWWmJKMHAraGlDNzBZWFFyRUY2dUlSaW8rbUd4MisiLCJ1aW4iOiIxNDg5NjQ3MTc5In0%3D&data=fa4zSsT_IdI4ftCT_wwpytYHf--TaTB35lH0Jac5JHVpYoyXw3_3bZ1l1NZejsOZnGJku5u3BCbf5_bgrCkhZg&svctype=4&tempid=h5_group_info)). Report issues or suggest features via [issues](https://github.com/zhyan0603/GPUMDkit/issues).
diff --git a/Scripts/utils/nep_modifier/README_zh-CN.md b/Scripts/utils/nep_modifier/README_zh-CN.md
new file mode 100644
index 0000000..e417d9a
--- /dev/null
+++ b/Scripts/utils/nep_modifier/README_zh-CN.md
@@ -0,0 +1,298 @@
+# NEP Model Modifier
+
+[English](./README.md) | **简体中文**
+
+> **注意**：此功能目前处于**测试阶段**。本文档由 AI 生成，可能存在错误。如有问题，请提交 [issue](https://github.com/zhyan0603/GPUMDkit/issues) 或加入 QQ 群：[825696376](https://qun.qq.com/universal-share/share?ac=1&authKey=buBNi1ADDzIFF2oZ1yA5FywG3LA9EL9yKZmb%2BN2MMz7nNuuxTas54wH7BgPEqP0s&busi_data=eyJncm91cENvZGUiOiI4MjU2OTYzNzYiLCJ0b2tlbiI6IlRxL1RLTDlOK3U2ekRSUXJ1TkNTUWd3ODNVV3BrdG9HN2lWWmJKMHAraGlDNzBZWFFyRUY2dUlSaW8rbUd4MisiLCJ1aW4iOiIxNDg5NjQ3MTc5In0%3D&data=fa4zSsT_IdI4ftCT_wwpytYHf--TaTB35lH0Jac5JHVpYoyXw3_3bZ1l1NZejsOZnGJku5u3BCbf5_bgrCkhZg&svctype=4&tempid=h5_group_info)。
+
+基于 [calorine](https://gitlab.com/materials-modeling/calorine) Python 包（Lindgren et al., [JOSS, 2024, 9(95), 6264](https://doi.org/10.21105/joss.06264)）的 NEP（神经演化势）模型交互式修改工具。
+
+已训练的 NEP 模型可以作为进一步开发的起点，而非最终产品。常见的使用场景包括：
+
+- **扩展容量**：当初始架构过小时，增加神经元数量或添加更高体阶的描述符项。
+- **添加电荷输出**：将普通势函数模型升级为带电荷感知的 qNEP 模型，附加电荷输出头后继续训练。
+- **元素操作**：将多元素模型裁剪为元素子集，或在不丢弃已学习势函数面的情况下扩展新元素。
+- **缩减容量**：移除对精度贡献较小的神经元或描述符项，以加速推理或作为在更窄数据集上微调的起点。
+
+## 功能特点
+
+| 操作 | 说明 | 是否需要重新训练 |
+|------|------|-----------------|
+| `augment()` | 扩展神经元、描述符，或添加电荷头 | 是 |
+| `prune()` | 减少神经元、移除描述符项，或删除电荷头 | 是 |
+| `remove_species()` | 移除一个或多个元素 | 否（可选） |
+| `keep_species()` | 保留元素子集，移除其他所有元素 | 否（可选） |
+| `add_species()` | 添加一个或多个元素 | 是 |
+
+所有操作返回新的 Model 实例，源模型不会被原地修改。
+
+## 依赖项
+
+本工具需要 `calorine` Python 包（>= 3.4）。
+
+```bash
+# 方式一：从 PyPI 安装
+pip install 'calorine>=3.4'
+
+# 方式二：从 GitLab 安装最新版本
+pip install git+https://gitlab.com/materials-modeling/calorine.git@master
+```
+
+## 输入文件
+
+| 文件 | 说明 | 是否必需 |
+|------|------|---------|
+| `nep.txt` | NEP 模型文件 | 是 |
+| `nep.restart` | SNES 重启文件（存储优化器状态，用于微调） | 否 |
+
+restart 文件为每个参数存储均值 `mu` 和标准差 `sigma`，分别代表 SNES 优化器对最优值的当前估计和探索宽度。加载 restart 文件对于 `augment`、`prune` 和 `add_species` 操作正确初始化新旧参数至关重要。
+
+## 使用方法
+
+#### 交互模式
+
+1. 打开终端，进入存放 NEP 模型文件的目录。
+
+2. 运行工具：
+
+    ```
+    python nep_tool.py
+    ```
+
+3. 启动时工具会显示引用信息，然后提示输入文件。直接按 **Enter** 使用默认值（当前目录下的 `nep.txt nep.restart`）：
+
+    ```
+    +----------------------------------------------------+
+    |         NEP Model Modifier (calorine)              |
+    +----------------------------------------------------+
+    |  Powered by calorine package. If you use this tool,|
+    |  please cite the following papers:                 |
+    |                                                    |
+    |   Calorine: A Python package for constructing and  |
+    |      sampling neuroevolution potential models.     |
+    |   Journal of Open Source Software, 2024, 9, 6264.  |
+    |      https://doi.org/10.21105/joss.06264           |
+    +----------------------------------------------------+
+    [!] WARNING: This feature is currently in TESTING.
+    [!] The tutorial/docs were generated by AI and may contain errors.
+    [!] Report issues or join the QQ group: 825696376
+    +----------------------------------------------------+
+
+     Input <nep.txt> <nep.restart> (Enter to use defaults):
+     ------------>>
+    ```
+
+4. 加载后，工具显示模型信息和操作菜单：
+
+    ```
+     -----------------------------------------------------
+     Version          : 4
+     Model type       : potential
+     Types            : ('H', 'Li', 'B', 'N', 'O', ...)
+     Radial cutoff    : 6.0
+     Angular cutoff   : 5.0
+     n_max (rad/ang)  : 6 / 6
+     basis_size       : 6 / 6
+     l_max (3b/4b/5b) : 4 / 2 / 1
+     n_neuron         : 50
+     n_parameters     : 218858
+     -----------------------------------------------------
+
+     Choose an operation:
+     1) augment          (expand neurons/descriptors/charge)
+     2) prune            (shrink neurons/descriptors)
+     3) add_species      (add element)
+     4) remove_species   (remove element)
+     5) keep_species     (keep selected elements only)
+     6) Show model info
+     7) Export model
+     0) Exit
+     ------------>>
+    ```
+
+#### 命令行模式
+
+也可通过 `gpumdkit.sh` 直接启动：
+
+```
+gpumdkit.sh -nep_modifier
+```
+
+## 操作说明
+
+### 1) augment - 扩展模型
+
+`augment()` 原子性地应用一项或多项结构变更，返回新模型。可选项：
+
+- **Increase n_neuron**：增加隐藏层神经元。已训练的权重保留，新神经元以 `mu=0`、`sigma=sigma_new` 初始化。
+- **Increase l_max_5b**：启用 5-body 描述符项。新增 `n_max_angular + 1` 个描述符维度。
+- **Add charge_head**：将普通 NEP 模型（`potential`）升级为带电荷感知的 qNEP 模型（`potential_with_charges`），每个元素增加第二个输出节点。
+
+扩展后，记得更新 `nep.in` 文件以匹配新架构，然后才能继续训练。
+
+### 2) prune - 裁剪模型
+
+`prune()` 返回架构更小的新模型。可选项：
+
+- **Reduce n_neuron**：按重要性得分对神经元排序，移除最不重要的神经元。
+- **Reduce l_max_4b**：移除 4-body 描述符项（设为 0 则完全移除）。
+
+存活的参数会收到自适应的 SNES sigma 值，重新开启搜索分布以进行下一轮训练。
+
+### 3) add_species - 添加元素
+
+扩展模型：
+- 为每个新元素添加新的 ANN 子网络
+- 添加所有涉及新元素的 `(species_1, species_2)` 描述符权重对
+
+新参数以 `mu` 从 [-1, 1] 均匀采样、`sigma = sigma_new` 初始化。模型需要进一步训练才能使新元素有意义。
+
+### 4) remove_species - 移除元素
+
+移除与指定元素相关的所有参数：ANN 子网络、描述符权重对及其 SNES 统计量。常见用途是从多元素势函数中提取单元素模型。
+
+### 5) keep_species - 仅保留指定元素
+
+当从大型基础模型中隔离小子集时，通过 `remove_species()` 列出所有要移除的元素并不实际。`keep_species()` 接受要保留的元素，自动推导移除列表。
+
+## 操作示例
+
+#### 示例 1：提取子模型
+
+从 36 元素基础模型中提取 Li、La、Zr、O：
+
+```
+ Input <nep.txt> <nep.restart> (Enter to use defaults):
+ ------------>>
+
+ Choose an operation:
+ 5) keep_species     (keep selected elements only)
+ ------------>>
+ 5
+
+ Input elements to keep (space-separated): (Li La Zr O)
+ ------------>>
+ Li La Zr O
+
+ Will keep: ['Li', 'La', 'Zr', 'O']
+ Confirm? (y/n)
+ ------------>>
+ y
+
+ Done: ('H', 'Li', ..., 'W') -> ('Li', 'O', 'Zr', 'La')
+ Params: 218858 -> 11818
+
+ Choose an operation:
+ 7) Export model
+ ------------>>
+ 7
+
+ Output directory: (.)
+ ------------>>
+ .
+
+ Written: nep_modified.txt
+ Written: nep_modified.restart
+```
+
+#### 示例 2：扩展模型容量
+
+将神经元从 50 增加到 80，并启用 5-body 描述符：
+
+```
+ Choose an operation:
+ 1) augment          (expand neurons/descriptors/charge)
+ ------------>>
+ 1
+
+ Choose what to augment:
+ 1) Increase n_neuron
+ 2) Increase l_max_5b
+ 3) Add charge_head
+ 0) Cancel
+ ------------>>
+ 1
+
+ Input new n_neuron: (60)
+ ------------>>
+ 80
+
+ Confirm augment? (y/n)
+ ------------>>
+ y
+
+ Done: 218858 -> 345258 parameters
+```
+
+#### 示例 3：替换元素
+
+移除 Pb 并添加 Bi（链式操作）：
+
+```
+ Choose an operation:
+ 4) remove_species   (remove element)
+ ------------>>
+ 4
+
+ Input elements to remove (space-separated):
+ ------------>>
+ Pb
+
+ Confirm? (y/n)
+ ------------>>
+ y
+
+ Done: ('Te', 'Pb') -> ('Te',)
+ Params: 2311 -> 1081
+
+ Choose an operation:
+ 3) add_species      (add element)
+ ------------>>
+ 3
+
+ Input elements to add (space-separated): (Bi Sn)
+ ------------>>
+ Bi
+
+ Confirm? (y/n)
+ ------------>>
+ y
+
+ Done: ('Te',) -> ('Te', 'Bi')
+ Params: 1081 -> 2491
+```
+
+## 输出文件
+
+| 文件 | 说明 |
+|------|------|
+| `nep_modified.txt` | 修改后的 NEP 模型文件 |
+| `nep_modified.restart` | 更新后的 SNES 重启文件（仅在加载了 restart 时生成） |
+| `nep_modified.in` | 包含更新架构的训练输入文件 |
+
+输出文件名自动添加 `_modified` 后缀，避免覆盖原始文件。如果同名文件已存在，则自动添加数字后缀（`_1`、`_2`……）。
+
+如需使用修改后的模型继续训练，请将 `nep_modified.txt` 和 `nep_modified.restart` 放入 GPUMD 工作目录，并相应更新 `nep.in`。
+
+## 注意事项
+
+- 所有操作返回**新的** Model 实例，源模型不会被原地修改。
+- 加载 restart 文件对于 `augment`、`prune` 和 `add_species` 操作的正确参数初始化至关重要。
+- `augment()` 添加新参数时，现有参数保留其训练值（`mu` 原样复制）；`sigma` 重新开启以允许自适应。
+- `prune()` 后，存活的参数收到自适应 sigma：`max(sigma_floor, sigma_factor * |mu|)`。
+- `training_parameters` 属性返回与 `write_nepfile()` 兼容的架构字段，可用于更新 `nep.in`。
+
+## 引用
+
+如果您在研究中使用了本工具，请同时引用 calorine 和 GPUMDkit：
+
+**calorine:**
+
+> Lindgren, E., Rahm, M., Fransson, E., Eriksson, F., Österbacka, N., Fan, Z., & Erhart, P. calorine: A Python package for constructing and sampling neuroevolution potential models. [Journal of Open Source Software, 2024, 9, 6264](https://doi.org/10.21105/joss.06264).
+
+**GPUMDkit:**
+
+> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, e70074](https://doi.org/10.1002/mgea.70074).
+
+## 加入我们
+
+欢迎加入 QQ 群（[825696376](https://qun.qq.com/universal-share/share?ac=1&authKey=buBNi1ADDzIFF2oZ1yA5FywG3LA9EL9yKZmb%2BN2MMz7nNuuxTas54wH7BgPEqP0s&busi_data=eyJncm91cENvZGUiOiI4MjU2OTYzNzYiLCJ0b2tlbiI6IlRxL1RLTDlOK3U2ekRSUXJ1TkNTUWd3ODNVV3BrdG9HN2lWWmJKMHAraGlDNzBZWFFyRUY2dUlSaW8rbUd4MisiLCJ1aW4iOiIxNDg5NjQ3MTc5In0%3D&data=fa4zSsT_IdI4ftCT_wwpytYHf--TaTB35lH0Jac5JHVpYoyXw3_3bZ1l1NZejsOZnGJku5u3BCbf5_bgrCkhZg&svctype=4&tempid=h5_group_info)）。如有问题或建议，请提交 [issue](https://github.com/zhyan0603/GPUMDkit/issues)。
diff --git a/Scripts/utils/nep_modifier/nep_modifier.py b/Scripts/utils/nep_modifier/nep_modifier.py
new file mode 100644
index 0000000..469efbd
--- /dev/null
+++ b/Scripts/utils/nep_modifier/nep_modifier.py
@@ -0,0 +1,337 @@
+"""
+=============================================================================
+GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
+Repository: https://github.com/zhyan0603/GPUMDkit
+Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
+          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+=============================================================================
+Script:     nep_modifier.py
+Category:   Model Modification Scripts
+Purpose:    Interactively modify NEP models using calorine.
+Usage:      python nep_modifier.py <input.nep>
+
+Author:     Zihan YAN (yanzihan@westlake.edu.cn)
+Last-modified: 2026-06-17
+=============================================================================
+"""
+
+import os
+import sys
+from pathlib import Path
+
+try:
+    from calorine.nep import read_model, read_nepfile, write_nepfile
+except ImportError:
+    print(" Error: calorine package (>=3.4) is required.")
+    print(" Install via pip:")
+    print("   pip install 'calorine>=3.4'")
+    print(" Or install the latest version from GitLab:")
+    print("   pip install git+https://gitlab.com/materials-modeling/calorine.git@master")
+    sys.exit(1)
+
+
+# ─── helpers ──────────────────────────────────────────────────────────────────
+
+def banner(title):
+    print(f" +---------------------------------------------------+")
+    print(f" | {title:<51}|")
+    print(f" +---------------------------------------------------+")
+
+
+def separator():
+    print(" -----------------------------------------------------")
+
+
+def ask(prompt, hint=None):
+    if hint:
+        print(f" {prompt} ({hint})")
+    else:
+        print(f" {prompt}")
+    print(" ------------>>")
+    return input(" ").strip()
+
+
+def confirm(msg):
+    print(f" {msg} (y/n)")
+    print(" ------------>>")
+    return input(" ").strip().lower() in ("y", "yes")
+
+
+def safe_output_path(out_dir, base_name, ext):
+    path = out_dir / f"{base_name}{ext}"
+    if not path.exists():
+        return path
+    i = 1
+    while True:
+        path = out_dir / f"{base_name}_{i}{ext}"
+        if not path.exists():
+            return path
+        i += 1
+
+
+# ─── core functions ───────────────────────────────────────────────────────────
+
+def show_model_info(model):
+    separator()
+    print(f" Version          : {model.version}")
+    print(f" Model type       : {model.model_type}")
+    print(f" Types            : {model.types}")
+    print(f" Radial cutoff    : {model.radial_cutoff}")
+    print(f" Angular cutoff   : {model.angular_cutoff}")
+    print(f" n_max (rad/ang)  : {model.n_max_radial} / {model.n_max_angular}")
+    print(f" basis_size       : {model.n_basis_radial} / {model.n_basis_angular}")
+    print(f" l_max (3b/4b/5b) : {model.l_max_3b} / {model.l_max_4b} / {model.l_max_5b}")
+    print(f" n_neuron         : {model.n_neuron}")
+    print(f" n_parameters     : {model.n_parameters}")
+    separator()
+
+
+def op_augment(model):
+    banner("augment: Expand Model")
+    print(f" Current: neuron={model.n_neuron}, l_max_5b={model.l_max_5b}")
+    separator()
+    print(" Choose what to augment:")
+    print(" 1) Increase n_neuron")
+    print(" 2) Increase l_max_5b")
+    print(" 3) Add charge_head")
+    print(" 0) Cancel")
+    print(" ------------>>")
+    choice = input(" ").strip()
+
+    kwargs = {}
+    if choice == "1":
+        val = ask(" Input new n_neuron:", str(model.n_neuron + 10))
+        kwargs["n_neuron"] = int(val)
+    elif choice == "2":
+        val = ask(" Input new l_max_5b:", "1")
+        kwargs["l_max_5b"] = int(val)
+    elif choice == "3":
+        kwargs["charge_head"] = True
+    else:
+        print(" Cancelled.")
+        return model
+
+    separator()
+    for k, v in kwargs.items():
+        print(f"   {k} = {v}")
+
+    if not confirm(" Confirm augment?"):
+        return model
+
+    new_model = model.augment(**kwargs)
+    print(f" Done: {model.n_parameters} -> {new_model.n_parameters} parameters")
+    return new_model
+
+
+def op_prune(model):
+    banner("prune: Shrink Model")
+    print(f" Current: neuron={model.n_neuron}, l_max_4b={model.l_max_4b}")
+    separator()
+    print(" Choose what to prune:")
+    print(" 1) Reduce n_neuron")
+    print(" 2) Reduce l_max_4b")
+    print(" 0) Cancel")
+    print(" ------------>>")
+    choice = input(" ").strip()
+
+    kwargs = {}
+    if choice == "1":
+        val = ask(" Input new n_neuron:", str(max(1, model.n_neuron - 10)))
+        kwargs["n_neuron"] = int(val)
+    elif choice == "2":
+        val = ask(" Input new l_max_4b (0 to remove):", "0")
+        kwargs["l_max_4b"] = int(val)
+    else:
+        print(" Cancelled.")
+        return model
+
+    separator()
+    for k, v in kwargs.items():
+        print(f"   {k} = {v}")
+
+    if not confirm(" Confirm prune?"):
+        return model
+
+    new_model = model.prune(**kwargs)
+    print(f" Done: {model.n_parameters} -> {new_model.n_parameters} parameters")
+    return new_model
+
+
+def op_add_species(model):
+    banner("add_species: Add Elements")
+    print(f" Current types: {model.types}")
+    val = ask(" Input elements to add (space-separated):", "Bi Sn")
+    species = val.split()
+    if not species:
+        print(" Cancelled.")
+        return model
+
+    separator()
+    print(f" Will add: {species}")
+    if not confirm(" Confirm?"):
+        return model
+
+    new_model = model.add_species(species)
+    print(f" Done: {model.types} -> {new_model.types}")
+    print(f" Params: {model.n_parameters} -> {new_model.n_parameters}")
+    return new_model
+
+
+def op_remove_species(model):
+    banner("remove_species: Remove Elements")
+    print(f" Current types: {model.types}")
+    val = ask(" Input elements to remove (space-separated):")
+    species = val.split()
+    if not species:
+        print(" Cancelled.")
+        return model
+
+    separator()
+    print(f" Will remove: {species}")
+    if not confirm(" Confirm?"):
+        return model
+
+    new_model = model.remove_species(species)
+    print(f" Done: {model.types} -> {new_model.types}")
+    print(f" Params: {model.n_parameters} -> {new_model.n_parameters}")
+    return new_model
+
+
+def op_keep_species(model):
+    banner("keep_species: Keep Elements Only")
+    print(f" Current types: {model.types}")
+    val = ask(" Input elements to keep (space-separated):", "Li La Zr O")
+    species = val.split()
+    if not species:
+        print(" Cancelled.")
+        return model
+
+    separator()
+    print(f" Will keep: {species}")
+    if not confirm(" Confirm?"):
+        return model
+
+    new_model = model.keep_species(species)
+    print(f" Done: {model.types} -> {new_model.types}")
+    print(f" Params: {model.n_parameters} -> {new_model.n_parameters}")
+    return new_model
+
+
+def op_export(model, original_path):
+    banner("Export Model Files")
+    out_dir = ask(" Output directory:", ".")
+    out_dir = Path(out_dir)
+    out_dir.mkdir(parents=True, exist_ok=True)
+
+    base = Path(original_path).stem
+    nep_out = safe_output_path(out_dir, base + "_modified", ".txt")
+    restart_out = out_dir / (nep_out.stem + ".restart")
+
+    model.write(str(nep_out))
+    print(f" Written: {nep_out}")
+
+    try:
+        model.write_restart(str(restart_out))
+        print(f" Written: {restart_out}")
+    except Exception:
+        print(" Skipped: nep.restart (no restart data loaded)")
+
+    try:
+        if hasattr(model, "training_parameters"):
+            nep_in = out_dir / (nep_out.stem + ".in")
+            params = model.training_parameters
+            if Path("nep.in").exists():
+                old = read_nepfile("nep.in")
+                old.update(params)
+                params = old
+            write_nepfile(params, str(out_dir))
+            default_in = out_dir / "nep.in"
+            if default_in.exists() and default_in != nep_in:
+                default_in.rename(nep_in)
+            print(f" Written: {nep_in}")
+    except Exception:
+        pass
+
+    separator()
+
+
+# ─── main ─────────────────────────────────────────────────────────────────────
+
+def main():
+    print("")
+    print(" +----------------------------------------------------+")
+    print(" |         NEP Model Modifier (calorine)              |")
+    print(" +----------------------------------------------------+")
+    print(" |  Powered by calorine package. If you use this tool,|")
+    print(" |  please cite the following papers:                 |")
+    print(" |                                                    |")
+    print(" |   Calorine: A Python package for constructing and  |")
+    print(" |      sampling neuroevolution potential models.     |")
+    print(" |   Journal of Open Source Software, 2024, 9, 6264.  |")
+    print(" |      https://doi.org/10.21105/joss.06264           |")
+    print(" +----------------------------------------------------+")
+    print(" [!] WARNING: This feature is currently in TESTING.")
+    print(" [!] The docs were generated by AI and may contain errors.")
+    print(" [!] Report issues or join the QQ group: 825696376")
+    print(" +----------------------------------------------------+")
+    print("")
+
+    val = ask(" Input <nep.txt> <nep.restart> (Enter to use defaults):")
+    parts = val.split()
+    nep_path = parts[0] if parts else "nep.txt"
+    restart_path = parts[1] if len(parts) > 1 else "nep.restart"
+
+    if not Path(nep_path).exists():
+        print(f" Error: file not found: {nep_path}")
+        return
+    if not Path(restart_path).exists():
+        print(f" Warning: {restart_path} not found, skipping restart.")
+        restart_path = None
+
+    separator()
+    print(" Loading model...")
+    if restart_path:
+        model = read_model(nep_path, restart_file=restart_path)
+    else:
+        model = read_model(nep_path)
+    print(" Model loaded successfully!")
+
+    show_model_info(model)
+
+    while True:
+        print("")
+        print(" Choose an operation:")
+        print(" 1) augment          (expand neurons/descriptors/charge)")
+        print(" 2) prune            (shrink neurons/descriptors)")
+        print(" 3) add_species      (add element)")
+        print(" 4) remove_species   (remove element)")
+        print(" 5) keep_species     (keep selected elements only)")
+        print(" 6) Show model info")
+        print(" 7) Export model")
+        print(" 0) Exit")
+        print(" ------------>>")
+        choice = input(" ").strip()
+
+        if choice == "0":
+            print(" Bye!")
+            break
+        elif choice == "1":
+            model = op_augment(model)
+        elif choice == "2":
+            model = op_prune(model)
+        elif choice == "3":
+            model = op_add_species(model)
+        elif choice == "4":
+            model = op_remove_species(model)
+        elif choice == "5":
+            model = op_keep_species(model)
+        elif choice == "6":
+            show_model_info(model)
+        elif choice == "7":
+            op_export(model, nep_path)
+        else:
+            print(" Invalid option, try again.")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/docs/updates.info b/docs/updates.info
index d218a66..4b02d14 100644
--- a/docs/updates.info
+++ b/docs/updates.info
@@ -1,13 +1,12 @@
 # === User Configuration Section: Only modify these variables ===
-VERSION="1.5.5"
-RELEASE_DATE="2026-05-18"
+VERSION="1.5.6"
+RELEASE_DATE="2026-06-17"
 HOME_PAGE="https://zhyan0603.github.io/GPUMDkit"
 CONTACT="yanzihan@westlake.edu.cn"
 
 # New features (one per line, in an array)
 NEW_FEATURES=(
-    "add -plt train_density"
-    "add -plt bec"
+    "add -nep_modifier"
 )
 
 # Bug fixes (one per line, in an array)
diff --git a/gpumdkit.sh b/gpumdkit.sh
index 985bc53..0d5396a 100755
--- a/gpumdkit.sh
+++ b/gpumdkit.sh
@@ -19,7 +19,7 @@ if [ -z "$GPUMDkit_path" ]; then
     exit 1
 fi
 
-VERSION="1.5.5 (dev) (2026-05-16)"
+VERSION="1.5.6 (dev) (2026-06-17)"
 
 plt_path="${GPUMDkit_path}/Scripts/plt_scripts"
 analyzer_path="${GPUMDkit_path}/Scripts/analyzer"
@@ -669,6 +669,9 @@ if [ ! -z "$1" ]; then
             source ${GPUMDkit_path}/src/f2_sample_structures.sh
             parallel_pynep_sample_structures ;;
 
+        -nep_modifier)
+            source ${GPUMDkit_path}/Scripts/utils/nep_modifier/nep_modifier.py ;;
+
         -frame_range)
             if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] && [ ! -z "$4" ] ; then
                 echo " Calling script by Zihan YAN "

From e1a730508e48ef6d2f8469e6de7b4faaf848cbdd Mon Sep 17 00:00:00 2001
From: yanzihan <yanzihan@westlake.edu.cn>
Date: Wed, 17 Jun 2026 16:52:19 +0800
Subject: [PATCH 07/24] fix typo

---
 Scripts/utils/nep_modifier/README_zh-CN.md | 2 +-
 gpumdkit.sh                                | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Scripts/utils/nep_modifier/README_zh-CN.md b/Scripts/utils/nep_modifier/README_zh-CN.md
index e417d9a..317fda3 100644
--- a/Scripts/utils/nep_modifier/README_zh-CN.md
+++ b/Scripts/utils/nep_modifier/README_zh-CN.md
@@ -55,7 +55,7 @@ restart 文件为每个参数存储均值 `mu` 和标准差 `sigma`，分别代
 2. 运行工具：
 
     ```
-    python nep_tool.py
+    python nep_modifier.py
     ```
 
 3. 启动时工具会显示引用信息，然后提示输入文件。直接按 **Enter** 使用默认值（当前目录下的 `nep.txt nep.restart`）：
diff --git a/gpumdkit.sh b/gpumdkit.sh
index 0d5396a..1100830 100755
--- a/gpumdkit.sh
+++ b/gpumdkit.sh
@@ -670,7 +670,7 @@ if [ ! -z "$1" ]; then
             parallel_pynep_sample_structures ;;
 
         -nep_modifier)
-            source ${GPUMDkit_path}/Scripts/utils/nep_modifier/nep_modifier.py ;;
+            python ${GPUMDkit_path}/Scripts/utils/nep_modifier/nep_modifier.py ;;
 
         -frame_range)
             if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] && [ ! -z "$4" ] ; then

From a0663e6c94c443aa3a1af61ccaf99fd316eb9a64 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Sat, 20 Jun 2026 22:22:44 +0800
Subject: [PATCH 08/24] add skill and new tutorials

---
 .gitignore                                 |   3 +
 docs/tutorials2/en/analyzers.md            | 289 +++++++++++++++++++
 docs/tutorials2/en/calculators.md          | 312 +++++++++++++++++++++
 docs/tutorials2/en/format_conversion.md    | 273 ++++++++++++++++++
 docs/tutorials2/en/index.md                | 160 +++++++++++
 docs/tutorials2/en/nep_training.md         | 299 ++++++++++++++++++++
 docs/tutorials2/en/quickstart.md           | 244 ++++++++++++++++
 docs/tutorials2/en/sampling.md             | 221 +++++++++++++++
 docs/tutorials2/en/visualization.md        | 226 +++++++++++++++
 docs/tutorials2/en/workflows.md            | 280 ++++++++++++++++++
 docs/tutorials2/zh/analyzers.md            | 289 +++++++++++++++++++
 docs/tutorials2/zh/calculators.md          | 312 +++++++++++++++++++++
 docs/tutorials2/zh/format_conversion.md    | 273 ++++++++++++++++++
 docs/tutorials2/zh/index.md                | 160 +++++++++++
 docs/tutorials2/zh/nep_training.md         | 299 ++++++++++++++++++++
 docs/tutorials2/zh/quickstart.md           | 244 ++++++++++++++++
 docs/tutorials2/zh/sampling.md             | 221 +++++++++++++++
 docs/tutorials2/zh/visualization.md        | 226 +++++++++++++++
 docs/tutorials2/zh/workflows.md            | 280 ++++++++++++++++++
 skills/README.md                           | 117 ++++++++
 skills/gpumdkit-analyzers/SKILL.md         | 235 ++++++++++++++++
 skills/gpumdkit-calculators/SKILL.md       | 241 ++++++++++++++++
 skills/gpumdkit-format-conversion/SKILL.md | 173 ++++++++++++
 skills/gpumdkit-main/SKILL.md              | 153 ++++++++++
 skills/gpumdkit-sampling/SKILL.md          | 228 +++++++++++++++
 skills/gpumdkit-visualization/SKILL.md     | 216 ++++++++++++++
 skills/gpumdkit-workflows/SKILL.md         | 224 +++++++++++++++
 27 files changed, 6198 insertions(+)
 create mode 100644 docs/tutorials2/en/analyzers.md
 create mode 100644 docs/tutorials2/en/calculators.md
 create mode 100644 docs/tutorials2/en/format_conversion.md
 create mode 100644 docs/tutorials2/en/index.md
 create mode 100644 docs/tutorials2/en/nep_training.md
 create mode 100644 docs/tutorials2/en/quickstart.md
 create mode 100644 docs/tutorials2/en/sampling.md
 create mode 100644 docs/tutorials2/en/visualization.md
 create mode 100644 docs/tutorials2/en/workflows.md
 create mode 100644 docs/tutorials2/zh/analyzers.md
 create mode 100644 docs/tutorials2/zh/calculators.md
 create mode 100644 docs/tutorials2/zh/format_conversion.md
 create mode 100644 docs/tutorials2/zh/index.md
 create mode 100644 docs/tutorials2/zh/nep_training.md
 create mode 100644 docs/tutorials2/zh/quickstart.md
 create mode 100644 docs/tutorials2/zh/sampling.md
 create mode 100644 docs/tutorials2/zh/visualization.md
 create mode 100644 docs/tutorials2/zh/workflows.md
 create mode 100644 skills/README.md
 create mode 100644 skills/gpumdkit-analyzers/SKILL.md
 create mode 100644 skills/gpumdkit-calculators/SKILL.md
 create mode 100644 skills/gpumdkit-format-conversion/SKILL.md
 create mode 100644 skills/gpumdkit-main/SKILL.md
 create mode 100644 skills/gpumdkit-sampling/SKILL.md
 create mode 100644 skills/gpumdkit-visualization/SKILL.md
 create mode 100644 skills/gpumdkit-workflows/SKILL.md

diff --git a/.gitignore b/.gitignore
index e95b54f..4314cfc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,6 +16,9 @@ build/
 .DS_Store
 Thumbs.db
 
+# Opencode
+.opencode
+
 # Temporary / generated files
 *.log
 temp_*.xyz
diff --git a/docs/tutorials2/en/analyzers.md b/docs/tutorials2/en/analyzers.md
new file mode 100644
index 0000000..892f39a
--- /dev/null
+++ b/docs/tutorials2/en/analyzers.md
@@ -0,0 +1,289 @@
+# Analyzers Guide
+
+<div align="center">
+  <p>
+    <a href="../zh/analyzers.md">中文</a> | <strong>English</strong>
+  </p>
+</div>
+
+This guide covers all analysis tools in GPUMDkit for structure validation, filtering, and quality control.
+
+## Available Tools
+
+| Tool | Command | Description |
+|------|---------|-------------|
+| Composition Analysis | `-analyze_comp` | Group structures by composition |
+| Outlier Detection | Menu 502 | Find high-error structures |
+| Chemical Species | Menu 503 | List unique elements |
+| Charge Balance | `-cbc` | Check oxidation-state balance |
+| Property Range | `-range` | Energy/force/virial statistics |
+| Distance Filter | Menu 506 | Filter by minimum distance (no PBC) |
+| Distance Filter (PBC) | Menu 506b | Filter by minimum distance (with PBC) |
+| Minimum Distance | `-min_dist` | Calculate min distances (no PBC) |
+| Minimum Distance (PBC) | `-min_dist_pbc` | Calculate min distances (with PBC) |
+| Probability Density | Menu 508 | 3D diffusion channel analysis |
+
+## Interactive Mode
+
+```bash
+gpumdkit.sh
+# Select: 5) Analyzer
+```
+
+You'll see:
+
+```
++------------------------------------------------------+
+|                    ANALYZER TOOLS                    |
++------------------------------------------------------+
+| 501) Analyze composition of extxyz                   |
+| 502) Find outliers of extxyz                         |
+| 503) Analyze chemical species of extxyz              |
+| 504) Check charge balance of extxyz                  |
+| 505) Analyze energy/force/virial range               |
+| 506) Filter structures by minimum distance           |
+| 507) Get minimum interatomic distance                |
+| 508) Probability density analysis                    |
++------------------------------------------------------+
+```
+
+## Command Reference
+
+### Composition Analysis
+
+Analyze and group structures by chemical composition.
+
+```bash
+gpumdkit.sh -analyze_comp train.xyz
+```
+
+**Output:** Table of unique compositions with atom counts and structure counts. Interactive selection to export specific compositions.
+
+### Property Range Analysis
+
+Compute the range (min, max) of energy, force, or virial in an extxyz file.
+
+```bash
+gpumdkit.sh -range <filename> <property> [hist]
+
+# Examples
+gpumdkit.sh -range train.xyz energy
+gpumdkit.sh -range train.xyz force
+gpumdkit.sh -range train.xyz virial
+gpumdkit.sh -range train.xyz force hist    # With histogram
+```
+
+**Output:** Min/max values. Optional histogram plot with `hist` argument.
+
+### Minimum Distance
+
+Calculate minimum interatomic distance for each element pair.
+
+```bash
+# Fast calculation (no PBC)
+gpumdkit.sh -min_dist dump.xyz
+
+# Accurate calculation (with PBC)
+gpumdkit.sh -min_dist_pbc dump.xyz
+```
+
+**Output:** Table of minimum distances for all element pairs
+
+### Charge Balance Check
+
+Check oxidation-state balance for all structures.
+
+```bash
+gpumdkit.sh -cbc train.xyz
+```
+
+**Output:**
+- `balanced.xyz` - Charge-balanced structures
+- `unbalanced.xyz` - Unbalanced structures
+- `indices.txt` - Summary
+
+### Chemical Species Identification
+
+List all unique chemical elements in the file.
+
+```bash
+# Interactive mode
+gpumdkit.sh  # Select: 5) Analyzer -> 503
+```
+
+**Output:** Sorted list of all elements
+
+### Structure Filtering
+
+#### By Minimum Distance (No PBC)
+
+```bash
+gpumdkit.sh  # Select: 5) Analyzer -> 506
+```
+
+**Input:** extxyz file, distance threshold
+**Output:** `filtered_<file>.xyz`, `filtered_out_<file>.xyz`
+
+#### By Minimum Distance (With PBC)
+
+```bash
+gpumdkit.sh  # Select: 5) Analyzer -> 506b
+```
+
+More accurate for periodic systems.
+
+#### By Element-Pair Distance Range
+
+```bash
+gpumdkit.sh -filter_range <file> <element1> <element2> <min_dist> <max_dist>
+
+# Example: Filter Li-Li distances between 1.9 and 2.0 Å
+gpumdkit.sh -filter_range dump.xyz Li Li 1.9 2.0
+```
+
+**Output:** `filtered_<elem1>_<elem2>_<min>_<max>.xyz`
+
+#### By Box Size
+
+```bash
+gpumdkit.sh -filter_box <file> <edge_limit>
+
+# Example: Filter structures with box edge > 20 Å
+gpumdkit.sh -filter_box dump.xyz 20
+```
+
+**Output:** `filtered_by_box.xyz`
+
+#### By Property Value
+
+```bash
+gpumdkit.sh -filter_value <file> <property> <threshold>
+
+# Example: Keep structures with force < 20 eV/Å
+gpumdkit.sh -filter_value train.xyz force 20
+```
+
+**Output:** `filtered.xyz`
+
+### Outlier Detection
+
+Find outlier structures based on RMSE thresholds.
+
+```bash
+gpumdkit.sh  # Select: 5) Analyzer -> 502
+```
+
+**Required files:**
+- `train.xyz`
+- `energy_train.out`
+- `force_train.out`
+- `stress_train.out`
+
+**Output:** `selected.xyz` (high-error), `remained.xyz` (low-error)
+
+### Probability Density Analysis
+
+Calculate 3D probability density of mobile ions from AIMD trajectory.
+
+```bash
+gpumdkit.sh  # Select: 5) Analyzer -> 508
+```
+
+**Parameters:**
+- Reference structure (POSCAR)
+- Trajectory file (extxyz)
+- Mobile species (e.g., Li)
+- Grid interval (e.g., 0.25 Å)
+
+**Output:** `probability_density_<interval>.vasp` (CHGCAR format)
+
+## Common Workflows
+
+### Data Quality Check
+
+```bash
+# 1. Check composition
+gpumdkit.sh -analyze_comp train.xyz
+
+# 2. Check minimum distances
+gpumdkit.sh -min_dist_pbc train.xyz
+
+# 3. Check force range
+gpumdkit.sh -range train.xyz force
+
+# 4. Check for outliers
+gpumdkit.sh  # Select: 5) Analyzer -> 502
+```
+
+### Structure Filtering Pipeline
+
+```bash
+# 1. Filter by distance
+gpumdkit.sh  # Select: 5) Analyzer -> 506
+
+# 2. Filter by box size
+gpumdkit.sh -filter_box filtered.xyz 20
+
+# 3. Filter by force value
+gpumdkit.sh -filter_value filtered_by_box.xyz force 15
+```
+
+### Diffusion Channel Analysis
+
+```bash
+# 1. Calculate probability density
+gpumdkit.sh  # Select: 5) Analyzer -> 508
+
+# 2. Visualize with VESTA or similar
+# Open probability_density_0.25.vasp
+```
+
+## Additional Tools
+
+### Time Monitoring
+
+```bash
+# Monitor GPUMD progress
+gpumdkit.sh -time gpumd
+
+# Monitor NEP training progress
+gpumdkit.sh -time nep
+```
+
+### Volume Analysis
+
+```bash
+# Get average volume per temperature
+python Scripts/analyzer/get_volume.py
+# Requires: */K/thermo.out directories
+```
+
+## CLI Reference
+
+| Flag | Description | Syntax |
+|------|-------------|--------|
+| `-analyze_comp` | Composition analysis | `gpumdkit.sh -analyze_comp <file>` |
+| `-range` | Property range | `gpumdkit.sh -range <file> <prop>` |
+| `-min_dist` | Min distance (no PBC) | `gpumdkit.sh -min_dist <file>` |
+| `-min_dist_pbc` | Min distance (PBC) | `gpumdkit.sh -min_dist_pbc <file>` |
+| `-cbc` | Charge balance | `gpumdkit.sh -cbc <file>` |
+| `-filter_range` | Filter by distance range | `gpumdkit.sh -filter_range <file> <e1> <e2> <min> <max>` |
+| `-filter_box` | Filter by box size | `gpumdkit.sh -filter_box <file> <limit>` |
+| `-filter_value` | Filter by property | `gpumdkit.sh -filter_value <file> <prop> <thresh>` |
+| `-time` | Time monitoring | `gpumdkit.sh -time <gpumd\|nep>` |
+
+## Dependencies
+
+| Tool | Required Packages |
+|------|------------------|
+| All Python scripts | `ase`, `numpy` |
+| Distance calculations | `scipy` |
+| Charge balance | `pymatgen`, `tqdm` |
+| Property range | `matplotlib` |
+| Probability density | `pymatgen` |
+
+## See Also
+
+- [Format Conversion](format_conversion.md) - Convert file formats
+- [Calculators](calculators.md) - Compute properties
+- [Visualization](visualization.md) - Plot results
diff --git a/docs/tutorials2/en/calculators.md b/docs/tutorials2/en/calculators.md
new file mode 100644
index 0000000..57a9112
--- /dev/null
+++ b/docs/tutorials2/en/calculators.md
@@ -0,0 +1,312 @@
+# Calculators Guide
+
+<div align="center">
+  <p>
+    <a href="../zh/calculators.md">中文</a> | <strong>English</strong>
+  </p>
+</div>
+
+This guide covers all calculator tools in GPUMDkit for computing material properties.
+
+## Available Calculators
+
+| Calculator | Command | Description |
+|------------|---------|-------------|
+| Ionic Conductivity | `-calc ionic-cond` | Calculate ionic conductivity from MSD |
+| NEP Properties | `-calc nep` | Compute energy/force/stress with NEP |
+| Descriptors | `-calc des` | Calculate NEP descriptors for analysis |
+| DOAS | `-calc doas` | Density of atomistic states |
+| NEB | Direct Python | Nudged elastic band calculation |
+| Neighbor List | `-calc nlist` | Build neighbor lists for analysis |
+| Displacement | `-calc disp` | Calculate atomic displacements |
+| Averaged Structure | `-calc avg-struct` | Time-averaged structure from trajectory |
+| Octahedral Tilt | `-calc oct-tilt` | Perovskite octahedral tilt angles |
+| Polarization | `-calc pol-abo3` | ABO3 local polarization |
+| Minimization | `-calc minimize` | Structure relaxation with NEP |
+| MSD | `-calc msd` | Mean square displacement from trajectory |
+
+## Interactive Mode
+
+```bash
+gpumdkit.sh
+# Select: 4) Calculators
+```
+
+You'll see:
+
+```
++----------------------------------------------------------+
+|                     CALCULATOR TOOLS                     |
++----------------------------------------------------------+
+| 401) Calc ionic conductivity                             |
+| 402) Calc properties by nep                              |
+| 403) Calc descriptors of specific elements               |
+| 404) Calc density of atomistic states (DOAS)             |
+| 405) Calc nudged elastic band (NEB) by nep               |
+| 406) Build neighbor list                                 |
+| 407) Calc displacement from trajectory                   |
+| 408) Calc averaged structure                             |
+| 409) Calc octahedral tilt                                |
+| 410) Calc polarization for ABO3                          |
+| 411) Minimize structure by nep                           |
+| 412) Calc mean square displacement (MSD) from trajectory |
++----------------------------------------------------------+
+```
+
+## Command Reference
+
+### Ionic Conductivity
+
+Calculate ionic conductivity from MSD data using the Nernst-Einstein equation.
+
+```bash
+gpumdkit.sh -calc ionic-cond <element> <charge>
+
+# Examples
+gpumdkit.sh -calc ionic-cond Li 1    # Lithium ion (Li+)
+gpumdkit.sh -calc ionic-cond Na 1    # Sodium ion (Na+)
+gpumdkit.sh -calc ionic-cond O -2    # Oxygen ion (O2-)
+```
+
+**Required files in current directory:**
+- `msd.out` - From GPUMD `compute_msd`
+- `thermo.out` - For temperature
+- `model.xyz` - For volume
+- `run.in` - For simulation parameters
+
+**Output:** Ionic diffusivity and conductivity values
+
+### NEP Property Prediction
+
+Calculate energies, forces, and stresses using a NEP model as a DFT surrogate.
+
+```bash
+gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>
+
+# Example
+gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
+```
+
+**Note:** Clean input with `gpumdkit.sh -clean_xyz` first to remove existing properties.
+
+### Descriptors
+
+Calculate NEP descriptors for dimensionality reduction and structure analysis.
+
+```bash
+gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>
+
+# Example
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+```
+
+**Visualize with:**
+```bash
+gpumdkit.sh -plt des pca    # PCA visualization
+gpumdkit.sh -plt des umap   # UMAP visualization
+```
+
+### Density of Atomistic States (DOAS)
+
+Calculate per-atom energy distributions grouped by element type.
+
+```bash
+gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>
+
+# Example
+gpumdkit.sh -calc doas structures.xyz nep.txt doas.out
+```
+
+**Visualize with:**
+```bash
+gpumdkit.sh -plt doas doas.out Li
+```
+
+### Mean Square Displacement (MSD)
+
+Calculate directional MSD from an extxyz trajectory.
+
+```bash
+gpumdkit.sh -calc msd <trajectory.xyz> <element> <dt_fs> [max_corr_steps]
+
+# Example: Li with 10 fs timestep
+gpumdkit.sh -calc msd dump.xyz Li 10
+```
+
+**Output:** `msd.out` (Time/ps, MSD_x, MSD_y, MSD_z)
+
+### Neighbor List
+
+Build neighbor lists for perovskite analysis.
+
+```bash
+gpumdkit.sh -calc nlist -i <input> -c <cutoff> -n <num_neighbors> -C <center_elements> -E <neighbor_elements>
+
+# Examples
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O
+```
+
+**Output:** `nl-<center>-<neighbor>.dat`
+
+### Displacement
+
+Calculate atomic displacements from trajectory using neighbor list.
+
+```bash
+gpumdkit.sh -calc disp -i <trajectory.xyz> -n <neighbor_list> -o <output>
+
+# Example
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Pb-O.dat -o displacements.dat
+```
+
+**Optional frame slicing:** `-s <start> -t <stop> -p <step> -l <last_fraction>`
+
+### Averaged Structure
+
+Generate time-averaged structure from trajectory.
+
+```bash
+gpumdkit.sh -calc avg-struct -i <trajectory.xyz> -l <fraction> -o <output>
+
+# Example: Average last 20% of frames
+gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged.xyz
+```
+
+### Octahedral Tilt
+
+Calculate octahedral tilt angles for perovskite systems.
+
+```bash
+gpumdkit.sh -calc oct-tilt -i <input.xyz> -n <B-O neighbor list> -o <output>
+
+# Example
+gpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o octahedral_tilt.dat
+```
+
+### Polarization (ABO3)
+
+Calculate local polarization for ABO3 perovskites.
+
+```bash
+gpumdkit.sh -calc pol-abo3 -i <input.xyz> \
+  --nl-ba <B-A neighbor list> \
+  --nl-bo <B-O neighbor list> \
+  --bec <Element=charge ...>
+
+# Example
+gpumdkit.sh -calc pol-abo3 -i model.xyz \
+  --nl-ba nl-Ti-Pb.dat \
+  --nl-bo nl-Ti-O.dat \
+  --bec Pb=2.5 Sr=2.0 Ti=4.0 O=-2.0
+```
+
+### Structure Minimization
+
+Relax structures using BFGS optimizer with NEP model.
+
+```bash
+gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]
+
+# Example
+gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
+```
+
+**Parameters:**
+- `fmax`: Force convergence threshold (default: 0.01 eV/Å)
+- `max_steps`: Maximum optimization steps (default: 1000)
+
+**Output:** `minimize.xyz` (optimization trajectory)
+
+### NEB Calculation
+
+Perform nudged elastic band calculations for migration barriers.
+
+```bash
+# Direct Python execution
+python Scripts/calculators/neb_calculation.py <initial.xyz> <final.xyz> <n_images> <nep.txt>
+
+# Example
+python Scripts/calculators/neb_calculation.py init.xyz fin.xyz 9 nep.txt
+```
+
+## Common Workflows
+
+### Ionic Transport Analysis
+
+```bash
+# 1. Run MD with compute_msd in run.in
+# 2. Calculate MSD
+gpumdkit.sh -calc msd dump.xyz Li 10
+
+# 3. Calculate conductivity
+gpumdkit.sh -calc ionic-cond Li 1
+
+# 4. Visualize
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+```
+
+### Descriptor Analysis
+
+```bash
+# 1. Calculate descriptors
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+
+# 2. Visualize with PCA
+gpumdkit.sh -plt des pca
+
+# 3. Or visualize with UMAP
+gpumdkit.sh -plt des umap
+```
+
+### Perovskite Analysis
+
+```bash
+# 1. Build neighbor lists
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E Pb
+
+# 2. Calculate displacements
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -o disp.dat
+
+# 3. Calculate tilt
+gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -o tilt.dat
+
+# 4. Calculate polarization
+gpumdkit.sh -calc pol-abo3 -i movie.xyz \
+  --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \
+  --bec Pb=2.5 Ti=4.0 O=-2.0
+```
+
+### Structure Relaxation
+
+```bash
+# 1. Minimize structure
+gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
+
+# 2. Use minimized structure for MD
+cp minimize.xyz relaxed_model.xyz
+```
+
+## Dependencies
+
+| Calculator | Required Packages |
+|------------|------------------|
+| All | `numpy`, `ase` |
+| ionic-cond | `scipy` |
+| nep, des, doas, minimize | `calorine` |
+| nlist, disp, oct-tilt, pol-abo3 | `ferrodispcalc` |
+| neb | `calorine`, `matplotlib` |
+
+Install dependencies:
+```bash
+pip install numpy ase scipy calorine matplotlib tqdm
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
+```
+
+## See Also
+
+- [Visualization](visualization.md) - Plot calculation results
+- [Analyzers](analyzers.md) - Structure analysis
+- [NEP Training Guide](nep_training.md) - Complete training workflow
diff --git a/docs/tutorials2/en/format_conversion.md b/docs/tutorials2/en/format_conversion.md
new file mode 100644
index 0000000..f4109bd
--- /dev/null
+++ b/docs/tutorials2/en/format_conversion.md
@@ -0,0 +1,273 @@
+# Format Conversion Guide
+
+<div align="center">
+  <p>
+    <a href="../zh/format_conversion.md">中文</a> | <strong>English</strong>
+  </p>
+</div>
+
+This guide covers all format conversion tools in GPUMDkit.
+
+## Supported Formats
+
+| Format | Extensions | Description |
+|--------|-----------|-------------|
+| VASP | POSCAR, OUTCAR, XDATCAR, vasprun.xml | Vienna Ab initio Simulation Package |
+| LAMMPS | .data, dump.* | Large-scale Atomic/Molecular Massively Parallel Simulator |
+| CP2K | .log, pos.xyz, frc.xyz, cell.cell | Quantum chemistry and solid state physics |
+| ABACUS | running_scf.log, running_md.log | Atomic-orbital Based Ab-initio Computation |
+| CIF | .cif | Crystallographic Information File |
+| MTP | .cfg | Moment Tensor Potential format |
+| ASE | .traj | Atomic Simulation Environment trajectory |
+| extxyz | .xyz | Extended XYZ (primary working format) |
+
+## Interactive Mode
+
+Launch the interactive menu and select option 1:
+
+```bash
+gpumdkit.sh
+# Select: 1) Format Conversion
+```
+
+You'll see:
+
+```
++-------------------------------------------------------------+
+|                   FORMAT CONVERSION TOOLS                   |
++-------------------------------------------------------------+
+| 101) VASP to extxyz            106) Add group labels        |
+| 102) MTP to extxyz             107) Add weight to extxyz    |
+| 103) CP2K to extxyz            108) Extract frame extxyz    |
+| 104) ABACUS to extxyz          109) Clean XYZ info          |
+| 105) extxyz to POSCAR          110) Replicate structure     |
++-------------------------------------------------------------+
+| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |
+| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |
+| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |
+| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|
++-------------------------------------------------------------+
+| 000) Return to main menu                                    |
++-------------------------------------------------------------+
+```
+
+## Command-Line Mode
+
+### VASP Conversions
+
+#### OUTCAR to extxyz
+
+```bash
+# Shell version (supports both OUTCAR and vasprun.xml)
+gpumdkit.sh -out2xyz <directory>
+
+# Python version (OUTCAR only)
+gpumdkit.sh -out2exyz <directory>
+
+# Example
+gpumdkit.sh -out2xyz ./vasp_results/
+```
+
+#### XDATCAR to extxyz
+
+```bash
+gpumdkit.sh -xdat2exyz XDATCAR output.xyz
+```
+
+#### POSCAR to extxyz
+
+```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+```
+
+#### extxyz to POSCAR
+
+```bash
+# Converts ALL frames to separate POSCAR files
+gpumdkit.sh -exyz2pos structures.xyz
+```
+
+### LAMMPS Conversions
+
+#### LAMMPS dump to extxyz
+
+```bash
+# IMPORTANT: Element symbols must match atom type IDs in dump file
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
+
+# Example
+gpumdkit.sh -lmp2exyz trajectory.dump Na Cl
+```
+
+#### POSCAR to LAMMPS data
+
+```bash
+gpumdkit.sh -pos2lmp POSCAR lammps.data
+```
+
+### CIF Conversions
+
+```bash
+# CIF to POSCAR
+gpumdkit.sh -cif2pos input.cif POSCAR.vasp
+
+# CIF to extxyz
+gpumdkit.sh -cif2exyz input.cif model.xyz
+```
+
+### Other Conversions
+
+```bash
+# ASE trajectory to extxyz
+gpumdkit.sh -traj2exyz input.traj output.xyz
+```
+
+## Structure Manipulation
+
+### Add Group Labels
+
+Group labels are required for GPUMD/NEP to identify atom types:
+
+```bash
+gpumdkit.sh -addgroup POSCAR <element1> <element2> ...
+
+# Example
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+```
+
+This creates `model.xyz` with group labels assigned to each atom.
+
+### Add Weights
+
+Add weight labels to structures for weighted training:
+
+```bash
+gpumdkit.sh -addweight input.xyz output.xyz <weight>
+
+# Example
+gpumdkit.sh -addweight train.xyz weighted.xyz 2.0
+```
+
+### Replicate Structure
+
+Create supercells from unit cells:
+
+```bash
+# By replication factors
+gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2
+
+# By target atom count
+gpumdkit.sh -replicate POSCAR supercell.vasp 256
+```
+
+### Extract Frame
+
+Extract a specific frame from a trajectory:
+
+```bash
+# 0-based index
+gpumdkit.sh -get_frame trajectory.xyz 1000
+```
+
+### Clean XYZ Metadata
+
+Remove extra metadata from extxyz files:
+
+```bash
+gpumdkit.sh -clean_xyz input.xyz clean.xyz
+```
+
+## Complete CLI Reference
+
+| Flag | Description | Syntax |
+|------|-------------|--------|
+| `-out2xyz` | OUTCAR to extxyz (shell) | `gpumdkit.sh -out2xyz <dir>` |
+| `-out2exyz` | OUTCAR to extxyz (python) | `gpumdkit.sh -out2exyz <dir>` |
+| `-pos2exyz` | POSCAR to extxyz | `gpumdkit.sh -pos2exyz <poscar> <xyz>` |
+| `-exyz2pos` | extxyz to POSCAR | `gpumdkit.sh -exyz2pos <xyz>` |
+| `-pos2lmp` | POSCAR to LAMMPS data | `gpumdkit.sh -pos2lmp <poscar> <lmp>` |
+| `-lmp2exyz` | LAMMPS dump to extxyz | `gpumdkit.sh -lmp2exyz <dump> <elem...>` |
+| `-cif2pos` | CIF to POSCAR | `gpumdkit.sh -cif2pos <cif> <output>` |
+| `-cif2exyz` | CIF to extxyz | `gpumdkit.sh -cif2exyz <cif> <output>` |
+| `-xdat2exyz` | XDATCAR to extxyz | `gpumdkit.sh -xdat2exyz XDATCAR dump.xyz` |
+| `-traj2exyz` | ASE traj to extxyz | `gpumdkit.sh -traj2exyz <traj> <xyz>` |
+| `-addgroup` | Add group labels | `gpumdkit.sh -addgroup <poscar> <elem...>` |
+| `-addweight` | Add weight | `gpumdkit.sh -addweight <in> <out> <weight>` |
+| `-replicate` | Replicate structure | `gpumdkit.sh -replicate <in> <out> a b c` |
+| `-get_frame` | Extract frame | `gpumdkit.sh -get_frame <xyz> <index>` |
+| `-clean_xyz` | Clean extxyz info | `gpumdkit.sh -clean_xyz <in> <out>` |
+
+## Examples
+
+### Example 1: Convert VASP MD Output
+
+```bash
+# Convert all OUTCAR files in current directory
+gpumdkit.sh -out2xyz .
+
+# Add group labels for NEP training
+gpumdkit.sh -addgroup POSCAR Pb Ti O
+
+# Result: model.xyz ready for NEP training
+```
+
+### Example 2: Prepare LAMMPS Simulation
+
+```bash
+# Convert POSCAR to LAMMPS data
+gpumdkit.sh -pos2lmp POSCAR system.data
+
+# After LAMMPS simulation, convert dump back
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li P S
+```
+
+### Example 3: Batch Conversion
+
+```bash
+# Convert multiple OUTCAR files
+for dir in run_*; do
+    gpumdkit.sh -out2xyz "$dir"
+    mv "$dir"/model.xyz "$dir"/trajectory.xyz
+done
+```
+
+### Example 4: Structure Replication
+
+```bash
+# Create 2x2x2 supercell
+gpumdkit.sh -replicate POSCAR supercell_222.vasp 2 2 2
+
+# Create supercell with ~256 atoms
+gpumdkit.sh -replicate POSCAR supercell_256.vasp 256
+```
+
+## Important Notes
+
+1. **extxyz is the primary format**: Most GPUMDkit tools work with extxyz files
+2. **Group labels are essential**: Required for GPUMD/NEP to identify atom types
+3. **Frame indexing is 0-based**: First frame is index 0
+4. **Element ordering matters for LAMMPS**: Must match atom type IDs in dump file
+5. **exyz2pos exports all frames**: Creates separate POSCAR for each frame
+
+## Dependencies
+
+Most Python scripts require:
+- `ase` (Atomic Simulation Environment)
+- `numpy`
+
+## Troubleshooting
+
+### Issue: Missing element information
+**Solution**: Ensure POSCAR has correct element names in the header
+
+### Issue: Incorrect atom count
+**Solution**: Check if POSCAR has selective dynamics enabled
+
+### Issue: LAMMPS conversion wrong species
+**Solution**: Verify element order matches atom type IDs in dump file
+
+## See Also
+
+- [Calculators](calculators.md) - Compute material properties
+- [Analyzers](analyzers.md) - Structure analysis
+- [NEP Training Guide](nep_training.md) - Complete training workflow
diff --git a/docs/tutorials2/en/index.md b/docs/tutorials2/en/index.md
new file mode 100644
index 0000000..079eec7
--- /dev/null
+++ b/docs/tutorials2/en/index.md
@@ -0,0 +1,160 @@
+# GPUMDkit Tutorials
+
+<div align="center">
+  <p>
+    <a href="../zh/index.md">中文</a> | <strong>English</strong>
+  </p>
+</div>
+
+Welcome to **GPUMDkit** - a powerful command-line toolkit for GPUMD and NEP!
+
+## What is GPUMDkit?
+
+GPUMDkit streamlines your molecular dynamics workflow with:
+
+- **Format Conversion**: Convert between VASP, LAMMPS, CP2K, ABACUS, CIF, and extxyz formats
+- **Calculators**: Compute ionic conductivity, descriptors, MSD, NEB, and more
+- **Analyzers**: Structure validation, filtering, composition analysis
+- **Visualization**: 31+ plot types for training, transport, and structural analysis
+- **Workflows**: Batch processing for DFT and MD simulations
+- **Sampling**: Structure selection using uniform, random, or FPS methods
+
+## Quick Start
+
+### Installation
+
+```bash
+# Clone the repository
+git clone https://github.com/zhyan0603/GPUMDkit.git
+
+# Install
+cd GPUMDkit
+source ./install.sh
+```
+
+### Dependencies
+
+```bash
+# Create conda environment
+conda create -n gpumdkit python=3.12
+conda activate gpumdkit
+
+# Install required packages
+pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
+```
+
+### Basic Usage
+
+```bash
+# Interactive mode (menu-driven)
+gpumdkit.sh
+
+# Command-line mode
+gpumdkit.sh -<option> [args...]
+
+# Get help
+gpumdkit.sh -h                    # General help
+gpumdkit.sh -<option> -h          # Specific command help
+gpumdkit.sh -plt -h               # Plot help
+gpumdkit.sh -calc -h              # Calculator help
+```
+
+## Tutorials
+
+| Tutorial | Description |
+|----------|-------------|
+| [Quick Start](quickstart.md) | Installation, configuration, and first steps |
+| [Format Conversion](format_conversion.md) | Convert between structure file formats |
+| [Calculators](calculators.md) | Compute material properties |
+| [Analyzers](analyzers.md) | Structure analysis and validation |
+| [Visualization](visualization.md) | Plotting and data visualization |
+| [Workflows](workflows.md) | Batch processing and automation |
+| [Structure Sampling](sampling.md) | Structure selection methods |
+| [NEP Training Guide](nep_training.md) | Complete NEP model training workflow |
+
+## Common Workflows
+
+### Workflow 1: NEP Model Training
+
+```bash
+# 1. Convert DFT data
+gpumdkit.sh -out2xyz ./vasp_results/
+
+# 2. Add group labels
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+
+# 3. Sample structures
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+
+# 4. Train NEP (external)
+# ...
+
+# 5. Validate
+gpumdkit.sh -plt train
+gpumdkit.sh -plt prediction
+```
+
+### Workflow 2: Ionic Conductivity
+
+```bash
+# 1. Calculate MSD
+gpumdkit.sh -calc msd trajectory.xyz Li 10
+
+# 2. Calculate conductivity
+gpumdkit.sh -calc ionic-cond Li 1
+
+# 3. Visualize
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+```
+
+### Workflow 3: Structure Analysis
+
+```bash
+# 1. Check composition
+gpumdkit.sh -analyze_comp train.xyz
+
+# 2. Check distances
+gpumdkit.sh -min_dist_pbc train.xyz
+
+# 3. Check force range
+gpumdkit.sh -range train.xyz force
+```
+
+## Module Overview
+
+| Module | Menu | CLI Flag | Description |
+|--------|------|----------|-------------|
+| Format Conversion | 1 | `-out2xyz`, `-pos2exyz`, etc. | Structure file conversion |
+| Sample Structures | 2 | `-pynep` | Structure sampling |
+| Workflows | 3 | - | Batch processing |
+| Calculators | 4 | `-calc <type>` | Property calculations |
+| Analyzers | 5 | `-range`, `-min_dist`, etc. | Structure analysis |
+| Visualization | 6 | `-plt <type>` | Plotting tools |
+| Utilities | 7 | `-time`, `-clean` | Utility functions |
+
+## Output File Conventions
+
+| File | Content |
+|------|---------|
+| `model.xyz` | Structure file in extxyz format |
+| `train.xyz` | Training dataset |
+| `nep.txt` | NEP model file |
+| `msd.out` | Mean square displacement data |
+| `thermo.out` | Thermodynamic properties |
+| `loss.out` | Training loss history |
+| `rdf.out` | Radial distribution function |
+| `sdc.out` | Self-diffusion coefficient data |
+
+## Getting Help
+
+- **General help**: `gpumdkit.sh -h`
+- **Plot help**: `gpumdkit.sh -plt -h`
+- **Calculator help**: `gpumdkit.sh -calc -h`
+- **Specific command**: `gpumdkit.sh -<option> -h`
+
+## Contact
+
+- **Developer**: Zihan YAN (yanzihan@westlake.edu.cn)
+- **GitHub**: https://github.com/zhyan0603/GPUMDkit
+- **Documentation**: https://zhyan0603.github.io/GPUMDkit/
diff --git a/docs/tutorials2/en/nep_training.md b/docs/tutorials2/en/nep_training.md
new file mode 100644
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--- /dev/null
+++ b/docs/tutorials2/en/nep_training.md
@@ -0,0 +1,299 @@
+# NEP Training Guide
+
+<div align="center">
+  <p>
+    <a href="../zh/nep_training.md">中文</a> | <strong>English</strong>
+  </p>
+</div>
+
+This guide provides a complete workflow for training NEP (Neuroevolution Potential) models using GPUMDkit.
+
+## Overview
+
+NEP training involves:
+
+1. **Data Preparation** - Convert and organize training data
+2. **Structure Sampling** - Select diverse structures
+3. **Model Training** - Train the NEP model (external)
+4. **Validation** - Check training quality
+5. **Active Learning** - Iteratively improve the model
+
+## Step 1: Data Preparation
+
+### Convert DFT Data to extxyz
+
+```bash
+# From VASP OUTCAR
+gpumdkit.sh -out2xyz ./vasp_results/
+
+# From VASP XDATCAR
+gpumdkit.sh -xdat2exyz XDATCAR trajectory.xyz
+
+# From CP2K
+gpumdkit.sh  # Select: 1) Format Conversion -> 103
+
+# From LAMMPS
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
+```
+
+### Add Group Labels
+
+Group labels are required for NEP to identify atom types:
+
+```bash
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+```
+
+This creates `model.xyz` with group labels.
+
+### Combine Training Data
+
+```bash
+# Combine multiple extxyz files
+cat file1.xyz file2.xyz file3.xyz > train.xyz
+
+# Or use composition analysis to select specific compositions
+gpumdkit.sh -analyze_comp all_structures.xyz
+```
+
+## Step 2: Data Quality Check
+
+### Check Composition
+
+```bash
+gpumdkit.sh -analyze_comp train.xyz
+```
+
+### Check Minimum Distances
+
+```bash
+# Fast check (no PBC)
+gpumdkit.sh -min_dist train.xyz
+
+# Accurate check (with PBC)
+gpumdkit.sh -min_dist_pbc train.xyz
+```
+
+### Check Property Ranges
+
+```bash
+# Check force range
+gpumdkit.sh -range train.xyz force
+
+# Check energy range
+gpumdkit.sh -range train.xyz energy
+
+# With histogram
+gpumdkit.sh -range train.xyz force hist
+```
+
+### Filter Structures
+
+```bash
+# Filter by minimum distance
+gpumdkit.sh -filter_dist_pbc train.xyz 1.0
+
+# Filter by box size
+gpumdkit.sh -filter_box train.xyz 20
+
+# Filter by force value
+gpumdkit.sh -filter_value train.xyz force 20
+```
+
+## Step 3: Structure Sampling
+
+### Sample Diverse Structures
+
+```bash
+# FPS sampling (preferred)
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+
+# Or uniform sampling
+python Scripts/sample_structures/sample_structures.py train.xyz uniform 100
+```
+
+### Perturb Structures
+
+Generate additional training data from existing structures:
+
+```bash
+python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
+```
+
+## Step 4: NEP Model Training
+
+### Prepare nep.in
+
+Create `nep.in` with training parameters:
+
+```
+type 3 Li Y Cl
+cutoff 6 4
+n_max 4
+l_max 4
+neuron 100
+batch 1000
+generation 100000
+```
+
+### Run Training
+
+```bash
+# External to GPUMDkit
+gpumd
+```
+
+## Step 5: Validation
+
+### Plot Training Results
+
+```bash
+# Plot training loss and parity plots
+gpumdkit.sh -plt train
+
+# Plot test predictions
+gpumdkit.sh -plt prediction
+
+# Combined train/test plots
+gpumdkit.sh -plt train_test
+
+# Force error analysis
+gpumdkit.sh -plt force_errors
+```
+
+### Check Convergence
+
+```bash
+# Plot loss curves
+gpumdkit.sh -plt train
+```
+
+Look for:
+- Smooth decrease in loss
+- No oscillations
+- Convergence to low values
+
+### Analyze Descriptors
+
+```bash
+# Calculate descriptors
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+
+# Visualize with PCA
+gpumdkit.sh -plt des pca
+
+# Or UMAP
+gpumdkit.sh -plt des umap
+```
+
+## Step 6: Active Learning
+
+### Run MD with Current NEP
+
+```bash
+# Setup MD simulation
+gpumdkit.sh  # Select: 3) Workflow -> 302
+```
+
+### Select Diverse Structures
+
+```bash
+# Filter by distance
+gpumdkit.sh -min_dist_pbc dump.xyz
+gpumdkit.sh -filter_box dump.xyz 13
+
+# Sample diverse structures
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+```
+
+### Compute DFT Reference
+
+```bash
+# Prepare SCF calculations
+gpumdkit.sh  # Select: 3) Workflow -> 301
+
+# Run DFT (external)
+```
+
+### Retrain Model
+
+```bash
+# Add new data to training set
+cat new_structures.xyz >> train.xyz
+
+# Retrain NEP (external)
+```
+
+## Complete Workflow Example
+
+```bash
+# 1. Convert DFT data
+gpumdkit.sh -out2xyz ./dft_results/
+
+# 2. Add group labels
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+
+# 3. Combine training data
+cat */model.xyz > train.xyz
+
+# 4. Check data quality
+gpumdkit.sh -analyze_comp train.xyz
+gpumdkit.sh -min_dist_pbc train.xyz
+gpumdkit.sh -range train.xyz force
+
+# 5. Filter structures
+gpumdkit.sh -filter_dist_pbc train.xyz 1.0
+
+# 6. Sample diverse structures
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+
+# 7. Train NEP (external)
+# ... create nep.in and run gpumd ...
+
+# 8. Validate training
+gpumdkit.sh -plt train
+gpumdkit.sh -plt prediction
+gpumdkit.sh -plt force_errors
+
+# 9. Analyze descriptors
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+gpumdkit.sh -plt des pca
+```
+
+## Tips for Better Training
+
+1. **Diverse Data**: Include various structures, temperatures, and compositions
+2. **Balanced Dataset**: Ensure all element types are well-represented
+3. **Quality Filter**: Remove structures with too-close atoms or high forces
+4. **Sufficient Data**: At least 1000-5000 structures for good accuracy
+5. **Validation Set**: Keep 10-20% of data for testing
+
+## Troubleshooting
+
+### Issue: High RMSE
+
+**Solution**: 
+- Add more diverse training data
+- Increase `neuron` and `n_max` parameters
+- Check for outliers in training data
+
+### Issue: Poor Predictions
+
+**Solution**:
+- Verify training data quality
+- Add structures from different phases/temperatures
+- Increase training `generation`
+
+### Issue: Overfitting
+
+**Solution**:
+- Use more training data
+- Reduce model complexity
+- Use regularization
+
+## See Also
+
+- [Format Conversion](format_conversion.md) - Convert file formats
+- [Calculators](calculators.md) - Compute properties
+- [Visualization](visualization.md) - Plot results
+- [Structure Sampling](sampling.md) - Sample structures
diff --git a/docs/tutorials2/en/quickstart.md b/docs/tutorials2/en/quickstart.md
new file mode 100644
index 0000000..49e0820
--- /dev/null
+++ b/docs/tutorials2/en/quickstart.md
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+# Quick Start Guide
+
+<div align="center">
+  <p>
+    <a href="../zh/quickstart.md">中文</a> | <strong>English</strong>
+  </p>
+</div>
+
+This guide will help you get started with GPUMDkit quickly.
+
+## Prerequisites
+
+Before installing GPUMDkit, ensure you have:
+
+- **Linux or macOS** (Windows via WSL)
+- **Bash** shell
+- **Python 3.8+** (3.12 recommended)
+- **Git** (for cloning the repository)
+
+## Installation
+
+### Step 1: Clone the Repository
+
+```bash
+git clone https://github.com/zhyan0603/GPUMDkit.git
+cd GPUMDkit
+```
+
+### Step 2: Run Installation Script
+
+```bash
+source ./install.sh
+```
+
+This script will:
+1. Add GPUMDkit to your PATH
+2. Set up bash completion
+3. Configure environment variables
+
+### Step 3: Reload Shell
+
+```bash
+source ~/.bashrc
+# or
+source ~/.zshrc
+```
+
+### Step 4: Verify Installation
+
+```bash
+gpumdkit.sh -h
+```
+
+You should see the help message with available commands.
+
+## Python Dependencies
+
+Some features require Python packages. Create a conda environment:
+
+```bash
+# Create environment
+conda create -n gpumdkit python=3.12
+conda activate gpumdkit
+
+# Install core packages
+pip install numpy ase scipy matplotlib
+
+# Install optional packages (for full functionality)
+pip install neptrain pymatgen dpdata
+
+# For perovskite analysis (optional)
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
+```
+
+## Two Usage Modes
+
+### Interactive Mode
+
+Launch the interactive menu:
+
+```bash
+gpumdkit.sh
+```
+
+You'll see:
+
+```
+       ____ ____  _   _ __  __ ____  _    _ _
+      / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
+     | |  _| |_) | | | | |\/| | | | | |/ / | __|
+     | |_| |  __/| |_| | |  | | |_| |   <| | |_
+      \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
+
+      GPUMDkit Version 1.5.5 (dev) (2026-05-10)
+Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+
+ ---------------------- GPUMD ------------------------
+ 1) Format Conversion          2) Sample Structures
+ 3) Workflow                   4) Calculators
+ 5) Analyzer                   6) Visualization
+ 7) Utilities                  8) Developing...
+ 0) Exit
+ ------------>>
+ Input the function number:
+```
+
+Navigate by entering the number of your desired function.
+
+### Command-Line Mode
+
+Execute commands directly:
+
+```bash
+# Show help
+gpumdkit.sh -h
+
+# Convert POSCAR to extxyz
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+
+# Plot training results
+gpumdkit.sh -plt train
+
+# Calculate ionic conductivity
+gpumdkit.sh -calc ionic-cond Li 1
+```
+
+## First Steps Example
+
+### Example 1: Convert a Structure
+
+```bash
+# Convert POSCAR to extxyz format
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+
+# Add group labels (required for NEP training)
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+```
+
+### Example 2: Analyze Training Data
+
+```bash
+# Check force range in training data
+gpumdkit.sh -range train.xyz force
+
+# Check minimum interatomic distances
+gpumdkit.sh -min_dist_pbc train.xyz
+
+# Analyze composition
+gpumdkit.sh -analyze_comp train.xyz
+```
+
+### Example 3: Plot Results
+
+```bash
+# Plot NEP training results
+gpumdkit.sh -plt train
+
+# Plot mean square displacement
+gpumdkit.sh -plt msd
+
+# Plot radial distribution function
+gpumdkit.sh -plt rdf
+```
+
+## Getting Help
+
+### General Help
+
+```bash
+gpumdkit.sh -h
+```
+
+### Module-Specific Help
+
+```bash
+# Plot help
+gpumdkit.sh -plt -h
+
+# Calculator help
+gpumdkit.sh -calc -h
+
+# Specific command help
+gpumdkit.sh -pos2exyz -h
+gpumdkit.sh -calc ionic-cond -h
+```
+
+### Interactive Mode Help
+
+In interactive mode, each submenu displays available options with descriptions.
+
+## Common Issues
+
+### Issue: Command not found
+
+**Solution**: Ensure GPUMDkit is in your PATH:
+
+```bash
+# Check if gpumdkit.sh is in PATH
+which gpumdkit.sh
+
+# If not found, add to PATH manually
+export GPUMDkit_path=/path/to/GPUMDkit
+export PATH=${GPUMDkit_path}:${PATH}
+```
+
+### Issue: Missing Python packages
+
+**Solution**: Activate the conda environment:
+
+```bash
+conda activate gpumdkit
+```
+
+### Issue: Permission denied
+
+**Solution**: Make the script executable:
+
+```bash
+chmod +x /path/to/GPUMDkit/gpumdkit.sh
+```
+
+## Next Steps
+
+Now that you have GPUMDkit installed, explore these tutorials:
+
+- [Format Conversion](format_conversion.md) - Learn to convert between file formats
+- [Calculators](calculators.md) - Compute material properties
+- [Visualization](visualization.md) - Create publication-ready plots
+- [NEP Training Guide](nep_training.md) - Complete training workflow
+
+## Updating GPUMDkit
+
+To update to the latest version:
+
+```bash
+gpumdkit.sh -update
+```
+
+Or manually:
+
+```bash
+cd /path/to/GPUMDkit
+git pull origin main
+```
diff --git a/docs/tutorials2/en/sampling.md b/docs/tutorials2/en/sampling.md
new file mode 100644
index 0000000..e4649ef
--- /dev/null
+++ b/docs/tutorials2/en/sampling.md
@@ -0,0 +1,221 @@
+# Structure Sampling Guide
+
+<div align="center">
+  <p>
+    <a href="../zh/sampling.md">中文</a> | <strong>English</strong>
+  </p>
+</div>
+
+This guide covers structure sampling and selection tools in GPUMDkit.
+
+## Available Methods
+
+| Method | Menu | Description |
+|--------|------|-------------|
+| Uniform/Random | 201 | Select evenly spaced or random frames |
+| FPS by PyNEP | 202 | Farthest point sampling (deprecated) |
+| FPS by NepTrain | 203 | Farthest point sampling (preferred) |
+| Perturbation | 204 | Generate perturbed structures |
+| Force Deviation | 205 | Select high-force-deviation structures |
+
+## Interactive Mode
+
+```bash
+gpumdkit.sh
+# Select: 2) Sample Structures
+```
+
+You'll see:
+
+```
++------------------------------------------------------+
+|                 SAMPLE STRUCTURE TOOLS               |
++------------------------------------------------------+
+| 201) Sample structures from extxyz                   |
+| 202) FPS sampling by PyNEP [deprecated]              |
+| 203) FPS sampling by NepTrain [preferred]            |
+| 204) Perturb structure                               |
+| 205) Select max force deviation structs              |
++------------------------------------------------------+
+```
+
+## Command Reference
+
+### Uniform/Random Sampling
+
+Select structures using uniform or random sampling.
+
+```bash
+python Scripts/sample_structures/sample_structures.py <input.xyz> <method> <num_samples> [skip_initial]
+
+# Examples
+python Scripts/sample_structures/sample_structures.py dump.xyz uniform 50
+python Scripts/sample_structures/sample_structures.py dump.xyz random 100 500
+```
+
+**Parameters:**
+- `input.xyz`: Input trajectory file
+- `method`: `uniform` or `random`
+- `num_samples`: Number of frames to select
+- `skip_initial`: (optional) Skip first N frames
+
+**How it works:**
+- **Uniform**: Uses `numpy.linspace` to select evenly spaced indices
+- **Random**: Uses `numpy.random.choice` to select random indices without replacement
+
+**Output:** `sampled_structures.xyz`
+
+### Farthest Point Sampling (FPS) - NepTrain (Preferred)
+
+Select diverse structures using FPS on NEP descriptors.
+
+```bash
+python Scripts/sample_structures/neptrain_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
+
+# Example
+python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
+```
+
+**Selection methods (interactive):**
+1. **Minimum distance**: Select until max distance to existing training set drops below threshold
+2. **Number of structures**: Select between `min_select` and `max_select` structures
+
+**Output:**
+- `selected.xyz`
+- `select.png` (PCA visualization)
+- `pca_sample.txt`, `pca_train.txt`, `pca_selected.txt`
+
+**Citation**: Chen et al., Comput. Phys. Commun., 2025, 317, 109859
+
+### Farthest Point Sampling (FPS) - PyNEP (Deprecated)
+
+```bash
+python Scripts/sample_structures/pynep_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
+```
+
+**Note**: PyNEP package is no longer actively maintained. Use NepTrain (method 203) instead.
+
+### Structure Perturbation
+
+Generate perturbed structures for training data.
+
+```bash
+python Scripts/sample_structures/perturb_structure.py <input.vasp> <pert_num> <cell_pert> <atom_pert> <style>
+
+# Example
+python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
+```
+
+**Parameters:**
+- `input.vasp`: POSCAR/CONTCAR file
+- `pert_num`: Number of perturbed structures (e.g., 20)
+- `cell_pert`: Cell perturbation fraction (e.g., 0.03 = 3%)
+- `atom_pert`: Atom perturbation distance in Angstrom (e.g., 0.2)
+- `style`: `normal`, `uniform`, or `const`
+
+**Output:** `POSCAR_01.vasp`, `POSCAR_02.vasp`, ..., `POSCAR_<N>.vasp`
+
+### Force Deviation Selection
+
+Select structures with high force deviations from active learning.
+
+```bash
+python Scripts/sample_structures/select_max_modev.py <top_n> <min_deviation>
+
+# Example
+python Scripts/sample_structures/select_max_modev.py 200 0.15
+```
+
+**Required files:**
+- `active.out` - Max force deviation per structure (from GPUMD `active` command)
+- `active.xyz` - Corresponding structures
+
+**Output:** `selected.xyz`
+
+### Frame Range Extraction
+
+Extract a range of frames from a trajectory.
+
+```bash
+python Scripts/sample_structures/frame_range.py <input.xyz> <start_fraction> <end_fraction>
+
+# Example: Extract first 80% of frames
+python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
+```
+
+**Output:** `dump_0.00_0.80.xyz`
+
+## Common Workflows
+
+### Training Data Preparation
+
+```bash
+# 1. Run MD simulation
+# ... generate trajectory ...
+
+# 2. Filter by distance
+gpumdkit.sh -min_dist_pbc dump.xyz
+gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
+
+# 3. Sample diverse structures
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+
+# 4. Add to training set
+cat selected.xyz >> train.xyz
+```
+
+### Active Learning Data Selection
+
+```bash
+# 1. Run MD with current NEP
+# ... generate active.out and active.xyz ...
+
+# 2. Select high-deviation structures
+python Scripts/sample_structures/select_max_modev.py 100 0.1
+
+# 3. Or use FPS for diversity
+python Scripts/sample_structures/neptrain_select_structs.py active.xyz train.xyz nep.txt
+```
+
+### Structure Perturbation for Initial Data
+
+```bash
+# 1. Start from equilibrium structure
+# 2. Generate perturbations
+python Scripts/sample_structures/perturb_structure.py POSCAR 50 0.05 0.3 uniform
+
+# 3. Run DFT on perturbed structures
+# ... DFT calculations ...
+
+# 4. Add to training set
+```
+
+## Dependencies
+
+| Method | Required Packages |
+|--------|------------------|
+| Uniform/Random | `numpy`, `ase` |
+| FPS (NepTrain) | `numpy`, `ase`, `matplotlib`, `scikit-learn`, `scipy`, `NepTrain` |
+| FPS (PyNEP) | `numpy`, `ase`, `matplotlib`, `scikit-learn`, `pynep` |
+| Perturbation | `dpdata` |
+| Force Deviation | `numpy`, `ase` |
+
+Install dependencies:
+```bash
+pip install numpy ase matplotlib scikit-learn scipy dpdata
+pip install neptrain  # For FPS by NepTrain
+```
+
+## Important Notes
+
+1. **FPS is preferred**: Farthest Point Sampling provides better diversity than uniform/random
+2. **NepTrain over PyNEP**: NepTrain is actively maintained; PyNEP is deprecated
+3. **Filter before sampling**: Remove unphysical structures (too close, too large) first
+4. **Frame indexing is 0-based**: First frame is index 0
+5. **Output is extxyz**: All sampling methods output extxyz format
+
+## See Also
+
+- [Format Conversion](format_conversion.md) - Convert file formats
+- [Analyzers](analyzers.md) - Filter and analyze structures
+- [NEP Training Guide](nep_training.md) - Complete training workflow
diff --git a/docs/tutorials2/en/visualization.md b/docs/tutorials2/en/visualization.md
new file mode 100644
index 0000000..b3dd066
--- /dev/null
+++ b/docs/tutorials2/en/visualization.md
@@ -0,0 +1,226 @@
+# Visualization Guide
+
+<div align="center">
+  <p>
+    <a href="../zh/visualization.md">中文</a> | <strong>English</strong>
+  </p>
+</div>
+
+This guide covers all plotting and visualization tools in GPUMDkit.
+
+## Quick Reference
+
+```bash
+gpumdkit.sh -plt <type>              # Display plot interactively
+gpumdkit.sh -plt <type> save         # Save plot as PNG
+gpumdkit.sh -plt <type> -h           # Get help for specific plot
+```
+
+## Plot Categories
+
+### NEP Training & Evaluation (12 plot types)
+
+| Command | Input Files | Description |
+|---------|-------------|-------------|
+| `train` | `loss.out`, `*_train.out` | Training loss curves and parity plots |
+| `prediction` / `test` | `*_test.out` | Test set parity plots |
+| `train_test` | `*_train.out`, `*_test.out` | Combined train/test parity plots |
+| `parity_density` | `*_train.out` | Density-based parity plots for large datasets |
+| `train_density` | `loss.out`, `*_train.out` | Training with density visualization |
+| `force_errors` | `force_train.out` | Force error analysis |
+| `restart` | `nep.restart` | NEP restart file visualization |
+| `charge` | `charge_train.out` | Charge distribution (qNEP) |
+| `born_charge` / `bec` | `bec_train.out`, `bec_test.out` | Born effective charges |
+| `dimer` | NEP model | Dimer interaction curves |
+| `des` | `descriptors.npy` | Descriptor PCA/UMAP visualization |
+| `lr` | `loss.out` (gnep) | Learning rate decay |
+
+```bash
+# Training results
+gpumdkit.sh -plt train
+gpumdkit.sh -plt prediction
+gpumdkit.sh -plt force_errors
+
+# Descriptor visualization (requires prior calculation)
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+gpumdkit.sh -plt des pca
+gpumdkit.sh -plt des umap
+
+# Dimer plot
+gpumdkit.sh -plt dimer Li Li nep.txt
+```
+
+### Transport Properties (9 plot types)
+
+| Command | Input Files | Description |
+|---------|-------------|-------------|
+| `msd` | `msd.out` | Mean square displacement |
+| `msd_conv` | `msd_step*.out` | MSD convergence check |
+| `msd_all` | `msd.out` (all_groups) | MSD per species |
+| `sdc` | `msd.out` | Self-diffusion coefficient |
+| `msd_sdc` | `msd.out` | MSD and SDC combined |
+| `sigma` / `arrhenius_sigma` | `*K/` directories | Arrhenius ionic conductivity |
+| `D` / `arrhenius_d` | `*K/` directories | Arrhenius diffusivity |
+| `sigma_xyz` | `*K/` directories | Directional Arrhenius conductivity |
+| `D_xyz` | `*K/` directories | Directional Arrhenius diffusivity |
+
+```bash
+# MSD and diffusion
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+gpumdkit.sh -plt msd_sdc
+
+# MSD for all species (requires all_groups in run.in)
+gpumdkit.sh -plt msd_all Li P S
+
+# Arrhenius plots (requires temperature-organized directories)
+# Directory structure: 300K/, 350K/, 400K/, ... each containing msd.out
+gpumdkit.sh -plt arrhenius_sigma
+gpumdkit.sh -plt arrhenius_d
+```
+
+### Structural Analysis (10 plot types)
+
+| Command | Input Files | Description |
+|---------|-------------|-------------|
+| `thermo` | `thermo.out` | Thermodynamic properties |
+| `thermo2` | `thermo.out` | Alternative thermo style |
+| `thermo3` | `thermo.out` | Third thermo style |
+| `rdf` | `rdf.out` | Radial distribution function |
+| `rdf_pmf` | `rdf.out` | RDF + potential of mean force |
+| `vac` | `sdc.out` | Velocity autocorrelation |
+| `cohesive` | `cohesive.out` | Cohesive energy curve |
+| `net_force` | extxyz file | Net force distribution |
+| `doas` | `doas.out` | Density of atomistic states |
+| `plane-grid` | `model.xyz`, `displacements.dat` | Displacement grid visualization |
+
+```bash
+# Thermodynamic properties
+gpumdkit.sh -plt thermo
+
+# RDF analysis
+gpumdkit.sh -plt rdf
+gpumdkit.sh -plt rdf 2              # Specific column
+gpumdkit.sh -plt rdf_pmf 300        # With PMF at 300K
+
+# DOAS visualization (requires prior calculation)
+gpumdkit.sh -plt doas doas.out Li
+
+# Plane-grid displacement
+gpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Pb Sr
+```
+
+### Heat Transport (4 plot types)
+
+| Command | Input Files | Description |
+|---------|-------------|-------------|
+| `emd` | EMD outputs | EMD thermal conductivity |
+| `nemd` | NEMD outputs | NEMD thermal transport |
+| `hnemd` | HNEMD outputs | HNEMD thermal transport |
+| `viscosity` | `viscosity.out` | Viscosity components |
+
+```bash
+# EMD thermal conductivity
+gpumdkit.sh -plt emd x
+
+# NEMD thermal transport
+# Parameters: real_length scale_eff_size cutoff_freq
+gpumdkit.sh -plt nemd <real_length> <scale_eff_size> <cutoff_freq> save
+
+# HNEMD thermal transport
+gpumdkit.sh -plt hnemd <scale_eff_size> <cutoff_freq> save
+
+# Viscosity
+gpumdkit.sh -plt viscosity save
+```
+
+### Phonons (1 plot type)
+
+| Command | Input Files | Description |
+|---------|-------------|-------------|
+| `pdos` | `model.xyz`, `run.in`, `dos.out`, `mvac.out` | Phonon DOS and heat capacity |
+
+```bash
+gpumdkit.sh -plt pdos save
+```
+
+## Common Workflows
+
+### NEP Training Validation
+
+```bash
+# 1. Plot training loss
+gpumdkit.sh -plt train
+
+# 2. Check test predictions
+gpumdkit.sh -plt prediction
+
+# 3. Analyze force errors
+gpumdkit.sh -plt force_errors
+
+# 4. Visualize descriptors
+gpumdkit.sh -plt des pca
+```
+
+### Diffusion Analysis
+
+```bash
+# 1. Plot MSD
+gpumdkit.sh -plt msd
+
+# 2. Plot self-diffusion coefficient
+gpumdkit.sh -plt sdc
+
+# 3. Combined MSD-SDC plot
+gpumdkit.sh -plt msd_sdc
+
+# 4. Arrhenius analysis (multi-temperature)
+gpumdkit.sh -plt arrhenius_d
+```
+
+### Thermal Transport
+
+```bash
+# 1. Plot thermodynamic properties
+gpumdkit.sh -plt thermo
+
+# 2. Plot thermal conductivity
+gpumdkit.sh -plt emd x
+
+# 3. Or NEMD/HNEMD
+gpumdkit.sh -plt nemd 10 1 60 save
+```
+
+## Output Files
+
+| Plot Type | PNG Filename (with `save`) |
+|-----------|---------------------------|
+| `train` | `train.png` |
+| `prediction` | `prediction.png` |
+| `train_test` | `train_test.png` |
+| `force_errors` | `force_errors.png` |
+| `des` | `descriptors.png` |
+| `msd` | `msd.png` |
+| `sdc` | `sdc.png` |
+| `msd_sdc` | `MSD_SDC.png` |
+| `thermo` | `thermo.png` |
+| `rdf` | `rdf.png` |
+| `arrhenius_sigma` | `Arrhenius_sigma.png` |
+| `arrhenius_d` | `Arrhenius_D.png` |
+| `emd` | `emd.png` |
+| `nemd` | `nemd.png` |
+| `hnemd` | `hnemd.png` |
+| `viscosity` | `viscosity.png` |
+| `cohesive` | `Cohesive.png` |
+
+## Dependencies
+
+All plotting scripts require:
+- `matplotlib`
+- `numpy`
+
+## See Also
+
+- [Calculators](calculators.md) - Compute properties to plot
+- [Analyzers](analyzers.md) - Analyze data before plotting
+- [NEP Training Guide](nep_training.md) - Complete training workflow
diff --git a/docs/tutorials2/en/workflows.md b/docs/tutorials2/en/workflows.md
new file mode 100644
index 0000000..667bbf9
--- /dev/null
+++ b/docs/tutorials2/en/workflows.md
@@ -0,0 +1,280 @@
+# Workflows Guide
+
+<div align="center">
+  <p>
+    <a href="../zh/workflows.md">中文</a> | <strong>English</strong>
+  </p>
+</div>
+
+This guide covers batch processing and workflow automation tools in GPUMDkit.
+
+## Available Workflows
+
+| Workflow | Menu | Description |
+|----------|------|-------------|
+| SCF Batch (VASP) | 301.1 | VASP single-point batch setup |
+| SCF Batch (CP2K) | 301.2 | CP2K single-point batch setup |
+| MD Batch (GPUMD) | 302 | GPUMD MD sampling batch setup |
+| MD Batch (LAMMPS) | 303 | LAMMPS MD sampling batch setup |
+
+## Interactive Mode
+
+```bash
+gpumdkit.sh
+# Select: 3) Workflow
+```
+
+You'll see:
+
+```
++---------------------------------------------------------+
+|                      WORKFLOW TOOLS                     |
++---------------------------------------------------------+
+| 301) SCF batch pretreatment                             |
+| 302) MD sample batch pretreatment (gpumd)               |
+| 303) MD sample batch pretreatment (lmp)                 |
++---------------------------------------------------------+
+```
+
+## SCF Batch Pretreatment
+
+### VASP SCF Batch
+
+Prepare batch single-point energy/force calculations for VASP.
+
+```bash
+gpumdkit.sh  # Select: 3) Workflow -> 301 -> VASP
+```
+
+**Prerequisites:**
+
+1. Place POSCAR files (or single `.xyz`) in current directory
+2. Prepare `fp/` directory with:
+   - `INCAR`
+   - `POTCAR`
+   - `KPOINTS`
+
+**Output Structure:**
+
+```
+struct_fp/
+├── POSCAR_1.vasp
+├── POSCAR_2.vasp
+└── ...
+fp/
+├── INCAR
+├── POTCAR
+└── KPOINTS
+<prefix>_1/
+├── POSCAR -> ../struct_fp/POSCAR_1.vasp
+├── POTCAR -> ../fp/POTCAR
+├── INCAR -> ../fp/INCAR
+└── KPOINTS -> ../fp/KPOINTS
+<prefix>_2/
+└── ...
+presub.sh
+```
+
+### CP2K SCF Batch
+
+Prepare batch single-point calculations for CP2K.
+
+```bash
+python Scripts/workflow/scf_batch_pretreatment_cp2k.py <extxyz_file> <template.inp> <prefix_name>
+
+# Example
+python Scripts/workflow/scf_batch_pretreatment_cp2k.py structures.xyz cp2k_template.inp H2O_batch
+```
+
+**Prerequisites:**
+
+1. Prepare CP2K input template (`cp2k_template.inp`)
+2. Template should read coordinates from `pos.xyz`
+
+**Output Structure:**
+
+```
+<prefix>_1/
+├── input.inp
+└── pos.xyz
+<prefix>_2/
+└── ...
+```
+
+## MD Sample Batch Pretreatment
+
+### GPUMD MD Batch
+
+Set up batch MD simulations for GPUMD.
+
+```bash
+gpumdkit.sh  # Select: 3) Workflow -> 302
+```
+
+**Prerequisites:**
+
+1. Place POSCAR files (or single `.xyz`) in current directory
+2. Prepare `md/` directory with:
+   - `nep.txt` (NEP model)
+   - `run_1.in`, `run_2.in`, ... (GPUMD input files)
+
+**Output Structure:**
+
+```
+struct_md/
+├── model_1.xyz
+├── model_2.xyz
+└── ...
+md/
+├── nep.txt
+├── run_1.in
+├── run_2.in
+└── ...
+sample_1/
+├── model.xyz -> ../struct_md/model_1.xyz
+├── nep.txt -> ../md/nep.txt
+└── run.in -> ../md/run_1.in
+sample_2/
+└── ...
+presub.sh
+```
+
+### LAMMPS MD Batch
+
+Set up batch MD simulations for LAMMPS.
+
+```bash
+gpumdkit.sh  # Select: 3) Workflow -> 303
+```
+
+**Prerequisites:**
+
+1. Place POSCAR files (or single `.xyz`) in current directory
+2. Prepare `md/` directory with:
+   - `nep.txt` (NEP model)
+   - `lmprun.in` (LAMMPS input file)
+
+**Output Structure:**
+
+```
+struct_md/
+├── lammps_1.data
+├── lammps_2.data
+└── ...
+md/
+├── nep.txt
+└── lmprun.in
+sample_1/
+├── lammps.data -> ../struct_md/lammps_1.data
+├── nep.txt -> ../md/nep.txt
+└── lmprun.in -> ../md/lmprun.in
+sample_2/
+└── ...
+presub.sh
+```
+
+## Active Learning Workflow
+
+### Overview
+
+Active learning iteratively improves NEP models by:
+
+1. Running MD with current NEP model
+2. Selecting diverse structures
+3. Computing DFT reference data
+4. Retraining NEP model
+
+### Manual Active Learning Loop
+
+```bash
+# Step 1: MD sampling with current NEP
+gpumdkit.sh  # Select: 3) Workflow -> 302
+
+# Step 2: Filter and sample structures
+gpumdkit.sh -min_dist_pbc dump.xyz
+gpumdkit.sh -filter_box dump.xyz 13
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+
+# Step 3: Prepare SCF calculations
+gpumdkit.sh  # Select: 3) Workflow -> 301
+
+# Step 4: Run DFT calculations (external)
+
+# Step 5: Convert and validate
+gpumdkit.sh -out2xyz ./scf_results/
+gpumdkit.sh -range new_data.xyz force
+
+# Step 6: Retrain NEP model (external)
+```
+
+### Configurable Parameters
+
+| Parameter | Description | Example |
+|-----------|-------------|---------|
+| `prefix_name` | Directory prefix | `LiF_iter01` |
+| `min_dist` | Minimum distance filter | `1.4` |
+| `box_limit` | Maximum box size filter | `13` |
+| `max_fp_num` | Maximum DFT calculations | `50` |
+| `sample_method` | Sampling method | `uniform`, `random`, or `pynep` |
+| `pynep_sample_dist` | FPS distance threshold | `0.01` |
+
+## Examples
+
+### Example 1: Temperature-Dependent MD
+
+```bash
+# Setup directories for multiple temperatures
+for temp in 300 500 700 900; do
+    mkdir -p "${temp}K"
+    cp model.xyz "${temp}K/"
+    cp nep.txt "${temp}K/"
+    sed "s/TEMPERATURE/$temp/g" run_template.in > "${temp}K/run.in"
+done
+```
+
+### Example 2: High-Throughput Screening
+
+```bash
+# Prepare structures for multiple calculations
+for struct in structures/*.vasp; do
+    name=$(basename "$struct" .vasp)
+    mkdir -p "calc_$name"
+    cp "$struct" "calc_$name/POSCAR"
+    ln -s ../POTCAR "calc_$name/"
+    ln -s ../INCAR "calc_$name/"
+    ln -s ../KPOINTS "calc_$name/"
+done
+```
+
+### Example 3: NEP Training Data Generation
+
+```bash
+# 1. Start with initial structures
+gpumdkit.sh -replicate POSCAR supercell.vasp 3 3 3
+
+# 2. Perturb structures
+python Scripts/sample_structures/perturb_structure.py supercell.vasp 20 0.03 0.2 uniform
+
+# 3. Run MD sampling
+gpumdkit.sh  # Select: 3) Workflow -> 302
+
+# 4. Select diverse structures
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+
+# 5. Prepare DFT calculations
+gpumdkit.sh  # Select: 3) Workflow -> 301
+```
+
+## Important Notes
+
+1. **Directory structure matters**: Workflows expect specific directory layouts
+2. **Symlinks are used**: Output directories use symlinks to save disk space
+3. **presub.sh**: Generated submission script may need modification for your cluster
+4. **Template files**: Ensure input templates are correct before batch processing
+5. **Backup important files**: Always backup your data before running workflows
+
+## See Also
+
+- [Format Conversion](format_conversion.md) - Convert file formats
+- [Structure Sampling](sampling.md) - Sample structures for training
+- [NEP Training Guide](nep_training.md) - Complete training workflow
diff --git a/docs/tutorials2/zh/analyzers.md b/docs/tutorials2/zh/analyzers.md
new file mode 100644
index 0000000..342a877
--- /dev/null
+++ b/docs/tutorials2/zh/analyzers.md
@@ -0,0 +1,289 @@
+# 分析工具指南
+
+<div align="center">
+  <p>
+    <strong>中文</strong> | <a href="../en/analyzers.md">English</a>
+  </p>
+</div>
+
+本指南介绍 GPUMDkit 中用于结构验证、过滤和质量控制的所有分析工具。
+
+## 可用工具
+
+| 工具 | 命令 | 描述 |
+|------|------|------|
+| 成分分析 | `-analyze_comp` | 按成分分组结构 |
+| 异常值检测 | 菜单 502 | 查找高误差结构 |
+| 化学物种 | 菜单 503 | 列出唯一元素 |
+| 电荷平衡 | `-cbc` | 检查氧化态平衡 |
+| 属性范围 | `-range` | 能量/力/应力统计 |
+| 距离过滤 | 菜单 506 | 按最小距离过滤（无 PBC） |
+| 距离过滤 (PBC) | 菜单 506b | 按最小距离过滤（带 PBC） |
+| 最小距离 | `-min_dist` | 计算最小距离（无 PBC） |
+| 最小距离 (PBC) | `-min_dist_pbc` | 计算最小距离（带 PBC） |
+| 概率密度 | 菜单 508 | 3D 扩散通道分析 |
+
+## 交互模式
+
+```bash
+gpumdkit.sh
+# 选择: 5) Analyzer
+```
+
+您将看到：
+
+```
++------------------------------------------------------+
+|                    ANALYZER TOOLS                    |
++------------------------------------------------------+
+| 501) Analyze composition of extxyz                   |
+| 502) Find outliers of extxyz                         |
+| 503) Analyze chemical species of extxyz              |
+| 504) Check charge balance of extxyz                  |
+| 505) Analyze energy/force/virial range               |
+| 506) Filter structures by minimum distance           |
+| 507) Get minimum interatomic distance                |
+| 508) Probability density analysis                    |
++------------------------------------------------------+
+```
+
+## 命令参考
+
+### 成分分析
+
+按化学成分分析和分组结构。
+
+```bash
+gpumdkit.sh -analyze_comp train.xyz
+```
+
+**输出：** 唯一成分的表格，包含原子数和结构数。可交互选择导出特定成分。
+
+### 属性范围分析
+
+计算 extxyz 文件中能量、力或应力的范围（最小值、最大值）。
+
+```bash
+gpumdkit.sh -range <文件名> <属性> [hist]
+
+# 示例
+gpumdkit.sh -range train.xyz energy
+gpumdkit.sh -range train.xyz force
+gpumdkit.sh -range train.xyz virial
+gpumdkit.sh -range train.xyz force hist    # 带直方图
+```
+
+**输出：** 最小/最大值。使用 `hist` 参数可选择直方图。
+
+### 最小距离
+
+计算每个元素对的最小原子间距离。
+
+```bash
+# 快速计算（无 PBC）
+gpumdkit.sh -min_dist dump.xyz
+
+# 精确计算（带 PBC）
+gpumdkit.sh -min_dist_pbc dump.xyz
+```
+
+**输出：** 所有元素对的最小距离表
+
+### 电荷平衡检查
+
+检查所有结构的氧化态平衡。
+
+```bash
+gpumdkit.sh -cbc train.xyz
+```
+
+**输出：**
+- `balanced.xyz` - 电荷平衡的结构
+- `unbalanced.xyz` - 不平衡的结构
+- `indices.txt` - 摘要
+
+### 化学物种识别
+
+列出文件中所有唯一的化学元素。
+
+```bash
+# 交互模式
+gpumdkit.sh  # 选择: 5) Analyzer -> 503
+```
+
+**输出：** 排序后的所有元素列表
+
+### 结构过滤
+
+#### 按最小距离（无 PBC）
+
+```bash
+gpumdkit.sh  # 选择: 5) Analyzer -> 506
+```
+
+**输入：** extxyz 文件，距离阈值
+**输出：** `filtered_<file>.xyz`，`filtered_out_<file>.xyz`
+
+#### 按最小距离（带 PBC）
+
+```bash
+gpumdkit.sh  # 选择: 5) Analyzer -> 506b
+```
+
+对周期性系统更精确。
+
+#### 按元素对距离范围
+
+```bash
+gpumdkit.sh -filter_range <文件> <元素1> <元素2> <最小距离> <最大距离>
+
+# 示例：过滤 Li-Li 距离在 1.9 到 2.0 Å 之间
+gpumdkit.sh -filter_range dump.xyz Li Li 1.9 2.0
+```
+
+**输出：** `filtered_<elem1>_<elem2>_<min>_<max>.xyz`
+
+#### 按盒子大小
+
+```bash
+gpumdkit.sh -filter_box <文件> <边缘限制>
+
+# 示例：过滤盒子边缘 > 20 Å 的结构
+gpumdkit.sh -filter_box dump.xyz 20
+```
+
+**输出：** `filtered_by_box.xyz`
+
+#### 按属性值
+
+```bash
+gpumdkit.sh -filter_value <文件> <属性> <阈值>
+
+# 示例：保留力 < 20 eV/Å 的结构
+gpumdkit.sh -filter_value train.xyz force 20
+```
+
+**输出：** `filtered.xyz`
+
+### 异常值检测
+
+基于 RMSE 阈值查找异常值结构。
+
+```bash
+gpumdkit.sh  # 选择: 5) Analyzer -> 502
+```
+
+**必需文件：**
+- `train.xyz`
+- `energy_train.out`
+- `force_train.out`
+- `stress_train.out`
+
+**输出：** `selected.xyz`（高误差），`remained.xyz`（低误差）
+
+### 概率密度分析
+
+从 AIMD 轨迹计算移动离子的 3D 概率密度。
+
+```bash
+gpumdkit.sh  # 选择: 5) Analyzer -> 508
+```
+
+**参数：**
+- 参考结构（POSCAR）
+- 轨迹文件（extxyz）
+- 移动物种（如 Li）
+- 网格间距（如 0.25 Å）
+
+**输出：** `probability_density_<interval>.vasp`（CHGCAR 格式）
+
+## 常见工作流程
+
+### 数据质量检查
+
+```bash
+# 1. 检查成分
+gpumdkit.sh -analyze_comp train.xyz
+
+# 2. 检查最小距离
+gpumdkit.sh -min_dist_pbc train.xyz
+
+# 3. 检查力范围
+gpumdkit.sh -range train.xyz force
+
+# 4. 检查异常值
+gpumdkit.sh  # 选择: 5) Analyzer -> 502
+```
+
+### 结构过滤管道
+
+```bash
+# 1. 按距离过滤
+gpumdkit.sh  # 选择: 5) Analyzer -> 506
+
+# 2. 按盒子大小过滤
+gpumdkit.sh -filter_box filtered.xyz 20
+
+# 3. 按力值过滤
+gpumdkit.sh -filter_value filtered_by_box.xyz force 15
+```
+
+### 扩散通道分析
+
+```bash
+# 1. 计算概率密度
+gpumdkit.sh  # 选择: 5) Analyzer -> 508
+
+# 2. 使用 VESTA 或类似软件可视化
+# 打开 probability_density_0.25.vasp
+```
+
+## 附加工具
+
+### 时间监控
+
+```bash
+# 监控 GPUMD 进度
+gpumdkit.sh -time gpumd
+
+# 监控 NEP 训练进度
+gpumdkit.sh -time nep
+```
+
+### 体积分析
+
+```bash
+# 获取每个温度的平均体积
+python Scripts/analyzer/get_volume.py
+# 需要：*/K/thermo.out 目录
+```
+
+## CLI 参考
+
+| 标志 | 描述 | 语法 |
+|------|------|------|
+| `-analyze_comp` | 成分分析 | `gpumdkit.sh -analyze_comp <file>` |
+| `-range` | 属性范围 | `gpumdkit.sh -range <file> <prop>` |
+| `-min_dist` | 最小距离（无 PBC） | `gpumdkit.sh -min_dist <file>` |
+| `-min_dist_pbc` | 最小距离（PBC） | `gpumdkit.sh -min_dist_pbc <file>` |
+| `-cbc` | 电荷平衡 | `gpumdkit.sh -cbc <file>` |
+| `-filter_range` | 按距离范围过滤 | `gpumdkit.sh -filter_range <file> <e1> <e2> <min> <max>` |
+| `-filter_box` | 按盒子大小过滤 | `gpumdkit.sh -filter_box <file> <limit>` |
+| `-filter_value` | 按属性过滤 | `gpumdkit.sh -filter_value <file> <prop> <thresh>` |
+| `-time` | 时间监控 | `gpumdkit.sh -time <gpumd\|nep>` |
+
+## 依赖
+
+| 工具 | 必需的包 |
+|------|----------|
+| 所有 Python 脚本 | `ase`, `numpy` |
+| 距离计算 | `scipy` |
+| 电荷平衡 | `pymatgen`, `tqdm` |
+| 属性范围 | `matplotlib` |
+| 概率密度 | `pymatgen` |
+
+## 参见
+
+- [格式转换](format_conversion.md) - 转换文件格式
+- [计算器](calculators.md) - 计算属性
+- [可视化](visualization.md) - 绘制结果
diff --git a/docs/tutorials2/zh/calculators.md b/docs/tutorials2/zh/calculators.md
new file mode 100644
index 0000000..ce648ad
--- /dev/null
+++ b/docs/tutorials2/zh/calculators.md
@@ -0,0 +1,312 @@
+# 计算器指南
+
+<div align="center">
+  <p>
+    <strong>中文</strong> | <a href="../en/calculators.md">English</a>
+  </p>
+</div>
+
+本指南介绍 GPUMDkit 中用于计算材料属性的所有计算器工具。
+
+## 可用计算器
+
+| 计算器 | 命令 | 描述 |
+|--------|------|------|
+| 离子电导率 | `-calc ionic-cond` | 从 MSD 计算离子电导率 |
+| NEP 属性 | `-calc nep` | 使用 NEP 计算能量/力/应力 |
+| 描述符 | `-calc des` | 计算 NEP 描述符用于分析 |
+| DOAS | `-calc doas` | 原子态密度 |
+| NEB | 直接 Python | 推移弹性带计算 |
+| 邻居列表 | `-calc nlist` | 构建用于分析的邻居列表 |
+| 位移 | `-calc disp` | 计算原子位移 |
+| 平均结构 | `-calc avg-struct` | 从轨迹计算时间平均结构 |
+| 八面体倾斜 | `-calc oct-tilt` | 钙钛矿八面体倾斜角 |
+| 极化 | `-calc pol-abo3` | ABO3 局部极化 |
+| 最小化 | `-calc minimize` | 使用 NEP 进行结构弛豫 |
+| MSD | `-calc msd` | 从轨迹计算均方位移 |
+
+## 交互模式
+
+```bash
+gpumdkit.sh
+# 选择: 4) Calculators
+```
+
+您将看到：
+
+```
++----------------------------------------------------------+
+|                     CALCULATOR TOOLS                     |
++----------------------------------------------------------+
+| 401) Calc ionic conductivity                             |
+| 402) Calc properties by nep                              |
+| 403) Calc descriptors of specific elements               |
+| 404) Calc density of atomistic states (DOAS)             |
+| 405) Calc nudged elastic band (NEB) by nep               |
+| 406) Build neighbor list                                 |
+| 407) Calc displacement from trajectory                   |
+| 408) Calc averaged structure                             |
+| 409) Calc octahedral tilt                                |
+| 410) Calc polarization for ABO3                          |
+| 411) Minimize structure by nep                           |
+| 412) Calc mean square displacement (MSD) from trajectory |
++----------------------------------------------------------+
+```
+
+## 命令参考
+
+### 离子电导率
+
+使用 Nernst-Einstein 方程从 MSD 数据计算离子电导率。
+
+```bash
+gpumdkit.sh -calc ionic-cond <元素> <电荷>
+
+# 示例
+gpumdkit.sh -calc ionic-cond Li 1    # 锂离子 (Li+)
+gpumdkit.sh -calc ionic-cond Na 1    # 钠离子 (Na+)
+gpumdkit.sh -calc ionic-cond O -2    # 氧离子 (O2-)
+```
+
+**当前目录中需要的文件：**
+- `msd.out` - 来自 GPUMD 的 `compute_msd`
+- `thermo.out` - 用于获取温度
+- `model.xyz` - 用于获取体积
+- `run.in` - 用于获取模拟参数
+
+**输出：** 离子扩散率和电导率值
+
+### NEP 属性预测
+
+使用 NEP 模型作为 DFT 代理计算能量、力和应力。
+
+```bash
+gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>
+
+# 示例
+gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
+```
+
+**注意：** 先使用 `gpumdkit.sh -clean_xyz` 清理输入以删除现有属性。
+
+### 描述符
+
+计算 NEP 描述符用于降维和结构分析。
+
+```bash
+gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <元素>
+
+# 示例
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+```
+
+**可视化：**
+```bash
+gpumdkit.sh -plt des pca    # PCA 可视化
+gpumdkit.sh -plt des umap   # UMAP 可视化
+```
+
+### 原子态密度 (DOAS)
+
+按元素类型分组计算每原子能量分布。
+
+```bash
+gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>
+
+# 示例
+gpumdkit.sh -calc doas structures.xyz nep.txt doas.out
+```
+
+**可视化：**
+```bash
+gpumdkit.sh -plt doas doas.out Li
+```
+
+### 均方位移 (MSD)
+
+从 extxyz 轨迹计算方向性 MSD。
+
+```bash
+gpumdkit.sh -calc msd <trajectory.xyz> <元素> <dt_fs> [max_corr_steps]
+
+# 示例：Li，时间步长 10 fs
+gpumdkit.sh -calc msd dump.xyz Li 10
+```
+
+**输出：** `msd.out`（时间/ps, MSD_x, MSD_y, MSD_z）
+
+### 邻居列表
+
+为钙钛矿分析构建邻居列表。
+
+```bash
+gpumdkit.sh -calc nlist -i <input> -c <cutoff> -n <num_neighbors> -C <中心元素> -E <邻居元素>
+
+# 示例
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O
+```
+
+**输出：** `nl-<center>-<neighbor>.dat`
+
+### 位移
+
+使用邻居列表从轨迹计算原子位移。
+
+```bash
+gpumdkit.sh -calc disp -i <trajectory.xyz> -n <邻居列表> -o <输出>
+
+# 示例
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Pb-O.dat -o displacements.dat
+```
+
+**可选帧切片：** `-s <start> -t <stop> -p <step> -l <last_fraction>`
+
+### 平均结构
+
+从轨迹生成时间平均结构。
+
+```bash
+gpumdkit.sh -calc avg-struct -i <trajectory.xyz> -l <比例> -o <输出>
+
+# 示例：平均最后 20% 的帧
+gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged.xyz
+```
+
+### 八面体倾斜
+
+计算钙钛矿体系的八面体倾斜角。
+
+```bash
+gpumdkit.sh -calc oct-tilt -i <input.xyz> -n <B-O 邻居列表> -o <输出>
+
+# 示例
+gpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o octahedral_tilt.dat
+```
+
+### 极化 (ABO3)
+
+计算 ABO3 钙钛矿的局部极化。
+
+```bash
+gpumdkit.sh -calc pol-abo3 -i <input.xyz> \
+  --nl-ba <B-A 邻居列表> \
+  --nl-bo <B-O 邻居列表> \
+  --bec <元素=电荷 ...>
+
+# 示例
+gpumdkit.sh -calc pol-abo3 -i model.xyz \
+  --nl-ba nl-Ti-Pb.dat \
+  --nl-bo nl-Ti-O.dat \
+  --bec Pb=2.5 Sr=2.0 Ti=4.0 O=-2.0
+```
+
+### 结构最小化
+
+使用 BFGS 优化器和 NEP 模型弛豫结构。
+
+```bash
+gpumdkit.sh -calc minimize <结构> <nep.txt> [fmax] [max_steps]
+
+# 示例
+gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
+```
+
+**参数：**
+- `fmax`：力收敛阈值（默认：0.01 eV/Å）
+- `max_steps`：最大优化步数（默认：1000）
+
+**输出：** `minimize.xyz`（优化轨迹）
+
+### NEB 计算
+
+进行推移弹性带计算以获得迁移势垒。
+
+```bash
+# 直接 Python 执行
+python Scripts/calculators/neb_calculation.py <initial.xyz> <final.xyz> <n_images> <nep.txt>
+
+# 示例
+python Scripts/calculators/neb_calculation.py init.xyz fin.xyz 9 nep.txt
+```
+
+## 常见工作流程
+
+### 离子传输分析
+
+```bash
+# 1. 在 run.in 中使用 compute_msd 运行 MD
+# 2. 计算 MSD
+gpumdkit.sh -calc msd dump.xyz Li 10
+
+# 3. 计算电导率
+gpumdkit.sh -calc ionic-cond Li 1
+
+# 4. 可视化
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+```
+
+### 描述符分析
+
+```bash
+# 1. 计算描述符
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+
+# 2. 使用 PCA 可视化
+gpumdkit.sh -plt des pca
+
+# 3. 或使用 UMAP 可视化
+gpumdkit.sh -plt des umap
+```
+
+### 钙钛矿分析
+
+```bash
+# 1. 构建邻居列表
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E Pb
+
+# 2. 计算位移
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -o disp.dat
+
+# 3. 计算倾斜
+gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -o tilt.dat
+
+# 4. 计算极化
+gpumdkit.sh -calc pol-abo3 -i movie.xyz \
+  --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \
+  --bec Pb=2.5 Ti=4.0 O=-2.0
+```
+
+### 结构弛豫
+
+```bash
+# 1. 最小化结构
+gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
+
+# 2. 使用最小化后的结构进行 MD
+cp minimize.xyz relaxed_model.xyz
+```
+
+## 依赖
+
+| 计算器 | 必需的包 |
+|--------|----------|
+| 所有 | `numpy`, `ase` |
+| ionic-cond | `scipy` |
+| nep, des, doas, minimize | `calorine` |
+| nlist, disp, oct-tilt, pol-abo3 | `ferrodispcalc` |
+| neb | `calorine`, `matplotlib` |
+
+安装依赖：
+```bash
+pip install numpy ase scipy calorine matplotlib tqdm
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
+```
+
+## 参见
+
+- [可视化](visualization.md) - 绘制计算结果
+- [分析工具](analyzers.md) - 结构分析
+- [NEP 训练指南](nep_training.md) - 完整的训练工作流
diff --git a/docs/tutorials2/zh/format_conversion.md b/docs/tutorials2/zh/format_conversion.md
new file mode 100644
index 0000000..615b6bd
--- /dev/null
+++ b/docs/tutorials2/zh/format_conversion.md
@@ -0,0 +1,273 @@
+# 格式转换指南
+
+<div align="center">
+  <p>
+    <strong>中文</strong> | <a href="../en/format_conversion.md">English</a>
+  </p>
+</div>
+
+本指南介绍 GPUMDkit 中的所有格式转换工具。
+
+## 支持的格式
+
+| 格式 | 扩展名 | 描述 |
+|------|--------|------|
+| VASP | POSCAR, OUTCAR, XDATCAR, vasprun.xml | 维也纳从头算模拟包 |
+| LAMMPS | .data, dump.* | 大规模原子/分子大规模并行模拟器 |
+| CP2K | .log, pos.xyz, frc.xyz, cell.cell | 量子化学和固态物理 |
+| ABACUS | running_scf.log, running_md.log | 基于原子轨道的从头算计算 |
+| CIF | .cif | 晶体学信息文件 |
+| MTP | .cfg | 矩量张量势格式 |
+| ASE | .traj | 原子模拟环境轨迹 |
+| extxyz | .xyz | 扩展 XYZ（主要工作格式） |
+
+## 交互模式
+
+启动交互式菜单并选择选项 1：
+
+```bash
+gpumdkit.sh
+# 选择: 1) Format Conversion
+```
+
+您将看到：
+
+```
++-------------------------------------------------------------+
+|                   FORMAT CONVERSION TOOLS                   |
++-------------------------------------------------------------+
+| 101) VASP to extxyz            106) Add group labels        |
+| 102) MTP to extxyz             107) Add weight to extxyz    |
+| 103) CP2K to extxyz            108) Extract frame extxyz    |
+| 104) ABACUS to extxyz          109) Clean XYZ info          |
+| 105) extxyz to POSCAR          110) Replicate structure     |
++-------------------------------------------------------------+
+| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |
+| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |
+| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |
+| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|
++-------------------------------------------------------------+
+| 000) Return to main menu                                    |
++-------------------------------------------------------------+
+```
+
+## 命令行模式
+
+### VASP 转换
+
+#### OUTCAR 转 extxyz
+
+```bash
+# Shell 版本（支持 OUTCAR 和 vasprun.xml）
+gpumdkit.sh -out2xyz <目录>
+
+# Python 版本（仅 OUTCAR）
+gpumdkit.sh -out2exyz <目录>
+
+# 示例
+gpumdkit.sh -out2xyz ./vasp_results/
+```
+
+#### XDATCAR 转 extxyz
+
+```bash
+gpumdkit.sh -xdat2exyz XDATCAR output.xyz
+```
+
+#### POSCAR 转 extxyz
+
+```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+```
+
+#### extxyz 转 POSCAR
+
+```bash
+# 将所有帧转换为单独的 POSCAR 文件
+gpumdkit.sh -exyz2pos structures.xyz
+```
+
+### LAMMPS 转换
+
+#### LAMMPS dump 转 extxyz
+
+```bash
+# 重要：元素符号必须与 dump 文件中的原子类型 ID 匹配
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
+
+# 示例
+gpumdkit.sh -lmp2exyz trajectory.dump Na Cl
+```
+
+#### POSCAR 转 LAMMPS data
+
+```bash
+gpumdkit.sh -pos2lmp POSCAR lammps.data
+```
+
+### CIF 转换
+
+```bash
+# CIF 转 POSCAR
+gpumdkit.sh -cif2pos input.cif POSCAR.vasp
+
+# CIF 转 extxyz
+gpumdkit.sh -cif2exyz input.cif model.xyz
+```
+
+### 其他转换
+
+```bash
+# ASE 轨迹转 extxyz
+gpumdkit.sh -traj2exyz input.traj output.xyz
+```
+
+## 结构操作
+
+### 添加组标签
+
+组标签是 GPUMD/NEP 识别原子类型所必需的：
+
+```bash
+gpumdkit.sh -addgroup POSCAR <元素1> <元素2> ...
+
+# 示例
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+```
+
+这将创建带有组标签的 `model.xyz` 文件。
+
+### 添加权重
+
+为结构添加权重标签用于加权训练：
+
+```bash
+gpumdkit.sh -addweight input.xyz output.xyz <权重>
+
+# 示例
+gpumdkit.sh -addweight train.xyz weighted.xyz 2.0
+```
+
+### 复制结构
+
+从单胞创建超胞：
+
+```bash
+# 按复制因子
+gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2
+
+# 按目标原子数
+gpumdkit.sh -replicate POSCAR supercell.vasp 256
+```
+
+### 提取帧
+
+从轨迹中提取特定帧：
+
+```bash
+# 从 0 开始的索引
+gpumdkit.sh -get_frame trajectory.xyz 1000
+```
+
+### 清理 XYZ 元数据
+
+从 extxyz 文件中删除额外的元数据：
+
+```bash
+gpumdkit.sh -clean_xyz input.xyz clean.xyz
+```
+
+## 完整 CLI 参考
+
+| 标志 | 描述 | 语法 |
+|------|------|------|
+| `-out2xyz` | OUTCAR 转 extxyz (shell) | `gpumdkit.sh -out2xyz <dir>` |
+| `-out2exyz` | OUTCAR 转 extxyz (python) | `gpumdkit.sh -out2exyz <dir>` |
+| `-pos2exyz` | POSCAR 转 extxyz | `gpumdkit.sh -pos2exyz <poscar> <xyz>` |
+| `-exyz2pos` | extxyz 转 POSCAR | `gpumdkit.sh -exyz2pos <xyz>` |
+| `-pos2lmp` | POSCAR 转 LAMMPS data | `gpumdkit.sh -pos2lmp <poscar> <lmp>` |
+| `-lmp2exyz` | LAMMPS dump 转 extxyz | `gpumdkit.sh -lmp2exyz <dump> <elem...>` |
+| `-cif2pos` | CIF 转 POSCAR | `gpumdkit.sh -cif2pos <cif> <output>` |
+| `-cif2exyz` | CIF 转 extxyz | `gpumdkit.sh -cif2exyz <cif> <output>` |
+| `-xdat2exyz` | XDATCAR 转 extxyz | `gpumdkit.sh -xdat2exyz XDATCAR dump.xyz` |
+| `-traj2exyz` | ASE 轨迹转 extxyz | `gpumdkit.sh -traj2exyz <traj> <xyz>` |
+| `-addgroup` | 添加组标签 | `gpumdkit.sh -addgroup <poscar> <elem...>` |
+| `-addweight` | 添加权重 | `gpumdkit.sh -addweight <in> <out> <weight>` |
+| `-replicate` | 复制结构 | `gpumdkit.sh -replicate <in> <out> a b c` |
+| `-get_frame` | 提取帧 | `gpumdkit.sh -get_frame <xyz> <index>` |
+| `-clean_xyz` | 清理 extxyz 信息 | `gpumdkit.sh -clean_xyz <in> <out>` |
+
+## 示例
+
+### 示例 1：转换 VASP MD 输出
+
+```bash
+# 转换当前目录中的所有 OUTCAR 文件
+gpumdkit.sh -out2xyz .
+
+# 为 NEP 训练添加组标签
+gpumdkit.sh -addgroup POSCAR Pb Ti O
+
+# 结果：准备好用于 NEP 训练的 model.xyz
+```
+
+### 示例 2：准备 LAMMPS 模拟
+
+```bash
+# 将 POSCAR 转换为 LAMMPS data
+gpumdkit.sh -pos2lmp POSCAR system.data
+
+# LAMMPS 模拟后，将 dump 转换回来
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li P S
+```
+
+### 示例 3：批量转换
+
+```bash
+# 转换多个 OUTCAR 文件
+for dir in run_*; do
+    gpumdkit.sh -out2xyz "$dir"
+    mv "$dir"/model.xyz "$dir"/trajectory.xyz
+done
+```
+
+### 示例 4：结构复制
+
+```bash
+# 创建 2x2x2 超胞
+gpumdkit.sh -replicate POSCAR supercell_222.vasp 2 2 2
+
+# 创建约 256 个原子的超胞
+gpumdkit.sh -replicate POSCAR supercell_256.vasp 256
+```
+
+## 重要提示
+
+1. **extxyz 是主要格式**：大多数 GPUMDkit 工具使用 extxyz 文件
+2. **组标签是必需的**：GPUMD/NEP 需要组标签来识别原子类型
+3. **帧索引从 0 开始**：第一帧的索引为 0
+4. **LAMMPS 的元素顺序很重要**：必须与 dump 文件中的原子类型 ID 匹配
+5. **exyz2pos 导出所有帧**：为每帧创建单独的 POSCAR 文件
+
+## 依赖
+
+大多数 Python 脚本需要：
+- `ase`（原子模拟环境）
+- `numpy`
+
+## 故障排除
+
+### 问题：缺少元素信息
+**解决方案**：确保 POSCAR 头部有正确的元素名称
+
+### 问题：原子数不正确
+**解决方案**：检查 POSCAR 是否启用了选择性动力学
+
+### 问题：LAMMPS 转换物种错误
+**解决方案**：验证元素顺序是否与 dump 文件中的原子类型 ID 匹配
+
+## 参见
+
+- [计算器](calculators.md) - 计算材料属性
+- [分析工具](analyzers.md) - 结构分析
+- [NEP 训练指南](nep_training.md) - 完整的训练工作流
diff --git a/docs/tutorials2/zh/index.md b/docs/tutorials2/zh/index.md
new file mode 100644
index 0000000..c78d9cc
--- /dev/null
+++ b/docs/tutorials2/zh/index.md
@@ -0,0 +1,160 @@
+# GPUMDkit 教程
+
+<div align="center">
+  <p>
+    <strong>中文</strong> | <a href="../en/index.md">English</a>
+  </p>
+</div>
+
+欢迎使用 **GPUMDkit** - 一个强大的 GPUMD 和 NEP 命令行工具包！
+
+## 什么是 GPUMDkit？
+
+GPUMDkit 可以简化您的分子动力学工作流程：
+
+- **格式转换**：在 VASP、LAMMPS、CP2K、ABACUS、CIF 和 extxyz 格式之间转换
+- **计算器**：计算离子电导率、描述符、MSD、NEB 等
+- **分析工具**：结构验证、过滤、成分分析
+- **可视化**：31+ 种绘图类型，用于训练、传输和结构分析
+- **工作流**：DFT 和 MD 模拟的批处理
+- **结构采样**：使用均匀、随机或 FPS 方法选择结构
+
+## 快速开始
+
+### 安装
+
+```bash
+# 克隆仓库
+git clone https://github.com/zhyan0603/GPUMDkit.git
+
+# 安装
+cd GPUMDkit
+source ./install.sh
+```
+
+### 依赖
+
+```bash
+# 创建 conda 环境
+conda create -n gpumdkit python=3.12
+conda activate gpumdkit
+
+# 安装必需的包
+pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
+```
+
+### 基本用法
+
+```bash
+# 交互模式（菜单驱动）
+gpumdkit.sh
+
+# 命令行模式
+gpumdkit.sh -<选项> [参数...]
+
+# 获取帮助
+gpumdkit.sh -h                    # 通用帮助
+gpumdkit.sh -<选项> -h            # 特定命令帮助
+gpumdkit.sh -plt -h               # 绘图帮助
+gpumdkit.sh -calc -h              # 计算器帮助
+```
+
+## 教程列表
+
+| 教程 | 描述 |
+|------|------|
+| [快速入门](quickstart.md) | 安装、配置和第一步 |
+| [格式转换](format_conversion.md) | 在结构文件格式之间转换 |
+| [计算器](calculators.md) | 计算材料属性 |
+| [分析工具](analyzers.md) | 结构分析和验证 |
+| [可视化](visualization.md) | 绘图和数据可视化 |
+| [工作流](workflows.md) | 批处理和自动化 |
+| [结构采样](sampling.md) | 结构选择方法 |
+| [NEP 训练指南](nep_training.md) | 完整的 NEP 模型训练工作流 |
+
+## 常见工作流程
+
+### 工作流 1：NEP 模型训练
+
+```bash
+# 1. 转换 DFT 数据
+gpumdkit.sh -out2xyz ./vasp_results/
+
+# 2. 添加组标签
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+
+# 3. 采样结构
+gpumdkit.sh  # 选择: 2) Sample Structures -> 203
+
+# 4. 训练 NEP（外部）
+# ...
+
+# 5. 验证
+gpumdkit.sh -plt train
+gpumdkit.sh -plt prediction
+```
+
+### 工作流 2：离子电导率计算
+
+```bash
+# 1. 计算 MSD
+gpumdkit.sh -calc msd trajectory.xyz Li 10
+
+# 2. 计算电导率
+gpumdkit.sh -calc ionic-cond Li 1
+
+# 3. 可视化
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+```
+
+### 工作流 3：结构分析
+
+```bash
+# 1. 检查成分
+gpumdkit.sh -analyze_comp train.xyz
+
+# 2. 检查距离
+gpumdkit.sh -min_dist_pbc train.xyz
+
+# 3. 检查力范围
+gpumdkit.sh -range train.xyz force
+```
+
+## 模块概览
+
+| 模块 | 菜单 | CLI 标志 | 描述 |
+|------|------|----------|------|
+| 格式转换 | 1 | `-out2xyz`, `-pos2exyz` 等 | 结构文件转换 |
+| 结构采样 | 2 | `-pynep` | 结构采样 |
+| 工作流 | 3 | - | 批处理 |
+| 计算器 | 4 | `-calc <类型>` | 属性计算 |
+| 分析工具 | 5 | `-range`, `-min_dist` 等 | 结构分析 |
+| 可视化 | 6 | `-plt <类型>` | 绘图工具 |
+| 实用工具 | 7 | `-time`, `-clean` | 实用功能 |
+
+## 输出文件约定
+
+| 文件 | 内容 |
+|------|------|
+| `model.xyz` | extxyz 格式的结构文件 |
+| `train.xyz` | 训练数据集 |
+| `nep.txt` | NEP 模型文件 |
+| `msd.out` | 均方位移数据 |
+| `thermo.out` | 热力学属性 |
+| `loss.out` | 训练损失历史 |
+| `rdf.out` | 径向分布函数 |
+| `sdc.out` | 自扩散系数数据 |
+
+## 获取帮助
+
+- **通用帮助**：`gpumdkit.sh -h`
+- **绘图帮助**：`gpumdkit.sh -plt -h`
+- **计算器帮助**：`gpumdkit.sh -calc -h`
+- **特定命令**：`gpumdkit.sh -<选项> -h`
+
+## 联系方式
+
+- **开发者**：严子涵 (yanzihan@westlake.edu.cn)
+- **GitHub**：https://github.com/zhyan0603/GPUMDkit
+- **文档**：https://zhyan0603.github.io/GPUMDkit/
diff --git a/docs/tutorials2/zh/nep_training.md b/docs/tutorials2/zh/nep_training.md
new file mode 100644
index 0000000..7d8408e
--- /dev/null
+++ b/docs/tutorials2/zh/nep_training.md
@@ -0,0 +1,299 @@
+# NEP 训练指南
+
+<div align="center">
+  <p>
+    <strong>中文</strong> | <a href="../en/nep_training.md">English</a>
+  </p>
+</div>
+
+本指南提供使用 GPUMDkit 训练 NEP（神经演化势）模型的完整工作流。
+
+## 概述
+
+NEP 训练包括：
+
+1. **数据准备** - 转换和组织训练数据
+2. **结构采样** - 选择多样化结构
+3. **模型训练** - 训练 NEP 模型（外部）
+4. **验证** - 检查训练质量
+5. **主动学习** - 迭代改进模型
+
+## 步骤 1：数据准备
+
+### 将 DFT 数据转换为 extxyz
+
+```bash
+# 从 VASP OUTCAR
+gpumdkit.sh -out2xyz ./vasp_results/
+
+# 从 VASP XDATCAR
+gpumdkit.sh -xdat2exyz XDATCAR trajectory.xyz
+
+# 从 CP2K
+gpumdkit.sh  # 选择: 1) Format Conversion -> 103
+
+# 从 LAMMPS
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
+```
+
+### 添加组标签
+
+组标签是 NEP 识别原子类型所必需的：
+
+```bash
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+```
+
+这将创建带有组标签的 `model.xyz`。
+
+### 合并训练数据
+
+```bash
+# 合并多个 extxyz 文件
+cat file1.xyz file2.xyz file3.xyz > train.xyz
+
+# 或使用成分分析选择特定成分
+gpumdkit.sh -analyze_comp all_structures.xyz
+```
+
+## 步骤 2：数据质量检查
+
+### 检查成分
+
+```bash
+gpumdkit.sh -analyze_comp train.xyz
+```
+
+### 检查最小距离
+
+```bash
+# 快速检查（无 PBC）
+gpumdkit.sh -min_dist train.xyz
+
+# 精确检查（带 PBC）
+gpumdkit.sh -min_dist_pbc train.xyz
+```
+
+### 检查属性范围
+
+```bash
+# 检查力范围
+gpumdkit.sh -range train.xyz force
+
+# 检查能量范围
+gpumdkit.sh -range train.xyz energy
+
+# 带直方图
+gpumdkit.sh -range train.xyz force hist
+```
+
+### 过滤结构
+
+```bash
+# 按最小距离过滤
+gpumdkit.sh -filter_dist_pbc train.xyz 1.0
+
+# 按盒子大小过滤
+gpumdkit.sh -filter_box train.xyz 20
+
+# 按力值过滤
+gpumdkit.sh -filter_value train.xyz force 20
+```
+
+## 步骤 3：结构采样
+
+### 采样多样化结构
+
+```bash
+# FPS 采样（首选）
+gpumdkit.sh  # 选择: 2) Sample Structures -> 203
+
+# 或均匀采样
+python Scripts/sample_structures/sample_structures.py train.xyz uniform 100
+```
+
+### 扰动结构
+
+从现有结构生成额外的训练数据：
+
+```bash
+python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
+```
+
+## 步骤 4：NEP 模型训练
+
+### 准备 nep.in
+
+创建包含训练参数的 `nep.in`：
+
+```
+type 3 Li Y Cl
+cutoff 6 4
+n_max 4
+l_max 4
+neuron 100
+batch 1000
+generation 100000
+```
+
+### 运行训练
+
+```bash
+# GPUMDkit 外部
+gpumd
+```
+
+## 步骤 5：验证
+
+### 绘制训练结果
+
+```bash
+# 绘制训练损失和对比图
+gpumdkit.sh -plt train
+
+# 绘制测试预测
+gpumdkit.sh -plt prediction
+
+# 组合训练/测试图
+gpumdkit.sh -plt train_test
+
+# 力误差分析
+gpumdkit.sh -plt force_errors
+```
+
+### 检查收敛性
+
+```bash
+# 绘制损失曲线
+gpumdkit.sh -plt train
+```
+
+观察：
+- 损失平滑下降
+- 无振荡
+- 收敛到低值
+
+### 分析描述符
+
+```bash
+# 计算描述符
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+
+# 使用 PCA 可视化
+gpumdkit.sh -plt des pca
+
+# 或 UMAP
+gpumdkit.sh -plt des umap
+```
+
+## 步骤 6：主动学习
+
+### 使用当前 NEP 运行 MD
+
+```bash
+# 设置 MD 模拟
+gpumdkit.sh  # 选择: 3) Workflow -> 302
+```
+
+### 选择多样化结构
+
+```bash
+# 按距离过滤
+gpumdkit.sh -min_dist_pbc dump.xyz
+gpumdkit.sh -filter_box dump.xyz 13
+
+# 采样多样化结构
+gpumdkit.sh  # 选择: 2) Sample Structures -> 203
+```
+
+### 计算 DFT 参考
+
+```bash
+# 准备 SCF 计算
+gpumdkit.sh  # 选择: 3) Workflow -> 301
+
+# 运行 DFT（外部）
+```
+
+### 重新训练模型
+
+```bash
+# 将新数据添加到训练集
+cat new_structures.xyz >> train.xyz
+
+# 重新训练 NEP（外部）
+```
+
+## 完整工作流示例
+
+```bash
+# 1. 转换 DFT 数据
+gpumdkit.sh -out2xyz ./dft_results/
+
+# 2. 添加组标签
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+
+# 3. 合并训练数据
+cat */model.xyz > train.xyz
+
+# 4. 检查数据质量
+gpumdkit.sh -analyze_comp train.xyz
+gpumdkit.sh -min_dist_pbc train.xyz
+gpumdkit.sh -range train.xyz force
+
+# 5. 过滤结构
+gpumdkit.sh -filter_dist_pbc train.xyz 1.0
+
+# 6. 采样多样化结构
+gpumdkit.sh  # 选择: 2) Sample Structures -> 203
+
+# 7. 训练 NEP（外部）
+# ... 创建 nep.in 并运行 gpumd ...
+
+# 8. 验证训练
+gpumdkit.sh -plt train
+gpumdkit.sh -plt prediction
+gpumdkit.sh -plt force_errors
+
+# 9. 分析描述符
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+gpumdkit.sh -plt des pca
+```
+
+## 更好训练的技巧
+
+1. **多样化数据**：包含各种结构、温度和成分
+2. **平衡数据集**：确保所有元素类型都有良好表示
+3. **质量过滤**：删除原子太近或力太大的结构
+4. **足够数据**：至少 1000-5000 个结构以获得良好精度
+5. **验证集**：保留 10-20% 的数据用于测试
+
+## 故障排除
+
+### 问题：高 RMSE
+
+**解决方案**：
+- 添加更多多样化训练数据
+- 增加 `neuron` 和 `n_max` 参数
+- 检查训练数据中的异常值
+
+### 问题：预测不准确
+
+**解决方案**：
+- 验证训练数据质量
+- 添加来自不同相/温度的结构
+- 增加训练 `generation`
+
+### 问题：过拟合
+
+**解决方案**：
+- 使用更多训练数据
+- 降低模型复杂度
+- 使用正则化
+
+## 参见
+
+- [格式转换](format_conversion.md) - 转换文件格式
+- [计算器](calculators.md) - 计算属性
+- [可视化](visualization.md) - 绘制结果
+- [结构采样](sampling.md) - 采样结构
diff --git a/docs/tutorials2/zh/quickstart.md b/docs/tutorials2/zh/quickstart.md
new file mode 100644
index 0000000..7a9a605
--- /dev/null
+++ b/docs/tutorials2/zh/quickstart.md
@@ -0,0 +1,244 @@
+# 快速入门指南
+
+<div align="center">
+  <p>
+    <strong>中文</strong> | <a href="../en/quickstart.md">English</a>
+  </p>
+</div>
+
+本指南将帮助您快速开始使用 GPUMDkit。
+
+## 前提条件
+
+在安装 GPUMDkit 之前，请确保您拥有：
+
+- **Linux 或 macOS**（Windows 通过 WSL）
+- **Bash** shell
+- **Python 3.8+**（推荐 3.12）
+- **Git**（用于克隆仓库）
+
+## 安装
+
+### 步骤 1：克隆仓库
+
+```bash
+git clone https://github.com/zhyan0603/GPUMDkit.git
+cd GPUMDkit
+```
+
+### 步骤 2：运行安装脚本
+
+```bash
+source ./install.sh
+```
+
+此脚本将：
+1. 将 GPUMDkit 添加到您的 PATH
+2. 设置 bash 自动补全
+3. 配置环境变量
+
+### 步骤 3：重新加载 Shell
+
+```bash
+source ~/.bashrc
+# 或
+source ~/.zshrc
+```
+
+### 步骤 4：验证安装
+
+```bash
+gpumdkit.sh -h
+```
+
+您应该看到包含可用命令的帮助信息。
+
+## Python 依赖
+
+某些功能需要 Python 包。创建 conda 环境：
+
+```bash
+# 创建环境
+conda create -n gpumdkit python=3.12
+conda activate gpumdkit
+
+# 安装核心包
+pip install numpy ase scipy matplotlib
+
+# 安装可选包（完整功能）
+pip install neptrain pymatgen dpdata
+
+# 用于钙钛矿分析（可选）
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
+```
+
+## 两种使用模式
+
+### 交互模式
+
+启动交互式菜单：
+
+```bash
+gpumdkit.sh
+```
+
+您将看到：
+
+```
+       ____ ____  _   _ __  __ ____  _    _ _
+      / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
+     | |  _| |_) | | | | |\/| | | | | |/ / | __|
+     | |_| |  __/| |_| | |  | | |_| |   <| | |_
+      \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
+
+      GPUMDkit Version 1.5.5 (dev) (2026-05-10)
+Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+
+ ---------------------- GPUMD ------------------------
+ 1) Format Conversion          2) Sample Structures
+ 3) Workflow                   4) Calculators
+ 5) Analyzer                   6) Visualization
+ 7) Utilities                  8) Developing...
+ 0) Exit
+ ------------>>
+ Input the function number:
+```
+
+输入所需功能的编号进行导航。
+
+### 命令行模式
+
+直接执行命令：
+
+```bash
+# 显示帮助
+gpumdkit.sh -h
+
+# 将 POSCAR 转换为 extxyz
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+
+# 绘制训练结果
+gpumdkit.sh -plt train
+
+# 计算离子电导率
+gpumdkit.sh -calc ionic-cond Li 1
+```
+
+## 第一步示例
+
+### 示例 1：转换结构
+
+```bash
+# 将 POSCAR 转换为 extxyz 格式
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+
+# 添加组标签（NEP 训练必需）
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+```
+
+### 示例 2：分析训练数据
+
+```bash
+# 检查训练数据中的力范围
+gpumdkit.sh -range train.xyz force
+
+# 检查最小原子间距离
+gpumdkit.sh -min_dist_pbc train.xyz
+
+# 分析成分
+gpumdkit.sh -analyze_comp train.xyz
+```
+
+### 示例 3：绘制结果
+
+```bash
+# 绘制 NEP 训练结果
+gpumdkit.sh -plt train
+
+# 绘制均方位移
+gpumdkit.sh -plt msd
+
+# 绘制径向分布函数
+gpumdkit.sh -plt rdf
+```
+
+## 获取帮助
+
+### 通用帮助
+
+```bash
+gpumdkit.sh -h
+```
+
+### 模块特定帮助
+
+```bash
+# 绘图帮助
+gpumdkit.sh -plt -h
+
+# 计算器帮助
+gpumdkit.sh -calc -h
+
+# 特定命令帮助
+gpumdkit.sh -pos2exyz -h
+gpumdkit.sh -calc ionic-cond -h
+```
+
+### 交互模式帮助
+
+在交互模式中，每个子菜单都会显示可用选项及其描述。
+
+## 常见问题
+
+### 问题：命令未找到
+
+**解决方案**：确保 GPUMDkit 在您的 PATH 中：
+
+```bash
+# 检查 gpumdkit.sh 是否在 PATH 中
+which gpumdkit.sh
+
+# 如果未找到，手动添加到 PATH
+export GPUMDkit_path=/path/to/GPUMDkit
+export PATH=${GPUMDkit_path}:${PATH}
+```
+
+### 问题：缺少 Python 包
+
+**解决方案**：激活 conda 环境：
+
+```bash
+conda activate gpumdkit
+```
+
+### 问题：权限被拒绝
+
+**解决方案**：使脚本可执行：
+
+```bash
+chmod +x /path/to/GPUMDkit/gpumdkit.sh
+```
+
+## 下一步
+
+现在您已经安装了 GPUMDkit，请探索以下教程：
+
+- [格式转换](format_conversion.md) - 学习在文件格式之间转换
+- [计算器](calculators.md) - 计算材料属性
+- [可视化](visualization.md) - 创建出版级图表
+- [NEP 训练指南](nep_training.md) - 完整的训练工作流
+
+## 更新 GPUMDkit
+
+更新到最新版本：
+
+```bash
+gpumdkit.sh -update
+```
+
+或手动更新：
+
+```bash
+cd /path/to/GPUMDkit
+git pull origin main
+```
diff --git a/docs/tutorials2/zh/sampling.md b/docs/tutorials2/zh/sampling.md
new file mode 100644
index 0000000..7acf8e9
--- /dev/null
+++ b/docs/tutorials2/zh/sampling.md
@@ -0,0 +1,221 @@
+# 结构采样指南
+
+<div align="center">
+  <p>
+    <strong>中文</strong> | <a href="../en/sampling.md">English</a>
+  </p>
+</div>
+
+本指南介绍 GPUMDkit 中的结构采样和选择工具。
+
+## 可用方法
+
+| 方法 | 菜单 | 描述 |
+|------|------|------|
+| 均匀/随机 | 201 | 选择均匀间隔或随机帧 |
+| FPS by PyNEP | 202 | 最远点采样（已弃用） |
+| FPS by NepTrain | 203 | 最远点采样（推荐） |
+| 扰动 | 204 | 生成扰动结构 |
+| 力偏差 | 205 | 选择高力偏差结构 |
+
+## 交互模式
+
+```bash
+gpumdkit.sh
+# 选择: 2) Sample Structures
+```
+
+您将看到：
+
+```
++------------------------------------------------------+
+|                 SAMPLE STRUCTURE TOOLS               |
++------------------------------------------------------+
+| 201) Sample structures from extxyz                   |
+| 202) FPS sampling by PyNEP [deprecated]              |
+| 203) FPS sampling by NepTrain [preferred]            |
+| 204) Perturb structure                               |
+| 205) Select max force deviation structs              |
++------------------------------------------------------+
+```
+
+## 命令参考
+
+### 均匀/随机采样
+
+使用均匀或随机采样选择结构。
+
+```bash
+python Scripts/sample_structures/sample_structures.py <input.xyz> <method> <num_samples> [skip_initial]
+
+# 示例
+python Scripts/sample_structures/sample_structures.py dump.xyz uniform 50
+python Scripts/sample_structures/sample_structures.py dump.xyz random 100 500
+```
+
+**参数：**
+- `input.xyz`：输入轨迹文件
+- `method`：`uniform` 或 `random`
+- `num_samples`：要选择的帧数
+- `skip_initial`：（可选）跳过前 N 帧
+
+**工作原理：**
+- **均匀**：使用 `numpy.linspace` 选择均匀间隔的索引
+- **随机**：使用 `numpy.random.choice` 无放回地选择随机索引
+
+**输出：** `sampled_structures.xyz`
+
+### 最远点采样 (FPS) - NepTrain（推荐）
+
+使用 NEP 描述符上的 FPS 选择多样化结构。
+
+```bash
+python Scripts/sample_structures/neptrain_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
+
+# 示例
+python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
+```
+
+**选择方法（交互式）：**
+1. **最小距离**：选择直到与现有训练集的最大距离低于阈值
+2. **结构数量**：选择 `min_select` 到 `max_select` 个结构
+
+**输出：**
+- `selected.xyz`
+- `select.png`（PCA 可视化）
+- `pca_sample.txt`, `pca_train.txt`, `pca_selected.txt`
+
+**引用**：Chen et al., Comput. Phys. Commun., 2025, 317, 109859
+
+### 最远点采样 (FPS) - PyNEP（已弃用）
+
+```bash
+python Scripts/sample_structures/pynep_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
+```
+
+**注意**：PyNEP 包不再积极维护。请使用 NepTrain（方法 203）。
+
+### 结构扰动
+
+为训练数据生成扰动结构。
+
+```bash
+python Scripts/sample_structures/perturb_structure.py <input.vasp> <pert_num> <cell_pert> <atom_pert> <style>
+
+# 示例
+python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
+```
+
+**参数：**
+- `input.vasp`：POSCAR/CONTCAR 文件
+- `pert_num`：扰动结构数量（如 20）
+- `cell_pert`：晶胞扰动比例（如 0.03 = 3%）
+- `atom_pert`：原子扰动距离（Å）（如 0.2）
+- `style`：`normal`、`uniform` 或 `const`
+
+**输出：** `POSCAR_01.vasp`, `POSCAR_02.vasp`, ..., `POSCAR_<N>.vasp`
+
+### 力偏差选择
+
+从主动学习中选择具有高力偏差的结构。
+
+```bash
+python Scripts/sample_structures/select_max_modev.py <top_n> <min_deviation>
+
+# 示例
+python Scripts/sample_structures/select_max_modev.py 200 0.15
+```
+
+**必需文件：**
+- `active.out` - 每个结构的最大力偏差（来自 GPUMD 的 `active` 命令）
+- `active.xyz` - 对应的结构
+
+**输出：** `selected.xyz`
+
+### 帧范围提取
+
+从轨迹中提取帧范围。
+
+```bash
+python Scripts/sample_structures/frame_range.py <input.xyz> <start_fraction> <end_fraction>
+
+# 示例：提取前 80% 的帧
+python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
+```
+
+**输出：** `dump_0.00_0.80.xyz`
+
+## 常见工作流程
+
+### 训练数据准备
+
+```bash
+# 1. 运行 MD 模拟
+# ... 生成轨迹 ...
+
+# 2. 按距离过滤
+gpumdkit.sh -min_dist_pbc dump.xyz
+gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
+
+# 3. 采样多样化结构
+gpumdkit.sh  # 选择: 2) Sample Structures -> 203
+
+# 4. 添加到训练集
+cat selected.xyz >> train.xyz
+```
+
+### 主动学习数据选择
+
+```bash
+# 1. 使用当前 NEP 运行 MD
+# ... 生成 active.out 和 active.xyz ...
+
+# 2. 选择高偏差结构
+python Scripts/sample_structures/select_max_modev.py 100 0.1
+
+# 3. 或使用 FPS 获取多样性
+python Scripts/sample_structures/neptrain_select_structs.py active.xyz train.xyz nep.txt
+```
+
+### 初始数据的结构扰动
+
+```bash
+# 1. 从平衡结构开始
+# 2. 生成扰动
+python Scripts/sample_structures/perturb_structure.py POSCAR 50 0.05 0.3 uniform
+
+# 3. 对扰动结构运行 DFT
+# ... DFT 计算 ...
+
+# 4. 添加到训练集
+```
+
+## 依赖
+
+| 方法 | 必需的包 |
+|------|----------|
+| 均匀/随机 | `numpy`, `ase` |
+| FPS (NepTrain) | `numpy`, `ase`, `matplotlib`, `scikit-learn`, `scipy`, `NepTrain` |
+| FPS (PyNEP) | `numpy`, `ase`, `matplotlib`, `scikit-learn`, `pynep` |
+| 扰动 | `dpdata` |
+| 力偏差 | `numpy`, `ase` |
+
+安装依赖：
+```bash
+pip install numpy ase matplotlib scikit-learn scipy dpdata
+pip install neptrain  # 用于 FPS by NepTrain
+```
+
+## 重要提示
+
+1. **FPS 是首选**：最远点采样提供比均匀/随机更好的多样性
+2. **NepTrain 优于 PyNEP**：NepTrain 积极维护；PyNEP 已弃用
+3. **采样前先过滤**：首先删除不合理的结构（太近、太大）
+4. **帧索引从 0 开始**：第一帧索引为 0
+5. **输出是 extxyz**：所有采样方法输出 extxyz 格式
+
+## 参见
+
+- [格式转换](format_conversion.md) - 转换文件格式
+- [分析工具](analyzers.md) - 过滤和分析结构
+- [NEP 训练指南](nep_training.md) - 完整的训练工作流
diff --git a/docs/tutorials2/zh/visualization.md b/docs/tutorials2/zh/visualization.md
new file mode 100644
index 0000000..41e9842
--- /dev/null
+++ b/docs/tutorials2/zh/visualization.md
@@ -0,0 +1,226 @@
+# 可视化指南
+
+<div align="center">
+  <p>
+    <strong>中文</strong> | <a href="../en/visualization.md">English</a>
+  </p>
+</div>
+
+本指南介绍 GPUMDkit 中的所有绘图和可视化工具。
+
+## 快速参考
+
+```bash
+gpumdkit.sh -plt <类型>              # 交互式显示图表
+gpumdkit.sh -plt <类型> save         # 保存为 PNG
+gpumdkit.sh -plt <类型> -h           # 获取特定图表的帮助
+```
+
+## 图表类别
+
+### NEP 训练和评估（12 种图表类型）
+
+| 命令 | 输入文件 | 描述 |
+|------|----------|------|
+| `train` | `loss.out`, `*_train.out` | 训练损失曲线和对比图 |
+| `prediction` / `test` | `*_test.out` | 测试集对比图 |
+| `train_test` | `*_train.out`, `*_test.out` | 组合训练/测试对比图 |
+| `parity_density` | `*_train.out` | 基于密度的对比图（大数据集） |
+| `train_density` | `loss.out`, `*_train.out` | 带密度可视化的训练 |
+| `force_errors` | `force_train.out` | 力误差分析 |
+| `restart` | `nep.restart` | NEP 重启文件可视化 |
+| `charge` | `charge_train.out` | 电荷分布 (qNEP) |
+| `born_charge` / `bec` | `bec_train.out`, `bec_test.out` | Born 有效电荷 |
+| `dimer` | NEP 模型 | 二聚体相互作用曲线 |
+| `des` | `descriptors.npy` | 描述符 PCA/UMAP 可视化 |
+| `lr` | `loss.out` (gnep) | 学习率衰减 |
+
+```bash
+# 训练结果
+gpumdkit.sh -plt train
+gpumdkit.sh -plt prediction
+gpumdkit.sh -plt force_errors
+
+# 描述符可视化（需要预先计算）
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+gpumdkit.sh -plt des pca
+gpumdkit.sh -plt des umap
+
+# 二聚体图
+gpumdkit.sh -plt dimer Li Li nep.txt
+```
+
+### 传输属性（9 种图表类型）
+
+| 命令 | 输入文件 | 描述 |
+|------|----------|------|
+| `msd` | `msd.out` | 均方位移 |
+| `msd_conv` | `msd_step*.out` | MSD 收敛检查 |
+| `msd_all` | `msd.out` (all_groups) | 每个物种的 MSD |
+| `sdc` | `msd.out` | 自扩散系数 |
+| `msd_sdc` | `msd.out` | MSD 和 SDC 组合 |
+| `sigma` / `arrhenius_sigma` | `*K/` 目录 | Arrhenius 离子电导率 |
+| `D` / `arrhenius_d` | `*K/` 目录 | Arrhenius 扩散率 |
+| `sigma_xyz` | `*K/` 目录 | 方向性 Arrhenius 电导率 |
+| `D_xyz` | `*K/` 目录 | 方向性 Arrhenius 扩散率 |
+
+```bash
+# MSD 和扩散
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+gpumdkit.sh -plt msd_sdc
+
+# 所有物种的 MSD（需要在 run.in 中设置 all_groups）
+gpumdkit.sh -plt msd_all Li P S
+
+# Arrhenius 图（需要按温度组织的目录）
+# 目录结构：300K/, 350K/, 400K/, ... 每个包含 msd.out
+gpumdkit.sh -plt arrhenius_sigma
+gpumdkit.sh -plt arrhenius_d
+```
+
+### 结构分析（10 种图表类型）
+
+| 命令 | 输入文件 | 描述 |
+|------|----------|------|
+| `thermo` | `thermo.out` | 热力学属性 |
+| `thermo2` | `thermo.out` | 替代热力学样式 |
+| `thermo3` | `thermo.out` | 第三种热力学样式 |
+| `rdf` | `rdf.out` | 径向分布函数 |
+| `rdf_pmf` | `rdf.out` | RDF + 平均力势 |
+| `vac` | `sdc.out` | 速度自相关 |
+| `cohesive` | `cohesive.out` | 内聚能曲线 |
+| `net_force` | extxyz 文件 | 净力分布 |
+| `doas` | `doas.out` | 原子态密度 |
+| `plane-grid` | `model.xyz`, `displacements.dat` | 位移网格可视化 |
+
+```bash
+# 热力学属性
+gpumdkit.sh -plt thermo
+
+# RDF 分析
+gpumdkit.sh -plt rdf
+gpumdkit.sh -plt rdf 2              # 特定列
+gpumdkit.sh -plt rdf_pmf 300        # 300K 时的 PMF
+
+# DOAS 可视化（需要预先计算）
+gpumdkit.sh -plt doas doas.out Li
+
+# 平面网格位移
+gpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Pb Sr
+```
+
+### 热传输（4 种图表类型）
+
+| 命令 | 输入文件 | 描述 |
+|------|----------|------|
+| `emd` | EMD 输出 | EMD 热导率 |
+| `nemd` | NEMD 输出 | NEMD 热传输 |
+| `hnemd` | HNEMD 输出 | HNEMD 热传输 |
+| `viscosity` | `viscosity.out` | 粘度分量 |
+
+```bash
+# EMD 热导率
+gpumdkit.sh -plt emd x
+
+# NEMD 热传输
+# 参数：real_length scale_eff_size cutoff_freq
+gpumdkit.sh -plt nemd <real_length> <scale_eff_size> <cutoff_freq> save
+
+# HNEMD 热传输
+gpumdkit.sh -plt hnemd <scale_eff_size> <cutoff_freq> save
+
+# 粘度
+gpumdkit.sh -plt viscosity save
+```
+
+### 声子（1 种图表类型）
+
+| 命令 | 输入文件 | 描述 |
+|------|----------|------|
+| `pdos` | `model.xyz`, `run.in`, `dos.out`, `mvac.out` | 声子态密度和热容 |
+
+```bash
+gpumdkit.sh -plt pdos save
+```
+
+## 常见工作流程
+
+### NEP 训练验证
+
+```bash
+# 1. 绘制训练损失
+gpumdkit.sh -plt train
+
+# 2. 检查测试预测
+gpumdkit.sh -plt prediction
+
+# 3. 分析力误差
+gpumdkit.sh -plt force_errors
+
+# 4. 可视化描述符
+gpumdkit.sh -plt des pca
+```
+
+### 扩散分析
+
+```bash
+# 1. 绘制 MSD
+gpumdkit.sh -plt msd
+
+# 2. 绘制自扩散系数
+gpumdkit.sh -plt sdc
+
+# 3. 组合 MSD-SDC 图
+gpumdkit.sh -plt msd_sdc
+
+# 4. Arrhenius 分析（多温度）
+gpumdkit.sh -plt arrhenius_d
+```
+
+### 热传输
+
+```bash
+# 1. 绘制热力学属性
+gpumdkit.sh -plt thermo
+
+# 2. 绘制热导率
+gpumdkit.sh -plt emd x
+
+# 3. 或 NEMD/HNEMD
+gpumdkit.sh -plt nemd 10 1 60 save
+```
+
+## 输出文件
+
+| 图表类型 | PNG 文件名（使用 `save`） |
+|----------|---------------------------|
+| `train` | `train.png` |
+| `prediction` | `prediction.png` |
+| `train_test` | `train_test.png` |
+| `force_errors` | `force_errors.png` |
+| `des` | `descriptors.png` |
+| `msd` | `msd.png` |
+| `sdc` | `sdc.png` |
+| `msd_sdc` | `MSD_SDC.png` |
+| `thermo` | `thermo.png` |
+| `rdf` | `rdf.png` |
+| `arrhenius_sigma` | `Arrhenius_sigma.png` |
+| `arrhenius_d` | `Arrhenius_D.png` |
+| `emd` | `emd.png` |
+| `nemd` | `nemd.png` |
+| `hnemd` | `hnemd.png` |
+| `viscosity` | `viscosity.png` |
+| `cohesive` | `Cohesive.png` |
+
+## 依赖
+
+所有绘图脚本需要：
+- `matplotlib`
+- `numpy`
+
+## 参见
+
+- [计算器](calculators.md) - 计算要绘制的属性
+- [分析工具](analyzers.md) - 在绘图前分析数据
+- [NEP 训练指南](nep_training.md) - 完整的训练工作流
diff --git a/docs/tutorials2/zh/workflows.md b/docs/tutorials2/zh/workflows.md
new file mode 100644
index 0000000..a2d49fb
--- /dev/null
+++ b/docs/tutorials2/zh/workflows.md
@@ -0,0 +1,280 @@
+# 工作流指南
+
+<div align="center">
+  <p>
+    <strong>中文</strong> | <a href="../en/workflows.md">English</a>
+  </p>
+</div>
+
+本指南介绍 GPUMDkit 中的批处理和工作流自动化工具。
+
+## 可用工作流
+
+| 工作流 | 菜单 | 描述 |
+|--------|------|------|
+| SCF 批处理 (VASP) | 301.1 | VASP 单点批处理设置 |
+| SCF 批处理 (CP2K) | 301.2 | CP2K 单点批处理设置 |
+| MD 批处理 (GPUMD) | 302 | GPUMD MD 采样批处理设置 |
+| MD 批处理 (LAMMPS) | 303 | LAMMPS MD 采样批处理设置 |
+
+## 交互模式
+
+```bash
+gpumdkit.sh
+# 选择: 3) Workflow
+```
+
+您将看到：
+
+```
++---------------------------------------------------------+
+|                      WORKFLOW TOOLS                     |
++---------------------------------------------------------+
+| 301) SCF batch pretreatment                             |
+| 302) MD sample batch pretreatment (gpumd)               |
+| 303) MD sample batch pretreatment (lmp)                 |
++---------------------------------------------------------+
+```
+
+## SCF 批处理
+
+### VASP SCF 批处理
+
+为 VASP 准备批量单点能量/力计算。
+
+```bash
+gpumdkit.sh  # 选择: 3) Workflow -> 301 -> VASP
+```
+
+**前提条件：**
+
+1. 将 POSCAR 文件（或单个 `.xyz`）放在当前目录
+2. 准备 `fp/` 目录，包含：
+   - `INCAR`
+   - `POTCAR`
+   - `KPOINTS`
+
+**输出结构：**
+
+```
+struct_fp/
+├── POSCAR_1.vasp
+├── POSCAR_2.vasp
+└── ...
+fp/
+├── INCAR
+├── POTCAR
+└── KPOINTS
+<prefix>_1/
+├── POSCAR -> ../struct_fp/POSCAR_1.vasp
+├── POTCAR -> ../fp/POTCAR
+├── INCAR -> ../fp/INCAR
+└── KPOINTS -> ../fp/KPOINTS
+<prefix>_2/
+└── ...
+presub.sh
+```
+
+### CP2K SCF 批处理
+
+为 CP2K 准备批量单点计算。
+
+```bash
+python Scripts/workflow/scf_batch_pretreatment_cp2k.py <extxyz_file> <template.inp> <prefix_name>
+
+# 示例
+python Scripts/workflow/scf_batch_pretreatment_cp2k.py structures.xyz cp2k_template.inp H2O_batch
+```
+
+**前提条件：**
+
+1. 准备 CP2K 输入模板（`cp2k_template.inp`）
+2. 模板应从 `pos.xyz` 读取坐标
+
+**输出结构：**
+
+```
+<prefix>_1/
+├── input.inp
+└── pos.xyz
+<prefix>_2/
+└── ...
+```
+
+## MD 采样批处理
+
+### GPUMD MD 批处理
+
+为 GPUMD 设置批量 MD 模拟。
+
+```bash
+gpumdkit.sh  # 选择: 3) Workflow -> 302
+```
+
+**前提条件：**
+
+1. 将 POSCAR 文件（或单个 `.xyz`）放在当前目录
+2. 准备 `md/` 目录，包含：
+   - `nep.txt`（NEP 模型）
+   - `run_1.in`, `run_2.in`, ...（GPUMD 输入文件）
+
+**输出结构：**
+
+```
+struct_md/
+├── model_1.xyz
+├── model_2.xyz
+└── ...
+md/
+├── nep.txt
+├── run_1.in
+├── run_2.in
+└── ...
+sample_1/
+├── model.xyz -> ../struct_md/model_1.xyz
+├── nep.txt -> ../md/nep.txt
+└── run.in -> ../md/run_1.in
+sample_2/
+└── ...
+presub.sh
+```
+
+### LAMMPS MD 批处理
+
+为 LAMMPS 设置批量 MD 模拟。
+
+```bash
+gpumdkit.sh  # 选择: 3) Workflow -> 303
+```
+
+**前提条件：**
+
+1. 将 POSCAR 文件（或单个 `.xyz`）放在当前目录
+2. 准备 `md/` 目录，包含：
+   - `nep.txt`（NEP 模型）
+   - `lmprun.in`（LAMMPS 输入文件）
+
+**输出结构：**
+
+```
+struct_md/
+├── lammps_1.data
+├── lammps_2.data
+└── ...
+md/
+├── nep.txt
+└── lmprun.in
+sample_1/
+├── lammps.data -> ../struct_md/lammps_1.data
+├── nep.txt -> ../md/nep.txt
+└── lmprun.in -> ../md/lmprun.in
+sample_2/
+└── ...
+presub.sh
+```
+
+## 主动学习工作流
+
+### 概述
+
+主动学习通过以下步骤迭代改进 NEP 模型：
+
+1. 使用当前 NEP 模型运行 MD
+2. 选择多样化的结构
+3. 计算 DFT 参考数据
+4. 重新训练 NEP 模型
+
+### 手动主动学习循环
+
+```bash
+# 步骤 1：使用当前 NEP 进行 MD 采样
+gpumdkit.sh  # 选择: 3) Workflow -> 302
+
+# 步骤 2：过滤和采样结构
+gpumdkit.sh -min_dist_pbc dump.xyz
+gpumdkit.sh -filter_box dump.xyz 13
+gpumdkit.sh  # 选择: 2) Sample Structures -> 203
+
+# 步骤 3：准备 SCF 计算
+gpumdkit.sh  # 选择: 3) Workflow -> 301
+
+# 步骤 4：运行 DFT 计算（外部）
+
+# 步骤 5：转换和验证
+gpumdkit.sh -out2xyz ./scf_results/
+gpumdkit.sh -range new_data.xyz force
+
+# 步骤 6：重新训练 NEP 模型（外部）
+```
+
+### 可配置参数
+
+| 参数 | 描述 | 示例 |
+|------|------|------|
+| `prefix_name` | 目录前缀 | `LiF_iter01` |
+| `min_dist` | 最小距离过滤 | `1.4` |
+| `box_limit` | 最大盒子大小过滤 | `13` |
+| `max_fp_num` | 最大 DFT 计算数 | `50` |
+| `sample_method` | 采样方法 | `uniform`, `random` 或 `pynep` |
+| `pynep_sample_dist` | FPS 距离阈值 | `0.01` |
+
+## 示例
+
+### 示例 1：温度依赖的 MD
+
+```bash
+# 为多个温度设置目录
+for temp in 300 500 700 900; do
+    mkdir -p "${temp}K"
+    cp model.xyz "${temp}K/"
+    cp nep.txt "${temp}K/"
+    sed "s/TEMPERATURE/$temp/g" run_template.in > "${temp}K/run.in"
+done
+```
+
+### 示例 2：高通量筛选
+
+```bash
+# 为多个计算准备结构
+for struct in structures/*.vasp; do
+    name=$(basename "$struct" .vasp)
+    mkdir -p "calc_$name"
+    cp "$struct" "calc_$name/POSCAR"
+    ln -s ../POTCAR "calc_$name/"
+    ln -s ../INCAR "calc_$name/"
+    ln -s ../KPOINTS "calc_$name/"
+done
+```
+
+### 示例 3：NEP 训练数据生成
+
+```bash
+# 1. 从初始结构开始
+gpumdkit.sh -replicate POSCAR supercell.vasp 3 3 3
+
+# 2. 扰动结构
+python Scripts/sample_structures/perturb_structure.py supercell.vasp 20 0.03 0.2 uniform
+
+# 3. 运行 MD 采样
+gpumdkit.sh  # 选择: 3) Workflow -> 302
+
+# 4. 选择多样化结构
+gpumdkit.sh  # 选择: 2) Sample Structures -> 203
+
+# 5. 准备 DFT 计算
+gpumdkit.sh  # 选择: 3) Workflow -> 301
+```
+
+## 重要提示
+
+1. **目录结构很重要**：工作流期望特定的目录布局
+2. **使用符号链接**：输出目录使用符号链接以节省磁盘空间
+3. **presub.sh**：生成的提交脚本可能需要为您的集群进行修改
+4. **模板文件**：在批处理之前确保输入模板正确
+5. **备份重要文件**：在运行工作流之前始终备份数据
+
+## 参见
+
+- [格式转换](format_conversion.md) - 转换文件格式
+- [结构采样](sampling.md) - 为训练采样结构
+- [NEP 训练指南](nep_training.md) - 完整的训练工作流
diff --git a/skills/README.md b/skills/README.md
new file mode 100644
index 0000000..dcebae2
--- /dev/null
+++ b/skills/README.md
@@ -0,0 +1,117 @@
+# GPUMDkit Skills
+
+This directory contains skill definitions for AI agent tools (opencode, Claude Code, etc.)
+to effectively use GPUMDkit functionality.
+
+## Available Skills
+
+| Skill | Description |
+|-------|-------------|
+| [gpumdkit-main](gpumdkit-main/SKILL.md) | Main entry point and overview |
+| [gpumdkit-format-conversion](gpumdkit-format-conversion/SKILL.md) | Structure file format conversion |
+| [gpumdkit-calculators](gpumdkit-calculators/SKILL.md) | Material property calculations |
+| [gpumdkit-analyzers](gpumdkit-analyzers/SKILL.md) | Structure analysis and validation |
+| [gpumdkit-visualization](gpumdkit-visualization/SKILL.md) | Plotting and visualization |
+| [gpumdkit-workflows](gpumdkit-workflows/SKILL.md) | Batch processing and automation |
+| [gpumdkit-sampling](gpumdkit-sampling/SKILL.md) | Structure sampling and selection |
+
+## Usage with Different Agent Tools
+
+### opencode (Recommended)
+
+Configure in `opencode.json` to load skills directly from the skills directory:
+
+```json
+{
+  "skills": {
+    "paths": ["./skills"]
+  }
+}
+```
+
+Or create symlinks manually:
+
+```bash
+# Run from GPUMDkit root directory
+mkdir -p .opencode/skills
+cd .opencode/skills
+ln -s ../../skills/gpumdkit-main .
+ln -s ../../skills/gpumdkit-format-conversion .
+ln -s ../../skills/gpumdkit-calculators .
+ln -s ../../skills/gpumdkit-analyzers .
+ln -s ../../skills/gpumdkit-visualization .
+ln -s ../../skills/gpumdkit-workflows .
+ln -s ../../skills/gpumdkit-sampling .
+cd ../..
+```
+
+### Claude Code
+
+Create symlinks from GPUMDkit root directory:
+
+```bash
+# Run from GPUMDkit root directory
+mkdir -p .claude/skills
+cd .claude/skills
+ln -s ../../skills/gpumdkit-main .
+ln -s ../../skills/gpumdkit-format-conversion .
+ln -s ../../skills/gpumdkit-calculators .
+ln -s ../../skills/gpumdkit-analyzers .
+ln -s ../../skills/gpumdkit-visualization .
+ln -s ../../skills/gpumdkit-workflows .
+ln -s ../../skills/gpumdkit-sampling .
+cd ../..
+```
+
+Or use a one-liner from GPUMDkit root:
+
+```bash
+mkdir -p .claude/skills && cd .claude/skills && for skill in ../../skills/gpumdkit-*/; do ln -s "$skill" .; done && cd ../..
+```
+
+### Other Agent Tools
+
+Any agent tool supporting the [Agent Skills](https://agentskills.io) standard can use these skills.
+Each skill directory contains:
+- `SKILL.md` - Main skill file with YAML frontmatter
+
+## Skill Design Principles
+
+1. **Modular**: Each skill focuses on a specific functionality
+2. **Self-contained**: Skills include all necessary information
+3. **Cross-platform**: Works with multiple agent tools
+4. **Well-documented**: Clear descriptions and examples
+5. **Maintainable**: Easy to update as GPUMDkit evolves
+
+## Skill Structure
+
+Each skill follows the Agent Skills standard:
+
+```markdown
+---
+name: skill-name
+description: >
+  Description of what the skill does and when to use it.
+allowed-tools: Bash(gpumdkit *)
+---
+
+# Skill Title
+
+## Content...
+```
+
+## Contributing
+
+When adding new features to GPUMDkit:
+
+1. Update the relevant skill file
+2. Add examples and usage instructions
+3. Update this README if adding new skills
+4. Test with at least one agent tool
+
+## References
+
+- [Agent Skills Standard](https://agentskills.io)
+- [opencode Documentation](https://opencode.ai)
+- [Claude Code Skills](https://docs.anthropic.com/en/docs/claude-code/skills)
+- [GPUMDkit Documentation](https://zhyan0603.github.io/GPUMDkit/)
diff --git a/skills/gpumdkit-analyzers/SKILL.md b/skills/gpumdkit-analyzers/SKILL.md
new file mode 100644
index 0000000..3eb946e
--- /dev/null
+++ b/skills/gpumdkit-analyzers/SKILL.md
@@ -0,0 +1,235 @@
+---
+name: gpumdkit-analyzers
+description: >
+  Use when analyzing, validating, or filtering molecular dynamics structures.
+  Provides composition analysis, outlier detection, chemical species identification,
+  charge balance check, distance calculations, property filtering, and probability density analysis.
+  Use when user asks about: structure analysis, data quality, minimum distance, composition,
+  charge balance, outlier detection, or structure filtering.
+allowed-tools: Bash(gpumdkit *) Bash(python3 *)
+---
+
+# GPUMDkit Analyzers
+
+## Available Tools
+
+| Tool | Command | Description |
+|------|---------|-------------|
+| Composition Analysis | `-analyze_comp` | Group structures by composition |
+| Outlier Detection | Menu 502 | Find high-error structures |
+| Chemical Species | Menu 503 | List unique elements |
+| Charge Balance | `-cbc` | Check oxidation-state balance |
+| Property Range | `-range` | Energy/force/virial statistics |
+| Distance Filter | Menu 506 | Filter by minimum distance (no PBC) |
+| Distance Filter (PBC) | Menu 506b | Filter by minimum distance (with PBC) |
+| Minimum Distance | `-min_dist` | Calculate min distances (no PBC) |
+| Minimum Distance (PBC) | `-min_dist_pbc` | Calculate min distances (with PBC) |
+| Probability Density | Menu 508 | 3D diffusion channel analysis |
+
+## Command Reference
+
+### Composition Analysis
+```bash
+# Analyze composition of extxyz file
+gpumdkit.sh -analyze_comp train.xyz
+
+# Output: Table of unique compositions with counts
+# Interactive: Select compositions to export as separate files
+```
+
+### Property Range Analysis
+```bash
+# Analyze energy range
+gpumdkit.sh -range train.xyz energy
+
+# Analyze force range
+gpumdkit.sh -range train.xyz force
+
+# Analyze virial range
+gpumdkit.sh -range train.xyz virial
+
+# With histogram plot
+gpumdkit.sh -range train.xyz force hist
+```
+
+### Minimum Distance
+```bash
+# Fast calculation (no PBC)
+gpumdkit.sh -min_dist dump.xyz
+
+# Accurate calculation (with PBC)
+gpumdkit.sh -min_dist_pbc dump.xyz
+
+# Output: Table of minimum distances for all element pairs
+```
+
+### Charge Balance Check
+```bash
+# Check charge balance
+gpumdkit.sh -cbc train.xyz
+
+# Output:
+# - balanced.xyz (charge-balanced structures)
+# - unbalanced.xyz (unbalanced structures)
+# - indices.txt (summary)
+```
+
+### Chemical Species Identification
+```bash
+# List unique elements (interactive mode)
+gpumdkit.sh  # Select: 5) Analyzer -> 503
+
+# Output: Sorted list of all elements in the file
+```
+
+### Structure Filtering
+
+#### By Minimum Distance (No PBC)
+```bash
+gpumdkit.sh  # Select: 5) Analyzer -> 506
+# Input: extxyz file, distance threshold
+# Output: filtered_<file>.xyz, filtered_out_<file>.xyz
+```
+
+#### By Minimum Distance (With PBC)
+```bash
+gpumdkit.sh  # Select: 5) Analyzer -> 506b
+# More accurate for periodic systems
+```
+
+#### By Element-Pair Distance Range
+```bash
+# Filter structures where Li-Li distance is between 1.9 and 2.0 Angstrom
+gpumdkit.sh -filter_range dump.xyz Li Li 1.9 2.0
+
+# Output: filtered_<elem1>_<elem2>_<min>_<max>.xyz
+```
+
+#### By Box Size
+```bash
+# Filter structures with box edge > 20 Angstrom
+gpumdkit.sh -filter_box dump.xyz 20
+
+# Output: filtered_by_box.xyz
+```
+
+#### By Property Value
+```bash
+# Keep structures with force < 20 eV/Angstrom
+gpumdkit.sh -filter_value train.xyz force 20
+
+# Output: filtered.xyz
+```
+
+### Outlier Detection
+```bash
+# Find outlier structures based on RMSE
+gpumdkit.sh  # Select: 5) Analyzer -> 502
+
+# Required files in current directory:
+# - train.xyz
+# - energy_train.out
+# - force_train.out
+# - stress_train.out
+
+# Output: selected.xyz (high-error), remained.xyz (low-error)
+```
+
+### Probability Density Analysis
+```bash
+# Calculate 3D probability density of mobile ions
+gpumdkit.sh  # Select: 5) Analyzer -> 508
+
+# Parameters (interactive):
+# - Reference structure (POSCAR)
+# - Trajectory file (extxyz)
+# - Mobile species (e.g., Li)
+# - Grid interval (e.g., 0.25 Angstrom)
+
+# Output: probability_density_<interval>.vasp (CHGCAR format)
+# Can be visualized with VESTA or similar software
+```
+
+## Common Workflows
+
+### Data Quality Check
+```bash
+# 1. Check composition
+gpumdkit.sh -analyze_comp train.xyz
+
+# 2. Check minimum distances
+gpumdkit.sh -min_dist_pbc train.xyz
+
+# 3. Check force range
+gpumdkit.sh -range train.xyz force
+
+# 4. Check for outliers
+gpumdkit.sh  # Select: 5) Analyzer -> 502
+```
+
+### Structure Filtering Pipeline
+```bash
+# 1. Filter by distance
+gpumdkit.sh  # Select: 5) Analyzer -> 506
+
+# 2. Filter by box size
+gpumdkit.sh -filter_box filtered.xyz 20
+
+# 3. Filter by force value
+gpumdkit.sh -filter_value filtered_by_box.xyz force 15
+```
+
+### Diffusion Channel Analysis
+```bash
+# 1. Calculate probability density
+gpumdkit.sh  # Select: 5) Analyzer -> 508
+
+# 2. Visualize with VESTA or similar
+# Open probability_density_0.25.vasp
+```
+
+## Additional Tools
+
+### Time Monitoring
+```bash
+# Monitor GPUMD progress
+gpumdkit.sh -time gpumd
+
+# Monitor NEP training progress
+gpumdkit.sh -time nep
+```
+
+### Volume Analysis
+```bash
+# Get average volume per temperature
+python Scripts/analyzer/get_volume.py
+# Requires: */K/thermo.out directories
+```
+
+## CLI Flag Reference
+
+| Flag | Description | Syntax |
+|------|-------------|--------|
+| `-analyze_comp` | Composition analysis | `gpumdkit.sh -analyze_comp <file>` |
+| `-range` | Property range | `gpumdkit.sh -range <file> <prop>` |
+| `-min_dist` | Min distance (no PBC) | `gpumdkit.sh -min_dist <file>` |
+| `-min_dist_pbc` | Min distance (PBC) | `gpumdkit.sh -min_dist_pbc <file>` |
+| `-cbc` | Charge balance | `gpumdkit.sh -cbc <file>` |
+| `-filter_range` | Filter by distance range | `gpumdkit.sh -filter_range <file> <e1> <e2> <min> <max>` |
+| `-filter_box` | Filter by box size | `gpumdkit.sh -filter_box <file> <limit>` |
+| `-filter_value` | Filter by property | `gpumdkit.sh -filter_value <file> <prop> <thresh>` |
+| `-time` | Time monitoring | `gpumdkit.sh -time <gpumd|nep>` |
+
+## Dependencies
+
+| Tool | Required Packages |
+|------|------------------|
+| All Python scripts | `ase`, `numpy` |
+| Distance calculations | `scipy` |
+| Charge balance | `pymatgen`, `tqdm` |
+| Property range | `matplotlib` |
+| Probability density | `pymatgen` |
+
+## Detailed Documentation
+
+See [analyzer.md](../../docs/tutorials/analyzer.md) for comprehensive guide.
diff --git a/skills/gpumdkit-calculators/SKILL.md b/skills/gpumdkit-calculators/SKILL.md
new file mode 100644
index 0000000..a1f71ef
--- /dev/null
+++ b/skills/gpumdkit-calculators/SKILL.md
@@ -0,0 +1,241 @@
+---
+name: gpumdkit-calculators
+description: >
+  Use when calculating material properties from molecular dynamics data.
+  Provides ionic conductivity, NEP property prediction, descriptors, DOAS, NEB, MSD,
+  neighbor lists, displacements, octahedral tilt, polarization, and structure minimization.
+  Use when user asks about: ionic conductivity, diffusion coefficient, descriptors, NEB,
+  mean square displacement, density of atomistic states, or structure relaxation.
+allowed-tools: Bash(gpumdkit *) Bash(python3 *)
+---
+
+# GPUMDkit Calculators
+
+## Available Calculators
+
+| Calculator | Command | Description |
+|------------|---------|-------------|
+| Ionic Conductivity | `-calc ionic-cond` | Calculate ionic conductivity from MSD |
+| NEP Properties | `-calc nep` | Compute energy/force/stress with NEP |
+| Descriptors | `-calc des` | Calculate NEP descriptors for analysis |
+| DOAS | `-calc doas` | Density of atomistic states |
+| NEB | Direct Python | Nudged elastic band calculation |
+| Neighbor List | `-calc nlist` | Build neighbor lists for analysis |
+| Displacement | `-calc disp` | Calculate atomic displacements |
+| Averaged Structure | `-calc avg-struct` | Time-averaged structure from trajectory |
+| Octahedral Tilt | `-calc oct-tilt` | Perovskite octahedral tilt angles |
+| Polarization | `-calc pol-abo3` | ABO3 local polarization |
+| Minimization | `-calc minimize` | Structure relaxation with NEP |
+| MSD | `-calc msd` | Mean square displacement from trajectory |
+
+## Command Reference
+
+### Ionic Conductivity
+```bash
+# Calculate ionic conductivity from MSD data
+gpumdkit.sh -calc ionic-cond <element> <charge>
+
+# Example: Lithium ion (Li+)
+gpumdkit.sh -calc ionic-cond Li 1
+
+# Example: Oxygen ion (O2-)
+gpumdkit.sh -calc ionic-cond O -2
+
+# Required files in current directory:
+# - msd.out (from GPUMD compute_msd)
+# - thermo.out (for temperature)
+# - model.xyz (for volume)
+# - run.in (for simulation parameters)
+```
+
+### NEP Property Prediction
+```bash
+# Calculate properties using NEP model
+gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>
+
+# Example
+gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
+
+# Note: Clean input with gpumdkit.sh -clean_xyz first to remove existing properties
+```
+
+### Descriptors
+```bash
+# Calculate NEP descriptors for specific element
+gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>
+
+# Example
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+
+# Visualize with: gpumdkit.sh -plt des pca
+# Or: gpumdkit.sh -plt des umap
+```
+
+### Density of Atomistic States (DOAS)
+```bash
+# Calculate DOAS
+gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>
+
+# Example
+gpumdkit.sh -calc doas structures.xyz nep.txt doas.out
+
+# Visualize with: gpumdkit.sh -plt doas doas.out Li
+```
+
+### Mean Square Displacement
+```bash
+# Calculate MSD from trajectory
+gpumdkit.sh -calc msd <trajectory.xyz> <element> <dt_fs> [max_corr_steps]
+
+# Example: Li with 10 fs timestep
+gpumdkit.sh -calc msd dump.xyz Li 10
+
+# Output: msd.out (Time/ps, MSD_x, MSD_y, MSD_z)
+```
+
+### Neighbor List
+```bash
+# Build neighbor list for perovskite analysis
+gpumdkit.sh -calc nlist -i <input> -c <cutoff> -n <num_neighbors> -C <center_elements> -E <neighbor_elements>
+
+# Example: Ti-O neighbors in BaTiO3
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
+
+# Example: Pb/Sr-O neighbors in PZT
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O
+
+# Output: nl-<center>-<neighbor>.dat
+```
+
+### Displacement
+```bash
+# Calculate displacements from trajectory
+gpumdkit.sh -calc disp -i <trajectory.xyz> -n <neighbor_list> -o <output>
+
+# Example
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Pb-O.dat -o displacements.dat
+
+# Optional frame slicing: -s <start> -t <stop> -p <step> -l <last_fraction>
+```
+
+### Averaged Structure
+```bash
+# Calculate time-averaged structure
+gpumdkit.sh -calc avg-struct -i <trajectory.xyz> -l <fraction> -o <output>
+
+# Example: Average last 20% of frames
+gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged.xyz
+```
+
+### Octahedral Tilt
+```bash
+# Calculate octahedral tilt angles
+gpumdkit.sh -calc oct-tilt -i <input.xyz> -n <B-O neighbor list> -o <output>
+
+# Example
+gpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o octahedral_tilt.dat
+```
+
+### Polarization (ABO3)
+```bash
+# Calculate local polarization for perovskites
+gpumdkit.sh -calc pol-abo3 -i <input.xyz> \
+  --nl-ba <B-A neighbor list> \
+  --nl-bo <B-O neighbor list> \
+  --bec <Element=charge ...>
+
+# Example
+gpumdkit.sh -calc pol-abo3 -i model.xyz \
+  --nl-ba nl-Ti-Pb.dat \
+  --nl-bo nl-Ti-O.dat \
+  --bec Pb=2.5 Sr=2.0 Ti=4.0 O=-2.0
+```
+
+### Structure Minimization
+```bash
+# Minimize structure with NEP
+gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]
+
+# Example
+gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
+
+# Output: minimize.xyz (optimization trajectory)
+# Default fmax: 0.01 eV/A, Default max_steps: 1000
+```
+
+### NEB Calculation
+```bash
+# Direct Python execution (no CLI shortcut)
+python Scripts/calculators/neb_calculation.py <initial.xyz> <final.xyz> <n_images> <nep.txt>
+
+# Example
+python Scripts/calculators/neb_calculation.py init.xyz fin.xyz 9 nep.txt
+
+# Alternative with NepTrainKit:
+python Scripts/calculators/neb_calculation_neptrain.py init.xyz fin.xyz 9 nep.txt
+```
+
+## Common Workflows
+
+### Ionic Transport Analysis
+```bash
+# 1. Run MD with compute_msd in run.in
+# 2. Calculate MSD
+gpumdkit.sh -calc msd dump.xyz Li 10
+# 3. Calculate conductivity
+gpumdkit.sh -calc ionic-cond Li 1
+# 4. Visualize
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+```
+
+### Descriptor Analysis
+```bash
+# 1. Calculate descriptors
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+# 2. Visualize with PCA
+gpumdkit.sh -plt des pca
+# 3. Or visualize with UMAP
+gpumdkit.sh -plt des umap
+```
+
+### Perovskite Analysis
+```bash
+# 1. Build neighbor lists
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E Pb
+# 2. Calculate displacements
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -o disp.dat
+# 3. Calculate tilt
+gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -o tilt.dat
+# 4. Calculate polarization
+gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat --bec Pb=2.5 Ti=4.0 O=-2.0
+```
+
+### Structure Relaxation
+```bash
+# 1. Minimize structure
+gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
+# 2. Check result
+gpumdkit.sh -plt thermo  # If running MD after relaxation
+```
+
+## Dependencies
+
+| Calculator | Required Packages |
+|------------|------------------|
+| All | `numpy`, `ase` |
+| ionic-cond | `scipy` |
+| nep, des, doas, minimize | `calorine` |
+| nlist, disp, oct-tilt, pol-abo3 | `ferrodispcalc` |
+| neb | `calorine`, `matplotlib` |
+
+Install dependencies:
+```bash
+pip install numpy ase scipy calorine matplotlib tqdm
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
+```
+
+## Detailed Documentation
+
+See [calculators.md](../../docs/tutorials/calculators.md) for comprehensive guide.
diff --git a/skills/gpumdkit-format-conversion/SKILL.md b/skills/gpumdkit-format-conversion/SKILL.md
new file mode 100644
index 0000000..630501e
--- /dev/null
+++ b/skills/gpumdkit-format-conversion/SKILL.md
@@ -0,0 +1,173 @@
+---
+name: gpumdkit-format-conversion
+description: >
+  Use when converting structure files between computational materials science formats.
+  Supports VASP (POSCAR/OUTCAR/XDATCAR), LAMMPS, CP2K, ABACUS, CIF, MTP, ASE trajectory, and extxyz.
+  Use when user asks about: format conversion, file conversion, structure conversion,
+  POSCAR to xyz, OUTCAR to extxyz, LAMMPS dump conversion, or adding group labels.
+allowed-tools: Bash(gpumdkit *) Bash(python3 *)
+---
+
+# GPUMDkit Format Conversion
+
+## Supported Formats
+
+| Format | Extensions | Description |
+|--------|-----------|-------------|
+| VASP | POSCAR, OUTCAR, XDATCAR, vasprun.xml | Vienna Ab initio Simulation Package |
+| LAMMPS | .data, dump.* | Large-scale Atomic/Molecular Massively Parallel Simulator |
+| CP2K | .log, pos.xyz, frc.xyz, cell.cell | Quantum chemistry and solid state physics |
+| ABACUS | running_scf.log, running_md.log | Atomic-orbital Based Ab-initio Computation at UStc |
+| CIF | .cif | Crystallographic Information File |
+| MTP | .cfg | Moment Tensor Potential format |
+| ASE | .traj | Atomic Simulation Environment trajectory |
+| extxyz | .xyz | Extended XYZ (primary working format) |
+
+## Command Reference
+
+### VASP Conversions
+
+```bash
+# OUTCAR to extxyz (directory, shell version)
+gpumdkit.sh -out2xyz <directory>
+
+# OUTCAR to extxyz (Python version)
+gpumdkit.sh -out2exyz <directory>
+
+# XDATCAR to extxyz
+gpumdkit.sh -xdat2exyz XDATCAR output.xyz
+
+# POSCAR to extxyz
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+
+# extxyz to POSCAR (all frames)
+gpumdkit.sh -exyz2pos structures.xyz
+```
+
+### LAMMPS Conversions
+
+```bash
+# LAMMPS dump to extxyz
+# IMPORTANT: Element symbols must match atom type IDs in dump file
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
+
+# POSCAR to LAMMPS data
+gpumdkit.sh -pos2lmp POSCAR lammps.data
+```
+
+### CIF Conversions
+
+```bash
+# CIF to POSCAR
+gpumdkit.sh -cif2pos input.cif POSCAR.vasp
+
+# CIF to extxyz
+gpumdkit.sh -cif2exyz input.cif model.xyz
+```
+
+### Other Conversions
+
+```bash
+# ASE trajectory to extxyz
+gpumdkit.sh -traj2exyz input.traj output.xyz
+```
+
+### Structure Manipulation
+
+```bash
+# Add group labels (required for GPUMD/NEP)
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+
+# Add weights to structures
+gpumdkit.sh -addweight input.xyz output.xyz 2.0
+
+# Replicate structure (by factors)
+gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2
+
+# Replicate structure (by target atom count)
+gpumdkit.sh -replicate POSCAR supercell.vasp 256
+
+# Extract specific frame (0-based index)
+gpumdkit.sh -get_frame trajectory.xyz 1000
+
+# Clean extxyz metadata
+gpumdkit.sh -clean_xyz input.xyz clean.xyz
+```
+
+## Detailed CLI Flag Reference
+
+| CLI Flag | Conversion | Syntax |
+|----------|-----------|--------|
+| `-out2xyz` | OUTCAR -> extxyz (shell) | `gpumdkit.sh -out2xyz <dir>` |
+| `-out2exyz` | OUTCAR -> extxyz (python) | `gpumdkit.sh -out2exyz <dir>` |
+| `-pos2exyz` | POSCAR -> extxyz | `gpumdkit.sh -pos2exyz <poscar> <xyz>` |
+| `-exyz2pos` | extxyz -> POSCAR | `gpumdkit.sh -exyz2pos <xyz>` |
+| `-pos2lmp` | POSCAR -> LAMMPS data | `gpumdkit.sh -pos2lmp <poscar> <lmp>` |
+| `-lmp2exyz` | LAMMPS dump -> extxyz | `gpumdkit.sh -lmp2exyz <dump> <elem...>` |
+| `-cif2pos` | CIF -> POSCAR | `gpumdkit.sh -cif2pos <cif> <output>` |
+| `-cif2exyz` | CIF -> extxyz | `gpumdkit.sh -cif2exyz <cif> <output>` |
+| `-xdat2exyz` | XDATCAR -> extxyz | `gpumdkit.sh -xdat2exyz XDATCAR dump.xyz` |
+| `-traj2exyz` | ASE traj -> extxyz | `gpumdkit.sh -traj2exyz <traj> <xyz>` |
+| `-addgroup` | Add group labels | `gpumdkit.sh -addgroup <poscar> <elem...>` |
+| `-addweight` | Add weight | `gpumdkit.sh -addweight <in> <out> <weight>` |
+| `-replicate` | Replicate structure | `gpumdkit.sh -replicate <in> <out> a b c` |
+| `-get_frame` | Extract frame | `gpumdkit.sh -get_frame <xyz> <index>` |
+| `-clean_xyz` | Clean extxyz info | `gpumdkit.sh -clean_xyz <in> <out>` |
+
+## Examples
+
+### Example 1: Convert VASP MD Output
+```bash
+# Convert all OUTCAR files in current directory
+gpumdkit.sh -out2xyz .
+
+# Add group labels for NEP training
+gpumdkit.sh -addgroup POSCAR Pb Ti O
+
+# Result: model.xyz ready for NEP training
+```
+
+### Example 2: Prepare LAMMPS Simulation
+```bash
+# Convert POSCAR to LAMMPS data
+gpumdkit.sh -pos2lmp POSCAR system.data
+
+# After LAMMPS simulation, convert dump back
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li P S
+```
+
+### Example 3: Batch Conversion
+```bash
+# Convert multiple OUTCAR files
+for dir in run_*; do
+    gpumdkit.sh -out2xyz "$dir"
+    mv "$dir"/model.xyz "$dir"/trajectory.xyz
+done
+```
+
+### Example 4: Structure Replication
+```bash
+# Replicate to 2x2x2 supercell
+gpumdkit.sh -replicate POSCAR supercell_222.vasp 2 2 2
+
+# Replicate to target ~256 atoms
+gpumdkit.sh -replicate POSCAR supercell_256.vasp 256
+```
+
+## Notes
+
+1. **extxyz is the primary format**: Most GPUMDkit tools work with extxyz files
+2. **Group labels are essential**: Required for GPUMD/NEP to identify atom types
+3. **Frame indexing is 0-based**: First frame is index 0
+4. **Element ordering matters for LAMMPS**: Must match atom type IDs in dump file
+5. **exyz2pos exports all frames**: Creates separate POSCAR for each frame
+
+## Dependencies
+
+Most Python scripts require:
+- `ase` (Atomic Simulation Environment)
+- `numpy`
+
+## Detailed Documentation
+
+See [format_conversion.md](../../docs/tutorials/format_conversion.md) for comprehensive guide.
diff --git a/skills/gpumdkit-main/SKILL.md b/skills/gpumdkit-main/SKILL.md
new file mode 100644
index 0000000..4015515
--- /dev/null
+++ b/skills/gpumdkit-main/SKILL.md
@@ -0,0 +1,153 @@
+---
+name: gpumdkit
+description: >
+  Use when working with GPUMD molecular dynamics or NEP potentials for computational materials science.
+  Provides format conversion, structure analysis, visualization, calculation tools, and workflow automation.
+  Supports VASP, LAMMPS, CP2K, ABACUS, CIF, and extxyz formats.
+  Use when user asks about: molecular dynamics, NEP training, structure conversion, ionic conductivity,
+  radial distribution function, mean square displacement, thermal conductivity, phonon DOS,
+  structure sampling, farthest point sampling, or computational materials analysis.
+allowed-tools: Bash(gpumdkit *) Bash(python3 *) Bash(python *)
+---
+
+# GPUMDkit - Molecular Dynamics Toolkit
+
+## Overview
+
+GPUMDkit is a command-line toolkit for GPUMD (Graphics Processing Units Molecular Dynamics) and
+NEP (Neuroevolution Potential) programs. It streamlines common tasks in computational materials science.
+
+## Quick Start
+
+### Installation
+```bash
+git clone https://github.com/zhyan0603/GPUMDkit.git
+cd GPUMDkit && source ./install.sh
+```
+
+### Dependencies
+```bash
+conda create -n gpumdkit python=3.12
+conda activate gpumdkit
+pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
+```
+
+### Basic Usage
+```bash
+# Interactive mode (menu-driven)
+gpumdkit.sh
+
+# Command-line mode
+gpumdkit.sh -<option> [args...]
+
+# Get help
+gpumdkit.sh -h                    # General help
+gpumdkit.sh -<option> -h          # Specific command help
+gpumdkit.sh -plt -h               # Plot help
+gpumdkit.sh -calc -h              # Calculator help
+```
+
+## Module Overview
+
+| Module | Description | Skill Reference |
+|--------|-------------|-----------------|
+| Format Conversion | Convert between VASP, LAMMPS, CP2K, ABACUS, CIF, extxyz | See [gpumdkit-format-conversion](../gpumdkit-format-conversion/SKILL.md) |
+| Calculators | Compute ionic conductivity, descriptors, MSD, NEB, etc. | See [gpumdkit-calculators](../gpumdkit-calculators/SKILL.md) |
+| Analyzers | Structure validation, filtering, composition analysis | See [gpumdkit-analyzers](../gpumdkit-analyzers/SKILL.md) |
+| Visualization | Plot training results, transport properties, structural data | See [gpumdkit-visualization](../gpumdkit-visualization/SKILL.md) |
+| Workflows | Batch processing for DFT and MD simulations | See [gpumdkit-workflows](../gpumdkit-workflows/SKILL.md) |
+| Sampling | Structure selection using uniform, random, or FPS methods | See [gpumdkit-sampling](../gpumdkit-sampling/SKILL.md) |
+
+## Common Workflows
+
+### Workflow 1: NEP Model Training Pipeline
+```bash
+# 1. Convert DFT data to extxyz
+gpumdkit.sh -out2xyz ./vasp_results/
+
+# 2. Add group labels
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+
+# 3. Sample diverse structures
+gpumdkit.sh  # Select: 2) Sample Structures -> 203) FPS by NepTrain
+
+# 4. Train NEP model (external)
+# ... train nep.txt ...
+
+# 5. Validate training
+gpumdkit.sh -plt train
+gpumdkit.sh -plt prediction
+
+# 6. Check data quality
+gpumdkit.sh -range train.xyz force
+gpumdkit.sh -min_dist_pbc train.xyz
+```
+
+### Workflow 2: Ionic Conductivity Calculation
+```bash
+# 1. Run MD simulation with GPUMD
+# ... generate msd.out ...
+
+# 2. Calculate MSD
+gpumdkit.sh -calc msd trajectory.xyz Li 10
+
+# 3. Calculate ionic conductivity
+gpumdkit.sh -calc ionic-cond Li 1
+
+# 4. Plot results
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+
+# 5. Arrhenius analysis (multiple temperatures)
+gpumdkit.sh -plt arrhenius_sigma
+gpumdkit.sh -plt arrhenius_d
+```
+
+### Workflow 3: Structure Analysis Pipeline
+```bash
+# 1. Check composition
+gpumdkit.sh -analyze_comp train.xyz
+
+# 2. Check minimum distances
+gpumdkit.sh -min_dist_pbc train.xyz
+
+# 3. Filter structures
+gpumdkit.sh  # Select: 5) Analyzer -> 506) Filter by distance
+
+# 4. Check energy/force range
+gpumdkit.sh -range train.xyz force
+gpumdkit.sh -range train.xyz energy
+```
+
+## Output File Conventions
+
+| File | Content |
+|------|---------|
+| `model.xyz` | Structure file in extxyz format |
+| `train.xyz` | Training dataset |
+| `nep.txt` | NEP model file |
+| `msd.out` | Mean square displacement data |
+| `thermo.out` | Thermodynamic properties |
+| `loss.out` | Training loss history |
+| `rdf.out` | Radial distribution function |
+| `sdc.out` | Self-diffusion coefficient data |
+
+## Troubleshooting
+
+**Issue**: Command not found
+**Solution**: Ensure GPUMDkit is installed and in PATH: `source ./install.sh`
+
+**Issue**: Missing Python packages
+**Solution**: Activate conda environment: `conda activate gpumdkit`
+
+**Issue**: Script errors
+**Solution**: Check input file format and required parameters with `-h` flag
+
+## Detailed Documentation
+
+- [Format Conversion Guide](../../docs/tutorials/format_conversion.md)
+- [Calculators Guide](../../docs/tutorials/calculators.md)
+- [Analyzer Guide](../../docs/tutorials/analyzer.md)
+- [Visualization Guide](../../docs/tutorials/plot_scripts.md)
+- [Workflow Guide](../../docs/tutorials/workflow.md)
+- [Sampling Guide](../../docs/tutorials/sample_structures.md)
diff --git a/skills/gpumdkit-sampling/SKILL.md b/skills/gpumdkit-sampling/SKILL.md
new file mode 100644
index 0000000..fe04dd8
--- /dev/null
+++ b/skills/gpumdkit-sampling/SKILL.md
@@ -0,0 +1,228 @@
+---
+name: gpumdkit-sampling
+description: >
+  Use when selecting or sampling structures from molecular dynamics trajectories.
+  Provides uniform sampling, random sampling, farthest point sampling (FPS), structure perturbation,
+  and force deviation selection.
+  Use when user asks about: structure sampling, FPS, farthest point sampling, structure selection,
+  perturbation, or training data preparation.
+allowed-tools: Bash(gpumdkit *) Bash(python3 *)
+---
+
+# GPUMDkit Structure Sampling
+
+## Available Methods
+
+| Method | Menu | Description |
+|--------|------|-------------|
+| Uniform/Random | 201 | Select evenly spaced or random frames |
+| FPS by PyNEP | 202 | Farthest point sampling (deprecated) |
+| FPS by NepTrain | 203 | Farthest point sampling (preferred) |
+| Perturbation | 204 | Generate perturbed structures |
+| Force Deviation | 205 | Select high-force-deviation structures |
+
+## Command Reference
+
+### Uniform/Random Sampling
+
+```bash
+# Direct Python execution
+python Scripts/sample_structures/sample_structures.py <input.xyz> <method> <num_samples> [skip_initial]
+
+# Examples
+python Scripts/sample_structures/sample_structures.py dump.xyz uniform 50
+python Scripts/sample_structures/sample_structures.py dump.xyz random 100 500
+
+# Parameters:
+# - input.xyz: Input trajectory file
+# - method: 'uniform' or 'random'
+# - num_samples: Number of frames to select
+# - skip_initial: (optional) Skip first N frames
+
+# Output: sampled_structures.xyz
+```
+
+**How it works:**
+- **Uniform**: Uses `numpy.linspace` to select evenly spaced indices across the trajectory
+- **Random**: Uses `numpy.random.choice` to select random indices without replacement
+
+### Farthest Point Sampling (FPS)
+
+#### Using NepTrain (Preferred)
+
+```bash
+# Interactive mode
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+
+# Direct Python execution
+python Scripts/sample_structures/neptrain_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
+
+# Example
+python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
+
+# Selection methods (interactive):
+# 1. Minimum distance: Select until max distance < threshold
+# 2. Number of structures: Select N structures
+
+# Output:
+# - selected.xyz
+# - select.png (PCA visualization)
+# - pca_sample.txt, pca_train.txt, pca_selected.txt
+```
+
+**Algorithm**: Farthest Point Sampling using NEP descriptors (mean descriptor per structure)
+
+**Citation**: Chen et al., Comput. Phys. Commun., 2025, 317, 109859
+
+#### Using PyNEP (Deprecated)
+
+```bash
+# Direct execution
+python Scripts/sample_structures/pynep_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
+
+# Note: PyNEP package is no longer actively maintained
+# Use NepTrain (method 203) instead
+```
+
+### Structure Perturbation
+
+```bash
+# Interactive mode
+gpumdkit.sh  # Select: 2) Sample Structures -> 204
+
+# Direct Python execution
+python Scripts/sample_structures/perturb_structure.py <input.vasp> <pert_num> <cell_pert> <atom_pert> <style>
+
+# Example
+python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
+
+# Parameters:
+# - input.vasp: POSCAR/CONTCAR file
+# - pert_num: Number of perturbed structures (e.g., 20)
+# - cell_pert: Cell perturbation fraction (e.g., 0.03 = 3%)
+# - atom_pert: Atom perturbation distance in Angstrom (e.g., 0.2)
+# - style: 'normal', 'uniform', or 'const'
+
+# Output: POSCAR_01.vasp, POSCAR_02.vasp, ..., POSCAR_<N>.vasp
+```
+
+**How it works**: Uses `dpdata.System.perturb()` to generate perturbed variants of the input structure, varying both cell vectors and atomic positions.
+
+### Force Deviation Selection
+
+```bash
+# Interactive mode
+gpumdkit.sh  # Select: 2) Sample Structures -> 205
+
+# Direct Python execution
+python Scripts/sample_structures/select_max_modev.py <top_n> <min_deviation>
+
+# Example
+python Scripts/sample_structures/select_max_modev.py 200 0.15
+
+# Required files in current directory:
+# - active.out (from GPUMD active command)
+# - active.xyz (corresponding structures)
+
+# Output: selected.xyz
+```
+
+**How it works**:
+1. Reads `active.out` and filters structures with force deviation above `min_deviation`
+2. Sorts by deviation (descending) and extracts the top N structures
+3. Reads corresponding frames from `active.xyz` and writes them to output
+
+### Frame Range Extraction
+
+```bash
+# Direct Python execution
+python Scripts/sample_structures/frame_range.py <input.xyz> <start_fraction> <end_fraction>
+
+# Example: Extract first 80% of frames
+python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
+
+# Output: dump_0.00_0.80.xyz
+```
+
+## Common Workflows
+
+### Training Data Preparation
+
+```bash
+# 1. Run MD simulation
+# ... generate trajectory ...
+
+# 2. Filter by distance
+gpumdkit.sh -min_dist_pbc dump.xyz
+gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
+
+# 3. Sample diverse structures
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+
+# 4. Add to training set
+cat selected.xyz >> train.xyz
+```
+
+### Active Learning Data Selection
+
+```bash
+# 1. Run MD with current NEP
+# ... generate active.out and active.xyz ...
+
+# 2. Select high-deviation structures
+python Scripts/sample_structures/select_max_modev.py 100 0.1
+
+# 3. Or use FPS for diversity
+python Scripts/sample_structures/neptrain_select_structs.py active.xyz train.xyz nep.txt
+```
+
+### Structure Perturbation for Initial Data
+
+```bash
+# 1. Start from equilibrium structure
+# 2. Generate perturbations
+python Scripts/sample_structures/perturb_structure.py POSCAR 50 0.05 0.3 uniform
+
+# 3. Run DFT on perturbed structures
+# ... DFT calculations ...
+
+# 4. Add to training set
+```
+
+### Parallel FPS Sampling (Advanced)
+
+```bash
+# Parallel version for large datasets
+python Scripts/sample_structures/parallel_pynep_select_structs.py <sample.xyz> <train.xyz> <nep.txt> [threads]
+
+# Example with 8 threads
+python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8
+```
+
+## Dependencies
+
+| Method | Required Packages |
+|--------|------------------|
+| Uniform/Random | `numpy`, `ase` |
+| FPS (NepTrain) | `numpy`, `ase`, `matplotlib`, `scikit-learn`, `scipy`, `NepTrain` |
+| FPS (PyNEP) | `numpy`, `ase`, `matplotlib`, `scikit-learn`, `pynep` |
+| Perturbation | `dpdata` |
+| Force Deviation | `numpy`, `ase` |
+
+Install dependencies:
+```bash
+pip install numpy ase matplotlib scikit-learn scipy dpdata
+pip install neptrain  # For FPS by NepTrain
+```
+
+## Notes
+
+1. **FPS is preferred**: Farthest Point Sampling provides better diversity than uniform/random
+2. **NepTrain over PyNEP**: NepTrain is actively maintained; PyNEP is deprecated
+3. **Filter before sampling**: Remove unphysical structures (too close, too large) first
+4. **Frame indexing is 0-based**: First frame is index 0
+5. **Output is extxyz**: All sampling methods output extxyz format
+
+## Detailed Documentation
+
+See [sample_structures.md](../../docs/tutorials/sample_structures.md) for comprehensive guide.
diff --git a/skills/gpumdkit-visualization/SKILL.md b/skills/gpumdkit-visualization/SKILL.md
new file mode 100644
index 0000000..74147ba
--- /dev/null
+++ b/skills/gpumdkit-visualization/SKILL.md
@@ -0,0 +1,216 @@
+---
+name: gpumdkit-visualization
+description: >
+  Use when plotting molecular dynamics simulation results, NEP training data, or transport properties.
+  Supports 31+ plot types including training loss, parity plots, MSD, SDC, RDF, thermodynamic properties,
+  Arrhenius plots, phonon DOS, thermal conductivity, and descriptor visualization.
+  Use when user asks about: plotting, visualization, training results, MSD plot, RDF plot,
+  thermal conductivity, Arrhenius plot, or NEP training visualization.
+allowed-tools: Bash(gpumdkit *)
+---
+
+# GPUMDkit Visualization
+
+## Quick Reference
+
+```bash
+gpumdkit.sh -plt <type>              # Display plot interactively
+gpumdkit.sh -plt <type> save         # Save plot as PNG
+gpumdkit.sh -plt <type> -h           # Get help for specific plot
+```
+
+## Plot Categories
+
+### NEP Training & Evaluation (12 plot types)
+
+| Command | Input Files | Description |
+|---------|-------------|-------------|
+| `train` | `loss.out`, `*_train.out` | Training loss curves and parity plots |
+| `prediction` / `test` | `*_test.out` | Test set parity plots |
+| `train_test` | `*_train.out`, `*_test.out` | Combined train/test parity plots |
+| `parity_density` | `*_train.out` | Density-based parity plots for large datasets |
+| `train_density` | `loss.out`, `*_train.out` | Training with density visualization |
+| `force_errors` | `force_train.out` | Force error analysis |
+| `restart` | `nep.restart` | NEP restart file visualization |
+| `charge` | `charge_train.out` | Charge distribution (qNEP) |
+| `born_charge` / `bec` | `bec_train.out`, `bec_test.out` | Born effective charges |
+| `dimer` | NEP model | Dimer interaction curves |
+| `des` | `descriptors.npy` | Descriptor PCA/UMAP visualization |
+| `lr` | `loss.out` (gnep) | Learning rate decay |
+
+```bash
+# Training results
+gpumdkit.sh -plt train
+gpumdkit.sh -plt prediction
+gpumdkit.sh -plt force_errors
+
+# Descriptor visualization (requires prior calculation)
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+gpumdkit.sh -plt des pca
+gpumdkit.sh -plt des umap
+
+# Dimer plot
+gpumdkit.sh -plt dimer Li Li nep.txt
+```
+
+### Transport Properties (9 plot types)
+
+| Command | Input Files | Description |
+|---------|-------------|-------------|
+| `msd` | `msd.out` | Mean square displacement |
+| `msd_conv` | `msd_step*.out` | MSD convergence check |
+| `msd_all` | `msd.out` (all_groups) | MSD per species |
+| `sdc` | `msd.out` | Self-diffusion coefficient |
+| `msd_sdc` | `msd.out` | MSD and SDC combined |
+| `sigma` / `arrhenius_sigma` | `*K/` directories | Arrhenius ionic conductivity |
+| `D` / `arrhenius_d` | `*K/` directories | Arrhenius diffusivity |
+| `sigma_xyz` | `*K/` directories | Directional Arrhenius conductivity |
+| `D_xyz` | `*K/` directories | Directional Arrhenius diffusivity |
+
+```bash
+# MSD and diffusion
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+gpumdkit.sh -plt msd_sdc
+
+# MSD for all species (requires all_groups in run.in)
+gpumdkit.sh -plt msd_all Li P S
+
+# Arrhenius plots (requires temperature-organized directories)
+# Directory structure: 300K/, 350K/, 400K/, ... each containing msd.out
+gpumdkit.sh -plt arrhenius_sigma
+gpumdkit.sh -plt arrhenius_d
+```
+
+### Structural Analysis (10 plot types)
+
+| Command | Input Files | Description |
+|---------|-------------|-------------|
+| `thermo` | `thermo.out` | Thermodynamic properties |
+| `thermo2` | `thermo.out` | Alternative thermo style |
+| `thermo3` | `thermo.out` | Third thermo style |
+| `rdf` | `rdf.out` | Radial distribution function |
+| `rdf_pmf` | `rdf.out` | RDF + potential of mean force |
+| `vac` | `sdc.out` | Velocity autocorrelation |
+| `cohesive` | `cohesive.out` | Cohesive energy curve |
+| `net_force` | extxyz file | Net force distribution |
+| `doas` | `doas.out` | Density of atomistic states |
+| `plane-grid` | `model.xyz`, `displacements.dat` | Displacement grid visualization |
+
+```bash
+# Thermodynamic properties
+gpumdkit.sh -plt thermo
+
+# RDF analysis
+gpumdkit.sh -plt rdf
+gpumdkit.sh -plt rdf 2              # Specific column
+gpumdkit.sh -plt rdf_pmf 300        # With PMF at 300K
+
+# DOAS visualization (requires prior calculation)
+gpumdkit.sh -plt doas doas.out Li
+
+# Plane-grid displacement
+gpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Pb Sr
+```
+
+### Heat Transport (4 plot types)
+
+| Command | Input Files | Description |
+|---------|-------------|-------------|
+| `emd` | EMD outputs | EMD thermal conductivity |
+| `nemd` | NEMD outputs | NEMD thermal transport |
+| `hnemd` | HNEMD outputs | HNEMD thermal transport |
+| `viscosity` | `viscosity.out` | Viscosity components |
+
+```bash
+# EMD thermal conductivity
+gpumdkit.sh -plt emd x
+
+# NEMD thermal transport
+# Parameters: real_length scale_eff_size cutoff_freq
+gpumdkit.sh -plt nemd <real_length> <scale_eff_size> <cutoff_freq> save
+
+# HNEMD thermal transport
+gpumdkit.sh -plt hnemd <scale_eff_size> <cutoff_freq> save
+
+# Viscosity
+gpumdkit.sh -plt viscosity save
+```
+
+### Phonons (1 plot type)
+
+| Command | Input Files | Description |
+|---------|-------------|-------------|
+| `pdos` | `model.xyz`, `run.in`, `dos.out`, `mvac.out` | Phonon DOS and heat capacity |
+
+```bash
+gpumdkit.sh -plt pdos save
+```
+
+## Common Workflows
+
+### NEP Training Validation
+```bash
+# 1. Plot training loss
+gpumdkit.sh -plt train
+# 2. Check test predictions
+gpumdkit.sh -plt prediction
+# 3. Analyze force errors
+gpumdkit.sh -plt force_errors
+# 4. Visualize descriptors
+gpumdkit.sh -plt des pca
+```
+
+### Diffusion Analysis
+```bash
+# 1. Plot MSD
+gpumdkit.sh -plt msd
+# 2. Plot self-diffusion coefficient
+gpumdkit.sh -plt sdc
+# 3. Combined MSD-SDC plot
+gpumdkit.sh -plt msd_sdc
+# 4. Arrhenius analysis (multi-temperature)
+gpumdkit.sh -plt arrhenius_d
+```
+
+### Thermal Transport
+```bash
+# 1. Plot thermodynamic properties
+gpumdkit.sh -plt thermo
+# 2. Plot thermal conductivity
+gpumdkit.sh -plt emd x
+# 3. Or NEMD/HNEMD
+gpumdkit.sh -plt nemd 10 1 60 save
+```
+
+## Output Files
+
+| Plot Type | PNG Filename (with `save`) |
+|-----------|---------------------------|
+| `train` | `train.png` |
+| `prediction` | `prediction.png` |
+| `train_test` | `train_test.png` |
+| `force_errors` | `force_errors.png` |
+| `des` | `descriptors.png` |
+| `msd` | `msd.png` |
+| `sdc` | `sdc.png` |
+| `msd_sdc` | `MSD_SDC.png` |
+| `thermo` | `thermo.png` |
+| `rdf` | `rdf.png` |
+| `arrhenius_sigma` | `Arrhenius_sigma.png` |
+| `arrhenius_d` | `Arrhenius_D.png` |
+| `emd` | `emd.png` |
+| `nemd` | `nemd.png` |
+| `hnemd` | `hnemd.png` |
+| `viscosity` | `viscosity.png` |
+| `cohesive` | `Cohesive.png` |
+
+## Dependencies
+
+All plotting scripts require:
+- `matplotlib`
+- `numpy`
+
+## Detailed Documentation
+
+See [plot_scripts.md](../../docs/tutorials/plot_scripts.md) for comprehensive guide.
diff --git a/skills/gpumdkit-workflows/SKILL.md b/skills/gpumdkit-workflows/SKILL.md
new file mode 100644
index 0000000..c0a52b8
--- /dev/null
+++ b/skills/gpumdkit-workflows/SKILL.md
@@ -0,0 +1,224 @@
+---
+name: gpumdkit-workflows
+description: >
+  Use when setting up batch calculations or high-throughput simulations.
+  Provides SCF batch pretreatment for VASP and CP2K, MD sample batch pretreatment for GPUMD and LAMMPS,
+  and active learning workflow automation.
+  Use when user asks about: batch calculation, workflow automation, SCF batch, MD sampling,
+  high-throughput simulation, or active learning.
+allowed-tools: Bash(gpumdkit *) Bash(python3 *)
+---
+
+# GPUMDkit Workflows
+
+## Available Workflows
+
+| Workflow | Menu | Description |
+|----------|------|-------------|
+| SCF Batch (VASP) | 301.1 | VASP single-point batch setup |
+| SCF Batch (CP2K) | 301.2 | CP2K single-point batch setup |
+| MD Batch (GPUMD) | 302 | GPUMD MD sampling batch setup |
+| MD Batch (LAMMPS) | 303 | LAMMPS MD sampling batch setup |
+
+## SCF Batch Pretreatment
+
+### VASP SCF Batch
+
+```bash
+# Interactive mode
+gpumdkit.sh  # Select: 3) Workflow -> 301 -> VASP
+```
+
+**Prerequisites:**
+1. Place POSCAR files (or single `.xyz`) in current directory
+2. Prepare `fp/` directory with:
+   - `INCAR`
+   - `POTCAR`
+   - `KPOINTS`
+
+**Output structure:**
+```
+struct_fp/POSCAR_1.vasp, POSCAR_2.vasp, ...
+fp/POTCAR, INCAR, KPOINTS          (user-provided)
+<prefix>_1/POSCAR -> struct_fp/POSCAR_1.vasp
+<prefix>_1/POTCAR -> fp/POTCAR
+<prefix>_2/...
+presub.sh
+```
+
+### CP2K SCF Batch
+
+```bash
+# Direct Python execution
+python Scripts/workflow/scf_batch_pretreatment_cp2k.py <extxyz_file> <template.inp> <prefix_name>
+
+# Example
+python Scripts/workflow/scf_batch_pretreatment_cp2k.py structures.xyz cp2k_template.inp H2O_batch
+```
+
+**Prerequisites:**
+1. Prepare CP2K input template (`cp2k_template.inp`)
+2. Template should read coordinates from `pos.xyz`
+
+**Output structure:**
+```
+<prefix>_1/input.inp, pos.xyz
+<prefix>_2/input.inp, pos.xyz
+...
+```
+
+## MD Sample Batch Pretreatment
+
+### GPUMD MD Batch
+
+```bash
+# Interactive mode
+gpumdkit.sh  # Select: 3) Workflow -> 302
+```
+
+**Prerequisites:**
+1. Place POSCAR files (or single `.xyz`) in current directory
+2. Prepare `md/` directory with:
+   - `nep.txt` (NEP model)
+   - `run_1.in`, `run_2.in`, ... (GPUMD input files)
+
+**Output structure:**
+```
+struct_md/model_1.xyz, model_2.xyz, ...
+md/nep.txt, run_1.in, run_2.in, ...   (user-provided)
+sample_1/model.xyz -> struct_md/model_1.xyz
+sample_1/nep.txt -> md/nep.txt
+sample_1/run.in -> md/run_1.in
+presub.sh
+```
+
+### LAMMPS MD Batch
+
+```bash
+# Interactive mode
+gpumdkit.sh  # Select: 3) Workflow -> 303
+```
+
+**Prerequisites:**
+1. Place POSCAR files (or single `.xyz`) in current directory
+2. Prepare `md/` directory with:
+   - `nep.txt` (NEP model)
+   - `lmprun.in` (LAMMPS input file)
+
+**Output structure:**
+```
+struct_md/lammps_1.data, lammps_2.data, ...
+md/lmprun.in, nep.txt                  (user-provided)
+sample_1/lammps.data -> struct_md/lammps_1.data
+sample_1/lmprun.in -> md/lmprun.in
+sample_1/nep.txt -> md/nep.txt
+presub.sh
+```
+
+## Active Learning Workflow
+
+### Overview
+
+Active learning iteratively improves NEP models by:
+1. Running MD with current NEP model
+2. Selecting diverse structures
+3. Computing DFT reference data
+4. Retraining NEP model
+
+### Manual Active Learning Loop
+
+```bash
+# Step 1: MD sampling with current NEP
+gpumdkit.sh  # Select: 3) Workflow -> 302
+
+# Step 2: Filter and sample structures
+gpumdkit.sh -min_dist_pbc dump.xyz
+gpumdkit.sh -filter_box dump.xyz 13
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+
+# Step 3: Prepare SCF calculations
+gpumdkit.sh  # Select: 3) Workflow -> 301
+
+# Step 4: Run DFT calculations (external)
+
+# Step 5: Convert and validate
+gpumdkit.sh -out2xyz ./scf_results/
+gpumdkit.sh -range new_data.xyz force
+
+# Step 6: Retrain NEP model (external)
+```
+
+### Automated Active Learning (Development)
+
+```bash
+# Scripts available but under development:
+# Scripts/workflow/workflow_active_learning_dev.sh
+# Scripts/workflow/workflow_active_learning_dev_multielement.sh
+```
+
+**Configurable parameters:**
+
+| Parameter | Description | Example |
+|-----------|-------------|---------|
+| `prefix_name` | Directory prefix | `LiF_iter01` |
+| `min_dist` | Minimum distance filter | `1.4` |
+| `box_limit` | Maximum box size filter | `13` |
+| `max_fp_num` | Maximum DFT calculations | `50` |
+| `sample_method` | Sampling method | `uniform`, `random`, or `pynep` |
+| `pynep_sample_dist` | FPS distance threshold | `0.01` |
+
+## Examples
+
+### Example 1: VASP High-Throughput Screening
+```bash
+# Prepare structures
+for struct in structures/*.vasp; do
+    name=$(basename "$struct" .vasp)
+    mkdir -p "calc_$name"
+    cp "$struct" "calc_$name/POSCAR"
+    ln -s ../POTCAR "calc_$name/"
+    ln -s ../INCAR "calc_$name/"
+    ln -s ../KPOINTS "calc_$name/"
+done
+```
+
+### Example 2: Temperature-Dependent MD
+```bash
+# Setup directories for multiple temperatures
+for temp in 300 500 700 900; do
+    mkdir -p "${temp}K"
+    cp model.xyz "${temp}K/"
+    cp nep.txt "${temp}K/"
+    sed "s/TEMPERATURE/$temp/g" run_template.in > "${temp}K/run.in"
+done
+```
+
+### Example 3: NEP Training Data Generation
+```bash
+# 1. Start with initial structures
+gpumdkit.sh -replicate POSCAR supercell.vasp 3 3 3
+
+# 2. Perturb structures
+python Scripts/sample_structures/perturb_structure.py supercell.vasp 20 0.03 0.2 uniform
+
+# 3. Run MD sampling
+gpumdkit.sh  # Select: 3) Workflow -> 302
+
+# 4. Select diverse structures
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+
+# 5. Prepare DFT calculations
+gpumdkit.sh  # Select: 3) Workflow -> 301
+```
+
+## Notes
+
+1. **Directory structure matters**: Workflows expect specific directory layouts
+2. **Symlinks are used**: Output directories use symlinks to save disk space
+3. **presub.sh**: Generated submission script may need modification for your cluster
+4. **Template files**: Ensure input templates are correct before batch processing
+
+## Detailed Documentation
+
+- [Workflow Guide](../../docs/tutorials/workflow.md)
+- [Active Learning Guide](../../docs/tutorials/workflow_active_learning.md)

From 38fba94fa827424a83ef71cfa35e106de3dab773 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Sat, 20 Jun 2026 22:55:57 +0800
Subject: [PATCH 09/24] update

---
 docs/tutorials2/en/README.md            | 104 ++++++++++
 docs/tutorials2/en/analyzers.md         | 257 +++--------------------
 docs/tutorials2/en/calculators.md       | 217 +++----------------
 docs/tutorials2/en/format_conversion.md | 265 ++++--------------------
 docs/tutorials2/en/index.md             | 160 --------------
 docs/tutorials2/en/nep_training.md      | 250 +++-------------------
 docs/tutorials2/en/quickstart.md        | 189 ++++-------------
 docs/tutorials2/en/sampling.md          | 185 +++--------------
 docs/tutorials2/en/visualization.md     | 218 +++++--------------
 docs/tutorials2/en/workflows.md         | 232 +++------------------
 docs/tutorials2/zh/README.md            | 104 ++++++++++
 docs/tutorials2/zh/analyzers.md         | 257 +++--------------------
 docs/tutorials2/zh/calculators.md       | 215 +++----------------
 docs/tutorials2/zh/format_conversion.md | 263 ++++-------------------
 docs/tutorials2/zh/index.md             | 160 --------------
 docs/tutorials2/zh/nep_training.md      | 250 +++-------------------
 docs/tutorials2/zh/quickstart.md        | 189 ++++-------------
 docs/tutorials2/zh/sampling.md          | 187 +++--------------
 docs/tutorials2/zh/visualization.md     | 216 +++++--------------
 docs/tutorials2/zh/workflows.md         | 232 +++------------------
 20 files changed, 770 insertions(+), 3380 deletions(-)
 create mode 100644 docs/tutorials2/en/README.md
 delete mode 100644 docs/tutorials2/en/index.md
 create mode 100644 docs/tutorials2/zh/README.md
 delete mode 100644 docs/tutorials2/zh/index.md

diff --git a/docs/tutorials2/en/README.md b/docs/tutorials2/en/README.md
new file mode 100644
index 0000000..bf09b0c
--- /dev/null
+++ b/docs/tutorials2/en/README.md
@@ -0,0 +1,104 @@
+<div align="center">
+  <h1>GPUMDkit Tutorials</h1>
+  <p>
+    <strong>English</strong> | <a href="../zh/README.md">简体中文</a>
+  </p>
+</div>
+
+Welcome to **GPUMDkit** - a command-line toolkit for GPUMD and NEP.
+
+## What is GPUMDkit?
+
+GPUMDkit streamlines common tasks in computational materials science:
+
+- **Format Conversion**: Convert between VASP, LAMMPS, CP2K, ABACUS, CIF, and extxyz formats
+- **Visualization**: Plotting tools for NEP training, MD simulations, and analysis
+- **Calculators**: Compute ionic conductivity, descriptors, MSD, NEB, and more
+- **Analyzers**: Structure validation, filtering, composition analysis
+- **Workflows**: Batch processing for DFT and MD simulations
+- **Sampling**: Structure selection using uniform, random, or FPS methods
+
+## Quick Start
+
+### Installation
+
+```bash
+git clone https://github.com/zhyan0603/GPUMDkit.git
+cd GPUMDkit
+source ./install.sh
+```
+
+### Dependencies
+
+```bash
+conda create -n gpumdkit python=3.12
+conda activate gpumdkit
+pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
+```
+
+### Usage
+
+```bash
+# Interactive mode
+gpumdkit.sh
+
+# Command-line mode
+gpumdkit.sh -<option> [args...]
+
+# Get help
+gpumdkit.sh -h
+```
+
+## Tutorials
+
+| Tutorial | Description |
+|----------|-------------|
+| [Quick Start](quickstart.md) | Installation and first steps |
+| [Format Conversion](format_conversion.md) | Convert between file formats |
+| [Calculators](calculators.md) | Compute material properties |
+| [Analyzers](analyzers.md) | Structure analysis and validation |
+| [Visualization](visualization.md) | Plotting and visualization |
+| [Workflows](workflows.md) | Batch processing and automation |
+| [Structure Sampling](sampling.md) | Structure selection methods |
+| [NEP Training](nep_training.md) | Complete NEP training workflow |
+
+## Example: NEP Training Pipeline
+
+```bash
+# Convert DFT data
+gpumdkit.sh -out2xyz ./vasp_results/
+
+# Add group labels
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+
+# Sample structures
+gpumdkit.sh  # Select: 2) Sample Structures -> 203
+
+# Validate training
+gpumdkit.sh -plt train
+```
+
+## Example: Ionic Conductivity
+
+```bash
+gpumdkit.sh -calc msd trajectory.xyz Li 10
+gpumdkit.sh -calc ionic-cond Li 1
+gpumdkit.sh -plt msd
+```
+
+## Module Overview
+
+| Module | Menu | CLI | Description |
+|--------|------|-----|-------------|
+| Format Conversion | 1 | `-out2xyz`, `-pos2exyz` | File conversion |
+| Sample Structures | 2 | `-pynep` | Structure sampling |
+| Workflow | 3 | - | Batch processing |
+| Calculators | 4 | `-calc <type>` | Property calculations |
+| Analyzer | 5 | `-range`, `-min_dist` | Structure analysis |
+| Visualization | 6 | `-plt <type>` | Plotting tools |
+| Utilities | 7 | `-time`, `-clean` | Utility functions |
+
+## Links
+
+- GitHub: https://github.com/zhyan0603/GPUMDkit
+- Documentation: https://zhyan0603.github.io/GPUMDkit/
diff --git a/docs/tutorials2/en/analyzers.md b/docs/tutorials2/en/analyzers.md
index 892f39a..0b47abe 100644
--- a/docs/tutorials2/en/analyzers.md
+++ b/docs/tutorials2/en/analyzers.md
@@ -1,289 +1,92 @@
-# Analyzers Guide
-
 <div align="center">
+  <h1>Analyzers</h1>
   <p>
-    <a href="../zh/analyzers.md">中文</a> | <strong>English</strong>
+    <strong>English</strong> | <a href="../zh/analyzers.md">简体中文</a>
   </p>
 </div>
 
-This guide covers all analysis tools in GPUMDkit for structure validation, filtering, and quality control.
+Structure analysis, validation, and filtering tools.
 
 ## Available Tools
 
 | Tool | Command | Description |
 |------|---------|-------------|
 | Composition Analysis | `-analyze_comp` | Group structures by composition |
-| Outlier Detection | Menu 502 | Find high-error structures |
-| Chemical Species | Menu 503 | List unique elements |
-| Charge Balance | `-cbc` | Check oxidation-state balance |
 | Property Range | `-range` | Energy/force/virial statistics |
-| Distance Filter | Menu 506 | Filter by minimum distance (no PBC) |
-| Distance Filter (PBC) | Menu 506b | Filter by minimum distance (with PBC) |
 | Minimum Distance | `-min_dist` | Calculate min distances (no PBC) |
 | Minimum Distance (PBC) | `-min_dist_pbc` | Calculate min distances (with PBC) |
-| Probability Density | Menu 508 | 3D diffusion channel analysis |
-
-## Interactive Mode
-
-```bash
-gpumdkit.sh
-# Select: 5) Analyzer
-```
-
-You'll see:
-
-```
-+------------------------------------------------------+
-|                    ANALYZER TOOLS                    |
-+------------------------------------------------------+
-| 501) Analyze composition of extxyz                   |
-| 502) Find outliers of extxyz                         |
-| 503) Analyze chemical species of extxyz              |
-| 504) Check charge balance of extxyz                  |
-| 505) Analyze energy/force/virial range               |
-| 506) Filter structures by minimum distance           |
-| 507) Get minimum interatomic distance                |
-| 508) Probability density analysis                    |
-+------------------------------------------------------+
-```
+| Charge Balance | `-cbc` | Check oxidation-state balance |
+| Distance Filter | `-filter_dist_pbc` | Filter by minimum distance |
+| Box Filter | `-filter_box` | Filter by box size |
+| Value Filter | `-filter_value` | Filter by property value |
+| Distance Range | `-filter_range` | Filter by element-pair distance |
+| Time Monitor | `-time` | Monitor GPUMD/NEP progress |
 
 ## Command Reference
 
 ### Composition Analysis
 
-Analyze and group structures by chemical composition.
-
 ```bash
 gpumdkit.sh -analyze_comp train.xyz
 ```
 
-**Output:** Table of unique compositions with atom counts and structure counts. Interactive selection to export specific compositions.
-
-### Property Range Analysis
-
-Compute the range (min, max) of energy, force, or virial in an extxyz file.
+### Property Range
 
 ```bash
-gpumdkit.sh -range <filename> <property> [hist]
+gpumdkit.sh -range <file> <property> [hist]
 
 # Examples
-gpumdkit.sh -range train.xyz energy
 gpumdkit.sh -range train.xyz force
-gpumdkit.sh -range train.xyz virial
-gpumdkit.sh -range train.xyz force hist    # With histogram
+gpumdkit.sh -range train.xyz energy
+gpumdkit.sh -range train.xyz force hist
 ```
 
-**Output:** Min/max values. Optional histogram plot with `hist` argument.
-
 ### Minimum Distance
 
-Calculate minimum interatomic distance for each element pair.
-
 ```bash
-# Fast calculation (no PBC)
+# Fast (no PBC)
 gpumdkit.sh -min_dist dump.xyz
 
-# Accurate calculation (with PBC)
+# Accurate (with PBC)
 gpumdkit.sh -min_dist_pbc dump.xyz
 ```
 
-**Output:** Table of minimum distances for all element pairs
-
-### Charge Balance Check
-
-Check oxidation-state balance for all structures.
+### Charge Balance
 
 ```bash
 gpumdkit.sh -cbc train.xyz
 ```
 
-**Output:**
-- `balanced.xyz` - Charge-balanced structures
-- `unbalanced.xyz` - Unbalanced structures
-- `indices.txt` - Summary
-
-### Chemical Species Identification
-
-List all unique chemical elements in the file.
-
-```bash
-# Interactive mode
-gpumdkit.sh  # Select: 5) Analyzer -> 503
-```
-
-**Output:** Sorted list of all elements
-
-### Structure Filtering
-
-#### By Minimum Distance (No PBC)
-
-```bash
-gpumdkit.sh  # Select: 5) Analyzer -> 506
-```
-
-**Input:** extxyz file, distance threshold
-**Output:** `filtered_<file>.xyz`, `filtered_out_<file>.xyz`
-
-#### By Minimum Distance (With PBC)
-
-```bash
-gpumdkit.sh  # Select: 5) Analyzer -> 506b
-```
-
-More accurate for periodic systems.
-
-#### By Element-Pair Distance Range
-
-```bash
-gpumdkit.sh -filter_range <file> <element1> <element2> <min_dist> <max_dist>
-
-# Example: Filter Li-Li distances between 1.9 and 2.0 Å
-gpumdkit.sh -filter_range dump.xyz Li Li 1.9 2.0
-```
-
-**Output:** `filtered_<elem1>_<elem2>_<min>_<max>.xyz`
+Output: `balanced.xyz`, `unbalanced.xyz`
 
-#### By Box Size
+### Filtering
 
 ```bash
-gpumdkit.sh -filter_box <file> <edge_limit>
+# By minimum distance
+gpumdkit.sh -filter_dist_pbc train.xyz 1.0
 
-# Example: Filter structures with box edge > 20 Å
+# By box size
 gpumdkit.sh -filter_box dump.xyz 20
-```
 
-**Output:** `filtered_by_box.xyz`
-
-#### By Property Value
-
-```bash
-gpumdkit.sh -filter_value <file> <property> <threshold>
-
-# Example: Keep structures with force < 20 eV/Å
+# By property value
 gpumdkit.sh -filter_value train.xyz force 20
-```
-
-**Output:** `filtered.xyz`
-
-### Outlier Detection
-
-Find outlier structures based on RMSE thresholds.
-
-```bash
-gpumdkit.sh  # Select: 5) Analyzer -> 502
-```
-
-**Required files:**
-- `train.xyz`
-- `energy_train.out`
-- `force_train.out`
-- `stress_train.out`
-
-**Output:** `selected.xyz` (high-error), `remained.xyz` (low-error)
-
-### Probability Density Analysis
-
-Calculate 3D probability density of mobile ions from AIMD trajectory.
 
-```bash
-gpumdkit.sh  # Select: 5) Analyzer -> 508
-```
-
-**Parameters:**
-- Reference structure (POSCAR)
-- Trajectory file (extxyz)
-- Mobile species (e.g., Li)
-- Grid interval (e.g., 0.25 Å)
-
-**Output:** `probability_density_<interval>.vasp` (CHGCAR format)
-
-## Common Workflows
-
-### Data Quality Check
-
-```bash
-# 1. Check composition
-gpumdkit.sh -analyze_comp train.xyz
-
-# 2. Check minimum distances
-gpumdkit.sh -min_dist_pbc train.xyz
-
-# 3. Check force range
-gpumdkit.sh -range train.xyz force
-
-# 4. Check for outliers
-gpumdkit.sh  # Select: 5) Analyzer -> 502
-```
-
-### Structure Filtering Pipeline
-
-```bash
-# 1. Filter by distance
-gpumdkit.sh  # Select: 5) Analyzer -> 506
-
-# 2. Filter by box size
-gpumdkit.sh -filter_box filtered.xyz 20
-
-# 3. Filter by force value
-gpumdkit.sh -filter_value filtered_by_box.xyz force 15
-```
-
-### Diffusion Channel Analysis
-
-```bash
-# 1. Calculate probability density
-gpumdkit.sh  # Select: 5) Analyzer -> 508
-
-# 2. Visualize with VESTA or similar
-# Open probability_density_0.25.vasp
+# By element-pair distance range
+gpumdkit.sh -filter_range dump.xyz Li Li 1.9 2.0
 ```
 
-## Additional Tools
-
 ### Time Monitoring
 
 ```bash
-# Monitor GPUMD progress
 gpumdkit.sh -time gpumd
-
-# Monitor NEP training progress
 gpumdkit.sh -time nep
 ```
 
-### Volume Analysis
-
-```bash
-# Get average volume per temperature
-python Scripts/analyzer/get_volume.py
-# Requires: */K/thermo.out directories
-```
-
-## CLI Reference
-
-| Flag | Description | Syntax |
-|------|-------------|--------|
-| `-analyze_comp` | Composition analysis | `gpumdkit.sh -analyze_comp <file>` |
-| `-range` | Property range | `gpumdkit.sh -range <file> <prop>` |
-| `-min_dist` | Min distance (no PBC) | `gpumdkit.sh -min_dist <file>` |
-| `-min_dist_pbc` | Min distance (PBC) | `gpumdkit.sh -min_dist_pbc <file>` |
-| `-cbc` | Charge balance | `gpumdkit.sh -cbc <file>` |
-| `-filter_range` | Filter by distance range | `gpumdkit.sh -filter_range <file> <e1> <e2> <min> <max>` |
-| `-filter_box` | Filter by box size | `gpumdkit.sh -filter_box <file> <limit>` |
-| `-filter_value` | Filter by property | `gpumdkit.sh -filter_value <file> <prop> <thresh>` |
-| `-time` | Time monitoring | `gpumdkit.sh -time <gpumd\|nep>` |
-
 ## Dependencies
 
-| Tool | Required Packages |
-|------|------------------|
-| All Python scripts | `ase`, `numpy` |
-| Distance calculations | `scipy` |
-| Charge balance | `pymatgen`, `tqdm` |
-| Property range | `matplotlib` |
-| Probability density | `pymatgen` |
-
-## See Also
-
-- [Format Conversion](format_conversion.md) - Convert file formats
-- [Calculators](calculators.md) - Compute properties
-- [Visualization](visualization.md) - Plot results
+| Tool | Packages |
+|------|----------|
+| All | ase, numpy |
+| Distance | scipy |
+| Charge balance | pymatgen, tqdm |
+| Property range | matplotlib |
diff --git a/docs/tutorials2/en/calculators.md b/docs/tutorials2/en/calculators.md
index 57a9112..2fbfc4f 100644
--- a/docs/tutorials2/en/calculators.md
+++ b/docs/tutorials2/en/calculators.md
@@ -1,12 +1,11 @@
-# Calculators Guide
-
 <div align="center">
+  <h1>Calculators</h1>
   <p>
-    <a href="../zh/calculators.md">中文</a> | <strong>English</strong>
+    <strong>English</strong> | <a href="../zh/calculators.md">简体中文</a>
   </p>
 </div>
 
-This guide covers all calculator tools in GPUMDkit for computing material properties.
+Compute material properties from molecular dynamics data.
 
 ## Available Calculators
 
@@ -16,69 +15,30 @@ This guide covers all calculator tools in GPUMDkit for computing material proper
 | NEP Properties | `-calc nep` | Compute energy/force/stress with NEP |
 | Descriptors | `-calc des` | Calculate NEP descriptors for analysis |
 | DOAS | `-calc doas` | Density of atomistic states |
-| NEB | Direct Python | Nudged elastic band calculation |
+| MSD | `-calc msd` | Mean square displacement from trajectory |
 | Neighbor List | `-calc nlist` | Build neighbor lists for analysis |
 | Displacement | `-calc disp` | Calculate atomic displacements |
 | Averaged Structure | `-calc avg-struct` | Time-averaged structure from trajectory |
 | Octahedral Tilt | `-calc oct-tilt` | Perovskite octahedral tilt angles |
 | Polarization | `-calc pol-abo3` | ABO3 local polarization |
 | Minimization | `-calc minimize` | Structure relaxation with NEP |
-| MSD | `-calc msd` | Mean square displacement from trajectory |
-
-## Interactive Mode
-
-```bash
-gpumdkit.sh
-# Select: 4) Calculators
-```
-
-You'll see:
-
-```
-+----------------------------------------------------------+
-|                     CALCULATOR TOOLS                     |
-+----------------------------------------------------------+
-| 401) Calc ionic conductivity                             |
-| 402) Calc properties by nep                              |
-| 403) Calc descriptors of specific elements               |
-| 404) Calc density of atomistic states (DOAS)             |
-| 405) Calc nudged elastic band (NEB) by nep               |
-| 406) Build neighbor list                                 |
-| 407) Calc displacement from trajectory                   |
-| 408) Calc averaged structure                             |
-| 409) Calc octahedral tilt                                |
-| 410) Calc polarization for ABO3                          |
-| 411) Minimize structure by nep                           |
-| 412) Calc mean square displacement (MSD) from trajectory |
-+----------------------------------------------------------+
-```
+| NEB | Direct Python | Nudged elastic band calculation |
 
 ## Command Reference
 
 ### Ionic Conductivity
 
-Calculate ionic conductivity from MSD data using the Nernst-Einstein equation.
-
 ```bash
 gpumdkit.sh -calc ionic-cond <element> <charge>
 
 # Examples
-gpumdkit.sh -calc ionic-cond Li 1    # Lithium ion (Li+)
-gpumdkit.sh -calc ionic-cond Na 1    # Sodium ion (Na+)
-gpumdkit.sh -calc ionic-cond O -2    # Oxygen ion (O2-)
+gpumdkit.sh -calc ionic-cond Li 1    # Li+
+gpumdkit.sh -calc ionic-cond O -2    # O2-
 ```
 
-**Required files in current directory:**
-- `msd.out` - From GPUMD `compute_msd`
-- `thermo.out` - For temperature
-- `model.xyz` - For volume
-- `run.in` - For simulation parameters
+Required files: `msd.out`, `thermo.out`, `model.xyz`, `run.in`
 
-**Output:** Ionic diffusivity and conductivity values
-
-### NEP Property Prediction
-
-Calculate energies, forces, and stresses using a NEP model as a DFT surrogate.
+### NEP Properties
 
 ```bash
 gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>
@@ -87,12 +47,8 @@ gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>
 gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
 ```
 
-**Note:** Clean input with `gpumdkit.sh -clean_xyz` first to remove existing properties.
-
 ### Descriptors
 
-Calculate NEP descriptors for dimensionality reduction and structure analysis.
-
 ```bash
 gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>
 
@@ -100,15 +56,9 @@ gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>
 gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
 ```
 
-**Visualize with:**
-```bash
-gpumdkit.sh -plt des pca    # PCA visualization
-gpumdkit.sh -plt des umap   # UMAP visualization
-```
-
-### Density of Atomistic States (DOAS)
+Visualize with: `gpumdkit.sh -plt des pca` or `gpumdkit.sh -plt des umap`
 
-Calculate per-atom energy distributions grouped by element type.
+### DOAS
 
 ```bash
 gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>
@@ -117,42 +67,28 @@ gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>
 gpumdkit.sh -calc doas structures.xyz nep.txt doas.out
 ```
 
-**Visualize with:**
-```bash
-gpumdkit.sh -plt doas doas.out Li
-```
-
-### Mean Square Displacement (MSD)
-
-Calculate directional MSD from an extxyz trajectory.
+### MSD
 
 ```bash
 gpumdkit.sh -calc msd <trajectory.xyz> <element> <dt_fs> [max_corr_steps]
 
-# Example: Li with 10 fs timestep
+# Example
 gpumdkit.sh -calc msd dump.xyz Li 10
 ```
 
-**Output:** `msd.out` (Time/ps, MSD_x, MSD_y, MSD_z)
+Output: `msd.out` (Time/ps, MSD_x, MSD_y, MSD_z)
 
 ### Neighbor List
 
-Build neighbor lists for perovskite analysis.
-
 ```bash
-gpumdkit.sh -calc nlist -i <input> -c <cutoff> -n <num_neighbors> -C <center_elements> -E <neighbor_elements>
+gpumdkit.sh -calc nlist -i <input> -c <cutoff> -n <num> -C <center> -E <neighbor>
 
-# Examples
+# Example
 gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
-gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O
 ```
 
-**Output:** `nl-<center>-<neighbor>.dat`
-
 ### Displacement
 
-Calculate atomic displacements from trajectory using neighbor list.
-
 ```bash
 gpumdkit.sh -calc disp -i <trajectory.xyz> -n <neighbor_list> -o <output>
 
@@ -160,12 +96,8 @@ gpumdkit.sh -calc disp -i <trajectory.xyz> -n <neighbor_list> -o <output>
 gpumdkit.sh -calc disp -i movie.xyz -n nl-Pb-O.dat -o displacements.dat
 ```
 
-**Optional frame slicing:** `-s <start> -t <stop> -p <step> -l <last_fraction>`
-
 ### Averaged Structure
 
-Generate time-averaged structure from trajectory.
-
 ```bash
 gpumdkit.sh -calc avg-struct -i <trajectory.xyz> -l <fraction> -o <output>
 
@@ -175,35 +107,23 @@ gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged.xyz
 
 ### Octahedral Tilt
 
-Calculate octahedral tilt angles for perovskite systems.
-
 ```bash
-gpumdkit.sh -calc oct-tilt -i <input.xyz> -n <B-O neighbor list> -o <output>
+gpumdkit.sh -calc oct-tilt -i <input.xyz> -n <B-O list> -o <output>
 
 # Example
-gpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o octahedral_tilt.dat
+gpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o tilt.dat
 ```
 
 ### Polarization (ABO3)
 
-Calculate local polarization for ABO3 perovskites.
-
 ```bash
-gpumdkit.sh -calc pol-abo3 -i <input.xyz> \
-  --nl-ba <B-A neighbor list> \
-  --nl-bo <B-O neighbor list> \
-  --bec <Element=charge ...>
+gpumdkit.sh -calc pol-abo3 -i <input.xyz> --nl-ba <B-A list> --nl-bo <B-O list> --bec <Element=charge ...>
 
 # Example
-gpumdkit.sh -calc pol-abo3 -i model.xyz \
-  --nl-ba nl-Ti-Pb.dat \
-  --nl-bo nl-Ti-O.dat \
-  --bec Pb=2.5 Sr=2.0 Ti=4.0 O=-2.0
+gpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat --bec Pb=2.5 Ti=4.0 O=-2.0
 ```
 
-### Structure Minimization
-
-Relax structures using BFGS optimizer with NEP model.
+### Minimization
 
 ```bash
 gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]
@@ -212,101 +132,22 @@ gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]
 gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
 ```
 
-**Parameters:**
-- `fmax`: Force convergence threshold (default: 0.01 eV/Å)
-- `max_steps`: Maximum optimization steps (default: 1000)
+Output: `minimize.xyz`
 
-**Output:** `minimize.xyz` (optimization trajectory)
-
-### NEB Calculation
-
-Perform nudged elastic band calculations for migration barriers.
+### NEB
 
 ```bash
-# Direct Python execution
 python Scripts/calculators/neb_calculation.py <initial.xyz> <final.xyz> <n_images> <nep.txt>
 
 # Example
 python Scripts/calculators/neb_calculation.py init.xyz fin.xyz 9 nep.txt
 ```
 
-## Common Workflows
-
-### Ionic Transport Analysis
-
-```bash
-# 1. Run MD with compute_msd in run.in
-# 2. Calculate MSD
-gpumdkit.sh -calc msd dump.xyz Li 10
-
-# 3. Calculate conductivity
-gpumdkit.sh -calc ionic-cond Li 1
-
-# 4. Visualize
-gpumdkit.sh -plt msd
-gpumdkit.sh -plt sdc
-```
-
-### Descriptor Analysis
-
-```bash
-# 1. Calculate descriptors
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-
-# 2. Visualize with PCA
-gpumdkit.sh -plt des pca
-
-# 3. Or visualize with UMAP
-gpumdkit.sh -plt des umap
-```
-
-### Perovskite Analysis
-
-```bash
-# 1. Build neighbor lists
-gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
-gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E Pb
-
-# 2. Calculate displacements
-gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -o disp.dat
-
-# 3. Calculate tilt
-gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -o tilt.dat
-
-# 4. Calculate polarization
-gpumdkit.sh -calc pol-abo3 -i movie.xyz \
-  --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \
-  --bec Pb=2.5 Ti=4.0 O=-2.0
-```
-
-### Structure Relaxation
-
-```bash
-# 1. Minimize structure
-gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
-
-# 2. Use minimized structure for MD
-cp minimize.xyz relaxed_model.xyz
-```
-
 ## Dependencies
 
-| Calculator | Required Packages |
-|------------|------------------|
-| All | `numpy`, `ase` |
-| ionic-cond | `scipy` |
-| nep, des, doas, minimize | `calorine` |
-| nlist, disp, oct-tilt, pol-abo3 | `ferrodispcalc` |
-| neb | `calorine`, `matplotlib` |
-
-Install dependencies:
-```bash
-pip install numpy ase scipy calorine matplotlib tqdm
-pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
-```
-
-## See Also
-
-- [Visualization](visualization.md) - Plot calculation results
-- [Analyzers](analyzers.md) - Structure analysis
-- [NEP Training Guide](nep_training.md) - Complete training workflow
+| Calculator | Packages |
+|------------|----------|
+| All | numpy, ase |
+| ionic-cond | scipy |
+| nep, des, doas, minimize | calorine |
+| nlist, disp, oct-tilt, pol-abo3 | ferrodispcalc |
diff --git a/docs/tutorials2/en/format_conversion.md b/docs/tutorials2/en/format_conversion.md
index f4109bd..0aca344 100644
--- a/docs/tutorials2/en/format_conversion.md
+++ b/docs/tutorials2/en/format_conversion.md
@@ -1,273 +1,100 @@
-# Format Conversion Guide
-
 <div align="center">
+  <h1>Format Conversion</h1>
   <p>
-    <a href="../zh/format_conversion.md">中文</a> | <strong>English</strong>
+    <strong>English</strong> | <a href="../zh/format_conversion.md">简体中文</a>
   </p>
 </div>
 
-This guide covers all format conversion tools in GPUMDkit.
+Convert between computational materials science file formats.
 
 ## Supported Formats
 
-| Format | Extensions | Description |
-|--------|-----------|-------------|
-| VASP | POSCAR, OUTCAR, XDATCAR, vasprun.xml | Vienna Ab initio Simulation Package |
-| LAMMPS | .data, dump.* | Large-scale Atomic/Molecular Massively Parallel Simulator |
-| CP2K | .log, pos.xyz, frc.xyz, cell.cell | Quantum chemistry and solid state physics |
-| ABACUS | running_scf.log, running_md.log | Atomic-orbital Based Ab-initio Computation |
-| CIF | .cif | Crystallographic Information File |
-| MTP | .cfg | Moment Tensor Potential format |
-| ASE | .traj | Atomic Simulation Environment trajectory |
-| extxyz | .xyz | Extended XYZ (primary working format) |
-
-## Interactive Mode
+| Format | Extensions | Software |
+|--------|-----------|----------|
+| VASP | POSCAR, OUTCAR, XDATCAR, vasprun.xml | VASP |
+| LAMMPS | .data, dump.* | LAMMPS |
+| CP2K | .log, pos.xyz, frc.xyz, cell.cell | CP2K |
+| ABACUS | running_scf.log, running_md.log | ABACUS |
+| CIF | .cif | Various |
+| MTP | .cfg | MTP |
+| ASE | .traj | ASE |
+| extxyz | .xyz | Various (primary format) |
 
-Launch the interactive menu and select option 1:
+## Quick Reference
 
 ```bash
-gpumdkit.sh
-# Select: 1) Format Conversion
-```
+# VASP
+gpumdkit.sh -out2xyz <dir>              # OUTCAR -> extxyz
+gpumdkit.sh -pos2exyz POSCAR model.xyz  # POSCAR -> extxyz
+gpumdkit.sh -exyz2pos structures.xyz    # extxyz -> POSCAR
 
-You'll see:
-
-```
-+-------------------------------------------------------------+
-|                   FORMAT CONVERSION TOOLS                   |
-+-------------------------------------------------------------+
-| 101) VASP to extxyz            106) Add group labels        |
-| 102) MTP to extxyz             107) Add weight to extxyz    |
-| 103) CP2K to extxyz            108) Extract frame extxyz    |
-| 104) ABACUS to extxyz          109) Clean XYZ info          |
-| 105) extxyz to POSCAR          110) Replicate structure     |
-+-------------------------------------------------------------+
-| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |
-| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |
-| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |
-| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|
-+-------------------------------------------------------------+
-| 000) Return to main menu                                    |
-+-------------------------------------------------------------+
-```
-
-## Command-Line Mode
-
-### VASP Conversions
-
-#### OUTCAR to extxyz
-
-```bash
-# Shell version (supports both OUTCAR and vasprun.xml)
-gpumdkit.sh -out2xyz <directory>
-
-# Python version (OUTCAR only)
-gpumdkit.sh -out2exyz <directory>
-
-# Example
-gpumdkit.sh -out2xyz ./vasp_results/
-```
-
-#### XDATCAR to extxyz
-
-```bash
-gpumdkit.sh -xdat2exyz XDATCAR output.xyz
-```
-
-#### POSCAR to extxyz
-
-```bash
-gpumdkit.sh -pos2exyz POSCAR model.xyz
-```
-
-#### extxyz to POSCAR
-
-```bash
-# Converts ALL frames to separate POSCAR files
-gpumdkit.sh -exyz2pos structures.xyz
-```
-
-### LAMMPS Conversions
-
-#### LAMMPS dump to extxyz
-
-```bash
-# IMPORTANT: Element symbols must match atom type IDs in dump file
-gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
-
-# Example
-gpumdkit.sh -lmp2exyz trajectory.dump Na Cl
-```
-
-#### POSCAR to LAMMPS data
-
-```bash
-gpumdkit.sh -pos2lmp POSCAR lammps.data
-```
-
-### CIF Conversions
-
-```bash
-# CIF to POSCAR
-gpumdkit.sh -cif2pos input.cif POSCAR.vasp
-
-# CIF to extxyz
-gpumdkit.sh -cif2exyz input.cif model.xyz
-```
+# LAMMPS
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl  # LAMMPS -> extxyz
+gpumdkit.sh -pos2lmp POSCAR lammps.data        # POSCAR -> LAMMPS
 
-### Other Conversions
+# CIF
+gpumdkit.sh -cif2pos input.cif POSCAR.vasp     # CIF -> POSCAR
+gpumdkit.sh -cif2exyz input.cif model.xyz      # CIF -> extxyz
 
-```bash
-# ASE trajectory to extxyz
-gpumdkit.sh -traj2exyz input.traj output.xyz
+# Other
+gpumdkit.sh -xdat2exyz XDATCAR output.xyz      # XDATCAR -> extxyz
+gpumdkit.sh -traj2exyz input.traj output.xyz   # ASE traj -> extxyz
 ```
 
 ## Structure Manipulation
 
-### Add Group Labels
-
-Group labels are required for GPUMD/NEP to identify atom types:
-
 ```bash
-gpumdkit.sh -addgroup POSCAR <element1> <element2> ...
-
-# Example
+# Add group labels (required for NEP)
 gpumdkit.sh -addgroup POSCAR Li Y Cl
-```
-
-This creates `model.xyz` with group labels assigned to each atom.
 
-### Add Weights
-
-Add weight labels to structures for weighted training:
-
-```bash
-gpumdkit.sh -addweight input.xyz output.xyz <weight>
-
-# Example
-gpumdkit.sh -addweight train.xyz weighted.xyz 2.0
-```
+# Add weights
+gpumdkit.sh -addweight input.xyz output.xyz 2.0
 
-### Replicate Structure
-
-Create supercells from unit cells:
-
-```bash
-# By replication factors
+# Replicate structure
 gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2
+gpumdkit.sh -replicate POSCAR supercell.vasp 256  # by atom count
 
-# By target atom count
-gpumdkit.sh -replicate POSCAR supercell.vasp 256
-```
-
-### Extract Frame
-
-Extract a specific frame from a trajectory:
-
-```bash
-# 0-based index
+# Extract frame (0-based)
 gpumdkit.sh -get_frame trajectory.xyz 1000
-```
-
-### Clean XYZ Metadata
 
-Remove extra metadata from extxyz files:
-
-```bash
+# Clean metadata
 gpumdkit.sh -clean_xyz input.xyz clean.xyz
 ```
 
-## Complete CLI Reference
-
-| Flag | Description | Syntax |
-|------|-------------|--------|
-| `-out2xyz` | OUTCAR to extxyz (shell) | `gpumdkit.sh -out2xyz <dir>` |
-| `-out2exyz` | OUTCAR to extxyz (python) | `gpumdkit.sh -out2exyz <dir>` |
-| `-pos2exyz` | POSCAR to extxyz | `gpumdkit.sh -pos2exyz <poscar> <xyz>` |
-| `-exyz2pos` | extxyz to POSCAR | `gpumdkit.sh -exyz2pos <xyz>` |
-| `-pos2lmp` | POSCAR to LAMMPS data | `gpumdkit.sh -pos2lmp <poscar> <lmp>` |
-| `-lmp2exyz` | LAMMPS dump to extxyz | `gpumdkit.sh -lmp2exyz <dump> <elem...>` |
-| `-cif2pos` | CIF to POSCAR | `gpumdkit.sh -cif2pos <cif> <output>` |
-| `-cif2exyz` | CIF to extxyz | `gpumdkit.sh -cif2exyz <cif> <output>` |
-| `-xdat2exyz` | XDATCAR to extxyz | `gpumdkit.sh -xdat2exyz XDATCAR dump.xyz` |
-| `-traj2exyz` | ASE traj to extxyz | `gpumdkit.sh -traj2exyz <traj> <xyz>` |
-| `-addgroup` | Add group labels | `gpumdkit.sh -addgroup <poscar> <elem...>` |
-| `-addweight` | Add weight | `gpumdkit.sh -addweight <in> <out> <weight>` |
-| `-replicate` | Replicate structure | `gpumdkit.sh -replicate <in> <out> a b c` |
-| `-get_frame` | Extract frame | `gpumdkit.sh -get_frame <xyz> <index>` |
-| `-clean_xyz` | Clean extxyz info | `gpumdkit.sh -clean_xyz <in> <out>` |
-
 ## Examples
 
-### Example 1: Convert VASP MD Output
+### Convert VASP Output
 
 ```bash
-# Convert all OUTCAR files in current directory
 gpumdkit.sh -out2xyz .
-
-# Add group labels for NEP training
 gpumdkit.sh -addgroup POSCAR Pb Ti O
-
-# Result: model.xyz ready for NEP training
 ```
 
-### Example 2: Prepare LAMMPS Simulation
+### Prepare LAMMPS Simulation
 
 ```bash
-# Convert POSCAR to LAMMPS data
 gpumdkit.sh -pos2lmp POSCAR system.data
-
-# After LAMMPS simulation, convert dump back
+# After simulation
 gpumdkit.sh -lmp2exyz dump.lammpstrj Li P S
 ```
 
-### Example 3: Batch Conversion
+### Batch Conversion
 
 ```bash
-# Convert multiple OUTCAR files
 for dir in run_*; do
     gpumdkit.sh -out2xyz "$dir"
-    mv "$dir"/model.xyz "$dir"/trajectory.xyz
 done
 ```
 
-### Example 4: Structure Replication
-
-```bash
-# Create 2x2x2 supercell
-gpumdkit.sh -replicate POSCAR supercell_222.vasp 2 2 2
-
-# Create supercell with ~256 atoms
-gpumdkit.sh -replicate POSCAR supercell_256.vasp 256
-```
-
-## Important Notes
+## Notes
 
-1. **extxyz is the primary format**: Most GPUMDkit tools work with extxyz files
-2. **Group labels are essential**: Required for GPUMD/NEP to identify atom types
-3. **Frame indexing is 0-based**: First frame is index 0
-4. **Element ordering matters for LAMMPS**: Must match atom type IDs in dump file
-5. **exyz2pos exports all frames**: Creates separate POSCAR for each frame
+- extxyz is the primary format for GPUMDkit
+- Group labels are required for GPUMD/NEP
+- Frame indexing is 0-based
+- LAMMPS element order must match atom type IDs
 
 ## Dependencies
 
-Most Python scripts require:
-- `ase` (Atomic Simulation Environment)
-- `numpy`
-
-## Troubleshooting
-
-### Issue: Missing element information
-**Solution**: Ensure POSCAR has correct element names in the header
-
-### Issue: Incorrect atom count
-**Solution**: Check if POSCAR has selective dynamics enabled
-
-### Issue: LAMMPS conversion wrong species
-**Solution**: Verify element order matches atom type IDs in dump file
-
-## See Also
-
-- [Calculators](calculators.md) - Compute material properties
-- [Analyzers](analyzers.md) - Structure analysis
-- [NEP Training Guide](nep_training.md) - Complete training workflow
+```bash
+pip install ase numpy
+```
diff --git a/docs/tutorials2/en/index.md b/docs/tutorials2/en/index.md
deleted file mode 100644
index 079eec7..0000000
--- a/docs/tutorials2/en/index.md
+++ /dev/null
@@ -1,160 +0,0 @@
-# GPUMDkit Tutorials
-
-<div align="center">
-  <p>
-    <a href="../zh/index.md">中文</a> | <strong>English</strong>
-  </p>
-</div>
-
-Welcome to **GPUMDkit** - a powerful command-line toolkit for GPUMD and NEP!
-
-## What is GPUMDkit?
-
-GPUMDkit streamlines your molecular dynamics workflow with:
-
-- **Format Conversion**: Convert between VASP, LAMMPS, CP2K, ABACUS, CIF, and extxyz formats
-- **Calculators**: Compute ionic conductivity, descriptors, MSD, NEB, and more
-- **Analyzers**: Structure validation, filtering, composition analysis
-- **Visualization**: 31+ plot types for training, transport, and structural analysis
-- **Workflows**: Batch processing for DFT and MD simulations
-- **Sampling**: Structure selection using uniform, random, or FPS methods
-
-## Quick Start
-
-### Installation
-
-```bash
-# Clone the repository
-git clone https://github.com/zhyan0603/GPUMDkit.git
-
-# Install
-cd GPUMDkit
-source ./install.sh
-```
-
-### Dependencies
-
-```bash
-# Create conda environment
-conda create -n gpumdkit python=3.12
-conda activate gpumdkit
-
-# Install required packages
-pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
-```
-
-### Basic Usage
-
-```bash
-# Interactive mode (menu-driven)
-gpumdkit.sh
-
-# Command-line mode
-gpumdkit.sh -<option> [args...]
-
-# Get help
-gpumdkit.sh -h                    # General help
-gpumdkit.sh -<option> -h          # Specific command help
-gpumdkit.sh -plt -h               # Plot help
-gpumdkit.sh -calc -h              # Calculator help
-```
-
-## Tutorials
-
-| Tutorial | Description |
-|----------|-------------|
-| [Quick Start](quickstart.md) | Installation, configuration, and first steps |
-| [Format Conversion](format_conversion.md) | Convert between structure file formats |
-| [Calculators](calculators.md) | Compute material properties |
-| [Analyzers](analyzers.md) | Structure analysis and validation |
-| [Visualization](visualization.md) | Plotting and data visualization |
-| [Workflows](workflows.md) | Batch processing and automation |
-| [Structure Sampling](sampling.md) | Structure selection methods |
-| [NEP Training Guide](nep_training.md) | Complete NEP model training workflow |
-
-## Common Workflows
-
-### Workflow 1: NEP Model Training
-
-```bash
-# 1. Convert DFT data
-gpumdkit.sh -out2xyz ./vasp_results/
-
-# 2. Add group labels
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-
-# 3. Sample structures
-gpumdkit.sh  # Select: 2) Sample Structures -> 203
-
-# 4. Train NEP (external)
-# ...
-
-# 5. Validate
-gpumdkit.sh -plt train
-gpumdkit.sh -plt prediction
-```
-
-### Workflow 2: Ionic Conductivity
-
-```bash
-# 1. Calculate MSD
-gpumdkit.sh -calc msd trajectory.xyz Li 10
-
-# 2. Calculate conductivity
-gpumdkit.sh -calc ionic-cond Li 1
-
-# 3. Visualize
-gpumdkit.sh -plt msd
-gpumdkit.sh -plt sdc
-```
-
-### Workflow 3: Structure Analysis
-
-```bash
-# 1. Check composition
-gpumdkit.sh -analyze_comp train.xyz
-
-# 2. Check distances
-gpumdkit.sh -min_dist_pbc train.xyz
-
-# 3. Check force range
-gpumdkit.sh -range train.xyz force
-```
-
-## Module Overview
-
-| Module | Menu | CLI Flag | Description |
-|--------|------|----------|-------------|
-| Format Conversion | 1 | `-out2xyz`, `-pos2exyz`, etc. | Structure file conversion |
-| Sample Structures | 2 | `-pynep` | Structure sampling |
-| Workflows | 3 | - | Batch processing |
-| Calculators | 4 | `-calc <type>` | Property calculations |
-| Analyzers | 5 | `-range`, `-min_dist`, etc. | Structure analysis |
-| Visualization | 6 | `-plt <type>` | Plotting tools |
-| Utilities | 7 | `-time`, `-clean` | Utility functions |
-
-## Output File Conventions
-
-| File | Content |
-|------|---------|
-| `model.xyz` | Structure file in extxyz format |
-| `train.xyz` | Training dataset |
-| `nep.txt` | NEP model file |
-| `msd.out` | Mean square displacement data |
-| `thermo.out` | Thermodynamic properties |
-| `loss.out` | Training loss history |
-| `rdf.out` | Radial distribution function |
-| `sdc.out` | Self-diffusion coefficient data |
-
-## Getting Help
-
-- **General help**: `gpumdkit.sh -h`
-- **Plot help**: `gpumdkit.sh -plt -h`
-- **Calculator help**: `gpumdkit.sh -calc -h`
-- **Specific command**: `gpumdkit.sh -<option> -h`
-
-## Contact
-
-- **Developer**: Zihan YAN (yanzihan@westlake.edu.cn)
-- **GitHub**: https://github.com/zhyan0603/GPUMDkit
-- **Documentation**: https://zhyan0603.github.io/GPUMDkit/
diff --git a/docs/tutorials2/en/nep_training.md b/docs/tutorials2/en/nep_training.md
index 1bec6d7..f41ce49 100644
--- a/docs/tutorials2/en/nep_training.md
+++ b/docs/tutorials2/en/nep_training.md
@@ -1,130 +1,63 @@
-# NEP Training Guide
-
 <div align="center">
+  <h1>NEP Training Guide</h1>
   <p>
-    <a href="../zh/nep_training.md">中文</a> | <strong>English</strong>
+    <strong>English</strong> | <a href="../zh/nep_training.md">简体中文</a>
   </p>
 </div>
 
-This guide provides a complete workflow for training NEP (Neuroevolution Potential) models using GPUMDkit.
+Complete workflow for training NEP (Neuroevolution Potential) models.
 
 ## Overview
 
-NEP training involves:
-
 1. **Data Preparation** - Convert and organize training data
-2. **Structure Sampling** - Select diverse structures
-3. **Model Training** - Train the NEP model (external)
-4. **Validation** - Check training quality
-5. **Active Learning** - Iteratively improve the model
+2. **Quality Check** - Validate and filter structures
+3. **Sampling** - Select diverse structures
+4. **Training** - Train the NEP model (external)
+5. **Validation** - Check training quality
+6. **Active Learning** - Iteratively improve the model
 
 ## Step 1: Data Preparation
 
-### Convert DFT Data to extxyz
-
 ```bash
-# From VASP OUTCAR
+# Convert DFT data
 gpumdkit.sh -out2xyz ./vasp_results/
 
-# From VASP XDATCAR
-gpumdkit.sh -xdat2exyz XDATCAR trajectory.xyz
-
-# From CP2K
-gpumdkit.sh  # Select: 1) Format Conversion -> 103
-
-# From LAMMPS
-gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
-```
-
-### Add Group Labels
-
-Group labels are required for NEP to identify atom types:
-
-```bash
+# Add group labels
 gpumdkit.sh -addgroup POSCAR Li Y Cl
-```
-
-This creates `model.xyz` with group labels.
-
-### Combine Training Data
 
-```bash
-# Combine multiple extxyz files
-cat file1.xyz file2.xyz file3.xyz > train.xyz
-
-# Or use composition analysis to select specific compositions
-gpumdkit.sh -analyze_comp all_structures.xyz
+# Combine training data
+cat */model.xyz > train.xyz
 ```
 
-## Step 2: Data Quality Check
-
-### Check Composition
+## Step 2: Quality Check
 
 ```bash
+# Check composition
 gpumdkit.sh -analyze_comp train.xyz
-```
-
-### Check Minimum Distances
 
-```bash
-# Fast check (no PBC)
-gpumdkit.sh -min_dist train.xyz
-
-# Accurate check (with PBC)
+# Check distances
 gpumdkit.sh -min_dist_pbc train.xyz
-```
 
-### Check Property Ranges
-
-```bash
 # Check force range
 gpumdkit.sh -range train.xyz force
 
-# Check energy range
-gpumdkit.sh -range train.xyz energy
-
-# With histogram
-gpumdkit.sh -range train.xyz force hist
-```
-
-### Filter Structures
-
-```bash
-# Filter by minimum distance
+# Filter structures
 gpumdkit.sh -filter_dist_pbc train.xyz 1.0
-
-# Filter by box size
-gpumdkit.sh -filter_box train.xyz 20
-
-# Filter by force value
-gpumdkit.sh -filter_value train.xyz force 20
 ```
 
-## Step 3: Structure Sampling
-
-### Sample Diverse Structures
+## Step 3: Sampling
 
 ```bash
-# FPS sampling (preferred)
+# FPS sampling (recommended)
 gpumdkit.sh  # Select: 2) Sample Structures -> 203
 
 # Or uniform sampling
 python Scripts/sample_structures/sample_structures.py train.xyz uniform 100
 ```
 
-### Perturb Structures
-
-Generate additional training data from existing structures:
-
-```bash
-python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
-```
-
-## Step 4: NEP Model Training
-
-### Prepare nep.in
+## Step 4: Training
 
-Create `nep.in` with training parameters:
+Create `nep.in`:
 
 ```
 type 3 Li Y Cl
@@ -136,164 +69,45 @@ batch 1000
 generation 100000
 ```
 
-### Run Training
+Run training:
 
 ```bash
-# External to GPUMDkit
 gpumd
 ```
 
 ## Step 5: Validation
 
-### Plot Training Results
-
 ```bash
-# Plot training loss and parity plots
+# Plot training results
 gpumdkit.sh -plt train
-
-# Plot test predictions
 gpumdkit.sh -plt prediction
-
-# Combined train/test plots
-gpumdkit.sh -plt train_test
-
-# Force error analysis
 gpumdkit.sh -plt force_errors
-```
-
-### Check Convergence
-
-```bash
-# Plot loss curves
-gpumdkit.sh -plt train
-```
-
-Look for:
-- Smooth decrease in loss
-- No oscillations
-- Convergence to low values
-
-### Analyze Descriptors
 
-```bash
-# Calculate descriptors
+# Analyze descriptors
 gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-
-# Visualize with PCA
 gpumdkit.sh -plt des pca
-
-# Or UMAP
-gpumdkit.sh -plt des umap
 ```
 
 ## Step 6: Active Learning
 
-### Run MD with Current NEP
-
 ```bash
-# Setup MD simulation
+# Run MD with current NEP
 gpumdkit.sh  # Select: 3) Workflow -> 302
-```
-
-### Select Diverse Structures
 
-```bash
-# Filter by distance
+# Filter and sample
 gpumdkit.sh -min_dist_pbc dump.xyz
 gpumdkit.sh -filter_box dump.xyz 13
 
-# Sample diverse structures
-gpumdkit.sh  # Select: 2) Sample Structures -> 203
-```
-
-### Compute DFT Reference
-
-```bash
-# Prepare SCF calculations
+# Prepare DFT calculations
 gpumdkit.sh  # Select: 3) Workflow -> 301
 
-# Run DFT (external)
-```
-
-### Retrain Model
-
-```bash
-# Add new data to training set
+# Retrain with new data
 cat new_structures.xyz >> train.xyz
-
-# Retrain NEP (external)
-```
-
-## Complete Workflow Example
-
-```bash
-# 1. Convert DFT data
-gpumdkit.sh -out2xyz ./dft_results/
-
-# 2. Add group labels
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-
-# 3. Combine training data
-cat */model.xyz > train.xyz
-
-# 4. Check data quality
-gpumdkit.sh -analyze_comp train.xyz
-gpumdkit.sh -min_dist_pbc train.xyz
-gpumdkit.sh -range train.xyz force
-
-# 5. Filter structures
-gpumdkit.sh -filter_dist_pbc train.xyz 1.0
-
-# 6. Sample diverse structures
-gpumdkit.sh  # Select: 2) Sample Structures -> 203
-
-# 7. Train NEP (external)
-# ... create nep.in and run gpumd ...
-
-# 8. Validate training
-gpumdkit.sh -plt train
-gpumdkit.sh -plt prediction
-gpumdkit.sh -plt force_errors
-
-# 9. Analyze descriptors
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-gpumdkit.sh -plt des pca
 ```
 
-## Tips for Better Training
-
-1. **Diverse Data**: Include various structures, temperatures, and compositions
-2. **Balanced Dataset**: Ensure all element types are well-represented
-3. **Quality Filter**: Remove structures with too-close atoms or high forces
-4. **Sufficient Data**: At least 1000-5000 structures for good accuracy
-5. **Validation Set**: Keep 10-20% of data for testing
-
-## Troubleshooting
-
-### Issue: High RMSE
-
-**Solution**: 
-- Add more diverse training data
-- Increase `neuron` and `n_max` parameters
-- Check for outliers in training data
-
-### Issue: Poor Predictions
-
-**Solution**:
-- Verify training data quality
-- Add structures from different phases/temperatures
-- Increase training `generation`
-
-### Issue: Overfitting
-
-**Solution**:
-- Use more training data
-- Reduce model complexity
-- Use regularization
-
-## See Also
+## Tips
 
-- [Format Conversion](format_conversion.md) - Convert file formats
-- [Calculators](calculators.md) - Compute properties
-- [Visualization](visualization.md) - Plot results
-- [Structure Sampling](sampling.md) - Sample structures
+- Include diverse structures, temperatures, and compositions
+- At least 1000-5000 structures for good accuracy
+- Keep 10-20% of data for testing
+- Check for outliers before training
diff --git a/docs/tutorials2/en/quickstart.md b/docs/tutorials2/en/quickstart.md
index 49e0820..63040e1 100644
--- a/docs/tutorials2/en/quickstart.md
+++ b/docs/tutorials2/en/quickstart.md
@@ -1,244 +1,137 @@
-# Quick Start Guide
-
 <div align="center">
+  <h1>Quick Start</h1>
   <p>
-    <a href="../zh/quickstart.md">中文</a> | <strong>English</strong>
+    <strong>English</strong> | <a href="../zh/quickstart.md">简体中文</a>
   </p>
 </div>
 
-This guide will help you get started with GPUMDkit quickly.
+Get up and running with GPUMDkit in 5 minutes.
 
 ## Prerequisites
 
-Before installing GPUMDkit, ensure you have:
-
-- **Linux or macOS** (Windows via WSL)
-- **Bash** shell
-- **Python 3.8+** (3.12 recommended)
-- **Git** (for cloning the repository)
+- Linux or macOS (Windows via WSL)
+- Python 3.8+ (3.12 recommended)
+- Git
 
 ## Installation
 
-### Step 1: Clone the Repository
+### Step 1: Clone
 
 ```bash
 git clone https://github.com/zhyan0603/GPUMDkit.git
 cd GPUMDkit
 ```
 
-### Step 2: Run Installation Script
+### Step 2: Install
 
 ```bash
 source ./install.sh
 ```
 
-This script will:
-1. Add GPUMDkit to your PATH
-2. Set up bash completion
-3. Configure environment variables
-
 ### Step 3: Reload Shell
 
 ```bash
-source ~/.bashrc
-# or
-source ~/.zshrc
+source ~/.bashrc  # or source ~/.zshrc
 ```
 
-### Step 4: Verify Installation
+### Step 4: Verify
 
 ```bash
 gpumdkit.sh -h
 ```
 
-You should see the help message with available commands.
-
 ## Python Dependencies
 
-Some features require Python packages. Create a conda environment:
-
 ```bash
-# Create environment
 conda create -n gpumdkit python=3.12
 conda activate gpumdkit
-
-# Install core packages
-pip install numpy ase scipy matplotlib
-
-# Install optional packages (for full functionality)
-pip install neptrain pymatgen dpdata
-
-# For perovskite analysis (optional)
-pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
+pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
 ```
 
-## Two Usage Modes
+> Make sure the `gpumdkit` environment is activated before using GPUMDkit.
 
-### Interactive Mode
+## Usage Modes
 
-Launch the interactive menu:
+### Interactive Mode
 
 ```bash
 gpumdkit.sh
 ```
 
-You'll see:
-
 ```
-       ____ ____  _   _ __  __ ____  _    _ _
-      / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
-     | |  _| |_) | | | | |\/| | | | | |/ / | __|
-     | |_| |  __/| |_| | |  | | |_| |   <| | |_
-      \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
+           ____ ____  _   _ __  __ ____  _    _ _
+          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
+         | |  _| |_) | | | | |\/| | | | | |/ / | __|
+         | |_| |  __/| |_| | |  | | |_| |   <| | |_
+          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
 
-      GPUMDkit Version 1.5.5 (dev) (2026-05-10)
-Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+          GPUMDkit Version 1.5.5 (dev) (2026-05-10)
 
  ---------------------- GPUMD ------------------------
- 1) Format Conversion          2) Sample Structures
- 3) Workflow                   4) Calculators
- 5) Analyzer                   6) Visualization
- 7) Utilities                  8) Developing...
- 0) Exit
+  1) Format Conversion          2) Sample Structures
+  3) Workflow                   4) Calculators
+  5) Analyzer                   6) Visualization
+  7) Utilities                  0) Exit
  ------------>>
- Input the function number:
 ```
 
-Navigate by entering the number of your desired function.
-
 ### Command-Line Mode
 
-Execute commands directly:
-
 ```bash
-# Show help
-gpumdkit.sh -h
-
-# Convert POSCAR to extxyz
-gpumdkit.sh -pos2exyz POSCAR model.xyz
-
-# Plot training results
-gpumdkit.sh -plt train
-
-# Calculate ionic conductivity
-gpumdkit.sh -calc ionic-cond Li 1
+gpumdkit.sh -h                    # Show help
+gpumdkit.sh -pos2exyz POSCAR model.xyz  # Direct command
 ```
 
-## First Steps Example
+## First Examples
 
-### Example 1: Convert a Structure
+### Convert Structure
 
 ```bash
-# Convert POSCAR to extxyz format
 gpumdkit.sh -pos2exyz POSCAR model.xyz
-
-# Add group labels (required for NEP training)
 gpumdkit.sh -addgroup POSCAR Li Y Cl
 ```
 
-### Example 2: Analyze Training Data
+### Analyze Data
 
 ```bash
-# Check force range in training data
 gpumdkit.sh -range train.xyz force
-
-# Check minimum interatomic distances
 gpumdkit.sh -min_dist_pbc train.xyz
-
-# Analyze composition
 gpumdkit.sh -analyze_comp train.xyz
 ```
 
-### Example 3: Plot Results
+### Plot Results
 
 ```bash
-# Plot NEP training results
 gpumdkit.sh -plt train
-
-# Plot mean square displacement
 gpumdkit.sh -plt msd
-
-# Plot radial distribution function
 gpumdkit.sh -plt rdf
 ```
 
 ## Getting Help
 
-### General Help
-
-```bash
-gpumdkit.sh -h
-```
-
-### Module-Specific Help
-
 ```bash
-# Plot help
-gpumdkit.sh -plt -h
-
-# Calculator help
-gpumdkit.sh -calc -h
-
-# Specific command help
-gpumdkit.sh -pos2exyz -h
-gpumdkit.sh -calc ionic-cond -h
+gpumdkit.sh -h              # General help
+gpumdkit.sh -plt -h         # Plot help
+gpumdkit.sh -calc -h        # Calculator help
+gpumdkit.sh -pos2exyz -h    # Specific command help
 ```
 
-### Interactive Mode Help
-
-In interactive mode, each submenu displays available options with descriptions.
-
-## Common Issues
-
-### Issue: Command not found
-
-**Solution**: Ensure GPUMDkit is in your PATH:
+## Troubleshooting
 
+**Command not found**
 ```bash
-# Check if gpumdkit.sh is in PATH
-which gpumdkit.sh
-
-# If not found, add to PATH manually
 export GPUMDkit_path=/path/to/GPUMDkit
 export PATH=${GPUMDkit_path}:${PATH}
 ```
 
-### Issue: Missing Python packages
-
-**Solution**: Activate the conda environment:
-
+**Missing packages**
 ```bash
 conda activate gpumdkit
 ```
 
-### Issue: Permission denied
-
-**Solution**: Make the script executable:
-
-```bash
-chmod +x /path/to/GPUMDkit/gpumdkit.sh
-```
-
 ## Next Steps
 
-Now that you have GPUMDkit installed, explore these tutorials:
-
-- [Format Conversion](format_conversion.md) - Learn to convert between file formats
-- [Calculators](calculators.md) - Compute material properties
-- [Visualization](visualization.md) - Create publication-ready plots
-- [NEP Training Guide](nep_training.md) - Complete training workflow
-
-## Updating GPUMDkit
-
-To update to the latest version:
-
-```bash
-gpumdkit.sh -update
-```
-
-Or manually:
-
-```bash
-cd /path/to/GPUMDkit
-git pull origin main
-```
+- [Format Conversion](format_conversion.md)
+- [Calculators](calculators.md)
+- [Visualization](visualization.md)
+- [NEP Training](nep_training.md)
diff --git a/docs/tutorials2/en/sampling.md b/docs/tutorials2/en/sampling.md
index e4649ef..d94c27d 100644
--- a/docs/tutorials2/en/sampling.md
+++ b/docs/tutorials2/en/sampling.md
@@ -1,73 +1,34 @@
-# Structure Sampling Guide
-
 <div align="center">
+  <h1>Structure Sampling</h1>
   <p>
-    <a href="../zh/sampling.md">中文</a> | <strong>English</strong>
+    <strong>English</strong> | <a href="../zh/sampling.md">简体中文</a>
   </p>
 </div>
 
-This guide covers structure sampling and selection tools in GPUMDkit.
+Structure selection and sampling tools.
 
 ## Available Methods
 
 | Method | Menu | Description |
 |--------|------|-------------|
 | Uniform/Random | 201 | Select evenly spaced or random frames |
-| FPS by PyNEP | 202 | Farthest point sampling (deprecated) |
 | FPS by NepTrain | 203 | Farthest point sampling (preferred) |
 | Perturbation | 204 | Generate perturbed structures |
 | Force Deviation | 205 | Select high-force-deviation structures |
 
-## Interactive Mode
+## Uniform/Random Sampling
 
 ```bash
-gpumdkit.sh
-# Select: 2) Sample Structures
-```
-
-You'll see:
-
-```
-+------------------------------------------------------+
-|                 SAMPLE STRUCTURE TOOLS               |
-+------------------------------------------------------+
-| 201) Sample structures from extxyz                   |
-| 202) FPS sampling by PyNEP [deprecated]              |
-| 203) FPS sampling by NepTrain [preferred]            |
-| 204) Perturb structure                               |
-| 205) Select max force deviation structs              |
-+------------------------------------------------------+
-```
-
-## Command Reference
-
-### Uniform/Random Sampling
-
-Select structures using uniform or random sampling.
-
-```bash
-python Scripts/sample_structures/sample_structures.py <input.xyz> <method> <num_samples> [skip_initial]
+python Scripts/sample_structures/sample_structures.py <input.xyz> <method> <num> [skip]
 
 # Examples
 python Scripts/sample_structures/sample_structures.py dump.xyz uniform 50
 python Scripts/sample_structures/sample_structures.py dump.xyz random 100 500
 ```
 
-**Parameters:**
-- `input.xyz`: Input trajectory file
-- `method`: `uniform` or `random`
-- `num_samples`: Number of frames to select
-- `skip_initial`: (optional) Skip first N frames
-
-**How it works:**
-- **Uniform**: Uses `numpy.linspace` to select evenly spaced indices
-- **Random**: Uses `numpy.random.choice` to select random indices without replacement
-
-**Output:** `sampled_structures.xyz`
+Output: `sampled_structures.xyz`
 
-### Farthest Point Sampling (FPS) - NepTrain (Preferred)
-
-Select diverse structures using FPS on NEP descriptors.
+## Farthest Point Sampling (FPS)
 
 ```bash
 python Scripts/sample_structures/neptrain_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
@@ -76,48 +37,26 @@ python Scripts/sample_structures/neptrain_select_structs.py <sample.xyz> <train.
 python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
 ```
 
-**Selection methods (interactive):**
-1. **Minimum distance**: Select until max distance to existing training set drops below threshold
-2. **Number of structures**: Select between `min_select` and `max_select` structures
-
-**Output:**
-- `selected.xyz`
-- `select.png` (PCA visualization)
-- `pca_sample.txt`, `pca_train.txt`, `pca_selected.txt`
+Output: `selected.xyz`, `select.png`
 
-**Citation**: Chen et al., Comput. Phys. Commun., 2025, 317, 109859
-
-### Farthest Point Sampling (FPS) - PyNEP (Deprecated)
+## Structure Perturbation
 
 ```bash
-python Scripts/sample_structures/pynep_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
-```
-
-**Note**: PyNEP package is no longer actively maintained. Use NepTrain (method 203) instead.
-
-### Structure Perturbation
-
-Generate perturbed structures for training data.
-
-```bash
-python Scripts/sample_structures/perturb_structure.py <input.vasp> <pert_num> <cell_pert> <atom_pert> <style>
+python Scripts/sample_structures/perturb_structure.py <input.vasp> <num> <cell_pert> <atom_pert> <style>
 
 # Example
 python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
 ```
 
-**Parameters:**
-- `input.vasp`: POSCAR/CONTCAR file
-- `pert_num`: Number of perturbed structures (e.g., 20)
+Parameters:
+- `num`: Number of perturbed structures
 - `cell_pert`: Cell perturbation fraction (e.g., 0.03 = 3%)
-- `atom_pert`: Atom perturbation distance in Angstrom (e.g., 0.2)
+- `atom_pert`: Atom perturbation distance (Angstrom)
 - `style`: `normal`, `uniform`, or `const`
 
-**Output:** `POSCAR_01.vasp`, `POSCAR_02.vasp`, ..., `POSCAR_<N>.vasp`
-
-### Force Deviation Selection
+Output: `POSCAR_01.vasp`, `POSCAR_02.vasp`, ...
 
-Select structures with high force deviations from active learning.
+## Force Deviation Selection
 
 ```bash
 python Scripts/sample_structures/select_max_modev.py <top_n> <min_deviation>
@@ -126,96 +65,24 @@ python Scripts/sample_structures/select_max_modev.py <top_n> <min_deviation>
 python Scripts/sample_structures/select_max_modev.py 200 0.15
 ```
 
-**Required files:**
-- `active.out` - Max force deviation per structure (from GPUMD `active` command)
-- `active.xyz` - Corresponding structures
+Required files: `active.out`, `active.xyz`
 
-**Output:** `selected.xyz`
+Output: `selected.xyz`
 
-### Frame Range Extraction
-
-Extract a range of frames from a trajectory.
+## Frame Range Extraction
 
 ```bash
-python Scripts/sample_structures/frame_range.py <input.xyz> <start_fraction> <end_fraction>
+python Scripts/sample_structures/frame_range.py <input.xyz> <start> <end>
 
-# Example: Extract first 80% of frames
+# Example: First 80% of frames
 python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
 ```
 
-**Output:** `dump_0.00_0.80.xyz`
-
-## Common Workflows
-
-### Training Data Preparation
-
-```bash
-# 1. Run MD simulation
-# ... generate trajectory ...
-
-# 2. Filter by distance
-gpumdkit.sh -min_dist_pbc dump.xyz
-gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
-
-# 3. Sample diverse structures
-gpumdkit.sh  # Select: 2) Sample Structures -> 203
-
-# 4. Add to training set
-cat selected.xyz >> train.xyz
-```
-
-### Active Learning Data Selection
-
-```bash
-# 1. Run MD with current NEP
-# ... generate active.out and active.xyz ...
-
-# 2. Select high-deviation structures
-python Scripts/sample_structures/select_max_modev.py 100 0.1
-
-# 3. Or use FPS for diversity
-python Scripts/sample_structures/neptrain_select_structs.py active.xyz train.xyz nep.txt
-```
-
-### Structure Perturbation for Initial Data
-
-```bash
-# 1. Start from equilibrium structure
-# 2. Generate perturbations
-python Scripts/sample_structures/perturb_structure.py POSCAR 50 0.05 0.3 uniform
-
-# 3. Run DFT on perturbed structures
-# ... DFT calculations ...
-
-# 4. Add to training set
-```
-
 ## Dependencies
 
-| Method | Required Packages |
-|--------|------------------|
-| Uniform/Random | `numpy`, `ase` |
-| FPS (NepTrain) | `numpy`, `ase`, `matplotlib`, `scikit-learn`, `scipy`, `NepTrain` |
-| FPS (PyNEP) | `numpy`, `ase`, `matplotlib`, `scikit-learn`, `pynep` |
-| Perturbation | `dpdata` |
-| Force Deviation | `numpy`, `ase` |
-
-Install dependencies:
-```bash
-pip install numpy ase matplotlib scikit-learn scipy dpdata
-pip install neptrain  # For FPS by NepTrain
-```
-
-## Important Notes
-
-1. **FPS is preferred**: Farthest Point Sampling provides better diversity than uniform/random
-2. **NepTrain over PyNEP**: NepTrain is actively maintained; PyNEP is deprecated
-3. **Filter before sampling**: Remove unphysical structures (too close, too large) first
-4. **Frame indexing is 0-based**: First frame is index 0
-5. **Output is extxyz**: All sampling methods output extxyz format
-
-## See Also
-
-- [Format Conversion](format_conversion.md) - Convert file formats
-- [Analyzers](analyzers.md) - Filter and analyze structures
-- [NEP Training Guide](nep_training.md) - Complete training workflow
+| Method | Packages |
+|--------|----------|
+| Uniform/Random | numpy, ase |
+| FPS | numpy, ase, matplotlib, scikit-learn, scipy, NepTrain |
+| Perturbation | dpdata |
+| Force Deviation | numpy, ase |
diff --git a/docs/tutorials2/en/visualization.md b/docs/tutorials2/en/visualization.md
index b3dd066..b698673 100644
--- a/docs/tutorials2/en/visualization.md
+++ b/docs/tutorials2/en/visualization.md
@@ -1,226 +1,106 @@
-# Visualization Guide
-
 <div align="center">
+  <h1>Visualization</h1>
   <p>
-    <a href="../zh/visualization.md">中文</a> | <strong>English</strong>
+    <strong>English</strong> | <a href="../zh/visualization.md">简体中文</a>
   </p>
 </div>
 
-This guide covers all plotting and visualization tools in GPUMDkit.
+Plotting and visualization tools for simulation results.
 
 ## Quick Reference
 
 ```bash
-gpumdkit.sh -plt <type>              # Display plot interactively
-gpumdkit.sh -plt <type> save         # Save plot as PNG
-gpumdkit.sh -plt <type> -h           # Get help for specific plot
+gpumdkit.sh -plt <type>              # Display plot
+gpumdkit.sh -plt <type> save         # Save as PNG
+gpumdkit.sh -plt <type> -h           # Get help
 ```
 
-## Plot Categories
-
-### NEP Training & Evaluation (12 plot types)
-
-| Command | Input Files | Description |
-|---------|-------------|-------------|
-| `train` | `loss.out`, `*_train.out` | Training loss curves and parity plots |
-| `prediction` / `test` | `*_test.out` | Test set parity plots |
-| `train_test` | `*_train.out`, `*_test.out` | Combined train/test parity plots |
-| `parity_density` | `*_train.out` | Density-based parity plots for large datasets |
-| `train_density` | `loss.out`, `*_train.out` | Training with density visualization |
-| `force_errors` | `force_train.out` | Force error analysis |
-| `restart` | `nep.restart` | NEP restart file visualization |
-| `charge` | `charge_train.out` | Charge distribution (qNEP) |
-| `born_charge` / `bec` | `bec_train.out`, `bec_test.out` | Born effective charges |
-| `dimer` | NEP model | Dimer interaction curves |
-| `des` | `descriptors.npy` | Descriptor PCA/UMAP visualization |
-| `lr` | `loss.out` (gnep) | Learning rate decay |
+## NEP Training Plots
+
+| Command | Description |
+|---------|-------------|
+| `train` | Training loss curves and parity plots |
+| `prediction` / `test` | Test set parity plots |
+| `train_test` | Combined train/test parity plots |
+| `force_errors` | Force error analysis |
+| `des` | Descriptor PCA/UMAP visualization |
+| `dimer` | Dimer interaction curves |
+| `charge` | Charge distribution (qNEP) |
+| `born_charge` / `bec` | Born effective charges |
 
 ```bash
-# Training results
 gpumdkit.sh -plt train
 gpumdkit.sh -plt prediction
 gpumdkit.sh -plt force_errors
-
-# Descriptor visualization (requires prior calculation)
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
 gpumdkit.sh -plt des pca
-gpumdkit.sh -plt des umap
-
-# Dimer plot
 gpumdkit.sh -plt dimer Li Li nep.txt
 ```
 
-### Transport Properties (9 plot types)
+## Transport Plots
 
-| Command | Input Files | Description |
-|---------|-------------|-------------|
-| `msd` | `msd.out` | Mean square displacement |
-| `msd_conv` | `msd_step*.out` | MSD convergence check |
-| `msd_all` | `msd.out` (all_groups) | MSD per species |
-| `sdc` | `msd.out` | Self-diffusion coefficient |
-| `msd_sdc` | `msd.out` | MSD and SDC combined |
-| `sigma` / `arrhenius_sigma` | `*K/` directories | Arrhenius ionic conductivity |
-| `D` / `arrhenius_d` | `*K/` directories | Arrhenius diffusivity |
-| `sigma_xyz` | `*K/` directories | Directional Arrhenius conductivity |
-| `D_xyz` | `*K/` directories | Directional Arrhenius diffusivity |
+| Command | Description |
+|---------|-------------|
+| `msd` | Mean square displacement |
+| `sdc` | Self-diffusion coefficient |
+| `msd_sdc` | MSD and SDC combined |
+| `arrhenius_sigma` | Arrhenius ionic conductivity |
+| `arrhenius_d` | Arrhenius diffusivity |
 
 ```bash
-# MSD and diffusion
 gpumdkit.sh -plt msd
 gpumdkit.sh -plt sdc
-gpumdkit.sh -plt msd_sdc
-
-# MSD for all species (requires all_groups in run.in)
-gpumdkit.sh -plt msd_all Li P S
-
-# Arrhenius plots (requires temperature-organized directories)
-# Directory structure: 300K/, 350K/, 400K/, ... each containing msd.out
 gpumdkit.sh -plt arrhenius_sigma
 gpumdkit.sh -plt arrhenius_d
 ```
 
-### Structural Analysis (10 plot types)
-
-| Command | Input Files | Description |
-|---------|-------------|-------------|
-| `thermo` | `thermo.out` | Thermodynamic properties |
-| `thermo2` | `thermo.out` | Alternative thermo style |
-| `thermo3` | `thermo.out` | Third thermo style |
-| `rdf` | `rdf.out` | Radial distribution function |
-| `rdf_pmf` | `rdf.out` | RDF + potential of mean force |
-| `vac` | `sdc.out` | Velocity autocorrelation |
-| `cohesive` | `cohesive.out` | Cohesive energy curve |
-| `net_force` | extxyz file | Net force distribution |
-| `doas` | `doas.out` | Density of atomistic states |
-| `plane-grid` | `model.xyz`, `displacements.dat` | Displacement grid visualization |
+## Structural Plots
+
+| Command | Description |
+|---------|-------------|
+| `thermo` | Thermodynamic properties |
+| `rdf` | Radial distribution function |
+| `rdf_pmf` | RDF + potential of mean force |
+| `vac` | Velocity autocorrelation |
+| `doas` | Density of atomistic states |
+| `net_force` | Net force distribution |
 
 ```bash
-# Thermodynamic properties
 gpumdkit.sh -plt thermo
-
-# RDF analysis
 gpumdkit.sh -plt rdf
-gpumdkit.sh -plt rdf 2              # Specific column
-gpumdkit.sh -plt rdf_pmf 300        # With PMF at 300K
-
-# DOAS visualization (requires prior calculation)
 gpumdkit.sh -plt doas doas.out Li
-
-# Plane-grid displacement
-gpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Pb Sr
+gpumdkit.sh -plt net_force train.xyz
 ```
 
-### Heat Transport (4 plot types)
+## Heat Transport Plots
 
-| Command | Input Files | Description |
-|---------|-------------|-------------|
-| `emd` | EMD outputs | EMD thermal conductivity |
-| `nemd` | NEMD outputs | NEMD thermal transport |
-| `hnemd` | HNEMD outputs | HNEMD thermal transport |
-| `viscosity` | `viscosity.out` | Viscosity components |
+| Command | Description |
+|---------|-------------|
+| `emd` | EMD thermal conductivity |
+| `nemd` | NEMD thermal transport |
+| `hnemd` | HNEMD thermal transport |
+| `viscosity` | Viscosity components |
 
 ```bash
-# EMD thermal conductivity
 gpumdkit.sh -plt emd x
-
-# NEMD thermal transport
-# Parameters: real_length scale_eff_size cutoff_freq
 gpumdkit.sh -plt nemd <real_length> <scale_eff_size> <cutoff_freq> save
-
-# HNEMD thermal transport
 gpumdkit.sh -plt hnemd <scale_eff_size> <cutoff_freq> save
-
-# Viscosity
-gpumdkit.sh -plt viscosity save
-```
-
-### Phonons (1 plot type)
-
-| Command | Input Files | Description |
-|---------|-------------|-------------|
-| `pdos` | `model.xyz`, `run.in`, `dos.out`, `mvac.out` | Phonon DOS and heat capacity |
-
-```bash
-gpumdkit.sh -plt pdos save
-```
-
-## Common Workflows
-
-### NEP Training Validation
-
-```bash
-# 1. Plot training loss
-gpumdkit.sh -plt train
-
-# 2. Check test predictions
-gpumdkit.sh -plt prediction
-
-# 3. Analyze force errors
-gpumdkit.sh -plt force_errors
-
-# 4. Visualize descriptors
-gpumdkit.sh -plt des pca
-```
-
-### Diffusion Analysis
-
-```bash
-# 1. Plot MSD
-gpumdkit.sh -plt msd
-
-# 2. Plot self-diffusion coefficient
-gpumdkit.sh -plt sdc
-
-# 3. Combined MSD-SDC plot
-gpumdkit.sh -plt msd_sdc
-
-# 4. Arrhenius analysis (multi-temperature)
-gpumdkit.sh -plt arrhenius_d
-```
-
-### Thermal Transport
-
-```bash
-# 1. Plot thermodynamic properties
-gpumdkit.sh -plt thermo
-
-# 2. Plot thermal conductivity
-gpumdkit.sh -plt emd x
-
-# 3. Or NEMD/HNEMD
-gpumdkit.sh -plt nemd 10 1 60 save
 ```
 
 ## Output Files
 
-| Plot Type | PNG Filename (with `save`) |
-|-----------|---------------------------|
+| Plot | PNG Filename |
+|------|--------------|
 | `train` | `train.png` |
 | `prediction` | `prediction.png` |
-| `train_test` | `train_test.png` |
-| `force_errors` | `force_errors.png` |
-| `des` | `descriptors.png` |
 | `msd` | `msd.png` |
 | `sdc` | `sdc.png` |
-| `msd_sdc` | `MSD_SDC.png` |
 | `thermo` | `thermo.png` |
 | `rdf` | `rdf.png` |
 | `arrhenius_sigma` | `Arrhenius_sigma.png` |
 | `arrhenius_d` | `Arrhenius_D.png` |
-| `emd` | `emd.png` |
-| `nemd` | `nemd.png` |
-| `hnemd` | `hnemd.png` |
-| `viscosity` | `viscosity.png` |
-| `cohesive` | `Cohesive.png` |
 
 ## Dependencies
 
-All plotting scripts require:
-- `matplotlib`
-- `numpy`
-
-## See Also
-
-- [Calculators](calculators.md) - Compute properties to plot
-- [Analyzers](analyzers.md) - Analyze data before plotting
-- [NEP Training Guide](nep_training.md) - Complete training workflow
+```bash
+pip install matplotlib numpy
+```
diff --git a/docs/tutorials2/en/workflows.md b/docs/tutorials2/en/workflows.md
index 667bbf9..f1d9d20 100644
--- a/docs/tutorials2/en/workflows.md
+++ b/docs/tutorials2/en/workflows.md
@@ -1,12 +1,11 @@
-# Workflows Guide
-
 <div align="center">
+  <h1>Workflows</h1>
   <p>
-    <a href="../zh/workflows.md">中文</a> | <strong>English</strong>
+    <strong>English</strong> | <a href="../zh/workflows.md">简体中文</a>
   </p>
 </div>
 
-This guide covers batch processing and workflow automation tools in GPUMDkit.
+Batch processing and workflow automation tools.
 
 ## Available Workflows
 
@@ -17,213 +16,75 @@ This guide covers batch processing and workflow automation tools in GPUMDkit.
 | MD Batch (GPUMD) | 302 | GPUMD MD sampling batch setup |
 | MD Batch (LAMMPS) | 303 | LAMMPS MD sampling batch setup |
 
-## Interactive Mode
-
-```bash
-gpumdkit.sh
-# Select: 3) Workflow
-```
-
-You'll see:
-
-```
-+---------------------------------------------------------+
-|                      WORKFLOW TOOLS                     |
-+---------------------------------------------------------+
-| 301) SCF batch pretreatment                             |
-| 302) MD sample batch pretreatment (gpumd)               |
-| 303) MD sample batch pretreatment (lmp)                 |
-+---------------------------------------------------------+
-```
-
 ## SCF Batch Pretreatment
 
-### VASP SCF Batch
-
-Prepare batch single-point energy/force calculations for VASP.
+### VASP
 
 ```bash
 gpumdkit.sh  # Select: 3) Workflow -> 301 -> VASP
 ```
 
-**Prerequisites:**
-
-1. Place POSCAR files (or single `.xyz`) in current directory
-2. Prepare `fp/` directory with:
-   - `INCAR`
-   - `POTCAR`
-   - `KPOINTS`
+Prerequisites:
+1. POSCAR files in current directory
+2. `fp/` directory with INCAR, POTCAR, KPOINTS
 
-**Output Structure:**
-
-```
-struct_fp/
-├── POSCAR_1.vasp
-├── POSCAR_2.vasp
-└── ...
-fp/
-├── INCAR
-├── POTCAR
-└── KPOINTS
-<prefix>_1/
-├── POSCAR -> ../struct_fp/POSCAR_1.vasp
-├── POTCAR -> ../fp/POTCAR
-├── INCAR -> ../fp/INCAR
-└── KPOINTS -> ../fp/KPOINTS
-<prefix>_2/
-└── ...
-presub.sh
-```
+Output: `<prefix>_1/`, `<prefix>_2/`, ..., `presub.sh`
 
-### CP2K SCF Batch
-
-Prepare batch single-point calculations for CP2K.
+### CP2K
 
 ```bash
-python Scripts/workflow/scf_batch_pretreatment_cp2k.py <extxyz_file> <template.inp> <prefix_name>
-
-# Example
-python Scripts/workflow/scf_batch_pretreatment_cp2k.py structures.xyz cp2k_template.inp H2O_batch
+python Scripts/workflow/scf_batch_pretreatment_cp2k.py <extxyz> <template.inp> <prefix>
 ```
 
-**Prerequisites:**
-
-1. Prepare CP2K input template (`cp2k_template.inp`)
-2. Template should read coordinates from `pos.xyz`
-
-**Output Structure:**
-
-```
-<prefix>_1/
-├── input.inp
-└── pos.xyz
-<prefix>_2/
-└── ...
-```
+## MD Batch Pretreatment
 
-## MD Sample Batch Pretreatment
-
-### GPUMD MD Batch
-
-Set up batch MD simulations for GPUMD.
+### GPUMD
 
 ```bash
 gpumdkit.sh  # Select: 3) Workflow -> 302
 ```
 
-**Prerequisites:**
-
-1. Place POSCAR files (or single `.xyz`) in current directory
-2. Prepare `md/` directory with:
-   - `nep.txt` (NEP model)
-   - `run_1.in`, `run_2.in`, ... (GPUMD input files)
+Prerequisites:
+1. POSCAR files in current directory
+2. `md/` directory with `nep.txt`, `run_*.in`
 
-**Output Structure:**
-
-```
-struct_md/
-├── model_1.xyz
-├── model_2.xyz
-└── ...
-md/
-├── nep.txt
-├── run_1.in
-├── run_2.in
-└── ...
-sample_1/
-├── model.xyz -> ../struct_md/model_1.xyz
-├── nep.txt -> ../md/nep.txt
-└── run.in -> ../md/run_1.in
-sample_2/
-└── ...
-presub.sh
-```
+Output: `sample_1/`, `sample_2/`, ..., `presub.sh`
 
-### LAMMPS MD Batch
-
-Set up batch MD simulations for LAMMPS.
+### LAMMPS
 
 ```bash
 gpumdkit.sh  # Select: 3) Workflow -> 303
 ```
 
-**Prerequisites:**
-
-1. Place POSCAR files (or single `.xyz`) in current directory
-2. Prepare `md/` directory with:
-   - `nep.txt` (NEP model)
-   - `lmprun.in` (LAMMPS input file)
-
-**Output Structure:**
-
-```
-struct_md/
-├── lammps_1.data
-├── lammps_2.data
-└── ...
-md/
-├── nep.txt
-└── lmprun.in
-sample_1/
-├── lammps.data -> ../struct_md/lammps_1.data
-├── nep.txt -> ../md/nep.txt
-└── lmprun.in -> ../md/lmprun.in
-sample_2/
-└── ...
-presub.sh
-```
-
-## Active Learning Workflow
+Prerequisites:
+1. POSCAR files in current directory
+2. `md/` directory with `nep.txt`, `lmprun.in`
 
-### Overview
+## Active Learning
 
-Active learning iteratively improves NEP models by:
-
-1. Running MD with current NEP model
-2. Selecting diverse structures
-3. Computing DFT reference data
-4. Retraining NEP model
-
-### Manual Active Learning Loop
+Iterative NEP model improvement:
 
 ```bash
-# Step 1: MD sampling with current NEP
+# 1. MD sampling
 gpumdkit.sh  # Select: 3) Workflow -> 302
 
-# Step 2: Filter and sample structures
+# 2. Filter and sample
 gpumdkit.sh -min_dist_pbc dump.xyz
 gpumdkit.sh -filter_box dump.xyz 13
-gpumdkit.sh  # Select: 2) Sample Structures -> 203
 
-# Step 3: Prepare SCF calculations
+# 3. Prepare SCF
 gpumdkit.sh  # Select: 3) Workflow -> 301
 
-# Step 4: Run DFT calculations (external)
-
-# Step 5: Convert and validate
-gpumdkit.sh -out2xyz ./scf_results/
-gpumdkit.sh -range new_data.xyz force
+# 4. Run DFT (external)
 
-# Step 6: Retrain NEP model (external)
+# 5. Retrain NEP
 ```
 
-### Configurable Parameters
-
-| Parameter | Description | Example |
-|-----------|-------------|---------|
-| `prefix_name` | Directory prefix | `LiF_iter01` |
-| `min_dist` | Minimum distance filter | `1.4` |
-| `box_limit` | Maximum box size filter | `13` |
-| `max_fp_num` | Maximum DFT calculations | `50` |
-| `sample_method` | Sampling method | `uniform`, `random`, or `pynep` |
-| `pynep_sample_dist` | FPS distance threshold | `0.01` |
-
 ## Examples
 
-### Example 1: Temperature-Dependent MD
+### Temperature-Dependent MD
 
 ```bash
-# Setup directories for multiple temperatures
 for temp in 300 500 700 900; do
     mkdir -p "${temp}K"
     cp model.xyz "${temp}K/"
@@ -232,49 +93,14 @@ for temp in 300 500 700 900; do
 done
 ```
 
-### Example 2: High-Throughput Screening
+### Batch Structure Preparation
 
 ```bash
-# Prepare structures for multiple calculations
 for struct in structures/*.vasp; do
     name=$(basename "$struct" .vasp)
     mkdir -p "calc_$name"
     cp "$struct" "calc_$name/POSCAR"
     ln -s ../POTCAR "calc_$name/"
     ln -s ../INCAR "calc_$name/"
-    ln -s ../KPOINTS "calc_$name/"
 done
 ```
-
-### Example 3: NEP Training Data Generation
-
-```bash
-# 1. Start with initial structures
-gpumdkit.sh -replicate POSCAR supercell.vasp 3 3 3
-
-# 2. Perturb structures
-python Scripts/sample_structures/perturb_structure.py supercell.vasp 20 0.03 0.2 uniform
-
-# 3. Run MD sampling
-gpumdkit.sh  # Select: 3) Workflow -> 302
-
-# 4. Select diverse structures
-gpumdkit.sh  # Select: 2) Sample Structures -> 203
-
-# 5. Prepare DFT calculations
-gpumdkit.sh  # Select: 3) Workflow -> 301
-```
-
-## Important Notes
-
-1. **Directory structure matters**: Workflows expect specific directory layouts
-2. **Symlinks are used**: Output directories use symlinks to save disk space
-3. **presub.sh**: Generated submission script may need modification for your cluster
-4. **Template files**: Ensure input templates are correct before batch processing
-5. **Backup important files**: Always backup your data before running workflows
-
-## See Also
-
-- [Format Conversion](format_conversion.md) - Convert file formats
-- [Structure Sampling](sampling.md) - Sample structures for training
-- [NEP Training Guide](nep_training.md) - Complete training workflow
diff --git a/docs/tutorials2/zh/README.md b/docs/tutorials2/zh/README.md
new file mode 100644
index 0000000..eb31e0e
--- /dev/null
+++ b/docs/tutorials2/zh/README.md
@@ -0,0 +1,104 @@
+<div align="center">
+  <h1>GPUMDkit 教程</h1>
+  <p>
+    <strong>简体中文</strong> | <a href="../en/README.md">English</a>
+  </p>
+</div>
+
+欢迎使用 **GPUMDkit** - GPUMD 和 NEP 的命令行工具包。
+
+## 什么是 GPUMDkit？
+
+GPUMDkit 简化了计算材料科学中的常见任务：
+
+- **格式转换**：在 VASP、LAMMPS、CP2K、ABACUS、CIF 和 extxyz 格式之间转换
+- **可视化**：用于 NEP 训练、MD 模拟和分析的绘图工具
+- **计算器**：计算离子电导率、描述符、MSD、NEB 等
+- **分析工具**：结构验证、过滤、成分分析
+- **工作流**：DFT 和 MD 模拟的批处理
+- **结构采样**：使用均匀、随机或 FPS 方法选择结构
+
+## 快速开始
+
+### 安装
+
+```bash
+git clone https://github.com/zhyan0603/GPUMDkit.git
+cd GPUMDkit
+source ./install.sh
+```
+
+### 依赖
+
+```bash
+conda create -n gpumdkit python=3.12
+conda activate gpumdkit
+pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
+```
+
+### 使用方法
+
+```bash
+# 交互模式
+gpumdkit.sh
+
+# 命令行模式
+gpumdkit.sh -<选项> [参数...]
+
+# 获取帮助
+gpumdkit.sh -h
+```
+
+## 教程列表
+
+| 教程 | 描述 |
+|------|------|
+| [快速入门](quickstart.md) | 安装和第一步 |
+| [格式转换](format_conversion.md) | 在文件格式之间转换 |
+| [计算器](calculators.md) | 计算材料属性 |
+| [分析工具](analyzers.md) | 结构分析和验证 |
+| [可视化](visualization.md) | 绘图和可视化 |
+| [工作流](workflows.md) | 批处理和自动化 |
+| [结构采样](sampling.md) | 结构选择方法 |
+| [NEP 训练](nep_training.md) | 完整的 NEP 训练工作流 |
+
+## 示例：NEP 训练流程
+
+```bash
+# 转换 DFT 数据
+gpumdkit.sh -out2xyz ./vasp_results/
+
+# 添加组标签
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+
+# 采样结构
+gpumdkit.sh  # 选择: 2) Sample Structures -> 203
+
+# 验证训练
+gpumdkit.sh -plt train
+```
+
+## 示例：离子电导率
+
+```bash
+gpumdkit.sh -calc msd trajectory.xyz Li 10
+gpumdkit.sh -calc ionic-cond Li 1
+gpumdkit.sh -plt msd
+```
+
+## 模块概览
+
+| 模块 | 菜单 | CLI | 描述 |
+|------|------|-----|------|
+| 格式转换 | 1 | `-out2xyz`, `-pos2exyz` | 文件转换 |
+| 结构采样 | 2 | `-pynep` | 结构采样 |
+| 工作流 | 3 | - | 批处理 |
+| 计算器 | 4 | `-calc <类型>` | 属性计算 |
+| 分析工具 | 5 | `-range`, `-min_dist` | 结构分析 |
+| 可视化 | 6 | `-plt <类型>` | 绘图工具 |
+| 实用工具 | 7 | `-time`, `-clean` | 实用功能 |
+
+## 链接
+
+- GitHub: https://github.com/zhyan0603/GPUMDkit
+- 文档: https://zhyan0603.github.io/GPUMDkit/
diff --git a/docs/tutorials2/zh/analyzers.md b/docs/tutorials2/zh/analyzers.md
index 342a877..b157391 100644
--- a/docs/tutorials2/zh/analyzers.md
+++ b/docs/tutorials2/zh/analyzers.md
@@ -1,289 +1,92 @@
-# 分析工具指南
-
 <div align="center">
+  <h1>分析工具</h1>
   <p>
-    <strong>中文</strong> | <a href="../en/analyzers.md">English</a>
+    <strong>简体中文</strong> | <a href="../en/analyzers.md">English</a>
   </p>
 </div>
 
-本指南介绍 GPUMDkit 中用于结构验证、过滤和质量控制的所有分析工具。
+结构分析、验证和过滤工具。
 
 ## 可用工具
 
 | 工具 | 命令 | 描述 |
 |------|------|------|
 | 成分分析 | `-analyze_comp` | 按成分分组结构 |
-| 异常值检测 | 菜单 502 | 查找高误差结构 |
-| 化学物种 | 菜单 503 | 列出唯一元素 |
-| 电荷平衡 | `-cbc` | 检查氧化态平衡 |
 | 属性范围 | `-range` | 能量/力/应力统计 |
-| 距离过滤 | 菜单 506 | 按最小距离过滤（无 PBC） |
-| 距离过滤 (PBC) | 菜单 506b | 按最小距离过滤（带 PBC） |
 | 最小距离 | `-min_dist` | 计算最小距离（无 PBC） |
 | 最小距离 (PBC) | `-min_dist_pbc` | 计算最小距离（带 PBC） |
-| 概率密度 | 菜单 508 | 3D 扩散通道分析 |
-
-## 交互模式
-
-```bash
-gpumdkit.sh
-# 选择: 5) Analyzer
-```
-
-您将看到：
-
-```
-+------------------------------------------------------+
-|                    ANALYZER TOOLS                    |
-+------------------------------------------------------+
-| 501) Analyze composition of extxyz                   |
-| 502) Find outliers of extxyz                         |
-| 503) Analyze chemical species of extxyz              |
-| 504) Check charge balance of extxyz                  |
-| 505) Analyze energy/force/virial range               |
-| 506) Filter structures by minimum distance           |
-| 507) Get minimum interatomic distance                |
-| 508) Probability density analysis                    |
-+------------------------------------------------------+
-```
+| 电荷平衡 | `-cbc` | 检查氧化态平衡 |
+| 距离过滤 | `-filter_dist_pbc` | 按最小距离过滤 |
+| 盒子过滤 | `-filter_box` | 按盒子大小过滤 |
+| 值过滤 | `-filter_value` | 按属性值过滤 |
+| 距离范围 | `-filter_range` | 按元素对距离过滤 |
+| 时间监控 | `-time` | 监控 GPUMD/NEP 进度 |
 
 ## 命令参考
 
 ### 成分分析
 
-按化学成分分析和分组结构。
-
 ```bash
 gpumdkit.sh -analyze_comp train.xyz
 ```
 
-**输出：** 唯一成分的表格，包含原子数和结构数。可交互选择导出特定成分。
-
-### 属性范围分析
-
-计算 extxyz 文件中能量、力或应力的范围（最小值、最大值）。
+### 属性范围
 
 ```bash
-gpumdkit.sh -range <文件名> <属性> [hist]
+gpumdkit.sh -range <文件> <属性> [hist]
 
 # 示例
-gpumdkit.sh -range train.xyz energy
 gpumdkit.sh -range train.xyz force
-gpumdkit.sh -range train.xyz virial
-gpumdkit.sh -range train.xyz force hist    # 带直方图
+gpumdkit.sh -range train.xyz energy
+gpumdkit.sh -range train.xyz force hist
 ```
 
-**输出：** 最小/最大值。使用 `hist` 参数可选择直方图。
-
 ### 最小距离
 
-计算每个元素对的最小原子间距离。
-
 ```bash
-# 快速计算（无 PBC）
+# 快速（无 PBC）
 gpumdkit.sh -min_dist dump.xyz
 
-# 精确计算（带 PBC）
+# 精确（带 PBC）
 gpumdkit.sh -min_dist_pbc dump.xyz
 ```
 
-**输出：** 所有元素对的最小距离表
-
-### 电荷平衡检查
-
-检查所有结构的氧化态平衡。
+### 电荷平衡
 
 ```bash
 gpumdkit.sh -cbc train.xyz
 ```
 
-**输出：**
-- `balanced.xyz` - 电荷平衡的结构
-- `unbalanced.xyz` - 不平衡的结构
-- `indices.txt` - 摘要
-
-### 化学物种识别
-
-列出文件中所有唯一的化学元素。
-
-```bash
-# 交互模式
-gpumdkit.sh  # 选择: 5) Analyzer -> 503
-```
-
-**输出：** 排序后的所有元素列表
-
-### 结构过滤
-
-#### 按最小距离（无 PBC）
-
-```bash
-gpumdkit.sh  # 选择: 5) Analyzer -> 506
-```
-
-**输入：** extxyz 文件，距离阈值
-**输出：** `filtered_<file>.xyz`，`filtered_out_<file>.xyz`
-
-#### 按最小距离（带 PBC）
-
-```bash
-gpumdkit.sh  # 选择: 5) Analyzer -> 506b
-```
-
-对周期性系统更精确。
-
-#### 按元素对距离范围
-
-```bash
-gpumdkit.sh -filter_range <文件> <元素1> <元素2> <最小距离> <最大距离>
-
-# 示例：过滤 Li-Li 距离在 1.9 到 2.0 Å 之间
-gpumdkit.sh -filter_range dump.xyz Li Li 1.9 2.0
-```
-
-**输出：** `filtered_<elem1>_<elem2>_<min>_<max>.xyz`
+输出：`balanced.xyz`, `unbalanced.xyz`
 
-#### 按盒子大小
+### 过滤
 
 ```bash
-gpumdkit.sh -filter_box <文件> <边缘限制>
+# 按最小距离
+gpumdkit.sh -filter_dist_pbc train.xyz 1.0
 
-# 示例：过滤盒子边缘 > 20 Å 的结构
+# 按盒子大小
 gpumdkit.sh -filter_box dump.xyz 20
-```
-
-**输出：** `filtered_by_box.xyz`
-
-#### 按属性值
-
-```bash
-gpumdkit.sh -filter_value <文件> <属性> <阈值>
 
-# 示例：保留力 < 20 eV/Å 的结构
+# 按属性值
 gpumdkit.sh -filter_value train.xyz force 20
-```
-
-**输出：** `filtered.xyz`
-
-### 异常值检测
-
-基于 RMSE 阈值查找异常值结构。
-
-```bash
-gpumdkit.sh  # 选择: 5) Analyzer -> 502
-```
-
-**必需文件：**
-- `train.xyz`
-- `energy_train.out`
-- `force_train.out`
-- `stress_train.out`
-
-**输出：** `selected.xyz`（高误差），`remained.xyz`（低误差）
-
-### 概率密度分析
-
-从 AIMD 轨迹计算移动离子的 3D 概率密度。
-
-```bash
-gpumdkit.sh  # 选择: 5) Analyzer -> 508
-```
-
-**参数：**
-- 参考结构（POSCAR）
-- 轨迹文件（extxyz）
-- 移动物种（如 Li）
-- 网格间距（如 0.25 Å）
-
-**输出：** `probability_density_<interval>.vasp`（CHGCAR 格式）
-
-## 常见工作流程
-
-### 数据质量检查
-
-```bash
-# 1. 检查成分
-gpumdkit.sh -analyze_comp train.xyz
-
-# 2. 检查最小距离
-gpumdkit.sh -min_dist_pbc train.xyz
-
-# 3. 检查力范围
-gpumdkit.sh -range train.xyz force
-
-# 4. 检查异常值
-gpumdkit.sh  # 选择: 5) Analyzer -> 502
-```
-
-### 结构过滤管道
-
-```bash
-# 1. 按距离过滤
-gpumdkit.sh  # 选择: 5) Analyzer -> 506
-
-# 2. 按盒子大小过滤
-gpumdkit.sh -filter_box filtered.xyz 20
-
-# 3. 按力值过滤
-gpumdkit.sh -filter_value filtered_by_box.xyz force 15
-```
-
-### 扩散通道分析
-
-```bash
-# 1. 计算概率密度
-gpumdkit.sh  # 选择: 5) Analyzer -> 508
 
-# 2. 使用 VESTA 或类似软件可视化
-# 打开 probability_density_0.25.vasp
+# 按元素对距离范围
+gpumdkit.sh -filter_range dump.xyz Li Li 1.9 2.0
 ```
 
-## 附加工具
-
 ### 时间监控
 
 ```bash
-# 监控 GPUMD 进度
 gpumdkit.sh -time gpumd
-
-# 监控 NEP 训练进度
 gpumdkit.sh -time nep
 ```
 
-### 体积分析
-
-```bash
-# 获取每个温度的平均体积
-python Scripts/analyzer/get_volume.py
-# 需要：*/K/thermo.out 目录
-```
-
-## CLI 参考
-
-| 标志 | 描述 | 语法 |
-|------|------|------|
-| `-analyze_comp` | 成分分析 | `gpumdkit.sh -analyze_comp <file>` |
-| `-range` | 属性范围 | `gpumdkit.sh -range <file> <prop>` |
-| `-min_dist` | 最小距离（无 PBC） | `gpumdkit.sh -min_dist <file>` |
-| `-min_dist_pbc` | 最小距离（PBC） | `gpumdkit.sh -min_dist_pbc <file>` |
-| `-cbc` | 电荷平衡 | `gpumdkit.sh -cbc <file>` |
-| `-filter_range` | 按距离范围过滤 | `gpumdkit.sh -filter_range <file> <e1> <e2> <min> <max>` |
-| `-filter_box` | 按盒子大小过滤 | `gpumdkit.sh -filter_box <file> <limit>` |
-| `-filter_value` | 按属性过滤 | `gpumdkit.sh -filter_value <file> <prop> <thresh>` |
-| `-time` | 时间监控 | `gpumdkit.sh -time <gpumd\|nep>` |
-
 ## 依赖
 
-| 工具 | 必需的包 |
-|------|----------|
-| 所有 Python 脚本 | `ase`, `numpy` |
-| 距离计算 | `scipy` |
-| 电荷平衡 | `pymatgen`, `tqdm` |
-| 属性范围 | `matplotlib` |
-| 概率密度 | `pymatgen` |
-
-## 参见
-
-- [格式转换](format_conversion.md) - 转换文件格式
-- [计算器](calculators.md) - 计算属性
-- [可视化](visualization.md) - 绘制结果
+| 工具 | 包 |
+|------|-----|
+| 所有 | ase, numpy |
+| 距离 | scipy |
+| 电荷平衡 | pymatgen, tqdm |
+| 属性范围 | matplotlib |
diff --git a/docs/tutorials2/zh/calculators.md b/docs/tutorials2/zh/calculators.md
index ce648ad..3f696bd 100644
--- a/docs/tutorials2/zh/calculators.md
+++ b/docs/tutorials2/zh/calculators.md
@@ -1,12 +1,11 @@
-# 计算器指南
-
 <div align="center">
+  <h1>计算器</h1>
   <p>
-    <strong>中文</strong> | <a href="../en/calculators.md">English</a>
+    <strong>简体中文</strong> | <a href="../en/calculators.md">English</a>
   </p>
 </div>
 
-本指南介绍 GPUMDkit 中用于计算材料属性的所有计算器工具。
+从分子动力学数据计算材料属性。
 
 ## 可用计算器
 
@@ -16,69 +15,30 @@
 | NEP 属性 | `-calc nep` | 使用 NEP 计算能量/力/应力 |
 | 描述符 | `-calc des` | 计算 NEP 描述符用于分析 |
 | DOAS | `-calc doas` | 原子态密度 |
-| NEB | 直接 Python | 推移弹性带计算 |
+| MSD | `-calc msd` | 从轨迹计算均方位移 |
 | 邻居列表 | `-calc nlist` | 构建用于分析的邻居列表 |
 | 位移 | `-calc disp` | 计算原子位移 |
 | 平均结构 | `-calc avg-struct` | 从轨迹计算时间平均结构 |
 | 八面体倾斜 | `-calc oct-tilt` | 钙钛矿八面体倾斜角 |
 | 极化 | `-calc pol-abo3` | ABO3 局部极化 |
 | 最小化 | `-calc minimize` | 使用 NEP 进行结构弛豫 |
-| MSD | `-calc msd` | 从轨迹计算均方位移 |
-
-## 交互模式
-
-```bash
-gpumdkit.sh
-# 选择: 4) Calculators
-```
-
-您将看到：
-
-```
-+----------------------------------------------------------+
-|                     CALCULATOR TOOLS                     |
-+----------------------------------------------------------+
-| 401) Calc ionic conductivity                             |
-| 402) Calc properties by nep                              |
-| 403) Calc descriptors of specific elements               |
-| 404) Calc density of atomistic states (DOAS)             |
-| 405) Calc nudged elastic band (NEB) by nep               |
-| 406) Build neighbor list                                 |
-| 407) Calc displacement from trajectory                   |
-| 408) Calc averaged structure                             |
-| 409) Calc octahedral tilt                                |
-| 410) Calc polarization for ABO3                          |
-| 411) Minimize structure by nep                           |
-| 412) Calc mean square displacement (MSD) from trajectory |
-+----------------------------------------------------------+
-```
+| NEB | 直接 Python | 推移弹性带计算 |
 
 ## 命令参考
 
 ### 离子电导率
 
-使用 Nernst-Einstein 方程从 MSD 数据计算离子电导率。
-
 ```bash
 gpumdkit.sh -calc ionic-cond <元素> <电荷>
 
 # 示例
-gpumdkit.sh -calc ionic-cond Li 1    # 锂离子 (Li+)
-gpumdkit.sh -calc ionic-cond Na 1    # 钠离子 (Na+)
-gpumdkit.sh -calc ionic-cond O -2    # 氧离子 (O2-)
+gpumdkit.sh -calc ionic-cond Li 1    # Li+
+gpumdkit.sh -calc ionic-cond O -2    # O2-
 ```
 
-**当前目录中需要的文件：**
-- `msd.out` - 来自 GPUMD 的 `compute_msd`
-- `thermo.out` - 用于获取温度
-- `model.xyz` - 用于获取体积
-- `run.in` - 用于获取模拟参数
+需要文件：`msd.out`, `thermo.out`, `model.xyz`, `run.in`
 
-**输出：** 离子扩散率和电导率值
-
-### NEP 属性预测
-
-使用 NEP 模型作为 DFT 代理计算能量、力和应力。
+### NEP 属性
 
 ```bash
 gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>
@@ -87,12 +47,8 @@ gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>
 gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
 ```
 
-**注意：** 先使用 `gpumdkit.sh -clean_xyz` 清理输入以删除现有属性。
-
 ### 描述符
 
-计算 NEP 描述符用于降维和结构分析。
-
 ```bash
 gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <元素>
 
@@ -100,15 +56,9 @@ gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <元素>
 gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
 ```
 
-**可视化：**
-```bash
-gpumdkit.sh -plt des pca    # PCA 可视化
-gpumdkit.sh -plt des umap   # UMAP 可视化
-```
-
-### 原子态密度 (DOAS)
+可视化：`gpumdkit.sh -plt des pca` 或 `gpumdkit.sh -plt des umap`
 
-按元素类型分组计算每原子能量分布。
+### DOAS
 
 ```bash
 gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>
@@ -117,42 +67,28 @@ gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>
 gpumdkit.sh -calc doas structures.xyz nep.txt doas.out
 ```
 
-**可视化：**
-```bash
-gpumdkit.sh -plt doas doas.out Li
-```
-
-### 均方位移 (MSD)
-
-从 extxyz 轨迹计算方向性 MSD。
+### MSD
 
 ```bash
 gpumdkit.sh -calc msd <trajectory.xyz> <元素> <dt_fs> [max_corr_steps]
 
-# 示例：Li，时间步长 10 fs
+# 示例
 gpumdkit.sh -calc msd dump.xyz Li 10
 ```
 
-**输出：** `msd.out`（时间/ps, MSD_x, MSD_y, MSD_z）
+输出：`msd.out`（时间/ps, MSD_x, MSD_y, MSD_z）
 
 ### 邻居列表
 
-为钙钛矿分析构建邻居列表。
-
 ```bash
-gpumdkit.sh -calc nlist -i <input> -c <cutoff> -n <num_neighbors> -C <中心元素> -E <邻居元素>
+gpumdkit.sh -calc nlist -i <input> -c <cutoff> -n <num> -C <中心元素> -E <邻居元素>
 
 # 示例
 gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
-gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O
 ```
 
-**输出：** `nl-<center>-<neighbor>.dat`
-
 ### 位移
 
-使用邻居列表从轨迹计算原子位移。
-
 ```bash
 gpumdkit.sh -calc disp -i <trajectory.xyz> -n <邻居列表> -o <输出>
 
@@ -160,12 +96,8 @@ gpumdkit.sh -calc disp -i <trajectory.xyz> -n <邻居列表> -o <输出>
 gpumdkit.sh -calc disp -i movie.xyz -n nl-Pb-O.dat -o displacements.dat
 ```
 
-**可选帧切片：** `-s <start> -t <stop> -p <step> -l <last_fraction>`
-
 ### 平均结构
 
-从轨迹生成时间平均结构。
-
 ```bash
 gpumdkit.sh -calc avg-struct -i <trajectory.xyz> -l <比例> -o <输出>
 
@@ -175,35 +107,23 @@ gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged.xyz
 
 ### 八面体倾斜
 
-计算钙钛矿体系的八面体倾斜角。
-
 ```bash
-gpumdkit.sh -calc oct-tilt -i <input.xyz> -n <B-O 邻居列表> -o <输出>
+gpumdkit.sh -calc oct-tilt -i <input.xyz> -n <B-O 列表> -o <输出>
 
 # 示例
-gpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o octahedral_tilt.dat
+gpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o tilt.dat
 ```
 
 ### 极化 (ABO3)
 
-计算 ABO3 钙钛矿的局部极化。
-
 ```bash
-gpumdkit.sh -calc pol-abo3 -i <input.xyz> \
-  --nl-ba <B-A 邻居列表> \
-  --nl-bo <B-O 邻居列表> \
-  --bec <元素=电荷 ...>
+gpumdkit.sh -calc pol-abo3 -i <input.xyz> --nl-ba <B-A 列表> --nl-bo <B-O 列表> --bec <元素=电荷 ...>
 
 # 示例
-gpumdkit.sh -calc pol-abo3 -i model.xyz \
-  --nl-ba nl-Ti-Pb.dat \
-  --nl-bo nl-Ti-O.dat \
-  --bec Pb=2.5 Sr=2.0 Ti=4.0 O=-2.0
+gpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat --bec Pb=2.5 Ti=4.0 O=-2.0
 ```
 
-### 结构最小化
-
-使用 BFGS 优化器和 NEP 模型弛豫结构。
+### 最小化
 
 ```bash
 gpumdkit.sh -calc minimize <结构> <nep.txt> [fmax] [max_steps]
@@ -212,101 +132,22 @@ gpumdkit.sh -calc minimize <结构> <nep.txt> [fmax] [max_steps]
 gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
 ```
 
-**参数：**
-- `fmax`：力收敛阈值（默认：0.01 eV/Å）
-- `max_steps`：最大优化步数（默认：1000）
-
-**输出：** `minimize.xyz`（优化轨迹）
+输出：`minimize.xyz`
 
-### NEB 计算
-
-进行推移弹性带计算以获得迁移势垒。
+### NEB
 
 ```bash
-# 直接 Python 执行
 python Scripts/calculators/neb_calculation.py <initial.xyz> <final.xyz> <n_images> <nep.txt>
 
 # 示例
 python Scripts/calculators/neb_calculation.py init.xyz fin.xyz 9 nep.txt
 ```
 
-## 常见工作流程
-
-### 离子传输分析
-
-```bash
-# 1. 在 run.in 中使用 compute_msd 运行 MD
-# 2. 计算 MSD
-gpumdkit.sh -calc msd dump.xyz Li 10
-
-# 3. 计算电导率
-gpumdkit.sh -calc ionic-cond Li 1
-
-# 4. 可视化
-gpumdkit.sh -plt msd
-gpumdkit.sh -plt sdc
-```
-
-### 描述符分析
-
-```bash
-# 1. 计算描述符
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-
-# 2. 使用 PCA 可视化
-gpumdkit.sh -plt des pca
-
-# 3. 或使用 UMAP 可视化
-gpumdkit.sh -plt des umap
-```
-
-### 钙钛矿分析
-
-```bash
-# 1. 构建邻居列表
-gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
-gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E Pb
-
-# 2. 计算位移
-gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -o disp.dat
-
-# 3. 计算倾斜
-gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -o tilt.dat
-
-# 4. 计算极化
-gpumdkit.sh -calc pol-abo3 -i movie.xyz \
-  --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \
-  --bec Pb=2.5 Ti=4.0 O=-2.0
-```
-
-### 结构弛豫
-
-```bash
-# 1. 最小化结构
-gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
-
-# 2. 使用最小化后的结构进行 MD
-cp minimize.xyz relaxed_model.xyz
-```
-
 ## 依赖
 
-| 计算器 | 必需的包 |
-|--------|----------|
-| 所有 | `numpy`, `ase` |
-| ionic-cond | `scipy` |
-| nep, des, doas, minimize | `calorine` |
-| nlist, disp, oct-tilt, pol-abo3 | `ferrodispcalc` |
-| neb | `calorine`, `matplotlib` |
-
-安装依赖：
-```bash
-pip install numpy ase scipy calorine matplotlib tqdm
-pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
-```
-
-## 参见
-
-- [可视化](visualization.md) - 绘制计算结果
-- [分析工具](analyzers.md) - 结构分析
-- [NEP 训练指南](nep_training.md) - 完整的训练工作流
+| 计算器 | 包 |
+|--------|-----|
+| 所有 | numpy, ase |
+| ionic-cond | scipy |
+| nep, des, doas, minimize | calorine |
+| nlist, disp, oct-tilt, pol-abo3 | ferrodispcalc |
diff --git a/docs/tutorials2/zh/format_conversion.md b/docs/tutorials2/zh/format_conversion.md
index 615b6bd..277c22b 100644
--- a/docs/tutorials2/zh/format_conversion.md
+++ b/docs/tutorials2/zh/format_conversion.md
@@ -1,273 +1,100 @@
-# 格式转换指南
-
 <div align="center">
+  <h1>格式转换</h1>
   <p>
-    <strong>中文</strong> | <a href="../en/format_conversion.md">English</a>
+    <strong>简体中文</strong> | <a href="../en/format_conversion.md">English</a>
   </p>
 </div>
 
-本指南介绍 GPUMDkit 中的所有格式转换工具。
+在计算材料科学文件格式之间转换。
 
 ## 支持的格式
 
-| 格式 | 扩展名 | 描述 |
+| 格式 | 扩展名 | 软件 |
 |------|--------|------|
-| VASP | POSCAR, OUTCAR, XDATCAR, vasprun.xml | 维也纳从头算模拟包 |
-| LAMMPS | .data, dump.* | 大规模原子/分子大规模并行模拟器 |
-| CP2K | .log, pos.xyz, frc.xyz, cell.cell | 量子化学和固态物理 |
-| ABACUS | running_scf.log, running_md.log | 基于原子轨道的从头算计算 |
-| CIF | .cif | 晶体学信息文件 |
-| MTP | .cfg | 矩量张量势格式 |
-| ASE | .traj | 原子模拟环境轨迹 |
-| extxyz | .xyz | 扩展 XYZ（主要工作格式） |
-
-## 交互模式
+| VASP | POSCAR, OUTCAR, XDATCAR, vasprun.xml | VASP |
+| LAMMPS | .data, dump.* | LAMMPS |
+| CP2K | .log, pos.xyz, frc.xyz, cell.cell | CP2K |
+| ABACUS | running_scf.log, running_md.log | ABACUS |
+| CIF | .cif | 各种软件 |
+| MTP | .cfg | MTP |
+| ASE | .traj | ASE |
+| extxyz | .xyz | 各种软件（主要格式） |
 
-启动交互式菜单并选择选项 1：
+## 快速参考
 
 ```bash
-gpumdkit.sh
-# 选择: 1) Format Conversion
-```
+# VASP
+gpumdkit.sh -out2xyz <目录>              # OUTCAR -> extxyz
+gpumdkit.sh -pos2exyz POSCAR model.xyz   # POSCAR -> extxyz
+gpumdkit.sh -exyz2pos structures.xyz     # extxyz -> POSCAR
 
-您将看到：
-
-```
-+-------------------------------------------------------------+
-|                   FORMAT CONVERSION TOOLS                   |
-+-------------------------------------------------------------+
-| 101) VASP to extxyz            106) Add group labels        |
-| 102) MTP to extxyz             107) Add weight to extxyz    |
-| 103) CP2K to extxyz            108) Extract frame extxyz    |
-| 104) ABACUS to extxyz          109) Clean XYZ info          |
-| 105) extxyz to POSCAR          110) Replicate structure     |
-+-------------------------------------------------------------+
-| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |
-| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |
-| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |
-| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|
-+-------------------------------------------------------------+
-| 000) Return to main menu                                    |
-+-------------------------------------------------------------+
-```
-
-## 命令行模式
-
-### VASP 转换
-
-#### OUTCAR 转 extxyz
-
-```bash
-# Shell 版本（支持 OUTCAR 和 vasprun.xml）
-gpumdkit.sh -out2xyz <目录>
-
-# Python 版本（仅 OUTCAR）
-gpumdkit.sh -out2exyz <目录>
-
-# 示例
-gpumdkit.sh -out2xyz ./vasp_results/
-```
-
-#### XDATCAR 转 extxyz
-
-```bash
-gpumdkit.sh -xdat2exyz XDATCAR output.xyz
-```
-
-#### POSCAR 转 extxyz
-
-```bash
-gpumdkit.sh -pos2exyz POSCAR model.xyz
-```
-
-#### extxyz 转 POSCAR
-
-```bash
-# 将所有帧转换为单独的 POSCAR 文件
-gpumdkit.sh -exyz2pos structures.xyz
-```
-
-### LAMMPS 转换
-
-#### LAMMPS dump 转 extxyz
-
-```bash
-# 重要：元素符号必须与 dump 文件中的原子类型 ID 匹配
-gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
-
-# 示例
-gpumdkit.sh -lmp2exyz trajectory.dump Na Cl
-```
-
-#### POSCAR 转 LAMMPS data
-
-```bash
-gpumdkit.sh -pos2lmp POSCAR lammps.data
-```
-
-### CIF 转换
-
-```bash
-# CIF 转 POSCAR
-gpumdkit.sh -cif2pos input.cif POSCAR.vasp
-
-# CIF 转 extxyz
-gpumdkit.sh -cif2exyz input.cif model.xyz
-```
+# LAMMPS
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl  # LAMMPS -> extxyz
+gpumdkit.sh -pos2lmp POSCAR lammps.data        # POSCAR -> LAMMPS
 
-### 其他转换
+# CIF
+gpumdkit.sh -cif2pos input.cif POSCAR.vasp     # CIF -> POSCAR
+gpumdkit.sh -cif2exyz input.cif model.xyz      # CIF -> extxyz
 
-```bash
-# ASE 轨迹转 extxyz
-gpumdkit.sh -traj2exyz input.traj output.xyz
+# 其他
+gpumdkit.sh -xdat2exyz XDATCAR output.xyz      # XDATCAR -> extxyz
+gpumdkit.sh -traj2exyz input.traj output.xyz   # ASE 轨迹 -> extxyz
 ```
 
 ## 结构操作
 
-### 添加组标签
-
-组标签是 GPUMD/NEP 识别原子类型所必需的：
-
 ```bash
-gpumdkit.sh -addgroup POSCAR <元素1> <元素2> ...
-
-# 示例
+# 添加组标签（NEP 必需）
 gpumdkit.sh -addgroup POSCAR Li Y Cl
-```
-
-这将创建带有组标签的 `model.xyz` 文件。
 
-### 添加权重
-
-为结构添加权重标签用于加权训练：
-
-```bash
-gpumdkit.sh -addweight input.xyz output.xyz <权重>
-
-# 示例
-gpumdkit.sh -addweight train.xyz weighted.xyz 2.0
-```
+# 添加权重
+gpumdkit.sh -addweight input.xyz output.xyz 2.0
 
-### 复制结构
-
-从单胞创建超胞：
-
-```bash
-# 按复制因子
+# 复制结构
 gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2
+gpumdkit.sh -replicate POSCAR supercell.vasp 256  # 按原子数
 
-# 按目标原子数
-gpumdkit.sh -replicate POSCAR supercell.vasp 256
-```
-
-### 提取帧
-
-从轨迹中提取特定帧：
-
-```bash
-# 从 0 开始的索引
+# 提取帧（从 0 开始）
 gpumdkit.sh -get_frame trajectory.xyz 1000
-```
-
-### 清理 XYZ 元数据
 
-从 extxyz 文件中删除额外的元数据：
-
-```bash
+# 清理元数据
 gpumdkit.sh -clean_xyz input.xyz clean.xyz
 ```
 
-## 完整 CLI 参考
-
-| 标志 | 描述 | 语法 |
-|------|------|------|
-| `-out2xyz` | OUTCAR 转 extxyz (shell) | `gpumdkit.sh -out2xyz <dir>` |
-| `-out2exyz` | OUTCAR 转 extxyz (python) | `gpumdkit.sh -out2exyz <dir>` |
-| `-pos2exyz` | POSCAR 转 extxyz | `gpumdkit.sh -pos2exyz <poscar> <xyz>` |
-| `-exyz2pos` | extxyz 转 POSCAR | `gpumdkit.sh -exyz2pos <xyz>` |
-| `-pos2lmp` | POSCAR 转 LAMMPS data | `gpumdkit.sh -pos2lmp <poscar> <lmp>` |
-| `-lmp2exyz` | LAMMPS dump 转 extxyz | `gpumdkit.sh -lmp2exyz <dump> <elem...>` |
-| `-cif2pos` | CIF 转 POSCAR | `gpumdkit.sh -cif2pos <cif> <output>` |
-| `-cif2exyz` | CIF 转 extxyz | `gpumdkit.sh -cif2exyz <cif> <output>` |
-| `-xdat2exyz` | XDATCAR 转 extxyz | `gpumdkit.sh -xdat2exyz XDATCAR dump.xyz` |
-| `-traj2exyz` | ASE 轨迹转 extxyz | `gpumdkit.sh -traj2exyz <traj> <xyz>` |
-| `-addgroup` | 添加组标签 | `gpumdkit.sh -addgroup <poscar> <elem...>` |
-| `-addweight` | 添加权重 | `gpumdkit.sh -addweight <in> <out> <weight>` |
-| `-replicate` | 复制结构 | `gpumdkit.sh -replicate <in> <out> a b c` |
-| `-get_frame` | 提取帧 | `gpumdkit.sh -get_frame <xyz> <index>` |
-| `-clean_xyz` | 清理 extxyz 信息 | `gpumdkit.sh -clean_xyz <in> <out>` |
-
 ## 示例
 
-### 示例 1：转换 VASP MD 输出
+### 转换 VASP 输出
 
 ```bash
-# 转换当前目录中的所有 OUTCAR 文件
 gpumdkit.sh -out2xyz .
-
-# 为 NEP 训练添加组标签
 gpumdkit.sh -addgroup POSCAR Pb Ti O
-
-# 结果：准备好用于 NEP 训练的 model.xyz
 ```
 
-### 示例 2：准备 LAMMPS 模拟
+### 准备 LAMMPS 模拟
 
 ```bash
-# 将 POSCAR 转换为 LAMMPS data
 gpumdkit.sh -pos2lmp POSCAR system.data
-
-# LAMMPS 模拟后，将 dump 转换回来
+# 模拟后
 gpumdkit.sh -lmp2exyz dump.lammpstrj Li P S
 ```
 
-### 示例 3：批量转换
+### 批量转换
 
 ```bash
-# 转换多个 OUTCAR 文件
 for dir in run_*; do
     gpumdkit.sh -out2xyz "$dir"
-    mv "$dir"/model.xyz "$dir"/trajectory.xyz
 done
 ```
 
-### 示例 4：结构复制
-
-```bash
-# 创建 2x2x2 超胞
-gpumdkit.sh -replicate POSCAR supercell_222.vasp 2 2 2
-
-# 创建约 256 个原子的超胞
-gpumdkit.sh -replicate POSCAR supercell_256.vasp 256
-```
-
-## 重要提示
+## 注意事项
 
-1. **extxyz 是主要格式**：大多数 GPUMDkit 工具使用 extxyz 文件
-2. **组标签是必需的**：GPUMD/NEP 需要组标签来识别原子类型
-3. **帧索引从 0 开始**：第一帧的索引为 0
-4. **LAMMPS 的元素顺序很重要**：必须与 dump 文件中的原子类型 ID 匹配
-5. **exyz2pos 导出所有帧**：为每帧创建单独的 POSCAR 文件
+- extxyz 是 GPUMDkit 的主要格式
+- GPUMD/NEP 需要组标签
+- 帧索引从 0 开始
+- LAMMPS 元素顺序必须与原子类型 ID 匹配
 
 ## 依赖
 
-大多数 Python 脚本需要：
-- `ase`（原子模拟环境）
-- `numpy`
-
-## 故障排除
-
-### 问题：缺少元素信息
-**解决方案**：确保 POSCAR 头部有正确的元素名称
-
-### 问题：原子数不正确
-**解决方案**：检查 POSCAR 是否启用了选择性动力学
-
-### 问题：LAMMPS 转换物种错误
-**解决方案**：验证元素顺序是否与 dump 文件中的原子类型 ID 匹配
-
-## 参见
-
-- [计算器](calculators.md) - 计算材料属性
-- [分析工具](analyzers.md) - 结构分析
-- [NEP 训练指南](nep_training.md) - 完整的训练工作流
+```bash
+pip install ase numpy
+```
diff --git a/docs/tutorials2/zh/index.md b/docs/tutorials2/zh/index.md
deleted file mode 100644
index c78d9cc..0000000
--- a/docs/tutorials2/zh/index.md
+++ /dev/null
@@ -1,160 +0,0 @@
-# GPUMDkit 教程
-
-<div align="center">
-  <p>
-    <strong>中文</strong> | <a href="../en/index.md">English</a>
-  </p>
-</div>
-
-欢迎使用 **GPUMDkit** - 一个强大的 GPUMD 和 NEP 命令行工具包！
-
-## 什么是 GPUMDkit？
-
-GPUMDkit 可以简化您的分子动力学工作流程：
-
-- **格式转换**：在 VASP、LAMMPS、CP2K、ABACUS、CIF 和 extxyz 格式之间转换
-- **计算器**：计算离子电导率、描述符、MSD、NEB 等
-- **分析工具**：结构验证、过滤、成分分析
-- **可视化**：31+ 种绘图类型，用于训练、传输和结构分析
-- **工作流**：DFT 和 MD 模拟的批处理
-- **结构采样**：使用均匀、随机或 FPS 方法选择结构
-
-## 快速开始
-
-### 安装
-
-```bash
-# 克隆仓库
-git clone https://github.com/zhyan0603/GPUMDkit.git
-
-# 安装
-cd GPUMDkit
-source ./install.sh
-```
-
-### 依赖
-
-```bash
-# 创建 conda 环境
-conda create -n gpumdkit python=3.12
-conda activate gpumdkit
-
-# 安装必需的包
-pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
-```
-
-### 基本用法
-
-```bash
-# 交互模式（菜单驱动）
-gpumdkit.sh
-
-# 命令行模式
-gpumdkit.sh -<选项> [参数...]
-
-# 获取帮助
-gpumdkit.sh -h                    # 通用帮助
-gpumdkit.sh -<选项> -h            # 特定命令帮助
-gpumdkit.sh -plt -h               # 绘图帮助
-gpumdkit.sh -calc -h              # 计算器帮助
-```
-
-## 教程列表
-
-| 教程 | 描述 |
-|------|------|
-| [快速入门](quickstart.md) | 安装、配置和第一步 |
-| [格式转换](format_conversion.md) | 在结构文件格式之间转换 |
-| [计算器](calculators.md) | 计算材料属性 |
-| [分析工具](analyzers.md) | 结构分析和验证 |
-| [可视化](visualization.md) | 绘图和数据可视化 |
-| [工作流](workflows.md) | 批处理和自动化 |
-| [结构采样](sampling.md) | 结构选择方法 |
-| [NEP 训练指南](nep_training.md) | 完整的 NEP 模型训练工作流 |
-
-## 常见工作流程
-
-### 工作流 1：NEP 模型训练
-
-```bash
-# 1. 转换 DFT 数据
-gpumdkit.sh -out2xyz ./vasp_results/
-
-# 2. 添加组标签
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-
-# 3. 采样结构
-gpumdkit.sh  # 选择: 2) Sample Structures -> 203
-
-# 4. 训练 NEP（外部）
-# ...
-
-# 5. 验证
-gpumdkit.sh -plt train
-gpumdkit.sh -plt prediction
-```
-
-### 工作流 2：离子电导率计算
-
-```bash
-# 1. 计算 MSD
-gpumdkit.sh -calc msd trajectory.xyz Li 10
-
-# 2. 计算电导率
-gpumdkit.sh -calc ionic-cond Li 1
-
-# 3. 可视化
-gpumdkit.sh -plt msd
-gpumdkit.sh -plt sdc
-```
-
-### 工作流 3：结构分析
-
-```bash
-# 1. 检查成分
-gpumdkit.sh -analyze_comp train.xyz
-
-# 2. 检查距离
-gpumdkit.sh -min_dist_pbc train.xyz
-
-# 3. 检查力范围
-gpumdkit.sh -range train.xyz force
-```
-
-## 模块概览
-
-| 模块 | 菜单 | CLI 标志 | 描述 |
-|------|------|----------|------|
-| 格式转换 | 1 | `-out2xyz`, `-pos2exyz` 等 | 结构文件转换 |
-| 结构采样 | 2 | `-pynep` | 结构采样 |
-| 工作流 | 3 | - | 批处理 |
-| 计算器 | 4 | `-calc <类型>` | 属性计算 |
-| 分析工具 | 5 | `-range`, `-min_dist` 等 | 结构分析 |
-| 可视化 | 6 | `-plt <类型>` | 绘图工具 |
-| 实用工具 | 7 | `-time`, `-clean` | 实用功能 |
-
-## 输出文件约定
-
-| 文件 | 内容 |
-|------|------|
-| `model.xyz` | extxyz 格式的结构文件 |
-| `train.xyz` | 训练数据集 |
-| `nep.txt` | NEP 模型文件 |
-| `msd.out` | 均方位移数据 |
-| `thermo.out` | 热力学属性 |
-| `loss.out` | 训练损失历史 |
-| `rdf.out` | 径向分布函数 |
-| `sdc.out` | 自扩散系数数据 |
-
-## 获取帮助
-
-- **通用帮助**：`gpumdkit.sh -h`
-- **绘图帮助**：`gpumdkit.sh -plt -h`
-- **计算器帮助**：`gpumdkit.sh -calc -h`
-- **特定命令**：`gpumdkit.sh -<选项> -h`
-
-## 联系方式
-
-- **开发者**：严子涵 (yanzihan@westlake.edu.cn)
-- **GitHub**：https://github.com/zhyan0603/GPUMDkit
-- **文档**：https://zhyan0603.github.io/GPUMDkit/
diff --git a/docs/tutorials2/zh/nep_training.md b/docs/tutorials2/zh/nep_training.md
index 7d8408e..449897d 100644
--- a/docs/tutorials2/zh/nep_training.md
+++ b/docs/tutorials2/zh/nep_training.md
@@ -1,130 +1,63 @@
-# NEP 训练指南
-
 <div align="center">
+  <h1>NEP 训练指南</h1>
   <p>
-    <strong>中文</strong> | <a href="../en/nep_training.md">English</a>
+    <strong>简体中文</strong> | <a href="../en/nep_training.md">English</a>
   </p>
 </div>
 
-本指南提供使用 GPUMDkit 训练 NEP（神经演化势）模型的完整工作流。
+训练 NEP（神经演化势）模型的完整工作流。
 
 ## 概述
 
-NEP 训练包括：
-
 1. **数据准备** - 转换和组织训练数据
-2. **结构采样** - 选择多样化结构
-3. **模型训练** - 训练 NEP 模型（外部）
-4. **验证** - 检查训练质量
-5. **主动学习** - 迭代改进模型
+2. **质量检查** - 验证和过滤结构
+3. **采样** - 选择多样化结构
+4. **训练** - 训练 NEP 模型（外部）
+5. **验证** - 检查训练质量
+6. **主动学习** - 迭代改进模型
 
 ## 步骤 1：数据准备
 
-### 将 DFT 数据转换为 extxyz
-
 ```bash
-# 从 VASP OUTCAR
+# 转换 DFT 数据
 gpumdkit.sh -out2xyz ./vasp_results/
 
-# 从 VASP XDATCAR
-gpumdkit.sh -xdat2exyz XDATCAR trajectory.xyz
-
-# 从 CP2K
-gpumdkit.sh  # 选择: 1) Format Conversion -> 103
-
-# 从 LAMMPS
-gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
-```
-
-### 添加组标签
-
-组标签是 NEP 识别原子类型所必需的：
-
-```bash
+# 添加组标签
 gpumdkit.sh -addgroup POSCAR Li Y Cl
-```
-
-这将创建带有组标签的 `model.xyz`。
-
-### 合并训练数据
 
-```bash
-# 合并多个 extxyz 文件
-cat file1.xyz file2.xyz file3.xyz > train.xyz
-
-# 或使用成分分析选择特定成分
-gpumdkit.sh -analyze_comp all_structures.xyz
+# 合并训练数据
+cat */model.xyz > train.xyz
 ```
 
-## 步骤 2：数据质量检查
-
-### 检查成分
+## 步骤 2：质量检查
 
 ```bash
+# 检查成分
 gpumdkit.sh -analyze_comp train.xyz
-```
-
-### 检查最小距离
 
-```bash
-# 快速检查（无 PBC）
-gpumdkit.sh -min_dist train.xyz
-
-# 精确检查（带 PBC）
+# 检查距离
 gpumdkit.sh -min_dist_pbc train.xyz
-```
 
-### 检查属性范围
-
-```bash
 # 检查力范围
 gpumdkit.sh -range train.xyz force
 
-# 检查能量范围
-gpumdkit.sh -range train.xyz energy
-
-# 带直方图
-gpumdkit.sh -range train.xyz force hist
-```
-
-### 过滤结构
-
-```bash
-# 按最小距离过滤
+# 过滤结构
 gpumdkit.sh -filter_dist_pbc train.xyz 1.0
-
-# 按盒子大小过滤
-gpumdkit.sh -filter_box train.xyz 20
-
-# 按力值过滤
-gpumdkit.sh -filter_value train.xyz force 20
 ```
 
-## 步骤 3：结构采样
-
-### 采样多样化结构
+## 步骤 3：采样
 
 ```bash
-# FPS 采样（首选）
+# FPS 采样（推荐）
 gpumdkit.sh  # 选择: 2) Sample Structures -> 203
 
 # 或均匀采样
 python Scripts/sample_structures/sample_structures.py train.xyz uniform 100
 ```
 
-### 扰动结构
-
-从现有结构生成额外的训练数据：
-
-```bash
-python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
-```
-
-## 步骤 4：NEP 模型训练
-
-### 准备 nep.in
+## 步骤 4：训练
 
-创建包含训练参数的 `nep.in`：
+创建 `nep.in`：
 
 ```
 type 3 Li Y Cl
@@ -136,164 +69,45 @@ batch 1000
 generation 100000
 ```
 
-### 运行训练
+运行训练：
 
 ```bash
-# GPUMDkit 外部
 gpumd
 ```
 
 ## 步骤 5：验证
 
-### 绘制训练结果
-
 ```bash
-# 绘制训练损失和对比图
+# 绘制训练结果
 gpumdkit.sh -plt train
-
-# 绘制测试预测
 gpumdkit.sh -plt prediction
-
-# 组合训练/测试图
-gpumdkit.sh -plt train_test
-
-# 力误差分析
 gpumdkit.sh -plt force_errors
-```
-
-### 检查收敛性
-
-```bash
-# 绘制损失曲线
-gpumdkit.sh -plt train
-```
-
-观察：
-- 损失平滑下降
-- 无振荡
-- 收敛到低值
-
-### 分析描述符
 
-```bash
-# 计算描述符
+# 分析描述符
 gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-
-# 使用 PCA 可视化
 gpumdkit.sh -plt des pca
-
-# 或 UMAP
-gpumdkit.sh -plt des umap
 ```
 
 ## 步骤 6：主动学习
 
-### 使用当前 NEP 运行 MD
-
 ```bash
-# 设置 MD 模拟
+# 使用当前 NEP 运行 MD
 gpumdkit.sh  # 选择: 3) Workflow -> 302
-```
-
-### 选择多样化结构
 
-```bash
-# 按距离过滤
+# 过滤和采样
 gpumdkit.sh -min_dist_pbc dump.xyz
 gpumdkit.sh -filter_box dump.xyz 13
 
-# 采样多样化结构
-gpumdkit.sh  # 选择: 2) Sample Structures -> 203
-```
-
-### 计算 DFT 参考
-
-```bash
-# 准备 SCF 计算
+# 准备 DFT 计算
 gpumdkit.sh  # 选择: 3) Workflow -> 301
 
-# 运行 DFT（外部）
-```
-
-### 重新训练模型
-
-```bash
-# 将新数据添加到训练集
+# 用新数据重新训练
 cat new_structures.xyz >> train.xyz
-
-# 重新训练 NEP（外部）
-```
-
-## 完整工作流示例
-
-```bash
-# 1. 转换 DFT 数据
-gpumdkit.sh -out2xyz ./dft_results/
-
-# 2. 添加组标签
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-
-# 3. 合并训练数据
-cat */model.xyz > train.xyz
-
-# 4. 检查数据质量
-gpumdkit.sh -analyze_comp train.xyz
-gpumdkit.sh -min_dist_pbc train.xyz
-gpumdkit.sh -range train.xyz force
-
-# 5. 过滤结构
-gpumdkit.sh -filter_dist_pbc train.xyz 1.0
-
-# 6. 采样多样化结构
-gpumdkit.sh  # 选择: 2) Sample Structures -> 203
-
-# 7. 训练 NEP（外部）
-# ... 创建 nep.in 并运行 gpumd ...
-
-# 8. 验证训练
-gpumdkit.sh -plt train
-gpumdkit.sh -plt prediction
-gpumdkit.sh -plt force_errors
-
-# 9. 分析描述符
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-gpumdkit.sh -plt des pca
 ```
 
-## 更好训练的技巧
-
-1. **多样化数据**：包含各种结构、温度和成分
-2. **平衡数据集**：确保所有元素类型都有良好表示
-3. **质量过滤**：删除原子太近或力太大的结构
-4. **足够数据**：至少 1000-5000 个结构以获得良好精度
-5. **验证集**：保留 10-20% 的数据用于测试
-
-## 故障排除
-
-### 问题：高 RMSE
-
-**解决方案**：
-- 添加更多多样化训练数据
-- 增加 `neuron` 和 `n_max` 参数
-- 检查训练数据中的异常值
-
-### 问题：预测不准确
-
-**解决方案**：
-- 验证训练数据质量
-- 添加来自不同相/温度的结构
-- 增加训练 `generation`
-
-### 问题：过拟合
-
-**解决方案**：
-- 使用更多训练数据
-- 降低模型复杂度
-- 使用正则化
-
-## 参见
+## 建议
 
-- [格式转换](format_conversion.md) - 转换文件格式
-- [计算器](calculators.md) - 计算属性
-- [可视化](visualization.md) - 绘制结果
-- [结构采样](sampling.md) - 采样结构
+- 包含多样化的结构、温度和成分
+- 至少 1000-5000 个结构以获得良好精度
+- 保留 10-20% 的数据用于测试
+- 训练前检查异常值
diff --git a/docs/tutorials2/zh/quickstart.md b/docs/tutorials2/zh/quickstart.md
index 7a9a605..b8c30f6 100644
--- a/docs/tutorials2/zh/quickstart.md
+++ b/docs/tutorials2/zh/quickstart.md
@@ -1,244 +1,137 @@
-# 快速入门指南
-
 <div align="center">
+  <h1>快速入门</h1>
   <p>
-    <strong>中文</strong> | <a href="../en/quickstart.md">English</a>
+    <strong>简体中文</strong> | <a href="../en/quickstart.md">English</a>
   </p>
 </div>
 
-本指南将帮助您快速开始使用 GPUMDkit。
+5 分钟内开始使用 GPUMDkit。
 
 ## 前提条件
 
-在安装 GPUMDkit 之前，请确保您拥有：
-
-- **Linux 或 macOS**（Windows 通过 WSL）
-- **Bash** shell
-- **Python 3.8+**（推荐 3.12）
-- **Git**（用于克隆仓库）
+- Linux 或 macOS（Windows 通过 WSL）
+- Python 3.8+（推荐 3.12）
+- Git
 
 ## 安装
 
-### 步骤 1：克隆仓库
+### 步骤 1：克隆
 
 ```bash
 git clone https://github.com/zhyan0603/GPUMDkit.git
 cd GPUMDkit
 ```
 
-### 步骤 2：运行安装脚本
+### 步骤 2：安装
 
 ```bash
 source ./install.sh
 ```
 
-此脚本将：
-1. 将 GPUMDkit 添加到您的 PATH
-2. 设置 bash 自动补全
-3. 配置环境变量
-
 ### 步骤 3：重新加载 Shell
 
 ```bash
-source ~/.bashrc
-# 或
-source ~/.zshrc
+source ~/.bashrc  # 或 source ~/.zshrc
 ```
 
-### 步骤 4：验证安装
+### 步骤 4：验证
 
 ```bash
 gpumdkit.sh -h
 ```
 
-您应该看到包含可用命令的帮助信息。
-
 ## Python 依赖
 
-某些功能需要 Python 包。创建 conda 环境：
-
 ```bash
-# 创建环境
 conda create -n gpumdkit python=3.12
 conda activate gpumdkit
-
-# 安装核心包
-pip install numpy ase scipy matplotlib
-
-# 安装可选包（完整功能）
-pip install neptrain pymatgen dpdata
-
-# 用于钙钛矿分析（可选）
-pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
+pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
 ```
 
-## 两种使用模式
+> 使用 GPUMDkit 前请确保已激活 `gpumdkit` 环境。
 
-### 交互模式
+## 使用模式
 
-启动交互式菜单：
+### 交互模式
 
 ```bash
 gpumdkit.sh
 ```
 
-您将看到：
-
 ```
-       ____ ____  _   _ __  __ ____  _    _ _
-      / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
-     | |  _| |_) | | | | |\/| | | | | |/ / | __|
-     | |_| |  __/| |_| | |  | | |_| |   <| | |_
-      \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
+           ____ ____  _   _ __  __ ____  _    _ _
+          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
+         | |  _| |_) | | | | |\/| | | | | |/ / | __|
+         | |_| |  __/| |_| | |  | | |_| |   <| | |_
+          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
 
-      GPUMDkit Version 1.5.5 (dev) (2026-05-10)
-Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+          GPUMDkit Version 1.5.5 (dev) (2026-05-10)
 
  ---------------------- GPUMD ------------------------
- 1) Format Conversion          2) Sample Structures
- 3) Workflow                   4) Calculators
- 5) Analyzer                   6) Visualization
- 7) Utilities                  8) Developing...
- 0) Exit
+  1) Format Conversion          2) Sample Structures
+  3) Workflow                   4) Calculators
+  5) Analyzer                   6) Visualization
+  7) Utilities                  0) Exit
  ------------>>
- Input the function number:
 ```
 
-输入所需功能的编号进行导航。
-
 ### 命令行模式
 
-直接执行命令：
-
 ```bash
-# 显示帮助
-gpumdkit.sh -h
-
-# 将 POSCAR 转换为 extxyz
-gpumdkit.sh -pos2exyz POSCAR model.xyz
-
-# 绘制训练结果
-gpumdkit.sh -plt train
-
-# 计算离子电导率
-gpumdkit.sh -calc ionic-cond Li 1
+gpumdkit.sh -h                    # 显示帮助
+gpumdkit.sh -pos2exyz POSCAR model.xyz  # 直接命令
 ```
 
-## 第一步示例
+## 第一个例子
 
-### 示例 1：转换结构
+### 转换结构
 
 ```bash
-# 将 POSCAR 转换为 extxyz 格式
 gpumdkit.sh -pos2exyz POSCAR model.xyz
-
-# 添加组标签（NEP 训练必需）
 gpumdkit.sh -addgroup POSCAR Li Y Cl
 ```
 
-### 示例 2：分析训练数据
+### 分析数据
 
 ```bash
-# 检查训练数据中的力范围
 gpumdkit.sh -range train.xyz force
-
-# 检查最小原子间距离
 gpumdkit.sh -min_dist_pbc train.xyz
-
-# 分析成分
 gpumdkit.sh -analyze_comp train.xyz
 ```
 
-### 示例 3：绘制结果
+### 绘制结果
 
 ```bash
-# 绘制 NEP 训练结果
 gpumdkit.sh -plt train
-
-# 绘制均方位移
 gpumdkit.sh -plt msd
-
-# 绘制径向分布函数
 gpumdkit.sh -plt rdf
 ```
 
 ## 获取帮助
 
-### 通用帮助
-
-```bash
-gpumdkit.sh -h
-```
-
-### 模块特定帮助
-
 ```bash
-# 绘图帮助
-gpumdkit.sh -plt -h
-
-# 计算器帮助
-gpumdkit.sh -calc -h
-
-# 特定命令帮助
-gpumdkit.sh -pos2exyz -h
-gpumdkit.sh -calc ionic-cond -h
+gpumdkit.sh -h              # 通用帮助
+gpumdkit.sh -plt -h         # 绘图帮助
+gpumdkit.sh -calc -h        # 计算器帮助
+gpumdkit.sh -pos2exyz -h    # 特定命令帮助
 ```
 
-### 交互模式帮助
-
-在交互模式中，每个子菜单都会显示可用选项及其描述。
-
-## 常见问题
-
-### 问题：命令未找到
-
-**解决方案**：确保 GPUMDkit 在您的 PATH 中：
+## 故障排除
 
+**命令未找到**
 ```bash
-# 检查 gpumdkit.sh 是否在 PATH 中
-which gpumdkit.sh
-
-# 如果未找到，手动添加到 PATH
 export GPUMDkit_path=/path/to/GPUMDkit
 export PATH=${GPUMDkit_path}:${PATH}
 ```
 
-### 问题：缺少 Python 包
-
-**解决方案**：激活 conda 环境：
-
+**缺少包**
 ```bash
 conda activate gpumdkit
 ```
 
-### 问题：权限被拒绝
-
-**解决方案**：使脚本可执行：
-
-```bash
-chmod +x /path/to/GPUMDkit/gpumdkit.sh
-```
-
 ## 下一步
 
-现在您已经安装了 GPUMDkit，请探索以下教程：
-
-- [格式转换](format_conversion.md) - 学习在文件格式之间转换
-- [计算器](calculators.md) - 计算材料属性
-- [可视化](visualization.md) - 创建出版级图表
-- [NEP 训练指南](nep_training.md) - 完整的训练工作流
-
-## 更新 GPUMDkit
-
-更新到最新版本：
-
-```bash
-gpumdkit.sh -update
-```
-
-或手动更新：
-
-```bash
-cd /path/to/GPUMDkit
-git pull origin main
-```
+- [格式转换](format_conversion.md)
+- [计算器](calculators.md)
+- [可视化](visualization.md)
+- [NEP 训练](nep_training.md)
diff --git a/docs/tutorials2/zh/sampling.md b/docs/tutorials2/zh/sampling.md
index 7acf8e9..056da8a 100644
--- a/docs/tutorials2/zh/sampling.md
+++ b/docs/tutorials2/zh/sampling.md
@@ -1,73 +1,34 @@
-# 结构采样指南
-
 <div align="center">
+  <h1>结构采样</h1>
   <p>
-    <strong>中文</strong> | <a href="../en/sampling.md">English</a>
+    <strong>简体中文</strong> | <a href="../en/sampling.md">English</a>
   </p>
 </div>
 
-本指南介绍 GPUMDkit 中的结构采样和选择工具。
+结构选择和采样工具。
 
 ## 可用方法
 
 | 方法 | 菜单 | 描述 |
 |------|------|------|
 | 均匀/随机 | 201 | 选择均匀间隔或随机帧 |
-| FPS by PyNEP | 202 | 最远点采样（已弃用） |
 | FPS by NepTrain | 203 | 最远点采样（推荐） |
 | 扰动 | 204 | 生成扰动结构 |
 | 力偏差 | 205 | 选择高力偏差结构 |
 
-## 交互模式
+## 均匀/随机采样
 
 ```bash
-gpumdkit.sh
-# 选择: 2) Sample Structures
-```
-
-您将看到：
-
-```
-+------------------------------------------------------+
-|                 SAMPLE STRUCTURE TOOLS               |
-+------------------------------------------------------+
-| 201) Sample structures from extxyz                   |
-| 202) FPS sampling by PyNEP [deprecated]              |
-| 203) FPS sampling by NepTrain [preferred]            |
-| 204) Perturb structure                               |
-| 205) Select max force deviation structs              |
-+------------------------------------------------------+
-```
-
-## 命令参考
-
-### 均匀/随机采样
-
-使用均匀或随机采样选择结构。
-
-```bash
-python Scripts/sample_structures/sample_structures.py <input.xyz> <method> <num_samples> [skip_initial]
+python Scripts/sample_structures/sample_structures.py <input.xyz> <method> <num> [skip]
 
 # 示例
 python Scripts/sample_structures/sample_structures.py dump.xyz uniform 50
 python Scripts/sample_structures/sample_structures.py dump.xyz random 100 500
 ```
 
-**参数：**
-- `input.xyz`：输入轨迹文件
-- `method`：`uniform` 或 `random`
-- `num_samples`：要选择的帧数
-- `skip_initial`：（可选）跳过前 N 帧
-
-**工作原理：**
-- **均匀**：使用 `numpy.linspace` 选择均匀间隔的索引
-- **随机**：使用 `numpy.random.choice` 无放回地选择随机索引
-
-**输出：** `sampled_structures.xyz`
+输出：`sampled_structures.xyz`
 
-### 最远点采样 (FPS) - NepTrain（推荐）
-
-使用 NEP 描述符上的 FPS 选择多样化结构。
+## 最远点采样 (FPS)
 
 ```bash
 python Scripts/sample_structures/neptrain_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
@@ -76,48 +37,26 @@ python Scripts/sample_structures/neptrain_select_structs.py <sample.xyz> <train.
 python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
 ```
 
-**选择方法（交互式）：**
-1. **最小距离**：选择直到与现有训练集的最大距离低于阈值
-2. **结构数量**：选择 `min_select` 到 `max_select` 个结构
-
-**输出：**
-- `selected.xyz`
-- `select.png`（PCA 可视化）
-- `pca_sample.txt`, `pca_train.txt`, `pca_selected.txt`
+输出：`selected.xyz`, `select.png`
 
-**引用**：Chen et al., Comput. Phys. Commun., 2025, 317, 109859
-
-### 最远点采样 (FPS) - PyNEP（已弃用）
+## 结构扰动
 
 ```bash
-python Scripts/sample_structures/pynep_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
-```
-
-**注意**：PyNEP 包不再积极维护。请使用 NepTrain（方法 203）。
-
-### 结构扰动
-
-为训练数据生成扰动结构。
-
-```bash
-python Scripts/sample_structures/perturb_structure.py <input.vasp> <pert_num> <cell_pert> <atom_pert> <style>
+python Scripts/sample_structures/perturb_structure.py <input.vasp> <num> <cell_pert> <atom_pert> <style>
 
 # 示例
 python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
 ```
 
-**参数：**
-- `input.vasp`：POSCAR/CONTCAR 文件
-- `pert_num`：扰动结构数量（如 20）
+参数：
+- `num`：扰动结构数量
 - `cell_pert`：晶胞扰动比例（如 0.03 = 3%）
-- `atom_pert`：原子扰动距离（Å）（如 0.2）
-- `style`：`normal`、`uniform` 或 `const`
-
-**输出：** `POSCAR_01.vasp`, `POSCAR_02.vasp`, ..., `POSCAR_<N>.vasp`
+- `atom_pert`：原子扰动距离（埃）
+- `style`：`normal`, `uniform` 或 `const`
 
-### 力偏差选择
+输出：`POSCAR_01.vasp`, `POSCAR_02.vasp`, ...
 
-从主动学习中选择具有高力偏差的结构。
+## 力偏差选择
 
 ```bash
 python Scripts/sample_structures/select_max_modev.py <top_n> <min_deviation>
@@ -126,96 +65,24 @@ python Scripts/sample_structures/select_max_modev.py <top_n> <min_deviation>
 python Scripts/sample_structures/select_max_modev.py 200 0.15
 ```
 
-**必需文件：**
-- `active.out` - 每个结构的最大力偏差（来自 GPUMD 的 `active` 命令）
-- `active.xyz` - 对应的结构
+需要文件：`active.out`, `active.xyz`
 
-**输出：** `selected.xyz`
+输出：`selected.xyz`
 
-### 帧范围提取
-
-从轨迹中提取帧范围。
+## 帧范围提取
 
 ```bash
-python Scripts/sample_structures/frame_range.py <input.xyz> <start_fraction> <end_fraction>
+python Scripts/sample_structures/frame_range.py <input.xyz> <start> <end>
 
-# 示例：提取前 80% 的帧
+# 示例：前 80% 的帧
 python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
 ```
 
-**输出：** `dump_0.00_0.80.xyz`
-
-## 常见工作流程
-
-### 训练数据准备
-
-```bash
-# 1. 运行 MD 模拟
-# ... 生成轨迹 ...
-
-# 2. 按距离过滤
-gpumdkit.sh -min_dist_pbc dump.xyz
-gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
-
-# 3. 采样多样化结构
-gpumdkit.sh  # 选择: 2) Sample Structures -> 203
-
-# 4. 添加到训练集
-cat selected.xyz >> train.xyz
-```
-
-### 主动学习数据选择
-
-```bash
-# 1. 使用当前 NEP 运行 MD
-# ... 生成 active.out 和 active.xyz ...
-
-# 2. 选择高偏差结构
-python Scripts/sample_structures/select_max_modev.py 100 0.1
-
-# 3. 或使用 FPS 获取多样性
-python Scripts/sample_structures/neptrain_select_structs.py active.xyz train.xyz nep.txt
-```
-
-### 初始数据的结构扰动
-
-```bash
-# 1. 从平衡结构开始
-# 2. 生成扰动
-python Scripts/sample_structures/perturb_structure.py POSCAR 50 0.05 0.3 uniform
-
-# 3. 对扰动结构运行 DFT
-# ... DFT 计算 ...
-
-# 4. 添加到训练集
-```
-
 ## 依赖
 
-| 方法 | 必需的包 |
-|------|----------|
-| 均匀/随机 | `numpy`, `ase` |
-| FPS (NepTrain) | `numpy`, `ase`, `matplotlib`, `scikit-learn`, `scipy`, `NepTrain` |
-| FPS (PyNEP) | `numpy`, `ase`, `matplotlib`, `scikit-learn`, `pynep` |
-| 扰动 | `dpdata` |
-| 力偏差 | `numpy`, `ase` |
-
-安装依赖：
-```bash
-pip install numpy ase matplotlib scikit-learn scipy dpdata
-pip install neptrain  # 用于 FPS by NepTrain
-```
-
-## 重要提示
-
-1. **FPS 是首选**：最远点采样提供比均匀/随机更好的多样性
-2. **NepTrain 优于 PyNEP**：NepTrain 积极维护；PyNEP 已弃用
-3. **采样前先过滤**：首先删除不合理的结构（太近、太大）
-4. **帧索引从 0 开始**：第一帧索引为 0
-5. **输出是 extxyz**：所有采样方法输出 extxyz 格式
-
-## 参见
-
-- [格式转换](format_conversion.md) - 转换文件格式
-- [分析工具](analyzers.md) - 过滤和分析结构
-- [NEP 训练指南](nep_training.md) - 完整的训练工作流
+| 方法 | 包 |
+|------|-----|
+| 均匀/随机 | numpy, ase |
+| FPS | numpy, ase, matplotlib, scikit-learn, scipy, NepTrain |
+| 扰动 | dpdata |
+| 力偏差 | numpy, ase |
diff --git a/docs/tutorials2/zh/visualization.md b/docs/tutorials2/zh/visualization.md
index 41e9842..cd58dbe 100644
--- a/docs/tutorials2/zh/visualization.md
+++ b/docs/tutorials2/zh/visualization.md
@@ -1,226 +1,106 @@
-# 可视化指南
-
 <div align="center">
+  <h1>可视化</h1>
   <p>
-    <strong>中文</strong> | <a href="../en/visualization.md">English</a>
+    <strong>简体中文</strong> | <a href="../en/visualization.md">English</a>
   </p>
 </div>
 
-本指南介绍 GPUMDkit 中的所有绘图和可视化工具。
+模拟结果的绘图和可视化工具。
 
 ## 快速参考
 
 ```bash
-gpumdkit.sh -plt <类型>              # 交互式显示图表
+gpumdkit.sh -plt <类型>              # 显示图表
 gpumdkit.sh -plt <类型> save         # 保存为 PNG
-gpumdkit.sh -plt <类型> -h           # 获取特定图表的帮助
+gpumdkit.sh -plt <类型> -h           # 获取帮助
 ```
 
-## 图表类别
-
-### NEP 训练和评估（12 种图表类型）
-
-| 命令 | 输入文件 | 描述 |
-|------|----------|------|
-| `train` | `loss.out`, `*_train.out` | 训练损失曲线和对比图 |
-| `prediction` / `test` | `*_test.out` | 测试集对比图 |
-| `train_test` | `*_train.out`, `*_test.out` | 组合训练/测试对比图 |
-| `parity_density` | `*_train.out` | 基于密度的对比图（大数据集） |
-| `train_density` | `loss.out`, `*_train.out` | 带密度可视化的训练 |
-| `force_errors` | `force_train.out` | 力误差分析 |
-| `restart` | `nep.restart` | NEP 重启文件可视化 |
-| `charge` | `charge_train.out` | 电荷分布 (qNEP) |
-| `born_charge` / `bec` | `bec_train.out`, `bec_test.out` | Born 有效电荷 |
-| `dimer` | NEP 模型 | 二聚体相互作用曲线 |
-| `des` | `descriptors.npy` | 描述符 PCA/UMAP 可视化 |
-| `lr` | `loss.out` (gnep) | 学习率衰减 |
+## NEP 训练图表
+
+| 命令 | 描述 |
+|------|------|
+| `train` | 训练损失曲线和对比图 |
+| `prediction` / `test` | 测试集对比图 |
+| `train_test` | 组合训练/测试对比图 |
+| `force_errors` | 力误差分析 |
+| `des` | 描述符 PCA/UMAP 可视化 |
+| `dimer` | 二聚体相互作用曲线 |
+| `charge` | 电荷分布 (qNEP) |
+| `born_charge` / `bec` | Born 有效电荷 |
 
 ```bash
-# 训练结果
 gpumdkit.sh -plt train
 gpumdkit.sh -plt prediction
 gpumdkit.sh -plt force_errors
-
-# 描述符可视化（需要预先计算）
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
 gpumdkit.sh -plt des pca
-gpumdkit.sh -plt des umap
-
-# 二聚体图
 gpumdkit.sh -plt dimer Li Li nep.txt
 ```
 
-### 传输属性（9 种图表类型）
+## 传输属性图表
 
-| 命令 | 输入文件 | 描述 |
-|------|----------|------|
-| `msd` | `msd.out` | 均方位移 |
-| `msd_conv` | `msd_step*.out` | MSD 收敛检查 |
-| `msd_all` | `msd.out` (all_groups) | 每个物种的 MSD |
-| `sdc` | `msd.out` | 自扩散系数 |
-| `msd_sdc` | `msd.out` | MSD 和 SDC 组合 |
-| `sigma` / `arrhenius_sigma` | `*K/` 目录 | Arrhenius 离子电导率 |
-| `D` / `arrhenius_d` | `*K/` 目录 | Arrhenius 扩散率 |
-| `sigma_xyz` | `*K/` 目录 | 方向性 Arrhenius 电导率 |
-| `D_xyz` | `*K/` 目录 | 方向性 Arrhenius 扩散率 |
+| 命令 | 描述 |
+|------|------|
+| `msd` | 均方位移 |
+| `sdc` | 自扩散系数 |
+| `msd_sdc` | MSD 和 SDC 组合 |
+| `arrhenius_sigma` | Arrhenius 离子电导率 |
+| `arrhenius_d` | Arrhenius 扩散率 |
 
 ```bash
-# MSD 和扩散
 gpumdkit.sh -plt msd
 gpumdkit.sh -plt sdc
-gpumdkit.sh -plt msd_sdc
-
-# 所有物种的 MSD（需要在 run.in 中设置 all_groups）
-gpumdkit.sh -plt msd_all Li P S
-
-# Arrhenius 图（需要按温度组织的目录）
-# 目录结构：300K/, 350K/, 400K/, ... 每个包含 msd.out
 gpumdkit.sh -plt arrhenius_sigma
 gpumdkit.sh -plt arrhenius_d
 ```
 
-### 结构分析（10 种图表类型）
-
-| 命令 | 输入文件 | 描述 |
-|------|----------|------|
-| `thermo` | `thermo.out` | 热力学属性 |
-| `thermo2` | `thermo.out` | 替代热力学样式 |
-| `thermo3` | `thermo.out` | 第三种热力学样式 |
-| `rdf` | `rdf.out` | 径向分布函数 |
-| `rdf_pmf` | `rdf.out` | RDF + 平均力势 |
-| `vac` | `sdc.out` | 速度自相关 |
-| `cohesive` | `cohesive.out` | 内聚能曲线 |
-| `net_force` | extxyz 文件 | 净力分布 |
-| `doas` | `doas.out` | 原子态密度 |
-| `plane-grid` | `model.xyz`, `displacements.dat` | 位移网格可视化 |
+## 结构图表
+
+| 命令 | 描述 |
+|------|------|
+| `thermo` | 热力学属性 |
+| `rdf` | 径向分布函数 |
+| `rdf_pmf` | RDF + 平均力势 |
+| `vac` | 速度自相关 |
+| `doas` | 原子态密度 |
+| `net_force` | 净力分布 |
 
 ```bash
-# 热力学属性
 gpumdkit.sh -plt thermo
-
-# RDF 分析
 gpumdkit.sh -plt rdf
-gpumdkit.sh -plt rdf 2              # 特定列
-gpumdkit.sh -plt rdf_pmf 300        # 300K 时的 PMF
-
-# DOAS 可视化（需要预先计算）
 gpumdkit.sh -plt doas doas.out Li
-
-# 平面网格位移
-gpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Pb Sr
+gpumdkit.sh -plt net_force train.xyz
 ```
 
-### 热传输（4 种图表类型）
+## 热传输图表
 
-| 命令 | 输入文件 | 描述 |
-|------|----------|------|
-| `emd` | EMD 输出 | EMD 热导率 |
-| `nemd` | NEMD 输出 | NEMD 热传输 |
-| `hnemd` | HNEMD 输出 | HNEMD 热传输 |
-| `viscosity` | `viscosity.out` | 粘度分量 |
+| 命令 | 描述 |
+|------|------|
+| `emd` | EMD 热导率 |
+| `nemd` | NEMD 热传输 |
+| `hnemd` | HNEMD 热传输 |
+| `viscosity` | 粘度分量 |
 
 ```bash
-# EMD 热导率
 gpumdkit.sh -plt emd x
-
-# NEMD 热传输
-# 参数：real_length scale_eff_size cutoff_freq
 gpumdkit.sh -plt nemd <real_length> <scale_eff_size> <cutoff_freq> save
-
-# HNEMD 热传输
 gpumdkit.sh -plt hnemd <scale_eff_size> <cutoff_freq> save
-
-# 粘度
-gpumdkit.sh -plt viscosity save
-```
-
-### 声子（1 种图表类型）
-
-| 命令 | 输入文件 | 描述 |
-|------|----------|------|
-| `pdos` | `model.xyz`, `run.in`, `dos.out`, `mvac.out` | 声子态密度和热容 |
-
-```bash
-gpumdkit.sh -plt pdos save
-```
-
-## 常见工作流程
-
-### NEP 训练验证
-
-```bash
-# 1. 绘制训练损失
-gpumdkit.sh -plt train
-
-# 2. 检查测试预测
-gpumdkit.sh -plt prediction
-
-# 3. 分析力误差
-gpumdkit.sh -plt force_errors
-
-# 4. 可视化描述符
-gpumdkit.sh -plt des pca
-```
-
-### 扩散分析
-
-```bash
-# 1. 绘制 MSD
-gpumdkit.sh -plt msd
-
-# 2. 绘制自扩散系数
-gpumdkit.sh -plt sdc
-
-# 3. 组合 MSD-SDC 图
-gpumdkit.sh -plt msd_sdc
-
-# 4. Arrhenius 分析（多温度）
-gpumdkit.sh -plt arrhenius_d
-```
-
-### 热传输
-
-```bash
-# 1. 绘制热力学属性
-gpumdkit.sh -plt thermo
-
-# 2. 绘制热导率
-gpumdkit.sh -plt emd x
-
-# 3. 或 NEMD/HNEMD
-gpumdkit.sh -plt nemd 10 1 60 save
 ```
 
 ## 输出文件
 
-| 图表类型 | PNG 文件名（使用 `save`） |
-|----------|---------------------------|
+| 图表 | PNG 文件名 |
+|------|-----------|
 | `train` | `train.png` |
 | `prediction` | `prediction.png` |
-| `train_test` | `train_test.png` |
-| `force_errors` | `force_errors.png` |
-| `des` | `descriptors.png` |
 | `msd` | `msd.png` |
 | `sdc` | `sdc.png` |
-| `msd_sdc` | `MSD_SDC.png` |
 | `thermo` | `thermo.png` |
 | `rdf` | `rdf.png` |
 | `arrhenius_sigma` | `Arrhenius_sigma.png` |
 | `arrhenius_d` | `Arrhenius_D.png` |
-| `emd` | `emd.png` |
-| `nemd` | `nemd.png` |
-| `hnemd` | `hnemd.png` |
-| `viscosity` | `viscosity.png` |
-| `cohesive` | `Cohesive.png` |
 
 ## 依赖
 
-所有绘图脚本需要：
-- `matplotlib`
-- `numpy`
-
-## 参见
-
-- [计算器](calculators.md) - 计算要绘制的属性
-- [分析工具](analyzers.md) - 在绘图前分析数据
-- [NEP 训练指南](nep_training.md) - 完整的训练工作流
+```bash
+pip install matplotlib numpy
+```
diff --git a/docs/tutorials2/zh/workflows.md b/docs/tutorials2/zh/workflows.md
index a2d49fb..14b6e51 100644
--- a/docs/tutorials2/zh/workflows.md
+++ b/docs/tutorials2/zh/workflows.md
@@ -1,12 +1,11 @@
-# 工作流指南
-
 <div align="center">
+  <h1>工作流</h1>
   <p>
-    <strong>中文</strong> | <a href="../en/workflows.md">English</a>
+    <strong>简体中文</strong> | <a href="../en/workflows.md">English</a>
   </p>
 </div>
 
-本指南介绍 GPUMDkit 中的批处理和工作流自动化工具。
+批处理和工作流自动化工具。
 
 ## 可用工作流
 
@@ -17,213 +16,75 @@
 | MD 批处理 (GPUMD) | 302 | GPUMD MD 采样批处理设置 |
 | MD 批处理 (LAMMPS) | 303 | LAMMPS MD 采样批处理设置 |
 
-## 交互模式
-
-```bash
-gpumdkit.sh
-# 选择: 3) Workflow
-```
-
-您将看到：
-
-```
-+---------------------------------------------------------+
-|                      WORKFLOW TOOLS                     |
-+---------------------------------------------------------+
-| 301) SCF batch pretreatment                             |
-| 302) MD sample batch pretreatment (gpumd)               |
-| 303) MD sample batch pretreatment (lmp)                 |
-+---------------------------------------------------------+
-```
-
 ## SCF 批处理
 
-### VASP SCF 批处理
-
-为 VASP 准备批量单点能量/力计算。
+### VASP
 
 ```bash
 gpumdkit.sh  # 选择: 3) Workflow -> 301 -> VASP
 ```
 
-**前提条件：**
-
-1. 将 POSCAR 文件（或单个 `.xyz`）放在当前目录
-2. 准备 `fp/` 目录，包含：
-   - `INCAR`
-   - `POTCAR`
-   - `KPOINTS`
+前提条件：
+1. POSCAR 文件在当前目录
+2. `fp/` 目录包含 INCAR, POTCAR, KPOINTS
 
-**输出结构：**
-
-```
-struct_fp/
-├── POSCAR_1.vasp
-├── POSCAR_2.vasp
-└── ...
-fp/
-├── INCAR
-├── POTCAR
-└── KPOINTS
-<prefix>_1/
-├── POSCAR -> ../struct_fp/POSCAR_1.vasp
-├── POTCAR -> ../fp/POTCAR
-├── INCAR -> ../fp/INCAR
-└── KPOINTS -> ../fp/KPOINTS
-<prefix>_2/
-└── ...
-presub.sh
-```
+输出：`<prefix>_1/`, `<prefix>_2/`, ..., `presub.sh`
 
-### CP2K SCF 批处理
-
-为 CP2K 准备批量单点计算。
+### CP2K
 
 ```bash
-python Scripts/workflow/scf_batch_pretreatment_cp2k.py <extxyz_file> <template.inp> <prefix_name>
-
-# 示例
-python Scripts/workflow/scf_batch_pretreatment_cp2k.py structures.xyz cp2k_template.inp H2O_batch
+python Scripts/workflow/scf_batch_pretreatment_cp2k.py <extxyz> <template.inp> <prefix>
 ```
 
-**前提条件：**
-
-1. 准备 CP2K 输入模板（`cp2k_template.inp`）
-2. 模板应从 `pos.xyz` 读取坐标
-
-**输出结构：**
-
-```
-<prefix>_1/
-├── input.inp
-└── pos.xyz
-<prefix>_2/
-└── ...
-```
+## MD 批处理
 
-## MD 采样批处理
-
-### GPUMD MD 批处理
-
-为 GPUMD 设置批量 MD 模拟。
+### GPUMD
 
 ```bash
 gpumdkit.sh  # 选择: 3) Workflow -> 302
 ```
 
-**前提条件：**
-
-1. 将 POSCAR 文件（或单个 `.xyz`）放在当前目录
-2. 准备 `md/` 目录，包含：
-   - `nep.txt`（NEP 模型）
-   - `run_1.in`, `run_2.in`, ...（GPUMD 输入文件）
+前提条件：
+1. POSCAR 文件在当前目录
+2. `md/` 目录包含 `nep.txt`, `run_*.in`
 
-**输出结构：**
-
-```
-struct_md/
-├── model_1.xyz
-├── model_2.xyz
-└── ...
-md/
-├── nep.txt
-├── run_1.in
-├── run_2.in
-└── ...
-sample_1/
-├── model.xyz -> ../struct_md/model_1.xyz
-├── nep.txt -> ../md/nep.txt
-└── run.in -> ../md/run_1.in
-sample_2/
-└── ...
-presub.sh
-```
+输出：`sample_1/`, `sample_2/`, ..., `presub.sh`
 
-### LAMMPS MD 批处理
-
-为 LAMMPS 设置批量 MD 模拟。
+### LAMMPS
 
 ```bash
 gpumdkit.sh  # 选择: 3) Workflow -> 303
 ```
 
-**前提条件：**
-
-1. 将 POSCAR 文件（或单个 `.xyz`）放在当前目录
-2. 准备 `md/` 目录，包含：
-   - `nep.txt`（NEP 模型）
-   - `lmprun.in`（LAMMPS 输入文件）
-
-**输出结构：**
-
-```
-struct_md/
-├── lammps_1.data
-├── lammps_2.data
-└── ...
-md/
-├── nep.txt
-└── lmprun.in
-sample_1/
-├── lammps.data -> ../struct_md/lammps_1.data
-├── nep.txt -> ../md/nep.txt
-└── lmprun.in -> ../md/lmprun.in
-sample_2/
-└── ...
-presub.sh
-```
-
-## 主动学习工作流
+前提条件：
+1. POSCAR 文件在当前目录
+2. `md/` 目录包含 `nep.txt`, `lmprun.in`
 
-### 概述
+## 主动学习
 
-主动学习通过以下步骤迭代改进 NEP 模型：
-
-1. 使用当前 NEP 模型运行 MD
-2. 选择多样化的结构
-3. 计算 DFT 参考数据
-4. 重新训练 NEP 模型
-
-### 手动主动学习循环
+迭代改进 NEP 模型：
 
 ```bash
-# 步骤 1：使用当前 NEP 进行 MD 采样
+# 1. MD 采样
 gpumdkit.sh  # 选择: 3) Workflow -> 302
 
-# 步骤 2：过滤和采样结构
+# 2. 过滤和采样
 gpumdkit.sh -min_dist_pbc dump.xyz
 gpumdkit.sh -filter_box dump.xyz 13
-gpumdkit.sh  # 选择: 2) Sample Structures -> 203
 
-# 步骤 3：准备 SCF 计算
+# 3. 准备 SCF
 gpumdkit.sh  # 选择: 3) Workflow -> 301
 
-# 步骤 4：运行 DFT 计算（外部）
-
-# 步骤 5：转换和验证
-gpumdkit.sh -out2xyz ./scf_results/
-gpumdkit.sh -range new_data.xyz force
+# 4. 运行 DFT（外部）
 
-# 步骤 6：重新训练 NEP 模型（外部）
+# 5. 重新训练 NEP
 ```
 
-### 可配置参数
-
-| 参数 | 描述 | 示例 |
-|------|------|------|
-| `prefix_name` | 目录前缀 | `LiF_iter01` |
-| `min_dist` | 最小距离过滤 | `1.4` |
-| `box_limit` | 最大盒子大小过滤 | `13` |
-| `max_fp_num` | 最大 DFT 计算数 | `50` |
-| `sample_method` | 采样方法 | `uniform`, `random` 或 `pynep` |
-| `pynep_sample_dist` | FPS 距离阈值 | `0.01` |
-
 ## 示例
 
-### 示例 1：温度依赖的 MD
+### 温度依赖的 MD
 
 ```bash
-# 为多个温度设置目录
 for temp in 300 500 700 900; do
     mkdir -p "${temp}K"
     cp model.xyz "${temp}K/"
@@ -232,49 +93,14 @@ for temp in 300 500 700 900; do
 done
 ```
 
-### 示例 2：高通量筛选
+### 批量结构准备
 
 ```bash
-# 为多个计算准备结构
 for struct in structures/*.vasp; do
     name=$(basename "$struct" .vasp)
     mkdir -p "calc_$name"
     cp "$struct" "calc_$name/POSCAR"
     ln -s ../POTCAR "calc_$name/"
     ln -s ../INCAR "calc_$name/"
-    ln -s ../KPOINTS "calc_$name/"
 done
 ```
-
-### 示例 3：NEP 训练数据生成
-
-```bash
-# 1. 从初始结构开始
-gpumdkit.sh -replicate POSCAR supercell.vasp 3 3 3
-
-# 2. 扰动结构
-python Scripts/sample_structures/perturb_structure.py supercell.vasp 20 0.03 0.2 uniform
-
-# 3. 运行 MD 采样
-gpumdkit.sh  # 选择: 3) Workflow -> 302
-
-# 4. 选择多样化结构
-gpumdkit.sh  # 选择: 2) Sample Structures -> 203
-
-# 5. 准备 DFT 计算
-gpumdkit.sh  # 选择: 3) Workflow -> 301
-```
-
-## 重要提示
-
-1. **目录结构很重要**：工作流期望特定的目录布局
-2. **使用符号链接**：输出目录使用符号链接以节省磁盘空间
-3. **presub.sh**：生成的提交脚本可能需要为您的集群进行修改
-4. **模板文件**：在批处理之前确保输入模板正确
-5. **备份重要文件**：在运行工作流之前始终备份数据
-
-## 参见
-
-- [格式转换](format_conversion.md) - 转换文件格式
-- [结构采样](sampling.md) - 为训练采样结构
-- [NEP 训练指南](nep_training.md) - 完整的训练工作流

From 7a58b0a5d110fb6d386edda2e0b261442e4abb47 Mon Sep 17 00:00:00 2001
From: yanzihan <yanzihan@westlake.edu.cn>
Date: Fri, 26 Jun 2026 10:27:52 +0800
Subject: [PATCH 10/24] update citation

---
 docs/index.html | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/index.html b/docs/index.html
index 0b038dd..f762b4b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -314,14 +314,14 @@ <h3>Join QQ Group</h3>
                                     </div>
                                     <h3>Citation</h3>
                                 </div>
-                                <a href="https://doi.org/10.48550/arXiv.2603.17367" class="modern-btn outline" target="_blank">
-                                    View on arXiv
+                                <a href="https://doi.org/10.1002/mgea.70074" class="modern-btn outline" target="_blank">
+                                    View on Wiley
                                 </a>
                             </div>
                             <div class="citation-body-modern">
                                 <h4 class="paper-title-modern">GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP</h4>
                                 <div class="paper-meta-modern">
-                                    <span class="meta-text">arXiv.2603.17367</span>
+                                    <span class="meta-text">MGE Advances, 2026, e70074</span>
                                 </div>
                                 <div class="paper-authors-modern">
                                     Zihan Yan, Denan Li, Xin Wu, Zhoulin Liu, Chen Hua, Boyi Situ, Hao Yang, Shengjie Tang, Benrui Tang, Ziyang Wang, Shangzhao Yi, Huan Wang, Dian Huang, Ke Li, Qilin Guo, Zherui Chen, Ke Xu, Yanzhou Wang, Ziliang Wang, Gang Tang, Shi Liu, Zheyong Fan, Yizhou Zhu

From 05d74fefb9cc8229f29db58dc9b6c6d50697c534 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Mon, 29 Jun 2026 15:04:07 +0800
Subject: [PATCH 11/24] update

---
 CONTRIBUTING.md                               |  134 +-
 README.md                                     |   20 +-
 Scripts/README.md                             |   19 +-
 Scripts/analyzer/README.md                    |   36 +-
 Scripts/analyzer/analyze_chem_species.py      |    8 +-
 Scripts/analyzer/charge_balance_check.py      |    2 +-
 .../analyzer/energy_force_virial_analyzer.py  |    3 +-
 Scripts/analyzer/filter_exyz_by_box.py        |    3 +-
 Scripts/analyzer/filter_exyz_by_value.py      |    6 +-
 Scripts/analyzer/find_outliers.py             |   11 +-
 .../analyzer/probability_density_analysis.py  |    4 +-
 Scripts/calculators/README.md                 |   83 +-
 Scripts/calculators/calc_descriptors.py       |   12 +-
 Scripts/calculators/calc_doas.py              |   12 +-
 Scripts/calculators/calc_minimize.py          |   10 +
 .../calculators/calc_properties_with_nep.py   |   10 +
 Scripts/calculators/neb_calculation.py        |   12 +-
 .../calculators/neb_calculation_neptrain.py   |    2 +-
 Scripts/format_conversion/README.md           |  174 +-
 Scripts/format_conversion/add_groups.py       |    4 +-
 Scripts/format_conversion/clean_xyz.py        |    4 +-
 Scripts/format_conversion/exyz2pos.py         |    4 +-
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 31f045c..21122c6 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,5 +1,10 @@
 # Contributing to GPUMDkit
 
+<p align="center">
+  <strong>English</strong>
+  &nbsp;·&nbsp;
+  <a href="./docs/CONTRIBUTING_zh-CN.md">简体中文</a>
+</p>
 
 Thank you for your interest in contributing to `GPUMDkit`! We appreciate your time and effort in helping improve this toolkit. `GPUMDkit` is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.
 
@@ -62,7 +67,9 @@ To maintain code quality and consistency across the project, please adhere to th
 ### Documentation
 
 - Ensure that help messages (e.g., `-h` flags) are clear and accurate.
-- Documentation files in the `docs/` directory will be updated by the maintainers, so you generally don't need to modify them.
+- Tutorial documentation lives in `docs/tutorials/en/` (English) and `docs/tutorials/zh/` (Chinese).
+  If you add a new feature, consider updating the relevant tutorial page.
+- After editing tutorial markdown files, rebuild the HTML with `mkdocs build -f docs/mkdocs.yml`.
 
 ---
 
@@ -124,7 +131,8 @@ Name your branch as you prefer.
 
 The structure of `GPUMDkit` consists of:
 - **`gpumdkit.sh`**: Main entry point (Bash script) handling both interactive menu mode and command-line mode
-- **`Scripts/`**: Python utility scripts organized by functionality
+- **`install.sh`**: Installation script that sets up environment variables and shell configuration
+- **`Scripts/`**: Python and Bash implementation scripts organized by functionality
   - `plt_scripts/`: Plotting scripts
   - `calculators/`: Calculation utilities
   - `format_conversion/`: Format conversion tools
@@ -140,7 +148,12 @@ The structure of `GPUMDkit` consists of:
   - `f5_analyzers.sh`
   - `f6_plots.sh`
   - `f7_utilities.sh`
+- **`skills/`**: AI agent skill definitions (SKILL.md files for opencode/Claude Code integration)
 - **`docs/`**: Documentation files
+  - `tutorials/en/` and `tutorials/zh/`: Bilingual tutorial pages
+  - `mkdocs.yml`: MkDocs configuration for building tutorial HTML
+  - `command_reference.tsv`: Machine-readable command reference
+  - `htmls/`: Generated HTML output from MkDocs
 
 #### Interactive Mode Contributions
 
@@ -163,18 +176,18 @@ To add a new feature accessible through the interactive menu:
    
    Add a new function:
    ```bash
-   function f106_new_converter(){
+   function f111_new_converter(){
    echo " >-------------------------------------------------<"
    echo " | Calling the script in Scripts/format_conversion |"
    echo " | Script: new_converter.py                        |"
    echo " | Developer: Your Name (your@email.com)           |"
    echo " >-------------------------------------------------<"
-   echo " Input the required parameters:"
-   echo " Examp: input.xyz output.lmp"
+   echo " Input <required_param1> <required_param2>"
+   echo " Example: input.xyz output.lmp"
    echo " ------------>>"
-   read -p " " converter_params
+   read -r -a converter_args
    echo " ---------------------------------------------------"
-   python ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py ${converter_params}
+   python ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py "${converter_args[@]}"
    echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py"
    echo " ---------------------------------------------------"
    }
@@ -185,7 +198,7 @@ To add a new feature accessible through the interactive menu:
    # Find the menu() function and update it if needed
    # Find the array_choice array and add your new choice number
    array_choice=(
-       "0" "1" "101" "102" "103" "104" "105" "106"  # Added "106"
+       "0" "1" "101" "102" "103" "104" "105" "106" "107" "108" "109" "110" "111"  # Added "111"
        # ... rest of choices
    )
    ```
@@ -199,9 +212,9 @@ To add a new feature accessible through the interactive menu:
            source ${GPUMDkit_path}/src/f1_format_conversions.sh
            case $choice in
                "1") f1_format_conversion ;;
-               "101") f101_out2xyz ;;
-               # ... existing cases ...
-               "106") f106_new_converter ;;  # Add your case
+                "101") f101_out2xyz ;;
+                # ... existing cases ...
+                "111") f111_new_converter ;;  # Add your case
            esac ;;
        # ...
    esac
@@ -222,36 +235,35 @@ To add a new command-line flag or subcommand:
    # Example: Scripts/analyzer/analyze_bonds.py
    import sys
    
-   def main():
-       if len(sys.argv) != 3:
-           print("Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>")
-           print("Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0")
-           sys.exit(1)
-       
-       input_file = sys.argv[1]
-       cutoff = float(sys.argv[2])
-       
-       # Your implementation here
-       
-   if __name__ == "__main__":
-       main()
+   if len(sys.argv) != 3:
+       print("Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>")
+       print("Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0")
+       sys.exit(1)
+   
+   input_file = sys.argv[1]
+   cutoff = float(sys.argv[2])
+   
+   # Your implementation here
    ```
+   
+   > **Note**: GPUMDkit Python scripts are designed to run directly (not imported as modules).
+   > You may use a `main()` function with `if __name__ == "__main__":` guard if you prefer,
+   > but it is not required. Most existing scripts execute at module level.
 
 3. **Add the command-line flag handler** in `gpumdkit.sh`:
    ```bash
-   # Find the command-line parsing section (after line ~167)
+   # Find the command-line parsing section (the large "case $1 in" block)
    # Add your new flag in the appropriate location
    
    case $1 in
        # ... existing cases ...
        -analyze_bonds)
-           if [ ! -z "$2" ] && [ ! -z "$3" ]; then
-               python ${analyzer_path}/analyze_bonds.py "$2" "$3"
+           if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ]; then
+               python ${analyzer_path}/analyze_bonds.py $2 $3
            else
                echo " Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>"
                echo " Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0"
                echo " Code path: ${analyzer_path}/analyze_bonds.py"
-               exit 1
            fi ;;
        # ... rest of cases ...
    esac
@@ -279,17 +291,23 @@ vim Scripts/utils/completion.sh
 Add your new flag to the `opts` variable:
 ```bash
 # Find the line with local opts=...
-local opts="-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ..."
-#                                                      ^^^^^^^^^^^^^^ Add your flag here
+local opts="-h -help -update -U -clean -time -plt -calc ... -your_new_flag ..."
+#                                                        Add your flag here
 ```
 
-If your flag accepts secondary options (like `-plt` or `-calc`), add a case for it:
+If your flag requires file arguments, add it to the existing file-completion case:
+```bash
+# Find the case for file-requiring flags and add yours with |
+-out2xyz|-out2exyz|-...|-your_new_flag)
+    COMPREPLY=($(compgen -f -- "$cur")) ;;
+```
+
+If your flag accepts secondary options (like `-plt` or `-calc`), add a new case:
 ```bash
 case "$prev" in
     # ... existing cases ...
-    -analyze_bonds)
-        COMPREPLY=($(compgen -f -- "$cur"))  # Complete with filenames
-        ;;
+    -your_new_flag)
+        COMPREPLY=($(compgen -W "option1 option2 option3" -- "$cur")) ;;
     # ... rest of cases ...
 esac
 ```
@@ -298,15 +316,53 @@ esac
 
 - **Shell Scripts**:
   - Use `${variable}` for variable expansion
-  - Write code that is clear and easy to maintain
+  - Use `[ ! -z "$var" ]` for non-empty checks (project convention)
+  - Interactive functions should follow the banner format:
+    ```bash
+    echo " >-------------------------------------------------<"
+    echo " | Calling the script in Scripts/<category>        |"
+    echo " | Script: <script_name>.py                        |"
+    echo " | Developer: <Name> (<email>)                     |"
+    echo " >-------------------------------------------------<"
+    ```
+  - Use `read -r -a varname` for multi-word input, then pass with `"${varname[@]}"`
+  - Shell scripts in `src/` should start with a file header block:
+    ```bash
+    # ============================================================
+    # GPUMDkit <module name> module
+    # Repository: https://github.com/zhyan0603/GPUMDkit
+    # Author: <Name> (<email>)
+    # ============================================================
+    ```
 
 - **Python Scripts**:
   - Write clear, maintainable code
   - Use meaningful variable names
+  - Use `sys.argv` for argument parsing (consistent with most existing scripts)
+  - Provide clear usage messages with `print("Usage: ...")` and `print("Example: ...")`
+  - If your script uses heavy/special packages (`NepTrain`, `calorine`, `dpdata`), add a
+    `print_dependency_notice()` function to inform users about citation recommendations
 
 ### Testing Your Changes
 
-Before submitting your contribution:
+Before submitting your contribution, run the relevant validation commands:
+
+```bash
+# Shell syntax checks (always run these)
+bash -n gpumdkit.sh
+find src Scripts -name '*.sh' -exec bash -n {} +
+
+# Python syntax checks (for modified Python files)
+python3 -m py_compile path/to/modified_script.py
+
+# MkDocs build (if you modified documentation)
+mkdocs build -f docs/mkdocs.yml
+
+# Check for trailing whitespace issues
+git diff --check
+```
+
+Then test functionality:
 
 1. **Test interactive mode** (if applicable):
    ```bash
@@ -345,10 +401,10 @@ Write clear, descriptive commit messages that explain what you changed. There ar
    git commit -m "your descriptive message"
    ```
 
-2. **Keep your branch updated** with the upstream `main` branch:
+2. **Keep your branch updated** with the latest `dev` branch:
    ```bash
-   git fetch upstream
-   git rebase upstream/main
+   git fetch origin
+   git rebase origin/dev
    ```
 
 3. **Push your branch** to your fork:
diff --git a/README.md b/README.md
index 0f7596f..e6bf2b4 100644
--- a/README.md
+++ b/README.md
@@ -4,10 +4,10 @@
 <p align="center">
   <strong>English</strong>
   &nbsp;·&nbsp;
-  <a href="./README_zh-CN.md">简体中文</a>
+  <a href="./docs/README_zh-CN.md">简体中文</a>
   &nbsp;·&nbsp;
   <a href="https://zhyan0603.github.io/GPUMDkit/">Website</a> &nbsp;·&nbsp;
-  <a href="https://zhyan0603.github.io/GPUMDkit/htmls/tutorials.html">Documentation</a>
+  <a href="https://zhyan0603.github.io/GPUMDkit/htmls/index.html">Documentation</a>
   &nbsp;·&nbsp;
   <a href="https://zhyan0603.github.io/GPUMDkit/gallery.html">Gallery</a>
   &nbsp;
@@ -102,7 +102,7 @@ There are two options, <u>*interactive mode*</u> and <u>*command-line mode*</u>
              | |_| |  __/| |_| | |  | | |_| |   <| | |_
               \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
     
-              GPUMDkit Version 1.5.5 (dev) (2026-05-10)
+              GPUMDkit Version 1.5.6 (dev) (2026-06-17)
         Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
      Main Contributors: Denan LI, Xin WU, Zhoulin LIU & Chen HUA
     
@@ -132,7 +132,7 @@ the help information:
 
 ```
 +-------------------------------------------------------------------------------------------------------+
-|                          GPUMDkit 1.5.5 (dev) (2026-05-10) Command Help                               |
+|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
 +-------------------------------------------------------------------------------------------------------+
 |                                          MAIN FUNCTIONS                                               |
 +-------------------------------------------------------------------------------------------------------+
@@ -158,8 +158,8 @@ the help information:
 | -chem_species Analyze chemical species        | -cbc               Charge balance check               |
 | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-| -pynep        FPS sampling by PyNEP           |                                                       |
+| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
+| -pynep        Deprecated PyNEP sampling       |                                                       |
 +-------------------------------------------------------------------------------------------------------+
 | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
 +-------------------------------------------------------------------------------------------------------+
@@ -175,7 +175,7 @@ the help information:
 
 ```
  +-----------------------------------------------------------------------------------------------+
- |                     GPUMDkit 1.5.5 (dev) (2026-05-10) PLOT & VISUALIZATION TOOLS              |
+ |                     GPUMDkit 1.5.6 (dev) (2026-06-17) PLOT & VISUALIZATION TOOLS              |
  +-----------------------------------------------------------------------------------------------+
  |  Usage: gpumdkit.sh -plt <type>                        Help: gpumdkit.sh -plt <type> -h       |
  +-----------------------------------------------------------------------------------------------+
@@ -265,13 +265,13 @@ You can also save images as PNG if your device doesn't support visualization:
 gpumdkit.sh -plt thermo save
 ```
 
-Refer to our [documentation](https://zhyan0603.github.io/GPUMDkit/htmls/tutorials.html) for more detailed examples and command options.
+Refer to our [documentation](https://zhyan0603.github.io/GPUMDkit/) for more detailed examples and command options.
 
 #### Custom Commands
 
 `GPUMDkit` now supports custom commands via `~/.gpumdkit.in`.
 
-You can add your own shortcuts (e.g., `gpumdkit.sh -yourcommand`) by defining some functions in this file. This allows you to extend `GPUMDkit` with personal scripts. See [here](https://zhyan0603.github.io/GPUMDkit/htmls/custom_commands.html) for the detail usage.
+You can add your own shortcuts (e.g., `gpumdkit.sh -yourcommand`) by defining functions in this file. This allows you to extend `GPUMDkit` with personal scripts. See [custom command documentation](https://zhyan0603.github.io/GPUMDkit/) for details.
 
 #### Tab Completion Support
 
@@ -297,4 +297,4 @@ Also, welcome to join our QQ group ([825696376](https://qun.qq.com/universal-sha
 
 **GPUMDkit** is an open-source tool freely available for everyone. If you find it helpful in your research or workflow, please ⭐ [star us on GitHub](https://github.com/zhyan0603/GPUMDkit). Additionally, if GPUMDkit contributes to your published work, please cite our paper:
 
-> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, e70074](https://doi.org/10.1002/mgea.70074). 
\ No newline at end of file
+> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, e70074](https://doi.org/10.1002/mgea.70074).
diff --git a/Scripts/README.md b/Scripts/README.md
index 52db86f..5b5a8df 100644
--- a/Scripts/README.md
+++ b/Scripts/README.md
@@ -88,8 +88,8 @@ Structure sampling and selection tools:
 
 **Quick Start:**
 ```bash
-gpumdkit.sh -pynep   # PyNEP sampling
-python sample_structures.py train.xyz uniform 100  # Uniform sampling
+gpumdkit.sh          # Select 2) Sample Structures, then 203) NepTrain sampling
+python Scripts/sample_structures/sample_structures.py train.xyz uniform 100
 ```
 
 ### 🛠️ [utils/](utils/README.md)
@@ -142,14 +142,16 @@ Navigate through numbered menus to access different functionalities.
        | |_| |  __/| |_| | |  | | |_| |   <| | |_
         \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
 
-        GPUMDkit Version 1.4.2 (dev) (2025-12-17)
+        GPUMDkit Version 1.5.6 (dev) (2026-06-17)
   Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+ Main Contributors: Denan LI, Xin WU, Zhoulin LIU & Chen HUA
 
  ----------------------- GPUMD -----------------------
- 1) Format Conversion          2) Sample Structures
- 3) Workflow                   4) Calculators
- 5) Analyzer                   6) Developing ...
- 0) Quit!
+  1) Format Conversion          2) Sample Structures
+  3) Workflow                   4) Calculators
+  5) Analyzer                   6) Visualization
+  7) Utilities                  8) Developing...
+  0) Exit
  ------------>>
  Input the function number:
 ```
@@ -186,7 +188,8 @@ See [CONTRIBUTING.md](../CONTRIBUTING.md) for detailed contribution guidelines.
 
 Different scripts have varying dependencies. Common requirements include:
 - **Python 3.x** with packages: `numpy`, `matplotlib`, `ase`
-- **Optional**: `calorine`, `pynep`, `neptrain`,`ovito` (for specific calculators)
+- **Optional for specific tools**: `NepTrain`, `calorine`, `dpdata`
+- **Deprecated compatibility**: PyNEP-based sampling is still kept, but only through `gpumdkit.sh -pynep`; function 203 with NepTrain is preferred in the interactive menu.
 
 Check individual subdirectory READMEs for specific requirements.
 
diff --git a/Scripts/analyzer/README.md b/Scripts/analyzer/README.md
index 48e340d..d15c48f 100644
--- a/Scripts/analyzer/README.md
+++ b/Scripts/analyzer/README.md
@@ -23,7 +23,7 @@ Access analyzers through `gpumdkit.sh` using various flags or run scripts direct
 
 ---
 
-This script analyze the composition of your `extxyz` file.
+This script analyzes the composition of your `extxyz` file.
 
 #### Usage
 
@@ -298,33 +298,7 @@ python find_outliers.py
  Enter stress RMSE threshold (GPa): 0.03
 ```
 
-After that, you will get `selected.xyz`, `remained.xyz`, and `slected_remained.png`
-
-
-
-### filter_exyz_by_value.py
-
----
-
-This script filter the structures by min_dist.
-
-#### Usage
-
-```sh
-python filter_exyz_by_value.py <extxyz_file> <min_dist>
-```
-
-#### Example
-
-```sh
-python filter_exyz_by_value.py dump.xyz 1.4
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -filter_value dump.xyz 1.4
-```
+After that, you will get `selected.xyz`, `remained.xyz`, and `selected_remained.png`
 
 
 
@@ -332,12 +306,12 @@ gpumdkit.sh -filter_value dump.xyz 1.4
 
 ---
 
-This script filter the structures by box limit.
+This script filters the structures by box limit.
 
 #### Usage
 
 ```
-python filter_exyz_by_box.py <extxyz_file> <min_dist>
+python filter_exyz_by_box.py <extxyz_file> <edge_limit>
 ```
 
 #### Example
@@ -358,7 +332,7 @@ gpumdkit.sh -filter_box dump.xyz 20
 
 ---
 
-This script filter the structures by specified value.
+This script filters the structures by specified value.
 
 #### Usage
 
diff --git a/Scripts/analyzer/analyze_chem_species.py b/Scripts/analyzer/analyze_chem_species.py
index 51f43fb..4a3877a 100644
--- a/Scripts/analyzer/analyze_chem_species.py
+++ b/Scripts/analyzer/analyze_chem_species.py
@@ -9,9 +9,9 @@
 Category:   Analyzer Scripts
 Purpose:    Identify all unique chemical elements present in an extxyz
             trajectory.
-Usage:      python analyze_chem_species.py <file.xyz>
+Usage:      python analyze_chem_species.py <input.xyz>
 Arguments:
-  file.xyz  Input extxyz file
+  input.xyz  Input extxyz file
 Output:
   List of unique chemical elements sorted by atomic number
 Author:     Zihan YAN (yanzihan@westlake.edu.cn)
@@ -27,7 +27,7 @@
 try:
     atoms_list = read(sys.argv[1], index=':')
 except IndexError:
-    print("Usage: python analyzer.py <filename.extxyz>")
+    print("Usage: python analyze_chem_species.py <input.xyz>")
     sys.exit(1)
 
 # Identify all unique elements present across all frames
@@ -41,4 +41,4 @@
 # Display results
 print(f'Total unique elements: {len(sorted_elements)}')
 print('Element list (Periodic Table order):')
-print(' '.join(sorted_elements))
\ No newline at end of file
+print(' '.join(sorted_elements))
diff --git a/Scripts/analyzer/charge_balance_check.py b/Scripts/analyzer/charge_balance_check.py
index 83c9e3c..cbbf2ab 100644
--- a/Scripts/analyzer/charge_balance_check.py
+++ b/Scripts/analyzer/charge_balance_check.py
@@ -77,7 +77,7 @@ def process_structure(idx_atoms):
 def main():
     # Check if input file is provided
     if len(sys.argv) != 2:
-        print("Usage: python process_structures.py <input.extxyz>", file=sys.stderr)
+        print("Usage: python charge_balance_check.py <input.extxyz>", file=sys.stderr)
         sys.exit(1)
     
     input_file = sys.argv[1]
diff --git a/Scripts/analyzer/energy_force_virial_analyzer.py b/Scripts/analyzer/energy_force_virial_analyzer.py
index 7137c26..5e275a1 100644
--- a/Scripts/analyzer/energy_force_virial_analyzer.py
+++ b/Scripts/analyzer/energy_force_virial_analyzer.py
@@ -65,7 +65,7 @@ def plot_histogram(values, property_name):
 if __name__ == "__main__":
     # Check if the required arguments are provided
     if len(sys.argv) < 3:
-        print("Usage: python script.py <filename> <property> [hist]")
+        print("Usage: python energy_force_virial_analyzer.py <filename> <property> [hist]")
         sys.exit(1)
     
     filename = sys.argv[1]
@@ -84,4 +84,3 @@ def plot_histogram(values, property_name):
     # Plot histogram if requested
     if plot_hist:
         plot_histogram(values, property_name)
-
diff --git a/Scripts/analyzer/filter_exyz_by_box.py b/Scripts/analyzer/filter_exyz_by_box.py
index 1cf71d6..9eafab8 100644
--- a/Scripts/analyzer/filter_exyz_by_box.py
+++ b/Scripts/analyzer/filter_exyz_by_box.py
@@ -49,7 +49,7 @@ def filter_frames(input_file, output_file, edge_limit):
 
 if __name__ == "__main__":
     if len(sys.argv) != 3:
-        print("Usage: python script.py <input_file> <edge_limit>")
+        print("Usage: python filter_exyz_by_box.py <input_file> <edge_limit>")
         sys.exit(1)
 
     input_file = sys.argv[1]
@@ -57,4 +57,3 @@ def filter_frames(input_file, output_file, edge_limit):
     edge_limit = float(sys.argv[2])
 
     filter_frames(input_file, output_file, edge_limit)
-
diff --git a/Scripts/analyzer/filter_exyz_by_value.py b/Scripts/analyzer/filter_exyz_by_value.py
index b97728b..59f8f1b 100644
--- a/Scripts/analyzer/filter_exyz_by_value.py
+++ b/Scripts/analyzer/filter_exyz_by_value.py
@@ -15,7 +15,7 @@
   threshold   Maximum allowed value for the specified property
 Output:
   filtered.xyz
-Author:     Zihan YAN (yanzihan@westlake.edu.cn)X
+Author:     Zihan YAN (yanzihan@westlake.edu.cn)
 Last-modified: 2026-05-16
 =============================================================================
 """
@@ -57,6 +57,6 @@ def main():
 
 if __name__ == "__main__":
     if len(sys.argv) != 4:
-        print("Usage: python script.py <input_file> <property> <threshold>")
+        print("Usage: python filter_exyz_by_value.py <input_file> <property> <threshold>")
         sys.exit(1)
-    main()
\ No newline at end of file
+    main()
diff --git a/Scripts/analyzer/find_outliers.py b/Scripts/analyzer/find_outliers.py
index 7778ec9..5e87669 100644
--- a/Scripts/analyzer/find_outliers.py
+++ b/Scripts/analyzer/find_outliers.py
@@ -30,6 +30,7 @@
 """
 
 import sys
+import os
 import matplotlib.pyplot as plt
 import numpy as np
 
@@ -104,6 +105,14 @@ def select_outliers(rmse_func, err_func, thresh, n_struct):
     return selected
 
 # Load data
+required_files = ['energy_train.out', 'force_train.out', 'stress_train.out', 'train.xyz']
+for f in required_files:
+    if not os.path.exists(f):
+        print(f"Error: Required file '{f}' not found.")
+        print(f"Please ensure the following files exist in the current directory:")
+        print(f"  train.xyz, energy_train.out, force_train.out, stress_train.out")
+        sys.exit(1)
+
 energy_train = np.loadtxt('energy_train.out')
 force_train = np.loadtxt('force_train.out')
 stress_train = np.loadtxt('stress_train.out')
@@ -259,4 +268,4 @@ def calculate_limits(data1, data2, padding=0.08):
 # Adjust layout
 plt.tight_layout()
 fig.subplots_adjust(top=0.968, bottom=0.16, left=0.086, right=0.983, hspace=0.2, wspace=0.25)
-plt.savefig('slected_remained.png', dpi=300)
+plt.savefig('selected_remained.png', dpi=300)
diff --git a/Scripts/analyzer/probability_density_analysis.py b/Scripts/analyzer/probability_density_analysis.py
index 7abc234..c707e66 100644
--- a/Scripts/analyzer/probability_density_analysis.py
+++ b/Scripts/analyzer/probability_density_analysis.py
@@ -30,7 +30,7 @@
 
 # Check if required arguments are provided
 if len(sys.argv) != 5:
-    print("Usage: python script.py <ref_struct> <trajectory_file> <species> <interval>")
+    print("Usage: python probability_density_analysis.py <ref_struct> <trajectory_file> <species> <interval>")
     sys.exit(1)
 
 # Parse command-line arguments
@@ -55,4 +55,4 @@
 )
 
 # Save probability density to CHGCAR file
-pda.to_chgcar(filename=f"probability_density_{interval}.vasp")
\ No newline at end of file
+pda.to_chgcar(filename=f"probability_density_{interval}.vasp")
diff --git a/Scripts/calculators/README.md b/Scripts/calculators/README.md
index 1ec3346..d69a4c5 100644
--- a/Scripts/calculators/README.md
+++ b/Scripts/calculators/README.md
@@ -93,7 +93,7 @@ Calculates energies, forces, and stresses for structures using a NEP model. You
 
 ***Note that you must know what you are doing and this is not a substitute for DFT calculations.***
 
-Unless you have a well-trained NEP model and you want to use it as a DFT surrogate, you probably shouldn't use this feature. See [this article]([ https://doi.org/10.48550/arXiv.2504.15925](https://doi.org/10.48550/arXiv.2504.15925)) if you are interesting in it.
+Unless you have a well-trained NEP model and you want to use it as a DFT surrogate, you probably shouldn't use this feature. See [this article](https://doi.org/10.48550/arXiv.2504.15925) if you are interested in it.
 
 #### Input Files
 - A clean structure file in `extxyz` format with energy, force, and virial/stress. 
@@ -168,7 +168,7 @@ gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
 - **Model comparison**: Compare descriptor distributions across different models
 
 #### Reference
-See [arXiv:2504.15925](https://doi.org/10.48550/arXiv.2504.15925) if you are interesting in it.
+See [arXiv:2504.15925](https://doi.org/10.48550/arXiv.2504.15925) if you are interested in it.
 
 ---
 
@@ -200,8 +200,8 @@ python calc_doas.py <input.xyz> <nep.txt> <doas.out>
 gpumdkit.sh -calc doas structures.xyz nep.txt doas.out
 
 # Visualize results
-gpumdkit.sh -plt doas doas.txt <species>
-gpumdkit.sh -plt doas doas.txt Li
+gpumdkit.sh -plt doas doas.out <species>
+gpumdkit.sh -plt doas doas.out Li
 ```
 
 #### Process
@@ -211,7 +211,7 @@ gpumdkit.sh -plt doas doas.txt Li
 4. Groups energies by element type
 5. Outputs distribution for each element
 
-You can also do the `minimize` and atomistic energy calculations in `gpumd`, which is prefered for large-scale structures.
+You can also do the `minimize` and atomistic energy calculations in `gpumd`, which is preferred for large-scale structures.
 
 ---
 
@@ -311,7 +311,12 @@ Performs nudged elastic band (NEB) calculations to find minimum energy pathways
 
 #### Usage
 
-**Direct execution only:**
+**Command-line mode:**
+```bash
+gpumdkit.sh -calc neb <initial.xyz> <final.xyz> <n_images> <nep.txt>
+```
+
+**Direct execution:**
 ```bash
 python neb_calculation.py <initial.xyz> <final.xyz> <n_images> <nep.txt>
 ```
@@ -326,7 +331,7 @@ python neb_calculation.py <initial.xyz> <final.xyz> <n_images> <nep.txt>
 
 ```bash
 # Calculate Li migration pathway with 9 intermediate images
-python neb_calculation.py init.xyz fin.xyz 9 nep.txt
+gpumdkit.sh -calc neb init.xyz fin.xyz 9 nep.txt
 ```
 
 #### Interactive Options
@@ -341,10 +346,12 @@ python neb_calculation.py init.xyz fin.xyz 9 nep.txt
  405) Calc nudged elastic band (NEB) by nep
  406) Build neighbor list
  407) Calc displacement from trajectory
- 408) Calc averaged structure
- 409) Calc octahedral tilt
- 410) Calc polarization for ABO3
- 000) Return to the main menu
+408) Calc averaged structure
+409) Calc octahedral tilt
+410) Calc polarization for ABO3
+411) Minimize structure by nep
+412) Calc mean square displacement (MSD) from trajectory
+000) Return to the main menu
  ------------>>
  Input the function number:
  405
@@ -354,12 +361,64 @@ python neb_calculation.py init.xyz fin.xyz 9 nep.txt
  | Developer: Zhoulin LIU (1776627910@qq.com)      |
  >-------------------------------------------------<
  Input <initial_struct> <final_struct> <n_image> <nep_model>
- Examp: IS.xyz FS.xyz 5 nep.txt
+ Example: IS.xyz FS.xyz 5 nep.txt
  ------------>>
 ```
 
 ---
 
+### calc_minimize.py
+
+Minimizes a structure using a NEP model through `calorine`.
+
+#### Usage
+
+**Command-line mode:**
+```bash
+gpumdkit.sh -calc minimize <structure_file> <nep.txt> [fmax] [max_steps]
+```
+
+**Direct execution:**
+```bash
+python calc_minimize.py <structure_file> <nep.txt> [fmax=0.01] [max_steps=1000]
+```
+
+#### Example
+
+```bash
+gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
+```
+
+The output file is `minimized.xyz`.
+
+---
+
+### calc_msd.py
+
+Calculates mean square displacement (MSD) from an extxyz trajectory for a selected element.
+
+#### Usage
+
+**Command-line mode:**
+```bash
+gpumdkit.sh -calc msd <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]
+```
+
+**Direct execution:**
+```bash
+python calc_msd.py <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]
+```
+
+#### Example
+
+```bash
+gpumdkit.sh -calc msd dump.xyz Li 10
+```
+
+The output file is `msd.out`.
+
+---
+
 ### Additional Requirement For Neighbor/Displacement/Polarization/Tilt/Plane Workflow
 
 The scripts `calc_neighbor_list.py`, `calc_displacement.py`, `calc_averaged_structure.py`, `calc_oct_tilt.py`, `calc_polarization_abo3.py`, and `plt_plane_grid.py` require:
diff --git a/Scripts/calculators/calc_descriptors.py b/Scripts/calculators/calc_descriptors.py
index 5d1850a..b9ea329 100644
--- a/Scripts/calculators/calc_descriptors.py
+++ b/Scripts/calculators/calc_descriptors.py
@@ -28,6 +28,14 @@
 import sys
 import os
 
+
+def print_dependency_notice():
+    print(" This function requires the calorine package.")
+    print(" If you use this function, we recommend citing:")
+    print(" Lindgren et al., J. Open Source Softw. 9, 6264 (2024).")
+    print(" https://doi.org/10.21105/joss.06264")
+
+
 def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, length=50, fill='█'):
     percent = ("{0:." + str(decimals) + "f}").format(100 * (iteration / float(total)))
     filled_length = int(length * iteration // total)
@@ -43,6 +51,8 @@ def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, lengt
 
 input_file, output_file, model_file, target_element = sys.argv[1:5]
 
+print_dependency_notice()
+
 # Check if input and model files exist
 if not os.path.isfile(input_file) or not os.path.isfile(model_file):
     print(" Error: Input file or NEP model file not found.")
@@ -94,4 +104,4 @@ def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, lengt
 
 # Print output summary
 print(f" Saved descriptors to '{output_file}'")
-print(f" Output shape: {all_descriptors.shape} ({all_descriptors.shape[0]} {target_element} atoms)")
\ No newline at end of file
+print(f" Output shape: {all_descriptors.shape} ({all_descriptors.shape[0]} {target_element} atoms)")
diff --git a/Scripts/calculators/calc_doas.py b/Scripts/calculators/calc_doas.py
index 0f6eed3..15cdb48 100644
--- a/Scripts/calculators/calc_doas.py
+++ b/Scripts/calculators/calc_doas.py
@@ -30,11 +30,21 @@
 from calorine.calculators import CPUNEP
 from collections import defaultdict
 
+
+def print_dependency_notice():
+    print(" This function requires the calorine package.")
+    print(" If you use this function, we recommend citing:")
+    print(" Lindgren et al., J. Open Source Softw. 9, 6264 (2024).")
+    print(" https://doi.org/10.21105/joss.06264")
+
+
 # Specify input and output files
 input_file = sys.argv[1]  # Input extxyz file
 model_path = sys.argv[2]  # Path to the model for CPUNEP
 output_file = sys.argv[3]  # Output text file for grouped atomic energies
 
+print_dependency_notice()
+
 # Read input file containing all structures
 structures = read(input_file, index=':')  # Read all frames
 
@@ -77,4 +87,4 @@
             f.write(f"{energy}\n")
         f.write("\n")  # Blank line to separate elements
 
-print(f"Results saved to {output_file}")
\ No newline at end of file
+print(f"Results saved to {output_file}")
diff --git a/Scripts/calculators/calc_minimize.py b/Scripts/calculators/calc_minimize.py
index 2435dc2..c8405eb 100644
--- a/Scripts/calculators/calc_minimize.py
+++ b/Scripts/calculators/calc_minimize.py
@@ -32,6 +32,14 @@
 from calorine.calculators import CPUNEP
 import os
 
+
+def print_dependency_notice():
+    print(" This function requires the calorine package.")
+    print(" If you use this function, we recommend citing:")
+    print(" Lindgren et al., J. Open Source Softw. 9, 6264 (2024).")
+    print(" https://doi.org/10.21105/joss.06264")
+
+
 class TrajectoryCallback:
     """Callback class to save trajectory during optimization."""
     def __init__(self, atoms):
@@ -51,6 +59,8 @@ def main():
         print("  max_steps: Maximum number of optimization steps (default: 1000)")
         sys.exit(1)
 
+    print_dependency_notice()
+
     structure_file = sys.argv[1]  # Structure file (POSCAR or extxyz)
     model_path = sys.argv[2]  # Path to the model for CPUNEP
 
diff --git a/Scripts/calculators/calc_properties_with_nep.py b/Scripts/calculators/calc_properties_with_nep.py
index 12fd12e..546b0ce 100644
--- a/Scripts/calculators/calc_properties_with_nep.py
+++ b/Scripts/calculators/calc_properties_with_nep.py
@@ -27,6 +27,14 @@
 from ase.io import read, write
 from calorine.calculators import CPUNEP
 
+
+def print_dependency_notice():
+    print(" This function requires the calorine package.")
+    print(" If you use this function, we recommend citing:")
+    print(" Lindgren et al., J. Open Source Softw. 9, 6264 (2024).")
+    print(" https://doi.org/10.21105/joss.06264")
+
+
 def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, length=50, fill='█'):
     percent = ("{0:." + str(decimals) + "f}").format(100 * (iteration / float(total)))
     filled_length = int(length * iteration // total)
@@ -39,6 +47,8 @@ def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, lengt
 input_file = sys.argv[1]  # Input file
 output_file = sys.argv[2]  # Output file
 
+print_dependency_notice()
+
 # Read input file containing all structures
 structures = read(input_file, index=':')  # Read all frames
 
diff --git a/Scripts/calculators/neb_calculation.py b/Scripts/calculators/neb_calculation.py
index 6e375a8..8519166 100644
--- a/Scripts/calculators/neb_calculation.py
+++ b/Scripts/calculators/neb_calculation.py
@@ -32,11 +32,21 @@
 from ase.constraints import FixAtoms
 from ase.io import Trajectory, write
 
+
+def print_dependency_notice():
+    print(" This function requires the calorine package.")
+    print(" If you use this function, we recommend citing:")
+    print(" Lindgren et al., J. Open Source Softw. 9, 6264 (2024).")
+    print(" https://doi.org/10.21105/joss.06264")
+
+
 # Check command-line arguments
 if len(sys.argv) != 5:
     print("python neb_calculation.py <initial_structure> <final_structure> <n_image> <nep_model>")
     sys.exit(1)
 
+print_dependency_notice()
+
 initial_file = sys.argv[1]
 final_file = sys.argv[2]
 n_images = int(sys.argv[3])
@@ -234,4 +244,4 @@
 
 plt.savefig('nep_barrier.png', dpi=300)
 print("Energy profile plot saved as nep_barrier.png")
-print(f"Fixed atoms indices saved to {fixed_atoms_file}")
\ No newline at end of file
+print(f"Fixed atoms indices saved to {fixed_atoms_file}")
diff --git a/Scripts/calculators/neb_calculation_neptrain.py b/Scripts/calculators/neb_calculation_neptrain.py
index f371551..a4e3958 100644
--- a/Scripts/calculators/neb_calculation_neptrain.py
+++ b/Scripts/calculators/neb_calculation_neptrain.py
@@ -38,7 +38,7 @@
 # ----------------------------------------------
 
 if len(sys.argv) != 5:
-    print("python neb_calculation.py <initial_structure> <final_structure> <n_image> <nep_model>")
+    print("python neb_calculation_neptrain.py <initial_structure> <final_structure> <n_image> <nep_model>")
     sys.exit(1)
 
 initial_file = sys.argv[1]
diff --git a/Scripts/format_conversion/README.md b/Scripts/format_conversion/README.md
index 47e0259..1b9183d 100644
--- a/Scripts/format_conversion/README.md
+++ b/Scripts/format_conversion/README.md
@@ -24,16 +24,18 @@ The format conversion scripts provide seamless interconversion between:
 | OUTCAR | extxyz | `gpumdkit.sh -out2exyz <dir>` |
 | POSCAR | extxyz | `gpumdkit.sh -pos2exyz <poscar> <xyz>` |
 | extxyz | POSCAR | `gpumdkit.sh -exyz2pos <xyz>` |
-| POSCAR | LAMMPS | `gpumdkit.sh -pos2lmp <poscar> <lmp> <elem...>` |
+| POSCAR | LAMMPS | `gpumdkit.sh -pos2lmp <poscar> <lmp>` |
 | XDATCAR | extxyz | `gpumdkit.sh -xdat2exyz XDATCAR dump.xyz` |
 | LAMMPS dump | extxyz | `gpumdkit.sh -lmp2exyz <dump> <elem...>` |
-| CIF | extxyz | `gpumdkit.sh -cif2exyz <cif>` |
-| CIF | POSCAR | `gpumdkit.sh -cif2pos <cif>` |
+| CIF | extxyz | `gpumdkit.sh -cif2exyz <input.cif> <output.xyz>` |
+| CIF | POSCAR | `gpumdkit.sh -cif2pos <input.cif> <output.vasp>` |
 | Add groups | - | `gpumdkit.sh -addgroup <poscar> <elem...>` |
 | Add weight | - | `gpumdkit.sh -addweight <in> <out> <weight>` |
 | Replicate1 | - | `gpumdkit.sh -replicate input.vasp output.vasp 2 2 2` |
 | Replicate2 | - | `gpumdkit.sh -replicate input.vasp output.vasp <target_num>` |
 | Get frame | - | `gpumdkit.sh -get_frame <extxyz> <index>` |
+| Clean extxyz | - | `gpumdkit.sh -clean_xyz <input.xyz> <output.xyz>` |
+| ASE traj | extxyz | `gpumdkit.sh -traj2exyz <input.traj> <output.xyz>` |
 
 ---
 
@@ -82,8 +84,8 @@ This script adds weight labels to structures.
 python add_weight.py <input_file> <output_file> <new_weight>
 ```
 
-- `<inputfile>`: The path to the input file (e.g., train.xyz).
-- `<outputfile>`: The path to the input file (e.g., train_weighted.xyz).
+- `<input_file>`: The path to the input file (e.g., train.xyz).
+- `<output_file>`: The path to the output file (e.g., train_weighted.xyz).
 - `<new_weight>`: The `weight` you need to change.
 
 #### Example
@@ -208,6 +210,112 @@ This command will split all frames in `extxyz_file` into separate files named `m
 
 
 
+### out2exyz.py
+
+---
+
+This script searches a directory for VASP `OUTCAR` files and writes the converged configurations to `train.xyz` in extxyz format.
+
+#### Usage
+
+```
+python out2exyz.py <directory>
+```
+
+#### Example
+
+```sh
+python out2exyz.py ./
+```
+
+#### Command-Line Mode Example
+
+```
+gpumdkit.sh -out2exyz ./
+```
+
+The output file is `train.xyz`.
+
+
+
+### cif2pos.py
+
+---
+
+This script converts a CIF file to VASP POSCAR format.
+
+#### Usage
+
+```
+python cif2pos.py <input.cif> <output.vasp>
+```
+
+#### Example
+
+```sh
+python cif2pos.py input.cif POSCAR.vasp
+```
+
+#### Command-Line Mode Example
+
+```
+gpumdkit.sh -cif2pos input.cif POSCAR.vasp
+```
+
+
+
+### cif2exyz.py
+
+---
+
+This script converts a CIF file to extxyz format.
+
+#### Usage
+
+```
+python cif2exyz.py <input.cif> <output.xyz>
+```
+
+#### Example
+
+```sh
+python cif2exyz.py input.cif model.xyz
+```
+
+#### Command-Line Mode Example
+
+```
+gpumdkit.sh -cif2exyz input.cif model.xyz
+```
+
+
+
+### xdatcar2exyz.py
+
+---
+
+This script converts a VASP `XDATCAR` trajectory to extxyz format.
+
+#### Usage
+
+```
+python xdatcar2exyz.py <XDATCAR> <output.xyz>
+```
+
+#### Example
+
+```sh
+python xdatcar2exyz.py XDATCAR dump.xyz
+```
+
+#### Command-Line Mode Example
+
+```
+gpumdkit.sh -xdat2exyz XDATCAR dump.xyz
+```
+
+
+
 ### lmp2exyz.py
 
 ---
@@ -243,7 +351,7 @@ It will convert the `dump.data` to `dump.xyz` file
 
 ---
 
-This script will read the `extxyz` file and return the specified frame by index..
+This script will read the `extxyz` file and return the specified frame by index.
 
 #### Usage
 
@@ -270,6 +378,58 @@ You will get the `frame_1000.xyz` file after perform the script.
 
 
 
+### clean_xyz.py
+
+---
+
+This script removes stress, virial, force, and calculator result information from an extxyz file and writes the cleaned structures to a new extxyz file.
+
+#### Usage
+
+```
+python clean_xyz.py <input.xyz> <output.xyz>
+```
+
+#### Example
+
+```sh
+python clean_xyz.py train.xyz train_clean.xyz
+```
+
+#### Command-Line Mode Example
+
+```
+gpumdkit.sh -clean_xyz train.xyz train_clean.xyz
+```
+
+
+
+### traj2exyz.py
+
+---
+
+This script converts an ASE `.traj` file to extxyz format.
+
+#### Usage
+
+```
+python traj2exyz.py <input.traj> <output.xyz>
+```
+
+#### Example
+
+```sh
+python traj2exyz.py input.traj output.xyz
+```
+
+#### Command-Line Mode Example
+
+```
+gpumdkit.sh -traj2exyz input.traj output.xyz
+```
+
+
+
 ## Contributing
 
 To add new format converters:
@@ -277,7 +437,7 @@ To add new format converters:
 1. **Follow naming**: `<source>2<target>.py`
 2. **Handle errors**: Validate input format before processing
 3. **Document**: Add usage to this README
-6. **Update gpumdkit.sh**: Add command-line flag if appropriate
+4. **Update gpumdkit.sh**: Add command-line flag if appropriate
 
 See [CONTRIBUTING.md](../../CONTRIBUTING.md) for detailed guidelines.
 
diff --git a/Scripts/format_conversion/add_groups.py b/Scripts/format_conversion/add_groups.py
index afbe12c..6dba5f9 100644
--- a/Scripts/format_conversion/add_groups.py
+++ b/Scripts/format_conversion/add_groups.py
@@ -8,13 +8,13 @@
 Script:     add_groups.py
 Category:   Format Conversion Scripts
 Purpose:    Add group information to atoms in a structure file based on
-            element types, outputting the result to stdout.
+            element types, outputting the result to model.xyz.
 Usage:      python add_groups.py <input.xyz> <element1> <element2> ...
 Arguments:
   input.xyz   Input structure file
   elementX    Element symbols to assign group indices
 Output:
-  Modified structure with group information (printed to stdout)
+  model.xyz  Structure with group information
 Author:     Zihan YAN (yanzihan@westlake.edu.cn)
 Last-modified: 2026-05-16
 =============================================================================
diff --git a/Scripts/format_conversion/clean_xyz.py b/Scripts/format_conversion/clean_xyz.py
index c9767d2..62faf75 100644
--- a/Scripts/format_conversion/clean_xyz.py
+++ b/Scripts/format_conversion/clean_xyz.py
@@ -9,10 +9,10 @@
 Category:   Format Conversion Scripts
 Purpose:    Remove stress, virial, and force information from an extxyz
             training file, keeping only structural information.
-Usage:      python clean_xyz.py <input.xyz> [output.xyz]
+Usage:      python clean_xyz.py <input.xyz> <output.xyz>
 Arguments:
   input.xyz    Input extxyz training file
-  output.xyz   Output cleaned extxyz file (optional)
+  output.xyz   Output cleaned extxyz file
 Output:
   Cleaned extxyz file with only structural information
 Author:     Zihan YAN (yanzihan@westlake.edu.cn)
diff --git a/Scripts/format_conversion/exyz2pos.py b/Scripts/format_conversion/exyz2pos.py
index 3f1b19b..bf00692 100644
--- a/Scripts/format_conversion/exyz2pos.py
+++ b/Scripts/format_conversion/exyz2pos.py
@@ -8,7 +8,7 @@
 Script:     exyz2pos.py
 Category:   Format Conversion Scripts
 Purpose:    Convert extended XYZ file(s) to VASP POSCAR format(s).
-Usage:      python exyz2pos.py [extxyz_file]
+Usage:      python exyz2pos.py <input.xyz>
 Arguments:
   extxyz_file Input extxyz file (default: train.xyz)
 Output:
@@ -48,4 +48,4 @@ def print_progress_bar(iteration, total, length=50):
     write(poscar_filename, frame)
     print_progress_bar(i + 1, total_frames)
 
-print(f' All frames have been converted.')
\ No newline at end of file
+print(f' All frames have been converted.')
diff --git a/Scripts/format_conversion/out2exyz.py b/Scripts/format_conversion/out2exyz.py
index c634115..72a4c7e 100644
--- a/Scripts/format_conversion/out2exyz.py
+++ b/Scripts/format_conversion/out2exyz.py
@@ -9,7 +9,7 @@
 Category:   Format Conversion Scripts
 Purpose:    Convert VASP OUTCAR files to extended XYZ format with energy,
             forces, stress, and virial information.
-Usage:      python out2exyz.py [directory with OUTCARs]
+Usage:      python out2exyz.py <directory>
 Output:
   Converted structures in extxyz format
 Author:     Zihan YAN (yanzihan@westlake.edu.cn)
@@ -131,4 +131,4 @@ def is_converged(outcar_path):
     for non_conv_filename in non_converged_list:
         print(non_conv_filename)
 else:
-    print(" All calculations are converged!")
\ No newline at end of file
+    print(" All calculations are converged!")
diff --git a/Scripts/plt_scripts/README.md b/Scripts/plt_scripts/README.md
index 7d50d14..6b31e32 100644
--- a/Scripts/plt_scripts/README.md
+++ b/Scripts/plt_scripts/README.md
@@ -418,7 +418,7 @@ gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]
 **Params:**
 
 ```
-real_length   : Real length of heat tranfer zone in nm (set to 'Auto', with auto-calculation)
+real_length   : Real length of heat transfer zone in nm (set to 'Auto', with auto-calculation)
 scale_eff_size: Optional, Scale factor for effective cross-sectional area (default: 1)
                • For 3D bulk systems: use 1
                • For low-dimensional systems with vacuum layer: S_box / S_eff
@@ -683,7 +683,7 @@ For quick reference, here's the complete command list:
 
 ```
  +-----------------------------------------------------------------------------------------------+
- |                     GPUMDkit 1.5.5 (dev) (2026-05-10) PLOT & VISUALIZATION TOOLS              |
+ |                     GPUMDkit 1.5.6 (dev) (2026-06-17) PLOT & VISUALIZATION TOOLS              |
  +-----------------------------------------------------------------------------------------------+
  |  Usage: gpumdkit.sh -plt <type>                        Help: gpumdkit.sh -plt <type> -h       |
  +-----------------------------------------------------------------------------------------------+
diff --git a/Scripts/plt_scripts/plt_descriptors.py b/Scripts/plt_scripts/plt_descriptors.py
index 2b22273..fc73f15 100644
--- a/Scripts/plt_scripts/plt_descriptors.py
+++ b/Scripts/plt_scripts/plt_descriptors.py
@@ -110,7 +110,7 @@ def plot_reduced_data(reduced_splits, labels, method):
 def main():
     # Check command-line arguments
     if len(sys.argv) < 3:
-        print("Usage: python scripts.py <method> <file1.npy> <file2.npy> ...")
+        print("Usage: python plt_descriptors.py <method> <file1.npy> <file2.npy> ...")
         print("Method: 'pca' or 'umap'")
         sys.exit(1)
     
@@ -131,4 +131,4 @@ def main():
     plot_reduced_data(reduced_splits, labels, method)
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()
diff --git a/Scripts/plt_scripts/plt_descriptors_compare.py b/Scripts/plt_scripts/plt_descriptors_compare.py
index aa3133d..c33f80c 100644
--- a/Scripts/plt_scripts/plt_descriptors_compare.py
+++ b/Scripts/plt_scripts/plt_descriptors_compare.py
@@ -30,6 +30,14 @@
 import os
 import matplotlib.pyplot as plt
 
+
+def print_dependency_notice():
+    print(" This function requires the calorine package.")
+    print(" If you use this function, we recommend citing:")
+    print(" Lindgren et al., J. Open Source Softw. 9, 6264 (2024).")
+    print(" https://doi.org/10.21105/joss.06264")
+
+
 plt.rcParams.update({
     "font.family": "sans-serif",
     "font.sans-serif": ["Arial", "DejaVu Sans", "Liberation Sans"],
@@ -46,7 +54,7 @@ def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, lengt
 
 # Check command-line arguments
 if len(sys.argv) < 5:
-    print(" Usage: python calc_descriptors.py method nep.txt element train1.xyz [train2.xyz ...]")
+    print(" Usage: python plt_descriptors_compare.py method nep.txt element train1.xyz [train2.xyz ...]")
     print(" method: 'pca' or 'umap'")
     print(" element: chemical symbol (e.g., Li) or 'total'")
     sys.exit(1)
@@ -54,6 +62,8 @@ def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, lengt
 method, model_file, target_element = sys.argv[1:4]
 xyz_files = sys.argv[4:]
 
+print_dependency_notice()
+
 # Validate method
 if method.lower() not in ['pca', 'umap']:
     print(" Error: Method must be 'pca' or 'umap'.")
@@ -173,4 +183,4 @@ def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, lengt
     print("The plot has been automatically saved as 'descriptors.png'.")
     plt.savefig('descriptors.png', dpi=300)
 else:
-    plt.show()
\ No newline at end of file
+    plt.show()
diff --git a/Scripts/plt_scripts/plt_dimer.py b/Scripts/plt_scripts/plt_dimer.py
index f9541b1..38a31c2 100644
--- a/Scripts/plt_scripts/plt_dimer.py
+++ b/Scripts/plt_scripts/plt_dimer.py
@@ -27,6 +27,14 @@
 from calorine.calculators import CPUNEP
 import sys
 
+
+def print_dependency_notice():
+    print(" This function requires the calorine package.")
+    print(" If you use this function, we recommend citing:")
+    print(" Lindgren et al., J. Open Source Softw. 9, 6264 (2024).")
+    print(" https://doi.org/10.21105/joss.06264")
+
+
 plt.rcParams.update({
     "font.family": "sans-serif",
     "font.sans-serif": ["Arial", "DejaVu Sans", "Liberation Sans"],
@@ -43,6 +51,8 @@
 symbol2 = sys.argv[2]  # Type of the second atom
 nep_path = sys.argv[3]  # Directory of the NEP potential file
 
+print_dependency_notice()
+
 # Set the range and step size for distances
 start_distance = 0.1  # Starting distance in Angstrom
 end_distance = 6.0    # Ending distance in Angstrom
@@ -123,4 +133,4 @@
         print(f"The plot has been automatically saved as 'dimer-{symbol1}-{symbol2}.png'.")
         plt.savefig(f'dimer-{symbol1}-{symbol2}.png', dpi=300)
     else:
-        plt.show()
\ No newline at end of file
+        plt.show()
diff --git a/Scripts/plt_scripts/plt_hnemd.py b/Scripts/plt_scripts/plt_hnemd.py
index 967a369..73e54fd 100644
--- a/Scripts/plt_scripts/plt_hnemd.py
+++ b/Scripts/plt_scripts/plt_hnemd.py
@@ -47,7 +47,7 @@ def set_fig_properties(ax_list, tl=4, tw=1.2, tlm=4):
 
 def print_usage():
     """Print usage instructions"""
-    print("Usage: gpumdkit -plt hnemd [scale_eff_size] [cutoff_freq] [save]")
+    print("Usage: gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]")
     print("Params:")
     print("  scale_eff_size: Optional, Scale factor for effective cross-sectional area (default: 1)")
     print("                   • For 3D bulk systems: use 1")
@@ -431,4 +431,4 @@ def _plot_results(self, Reformed_HNEMD_data, Reformed_SHC_data, res_h, res_s,
 
     processor = HNEMD_Processor(directory, scale_eff_size, cutoff_freq)
     processor.process()
-    # python plt_hnemd.py [scale_eff_size] [cutoff_freq] [save]
\ No newline at end of file
+    # python plt_hnemd.py [scale_eff_size] [cutoff_freq] [save]
diff --git a/Scripts/plt_scripts/plt_nemd.py b/Scripts/plt_scripts/plt_nemd.py
index 428f360..2bee6db 100644
--- a/Scripts/plt_scripts/plt_nemd.py
+++ b/Scripts/plt_scripts/plt_nemd.py
@@ -47,7 +47,7 @@ def set_fig_properties(ax_list, tl=4, tw=1.2, tlm=4):
 
 def print_usage():
     """Print usage instructions"""
-    print("Usage: gpumdkit -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]")
+    print("Usage: gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]")
     print("Params:")
     print("  real_length   : Real length of heat tranfer zone in nm (set to 'Auto', with auto-calculation)")
     print("  scale_eff_size: Optional, Scale factor for effective cross-sectional area (default: 1)")
@@ -449,4 +449,4 @@ def _plot_results(self, Reformed_NEMD_data, Reformed_SHC_data, res_s,
 
     processor = NEMD_Processor(directory, real_length, scale_eff_size, cutoff_freq)
     processor.process()
-    # python plt_nemd.py [real_length] [scale_eff_size] [cutoff_freq] [save]
\ No newline at end of file
+    # python plt_nemd.py [real_length] [scale_eff_size] [cutoff_freq] [save]
diff --git a/Scripts/plt_scripts/plt_pdos.py b/Scripts/plt_scripts/plt_pdos.py
index 3fa9a18..5006c5e 100644
--- a/Scripts/plt_scripts/plt_pdos.py
+++ b/Scripts/plt_scripts/plt_pdos.py
@@ -45,7 +45,7 @@ def set_fig_properties(ax_list, tl=4, tw=1.2, tlm=4):
 trap = np.trapezoid if hasattr(np, "trapezoid") else np.trapz
 
 def print_usage():
-    print("Usage: python plt_vac_dos.py [save]")
+    print("Usage: python plt_pdos.py [save]")
     print("  save : Optional. If provided, saves figures (.png) and data (.xlsx).")
 
 class VAC_DOS_Processor:
@@ -370,4 +370,4 @@ def _save_excel(self, nu, dx, dy, dz, T, cx, cy, cz):
 
     directory = os.getcwd()
     processor = VAC_DOS_Processor(directory)
-    processor.process(save_mode)
\ No newline at end of file
+    processor.process(save_mode)
diff --git a/Scripts/sample_structures/README.md b/Scripts/sample_structures/README.md
index 76130f6..511ca8a 100644
--- a/Scripts/sample_structures/README.md
+++ b/Scripts/sample_structures/README.md
@@ -25,21 +25,23 @@ Structure sampling is crucial for creating diverse configurations. These scripts
        | |_| |  __/| |_| | |  | | |_| |   <| | |_
         \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
 
-        GPUMDkit Version 1.4.2 (dev) (2025-12-17)
+        GPUMDkit Version 1.5.6 (dev) (2026-06-17)
   Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+ Main Contributors: Denan LI, Xin WU, Zhoulin LIU & Chen HUA
 
  ----------------------- GPUMD -----------------------
- 1) Format Conversion          2) Sample Structures
- 3) Workflow                   4) Calculators
- 5) Analyzer                   6) Developing ...
- 0) Quit!
+  1) Format Conversion          2) Sample Structures
+  3) Workflow                   4) Calculators
+  5) Analyzer                   6) Visualization
+  7) Utilities                  8) Developing...
+  0) Exit
  ------------>>
  Input the function number:
  2
  ------------>>
  201) Sample structures from extxyz
- 202) Sample structures by pynep
- 203) Sample structures by neptrain
+ 202) PyNEP sampling [deprecated]
+ 203) FPS sampling by NepTrain [preferred]
  204) Perturb structure
  205) Select max force deviation structs
  000) Return to the main menu
@@ -47,6 +49,155 @@ Structure sampling is crucial for creating diverse configurations. These scripts
  Input the function number:
 ```
 
+---
+
+## Scripts
+
+### sample_structures.py
+
+This script samples frames from an extxyz trajectory using either uniform or random sampling.
+
+#### Usage
+
+```sh
+python sample_structures.py <extxyz_file> <sampling_method> <num_samples> [skip_initial]
+```
+
+- `<sampling_method>`: `uniform` or `random`
+- `[skip_initial]`: optional number of initial frames to skip; default is `0`
+
+#### Example
+
+```sh
+python sample_structures.py train.xyz uniform 50
+```
+
+#### Interactive Mode Example
+
+```
+201) Sample structures from extxyz
+Input <extxyz_file> <sampling_method> <num_samples> [skip_num]
+[skip_num]: number of initial frames to skip, default value is 0
+Sampling_method: 'uniform' or 'random'
+Example: train.xyz uniform 50
+```
+
+The output file is `sampled_structures.xyz`.
+
+
+
+### pynep_select_structs.py / parallel_pynep_select_structs.py
+
+PyNEP-based FPS sampling is kept for compatibility, but it is only executed through `gpumdkit.sh -pynep`. The interactive `202` entry only prints a notice and does not run PyNEP. The interactive sampling menu uses `203) FPS sampling by NepTrain` for descriptor-based FPS.
+
+#### Direct Usage
+
+```sh
+python pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file>
+python parallel_pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file> <threads>
+```
+
+#### GPUMDkit Entry
+
+```sh
+gpumdkit.sh -pynep
+```
+
+Then input:
+
+```sh
+dump.xyz train.xyz nep.txt 8
+```
+
+
+
+### neptrain_select_structs.py
+
+This script selects diverse structures from candidate structures using NepTrain descriptors and farthest-point sampling.
+
+#### Usage
+
+```sh
+python neptrain_select_structs.py <sampledata_file> <traindata_file> <nep_model_file>
+```
+
+#### Example
+
+```sh
+python neptrain_select_structs.py dump.xyz train.xyz nep.txt
+```
+
+#### Interactive Mode Example
+
+```
+203) FPS sampling by NepTrain [preferred]
+Input <sample.xyz> <train.xyz> <nep_model>
+Example: dump.xyz train.xyz nep.txt
+```
+
+This function requires the `NepTrain` package. If you use this function, we recommend citing the NepTrain paper.
+
+
+
+### perturb_structure.py
+
+This script generates perturbed structures from an input VASP structure.
+
+#### Usage
+
+```sh
+python perturb_structure.py <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>
+```
+
+#### Example
+
+```sh
+python perturb_structure.py POSCAR 20 0.03 0.2 uniform
+```
+
+#### Interactive Mode Example
+
+```
+204) Perturb structure
+Input <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>
+The default parameters for perturb are 20 0.03 0.2 uniform
+Example: POSCAR 20 0.03 0.2 uniform
+```
+
+This function requires the `dpdata` package. If you use this function, we recommend citing dpdata.
+
+
+
+### select_max_modev.py
+
+This script selects structures with large maximum force deviation from GPUMD active-learning output files.
+
+#### Required Files
+
+- `active.out`
+- `active.xyz`
+
+#### Usage
+
+```sh
+python select_max_modev.py <top_n> <min_deviation>
+```
+
+#### Example
+
+```sh
+python select_max_modev.py 200 0.15
+```
+
+#### Interactive Mode Example
+
+```
+205) Select max force deviation structs
+Input <structs_num> <threshold> (eg. 200 0.15)
+```
+
+The output file is `selected.xyz`.
+
 ## Contributing
 
 See [CONTRIBUTING.md](../../CONTRIBUTING.md) for detailed guidelines.
diff --git a/Scripts/sample_structures/neptrain_select_structs.py b/Scripts/sample_structures/neptrain_select_structs.py
index b500029..5125d57 100644
--- a/Scripts/sample_structures/neptrain_select_structs.py
+++ b/Scripts/sample_structures/neptrain_select_structs.py
@@ -33,6 +33,13 @@
 from scipy.spatial.distance import cdist
 
 
+def print_dependency_notice():
+    print(" This function requires the NepTrain package.")
+    print(" If you use this function, we recommend citing:")
+    print(" Chen et al., Comput. Phys. Commun. 317, 109859 (2025).")
+    print(" https://doi.org/10.1016/j.cpc.2025.109859")
+
+
 def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, length=50, fill='█'):
     percent = ("{0:." + str(decimals) + "f}").format(100 * (iteration / float(total)))
     filled_length = int(length * iteration // total)
@@ -89,10 +96,12 @@ def FarthestPointSample(new_data, now_data=[], min_distance=None, min_select=1,
 
 # Check command line arguments
 if len(sys.argv) < 4:
-    print(" Usage: python pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file>")
-    print(" Examp: python pynep_select_structs.py dump.xyz train.xyz nep.txt")
+    print(" Usage: python neptrain_select_structs.py <sampledata_file> <traindata_file> <nep_model_file>")
+    print(" Example: python neptrain_select_structs.py dump.xyz train.xyz nep.txt")
     sys.exit(1)
 
+print_dependency_notice()
+
 # Load data
 sampledata = read(sys.argv[1], ':')
 traindata = read(sys.argv[2], ':')
diff --git a/Scripts/sample_structures/parallel_pynep_select_structs.py b/Scripts/sample_structures/parallel_pynep_select_structs.py
index 66ef14c..03e68b1 100644
--- a/Scripts/sample_structures/parallel_pynep_select_structs.py
+++ b/Scripts/sample_structures/parallel_pynep_select_structs.py
@@ -10,12 +10,12 @@
 Purpose:    Parallelized version of pynep_select_structs.py. Select diverse
             structures using farthest-point sampling on pynep descriptors
             with multi-processing for descriptor computation and I/O.
-Usage:      python parallel_pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file> [threads]
+Usage:      python parallel_pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file> <threads>
 Arguments:
   sampledata_file  Extxyz file with candidate structures
   traindata_file   Extxyz file with existing training structures
   nep_model_file   NEP model file (e.g., nep.txt)
-  threads          (optional) Number of parallel workers
+  threads          Number of parallel workers
 Output:
   selected.xyz     Selected diverse structures
   select.png       PCA visualization of descriptor space
@@ -37,6 +37,12 @@
 import time
 import os
 
+
+def print_dependency_notice():
+    print(" This function requires the pynep package.")
+    print(" This PyNEP sampling entry is deprecated. We recommend using NepTrain sampling instead.")
+
+
 def get_num_frames(file_path):
     count = 0
     with open(file_path, 'r') as f:
@@ -120,8 +126,8 @@ def calculate_descriptors(data, desc_type, max_workers=None):
 
 # Check command line arguments
 if len(sys.argv) < 4:
-    print(" Usage: python pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file>")
-    print(" Examp: python pynep_select_structs.py dump.xyz train.xyz nep.txt")
+    print(" Usage: python parallel_pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file> <threads>")
+    print(" Example: python parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8")
     sys.exit(1)
 
 # Parse command-line arguments
@@ -132,6 +138,8 @@ def calculate_descriptors(data, desc_type, max_workers=None):
 parser.add_argument('threads', type=int, default=multiprocessing.cpu_count(), help='Number of threads for parallel processing')
 args = parser.parse_args()
 
+print_dependency_notice()
+
 # Function to load data from file
 def load_data(file_path):
     return read(file_path, ':')
diff --git a/Scripts/sample_structures/perturb_structure.py b/Scripts/sample_structures/perturb_structure.py
index 012c2bb..53c6a8e 100644
--- a/Scripts/sample_structures/perturb_structure.py
+++ b/Scripts/sample_structures/perturb_structure.py
@@ -28,9 +28,15 @@
 import sys
 import dpdata
 
+
+def print_dependency_notice():
+    print(" This function requires the dpdata package.")
+    print(" If you use this function, we recommend citing dpdata according to its official documentation.")
+
+
 def parse_args():
     parser = argparse.ArgumentParser(
-             description="Usage: python script.py <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>")
+             description="Usage: python perturb_structure.py <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>")
     parser.add_argument('input_file', help='The path to POSCAR/CONTCAR file')
     parser.add_argument('pert_num', type=int, default=20, help='The perturbation number')
     parser.add_argument('cell_pert_fraction', type=float, default=0.03, help='The fraction of cell perturbation')
@@ -47,6 +53,8 @@ def main():
         print("dpdata documentation: https://docs.deepmodeling.com/projects/dpdata/en/master/index.html \n")
         sys.exit(1)
 
+    print_dependency_notice()
+
     # Read the POSCAR file and perform perturbation
     system = dpdata.System(args.input_file, fmt='vasp/poscar')
     perturbed_systems = system.perturb(pert_num=args.pert_num,
diff --git a/Scripts/sample_structures/pynep_select_structs.py b/Scripts/sample_structures/pynep_select_structs.py
index 51e87a8..00dd7df 100644
--- a/Scripts/sample_structures/pynep_select_structs.py
+++ b/Scripts/sample_structures/pynep_select_structs.py
@@ -31,6 +31,12 @@
 from pynep.calculate import NEP
 from pynep.select import FarthestPointSample
 
+
+def print_dependency_notice():
+    print(" This function requires the pynep package.")
+    print(" This PyNEP sampling entry is deprecated. We recommend using NepTrain sampling instead.")
+
+
 def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, length=50, fill='█'):
     percent = ("{0:." + str(decimals) + "f}").format(100 * (iteration / float(total)))
     filled_length = int(length * iteration // total)
@@ -66,9 +72,11 @@ def calculate_descriptors():
 # Check command line arguments
 if len(sys.argv) < 4:
     print(" Usage: python pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file>")
-    print(" Examp: python pynep_select_structs.py dump.xyz train.xyz nep.txt")
+    print(" Example: python pynep_select_structs.py dump.xyz train.xyz nep.txt")
     sys.exit(1)
 
+print_dependency_notice()
+
 # Load data
 sampledata = read(sys.argv[1], ':')
 traindata = read(sys.argv[2], ':')
@@ -153,4 +161,4 @@ def calculate_descriptors():
 
 plt.tight_layout()
 #plt.show()
-plt.savefig('select.png')
\ No newline at end of file
+plt.savefig('select.png')
diff --git a/Scripts/utils/clean_extra_files.sh b/Scripts/utils/clean_extra_files.sh
index d59a220..8fc905f 100644
--- a/Scripts/utils/clean_extra_files.sh
+++ b/Scripts/utils/clean_extra_files.sh
@@ -33,7 +33,7 @@ done
 # Display files to delete
 if [ ${#delete_files[@]} -eq 0 ]; then
     echo "No files to delete."
-    exit 0
+    return 0
 else
     echo "The following files will be deleted:"
     echo "---------------------------------------"
@@ -57,7 +57,7 @@ if [[ "$user_input" == "y" || "$user_input" == "yes" ]]; then
     echo "Files deleted."
 elif [[ "$user_input" == "n" || "$user_input" == "no" ]]; then
     echo "Operation canceled. No files were deleted."
-    exit 0
+    return 0
 else
     # Add extra files to keep based on user input
     extra_keep_files=($user_input)
diff --git a/Scripts/utils/completion.sh b/Scripts/utils/completion.sh
index 2f4b4e4..81d77aa 100644
--- a/Scripts/utils/completion.sh
+++ b/Scripts/utils/completion.sh
@@ -13,7 +13,7 @@ _gpumdkit_completions() {
     prev="${COMP_WORDS[COMP_CWORD-1]}" # Previous word
 
     # List of primary options (extracted from gpumdkit.sh)
-    local opts="-h -update -help -clean -time -plt -calc -cbc -range -out2xyz -xml2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -pos2lmp -lmp2exyz -traj2exyz -cp2k2xyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -get_frame -clean_xyz -get_volume -analyze_comp -replicate -hbond -pda -pynep -frame_range -chem_species -xdat2exyz -nep_modifier"
+    local opts="-h -help -update -U -clean -time -plt -calc -cbc -range -out2xyz -out2exyz -cp2k2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -xdat2exyz -pos2lmp -lmp2exyz -traj2exyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -filter_range -get_frame -clean_xyz -get_volume -analyze_comp -chem_species -replicate -hbond -pda -pynep -frame_range -re_atoms -nep_modifier"
 
     # Provide secondary completion based on the previous word
     case "$prev" in
@@ -23,14 +23,14 @@ _gpumdkit_completions() {
 
         # Secondary options for -plt
         -plt)
-            COMPREPLY=($(compgen -W "thermo thermo2 thermo3 train train_density prediction test train_test msd msd_all msd_conv sdc rdf vac restart dimer force_error des doas charge lr parity_density arrhenius_d arrhenius_sigma sigma D sigma_xyz D_xyz net_force emd nemd hnemd pdos plane-grid cohesive viscosity rdf_pmf bec born_charge" -- "$cur")) ;;
+            COMPREPLY=($(compgen -W "thermo thermo2 thermo3 train train_density prediction test train_test parity_density born_charge bec msd msd_all msd_conv msd_sdc sdc rdf rdf_pmf vac restart dimer force_errors des doas charge lr arrhenius_d arrhenius_sigma sigma D sigma_xyz D_xyz net_force emd nemd hnemd pdos plane-grid cohesive viscosity" -- "$cur")) ;;
 
         # Secondary options for -calc
         -calc)
-            COMPREPLY=($(compgen -W "ionic-cond nep des doas neb nlist disp avg-struct oct-tilt pol-abo3" -- "$cur")) ;;
+            COMPREPLY=($(compgen -W "ionic-cond nep des doas neb minimize msd nlist disp avg-struct oct-tilt pol-abo3" -- "$cur")) ;;
             
         # Options requiring files or directories, complete with filenames
-        -out2xyz|-cp2k2xyz|-exyz2pos|-min_dist|-min_dist_pbc|-filter_dist|-filter_dist_pbc|-filter_box|-get_frame|-clean_xyz|-mtp2xyz|-pos2exyz|-cif2exyz|-cif2pos|-pos2lmp|-lmp2exyz|-traj2exyz|-addgroup|-addlabel|-addweight|-analyze_comp|-replicate|-pda|-cbc|-frame_range|-xml2xyz|-chem_species|-xdat2exyz)
+        -out2xyz|-out2exyz|-cp2k2xyz|-exyz2pos|-min_dist|-min_dist_pbc|-filter_dist|-filter_dist_pbc|-filter_box|-filter_value|-filter_range|-get_frame|-clean_xyz|-pos2exyz|-cif2exyz|-cif2pos|-pos2lmp|-lmp2exyz|-traj2exyz|-addgroup|-addlabel|-addweight|-analyze_comp|-replicate|-pda|-cbc|-frame_range|-chem_species|-xdat2exyz|-re_atoms)
             COMPREPLY=($(compgen -f -- "$cur")) ;;
 
         # Default case: complete primary options
diff --git a/Scripts/utils/nep_modifier/nep_modifier.py b/Scripts/utils/nep_modifier/nep_modifier.py
index 469efbd..ed59ccc 100644
--- a/Scripts/utils/nep_modifier/nep_modifier.py
+++ b/Scripts/utils/nep_modifier/nep_modifier.py
@@ -30,6 +30,13 @@
     sys.exit(1)
 
 
+def print_dependency_notice():
+    print(" This function requires the calorine package.")
+    print(" If you use this function, we recommend citing:")
+    print(" Lindgren et al., J. Open Source Softw. 9, 6264 (2024).")
+    print(" https://doi.org/10.21105/joss.06264")
+
+
 # ─── helpers ──────────────────────────────────────────────────────────────────
 
 def banner(title):
@@ -334,4 +341,5 @@ def main():
 
 
 if __name__ == "__main__":
+    print_dependency_notice()
     main()
diff --git a/Scripts/workflow/README.md b/Scripts/workflow/README.md
index 1d9d743..349f111 100644
--- a/Scripts/workflow/README.md
+++ b/Scripts/workflow/README.md
@@ -7,7 +7,7 @@
 
 Workflow scripts automate repetitive tasks in computational materials research:
 
-- **SCF Batch preprocessin**: Set up VASP/CP2K single-point energy calculations
+- **SCF batch preprocessing**: Set up VASP/CP2K single-point energy calculations
 - **MD sampling**: Prepare molecular dynamics simulations with GPUMD/LAMMPS
 - **Active learning**: Iterative NEP model improvement workflows
 
@@ -24,14 +24,16 @@ Access workflow tools through `gpumdkit.sh` interactive mode:
        | |_| |  __/| |_| | |  | | |_| |   <| | |_
         \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
 
-        GPUMDkit Version 1.4.2 (dev) (2025-12-17)
+        GPUMDkit Version 1.5.6 (dev) (2026-06-17)
   Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+ Main Contributors: Denan LI, Xin WU, Zhoulin LIU & Chen HUA
 
  ----------------------- GPUMD -----------------------
- 1) Format Conversion          2) Sample Structures
- 3) Workflow                   4) Calculators
- 5) Analyzer                   6) Developing ...
- 0) Quit!
+  1) Format Conversion          2) Sample Structures
+  3) Workflow                   4) Calculators
+  5) Analyzer                   6) Visualization
+  7) Utilities                  8) Developing...
+  0) Exit
  ------------>>
  Input the function number:
  3
@@ -46,6 +48,47 @@ Access workflow tools through `gpumdkit.sh` interactive mode:
 
 ---
 
+## Workflow Entries
+
+### 301) SCF batch pretreatment
+
+This entry prepares folders for single-point calculations. For VASP, keep either `.vasp` structures or one `.xyz` file in the current directory before running the script.
+
+- If `.vasp` files are present, the script processes the `.vasp` files.
+- If both `.vasp` and `.xyz` files are present, the script prints a notice and only processes `.vasp` files.
+- If no `.vasp` file is present and multiple `.xyz` files are detected, the script asks which `.xyz` file to process.
+
+After running, the script creates `struct_fp/`, `fp/`, and `fp_sample_*` directories. Put `INCAR`, `POTCAR`, and `KPOINTS` into the generated `fp/` directory; each calculation folder links to these files.
+
+For CP2K, enter `3) Workflow`, then `301) SCF batch pretreatment`, and choose the CP2K branch. The CP2K script asks for:
+
+```text
+<input.xyz> <template.inp> <prefix>
+```
+
+The repository provides `Scripts/workflow/cp2k_template.inp` as a starting template.
+
+
+
+### 302) MD sample batch pretreatment (GPUMD)
+
+This entry prepares GPUMD MD sampling folders. Start from `.vasp` structures, or from one selected `.xyz` trajectory/structure file if no `.vasp` files are present.
+
+- If `.vasp` files are present, they are converted to extxyz files and processed.
+- If both `.vasp` and `.xyz` files are present, only `.vasp` files are processed.
+- If multiple `.xyz` files are detected without `.vasp` files, the script asks which one to use.
+
+After running, put `nep.txt` and `run_*.in` files into the generated `md/` directory. The sample folders link `run_1.in`, `run_2.in`, ... as their `run.in`.
+
+
+
+### 303) MD sample batch pretreatment (LAMMPS)
+
+This entry prepares LAMMPS MD sampling folders. The input-file selection rules are the same as function 302.
+
+After running, put `lmprun.in` and `nep.txt` into the generated `md/` directory. The sample folders link `lammps.data`, `lmprun.in`, and `nep.txt`.
+
+
 ### workflow_active_learning_dev.sh
 
 Implements automated active learning cycles for iterative NEP model improvement.
diff --git a/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh b/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
index 79de851..053e323 100644
--- a/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
+++ b/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
@@ -26,6 +26,10 @@ function f302_md_sample_batch_pretreatment_gpumd(){
 
 	# Check if there are any .vasp files
 	if [ $num_vasp_files -gt 0 ]; then
+	    if [ $num_xyz_files -gt 0 ]; then
+	        echo " Notice: Found both .vasp and .xyz files in the current directory."
+	        echo " This workflow prioritizes .vasp files and will ignore .xyz files."
+	    fi
 	    # Create the struct directory and move .vasp files into it
 	    mkdir -p struct_md
 	    rename_seq=1
@@ -44,11 +48,22 @@ function f302_md_sample_batch_pretreatment_gpumd(){
 		done
 		num_xyz_files=$(find ./struct_md -maxdepth 1 -name "*.xyz" | wc -l)
 	else
-	    # Check if there is exactly one XYZ file
-	    if [ $num_xyz_files -eq 1 ]; then
-	        echo " No .vasp files found, but found one XYZ file."
-	        echo " Converting it to model.xyz using GPUMDkit..."
-	        python ${GPUMDkit_path}/Scripts/format_conversion/split_single_xyz.py *.xyz
+	    # Check available XYZ files
+	    if [ $num_xyz_files -ge 1 ]; then
+	        if [ $num_xyz_files -eq 1 ]; then
+	            xyz_file=$(find . -maxdepth 1 -name "*.xyz" | head -n 1)
+	            echo " No .vasp files found, but found one XYZ file: ${xyz_file#./}"
+	        else
+	            echo " No .vasp files found, but found multiple XYZ files:"
+	            select xyz_file in *.xyz; do
+	                if [ -n "$xyz_file" ]; then
+	                    break
+	                fi
+	                echo " Invalid selection. Please choose one XYZ file."
+	            done
+	        fi
+	        echo " Splitting ${xyz_file#./} to model_*.xyz using GPUMDkit..."
+	        python ${GPUMDkit_path}/Scripts/format_conversion/split_single_xyz.py "$xyz_file"
 	        
 	        mkdir -p struct_md
 	        mv *.xyz ./struct_md
@@ -56,7 +71,7 @@ function f302_md_sample_batch_pretreatment_gpumd(){
 	        
 	        # Perform additional operations if needed after moving .vasp files
 	    else
-	        echo " No .vasp files found and the XYZ file is not unique."
+	        echo " No .vasp files or .xyz files found."
 	        exit 1
 	    fi
 	fi
diff --git a/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh b/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
index da809bd..f77fc4a 100644
--- a/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
+++ b/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
@@ -26,6 +26,10 @@ function f303_md_sample_batch_pretreatment_lmp(){
 
 	# Check if there are any .vasp files
 	if [ $num_vasp_files -gt 0 ]; then
+	    if [ $num_xyz_files -gt 0 ]; then
+	        echo " Notice: Found both .vasp and .xyz files in the current directory."
+	        echo " This workflow prioritizes .vasp files and will ignore .xyz files."
+	    fi
 	    # Create the struct directory and move .vasp files into it
 	    mkdir -p struct_md
 	    rename_seq=1
@@ -46,11 +50,22 @@ function f303_md_sample_batch_pretreatment_lmp(){
 		done
 		num_lmp_files=$(find ./struct_md -maxdepth 1 -name "*.data" | wc -l)
 	else
-	    # Check if there is exactly one XYZ file
-	    if [ $num_xyz_files -eq 1 ]; then
-	        echo " No .vasp files found, but found one XYZ file."
-	        echo " Converting it to model.xyz using GPUMDkit..."
-	        python ${GPUMDkit_path}/Scripts/format_conversion/split_single_xyz.py *.xyz
+	    # Check available XYZ files
+	    if [ $num_xyz_files -ge 1 ]; then
+	        if [ $num_xyz_files -eq 1 ]; then
+	            xyz_file=$(find . -maxdepth 1 -name "*.xyz" | head -n 1)
+	            echo " No .vasp files found, but found one XYZ file: ${xyz_file#./}"
+	        else
+	            echo " No .vasp files found, but found multiple XYZ files:"
+	            select xyz_file in *.xyz; do
+	                if [ -n "$xyz_file" ]; then
+	                    break
+	                fi
+	                echo " Invalid selection. Please choose one XYZ file."
+	            done
+	        fi
+	        echo " Splitting ${xyz_file#./} to model_*.xyz using GPUMDkit..."
+	        python ${GPUMDkit_path}/Scripts/format_conversion/split_single_xyz.py "$xyz_file"
 	        
 	        mkdir -p struct_md
 	        mv *.xyz ./struct_md
@@ -69,7 +84,7 @@ function f303_md_sample_batch_pretreatment_lmp(){
 	        
 	        # Perform additional operations if needed after moving .vasp files
 	    else
-	        echo " No .vasp files found and the XYZ file is not unique."
+	        echo " No .vasp files or .xyz files found."
 	        exit 1
 	    fi
 	fi
diff --git a/Scripts/workflow/scf_batch_pretreatment_cp2k.py b/Scripts/workflow/scf_batch_pretreatment_cp2k.py
index 70037e0..13ea9c3 100644
--- a/Scripts/workflow/scf_batch_pretreatment_cp2k.py
+++ b/Scripts/workflow/scf_batch_pretreatment_cp2k.py
@@ -10,12 +10,13 @@
 Purpose:    Batch pretreatment of structures for CP2K SCF calculations.
             Reads structures from extxyz/VASP files, copies a CP2K template,
             and populates the CELL section with the correct lattice vectors.
-Usage:      python scf_batch_pretreatment_cp2k.py <xyz_file> [template]
+Usage:      python scf_batch_pretreatment_cp2k.py <extxyz_file> <template_inp> <prefix>
 Arguments:
-  xyz_file  Input extxyz file with structures
-  template  (optional) CP2K input template (default: cp2k_template.inp)
+  extxyz_file   Input extxyz file with structures
+  template_inp  CP2K input template
+  prefix        Prefix for output directories
 Output:
-  struct_fp/ directory with POSCAR_*.vasp and cp2k input files
+  <prefix>_<index>/ directories with input.inp and pos.xyz files
 Author:     Zihan YAN (yanzihan@westlake.edu.cn)
 Last-modified: 2026-05-16
 =============================================================================
diff --git a/Scripts/workflow/scf_batch_pretreatment_vasp.sh b/Scripts/workflow/scf_batch_pretreatment_vasp.sh
index bd42d44..c75f57d 100644
--- a/Scripts/workflow/scf_batch_pretreatment_vasp.sh
+++ b/Scripts/workflow/scf_batch_pretreatment_vasp.sh
@@ -26,6 +26,10 @@ function vasp_scf_batch_pretreatment(){
 
 	# Check if there are any .vasp files
 	if [ $num_vasp_files -gt 0 ]; then
+	    if [ $num_xyz_files -gt 0 ]; then
+	        echo " Notice: Found both .vasp and .xyz files in the current directory."
+	        echo " This workflow prioritizes .vasp files and will ignore .xyz files."
+	    fi
 	    # Create the struct directory and move .vasp files into it
 	    mkdir -p struct_fp
 	    rename_seq=1
@@ -36,11 +40,22 @@ function vasp_scf_batch_pretreatment(){
 		done
         num_vasp_files=$(find ./struct_fp -maxdepth 1 -name "*.vasp" | wc -l)
 	else
-	    # Check if there is exactly one XYZ file
-	    if [ $num_xyz_files -eq 1 ]; then
-	        echo " No .vasp files found, but found one XYZ file."
-	        echo " Converting it to POSCAR using GPUMDkit..."
-	        python ${GPUMDkit_path}/Scripts/format_conversion/exyz2pos.py *.xyz
+	    # Check available XYZ files
+	    if [ $num_xyz_files -ge 1 ]; then
+	        if [ $num_xyz_files -eq 1 ]; then
+	            xyz_file=$(find . -maxdepth 1 -name "*.xyz" | head -n 1)
+	            echo " No .vasp files found, but found one XYZ file: ${xyz_file#./}"
+	        else
+	            echo " No .vasp files found, but found multiple XYZ files:"
+	            select xyz_file in *.xyz; do
+	                if [ -n "$xyz_file" ]; then
+	                    break
+	                fi
+	                echo " Invalid selection. Please choose one XYZ file."
+	            done
+	        fi
+	        echo " Converting ${xyz_file#./} to POSCAR files using GPUMDkit..."
+	        python ${GPUMDkit_path}/Scripts/format_conversion/exyz2pos.py "$xyz_file"
 	        
 	        mkdir -p struct_fp
 	        mv *.vasp ./struct_fp
@@ -48,7 +63,7 @@ function vasp_scf_batch_pretreatment(){
 	        
 	        # Perform additional operations if needed after moving .vasp files
 	    else
-	        echo " No .vasp files found and the XYZ file is not unique."
+	        echo " No .vasp files or .xyz files found."
 	        exit 1
 	    fi
 	fi
diff --git a/Scripts/workflow/submit_template.sh b/Scripts/workflow/submit_template.sh
index 5227816..924fe19 100644
--- a/Scripts/workflow/submit_template.sh
+++ b/Scripts/workflow/submit_template.sh
@@ -1,4 +1,4 @@
-#!bin/bash
+#!/bin/bash
 
 function submit_gpumd_array(){
 cat > submit.slurm <<-EOF
diff --git a/Scripts/workflow/workflow_active_learning_dev.sh b/Scripts/workflow/workflow_active_learning_dev.sh
index 356d860..a6bb63f 100644
--- a/Scripts/workflow/workflow_active_learning_dev.sh
+++ b/Scripts/workflow/workflow_active_learning_dev.sh
@@ -11,7 +11,7 @@ cd $SLURM_SUBMIT_DIR
 # It is recommended that you copy it to another path,
 # otherwise there will be code conflicts when use 'git pull' command to update GPUMDkit.
 source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  
-python_pynep=/storage/zhuyizhouLab/yanzhihan/soft/conda/envs/gpumd/bin/python  # python executable for pynep
+python_pynep=python  # python executable for deprecated pynep branch if needed
 
 work_dir=${PWD}  # work directory
 prefix_name=LiF_iter01  # prefix name for this workflow, used for the scf calculations
@@ -117,7 +117,7 @@ case $sample_method in
     "pynep")
         echo $(date -d "2 second" +"%Y-%m-%d %H:%M:%S") "Performing pynep sampling..." 
         # This function still needs to be improved in the future. 
-        (echo 202; echo "filtered_by_box.xyz train.xyz nep.txt"; echo 1; echo ${pynep_sample_dist}) | gpumdkit.sh >> /dev/null
+        (echo "filtered_by_box.xyz train.xyz nep.txt 1"; echo 1; echo ${pynep_sample_dist}) | gpumdkit.sh -pynep >> /dev/null
         #${python_pynep} ${GPUMDkit_path}/Scripts/sample_structures/pynep_select_structs.py filtered_by_box.xyz train.xyz nep.txt ${pynep_sample_dist}
         # Check the number of structures in selected.xyz
         selected_struct_num=$(grep -c Lat selected.xyz)
@@ -178,4 +178,3 @@ submit_nep_prediction
 sbatch submit.slurm
 gpumdkit.sh -plt prediction save
 echo $(date -d "2 second" +"%Y-%m-%d %H:%M:%S") "Prediction finished."
-
diff --git a/Scripts/workflow/workflow_active_learning_dev_multielement.sh b/Scripts/workflow/workflow_active_learning_dev_multielement.sh
index 9f7513e..1fb698b 100644
--- a/Scripts/workflow/workflow_active_learning_dev_multielement.sh
+++ b/Scripts/workflow/workflow_active_learning_dev_multielement.sh
@@ -11,7 +11,7 @@ cd $SLURM_SUBMIT_DIR
 # It is recommended that you copy it to another path,
 # otherwise there will be code conflicts when use 'git pull' command to update GPUMDkit.
 source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  
-python_pynep=/storage/zhuyizhouLab/yanzhihan/soft/conda/envs/gpumd/bin/python  # python executable for pynep
+python_pynep=python  # python executable for deprecated pynep branch if needed
 
 work_dir=${PWD}  # work directory
 prefix_name=LiF_iter01  # prefix name for this workflow, used for the scf calculations
@@ -117,7 +117,7 @@ case $sample_method in
     "pynep")
         echo $(date -d "2 second" +"%Y-%m-%d %H:%M:%S") "Performing pynep sampling..." 
         # This function still needs to be improved in the future. 
-        (echo 202; echo "filtered_by_box.xyz train.xyz nep.txt"; echo 1; echo ${pynep_sample_dist}) | gpumdkit.sh >> /dev/null
+        (echo "filtered_by_box.xyz train.xyz nep.txt 1"; echo 1; echo ${pynep_sample_dist}) | gpumdkit.sh -pynep >> /dev/null
         #${python_pynep} ${GPUMDkit_path}/Scripts/sample_structures/pynep_select_structs.py filtered_by_box.xyz train.xyz nep.txt ${pynep_sample_dist}
         # Check the number of structures in selected.xyz
         selected_struct_num=$(grep -c Lat selected.xyz)
@@ -179,4 +179,3 @@ submit_nep_prediction
 sbatch submit.slurm
 gpumdkit.sh -plt prediction save
 echo $(date -d "2 second" +"%Y-%m-%d %H:%M:%S") "Prediction finished."
-
diff --git a/docs/CONTRIBUTING_zh-CN.md b/docs/CONTRIBUTING_zh-CN.md
new file mode 100644
index 0000000..3ff14e1
--- /dev/null
+++ b/docs/CONTRIBUTING_zh-CN.md
@@ -0,0 +1,443 @@
+# 为 GPUMDkit 贡献代码
+
+<p align="center">
+  <a href="../CONTRIBUTING.md">English</a>
+  &nbsp;·&nbsp;
+  <strong>简体中文</strong>
+</p>
+
+感谢你有兴趣为 `GPUMDkit` 做出贡献！我们感谢你为改善这个工具包所付出的时间和努力。`GPUMDkit` 是一个开源项目，我们欢迎社区的各种贡献，无论是修复 bug、添加新功能、改进文档还是提出建议。
+
+---
+
+## 目录
+
+- [开发规范与准则](#开发规范与准则)
+- [报告问题](#报告问题)
+- [功能建议](#功能建议)
+- [贡献代码](#贡献代码)
+  - [Fork 并克隆仓库](#fork-并克隆仓库)
+  - [创建功能分支](#创建功能分支)
+  - [进行修改](#进行修改)
+    - [交互模式贡献](#交互模式贡献)
+    - [命令行模式贡献](#命令行模式贡献)
+    - [更新 Tab 补全](#更新-tab-补全)
+  - [代码风格与最佳实践](#代码风格与最佳实践)
+  - [测试你的修改](#测试你的修改)
+  - [提交信息](#提交信息)
+  - [推送并创建 Pull Request](#推送并创建-pull-request)
+
+---
+
+## 开发规范与准则
+
+为保持代码质量和项目一致性，请遵循以下准则：
+
+### 语言要求
+
+- **所有代码应使用英文编写**：包括变量名、函数名、注释、文档字符串、提交信息和文档。
+- 虽然我们理解贡献者来自不同背景，但使用英文能确保代码库对最广泛的用户群体可访问。
+
+### 模块化与可复用性
+
+- **编写模块化和可复用的代码**：函数和脚本的设计应具有灵活性。
+- **优先传递参数而非硬编码值**：使用函数参数、命令行参数或配置文件来替代硬编码值。但某些文件名由 GPUMD 和 NEP 程序固定要求（如 `train.xyz`、`thermo.out`），这些可以按需硬编码。
+- **示例**：
+  ```bash
+  # 好的做法：接受参数
+  function convert_file() {
+      local input_file=$1
+      local output_file=$2
+      # 处理逻辑
+  }
+  
+  # 避免：硬编码值（除非 GPUMD/NEP 要求）
+  function convert_file() {
+      local input_file="hardcoded_input.xyz"
+      # 处理逻辑
+  }
+  ```
+
+### 代码风格
+
+- 编写清晰、易于他人维护和修改的代码。
+- 使用有意义的变量和函数名。
+- 在必要处添加注释以解释复杂逻辑。
+
+### 文档
+
+- 确保帮助信息（如 `-h` 标志）清晰准确。
+- 教程文档位于 `docs/tutorials/en/`（英文）和 `docs/tutorials/zh/`（中文）。如果你添加了新功能，请考虑更新相关教程页面。
+- 编辑教程 Markdown 文件后，使用 `mkdocs build -f docs/mkdocs.yml` 重新构建 HTML。
+
+---
+
+## 报告问题
+
+如果你遇到 bug，请通过 GitHub Issues 帮助我们修复：
+
+1. **搜索现有 issues** 查看该 bug 是否已被报告。
+2. **创建新 issue**（如果尚未被报告）：[创建 Issue](https://github.com/zhyan0603/GPUMDkit/issues/new)
+3. **详细描述问题**，如果可能请提供测试文件。
+
+你也可以通过以下方式联系我们：
+- **QQ 群**：825696376
+- **邮箱**：yanzihan@westlake.edu.cn
+- **脚本开发者**：联系脚本头部列出的开发者
+
+---
+
+## 功能建议
+
+我们欢迎功能建议！提出新功能：
+
+1. **搜索现有 issues** 查看是否已有人提出。
+2. **创建新功能请求**：[创建功能请求](https://github.com/zhyan0603/GPUMDkit/issues/new) 并 mention @zhyan0603
+3. **清楚描述你的需求** 并解释其用途。
+
+---
+
+## 贡献代码
+
+### Fork 并克隆仓库
+
+1. 在 GitHub 上 **Fork 仓库**，点击 [仓库页面](https://github.com/zhyan0603/GPUMDkit) 右上角的 "Fork" 按钮。
+
+2. **克隆你的 fork** 到本地：
+
+   ```bash
+   git clone https://github.com/YOUR_USERNAME/GPUMDkit.git
+   cd GPUMDkit
+   ```
+
+3. **设置 upstream remote** 以保持 fork 同步：
+   ```bash
+   git remote add upstream https://github.com/zhyan0603/GPUMDkit.git
+   ```
+
+### 创建功能分支
+
+为你的修改创建新分支：
+
+```bash
+# 从 main 创建并切换到新分支
+git checkout -b your-branch-name
+```
+
+分支名称随意。
+
+### 进行修改
+
+`GPUMDkit` 的结构包括：
+- **`gpumdkit.sh`**：主入口（Bash 脚本），处理交互菜单模式和命令行模式
+- **`install.sh`**：安装脚本，设置环境变量和 shell 配置
+- **`Scripts/`**：按功能组织的 Python 和 Bash 实现脚本
+  - `plt_scripts/`：绘图脚本
+  - `calculators/`：计算工具
+  - `format_conversion/`：格式转换工具
+  - `workflow/`：工作流自动化
+  - `sample_structures/`：结构采样工具
+  - `analyzer/`：分析工具
+  - `utils/`：实用函数（包括 `completion.sh` Tab 补全）
+- **`src/`**：交互模式菜单函数的 Shell 脚本
+  - `f1_format_conversions.sh`
+  - `f2_sample_structures.sh`
+  - `f3_workflows.sh`
+  - `f4_calculators.sh`
+  - `f5_analyzers.sh`
+  - `f6_plots.sh`
+  - `f7_utilities.sh`
+- **`skills/`**：AI agent 技能定义（用于 opencode/Claude Code 集成的 SKILL.md 文件）
+- **`docs/`**：文档文件
+  - `tutorials/en/` 和 `tutorials/zh/`：双语教程页面
+  - `mkdocs.yml`：构建教程 HTML 的 MkDocs 配置
+  - `command_reference.tsv`：机器可读的命令参考
+  - `htmls/`：MkDocs 生成的 HTML 输出
+
+#### 交互模式贡献
+
+要添加通过交互菜单访问的新功能：
+
+1. **在相应的 `Scripts/` 子目录中创建实现脚本**：
+
+   ```bash
+   # 示例：添加新的格式转换脚本
+   touch Scripts/format_conversion/new_converter.py
+   ```
+
+2. **实现你的功能**，遵循模块化准则（接受参数，避免硬编码）。
+
+3. **在相应的 `src/` 文件中添加包装函数**：
+   ```bash
+   # 示例：编辑 src/f1_format_conversions.sh
+   vim src/f1_format_conversions.sh
+   ```
+
+   添加新函数：
+   ```bash
+   function f111_new_converter(){
+   echo " >-------------------------------------------------<"
+   echo " | Calling the script in Scripts/format_conversion |"
+   echo " | Script: new_converter.py                        |"
+   echo " | Developer: Your Name (your@email.com)           |"
+   echo " >-------------------------------------------------<"
+   echo " Input <required_param1> <required_param2>"
+   echo " Example: input.xyz output.lmp"
+   echo " ------------>>"
+   read -r -a converter_args
+   echo " ---------------------------------------------------"
+   python ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py "${converter_args[@]}"
+   echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py"
+   echo " ---------------------------------------------------"
+   }
+   ```
+
+4. **在 `gpumdkit.sh` 中更新菜单显示**：
+   ```bash
+   # 找到 menu() 函数并按需更新
+   # 找到 array_choice 数组并添加你的新选择编号
+   array_choice=(
+       "0" "1" "101" "102" "103" "104" "105" "106" "107" "108" "109" "110" "111"  # 添加 "111"
+       # ... 其余选择
+   )
+   ```
+
+5. **在 `gpumdkit.sh` 中添加 case 语句**：
+   ```bash
+   # 在 main() 函数中找到相应的 case 语句
+   case "${choice:0:1}" in
+       # ...
+       "1")
+           source ${GPUMDkit_path}/src/f1_format_conversions.sh
+           case $choice in
+               "1") f1_format_conversion ;;
+               "101") f101_out2xyz ;;
+               # ... 现有 case ...
+               "111") f111_new_converter ;;  # 添加你的 case
+           esac ;;
+       # ...
+   esac
+   ```
+
+#### 命令行模式贡献
+
+要添加新的命令行标志或子命令：
+
+1. **在相应的 `Scripts/` 子目录中创建实现脚本**：
+   ```bash
+   # 示例：添加新的分析器脚本
+   touch Scripts/analyzer/analyze_bonds.py
+   ```
+
+2. **实现你的功能**，明确参数要求：
+   ```python
+   # 示例：Scripts/analyzer/analyze_bonds.py
+   import sys
+   
+   if len(sys.argv) != 3:
+       print("Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>")
+       print("Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0")
+       sys.exit(1)
+   
+   input_file = sys.argv[1]
+   cutoff = float(sys.argv[2])
+   
+   # 你的实现
+   ```
+
+   > **注意**：GPUMDkit Python 脚本设计为直接运行（不作为模块导入）。
+   > 如果你愿意，可以使用 `main()` 函数配合 `if __name__ == "__main__":` 保护，
+   > 但这不是必需的。大多数现有脚本在模块级别执行。
+
+3. **在 `gpumdkit.sh` 中添加命令行标志处理**：
+   ```bash
+   # 找到命令行解析部分（大的 "case $1 in" 块）
+   # 在适当位置添加你的新标志
+   
+   case $1 in
+       # ... 现有 case ...
+       -analyze_bonds)
+           if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ]; then
+               python ${analyzer_path}/analyze_bonds.py $2 $3
+           else
+               echo " Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>"
+               echo " Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0"
+               echo " Code path: ${analyzer_path}/analyze_bonds.py"
+           fi ;;
+       # ... 其余 case ...
+   esac
+   ```
+
+4. **在 `gpumdkit.sh` 中更新帮助信息**：
+   ```bash
+   # 找到 help_info_table() 函数并添加你的命令
+   function help_info_table(){
+       echo "+====================================== Analysis ===============================================+"
+       echo "| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |"
+       # ... 其余帮助表 ...
+   }
+   ```
+
+#### 更新 Tab 补全
+
+添加新的命令行标志时，更新 Tab 补全脚本：
+
+```bash
+# 编辑 Scripts/utils/completion.sh
+vim Scripts/utils/completion.sh
+```
+
+将你的新标志添加到 `opts` 变量：
+```bash
+# 找到 local opts=... 行
+local opts="-h -help -update -U -clean -time -plt -calc ... -your_new_flag ..."
+#                                                        在此添加你的标志
+```
+
+如果你的标志需要文件参数，将其添加到现有的文件补全 case 中：
+```bash
+# 找到需要文件参数的 case 并用 | 添加你的标志
+-out2xyz|-out2exyz|-...|-your_new_flag)
+    COMPREPLY=($(compgen -f -- "$cur")) ;;
+```
+
+如果你的标志接受二级选项（如 `-plt` 或 `-calc`），添加新 case：
+```bash
+case "$prev" in
+    # ... 现有 case ...
+    -your_new_flag)
+        COMPREPLY=($(compgen -W "option1 option2 option3" -- "$cur")) ;;
+    # ... 其余 case ...
+esac
+```
+
+### 代码风格与最佳实践
+
+- **Shell 脚本**：
+  - 使用 `${variable}` 进行变量展开
+  - 使用 `[ ! -z "$var" ]` 进行非空检查（项目约定）
+  - 交互函数应遵循 banner 格式：
+    ```bash
+    echo " >-------------------------------------------------<"
+    echo " | Calling the script in Scripts/<category>        |"
+    echo " | Script: <script_name>.py                        |"
+    echo " | Developer: <Name> (<email>)                     |"
+    echo " >-------------------------------------------------<"
+    ```
+  - 使用 `read -r -a varname` 读取多词输入，然后用 `"${varname[@]}"` 传递
+  - `src/` 中的 Shell 脚本应以文件头注释块开始：
+    ```bash
+    # ============================================================
+    # GPUMDkit <module name> module
+    # Repository: https://github.com/zhyan0603/GPUMDkit
+    # Author: <Name> (<email>)
+    # ============================================================
+    ```
+
+- **Python 脚本**：
+  - 编写清晰、可维护的代码
+  - 使用有意义的变量名
+  - 使用 `sys.argv` 进行参数解析（与大多数现有脚本一致）
+  - 提供清晰的使用信息：`print("Usage: ...")` 和 `print("Example: ...")`
+  - 如果你的脚本使用重型/特殊包（`NepTrain`、`calorine`、`dpdata`），请添加
+    `print_dependency_notice()` 函数以通知用户引用建议
+
+### 测试你的修改
+
+提交贡献前，运行相关验证命令：
+
+```bash
+# Shell 语法检查（始终运行）
+bash -n gpumdkit.sh
+find src Scripts -name '*.sh' -exec bash -n {} +
+
+# Python 语法检查（针对修改的 Python 文件）
+python3 -m py_compile path/to/modified_script.py
+
+# MkDocs 构建（如果修改了文档）
+mkdocs build -f docs/mkdocs.yml
+
+# 检查尾随空格问题
+git diff --check
+```
+
+然后测试功能：
+
+1. **测试交互模式**（如适用）：
+   ```bash
+   gpumdkit.sh
+   # 导航到你的新功能并充分测试
+   ```
+
+2. **测试命令行模式**（如适用）：
+   ```bash
+   gpumdkit.sh -your_new_flag [arguments]
+   gpumdkit.sh -your_new_flag -h  # 测试帮助信息
+   ```
+
+3. **测试 Tab 补全**（如果你修改了 `completion.sh`）：
+   ```bash
+   source Scripts/utils/completion.sh
+   gpumdkit.sh -<TAB>  # 应显示你的新标志
+   ```
+
+4. **用各种输入测试**：
+   - 用典型输入测试
+   - 用边缘情况测试（空文件、大文件等）
+   - 测试错误处理（缺少文件、无效参数）
+
+5. **验证无回归**：确保现有功能仍然正常工作。
+
+### 提交信息
+
+编写清晰、描述性的提交信息来解释你做了什么更改。没有严格的格式要求——只要确保你的信息是可理解的。
+
+### 推送并创建 Pull Request
+
+1. **提交你的修改**：
+   ```bash
+   git add .
+   git commit -m "你的描述性信息"
+   ```
+
+2. **保持你的分支与最新的 `dev` 分支同步**：
+   ```bash
+   git fetch origin
+   git rebase origin/dev
+   ```
+
+3. **推送你的分支**到你的 fork：
+   ```bash
+   git push origin your-branch-name
+   ```
+
+4. **创建 Pull Request**：
+   - 前往 [GPUMDkit 仓库](https://github.com/zhyan0603/GPUMDkit)
+   - 点击 "Pull Requests" → "New Pull Request"
+   - 设置目标分支为 `dev` 进行代码审查
+   - 设置比较分支为你的功能分支
+   - 填写 PR 描述：
+     - **标题**：简要描述更改
+     - **描述**：详细解释更改内容和原因
+     - **测试**：描述你如何测试这些更改
+
+5. **回应审查反馈**：
+   - 对建议和建设性批评保持开放
+   - 及时进行请求的修改
+   - 推送额外提交到你的分支（它们会自动出现在 PR 中）
+
+6. **批准后**：维护者将合并你的 PR。
+
+---
+
+## 有问题或需要帮助？
+
+如果你对贡献有疑问或需要帮助：
+
+- **发起讨论**：使用 [GitHub Discussions](https://github.com/zhyan0603/GPUMDkit/discussions) 提出一般性问题
+- **在 issue 中提问**：在相关 issue 中评论以获取具体问题的帮助
+- **联系维护者**：联系 README 中列出的核心开发者
+
+---
+
+再次感谢你为 `GPUMDkit` 做出贡献！你的努力帮助这个工具包为整个 GPUMD 和 NEP 社区变得更好。🚀
diff --git a/README_zh-CN.md b/docs/README_zh-CN.md
similarity index 93%
rename from README_zh-CN.md
rename to docs/README_zh-CN.md
index 2c162e0..724f605 100644
--- a/README_zh-CN.md
+++ b/docs/README_zh-CN.md
@@ -1,13 +1,13 @@
 <p align="center">
-  <img src="./docs/Gallery/gpumdkit_logo_lateral.png" width="55%" alt="GPUMDkit Logo">
+  <img src="./Gallery/gpumdkit_logo_lateral.png" width="55%" alt="GPUMDkit Logo">
 </p>
 <p align="center">
-  <a href="./README.md">English</a>
+  <a href="../README.md">English</a>
   &nbsp;·&nbsp;
   <strong>简体中文</strong>
   &nbsp;·&nbsp;
   <a href="https://zhyan0603.github.io/GPUMDkit/">Website</a> &nbsp;·&nbsp;
-  <a href="https://zhyan0603.github.io/GPUMDkit/htmls/tutorials.html">Documentation</a>
+  <a href="https://zhyan0603.github.io/GPUMDkit/htmls/index.html">Documentation</a>
   &nbsp;·&nbsp;
   <a href="https://zhyan0603.github.io/GPUMDkit/gallery.html">Gallery</a>
   &nbsp;
@@ -103,7 +103,7 @@ wget https://github.com/zhyan0603/GPUMDkit/archive/refs/heads/main.zip
              | |_| |  __/| |_| | |  | | |_| |   <| | |_
               \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
     
-              GPUMDkit Version 1.5.5 (dev) (2026-05-10)
+              GPUMDkit Version 1.5.6 (dev) (2026-06-17)
         Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
      Main Contributors: Denan LI, Xin WU, Zhoulin LIU & Chen HUA
     
@@ -133,7 +133,7 @@ gpumdkit.sh -h
 
 ```
 +-------------------------------------------------------------------------------------------------------+
-|                          GPUMDkit 1.5.5 (dev) (2026-05-10) Command Help                               |
+|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
 +-------------------------------------------------------------------------------------------------------+
 |                                          MAIN FUNCTIONS                                               |
 +-------------------------------------------------------------------------------------------------------+
@@ -159,8 +159,8 @@ gpumdkit.sh -h
 | -chem_species Analyze chemical species        | -cbc               Charge balance check               |
 | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-| -pynep        FPS sampling by PyNEP           |                                                       |
+| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
+| -pynep        Deprecated PyNEP sampling       |                                                       |
 +-------------------------------------------------------------------------------------------------------+
 | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
 +-------------------------------------------------------------------------------------------------------+
@@ -176,7 +176,7 @@ gpumdkit.sh -plt -h
 
 ```
  +-----------------------------------------------------------------------------------------------+
- |                     GPUMDkit 1.5.5 (dev) (2026-05-10) PLOT & VISUALIZATION TOOLS              |
+ |                     GPUMDkit 1.5.6 (dev) (2026-06-17) PLOT & VISUALIZATION TOOLS              |
  +-----------------------------------------------------------------------------------------------+
  |  Usage: gpumdkit.sh -plt <type>                        Help: gpumdkit.sh -plt <type> -h       |
  +-----------------------------------------------------------------------------------------------+
@@ -235,7 +235,7 @@ gpumdkit.sh -plt train
 ```
 
 <div align="center">
-    <img src="./docs/Gallery/train.png" alt="msd" width="75%" />
+    <img src="./Gallery/train.png" alt="msd" width="75%" />
 </div>
 
 ##### 示例 5：绘制 parity 图
@@ -245,7 +245,7 @@ gpumdkit.sh -plt test
 ```
 
 <div align="center">
-    <img src="./docs/Gallery/prediction.png" alt="msd" width="95%" />
+    <img src="./Gallery/prediction.png" alt="msd" width="95%" />
 </div>
 
 ##### 示例 6：绘制 thermo 演化图
@@ -256,7 +256,7 @@ gpumdkit.sh -plt test
 gpumdkit.sh -plt thermo
 ```
 
-![](./docs/Gallery/thermo.png)
+![](./Gallery/thermo.png)
 
 如果当前设备不支持显示图形，也可以将图片保存为 PNG：
 
@@ -264,13 +264,13 @@ gpumdkit.sh -plt thermo
 gpumdkit.sh -plt thermo save
 ```
 
-更多详细示例和命令选项请参考我们的[文档](https://zhyan0603.github.io/GPUMDkit/htmls/tutorials.html)。
+更多详细示例和命令选项请参考我们的[文档](https://zhyan0603.github.io/GPUMDkit/)。
 
 #### 自定义命令
 
 `GPUMDkit` 支持通过 `~/.gpumdkit.in` 文件自定义命令。
 
-你可以在该文件中定义函数来添加自己的快捷命令（例如 `gpumdkit.sh -yourcommand`），从而扩展 `GPUMDkit` 的功能。详细用法请参见[此处](https://zhyan0603.github.io/GPUMDkit/htmls/custom_commands.html)。
+你可以在该文件中定义函数来添加自己的快捷命令（例如 `gpumdkit.sh -yourcommand`），从而扩展 `GPUMDkit` 的功能。详细用法请参见[自定义命令文档](https://zhyan0603.github.io/GPUMDkit/)。
 
 #### Tab 补全支持
 
diff --git a/docs/command_reference.tsv b/docs/command_reference.tsv
new file mode 100644
index 0000000..6799d2f
--- /dev/null
+++ b/docs/command_reference.tsv
@@ -0,0 +1,49 @@
+category	command	syntax	description_en	description_zh	status
+main	-h	gpumdkit.sh -h	Show general command help	显示通用命令帮助	stable
+main	-update	gpumdkit.sh -update	Update GPUMDkit from GitHub	从 GitHub 更新 GPUMDkit	stable
+main	-clean	gpumdkit.sh -clean	Clean extra files in current directory	清理当前目录中的冗余文件	stable
+format	-out2xyz	gpumdkit.sh -out2xyz <dir>	Convert VASP OUTCAR files to extxyz (shell version)	将 VASP OUTCAR 转换为 extxyz（shell 版本）	stable
+format	-out2exyz	gpumdkit.sh -out2exyz <dir>	Convert VASP OUTCAR files to extxyz (Python version)	将 VASP OUTCAR 转换为 extxyz（Python 版本）	stable
+format	-cp2k2xyz	gpumdkit.sh -cp2k2xyz	Convert CP2K output to xyz/extxyz	转换 CP2K 输出为 xyz/extxyz	stable
+format	-xdat2exyz	gpumdkit.sh -xdat2exyz <XDATCAR> <output.xyz>	Convert XDATCAR to extxyz	将 XDATCAR 转换为 extxyz	stable
+format	-cif2pos	gpumdkit.sh -cif2pos <input.cif> <output.vasp>	Convert CIF to POSCAR/VASP	将 CIF 转换为 POSCAR/VASP	stable
+format	-cif2exyz	gpumdkit.sh -cif2exyz <input.cif> <output.xyz>	Convert CIF to extxyz	将 CIF 转换为 extxyz	stable
+format	-pos2exyz	gpumdkit.sh -pos2exyz <POSCAR> <output.xyz>	Convert POSCAR to extxyz	将 POSCAR 转换为 extxyz	stable
+format	-exyz2pos	gpumdkit.sh -exyz2pos <input.xyz>	Convert extxyz frames to POSCAR files	将 extxyz 帧转换为 POSCAR 文件	stable
+format	-pos2lmp	gpumdkit.sh -pos2lmp <POSCAR> <output.data>	Convert POSCAR to LAMMPS data	将 POSCAR 转换为 LAMMPS data	stable
+format	-lmp2exyz	gpumdkit.sh -lmp2exyz <dump> <element...>	Convert LAMMPS dump to extxyz	将 LAMMPS dump 转换为 extxyz	stable
+format	-traj2exyz	gpumdkit.sh -traj2exyz <input.traj> <output.xyz>	Convert ASE trajectory to extxyz	将 ASE trajectory 转换为 extxyz	stable
+format	-replicate	gpumdkit.sh -replicate <input> <output> a b c	Replicate a structure by cell factors	按晶胞倍数扩胞	stable
+format	-replicate	gpumdkit.sh -replicate <input> <output> <target_num>	Replicate a structure toward a target atom count	按目标原子数扩胞	stable
+format	-addgroup	gpumdkit.sh -addgroup <POSCAR> <element...>	Add GPUMD group labels	添加 GPUMD group 标签	stable
+format	-addweight	gpumdkit.sh -addweight <input.xyz> <output.xyz> <weight>	Add structure weights to extxyz	为 extxyz 添加结构权重	stable
+format	-get_frame	gpumdkit.sh -get_frame <input.xyz> <frame_index>	Extract one frame from extxyz	从 extxyz 提取单帧	stable
+format	-clean_xyz	gpumdkit.sh -clean_xyz <input.xyz> <output.xyz>	Remove extra properties from extxyz	清理 extxyz 中的冗余属性	stable
+format	-frame_range	gpumdkit.sh -frame_range <input.xyz> <start_frac> <end_frac>	Extract frames by fractional range	按比例范围提取帧	stable
+sampling	-pynep	gpumdkit.sh -pynep	Run PyNEP FPS sampling	运行 PyNEP FPS 采样	deprecated
+calc	-calc ionic-cond	gpumdkit.sh -calc ionic-cond <element> <charge>	Calculate ionic conductivity	计算离子电导率	stable
+calc	-calc nep	gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>	Predict properties with a NEP model	使用 NEP 模型预测性质	stable
+calc	-calc des	gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>	Calculate NEP descriptors	计算 NEP 描述符	stable
+calc	-calc doas	gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>	Calculate density of atomistic states	计算原子态密度	stable
+calc	-calc neb	gpumdkit.sh -calc neb <initial.xyz> <final.xyz> <n_images> <nep.txt>	Run NEB with a NEP model	使用 NEP 模型运行 NEB	stable
+calc	-calc minimize	gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]	Minimize a structure with a NEP model	使用 NEP 模型优化结构	stable
+calc	-calc msd	gpumdkit.sh -calc msd <trajectory.xyz> <element> <dt_fs> [max_corr_steps]	Calculate MSD from trajectory	从轨迹计算 MSD	stable
+calc	-calc nlist	gpumdkit.sh -calc nlist [args...]	Build neighbor lists	构建邻居列表	stable
+calc	-calc disp	gpumdkit.sh -calc disp [args...]	Calculate displacements	计算位移	stable
+calc	-calc avg-struct	gpumdkit.sh -calc avg-struct [args...]	Calculate averaged structure	计算平均结构	stable
+calc	-calc oct-tilt	gpumdkit.sh -calc oct-tilt [args...]	Calculate octahedral tilt	计算八面体倾斜	stable
+calc	-calc pol-abo3	gpumdkit.sh -calc pol-abo3 [args...]	Calculate ABO3 local polarization	计算 ABO3 局域极化	stable
+analyze	-range	gpumdkit.sh -range <input.xyz> <energy|force|virial> [hist]	Analyze property ranges	分析性质范围	stable
+analyze	-analyze_comp	gpumdkit.sh -analyze_comp <input.xyz>	Analyze structure composition	分析结构成分	stable
+analyze	-chem_species	gpumdkit.sh -chem_species <input.xyz>	List chemical species	列出化学元素	stable
+analyze	-cbc	gpumdkit.sh -cbc <input.xyz>	Check charge balance	检查电荷平衡	stable
+analyze	-min_dist	gpumdkit.sh -min_dist <input.xyz>	Calculate minimum distance without PBC	计算无 PBC 最小距离	stable
+analyze	-min_dist_pbc	gpumdkit.sh -min_dist_pbc <input.xyz>	Calculate minimum distance with PBC	计算带 PBC 最小距离	stable
+analyze	-filter_dist	gpumdkit.sh -filter_dist <input.xyz> <min_dist>	Filter structures by minimum distance	按最小距离过滤结构	stable
+analyze	-filter_dist_pbc	gpumdkit.sh -filter_dist_pbc <input.xyz> <min_dist>	Filter structures by minimum distance with PBC	按带 PBC 最小距离过滤结构	stable
+analyze	-filter_box	gpumdkit.sh -filter_box <input.xyz> <edge_limit>	Filter structures by box-edge limit	按盒子边长过滤结构	stable
+analyze	-filter_value	gpumdkit.sh -filter_value <input.xyz> <property> <threshold>	Filter structures by property threshold	按性质阈值过滤结构	stable
+analyze	-filter_range	gpumdkit.sh -filter_range <input.xyz> <element1> <element2> <min_dist> <max_dist>	Filter by element-pair distance range	按元素对距离范围过滤	stable
+analyze	-pda	gpumdkit.sh -pda <ref_struct> <trajectory.xyz> <species> <interval>	Calculate probability density	计算概率密度	stable
+utility	-time	gpumdkit.sh -time <gpumd|nep>	Monitor GPUMD or NEP progress	监控 GPUMD 或 NEP 进度	stable
+utility	-nep_modifier	gpumdkit.sh -nep_modifier	Modify NEP model interactively	交互式修改 NEP 模型	stable
diff --git a/docs/gallery.html b/docs/gallery.html
index 932b19d..9f8a223 100644
--- a/docs/gallery.html
+++ b/docs/gallery.html
@@ -220,7 +220,7 @@
         <button class="mobile-menu-btn" style="display: none;">☰</button>
         <nav class="nav-links">
             <a href="index.html" class="nav-item">Home</a>            
-            <a href="htmls/tutorials.html" class="nav-item">Documentation</a>
+            <a href="htmls/index.html" class="nav-item">Documentation</a>
             <a href="gallery.html" class="nav-item" style="color: var(--text-gpumd);">Gallery</a>
             <a href="publications.html" class="nav-item">Publications</a>            
             <!-- <a href="https://github.com/zhyan0603/GPUMDkit" class="nav-item">Join Us</a> -->
@@ -250,7 +250,7 @@
                 <div class="footer-column">
                     <h4>Quick Links</h4>
                     <ul>
-                        <li><a href="htmls/tutorials.html">Documentation</a></li>
+                        <li><a href="htmls/index.html">Documentation</a></li>
                         <li><a href="gallery.html">Gallery</a></li>
                         <li><a href="publications.html">Publications</a></li>
                         <li><a href="https://github.com/zhyan0603/GPUMDkit/archive/refs/heads/main.zip">Download</a></li>
diff --git a/docs/htmls/404.html b/docs/htmls/404.html
new file mode 100644
index 0000000..f5696e3
--- /dev/null
+++ b/docs/htmls/404.html
@@ -0,0 +1,1274 @@
+
+<!doctype html>
+<html lang="en" class="no-js">
+  <head>
+    
+      <meta charset="utf-8">
+      <meta name="viewport" content="width=device-width,initial-scale=1">
+      
+        <meta name="description" content="Tutorials for GPUMDkit.">
+      
+      
+        <meta name="author" content="Zihan YAN">
+      
+      
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+      
+      <link rel="icon" href="/GPUMDkit/assets/images/favicon.png">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.7.6">
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+    
+      
+        <title>GPUMDkit Tutorial</title>
+      
+    
+    
+      <link rel="stylesheet" href="/GPUMDkit/assets/stylesheets/main.484c7ddc.min.css">
+      
+        
+        <link rel="stylesheet" href="/GPUMDkit/assets/stylesheets/palette.ab4e12ef.min.css">
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+      <a href="/GPUMDkit/index.html" class="md-nav__link">
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+      <a href="/GPUMDkit/en/index.html" class="md-nav__link">
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+    <li class="md-nav__item">
+      <a href="/GPUMDkit/en/quick_start.html" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Quick Start
+  
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+  
+  
+
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+    </li>
+  
+
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+      <a href="/GPUMDkit/en/command_reference.html" class="md-nav__link">
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+    
+  
+    Command Reference
+  
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+  </span>
+  
+  
+
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+  
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+              
+            
+              
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+  
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+    <li class="md-nav__item">
+      <a href="/GPUMDkit/en/format_conversion.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Format Conversion
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/GPUMDkit/en/structure_sampling.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Structure Sampling
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
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+  
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+    <li class="md-nav__item">
+      <a href="/GPUMDkit/en/workflow_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Workflow Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/GPUMDkit/en/calculator_scripts.html" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Calculator Scripts
+  
+
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+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/GPUMDkit/en/analyzer_scripts.html" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Analyzer Scripts
+  
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+  
+  
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+  
+
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+            
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+    <li class="md-nav__item">
+      <a href="/GPUMDkit/en/plot_scripts.html" class="md-nav__link">
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+    
+  
+    Plot Scripts
+  
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+  
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+    </li>
+  
+
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+    <li class="md-nav__item">
+      <a href="/GPUMDkit/en/custom_commands.html" class="md-nav__link">
+        
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+    
+  
+    Custom Commands
+  
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+  
+  
+
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+    </li>
+  
+
+              
+            
+              
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+  
+  
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+    <li class="md-nav__item">
+      <a href="/GPUMDkit/en/active_learning_workflow.html" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
+  
+    Active Learning Workflow
+  
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+    
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+  
+  
+
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+  
+
+              
+            
+              
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+    <li class="md-nav__item">
+      <a href="/GPUMDkit/en/polar_material_analysis.html" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Polar Material Analysis
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
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+    <li class="md-nav__item">
+      <a href="/GPUMDkit/en/contributing_to_gpumdkit.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
+
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+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
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+      
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+            
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+    
+  
+    简体中文
+  
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+  
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+        
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+      <a href="/GPUMDkit/zh/index.html" class="md-nav__link">
+        
+  
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+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit 教程
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
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+      <a href="/GPUMDkit/zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/GPUMDkit/zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/GPUMDkit/zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/GPUMDkit/zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/GPUMDkit/zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/GPUMDkit/zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/GPUMDkit/zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
+              
+                
+  
+  
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rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}.statediagram-state rect.divider{fill:var(--md-default-fg-color--lightest);stroke:var(--md-default-fg-color--lighter)}defs #statediagram-barbEnd{stroke:var(--md-mermaid-edge-color)}[id^=entity] path,[id^=entity] rect{fill:var(--md-default-bg-color)}.relationshipLine{stroke:var(--md-mermaid-edge-color)}defs .marker.oneOrMore.er *,defs .marker.onlyOne.er *,defs .marker.zeroOrMore.er *,defs .marker.zeroOrOne.er *{stroke:var(--md-mermaid-edge-color)!important}text:not([class]):last-child{fill:var(--md-mermaid-label-fg-color)}.actor{fill:var(--md-mermaid-sequence-actor-bg-color);stroke:var(--md-mermaid-sequence-actor-border-color)}text.actor>tspan{fill:var(--md-mermaid-sequence-actor-fg-color);font-family:var(--md-mermaid-font-family)}line{stroke:var(--md-mermaid-sequence-actor-line-color)}.actor-man circle,.actor-man 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H(()=>{let r=new T;r.subscribe({next({active:n}){e.classList.toggle("md-header__title--active",n)},complete(){e.classList.remove("md-header__title--active")}});let o=ue(".md-content h1");return typeof o=="undefined"?y:fs(o,t).pipe(O(n=>r.next(n)),A(()=>r.complete()),m(n=>P({ref:e},n)))})}function pi(e,{viewport$:t,header$:r}){let o=r.pipe(m(({height:i})=>i),Y()),n=o.pipe(b(()=>Le(e).pipe(m(({height:i})=>({top:e.offsetTop,bottom:e.offsetTop+i})),ne("bottom"))));return z([o,n,t]).pipe(m(([i,{top:s,bottom:a},{offset:{y:c},size:{height:p}}])=>(p=Math.max(0,p-Math.max(0,s-c,i)-Math.max(0,p+c-a)),{offset:s-i,height:p,active:s-i<=c})),Y((i,s)=>i.offset===s.offset&&i.height===s.height&&i.active===s.active))}function us(e){let t=__md_get("__palette")||{index:e.findIndex(o=>matchMedia(o.getAttribute("data-md-color-media")).matches)},r=Math.max(0,Math.min(t.index,e.length-1));return 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ji({document$:e,tablet$:t}){e.pipe(b(()=>M(".md-toggle--indeterminate")),O(r=>{r.indeterminate=!0,r.checked=!1}),J(r=>h(r,"change").pipe(Jr(()=>r.classList.contains("md-toggle--indeterminate")),m(()=>r))),te(t)).subscribe(([r,o])=>{r.classList.remove("md-toggle--indeterminate"),o&&(r.checked=!1)})}function Cs(){return/(iPad|iPhone|iPod)/.test(navigator.userAgent)}function Ui({document$:e}){e.pipe(b(()=>M("[data-md-scrollfix]")),O(t=>t.removeAttribute("data-md-scrollfix")),g(Cs),J(t=>h(t,"touchstart").pipe(m(()=>t)))).subscribe(t=>{let r=t.scrollTop;r===0?t.scrollTop=1:r+t.offsetHeight===t.scrollHeight&&(t.scrollTop=r-1)})}function Wi({viewport$:e,tablet$:t}){z([Je("search"),t]).pipe(m(([r,o])=>r&&!o),b(r=>$(r).pipe(nt(r?400:100))),te(e)).subscribe(([r,{offset:{y:o}}])=>{if(r)document.body.setAttribute("data-md-scrolllock",""),document.body.style.top=`-${o}px`;else{let 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ft=ai(Ce("header"),{viewport$:ke}),qt=ct.pipe(m(()=>Ce("main")),b(e=>pi(e,{viewport$:ke,header$:ft})),Z(1)),Hs=L(...me("consent").map(e=>An(e,{target$:Ht})),...me("dialog").map(e=>ni(e,{alert$:fo})),...me("palette").map(e=>li(e)),...me("progress").map(e=>mi(e,{progress$:uo})),...me("search").map(e=>_i(e,{index$:zi,keyboard$:mo})),...me("source").map(e=>$i(e))),$s=H(()=>L(...me("announce").map(e=>_n(e)),...me("content").map(e=>oi(e,{sitemap$:qi,viewport$:ke,target$:Ht,print$:Ni})),...me("content").map(e=>V("search.highlight")?Ai(e,{index$:zi,location$:Kt}):y),...me("header").map(e=>si(e,{viewport$:ke,header$:ft,main$:qt})),...me("header-title").map(e=>ci(e,{viewport$:ke,header$:ft})),...me("sidebar").map(e=>e.getAttribute("data-md-type")==="navigation"?eo(Vi,()=>lo(e,{viewport$:ke,header$:ft,main$:qt})):eo(Lr,()=>lo(e,{viewport$:ke,header$:ft,main$:qt}))),...me("tabs").map(e=>Pi(e,{viewport$:ke,header$:ft})),...me("toc").map(e=>Ri(e,{viewport$:ke,header$:ft,main$:qt,target$:Ht})),...me("top").map(e=>Ii(e,{viewport$:ke,header$:ft,main$:qt,target$:Ht})))),Ki=ct.pipe(b(()=>$s),Ve(Hs),Z(1));Ki.subscribe();window.document$=ct;window.location$=Kt;window.target$=Ht;window.keyboard$=mo;window.viewport$=ke;window.tablet$=Lr;window.screen$=Vi;window.print$=Ni;window.alert$=fo;window.progress$=uo;window.component$=Ki;})();
+//# sourceMappingURL=bundle.79ae519e.min.js.map
+
diff --git a/docs/htmls/assets/javascripts/bundle.79ae519e.min.js.map b/docs/htmls/assets/javascripts/bundle.79ae519e.min.js.map
new file mode 100644
index 0000000..5cf0289
--- /dev/null
+++ b/docs/htmls/assets/javascripts/bundle.79ae519e.min.js.map
@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["node_modules/focus-visible/dist/focus-visible.js", "node_modules/escape-html/index.js", "node_modules/clipboard/dist/clipboard.js", "src/templates/assets/javascripts/bundle.ts", "node_modules/tslib/tslib.es6.mjs", "node_modules/rxjs/src/internal/util/isFunction.ts", "node_modules/rxjs/src/internal/util/createErrorClass.ts", "node_modules/rxjs/src/internal/util/UnsubscriptionError.ts", "node_modules/rxjs/src/internal/util/arrRemove.ts", "node_modules/rxjs/src/internal/Subscription.ts", "node_modules/rxjs/src/internal/config.ts", "node_modules/rxjs/src/internal/scheduler/timeoutProvider.ts", "node_modules/rxjs/src/internal/util/reportUnhandledError.ts", "node_modules/rxjs/src/internal/util/noop.ts", "node_modules/rxjs/src/internal/NotificationFactories.ts", "node_modules/rxjs/src/internal/util/errorContext.ts", "node_modules/rxjs/src/internal/Subscriber.ts", "node_modules/rxjs/src/internal/symbol/observable.ts", "node_modules/rxjs/src/internal/util/identity.ts", 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+  "sourcesContent": ["(function (global, factory) {\n  typeof exports === 'object' && typeof module !== 'undefined' ? factory() :\n  typeof define === 'function' && define.amd ? define(factory) :\n  (factory());\n}(this, (function () { 'use strict';\n\n  /**\n   * Applies the :focus-visible polyfill at the given scope.\n   * A scope in this case is either the top-level Document or a Shadow Root.\n   *\n   * @param {(Document|ShadowRoot)} scope\n   * @see https://github.com/WICG/focus-visible\n   */\n  function applyFocusVisiblePolyfill(scope) {\n    var hadKeyboardEvent = true;\n    var hadFocusVisibleRecently = false;\n    var hadFocusVisibleRecentlyTimeout = null;\n\n    var inputTypesAllowlist = {\n      text: true,\n      search: true,\n      url: true,\n      tel: true,\n      email: true,\n      password: true,\n      number: true,\n      date: true,\n      month: true,\n      week: true,\n      time: true,\n      datetime: true,\n      'datetime-local': true\n    };\n\n    /**\n     * Helper function for legacy browsers and iframes which sometimes focus\n     * elements like document, body, and non-interactive SVG.\n     * @param {Element} el\n     */\n    function isValidFocusTarget(el) {\n      if (\n        el &&\n        el !== document &&\n        el.nodeName !== 'HTML' &&\n        el.nodeName !== 'BODY' &&\n        'classList' in el &&\n        'contains' in el.classList\n      ) {\n        return true;\n      }\n      return false;\n    }\n\n    /**\n     * Computes whether the given element should automatically trigger the\n     * `focus-visible` class being added, i.e. whether it should always match\n     * `:focus-visible` when focused.\n     * @param {Element} el\n     * @return {boolean}\n     */\n    function focusTriggersKeyboardModality(el) {\n      var type = el.type;\n      var tagName = el.tagName;\n\n      if (tagName === 'INPUT' && inputTypesAllowlist[type] && !el.readOnly) {\n        return true;\n      }\n\n      if (tagName === 'TEXTAREA' && !el.readOnly) {\n        return true;\n      }\n\n      if (el.isContentEditable) {\n        return true;\n      }\n\n      return false;\n    }\n\n    /**\n     * Add the `focus-visible` class to the given element if it was not added by\n     * the author.\n     * @param {Element} el\n     */\n    function addFocusVisibleClass(el) {\n      if (el.classList.contains('focus-visible')) {\n        return;\n      }\n      el.classList.add('focus-visible');\n      el.setAttribute('data-focus-visible-added', '');\n    }\n\n    /**\n     * Remove the `focus-visible` class from the given element if it was not\n     * originally added by the author.\n     * @param {Element} el\n     */\n    function removeFocusVisibleClass(el) {\n      if (!el.hasAttribute('data-focus-visible-added')) {\n        return;\n      }\n      el.classList.remove('focus-visible');\n      el.removeAttribute('data-focus-visible-added');\n    }\n\n    /**\n     * If the most recent user interaction was via the keyboard;\n     * and the key press did not include a meta, alt/option, or control key;\n     * then the modality is keyboard. Otherwise, the modality is not keyboard.\n     * Apply `focus-visible` to any current active element and keep track\n     * of our keyboard modality state with `hadKeyboardEvent`.\n     * @param {KeyboardEvent} e\n     */\n    function onKeyDown(e) {\n      if (e.metaKey || e.altKey || e.ctrlKey) {\n        return;\n      }\n\n      if (isValidFocusTarget(scope.activeElement)) {\n        addFocusVisibleClass(scope.activeElement);\n      }\n\n      hadKeyboardEvent = true;\n    }\n\n    /**\n     * If at any point a user clicks with a pointing device, ensure that we change\n     * the modality away from keyboard.\n     * This avoids the situation where a user presses a key on an already focused\n     * element, and then clicks on a different element, focusing it with a\n     * pointing device, while we still think we're in keyboard modality.\n     * @param {Event} e\n     */\n    function onPointerDown(e) {\n      hadKeyboardEvent = false;\n    }\n\n    /**\n     * On `focus`, add the `focus-visible` class to the target if:\n     * - the target received focus as a result of keyboard navigation, or\n     * - the event target is an element that will likely require interaction\n     *   via the keyboard (e.g. a text box)\n     * @param {Event} e\n     */\n    function onFocus(e) {\n      // Prevent IE from focusing the document or HTML element.\n      if (!isValidFocusTarget(e.target)) {\n        return;\n      }\n\n      if (hadKeyboardEvent || focusTriggersKeyboardModality(e.target)) {\n        addFocusVisibleClass(e.target);\n      }\n    }\n\n    /**\n     * On `blur`, remove the `focus-visible` class from the target.\n     * @param {Event} e\n     */\n    function onBlur(e) {\n      if (!isValidFocusTarget(e.target)) {\n        return;\n      }\n\n      if (\n        e.target.classList.contains('focus-visible') ||\n        e.target.hasAttribute('data-focus-visible-added')\n      ) {\n        // To detect a tab/window switch, we look for a blur event followed\n        // rapidly by a visibility change.\n        // If we don't see a visibility change within 100ms, it's probably a\n        // regular focus change.\n        hadFocusVisibleRecently = true;\n        window.clearTimeout(hadFocusVisibleRecentlyTimeout);\n        hadFocusVisibleRecentlyTimeout = window.setTimeout(function() {\n          hadFocusVisibleRecently = false;\n        }, 100);\n        removeFocusVisibleClass(e.target);\n      }\n    }\n\n    /**\n     * If the user changes tabs, keep track of whether or not the previously\n     * focused element had .focus-visible.\n     * @param {Event} e\n     */\n    function onVisibilityChange(e) {\n      if (document.visibilityState === 'hidden') {\n        // If the tab becomes active again, the browser will handle calling focus\n        // on the element (Safari actually calls it twice).\n        // If this tab change caused a blur on an element with focus-visible,\n        // re-apply the class when the user switches back to the tab.\n        if (hadFocusVisibleRecently) {\n          hadKeyboardEvent = true;\n        }\n        addInitialPointerMoveListeners();\n      }\n    }\n\n    /**\n     * Add a group of listeners to detect usage of any pointing devices.\n     * These listeners will be added when the polyfill first loads, and anytime\n     * the window is blurred, so that they are active when the window regains\n     * focus.\n     */\n    function addInitialPointerMoveListeners() {\n      document.addEventListener('mousemove', onInitialPointerMove);\n      document.addEventListener('mousedown', onInitialPointerMove);\n      document.addEventListener('mouseup', onInitialPointerMove);\n      document.addEventListener('pointermove', onInitialPointerMove);\n      document.addEventListener('pointerdown', onInitialPointerMove);\n      document.addEventListener('pointerup', onInitialPointerMove);\n      document.addEventListener('touchmove', onInitialPointerMove);\n      document.addEventListener('touchstart', onInitialPointerMove);\n      document.addEventListener('touchend', onInitialPointerMove);\n    }\n\n    function removeInitialPointerMoveListeners() {\n      document.removeEventListener('mousemove', onInitialPointerMove);\n      document.removeEventListener('mousedown', onInitialPointerMove);\n      document.removeEventListener('mouseup', onInitialPointerMove);\n      document.removeEventListener('pointermove', onInitialPointerMove);\n      document.removeEventListener('pointerdown', onInitialPointerMove);\n      document.removeEventListener('pointerup', onInitialPointerMove);\n      document.removeEventListener('touchmove', onInitialPointerMove);\n      document.removeEventListener('touchstart', onInitialPointerMove);\n      document.removeEventListener('touchend', onInitialPointerMove);\n    }\n\n    /**\n     * When the polfyill first loads, assume the user is in keyboard modality.\n     * If any event is received from a pointing device (e.g. mouse, pointer,\n     * touch), turn off keyboard modality.\n     * This accounts for situations where focus enters the page from the URL bar.\n     * @param {Event} e\n     */\n    function onInitialPointerMove(e) {\n      // Work around a Safari quirk that fires a mousemove on <html> whenever the\n      // window blurs, even if you're tabbing out of the page. \u00AF\\_(\u30C4)_/\u00AF\n      if (e.target.nodeName && e.target.nodeName.toLowerCase() === 'html') {\n        return;\n      }\n\n      hadKeyboardEvent = false;\n      removeInitialPointerMoveListeners();\n    }\n\n    // For some kinds of state, we are interested in changes at the global scope\n    // only. For example, global pointer input, global key presses and global\n    // visibility change should affect the state at every scope:\n    document.addEventListener('keydown', onKeyDown, true);\n    document.addEventListener('mousedown', onPointerDown, true);\n    document.addEventListener('pointerdown', onPointerDown, true);\n    document.addEventListener('touchstart', onPointerDown, true);\n    document.addEventListener('visibilitychange', onVisibilityChange, true);\n\n    addInitialPointerMoveListeners();\n\n    // For focus and blur, we specifically care about state changes in the local\n    // scope. This is because focus / blur events that originate from within a\n    // shadow root are not re-dispatched from the host element if it was already\n    // the active element in its own scope:\n    scope.addEventListener('focus', onFocus, true);\n    scope.addEventListener('blur', onBlur, true);\n\n    // We detect that a node is a ShadowRoot by ensuring that it is a\n    // DocumentFragment and also has a host property. This check covers native\n    // implementation and polyfill implementation transparently. If we only cared\n    // about the native implementation, we could just check if the scope was\n    // an instance of a ShadowRoot.\n    if (scope.nodeType === Node.DOCUMENT_FRAGMENT_NODE && scope.host) {\n      // Since a ShadowRoot is a special kind of DocumentFragment, it does not\n      // have a root element to add a class to. So, we add this attribute to the\n      // host element instead:\n      scope.host.setAttribute('data-js-focus-visible', '');\n    } else if (scope.nodeType === Node.DOCUMENT_NODE) {\n      document.documentElement.classList.add('js-focus-visible');\n      document.documentElement.setAttribute('data-js-focus-visible', '');\n    }\n  }\n\n  // It is important to wrap all references to global window and document in\n  // these checks to support server-side rendering use cases\n  // @see https://github.com/WICG/focus-visible/issues/199\n  if (typeof window !== 'undefined' && typeof document !== 'undefined') {\n    // Make the polyfill helper globally available. This can be used as a signal\n    // to interested libraries that wish to coordinate with the polyfill for e.g.,\n    // applying the polyfill to a shadow root:\n    window.applyFocusVisiblePolyfill = applyFocusVisiblePolyfill;\n\n    // Notify interested libraries of the polyfill's presence, in case the\n    // polyfill was loaded lazily:\n    var event;\n\n    try {\n      event = new CustomEvent('focus-visible-polyfill-ready');\n    } catch (error) {\n      // IE11 does not support using CustomEvent as a constructor directly:\n      event = document.createEvent('CustomEvent');\n      event.initCustomEvent('focus-visible-polyfill-ready', false, false, {});\n    }\n\n    window.dispatchEvent(event);\n  }\n\n  if (typeof document !== 'undefined') {\n    // Apply the polyfill to the global document, so that no JavaScript\n    // coordination is required to use the polyfill in the top-level document:\n    applyFocusVisiblePolyfill(document);\n  }\n\n})));\n", "/*!\n * escape-html\n * Copyright(c) 2012-2013 TJ Holowaychuk\n * Copyright(c) 2015 Andreas Lubbe\n * Copyright(c) 2015 Tiancheng \"Timothy\" Gu\n * MIT Licensed\n */\n\n'use strict';\n\n/**\n * Module variables.\n * @private\n */\n\nvar matchHtmlRegExp = /[\"'&<>]/;\n\n/**\n * Module exports.\n * @public\n */\n\nmodule.exports = escapeHtml;\n\n/**\n * Escape special characters in the given string of html.\n *\n * @param  {string} string The string to escape for inserting into HTML\n * @return {string}\n * @public\n */\n\nfunction escapeHtml(string) {\n  var str = '' + string;\n  var match = matchHtmlRegExp.exec(str);\n\n  if (!match) {\n    return str;\n  }\n\n  var escape;\n  var html = '';\n  var index = 0;\n  var lastIndex = 0;\n\n  for (index = match.index; index < str.length; index++) {\n    switch (str.charCodeAt(index)) {\n      case 34: // \"\n        escape = '&quot;';\n        break;\n      case 38: // &\n        escape = '&amp;';\n        break;\n      case 39: // '\n        escape = '&#39;';\n        break;\n      case 60: // <\n        escape = '&lt;';\n        break;\n      case 62: // >\n        escape = '&gt;';\n        break;\n      default:\n        continue;\n    }\n\n    if (lastIndex !== index) {\n      html += str.substring(lastIndex, index);\n    }\n\n    lastIndex = index + 1;\n    html += escape;\n  }\n\n  return lastIndex !== index\n    ? html + str.substring(lastIndex, index)\n    : html;\n}\n", "/*!\n * clipboard.js v2.0.11\n * https://clipboardjs.com/\n *\n * Licensed MIT \u00A9 Zeno Rocha\n */\n(function webpackUniversalModuleDefinition(root, factory) {\n\tif(typeof exports === 'object' && typeof module === 'object')\n\t\tmodule.exports = factory();\n\telse if(typeof define === 'function' && define.amd)\n\t\tdefine([], factory);\n\telse if(typeof exports === 'object')\n\t\texports[\"ClipboardJS\"] = factory();\n\telse\n\t\troot[\"ClipboardJS\"] = factory();\n})(this, function() {\nreturn /******/ (function() { // webpackBootstrap\n/******/ \tvar __webpack_modules__ = ({\n\n/***/ 686:\n/***/ (function(__unused_webpack_module, __webpack_exports__, __webpack_require__) {\n\n\"use strict\";\n\n// EXPORTS\n__webpack_require__.d(__webpack_exports__, {\n  \"default\": function() { return /* binding */ clipboard; }\n});\n\n// EXTERNAL MODULE: ./node_modules/tiny-emitter/index.js\nvar tiny_emitter = __webpack_require__(279);\nvar tiny_emitter_default = /*#__PURE__*/__webpack_require__.n(tiny_emitter);\n// EXTERNAL MODULE: ./node_modules/good-listener/src/listen.js\nvar listen = __webpack_require__(370);\nvar listen_default = /*#__PURE__*/__webpack_require__.n(listen);\n// EXTERNAL MODULE: ./node_modules/select/src/select.js\nvar src_select = __webpack_require__(817);\nvar select_default = /*#__PURE__*/__webpack_require__.n(src_select);\n;// CONCATENATED MODULE: ./src/common/command.js\n/**\n * Executes a given operation type.\n * @param {String} type\n * @return {Boolean}\n */\nfunction command(type) {\n  try {\n    return document.execCommand(type);\n  } catch (err) {\n    return false;\n  }\n}\n;// CONCATENATED MODULE: ./src/actions/cut.js\n\n\n/**\n * Cut action wrapper.\n * @param {String|HTMLElement} target\n * @return {String}\n */\n\nvar ClipboardActionCut = function ClipboardActionCut(target) {\n  var selectedText = select_default()(target);\n  command('cut');\n  return selectedText;\n};\n\n/* harmony default export */ var actions_cut = (ClipboardActionCut);\n;// CONCATENATED MODULE: ./src/common/create-fake-element.js\n/**\n * Creates a fake textarea element with a value.\n * @param {String} value\n * @return {HTMLElement}\n */\nfunction createFakeElement(value) {\n  var isRTL = document.documentElement.getAttribute('dir') === 'rtl';\n  var fakeElement = document.createElement('textarea'); // Prevent zooming on iOS\n\n  fakeElement.style.fontSize = '12pt'; // Reset box model\n\n  fakeElement.style.border = '0';\n  fakeElement.style.padding = '0';\n  fakeElement.style.margin = '0'; // Move element out of screen horizontally\n\n  fakeElement.style.position = 'absolute';\n  fakeElement.style[isRTL ? 'right' : 'left'] = '-9999px'; // Move element to the same position vertically\n\n  var yPosition = window.pageYOffset || document.documentElement.scrollTop;\n  fakeElement.style.top = \"\".concat(yPosition, \"px\");\n  fakeElement.setAttribute('readonly', '');\n  fakeElement.value = value;\n  return fakeElement;\n}\n;// CONCATENATED MODULE: ./src/actions/copy.js\n\n\n\n/**\n * Create fake copy action wrapper using a fake element.\n * @param {String} target\n * @param {Object} options\n * @return {String}\n */\n\nvar fakeCopyAction = function fakeCopyAction(value, options) {\n  var fakeElement = createFakeElement(value);\n  options.container.appendChild(fakeElement);\n  var selectedText = select_default()(fakeElement);\n  command('copy');\n  fakeElement.remove();\n  return selectedText;\n};\n/**\n * Copy action wrapper.\n * @param {String|HTMLElement} target\n * @param {Object} options\n * @return {String}\n */\n\n\nvar ClipboardActionCopy = function ClipboardActionCopy(target) {\n  var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n    container: document.body\n  };\n  var selectedText = '';\n\n  if (typeof target === 'string') {\n    selectedText = fakeCopyAction(target, options);\n  } else if (target instanceof HTMLInputElement && !['text', 'search', 'url', 'tel', 'password'].includes(target === null || target === void 0 ? void 0 : target.type)) {\n    // If input type doesn't support `setSelectionRange`. Simulate it. https://developer.mozilla.org/en-US/docs/Web/API/HTMLInputElement/setSelectionRange\n    selectedText = fakeCopyAction(target.value, options);\n  } else {\n    selectedText = select_default()(target);\n    command('copy');\n  }\n\n  return selectedText;\n};\n\n/* harmony default export */ var actions_copy = (ClipboardActionCopy);\n;// CONCATENATED MODULE: ./src/actions/default.js\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { _typeof = function _typeof(obj) { return typeof obj; }; } else { _typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return _typeof(obj); }\n\n\n\n/**\n * Inner function which performs selection from either `text` or `target`\n * properties and then executes copy or cut operations.\n * @param {Object} options\n */\n\nvar ClipboardActionDefault = function ClipboardActionDefault() {\n  var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n  // Defines base properties passed from constructor.\n  var _options$action = options.action,\n      action = _options$action === void 0 ? 'copy' : _options$action,\n      container = options.container,\n      target = options.target,\n      text = options.text; // Sets the `action` to be performed which can be either 'copy' or 'cut'.\n\n  if (action !== 'copy' && action !== 'cut') {\n    throw new Error('Invalid \"action\" value, use either \"copy\" or \"cut\"');\n  } // Sets the `target` property using an element that will be have its content copied.\n\n\n  if (target !== undefined) {\n    if (target && _typeof(target) === 'object' && target.nodeType === 1) {\n      if (action === 'copy' && target.hasAttribute('disabled')) {\n        throw new Error('Invalid \"target\" attribute. Please use \"readonly\" instead of \"disabled\" attribute');\n      }\n\n      if (action === 'cut' && (target.hasAttribute('readonly') || target.hasAttribute('disabled'))) {\n        throw new Error('Invalid \"target\" attribute. You can\\'t cut text from elements with \"readonly\" or \"disabled\" attributes');\n      }\n    } else {\n      throw new Error('Invalid \"target\" value, use a valid Element');\n    }\n  } // Define selection strategy based on `text` property.\n\n\n  if (text) {\n    return actions_copy(text, {\n      container: container\n    });\n  } // Defines which selection strategy based on `target` property.\n\n\n  if (target) {\n    return action === 'cut' ? actions_cut(target) : actions_copy(target, {\n      container: container\n    });\n  }\n};\n\n/* harmony default export */ var actions_default = (ClipboardActionDefault);\n;// CONCATENATED MODULE: ./src/clipboard.js\nfunction clipboard_typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { clipboard_typeof = function _typeof(obj) { return typeof obj; }; } else { clipboard_typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return clipboard_typeof(obj); }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (clipboard_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Date.prototype.toString.call(Reflect.construct(Date, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n\n\n\n\n\n/**\n * Helper function to retrieve attribute value.\n * @param {String} suffix\n * @param {Element} element\n */\n\nfunction getAttributeValue(suffix, element) {\n  var attribute = \"data-clipboard-\".concat(suffix);\n\n  if (!element.hasAttribute(attribute)) {\n    return;\n  }\n\n  return element.getAttribute(attribute);\n}\n/**\n * Base class which takes one or more elements, adds event listeners to them,\n * and instantiates a new `ClipboardAction` on each click.\n */\n\n\nvar Clipboard = /*#__PURE__*/function (_Emitter) {\n  _inherits(Clipboard, _Emitter);\n\n  var _super = _createSuper(Clipboard);\n\n  /**\n   * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n   * @param {Object} options\n   */\n  function Clipboard(trigger, options) {\n    var _this;\n\n    _classCallCheck(this, Clipboard);\n\n    _this = _super.call(this);\n\n    _this.resolveOptions(options);\n\n    _this.listenClick(trigger);\n\n    return _this;\n  }\n  /**\n   * Defines if attributes would be resolved using internal setter functions\n   * or custom functions that were passed in the constructor.\n   * @param {Object} options\n   */\n\n\n  _createClass(Clipboard, [{\n    key: \"resolveOptions\",\n    value: function resolveOptions() {\n      var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n      this.action = typeof options.action === 'function' ? options.action : this.defaultAction;\n      this.target = typeof options.target === 'function' ? options.target : this.defaultTarget;\n      this.text = typeof options.text === 'function' ? options.text : this.defaultText;\n      this.container = clipboard_typeof(options.container) === 'object' ? options.container : document.body;\n    }\n    /**\n     * Adds a click event listener to the passed trigger.\n     * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n     */\n\n  }, {\n    key: \"listenClick\",\n    value: function listenClick(trigger) {\n      var _this2 = this;\n\n      this.listener = listen_default()(trigger, 'click', function (e) {\n        return _this2.onClick(e);\n      });\n    }\n    /**\n     * Defines a new `ClipboardAction` on each click event.\n     * @param {Event} e\n     */\n\n  }, {\n    key: \"onClick\",\n    value: function onClick(e) {\n      var trigger = e.delegateTarget || e.currentTarget;\n      var action = this.action(trigger) || 'copy';\n      var text = actions_default({\n        action: action,\n        container: this.container,\n        target: this.target(trigger),\n        text: this.text(trigger)\n      }); // Fires an event based on the copy operation result.\n\n      this.emit(text ? 'success' : 'error', {\n        action: action,\n        text: text,\n        trigger: trigger,\n        clearSelection: function clearSelection() {\n          if (trigger) {\n            trigger.focus();\n          }\n\n          window.getSelection().removeAllRanges();\n        }\n      });\n    }\n    /**\n     * Default `action` lookup function.\n     * @param {Element} trigger\n     */\n\n  }, {\n    key: \"defaultAction\",\n    value: function defaultAction(trigger) {\n      return getAttributeValue('action', trigger);\n    }\n    /**\n     * Default `target` lookup function.\n     * @param {Element} trigger\n     */\n\n  }, {\n    key: \"defaultTarget\",\n    value: function defaultTarget(trigger) {\n      var selector = getAttributeValue('target', trigger);\n\n      if (selector) {\n        return document.querySelector(selector);\n      }\n    }\n    /**\n     * Allow fire programmatically a copy action\n     * @param {String|HTMLElement} target\n     * @param {Object} options\n     * @returns Text copied.\n     */\n\n  }, {\n    key: \"defaultText\",\n\n    /**\n     * Default `text` lookup function.\n     * @param {Element} trigger\n     */\n    value: function defaultText(trigger) {\n      return getAttributeValue('text', trigger);\n    }\n    /**\n     * Destroy lifecycle.\n     */\n\n  }, {\n    key: \"destroy\",\n    value: function destroy() {\n      this.listener.destroy();\n    }\n  }], [{\n    key: \"copy\",\n    value: function copy(target) {\n      var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n        container: document.body\n      };\n      return actions_copy(target, options);\n    }\n    /**\n     * Allow fire programmatically a cut action\n     * @param {String|HTMLElement} target\n     * @returns Text cutted.\n     */\n\n  }, {\n    key: \"cut\",\n    value: function cut(target) {\n      return actions_cut(target);\n    }\n    /**\n     * Returns the support of the given action, or all actions if no action is\n     * given.\n     * @param {String} [action]\n     */\n\n  }, {\n    key: \"isSupported\",\n    value: function isSupported() {\n      var action = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : ['copy', 'cut'];\n      var actions = typeof action === 'string' ? [action] : action;\n      var support = !!document.queryCommandSupported;\n      actions.forEach(function (action) {\n        support = support && !!document.queryCommandSupported(action);\n      });\n      return support;\n    }\n  }]);\n\n  return Clipboard;\n}((tiny_emitter_default()));\n\n/* harmony default export */ var clipboard = (Clipboard);\n\n/***/ }),\n\n/***/ 828:\n/***/ (function(module) {\n\nvar DOCUMENT_NODE_TYPE = 9;\n\n/**\n * A polyfill for Element.matches()\n */\nif (typeof Element !== 'undefined' && !Element.prototype.matches) {\n    var proto = Element.prototype;\n\n    proto.matches = proto.matchesSelector ||\n                    proto.mozMatchesSelector ||\n                    proto.msMatchesSelector ||\n                    proto.oMatchesSelector ||\n                    proto.webkitMatchesSelector;\n}\n\n/**\n * Finds the closest parent that matches a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @return {Function}\n */\nfunction closest (element, selector) {\n    while (element && element.nodeType !== DOCUMENT_NODE_TYPE) {\n        if (typeof element.matches === 'function' &&\n            element.matches(selector)) {\n          return element;\n        }\n        element = element.parentNode;\n    }\n}\n\nmodule.exports = closest;\n\n\n/***/ }),\n\n/***/ 438:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar closest = __webpack_require__(828);\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction _delegate(element, selector, type, callback, useCapture) {\n    var listenerFn = listener.apply(this, arguments);\n\n    element.addEventListener(type, listenerFn, useCapture);\n\n    return {\n        destroy: function() {\n            element.removeEventListener(type, listenerFn, useCapture);\n        }\n    }\n}\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element|String|Array} [elements]\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction delegate(elements, selector, type, callback, useCapture) {\n    // Handle the regular Element usage\n    if (typeof elements.addEventListener === 'function') {\n        return _delegate.apply(null, arguments);\n    }\n\n    // Handle Element-less usage, it defaults to global delegation\n    if (typeof type === 'function') {\n        // Use `document` as the first parameter, then apply arguments\n        // This is a short way to .unshift `arguments` without running into deoptimizations\n        return _delegate.bind(null, document).apply(null, arguments);\n    }\n\n    // Handle Selector-based usage\n    if (typeof elements === 'string') {\n        elements = document.querySelectorAll(elements);\n    }\n\n    // Handle Array-like based usage\n    return Array.prototype.map.call(elements, function (element) {\n        return _delegate(element, selector, type, callback, useCapture);\n    });\n}\n\n/**\n * Finds closest match and invokes callback.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Function}\n */\nfunction listener(element, selector, type, callback) {\n    return function(e) {\n        e.delegateTarget = closest(e.target, selector);\n\n        if (e.delegateTarget) {\n            callback.call(element, e);\n        }\n    }\n}\n\nmodule.exports = delegate;\n\n\n/***/ }),\n\n/***/ 879:\n/***/ (function(__unused_webpack_module, exports) {\n\n/**\n * Check if argument is a HTML element.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.node = function(value) {\n    return value !== undefined\n        && value instanceof HTMLElement\n        && value.nodeType === 1;\n};\n\n/**\n * Check if argument is a list of HTML elements.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.nodeList = function(value) {\n    var type = Object.prototype.toString.call(value);\n\n    return value !== undefined\n        && (type === '[object NodeList]' || type === '[object HTMLCollection]')\n        && ('length' in value)\n        && (value.length === 0 || exports.node(value[0]));\n};\n\n/**\n * Check if argument is a string.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.string = function(value) {\n    return typeof value === 'string'\n        || value instanceof String;\n};\n\n/**\n * Check if argument is a function.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.fn = function(value) {\n    var type = Object.prototype.toString.call(value);\n\n    return type === '[object Function]';\n};\n\n\n/***/ }),\n\n/***/ 370:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar is = __webpack_require__(879);\nvar delegate = __webpack_require__(438);\n\n/**\n * Validates all params and calls the right\n * listener function based on its target type.\n *\n * @param {String|HTMLElement|HTMLCollection|NodeList} target\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listen(target, type, callback) {\n    if (!target && !type && !callback) {\n        throw new Error('Missing required arguments');\n    }\n\n    if (!is.string(type)) {\n        throw new TypeError('Second argument must be a String');\n    }\n\n    if (!is.fn(callback)) {\n        throw new TypeError('Third argument must be a Function');\n    }\n\n    if (is.node(target)) {\n        return listenNode(target, type, callback);\n    }\n    else if (is.nodeList(target)) {\n        return listenNodeList(target, type, callback);\n    }\n    else if (is.string(target)) {\n        return listenSelector(target, type, callback);\n    }\n    else {\n        throw new TypeError('First argument must be a String, HTMLElement, HTMLCollection, or NodeList');\n    }\n}\n\n/**\n * Adds an event listener to a HTML element\n * and returns a remove listener function.\n *\n * @param {HTMLElement} node\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNode(node, type, callback) {\n    node.addEventListener(type, callback);\n\n    return {\n        destroy: function() {\n            node.removeEventListener(type, callback);\n        }\n    }\n}\n\n/**\n * Add an event listener to a list of HTML elements\n * and returns a remove listener function.\n *\n * @param {NodeList|HTMLCollection} nodeList\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNodeList(nodeList, type, callback) {\n    Array.prototype.forEach.call(nodeList, function(node) {\n        node.addEventListener(type, callback);\n    });\n\n    return {\n        destroy: function() {\n            Array.prototype.forEach.call(nodeList, function(node) {\n                node.removeEventListener(type, callback);\n            });\n        }\n    }\n}\n\n/**\n * Add an event listener to a selector\n * and returns a remove listener function.\n *\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenSelector(selector, type, callback) {\n    return delegate(document.body, selector, type, callback);\n}\n\nmodule.exports = listen;\n\n\n/***/ }),\n\n/***/ 817:\n/***/ (function(module) {\n\nfunction select(element) {\n    var selectedText;\n\n    if (element.nodeName === 'SELECT') {\n        element.focus();\n\n        selectedText = element.value;\n    }\n    else if (element.nodeName === 'INPUT' || element.nodeName === 'TEXTAREA') {\n        var isReadOnly = element.hasAttribute('readonly');\n\n        if (!isReadOnly) {\n            element.setAttribute('readonly', '');\n        }\n\n        element.select();\n        element.setSelectionRange(0, element.value.length);\n\n        if (!isReadOnly) {\n            element.removeAttribute('readonly');\n        }\n\n        selectedText = element.value;\n    }\n    else {\n        if (element.hasAttribute('contenteditable')) {\n            element.focus();\n        }\n\n        var selection = window.getSelection();\n        var range = document.createRange();\n\n        range.selectNodeContents(element);\n        selection.removeAllRanges();\n        selection.addRange(range);\n\n        selectedText = selection.toString();\n    }\n\n    return selectedText;\n}\n\nmodule.exports = select;\n\n\n/***/ }),\n\n/***/ 279:\n/***/ (function(module) {\n\nfunction E () {\n  // Keep this empty so it's easier to inherit from\n  // (via https://github.com/lipsmack from https://github.com/scottcorgan/tiny-emitter/issues/3)\n}\n\nE.prototype = {\n  on: function (name, callback, ctx) {\n    var e = this.e || (this.e = {});\n\n    (e[name] || (e[name] = [])).push({\n      fn: callback,\n      ctx: ctx\n    });\n\n    return this;\n  },\n\n  once: function (name, callback, ctx) {\n    var self = this;\n    function listener () {\n      self.off(name, listener);\n      callback.apply(ctx, arguments);\n    };\n\n    listener._ = callback\n    return this.on(name, listener, ctx);\n  },\n\n  emit: function (name) {\n    var data = [].slice.call(arguments, 1);\n    var evtArr = ((this.e || (this.e = {}))[name] || []).slice();\n    var i = 0;\n    var len = evtArr.length;\n\n    for (i; i < len; i++) {\n      evtArr[i].fn.apply(evtArr[i].ctx, data);\n    }\n\n    return this;\n  },\n\n  off: function (name, callback) {\n    var e = this.e || (this.e = {});\n    var evts = e[name];\n    var liveEvents = [];\n\n    if (evts && callback) {\n      for (var i = 0, len = evts.length; i < len; i++) {\n        if (evts[i].fn !== callback && evts[i].fn._ !== callback)\n          liveEvents.push(evts[i]);\n      }\n    }\n\n    // Remove event from queue to prevent memory leak\n    // Suggested by https://github.com/lazd\n    // Ref: https://github.com/scottcorgan/tiny-emitter/commit/c6ebfaa9bc973b33d110a84a307742b7cf94c953#commitcomment-5024910\n\n    (liveEvents.length)\n      ? e[name] = liveEvents\n      : delete e[name];\n\n    return this;\n  }\n};\n\nmodule.exports = E;\nmodule.exports.TinyEmitter = E;\n\n\n/***/ })\n\n/******/ \t});\n/************************************************************************/\n/******/ \t// The module cache\n/******/ \tvar __webpack_module_cache__ = {};\n/******/ \t\n/******/ \t// The require function\n/******/ \tfunction __webpack_require__(moduleId) {\n/******/ \t\t// Check if module is in cache\n/******/ \t\tif(__webpack_module_cache__[moduleId]) {\n/******/ \t\t\treturn __webpack_module_cache__[moduleId].exports;\n/******/ \t\t}\n/******/ \t\t// Create a new module (and put it into the cache)\n/******/ \t\tvar module = __webpack_module_cache__[moduleId] = {\n/******/ \t\t\t// no module.id needed\n/******/ \t\t\t// no module.loaded needed\n/******/ \t\t\texports: {}\n/******/ \t\t};\n/******/ \t\n/******/ \t\t// Execute the module function\n/******/ \t\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n/******/ \t\n/******/ \t\t// Return the exports of the module\n/******/ \t\treturn module.exports;\n/******/ \t}\n/******/ \t\n/************************************************************************/\n/******/ \t/* webpack/runtime/compat get default export */\n/******/ \t!function() {\n/******/ \t\t// getDefaultExport function for compatibility with non-harmony modules\n/******/ \t\t__webpack_require__.n = function(module) {\n/******/ \t\t\tvar getter = module && module.__esModule ?\n/******/ \t\t\t\tfunction() { return module['default']; } :\n/******/ \t\t\t\tfunction() { return module; };\n/******/ \t\t\t__webpack_require__.d(getter, { a: getter });\n/******/ \t\t\treturn getter;\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/define property getters */\n/******/ \t!function() {\n/******/ \t\t// define getter functions for harmony exports\n/******/ \t\t__webpack_require__.d = function(exports, definition) {\n/******/ \t\t\tfor(var key in definition) {\n/******/ \t\t\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n/******/ \t\t\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n/******/ \t\t\t\t}\n/******/ \t\t\t}\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/hasOwnProperty shorthand */\n/******/ \t!function() {\n/******/ \t\t__webpack_require__.o = function(obj, prop) { return Object.prototype.hasOwnProperty.call(obj, prop); }\n/******/ \t}();\n/******/ \t\n/************************************************************************/\n/******/ \t// module exports must be returned from runtime so entry inlining is disabled\n/******/ \t// startup\n/******/ \t// Load entry module and return exports\n/******/ \treturn __webpack_require__(686);\n/******/ })()\n.default;\n});", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport \"focus-visible\"\n\nimport {\n  EMPTY,\n  NEVER,\n  Observable,\n  Subject,\n  defer,\n  delay,\n  filter,\n  map,\n  merge,\n  mergeWith,\n  shareReplay,\n  switchMap\n} from \"rxjs\"\n\nimport { configuration, feature } from \"./_\"\nimport {\n  at,\n  getActiveElement,\n  getOptionalElement,\n  requestJSON,\n  setLocation,\n  setToggle,\n  watchDocument,\n  watchKeyboard,\n  watchLocation,\n  watchLocationTarget,\n  watchMedia,\n  watchPrint,\n  watchScript,\n  watchViewport\n} from \"./browser\"\nimport {\n  getComponentElement,\n  getComponentElements,\n  mountAnnounce,\n  mountBackToTop,\n  mountConsent,\n  mountContent,\n  mountDialog,\n  mountHeader,\n  mountHeaderTitle,\n  mountPalette,\n  mountProgress,\n  mountSearch,\n  mountSearchHiglight,\n  mountSidebar,\n  mountSource,\n  mountTableOfContents,\n  mountTabs,\n  watchHeader,\n  watchMain\n} from \"./components\"\nimport {\n  SearchIndex,\n  fetchSitemap,\n  setupAlternate,\n  setupClipboardJS,\n  setupInstantNavigation,\n  setupVersionSelector\n} from \"./integrations\"\nimport {\n  patchEllipsis,\n  patchIndeterminate,\n  patchScrollfix,\n  patchScrolllock\n} from \"./patches\"\nimport \"./polyfills\"\n\n/* ----------------------------------------------------------------------------\n * Functions - @todo refactor\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch search index\n *\n * @returns Search index observable\n */\nfunction fetchSearchIndex(): Observable<SearchIndex> {\n  if (location.protocol === \"file:\") {\n    return watchScript(\n      `${new URL(\"search/search_index.js\", config.base)}`\n    )\n      .pipe(\n        // @ts-ignore - @todo fix typings\n        map(() => __index),\n        shareReplay(1)\n      )\n  } else {\n    return requestJSON<SearchIndex>(\n      new URL(\"search/search_index.json\", config.base)\n    )\n  }\n}\n\n/* ----------------------------------------------------------------------------\n * Application\n * ------------------------------------------------------------------------- */\n\n/* Yay, JavaScript is available */\ndocument.documentElement.classList.remove(\"no-js\")\ndocument.documentElement.classList.add(\"js\")\n\n/* Set up navigation observables and subjects */\nconst document$ = watchDocument()\nconst location$ = watchLocation()\nconst target$   = watchLocationTarget(location$)\nconst keyboard$ = watchKeyboard()\n\n/* Set up media observables */\nconst viewport$ = watchViewport()\nconst tablet$   = watchMedia(\"(min-width: 60em)\")\nconst screen$   = watchMedia(\"(min-width: 76.25em)\")\nconst print$    = watchPrint()\n\n/* Retrieve search index, if search is enabled */\nconst config = configuration()\nconst index$ = document.forms.namedItem(\"search\")\n  ? fetchSearchIndex()\n  : NEVER\n\n/* Set up Clipboard.js integration */\nconst alert$ = new Subject<string>()\nsetupClipboardJS({ alert$ })\n\n/* Set up language selector */\nsetupAlternate({ document$ })\n\n/* Set up progress indicator */\nconst progress$ = new Subject<number>()\n\n/* Set up sitemap for instant navigation and previews */\nconst sitemap$ = fetchSitemap(config.base)\n\n/* Set up instant navigation, if enabled */\nif (feature(\"navigation.instant\"))\n  setupInstantNavigation({ sitemap$, location$, viewport$, progress$ })\n    .subscribe(document$)\n\n/* Set up version selector */\nif (config.version?.provider === \"mike\")\n  setupVersionSelector({ document$ })\n\n/* Always close drawer and search on navigation */\nmerge(location$, target$)\n  .pipe(\n    delay(125)\n  )\n    .subscribe(() => {\n      setToggle(\"drawer\", false)\n      setToggle(\"search\", false)\n    })\n\n/* Set up global keyboard handlers */\nkeyboard$\n  .pipe(\n    filter(({ mode }) => mode === \"global\")\n  )\n    .subscribe(key => {\n      switch (key.type) {\n\n        /* Go to previous page */\n        case \"p\":\n        case \",\":\n          const prev = getOptionalElement<HTMLLinkElement>(\"link[rel=prev]\")\n          if (typeof prev !== \"undefined\")\n            setLocation(prev)\n          break\n\n        /* Go to next page */\n        case \"n\":\n        case \".\":\n          const next = getOptionalElement<HTMLLinkElement>(\"link[rel=next]\")\n          if (typeof next !== \"undefined\")\n            setLocation(next)\n          break\n\n        /* Expand navigation, see https://bit.ly/3ZjG5io */\n        case \"Enter\":\n          const active = getActiveElement()\n          if (active instanceof HTMLLabelElement)\n            active.click()\n      }\n    })\n\n/* Set up patches */\npatchEllipsis({ viewport$, document$ })\npatchIndeterminate({ document$, tablet$ })\npatchScrollfix({ document$ })\npatchScrolllock({ viewport$, tablet$ })\n\n/* Set up header and main area observable */\nconst header$ = watchHeader(getComponentElement(\"header\"), { viewport$ })\nconst main$ = document$\n  .pipe(\n    map(() => getComponentElement(\"main\")),\n    switchMap(el => watchMain(el, { viewport$, header$ })),\n    shareReplay(1)\n  )\n\n/* Set up control component observables */\nconst control$ = merge(\n\n  /* Consent */\n  ...getComponentElements(\"consent\")\n    .map(el => mountConsent(el, { target$ })),\n\n  /* Dialog */\n  ...getComponentElements(\"dialog\")\n    .map(el => mountDialog(el, { alert$ })),\n\n  /* Color palette */\n  ...getComponentElements(\"palette\")\n    .map(el => mountPalette(el)),\n\n  /* Progress bar */\n  ...getComponentElements(\"progress\")\n    .map(el => mountProgress(el, { progress$ })),\n\n  /* Search */\n  ...getComponentElements(\"search\")\n    .map(el => mountSearch(el, { index$, keyboard$ })),\n\n  /* Repository information */\n  ...getComponentElements(\"source\")\n    .map(el => mountSource(el))\n)\n\n/* Set up content component observables */\nconst content$ = defer(() => merge(\n\n  /* Announcement bar */\n  ...getComponentElements(\"announce\")\n    .map(el => mountAnnounce(el)),\n\n  /* Content */\n  ...getComponentElements(\"content\")\n    .map(el => mountContent(el, { sitemap$, viewport$, target$, print$ })),\n\n  /* Search highlighting */\n  ...getComponentElements(\"content\")\n    .map(el => feature(\"search.highlight\")\n      ? mountSearchHiglight(el, { index$, location$ })\n      : EMPTY\n    ),\n\n  /* Header */\n  ...getComponentElements(\"header\")\n    .map(el => mountHeader(el, { viewport$, header$, main$ })),\n\n  /* Header title */\n  ...getComponentElements(\"header-title\")\n    .map(el => mountHeaderTitle(el, { viewport$, header$ })),\n\n  /* Sidebar */\n  ...getComponentElements(\"sidebar\")\n    .map(el => el.getAttribute(\"data-md-type\") === \"navigation\"\n      ? at(screen$, () => mountSidebar(el, { viewport$, header$, main$ }))\n      : at(tablet$, () => mountSidebar(el, { viewport$, header$, main$ }))\n    ),\n\n  /* Navigation tabs */\n  ...getComponentElements(\"tabs\")\n    .map(el => mountTabs(el, { viewport$, header$ })),\n\n  /* Table of contents */\n  ...getComponentElements(\"toc\")\n    .map(el => mountTableOfContents(el, {\n      viewport$, header$, main$, target$\n    })),\n\n  /* Back-to-top button */\n  ...getComponentElements(\"top\")\n    .map(el => mountBackToTop(el, { viewport$, header$, main$, target$ }))\n))\n\n/* Set up component observables */\nconst component$ = document$\n  .pipe(\n    switchMap(() => content$),\n    mergeWith(control$),\n    shareReplay(1)\n  )\n\n/* Subscribe to all components */\ncomponent$.subscribe()\n\n/* ----------------------------------------------------------------------------\n * Exports\n * ------------------------------------------------------------------------- */\n\nwindow.document$  = document$          /* Document observable */\nwindow.location$  = location$          /* Location subject */\nwindow.target$    = target$            /* Location target observable */\nwindow.keyboard$  = keyboard$          /* Keyboard observable */\nwindow.viewport$  = viewport$          /* Viewport observable */\nwindow.tablet$    = tablet$            /* Media tablet observable */\nwindow.screen$    = screen$            /* Media screen observable */\nwindow.print$     = print$             /* Media print observable */\nwindow.alert$     = alert$             /* Alert subject */\nwindow.progress$  = progress$          /* Progress indicator subject */\nwindow.component$ = component$         /* Component observable */\n", "/******************************************************************************\nCopyright (c) Microsoft Corporation.\n\nPermission to use, copy, modify, and/or distribute this software for any\npurpose with or without fee is hereby granted.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH\nREGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY\nAND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,\nINDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM\nLOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR\nOTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR\nPERFORMANCE OF THIS SOFTWARE.\n***************************************************************************** */\n/* global Reflect, Promise, SuppressedError, Symbol, Iterator */\n\nvar extendStatics = function(d, b) {\n  extendStatics = Object.setPrototypeOf ||\n      ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||\n      function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };\n  return extendStatics(d, b);\n};\n\nexport function __extends(d, b) {\n  if (typeof b !== \"function\" && b !== null)\n      throw new TypeError(\"Class extends value \" + String(b) + \" is not a constructor or null\");\n  extendStatics(d, b);\n  function __() { this.constructor = d; }\n  d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());\n}\n\nexport var __assign = function() {\n  __assign = Object.assign || function __assign(t) {\n      for (var s, i = 1, n = arguments.length; i < n; i++) {\n          s = arguments[i];\n          for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p)) t[p] = s[p];\n      }\n      return t;\n  }\n  return __assign.apply(this, arguments);\n}\n\nexport function __rest(s, e) {\n  var t = {};\n  for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)\n      t[p] = s[p];\n  if (s != null && typeof Object.getOwnPropertySymbols === \"function\")\n      for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {\n          if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))\n              t[p[i]] = s[p[i]];\n      }\n  return t;\n}\n\nexport function __decorate(decorators, target, key, desc) {\n  var c = arguments.length, r = c < 3 ? target : desc === null ? desc = Object.getOwnPropertyDescriptor(target, key) : desc, d;\n  if (typeof Reflect === \"object\" && typeof Reflect.decorate === \"function\") r = Reflect.decorate(decorators, target, key, desc);\n  else for (var i = decorators.length - 1; i >= 0; i--) if (d = decorators[i]) r = (c < 3 ? d(r) : c > 3 ? d(target, key, r) : d(target, key)) || r;\n  return c > 3 && r && Object.defineProperty(target, key, r), r;\n}\n\nexport function __param(paramIndex, decorator) {\n  return function (target, key) { decorator(target, key, paramIndex); }\n}\n\nexport function __esDecorate(ctor, descriptorIn, decorators, contextIn, initializers, extraInitializers) {\n  function accept(f) { if (f !== void 0 && typeof f !== \"function\") throw new TypeError(\"Function expected\"); return f; }\n  var kind = contextIn.kind, key = kind === \"getter\" ? \"get\" : kind === \"setter\" ? \"set\" : \"value\";\n  var target = !descriptorIn && ctor ? contextIn[\"static\"] ? ctor : ctor.prototype : null;\n  var descriptor = descriptorIn || (target ? Object.getOwnPropertyDescriptor(target, contextIn.name) : {});\n  var _, done = false;\n  for (var i = decorators.length - 1; i >= 0; i--) {\n      var context = {};\n      for (var p in contextIn) context[p] = p === \"access\" ? {} : contextIn[p];\n      for (var p in contextIn.access) context.access[p] = contextIn.access[p];\n      context.addInitializer = function (f) { if (done) throw new TypeError(\"Cannot add initializers after decoration has completed\"); extraInitializers.push(accept(f || null)); };\n      var result = (0, decorators[i])(kind === \"accessor\" ? { get: descriptor.get, set: descriptor.set } : descriptor[key], context);\n      if (kind === \"accessor\") {\n          if (result === void 0) continue;\n          if (result === null || typeof result !== \"object\") throw new TypeError(\"Object expected\");\n          if (_ = accept(result.get)) descriptor.get = _;\n          if (_ = accept(result.set)) descriptor.set = _;\n          if (_ = accept(result.init)) initializers.unshift(_);\n      }\n      else if (_ = accept(result)) {\n          if (kind === \"field\") initializers.unshift(_);\n          else descriptor[key] = _;\n      }\n  }\n  if (target) Object.defineProperty(target, contextIn.name, descriptor);\n  done = true;\n};\n\nexport function __runInitializers(thisArg, initializers, value) {\n  var useValue = arguments.length > 2;\n  for (var i = 0; i < initializers.length; i++) {\n      value = useValue ? initializers[i].call(thisArg, value) : initializers[i].call(thisArg);\n  }\n  return useValue ? value : void 0;\n};\n\nexport function __propKey(x) {\n  return typeof x === \"symbol\" ? x : \"\".concat(x);\n};\n\nexport function __setFunctionName(f, name, prefix) {\n  if (typeof name === \"symbol\") name = name.description ? \"[\".concat(name.description, \"]\") : \"\";\n  return Object.defineProperty(f, \"name\", { configurable: true, value: prefix ? \"\".concat(prefix, \" \", name) : name });\n};\n\nexport function __metadata(metadataKey, metadataValue) {\n  if (typeof Reflect === \"object\" && typeof Reflect.metadata === \"function\") return Reflect.metadata(metadataKey, metadataValue);\n}\n\nexport function __awaiter(thisArg, _arguments, P, generator) {\n  function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }\n  return new (P || (P = Promise))(function (resolve, reject) {\n      function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }\n      function rejected(value) { try { step(generator[\"throw\"](value)); } catch (e) { reject(e); } }\n      function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }\n      step((generator = generator.apply(thisArg, _arguments || [])).next());\n  });\n}\n\nexport function __generator(thisArg, body) {\n  var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g = Object.create((typeof Iterator === \"function\" ? Iterator : Object).prototype);\n  return g.next = verb(0), g[\"throw\"] = verb(1), g[\"return\"] = verb(2), typeof Symbol === \"function\" && (g[Symbol.iterator] = function() { return this; }), g;\n  function verb(n) { return function (v) { return step([n, v]); }; }\n  function step(op) {\n      if (f) throw new TypeError(\"Generator is already executing.\");\n      while (g && (g = 0, op[0] && (_ = 0)), _) try {\n          if (f = 1, y && (t = op[0] & 2 ? y[\"return\"] : op[0] ? y[\"throw\"] || ((t = y[\"return\"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;\n          if (y = 0, t) op = [op[0] & 2, t.value];\n          switch (op[0]) {\n              case 0: case 1: t = op; break;\n              case 4: _.label++; return { value: op[1], done: false };\n              case 5: _.label++; y = op[1]; op = [0]; continue;\n              case 7: op = _.ops.pop(); _.trys.pop(); continue;\n              default:\n                  if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }\n                  if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }\n                  if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }\n                  if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }\n                  if (t[2]) _.ops.pop();\n                  _.trys.pop(); continue;\n          }\n          op = body.call(thisArg, _);\n      } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }\n      if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };\n  }\n}\n\nexport var __createBinding = Object.create ? (function(o, m, k, k2) {\n  if (k2 === undefined) k2 = k;\n  var desc = Object.getOwnPropertyDescriptor(m, k);\n  if (!desc || (\"get\" in desc ? !m.__esModule : desc.writable || desc.configurable)) {\n      desc = { enumerable: true, get: function() { return m[k]; } };\n  }\n  Object.defineProperty(o, k2, desc);\n}) : (function(o, m, k, k2) {\n  if (k2 === undefined) k2 = k;\n  o[k2] = m[k];\n});\n\nexport function __exportStar(m, o) {\n  for (var p in m) if (p !== \"default\" && !Object.prototype.hasOwnProperty.call(o, p)) __createBinding(o, m, p);\n}\n\nexport function __values(o) {\n  var s = typeof Symbol === \"function\" && Symbol.iterator, m = s && o[s], i = 0;\n  if (m) return m.call(o);\n  if (o && typeof o.length === \"number\") return {\n      next: function () {\n          if (o && i >= o.length) o = void 0;\n          return { value: o && o[i++], done: !o };\n      }\n  };\n  throw new TypeError(s ? \"Object is not iterable.\" : \"Symbol.iterator is not defined.\");\n}\n\nexport function __read(o, n) {\n  var m = typeof Symbol === \"function\" && o[Symbol.iterator];\n  if (!m) return o;\n  var i = m.call(o), r, ar = [], e;\n  try {\n      while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);\n  }\n  catch (error) { e = { error: error }; }\n  finally {\n      try {\n          if (r && !r.done && (m = i[\"return\"])) m.call(i);\n      }\n      finally { if (e) throw e.error; }\n  }\n  return ar;\n}\n\n/** @deprecated */\nexport function __spread() {\n  for (var ar = [], i = 0; i < arguments.length; i++)\n      ar = ar.concat(__read(arguments[i]));\n  return ar;\n}\n\n/** @deprecated */\nexport function __spreadArrays() {\n  for (var s = 0, i = 0, il = arguments.length; i < il; i++) s += arguments[i].length;\n  for (var r = Array(s), k = 0, i = 0; i < il; i++)\n      for (var a = arguments[i], j = 0, jl = a.length; j < jl; j++, k++)\n          r[k] = a[j];\n  return r;\n}\n\nexport function __spreadArray(to, from, pack) {\n  if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {\n      if (ar || !(i in from)) {\n          if (!ar) ar = Array.prototype.slice.call(from, 0, i);\n          ar[i] = from[i];\n      }\n  }\n  return to.concat(ar || Array.prototype.slice.call(from));\n}\n\nexport function __await(v) {\n  return this instanceof __await ? (this.v = v, this) : new __await(v);\n}\n\nexport function __asyncGenerator(thisArg, _arguments, generator) {\n  if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\n  var g = generator.apply(thisArg, _arguments || []), i, q = [];\n  return i = Object.create((typeof AsyncIterator === \"function\" ? AsyncIterator : Object).prototype), verb(\"next\"), verb(\"throw\"), verb(\"return\", awaitReturn), i[Symbol.asyncIterator] = function () { return this; }, i;\n  function awaitReturn(f) { return function (v) { return Promise.resolve(v).then(f, reject); }; }\n  function verb(n, f) { if (g[n]) { i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; if (f) i[n] = f(i[n]); } }\n  function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }\n  function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }\n  function fulfill(value) { resume(\"next\", value); }\n  function reject(value) { resume(\"throw\", value); }\n  function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }\n}\n\nexport function __asyncDelegator(o) {\n  var i, p;\n  return i = {}, verb(\"next\"), verb(\"throw\", function (e) { throw e; }), verb(\"return\"), i[Symbol.iterator] = function () { return this; }, i;\n  function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: false } : f ? f(v) : v; } : f; }\n}\n\nexport function __asyncValues(o) {\n  if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\n  var m = o[Symbol.asyncIterator], i;\n  return m ? m.call(o) : (o = typeof __values === \"function\" ? __values(o) : o[Symbol.iterator](), i = {}, verb(\"next\"), verb(\"throw\"), verb(\"return\"), i[Symbol.asyncIterator] = function () { return this; }, i);\n  function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }\n  function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }\n}\n\nexport function __makeTemplateObject(cooked, raw) {\n  if (Object.defineProperty) { Object.defineProperty(cooked, \"raw\", { value: raw }); } else { cooked.raw = raw; }\n  return cooked;\n};\n\nvar __setModuleDefault = Object.create ? (function(o, v) {\n  Object.defineProperty(o, \"default\", { enumerable: true, value: v });\n}) : function(o, v) {\n  o[\"default\"] = v;\n};\n\nexport function __importStar(mod) {\n  if (mod && mod.__esModule) return mod;\n  var result = {};\n  if (mod != null) for (var k in mod) if (k !== \"default\" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);\n  __setModuleDefault(result, mod);\n  return result;\n}\n\nexport function __importDefault(mod) {\n  return (mod && mod.__esModule) ? mod : { default: mod };\n}\n\nexport function __classPrivateFieldGet(receiver, state, kind, f) {\n  if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a getter\");\n  if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot read private member from an object whose class did not declare it\");\n  return kind === \"m\" ? f : kind === \"a\" ? f.call(receiver) : f ? f.value : state.get(receiver);\n}\n\nexport function __classPrivateFieldSet(receiver, state, value, kind, f) {\n  if (kind === \"m\") throw new TypeError(\"Private method is not writable\");\n  if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a setter\");\n  if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot write private member to an object whose class did not declare it\");\n  return (kind === \"a\" ? f.call(receiver, value) : f ? f.value = value : state.set(receiver, value)), value;\n}\n\nexport function __classPrivateFieldIn(state, receiver) {\n  if (receiver === null || (typeof receiver !== \"object\" && typeof receiver !== \"function\")) throw new TypeError(\"Cannot use 'in' operator on non-object\");\n  return typeof state === \"function\" ? receiver === state : state.has(receiver);\n}\n\nexport function __addDisposableResource(env, value, async) {\n  if (value !== null && value !== void 0) {\n    if (typeof value !== \"object\" && typeof value !== \"function\") throw new TypeError(\"Object expected.\");\n    var dispose, inner;\n    if (async) {\n      if (!Symbol.asyncDispose) throw new TypeError(\"Symbol.asyncDispose is not defined.\");\n      dispose = value[Symbol.asyncDispose];\n    }\n    if (dispose === void 0) {\n      if (!Symbol.dispose) throw new TypeError(\"Symbol.dispose is not defined.\");\n      dispose = value[Symbol.dispose];\n      if (async) inner = dispose;\n    }\n    if (typeof dispose !== \"function\") throw new TypeError(\"Object not disposable.\");\n    if (inner) dispose = function() { try { inner.call(this); } catch (e) { return Promise.reject(e); } };\n    env.stack.push({ value: value, dispose: dispose, async: async });\n  }\n  else if (async) {\n    env.stack.push({ async: true });\n  }\n  return value;\n}\n\nvar _SuppressedError = typeof SuppressedError === \"function\" ? SuppressedError : function (error, suppressed, message) {\n  var e = new Error(message);\n  return e.name = \"SuppressedError\", e.error = error, e.suppressed = suppressed, e;\n};\n\nexport function __disposeResources(env) {\n  function fail(e) {\n    env.error = env.hasError ? new _SuppressedError(e, env.error, \"An error was suppressed during disposal.\") : e;\n    env.hasError = true;\n  }\n  var r, s = 0;\n  function next() {\n    while (r = env.stack.pop()) {\n      try {\n        if (!r.async && s === 1) return s = 0, env.stack.push(r), Promise.resolve().then(next);\n        if (r.dispose) {\n          var result = r.dispose.call(r.value);\n          if (r.async) return s |= 2, Promise.resolve(result).then(next, function(e) { fail(e); return next(); });\n        }\n        else s |= 1;\n      }\n      catch (e) {\n        fail(e);\n      }\n    }\n    if (s === 1) return env.hasError ? Promise.reject(env.error) : Promise.resolve();\n    if (env.hasError) throw env.error;\n  }\n  return next();\n}\n\nexport default {\n  __extends,\n  __assign,\n  __rest,\n  __decorate,\n  __param,\n  __metadata,\n  __awaiter,\n  __generator,\n  __createBinding,\n  __exportStar,\n  __values,\n  __read,\n  __spread,\n  __spreadArrays,\n  __spreadArray,\n  __await,\n  __asyncGenerator,\n  __asyncDelegator,\n  __asyncValues,\n  __makeTemplateObject,\n  __importStar,\n  __importDefault,\n  __classPrivateFieldGet,\n  __classPrivateFieldSet,\n  __classPrivateFieldIn,\n  __addDisposableResource,\n  __disposeResources,\n};\n", "/**\n * Returns true if the object is a function.\n * @param value The value to check\n */\nexport function isFunction(value: any): value is (...args: any[]) => any {\n  return typeof value === 'function';\n}\n", "/**\n * Used to create Error subclasses until the community moves away from ES5.\n *\n * This is because compiling from TypeScript down to ES5 has issues with subclassing Errors\n * as well as other built-in types: https://github.com/Microsoft/TypeScript/issues/12123\n *\n * @param createImpl A factory function to create the actual constructor implementation. The returned\n * function should be a named function that calls `_super` internally.\n */\nexport function createErrorClass<T>(createImpl: (_super: any) => any): T {\n  const _super = (instance: any) => {\n    Error.call(instance);\n    instance.stack = new Error().stack;\n  };\n\n  const ctorFunc = createImpl(_super);\n  ctorFunc.prototype = Object.create(Error.prototype);\n  ctorFunc.prototype.constructor = ctorFunc;\n  return ctorFunc;\n}\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface UnsubscriptionError extends Error {\n  readonly errors: any[];\n}\n\nexport interface UnsubscriptionErrorCtor {\n  /**\n   * @deprecated Internal implementation detail. Do not construct error instances.\n   * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n   */\n  new (errors: any[]): UnsubscriptionError;\n}\n\n/**\n * An error thrown when one or more errors have occurred during the\n * `unsubscribe` of a {@link Subscription}.\n */\nexport const UnsubscriptionError: UnsubscriptionErrorCtor = createErrorClass(\n  (_super) =>\n    function UnsubscriptionErrorImpl(this: any, errors: (Error | string)[]) {\n      _super(this);\n      this.message = errors\n        ? `${errors.length} errors occurred during unsubscription:\n${errors.map((err, i) => `${i + 1}) ${err.toString()}`).join('\\n  ')}`\n        : '';\n      this.name = 'UnsubscriptionError';\n      this.errors = errors;\n    }\n);\n", "/**\n * Removes an item from an array, mutating it.\n * @param arr The array to remove the item from\n * @param item The item to remove\n */\nexport function arrRemove<T>(arr: T[] | undefined | null, item: T) {\n  if (arr) {\n    const index = arr.indexOf(item);\n    0 <= index && arr.splice(index, 1);\n  }\n}\n", "import { isFunction } from './util/isFunction';\nimport { UnsubscriptionError } from './util/UnsubscriptionError';\nimport { SubscriptionLike, TeardownLogic, Unsubscribable } from './types';\nimport { arrRemove } from './util/arrRemove';\n\n/**\n * Represents a disposable resource, such as the execution of an Observable. A\n * Subscription has one important method, `unsubscribe`, that takes no argument\n * and just disposes the resource held by the subscription.\n *\n * Additionally, subscriptions may be grouped together through the `add()`\n * method, which will attach a child Subscription to the current Subscription.\n * When a Subscription is unsubscribed, all its children (and its grandchildren)\n * will be unsubscribed as well.\n */\nexport class Subscription implements SubscriptionLike {\n  public static EMPTY = (() => {\n    const empty = new Subscription();\n    empty.closed = true;\n    return empty;\n  })();\n\n  /**\n   * A flag to indicate whether this Subscription has already been unsubscribed.\n   */\n  public closed = false;\n\n  private _parentage: Subscription[] | Subscription | null = null;\n\n  /**\n   * The list of registered finalizers to execute upon unsubscription. Adding and removing from this\n   * list occurs in the {@link #add} and {@link #remove} methods.\n   */\n  private _finalizers: Exclude<TeardownLogic, void>[] | null = null;\n\n  /**\n   * @param initialTeardown A function executed first as part of the finalization\n   * process that is kicked off when {@link #unsubscribe} is called.\n   */\n  constructor(private initialTeardown?: () => void) {}\n\n  /**\n   * Disposes the resources held by the subscription. May, for instance, cancel\n   * an ongoing Observable execution or cancel any other type of work that\n   * started when the Subscription was created.\n   */\n  unsubscribe(): void {\n    let errors: any[] | undefined;\n\n    if (!this.closed) {\n      this.closed = true;\n\n      // Remove this from it's parents.\n      const { _parentage } = this;\n      if (_parentage) {\n        this._parentage = null;\n        if (Array.isArray(_parentage)) {\n          for (const parent of _parentage) {\n            parent.remove(this);\n          }\n        } else {\n          _parentage.remove(this);\n        }\n      }\n\n      const { initialTeardown: initialFinalizer } = this;\n      if (isFunction(initialFinalizer)) {\n        try {\n          initialFinalizer();\n        } catch (e) {\n          errors = e instanceof UnsubscriptionError ? e.errors : [e];\n        }\n      }\n\n      const { _finalizers } = this;\n      if (_finalizers) {\n        this._finalizers = null;\n        for (const finalizer of _finalizers) {\n          try {\n            execFinalizer(finalizer);\n          } catch (err) {\n            errors = errors ?? [];\n            if (err instanceof UnsubscriptionError) {\n              errors = [...errors, ...err.errors];\n            } else {\n              errors.push(err);\n            }\n          }\n        }\n      }\n\n      if (errors) {\n        throw new UnsubscriptionError(errors);\n      }\n    }\n  }\n\n  /**\n   * Adds a finalizer to this subscription, so that finalization will be unsubscribed/called\n   * when this subscription is unsubscribed. If this subscription is already {@link #closed},\n   * because it has already been unsubscribed, then whatever finalizer is passed to it\n   * will automatically be executed (unless the finalizer itself is also a closed subscription).\n   *\n   * Closed Subscriptions cannot be added as finalizers to any subscription. Adding a closed\n   * subscription to a any subscription will result in no operation. (A noop).\n   *\n   * Adding a subscription to itself, or adding `null` or `undefined` will not perform any\n   * operation at all. (A noop).\n   *\n   * `Subscription` instances that are added to this instance will automatically remove themselves\n   * if they are unsubscribed. Functions and {@link Unsubscribable} objects that you wish to remove\n   * will need to be removed manually with {@link #remove}\n   *\n   * @param teardown The finalization logic to add to this subscription.\n   */\n  add(teardown: TeardownLogic): void {\n    // Only add the finalizer if it's not undefined\n    // and don't add a subscription to itself.\n    if (teardown && teardown !== this) {\n      if (this.closed) {\n        // If this subscription is already closed,\n        // execute whatever finalizer is handed to it automatically.\n        execFinalizer(teardown);\n      } else {\n        if (teardown instanceof Subscription) {\n          // We don't add closed subscriptions, and we don't add the same subscription\n          // twice. Subscription unsubscribe is idempotent.\n          if (teardown.closed || teardown._hasParent(this)) {\n            return;\n          }\n          teardown._addParent(this);\n        }\n        (this._finalizers = this._finalizers ?? []).push(teardown);\n      }\n    }\n  }\n\n  /**\n   * Checks to see if a this subscription already has a particular parent.\n   * This will signal that this subscription has already been added to the parent in question.\n   * @param parent the parent to check for\n   */\n  private _hasParent(parent: Subscription) {\n    const { _parentage } = this;\n    return _parentage === parent || (Array.isArray(_parentage) && _parentage.includes(parent));\n  }\n\n  /**\n   * Adds a parent to this subscription so it can be removed from the parent if it\n   * unsubscribes on it's own.\n   *\n   * NOTE: THIS ASSUMES THAT {@link _hasParent} HAS ALREADY BEEN CHECKED.\n   * @param parent The parent subscription to add\n   */\n  private _addParent(parent: Subscription) {\n    const { _parentage } = this;\n    this._parentage = Array.isArray(_parentage) ? (_parentage.push(parent), _parentage) : _parentage ? [_parentage, parent] : parent;\n  }\n\n  /**\n   * Called on a child when it is removed via {@link #remove}.\n   * @param parent The parent to remove\n   */\n  private _removeParent(parent: Subscription) {\n    const { _parentage } = this;\n    if (_parentage === parent) {\n      this._parentage = null;\n    } else if (Array.isArray(_parentage)) {\n      arrRemove(_parentage, parent);\n    }\n  }\n\n  /**\n   * Removes a finalizer from this subscription that was previously added with the {@link #add} method.\n   *\n   * Note that `Subscription` instances, when unsubscribed, will automatically remove themselves\n   * from every other `Subscription` they have been added to. This means that using the `remove` method\n   * is not a common thing and should be used thoughtfully.\n   *\n   * If you add the same finalizer instance of a function or an unsubscribable object to a `Subscription` instance\n   * more than once, you will need to call `remove` the same number of times to remove all instances.\n   *\n   * All finalizer instances are removed to free up memory upon unsubscription.\n   *\n   * @param teardown The finalizer to remove from this subscription\n   */\n  remove(teardown: Exclude<TeardownLogic, void>): void {\n    const { _finalizers } = this;\n    _finalizers && arrRemove(_finalizers, teardown);\n\n    if (teardown instanceof Subscription) {\n      teardown._removeParent(this);\n    }\n  }\n}\n\nexport const EMPTY_SUBSCRIPTION = Subscription.EMPTY;\n\nexport function isSubscription(value: any): value is Subscription {\n  return (\n    value instanceof Subscription ||\n    (value && 'closed' in value && isFunction(value.remove) && isFunction(value.add) && isFunction(value.unsubscribe))\n  );\n}\n\nfunction execFinalizer(finalizer: Unsubscribable | (() => void)) {\n  if (isFunction(finalizer)) {\n    finalizer();\n  } else {\n    finalizer.unsubscribe();\n  }\n}\n", "import { Subscriber } from './Subscriber';\nimport { ObservableNotification } from './types';\n\n/**\n * The {@link GlobalConfig} object for RxJS. It is used to configure things\n * like how to react on unhandled errors.\n */\nexport const config: GlobalConfig = {\n  onUnhandledError: null,\n  onStoppedNotification: null,\n  Promise: undefined,\n  useDeprecatedSynchronousErrorHandling: false,\n  useDeprecatedNextContext: false,\n};\n\n/**\n * The global configuration object for RxJS, used to configure things\n * like how to react on unhandled errors. Accessible via {@link config}\n * object.\n */\nexport interface GlobalConfig {\n  /**\n   * A registration point for unhandled errors from RxJS. These are errors that\n   * cannot were not handled by consuming code in the usual subscription path. For\n   * example, if you have this configured, and you subscribe to an observable without\n   * providing an error handler, errors from that subscription will end up here. This\n   * will _always_ be called asynchronously on another job in the runtime. This is because\n   * we do not want errors thrown in this user-configured handler to interfere with the\n   * behavior of the library.\n   */\n  onUnhandledError: ((err: any) => void) | null;\n\n  /**\n   * A registration point for notifications that cannot be sent to subscribers because they\n   * have completed, errored or have been explicitly unsubscribed. By default, next, complete\n   * and error notifications sent to stopped subscribers are noops. However, sometimes callers\n   * might want a different behavior. For example, with sources that attempt to report errors\n   * to stopped subscribers, a caller can configure RxJS to throw an unhandled error instead.\n   * This will _always_ be called asynchronously on another job in the runtime. This is because\n   * we do not want errors thrown in this user-configured handler to interfere with the\n   * behavior of the library.\n   */\n  onStoppedNotification: ((notification: ObservableNotification<any>, subscriber: Subscriber<any>) => void) | null;\n\n  /**\n   * The promise constructor used by default for {@link Observable#toPromise toPromise} and {@link Observable#forEach forEach}\n   * methods.\n   *\n   * @deprecated As of version 8, RxJS will no longer support this sort of injection of a\n   * Promise constructor. If you need a Promise implementation other than native promises,\n   * please polyfill/patch Promise as you see appropriate. Will be removed in v8.\n   */\n  Promise?: PromiseConstructorLike;\n\n  /**\n   * If true, turns on synchronous error rethrowing, which is a deprecated behavior\n   * in v6 and higher. This behavior enables bad patterns like wrapping a subscribe\n   * call in a try/catch block. It also enables producer interference, a nasty bug\n   * where a multicast can be broken for all observers by a downstream consumer with\n   * an unhandled error. DO NOT USE THIS FLAG UNLESS IT'S NEEDED TO BUY TIME\n   * FOR MIGRATION REASONS.\n   *\n   * @deprecated As of version 8, RxJS will no longer support synchronous throwing\n   * of unhandled errors. All errors will be thrown on a separate call stack to prevent bad\n   * behaviors described above. Will be removed in v8.\n   */\n  useDeprecatedSynchronousErrorHandling: boolean;\n\n  /**\n   * If true, enables an as-of-yet undocumented feature from v5: The ability to access\n   * `unsubscribe()` via `this` context in `next` functions created in observers passed\n   * to `subscribe`.\n   *\n   * This is being removed because the performance was severely problematic, and it could also cause\n   * issues when types other than POJOs are passed to subscribe as subscribers, as they will likely have\n   * their `this` context overwritten.\n   *\n   * @deprecated As of version 8, RxJS will no longer support altering the\n   * context of next functions provided as part of an observer to Subscribe. Instead,\n   * you will have access to a subscription or a signal or token that will allow you to do things like\n   * unsubscribe and test closed status. Will be removed in v8.\n   */\n  useDeprecatedNextContext: boolean;\n}\n", "import type { TimerHandle } from './timerHandle';\ntype SetTimeoutFunction = (handler: () => void, timeout?: number, ...args: any[]) => TimerHandle;\ntype ClearTimeoutFunction = (handle: TimerHandle) => void;\n\ninterface TimeoutProvider {\n  setTimeout: SetTimeoutFunction;\n  clearTimeout: ClearTimeoutFunction;\n  delegate:\n    | {\n        setTimeout: SetTimeoutFunction;\n        clearTimeout: ClearTimeoutFunction;\n      }\n    | undefined;\n}\n\nexport const timeoutProvider: TimeoutProvider = {\n  // When accessing the delegate, use the variable rather than `this` so that\n  // the functions can be called without being bound to the provider.\n  setTimeout(handler: () => void, timeout?: number, ...args) {\n    const { delegate } = timeoutProvider;\n    if (delegate?.setTimeout) {\n      return delegate.setTimeout(handler, timeout, ...args);\n    }\n    return setTimeout(handler, timeout, ...args);\n  },\n  clearTimeout(handle) {\n    const { delegate } = timeoutProvider;\n    return (delegate?.clearTimeout || clearTimeout)(handle as any);\n  },\n  delegate: undefined,\n};\n", "import { config } from '../config';\nimport { timeoutProvider } from '../scheduler/timeoutProvider';\n\n/**\n * Handles an error on another job either with the user-configured {@link onUnhandledError},\n * or by throwing it on that new job so it can be picked up by `window.onerror`, `process.on('error')`, etc.\n *\n * This should be called whenever there is an error that is out-of-band with the subscription\n * or when an error hits a terminal boundary of the subscription and no error handler was provided.\n *\n * @param err the error to report\n */\nexport function reportUnhandledError(err: any) {\n  timeoutProvider.setTimeout(() => {\n    const { onUnhandledError } = config;\n    if (onUnhandledError) {\n      // Execute the user-configured error handler.\n      onUnhandledError(err);\n    } else {\n      // Throw so it is picked up by the runtime's uncaught error mechanism.\n      throw err;\n    }\n  });\n}\n", "/* tslint:disable:no-empty */\nexport function noop() { }\n", "import { CompleteNotification, NextNotification, ErrorNotification } from './types';\n\n/**\n * A completion object optimized for memory use and created to be the\n * same \"shape\" as other notifications in v8.\n * @internal\n */\nexport const COMPLETE_NOTIFICATION = (() => createNotification('C', undefined, undefined) as CompleteNotification)();\n\n/**\n * Internal use only. Creates an optimized error notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function errorNotification(error: any): ErrorNotification {\n  return createNotification('E', undefined, error) as any;\n}\n\n/**\n * Internal use only. Creates an optimized next notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function nextNotification<T>(value: T) {\n  return createNotification('N', value, undefined) as NextNotification<T>;\n}\n\n/**\n * Ensures that all notifications created internally have the same \"shape\" in v8.\n *\n * TODO: This is only exported to support a crazy legacy test in `groupBy`.\n * @internal\n */\nexport function createNotification(kind: 'N' | 'E' | 'C', value: any, error: any) {\n  return {\n    kind,\n    value,\n    error,\n  };\n}\n", "import { config } from '../config';\n\nlet context: { errorThrown: boolean; error: any } | null = null;\n\n/**\n * Handles dealing with errors for super-gross mode. Creates a context, in which\n * any synchronously thrown errors will be passed to {@link captureError}. Which\n * will record the error such that it will be rethrown after the call back is complete.\n * TODO: Remove in v8\n * @param cb An immediately executed function.\n */\nexport function errorContext(cb: () => void) {\n  if (config.useDeprecatedSynchronousErrorHandling) {\n    const isRoot = !context;\n    if (isRoot) {\n      context = { errorThrown: false, error: null };\n    }\n    cb();\n    if (isRoot) {\n      const { errorThrown, error } = context!;\n      context = null;\n      if (errorThrown) {\n        throw error;\n      }\n    }\n  } else {\n    // This is the general non-deprecated path for everyone that\n    // isn't crazy enough to use super-gross mode (useDeprecatedSynchronousErrorHandling)\n    cb();\n  }\n}\n\n/**\n * Captures errors only in super-gross mode.\n * @param err the error to capture\n */\nexport function captureError(err: any) {\n  if (config.useDeprecatedSynchronousErrorHandling && context) {\n    context.errorThrown = true;\n    context.error = err;\n  }\n}\n", "import { isFunction } from './util/isFunction';\nimport { Observer, ObservableNotification } from './types';\nimport { isSubscription, Subscription } from './Subscription';\nimport { config } from './config';\nimport { reportUnhandledError } from './util/reportUnhandledError';\nimport { noop } from './util/noop';\nimport { nextNotification, errorNotification, COMPLETE_NOTIFICATION } from './NotificationFactories';\nimport { timeoutProvider } from './scheduler/timeoutProvider';\nimport { captureError } from './util/errorContext';\n\n/**\n * Implements the {@link Observer} interface and extends the\n * {@link Subscription} class. While the {@link Observer} is the public API for\n * consuming the values of an {@link Observable}, all Observers get converted to\n * a Subscriber, in order to provide Subscription-like capabilities such as\n * `unsubscribe`. Subscriber is a common type in RxJS, and crucial for\n * implementing operators, but it is rarely used as a public API.\n */\nexport class Subscriber<T> extends Subscription implements Observer<T> {\n  /**\n   * A static factory for a Subscriber, given a (potentially partial) definition\n   * of an Observer.\n   * @param next The `next` callback of an Observer.\n   * @param error The `error` callback of an\n   * Observer.\n   * @param complete The `complete` callback of an\n   * Observer.\n   * @return A Subscriber wrapping the (partially defined)\n   * Observer represented by the given arguments.\n   * @deprecated Do not use. Will be removed in v8. There is no replacement for this\n   * method, and there is no reason to be creating instances of `Subscriber` directly.\n   * If you have a specific use case, please file an issue.\n   */\n  static create<T>(next?: (x?: T) => void, error?: (e?: any) => void, complete?: () => void): Subscriber<T> {\n    return new SafeSubscriber(next, error, complete);\n  }\n\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  protected isStopped: boolean = false;\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  protected destination: Subscriber<any> | Observer<any>; // this `any` is the escape hatch to erase extra type param (e.g. R)\n\n  /**\n   * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n   * There is no reason to directly create an instance of Subscriber. This type is exported for typings reasons.\n   */\n  constructor(destination?: Subscriber<any> | Observer<any>) {\n    super();\n    if (destination) {\n      this.destination = destination;\n      // Automatically chain subscriptions together here.\n      // if destination is a Subscription, then it is a Subscriber.\n      if (isSubscription(destination)) {\n        destination.add(this);\n      }\n    } else {\n      this.destination = EMPTY_OBSERVER;\n    }\n  }\n\n  /**\n   * The {@link Observer} callback to receive notifications of type `next` from\n   * the Observable, with a value. The Observable may call this method 0 or more\n   * times.\n   * @param value The `next` value.\n   */\n  next(value: T): void {\n    if (this.isStopped) {\n      handleStoppedNotification(nextNotification(value), this);\n    } else {\n      this._next(value!);\n    }\n  }\n\n  /**\n   * The {@link Observer} callback to receive notifications of type `error` from\n   * the Observable, with an attached `Error`. Notifies the Observer that\n   * the Observable has experienced an error condition.\n   * @param err The `error` exception.\n   */\n  error(err?: any): void {\n    if (this.isStopped) {\n      handleStoppedNotification(errorNotification(err), this);\n    } else {\n      this.isStopped = true;\n      this._error(err);\n    }\n  }\n\n  /**\n   * The {@link Observer} callback to receive a valueless notification of type\n   * `complete` from the Observable. Notifies the Observer that the Observable\n   * has finished sending push-based notifications.\n   */\n  complete(): void {\n    if (this.isStopped) {\n      handleStoppedNotification(COMPLETE_NOTIFICATION, this);\n    } else {\n      this.isStopped = true;\n      this._complete();\n    }\n  }\n\n  unsubscribe(): void {\n    if (!this.closed) {\n      this.isStopped = true;\n      super.unsubscribe();\n      this.destination = null!;\n    }\n  }\n\n  protected _next(value: T): void {\n    this.destination.next(value);\n  }\n\n  protected _error(err: any): void {\n    try {\n      this.destination.error(err);\n    } finally {\n      this.unsubscribe();\n    }\n  }\n\n  protected _complete(): void {\n    try {\n      this.destination.complete();\n    } finally {\n      this.unsubscribe();\n    }\n  }\n}\n\n/**\n * This bind is captured here because we want to be able to have\n * compatibility with monoid libraries that tend to use a method named\n * `bind`. In particular, a library called Monio requires this.\n */\nconst _bind = Function.prototype.bind;\n\nfunction bind<Fn extends (...args: any[]) => any>(fn: Fn, thisArg: any): Fn {\n  return _bind.call(fn, thisArg);\n}\n\n/**\n * Internal optimization only, DO NOT EXPOSE.\n * @internal\n */\nclass ConsumerObserver<T> implements Observer<T> {\n  constructor(private partialObserver: Partial<Observer<T>>) {}\n\n  next(value: T): void {\n    const { partialObserver } = this;\n    if (partialObserver.next) {\n      try {\n        partialObserver.next(value);\n      } catch (error) {\n        handleUnhandledError(error);\n      }\n    }\n  }\n\n  error(err: any): void {\n    const { partialObserver } = this;\n    if (partialObserver.error) {\n      try {\n        partialObserver.error(err);\n      } catch (error) {\n        handleUnhandledError(error);\n      }\n    } else {\n      handleUnhandledError(err);\n    }\n  }\n\n  complete(): void {\n    const { partialObserver } = this;\n    if (partialObserver.complete) {\n      try {\n        partialObserver.complete();\n      } catch (error) {\n        handleUnhandledError(error);\n      }\n    }\n  }\n}\n\nexport class SafeSubscriber<T> extends Subscriber<T> {\n  constructor(\n    observerOrNext?: Partial<Observer<T>> | ((value: T) => void) | null,\n    error?: ((e?: any) => void) | null,\n    complete?: (() => void) | null\n  ) {\n    super();\n\n    let partialObserver: Partial<Observer<T>>;\n    if (isFunction(observerOrNext) || !observerOrNext) {\n      // The first argument is a function, not an observer. The next\n      // two arguments *could* be observers, or they could be empty.\n      partialObserver = {\n        next: (observerOrNext ?? undefined) as ((value: T) => void) | undefined,\n        error: error ?? undefined,\n        complete: complete ?? undefined,\n      };\n    } else {\n      // The first argument is a partial observer.\n      let context: any;\n      if (this && config.useDeprecatedNextContext) {\n        // This is a deprecated path that made `this.unsubscribe()` available in\n        // next handler functions passed to subscribe. This only exists behind a flag\n        // now, as it is *very* slow.\n        context = Object.create(observerOrNext);\n        context.unsubscribe = () => this.unsubscribe();\n        partialObserver = {\n          next: observerOrNext.next && bind(observerOrNext.next, context),\n          error: observerOrNext.error && bind(observerOrNext.error, context),\n          complete: observerOrNext.complete && bind(observerOrNext.complete, context),\n        };\n      } else {\n        // The \"normal\" path. Just use the partial observer directly.\n        partialObserver = observerOrNext;\n      }\n    }\n\n    // Wrap the partial observer to ensure it's a full observer, and\n    // make sure proper error handling is accounted for.\n    this.destination = new ConsumerObserver(partialObserver);\n  }\n}\n\nfunction handleUnhandledError(error: any) {\n  if (config.useDeprecatedSynchronousErrorHandling) {\n    captureError(error);\n  } else {\n    // Ideal path, we report this as an unhandled error,\n    // which is thrown on a new call stack.\n    reportUnhandledError(error);\n  }\n}\n\n/**\n * An error handler used when no error handler was supplied\n * to the SafeSubscriber -- meaning no error handler was supplied\n * do the `subscribe` call on our observable.\n * @param err The error to handle\n */\nfunction defaultErrorHandler(err: any) {\n  throw err;\n}\n\n/**\n * A handler for notifications that cannot be sent to a stopped subscriber.\n * @param notification The notification being sent.\n * @param subscriber The stopped subscriber.\n */\nfunction handleStoppedNotification(notification: ObservableNotification<any>, subscriber: Subscriber<any>) {\n  const { onStoppedNotification } = config;\n  onStoppedNotification && timeoutProvider.setTimeout(() => onStoppedNotification(notification, subscriber));\n}\n\n/**\n * The observer used as a stub for subscriptions where the user did not\n * pass any arguments to `subscribe`. Comes with the default error handling\n * behavior.\n */\nexport const EMPTY_OBSERVER: Readonly<Observer<any>> & { closed: true } = {\n  closed: true,\n  next: noop,\n  error: defaultErrorHandler,\n  complete: noop,\n};\n", "/**\n * Symbol.observable or a string \"@@observable\". Used for interop\n *\n * @deprecated We will no longer be exporting this symbol in upcoming versions of RxJS.\n * Instead polyfill and use Symbol.observable directly *or* use https://www.npmjs.com/package/symbol-observable\n */\nexport const observable: string | symbol = (() => (typeof Symbol === 'function' && Symbol.observable) || '@@observable')();\n", "/**\n * This function takes one parameter and just returns it. Simply put,\n * this is like `<T>(x: T): T => x`.\n *\n * ## Examples\n *\n * This is useful in some cases when using things like `mergeMap`\n *\n * ```ts\n * import { interval, take, map, range, mergeMap, identity } from 'rxjs';\n *\n * const source$ = interval(1000).pipe(take(5));\n *\n * const result$ = source$.pipe(\n *   map(i => range(i)),\n *   mergeMap(identity) // same as mergeMap(x => x)\n * );\n *\n * result$.subscribe({\n *   next: console.log\n * });\n * ```\n *\n * Or when you want to selectively apply an operator\n *\n * ```ts\n * import { interval, take, identity } from 'rxjs';\n *\n * const shouldLimit = () => Math.random() < 0.5;\n *\n * const source$ = interval(1000);\n *\n * const result$ = source$.pipe(shouldLimit() ? take(5) : identity);\n *\n * result$.subscribe({\n *   next: console.log\n * });\n * ```\n *\n * @param x Any value that is returned by this function\n * @returns The value passed as the first parameter to this function\n */\nexport function identity<T>(x: T): T {\n  return x;\n}\n", "import { identity } from './identity';\nimport { UnaryFunction } from '../types';\n\nexport function pipe(): typeof identity;\nexport function pipe<T, A>(fn1: UnaryFunction<T, A>): UnaryFunction<T, A>;\nexport function pipe<T, A, B>(fn1: UnaryFunction<T, A>, fn2: UnaryFunction<A, B>): UnaryFunction<T, B>;\nexport function pipe<T, A, B, C>(fn1: UnaryFunction<T, A>, fn2: UnaryFunction<A, B>, fn3: UnaryFunction<B, C>): UnaryFunction<T, C>;\nexport function pipe<T, A, B, C, D>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>\n): UnaryFunction<T, D>;\nexport function pipe<T, A, B, C, D, E>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>\n): UnaryFunction<T, E>;\nexport function pipe<T, A, B, C, D, E, F>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>,\n  fn6: UnaryFunction<E, F>\n): UnaryFunction<T, F>;\nexport function pipe<T, A, B, C, D, E, F, G>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>,\n  fn6: UnaryFunction<E, F>,\n  fn7: UnaryFunction<F, G>\n): UnaryFunction<T, G>;\nexport function pipe<T, A, B, C, D, E, F, G, H>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>,\n  fn6: UnaryFunction<E, F>,\n  fn7: UnaryFunction<F, G>,\n  fn8: UnaryFunction<G, H>\n): UnaryFunction<T, H>;\nexport function pipe<T, A, B, C, D, E, F, G, H, I>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>,\n  fn6: UnaryFunction<E, F>,\n  fn7: UnaryFunction<F, G>,\n  fn8: UnaryFunction<G, H>,\n  fn9: UnaryFunction<H, I>\n): UnaryFunction<T, I>;\nexport function pipe<T, A, B, C, D, E, F, G, H, I>(\n  fn1: UnaryFunction<T, A>,\n  fn2: UnaryFunction<A, B>,\n  fn3: UnaryFunction<B, C>,\n  fn4: UnaryFunction<C, D>,\n  fn5: UnaryFunction<D, E>,\n  fn6: UnaryFunction<E, F>,\n  fn7: UnaryFunction<F, G>,\n  fn8: UnaryFunction<G, H>,\n  fn9: UnaryFunction<H, I>,\n  ...fns: UnaryFunction<any, any>[]\n): UnaryFunction<T, unknown>;\n\n/**\n * pipe() can be called on one or more functions, each of which can take one argument (\"UnaryFunction\")\n * and uses it to return a value.\n * It returns a function that takes one argument, passes it to the first UnaryFunction, and then\n * passes the result to the next one, passes that result to the next one, and so on.  \n */\nexport function pipe(...fns: Array<UnaryFunction<any, any>>): UnaryFunction<any, any> {\n  return pipeFromArray(fns);\n}\n\n/** @internal */\nexport function pipeFromArray<T, R>(fns: Array<UnaryFunction<T, R>>): UnaryFunction<T, R> {\n  if (fns.length === 0) {\n    return identity as UnaryFunction<any, any>;\n  }\n\n  if (fns.length === 1) {\n    return fns[0];\n  }\n\n  return function piped(input: T): R {\n    return fns.reduce((prev: any, fn: UnaryFunction<T, R>) => fn(prev), input as any);\n  };\n}\n", "import { Operator } from './Operator';\nimport { SafeSubscriber, Subscriber } from './Subscriber';\nimport { isSubscription, Subscription } from './Subscription';\nimport { TeardownLogic, OperatorFunction, Subscribable, Observer } from './types';\nimport { observable as Symbol_observable } from './symbol/observable';\nimport { pipeFromArray } from './util/pipe';\nimport { config } from './config';\nimport { isFunction } from './util/isFunction';\nimport { errorContext } from './util/errorContext';\n\n/**\n * A representation of any set of values over any amount of time. This is the most basic building block\n * of RxJS.\n */\nexport class Observable<T> implements Subscribable<T> {\n  /**\n   * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n   */\n  source: Observable<any> | undefined;\n\n  /**\n   * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n   */\n  operator: Operator<any, T> | undefined;\n\n  /**\n   * @param subscribe The function that is called when the Observable is\n   * initially subscribed to. This function is given a Subscriber, to which new values\n   * can be `next`ed, or an `error` method can be called to raise an error, or\n   * `complete` can be called to notify of a successful completion.\n   */\n  constructor(subscribe?: (this: Observable<T>, subscriber: Subscriber<T>) => TeardownLogic) {\n    if (subscribe) {\n      this._subscribe = subscribe;\n    }\n  }\n\n  // HACK: Since TypeScript inherits static properties too, we have to\n  // fight against TypeScript here so Subject can have a different static create signature\n  /**\n   * Creates a new Observable by calling the Observable constructor\n   * @param subscribe the subscriber function to be passed to the Observable constructor\n   * @return A new observable.\n   * @deprecated Use `new Observable()` instead. Will be removed in v8.\n   */\n  static create: (...args: any[]) => any = <T>(subscribe?: (subscriber: Subscriber<T>) => TeardownLogic) => {\n    return new Observable<T>(subscribe);\n  };\n\n  /**\n   * Creates a new Observable, with this Observable instance as the source, and the passed\n   * operator defined as the new observable's operator.\n   * @param operator the operator defining the operation to take on the observable\n   * @return A new observable with the Operator applied.\n   * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n   * If you have implemented an operator using `lift`, it is recommended that you create an\n   * operator by simply returning `new Observable()` directly. See \"Creating new operators from\n   * scratch\" section here: https://rxjs.dev/guide/operators\n   */\n  lift<R>(operator?: Operator<T, R>): Observable<R> {\n    const observable = new Observable<R>();\n    observable.source = this;\n    observable.operator = operator;\n    return observable;\n  }\n\n  subscribe(observerOrNext?: Partial<Observer<T>> | ((value: T) => void)): Subscription;\n  /** @deprecated Instead of passing separate callback arguments, use an observer argument. Signatures taking separate callback arguments will be removed in v8. Details: https://rxjs.dev/deprecations/subscribe-arguments */\n  subscribe(next?: ((value: T) => void) | null, error?: ((error: any) => void) | null, complete?: (() => void) | null): Subscription;\n  /**\n   * Invokes an execution of an Observable and registers Observer handlers for notifications it will emit.\n   *\n   * <span class=\"informal\">Use it when you have all these Observables, but still nothing is happening.</span>\n   *\n   * `subscribe` is not a regular operator, but a method that calls Observable's internal `subscribe` function. It\n   * might be for example a function that you passed to Observable's constructor, but most of the time it is\n   * a library implementation, which defines what will be emitted by an Observable, and when it be will emitted. This means\n   * that calling `subscribe` is actually the moment when Observable starts its work, not when it is created, as it is often\n   * the thought.\n   *\n   * Apart from starting the execution of an Observable, this method allows you to listen for values\n   * that an Observable emits, as well as for when it completes or errors. You can achieve this in two\n   * of the following ways.\n   *\n   * The first way is creating an object that implements {@link Observer} interface. It should have methods\n   * defined by that interface, but note that it should be just a regular JavaScript object, which you can create\n   * yourself in any way you want (ES6 class, classic function constructor, object literal etc.). In particular, do\n   * not attempt to use any RxJS implementation details to create Observers - you don't need them. Remember also\n   * that your object does not have to implement all methods. If you find yourself creating a method that doesn't\n   * do anything, you can simply omit it. Note however, if the `error` method is not provided and an error happens,\n   * it will be thrown asynchronously. Errors thrown asynchronously cannot be caught using `try`/`catch`. Instead,\n   * use the {@link onUnhandledError} configuration option or use a runtime handler (like `window.onerror` or\n   * `process.on('error)`) to be notified of unhandled errors. Because of this, it's recommended that you provide\n   * an `error` method to avoid missing thrown errors.\n   *\n   * The second way is to give up on Observer object altogether and simply provide callback functions in place of its methods.\n   * This means you can provide three functions as arguments to `subscribe`, where the first function is equivalent\n   * of a `next` method, the second of an `error` method and the third of a `complete` method. Just as in case of an Observer,\n   * if you do not need to listen for something, you can omit a function by passing `undefined` or `null`,\n   * since `subscribe` recognizes these functions by where they were placed in function call. When it comes\n   * to the `error` function, as with an Observer, if not provided, errors emitted by an Observable will be thrown asynchronously.\n   *\n   * You can, however, subscribe with no parameters at all. This may be the case where you're not interested in terminal events\n   * and you also handled emissions internally by using operators (e.g. using `tap`).\n   *\n   * Whichever style of calling `subscribe` you use, in both cases it returns a Subscription object.\n   * This object allows you to call `unsubscribe` on it, which in turn will stop the work that an Observable does and will clean\n   * up all resources that an Observable used. Note that cancelling a subscription will not call `complete` callback\n   * provided to `subscribe` function, which is reserved for a regular completion signal that comes from an Observable.\n   *\n   * Remember that callbacks provided to `subscribe` are not guaranteed to be called asynchronously.\n   * It is an Observable itself that decides when these functions will be called. For example {@link of}\n   * by default emits all its values synchronously. Always check documentation for how given Observable\n   * will behave when subscribed and if its default behavior can be modified with a `scheduler`.\n   *\n   * #### Examples\n   *\n   * Subscribe with an {@link guide/observer Observer}\n   *\n   * ```ts\n   * import { of } from 'rxjs';\n   *\n   * const sumObserver = {\n   *   sum: 0,\n   *   next(value) {\n   *     console.log('Adding: ' + value);\n   *     this.sum = this.sum + value;\n   *   },\n   *   error() {\n   *     // We actually could just remove this method,\n   *     // since we do not really care about errors right now.\n   *   },\n   *   complete() {\n   *     console.log('Sum equals: ' + this.sum);\n   *   }\n   * };\n   *\n   * of(1, 2, 3) // Synchronously emits 1, 2, 3 and then completes.\n   *   .subscribe(sumObserver);\n   *\n   * // Logs:\n   * // 'Adding: 1'\n   * // 'Adding: 2'\n   * // 'Adding: 3'\n   * // 'Sum equals: 6'\n   * ```\n   *\n   * Subscribe with functions ({@link deprecations/subscribe-arguments deprecated})\n   *\n   * ```ts\n   * import { of } from 'rxjs'\n   *\n   * let sum = 0;\n   *\n   * of(1, 2, 3).subscribe(\n   *   value => {\n   *     console.log('Adding: ' + value);\n   *     sum = sum + value;\n   *   },\n   *   undefined,\n   *   () => console.log('Sum equals: ' + sum)\n   * );\n   *\n   * // Logs:\n   * // 'Adding: 1'\n   * // 'Adding: 2'\n   * // 'Adding: 3'\n   * // 'Sum equals: 6'\n   * ```\n   *\n   * Cancel a subscription\n   *\n   * ```ts\n   * import { interval } from 'rxjs';\n   *\n   * const subscription = interval(1000).subscribe({\n   *   next(num) {\n   *     console.log(num)\n   *   },\n   *   complete() {\n   *     // Will not be called, even when cancelling subscription.\n   *     console.log('completed!');\n   *   }\n   * });\n   *\n   * setTimeout(() => {\n   *   subscription.unsubscribe();\n   *   console.log('unsubscribed!');\n   * }, 2500);\n   *\n   * // Logs:\n   * // 0 after 1s\n   * // 1 after 2s\n   * // 'unsubscribed!' after 2.5s\n   * ```\n   *\n   * @param observerOrNext Either an {@link Observer} with some or all callback methods,\n   * or the `next` handler that is called for each value emitted from the subscribed Observable.\n   * @param error A handler for a terminal event resulting from an error. If no error handler is provided,\n   * the error will be thrown asynchronously as unhandled.\n   * @param complete A handler for a terminal event resulting from successful completion.\n   * @return A subscription reference to the registered handlers.\n   */\n  subscribe(\n    observerOrNext?: Partial<Observer<T>> | ((value: T) => void) | null,\n    error?: ((error: any) => void) | null,\n    complete?: (() => void) | null\n  ): Subscription {\n    const subscriber = isSubscriber(observerOrNext) ? observerOrNext : new SafeSubscriber(observerOrNext, error, complete);\n\n    errorContext(() => {\n      const { operator, source } = this;\n      subscriber.add(\n        operator\n          ? // We're dealing with a subscription in the\n            // operator chain to one of our lifted operators.\n            operator.call(subscriber, source)\n          : source\n          ? // If `source` has a value, but `operator` does not, something that\n            // had intimate knowledge of our API, like our `Subject`, must have\n            // set it. We're going to just call `_subscribe` directly.\n            this._subscribe(subscriber)\n          : // In all other cases, we're likely wrapping a user-provided initializer\n            // function, so we need to catch errors and handle them appropriately.\n            this._trySubscribe(subscriber)\n      );\n    });\n\n    return subscriber;\n  }\n\n  /** @internal */\n  protected _trySubscribe(sink: Subscriber<T>): TeardownLogic {\n    try {\n      return this._subscribe(sink);\n    } catch (err) {\n      // We don't need to return anything in this case,\n      // because it's just going to try to `add()` to a subscription\n      // above.\n      sink.error(err);\n    }\n  }\n\n  /**\n   * Used as a NON-CANCELLABLE means of subscribing to an observable, for use with\n   * APIs that expect promises, like `async/await`. You cannot unsubscribe from this.\n   *\n   * **WARNING**: Only use this with observables you *know* will complete. If the source\n   * observable does not complete, you will end up with a promise that is hung up, and\n   * potentially all of the state of an async function hanging out in memory. To avoid\n   * this situation, look into adding something like {@link timeout}, {@link take},\n   * {@link takeWhile}, or {@link takeUntil} amongst others.\n   *\n   * #### Example\n   *\n   * ```ts\n   * import { interval, take } from 'rxjs';\n   *\n   * const source$ = interval(1000).pipe(take(4));\n   *\n   * async function getTotal() {\n   *   let total = 0;\n   *\n   *   await source$.forEach(value => {\n   *     total += value;\n   *     console.log('observable -> ' + value);\n   *   });\n   *\n   *   return total;\n   * }\n   *\n   * getTotal().then(\n   *   total => console.log('Total: ' + total)\n   * );\n   *\n   * // Expected:\n   * // 'observable -> 0'\n   * // 'observable -> 1'\n   * // 'observable -> 2'\n   * // 'observable -> 3'\n   * // 'Total: 6'\n   * ```\n   *\n   * @param next A handler for each value emitted by the observable.\n   * @return A promise that either resolves on observable completion or\n   * rejects with the handled error.\n   */\n  forEach(next: (value: T) => void): Promise<void>;\n\n  /**\n   * @param next a handler for each value emitted by the observable\n   * @param promiseCtor a constructor function used to instantiate the Promise\n   * @return a promise that either resolves on observable completion or\n   *  rejects with the handled error\n   * @deprecated Passing a Promise constructor will no longer be available\n   * in upcoming versions of RxJS. This is because it adds weight to the library, for very\n   * little benefit. If you need this functionality, it is recommended that you either\n   * polyfill Promise, or you create an adapter to convert the returned native promise\n   * to whatever promise implementation you wanted. Will be removed in v8.\n   */\n  forEach(next: (value: T) => void, promiseCtor: PromiseConstructorLike): Promise<void>;\n\n  forEach(next: (value: T) => void, promiseCtor?: PromiseConstructorLike): Promise<void> {\n    promiseCtor = getPromiseCtor(promiseCtor);\n\n    return new promiseCtor<void>((resolve, reject) => {\n      const subscriber = new SafeSubscriber<T>({\n        next: (value) => {\n          try {\n            next(value);\n          } catch (err) {\n            reject(err);\n            subscriber.unsubscribe();\n          }\n        },\n        error: reject,\n        complete: resolve,\n      });\n      this.subscribe(subscriber);\n    }) as Promise<void>;\n  }\n\n  /** @internal */\n  protected _subscribe(subscriber: Subscriber<any>): TeardownLogic {\n    return this.source?.subscribe(subscriber);\n  }\n\n  /**\n   * An interop point defined by the es7-observable spec https://github.com/zenparsing/es-observable\n   * @return This instance of the observable.\n   */\n  [Symbol_observable]() {\n    return this;\n  }\n\n  /* tslint:disable:max-line-length */\n  pipe(): Observable<T>;\n  pipe<A>(op1: OperatorFunction<T, A>): Observable<A>;\n  pipe<A, B>(op1: OperatorFunction<T, A>, op2: OperatorFunction<A, B>): Observable<B>;\n  pipe<A, B, C>(op1: OperatorFunction<T, A>, op2: OperatorFunction<A, B>, op3: OperatorFunction<B, C>): Observable<C>;\n  pipe<A, B, C, D>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>\n  ): Observable<D>;\n  pipe<A, B, C, D, E>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>\n  ): Observable<E>;\n  pipe<A, B, C, D, E, F>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>,\n    op6: OperatorFunction<E, F>\n  ): Observable<F>;\n  pipe<A, B, C, D, E, F, G>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>,\n    op6: OperatorFunction<E, F>,\n    op7: OperatorFunction<F, G>\n  ): Observable<G>;\n  pipe<A, B, C, D, E, F, G, H>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>,\n    op6: OperatorFunction<E, F>,\n    op7: OperatorFunction<F, G>,\n    op8: OperatorFunction<G, H>\n  ): Observable<H>;\n  pipe<A, B, C, D, E, F, G, H, I>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>,\n    op6: OperatorFunction<E, F>,\n    op7: OperatorFunction<F, G>,\n    op8: OperatorFunction<G, H>,\n    op9: OperatorFunction<H, I>\n  ): Observable<I>;\n  pipe<A, B, C, D, E, F, G, H, I>(\n    op1: OperatorFunction<T, A>,\n    op2: OperatorFunction<A, B>,\n    op3: OperatorFunction<B, C>,\n    op4: OperatorFunction<C, D>,\n    op5: OperatorFunction<D, E>,\n    op6: OperatorFunction<E, F>,\n    op7: OperatorFunction<F, G>,\n    op8: OperatorFunction<G, H>,\n    op9: OperatorFunction<H, I>,\n    ...operations: OperatorFunction<any, any>[]\n  ): Observable<unknown>;\n  /* tslint:enable:max-line-length */\n\n  /**\n   * Used to stitch together functional operators into a chain.\n   *\n   * ## Example\n   *\n   * ```ts\n   * import { interval, filter, map, scan } from 'rxjs';\n   *\n   * interval(1000)\n   *   .pipe(\n   *     filter(x => x % 2 === 0),\n   *     map(x => x + x),\n   *     scan((acc, x) => acc + x)\n   *   )\n   *   .subscribe(x => console.log(x));\n   * ```\n   *\n   * @return The Observable result of all the operators having been called\n   * in the order they were passed in.\n   */\n  pipe(...operations: OperatorFunction<any, any>[]): Observable<any> {\n    return pipeFromArray(operations)(this);\n  }\n\n  /* tslint:disable:max-line-length */\n  /** @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise */\n  toPromise(): Promise<T | undefined>;\n  /** @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise */\n  toPromise(PromiseCtor: typeof Promise): Promise<T | undefined>;\n  /** @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise */\n  toPromise(PromiseCtor: PromiseConstructorLike): Promise<T | undefined>;\n  /* tslint:enable:max-line-length */\n\n  /**\n   * Subscribe to this Observable and get a Promise resolving on\n   * `complete` with the last emission (if any).\n   *\n   * **WARNING**: Only use this with observables you *know* will complete. If the source\n   * observable does not complete, you will end up with a promise that is hung up, and\n   * potentially all of the state of an async function hanging out in memory. To avoid\n   * this situation, look into adding something like {@link timeout}, {@link take},\n   * {@link takeWhile}, or {@link takeUntil} amongst others.\n   *\n   * @param [promiseCtor] a constructor function used to instantiate\n   * the Promise\n   * @return A Promise that resolves with the last value emit, or\n   * rejects on an error. If there were no emissions, Promise\n   * resolves with undefined.\n   * @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise\n   */\n  toPromise(promiseCtor?: PromiseConstructorLike): Promise<T | undefined> {\n    promiseCtor = getPromiseCtor(promiseCtor);\n\n    return new promiseCtor((resolve, reject) => {\n      let value: T | undefined;\n      this.subscribe(\n        (x: T) => (value = x),\n        (err: any) => reject(err),\n        () => resolve(value)\n      );\n    }) as Promise<T | undefined>;\n  }\n}\n\n/**\n * Decides between a passed promise constructor from consuming code,\n * A default configured promise constructor, and the native promise\n * constructor and returns it. If nothing can be found, it will throw\n * an error.\n * @param promiseCtor The optional promise constructor to passed by consuming code\n */\nfunction getPromiseCtor(promiseCtor: PromiseConstructorLike | undefined) {\n  return promiseCtor ?? config.Promise ?? Promise;\n}\n\nfunction isObserver<T>(value: any): value is Observer<T> {\n  return value && isFunction(value.next) && isFunction(value.error) && isFunction(value.complete);\n}\n\nfunction isSubscriber<T>(value: any): value is Subscriber<T> {\n  return (value && value instanceof Subscriber) || (isObserver(value) && isSubscription(value));\n}\n", "import { Observable } from '../Observable';\nimport { Subscriber } from '../Subscriber';\nimport { OperatorFunction } from '../types';\nimport { isFunction } from './isFunction';\n\n/**\n * Used to determine if an object is an Observable with a lift function.\n */\nexport function hasLift(source: any): source is { lift: InstanceType<typeof Observable>['lift'] } {\n  return isFunction(source?.lift);\n}\n\n/**\n * Creates an `OperatorFunction`. Used to define operators throughout the library in a concise way.\n * @param init The logic to connect the liftedSource to the subscriber at the moment of subscription.\n */\nexport function operate<T, R>(\n  init: (liftedSource: Observable<T>, subscriber: Subscriber<R>) => (() => void) | void\n): OperatorFunction<T, R> {\n  return (source: Observable<T>) => {\n    if (hasLift(source)) {\n      return source.lift(function (this: Subscriber<R>, liftedSource: Observable<T>) {\n        try {\n          return init(liftedSource, this);\n        } catch (err) {\n          this.error(err);\n        }\n      });\n    }\n    throw new TypeError('Unable to lift unknown Observable type');\n  };\n}\n", "import { Subscriber } from '../Subscriber';\n\n/**\n * Creates an instance of an `OperatorSubscriber`.\n * @param destination The downstream subscriber.\n * @param onNext Handles next values, only called if this subscriber is not stopped or closed. Any\n * error that occurs in this function is caught and sent to the `error` method of this subscriber.\n * @param onError Handles errors from the subscription, any errors that occur in this handler are caught\n * and send to the `destination` error handler.\n * @param onComplete Handles completion notification from the subscription. Any errors that occur in\n * this handler are sent to the `destination` error handler.\n * @param onFinalize Additional teardown logic here. This will only be called on teardown if the\n * subscriber itself is not already closed. This is called after all other teardown logic is executed.\n */\nexport function createOperatorSubscriber<T>(\n  destination: Subscriber<any>,\n  onNext?: (value: T) => void,\n  onComplete?: () => void,\n  onError?: (err: any) => void,\n  onFinalize?: () => void\n): Subscriber<T> {\n  return new OperatorSubscriber(destination, onNext, onComplete, onError, onFinalize);\n}\n\n/**\n * A generic helper for allowing operators to be created with a Subscriber and\n * use closures to capture necessary state from the operator function itself.\n */\nexport class OperatorSubscriber<T> extends Subscriber<T> {\n  /**\n   * Creates an instance of an `OperatorSubscriber`.\n   * @param destination The downstream subscriber.\n   * @param onNext Handles next values, only called if this subscriber is not stopped or closed. Any\n   * error that occurs in this function is caught and sent to the `error` method of this subscriber.\n   * @param onError Handles errors from the subscription, any errors that occur in this handler are caught\n   * and send to the `destination` error handler.\n   * @param onComplete Handles completion notification from the subscription. Any errors that occur in\n   * this handler are sent to the `destination` error handler.\n   * @param onFinalize Additional finalization logic here. This will only be called on finalization if the\n   * subscriber itself is not already closed. This is called after all other finalization logic is executed.\n   * @param shouldUnsubscribe An optional check to see if an unsubscribe call should truly unsubscribe.\n   * NOTE: This currently **ONLY** exists to support the strange behavior of {@link groupBy}, where unsubscription\n   * to the resulting observable does not actually disconnect from the source if there are active subscriptions\n   * to any grouped observable. (DO NOT EXPOSE OR USE EXTERNALLY!!!)\n   */\n  constructor(\n    destination: Subscriber<any>,\n    onNext?: (value: T) => void,\n    onComplete?: () => void,\n    onError?: (err: any) => void,\n    private onFinalize?: () => void,\n    private shouldUnsubscribe?: () => boolean\n  ) {\n    // It's important - for performance reasons - that all of this class's\n    // members are initialized and that they are always initialized in the same\n    // order. This will ensure that all OperatorSubscriber instances have the\n    // same hidden class in V8. This, in turn, will help keep the number of\n    // hidden classes involved in property accesses within the base class as\n    // low as possible. If the number of hidden classes involved exceeds four,\n    // the property accesses will become megamorphic and performance penalties\n    // will be incurred - i.e. inline caches won't be used.\n    //\n    // The reasons for ensuring all instances have the same hidden class are\n    // further discussed in this blog post from Benedikt Meurer:\n    // https://benediktmeurer.de/2018/03/23/impact-of-polymorphism-on-component-based-frameworks-like-react/\n    super(destination);\n    this._next = onNext\n      ? function (this: OperatorSubscriber<T>, value: T) {\n          try {\n            onNext(value);\n          } catch (err) {\n            destination.error(err);\n          }\n        }\n      : super._next;\n    this._error = onError\n      ? function (this: OperatorSubscriber<T>, err: any) {\n          try {\n            onError(err);\n          } catch (err) {\n            // Send any errors that occur down stream.\n            destination.error(err);\n          } finally {\n            // Ensure finalization.\n            this.unsubscribe();\n          }\n        }\n      : super._error;\n    this._complete = onComplete\n      ? function (this: OperatorSubscriber<T>) {\n          try {\n            onComplete();\n          } catch (err) {\n            // Send any errors that occur down stream.\n            destination.error(err);\n          } finally {\n            // Ensure finalization.\n            this.unsubscribe();\n          }\n        }\n      : super._complete;\n  }\n\n  unsubscribe() {\n    if (!this.shouldUnsubscribe || this.shouldUnsubscribe()) {\n      const { closed } = this;\n      super.unsubscribe();\n      // Execute additional teardown if we have any and we didn't already do so.\n      !closed && this.onFinalize?.();\n    }\n  }\n}\n", "import { Subscription } from '../Subscription';\n\ninterface AnimationFrameProvider {\n  schedule(callback: FrameRequestCallback): Subscription;\n  requestAnimationFrame: typeof requestAnimationFrame;\n  cancelAnimationFrame: typeof cancelAnimationFrame;\n  delegate:\n    | {\n        requestAnimationFrame: typeof requestAnimationFrame;\n        cancelAnimationFrame: typeof cancelAnimationFrame;\n      }\n    | undefined;\n}\n\nexport const animationFrameProvider: AnimationFrameProvider = {\n  // When accessing the delegate, use the variable rather than `this` so that\n  // the functions can be called without being bound to the provider.\n  schedule(callback) {\n    let request = requestAnimationFrame;\n    let cancel: typeof cancelAnimationFrame | undefined = cancelAnimationFrame;\n    const { delegate } = animationFrameProvider;\n    if (delegate) {\n      request = delegate.requestAnimationFrame;\n      cancel = delegate.cancelAnimationFrame;\n    }\n    const handle = request((timestamp) => {\n      // Clear the cancel function. The request has been fulfilled, so\n      // attempting to cancel the request upon unsubscription would be\n      // pointless.\n      cancel = undefined;\n      callback(timestamp);\n    });\n    return new Subscription(() => cancel?.(handle));\n  },\n  requestAnimationFrame(...args) {\n    const { delegate } = animationFrameProvider;\n    return (delegate?.requestAnimationFrame || requestAnimationFrame)(...args);\n  },\n  cancelAnimationFrame(...args) {\n    const { delegate } = animationFrameProvider;\n    return (delegate?.cancelAnimationFrame || cancelAnimationFrame)(...args);\n  },\n  delegate: undefined,\n};\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface ObjectUnsubscribedError extends Error {}\n\nexport interface ObjectUnsubscribedErrorCtor {\n  /**\n   * @deprecated Internal implementation detail. Do not construct error instances.\n   * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n   */\n  new (): ObjectUnsubscribedError;\n}\n\n/**\n * An error thrown when an action is invalid because the object has been\n * unsubscribed.\n *\n * @see {@link Subject}\n * @see {@link BehaviorSubject}\n *\n * @class ObjectUnsubscribedError\n */\nexport const ObjectUnsubscribedError: ObjectUnsubscribedErrorCtor = createErrorClass(\n  (_super) =>\n    function ObjectUnsubscribedErrorImpl(this: any) {\n      _super(this);\n      this.name = 'ObjectUnsubscribedError';\n      this.message = 'object unsubscribed';\n    }\n);\n", "import { Operator } from './Operator';\nimport { Observable } from './Observable';\nimport { Subscriber } from './Subscriber';\nimport { Subscription, EMPTY_SUBSCRIPTION } from './Subscription';\nimport { Observer, SubscriptionLike, TeardownLogic } from './types';\nimport { ObjectUnsubscribedError } from './util/ObjectUnsubscribedError';\nimport { arrRemove } from './util/arrRemove';\nimport { errorContext } from './util/errorContext';\n\n/**\n * A Subject is a special type of Observable that allows values to be\n * multicasted to many Observers. Subjects are like EventEmitters.\n *\n * Every Subject is an Observable and an Observer. You can subscribe to a\n * Subject, and you can call next to feed values as well as error and complete.\n */\nexport class Subject<T> extends Observable<T> implements SubscriptionLike {\n  closed = false;\n\n  private currentObservers: Observer<T>[] | null = null;\n\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  observers: Observer<T>[] = [];\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  isStopped = false;\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  hasError = false;\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  thrownError: any = null;\n\n  /**\n   * Creates a \"subject\" by basically gluing an observer to an observable.\n   *\n   * @deprecated Recommended you do not use. Will be removed at some point in the future. Plans for replacement still under discussion.\n   */\n  static create: (...args: any[]) => any = <T>(destination: Observer<T>, source: Observable<T>): AnonymousSubject<T> => {\n    return new AnonymousSubject<T>(destination, source);\n  };\n\n  constructor() {\n    // NOTE: This must be here to obscure Observable's constructor.\n    super();\n  }\n\n  /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n  lift<R>(operator: Operator<T, R>): Observable<R> {\n    const subject = new AnonymousSubject(this, this);\n    subject.operator = operator as any;\n    return subject as any;\n  }\n\n  /** @internal */\n  protected _throwIfClosed() {\n    if (this.closed) {\n      throw new ObjectUnsubscribedError();\n    }\n  }\n\n  next(value: T) {\n    errorContext(() => {\n      this._throwIfClosed();\n      if (!this.isStopped) {\n        if (!this.currentObservers) {\n          this.currentObservers = Array.from(this.observers);\n        }\n        for (const observer of this.currentObservers) {\n          observer.next(value);\n        }\n      }\n    });\n  }\n\n  error(err: any) {\n    errorContext(() => {\n      this._throwIfClosed();\n      if (!this.isStopped) {\n        this.hasError = this.isStopped = true;\n        this.thrownError = err;\n        const { observers } = this;\n        while (observers.length) {\n          observers.shift()!.error(err);\n        }\n      }\n    });\n  }\n\n  complete() {\n    errorContext(() => {\n      this._throwIfClosed();\n      if (!this.isStopped) {\n        this.isStopped = true;\n        const { observers } = this;\n        while (observers.length) {\n          observers.shift()!.complete();\n        }\n      }\n    });\n  }\n\n  unsubscribe() {\n    this.isStopped = this.closed = true;\n    this.observers = this.currentObservers = null!;\n  }\n\n  get observed() {\n    return this.observers?.length > 0;\n  }\n\n  /** @internal */\n  protected _trySubscribe(subscriber: Subscriber<T>): TeardownLogic {\n    this._throwIfClosed();\n    return super._trySubscribe(subscriber);\n  }\n\n  /** @internal */\n  protected _subscribe(subscriber: Subscriber<T>): Subscription {\n    this._throwIfClosed();\n    this._checkFinalizedStatuses(subscriber);\n    return this._innerSubscribe(subscriber);\n  }\n\n  /** @internal */\n  protected _innerSubscribe(subscriber: Subscriber<any>) {\n    const { hasError, isStopped, observers } = this;\n    if (hasError || isStopped) {\n      return EMPTY_SUBSCRIPTION;\n    }\n    this.currentObservers = null;\n    observers.push(subscriber);\n    return new Subscription(() => {\n      this.currentObservers = null;\n      arrRemove(observers, subscriber);\n    });\n  }\n\n  /** @internal */\n  protected _checkFinalizedStatuses(subscriber: Subscriber<any>) {\n    const { hasError, thrownError, isStopped } = this;\n    if (hasError) {\n      subscriber.error(thrownError);\n    } else if (isStopped) {\n      subscriber.complete();\n    }\n  }\n\n  /**\n   * Creates a new Observable with this Subject as the source. You can do this\n   * to create custom Observer-side logic of the Subject and conceal it from\n   * code that uses the Observable.\n   * @return Observable that this Subject casts to.\n   */\n  asObservable(): Observable<T> {\n    const observable: any = new Observable<T>();\n    observable.source = this;\n    return observable;\n  }\n}\n\nexport class AnonymousSubject<T> extends Subject<T> {\n  constructor(\n    /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n    public destination?: Observer<T>,\n    source?: Observable<T>\n  ) {\n    super();\n    this.source = source;\n  }\n\n  next(value: T) {\n    this.destination?.next?.(value);\n  }\n\n  error(err: any) {\n    this.destination?.error?.(err);\n  }\n\n  complete() {\n    this.destination?.complete?.();\n  }\n\n  /** @internal */\n  protected _subscribe(subscriber: Subscriber<T>): Subscription {\n    return this.source?.subscribe(subscriber) ?? EMPTY_SUBSCRIPTION;\n  }\n}\n", "import { Subject } from './Subject';\nimport { Subscriber } from './Subscriber';\nimport { Subscription } from './Subscription';\n\n/**\n * A variant of Subject that requires an initial value and emits its current\n * value whenever it is subscribed to.\n */\nexport class BehaviorSubject<T> extends Subject<T> {\n  constructor(private _value: T) {\n    super();\n  }\n\n  get value(): T {\n    return this.getValue();\n  }\n\n  /** @internal */\n  protected _subscribe(subscriber: Subscriber<T>): Subscription {\n    const subscription = super._subscribe(subscriber);\n    !subscription.closed && subscriber.next(this._value);\n    return subscription;\n  }\n\n  getValue(): T {\n    const { hasError, thrownError, _value } = this;\n    if (hasError) {\n      throw thrownError;\n    }\n    this._throwIfClosed();\n    return _value;\n  }\n\n  next(value: T): void {\n    super.next((this._value = value));\n  }\n}\n", "import { TimestampProvider } from '../types';\n\ninterface DateTimestampProvider extends TimestampProvider {\n  delegate: TimestampProvider | undefined;\n}\n\nexport const dateTimestampProvider: DateTimestampProvider = {\n  now() {\n    // Use the variable rather than `this` so that the function can be called\n    // without being bound to the provider.\n    return (dateTimestampProvider.delegate || Date).now();\n  },\n  delegate: undefined,\n};\n", "import { Subject } from './Subject';\nimport { TimestampProvider } from './types';\nimport { Subscriber } from './Subscriber';\nimport { Subscription } from './Subscription';\nimport { dateTimestampProvider } from './scheduler/dateTimestampProvider';\n\n/**\n * A variant of {@link Subject} that \"replays\" old values to new subscribers by emitting them when they first subscribe.\n *\n * `ReplaySubject` has an internal buffer that will store a specified number of values that it has observed. Like `Subject`,\n * `ReplaySubject` \"observes\" values by having them passed to its `next` method. When it observes a value, it will store that\n * value for a time determined by the configuration of the `ReplaySubject`, as passed to its constructor.\n *\n * When a new subscriber subscribes to the `ReplaySubject` instance, it will synchronously emit all values in its buffer in\n * a First-In-First-Out (FIFO) manner. The `ReplaySubject` will also complete, if it has observed completion; and it will\n * error if it has observed an error.\n *\n * There are two main configuration items to be concerned with:\n *\n * 1. `bufferSize` - This will determine how many items are stored in the buffer, defaults to infinite.\n * 2. `windowTime` - The amount of time to hold a value in the buffer before removing it from the buffer.\n *\n * Both configurations may exist simultaneously. So if you would like to buffer a maximum of 3 values, as long as the values\n * are less than 2 seconds old, you could do so with a `new ReplaySubject(3, 2000)`.\n *\n * ### Differences with BehaviorSubject\n *\n * `BehaviorSubject` is similar to `new ReplaySubject(1)`, with a couple of exceptions:\n *\n * 1. `BehaviorSubject` comes \"primed\" with a single value upon construction.\n * 2. `ReplaySubject` will replay values, even after observing an error, where `BehaviorSubject` will not.\n *\n * @see {@link Subject}\n * @see {@link BehaviorSubject}\n * @see {@link shareReplay}\n */\nexport class ReplaySubject<T> extends Subject<T> {\n  private _buffer: (T | number)[] = [];\n  private _infiniteTimeWindow = true;\n\n  /**\n   * @param _bufferSize The size of the buffer to replay on subscription\n   * @param _windowTime The amount of time the buffered items will stay buffered\n   * @param _timestampProvider An object with a `now()` method that provides the current timestamp. This is used to\n   * calculate the amount of time something has been buffered.\n   */\n  constructor(\n    private _bufferSize = Infinity,\n    private _windowTime = Infinity,\n    private _timestampProvider: TimestampProvider = dateTimestampProvider\n  ) {\n    super();\n    this._infiniteTimeWindow = _windowTime === Infinity;\n    this._bufferSize = Math.max(1, _bufferSize);\n    this._windowTime = Math.max(1, _windowTime);\n  }\n\n  next(value: T): void {\n    const { isStopped, _buffer, _infiniteTimeWindow, _timestampProvider, _windowTime } = this;\n    if (!isStopped) {\n      _buffer.push(value);\n      !_infiniteTimeWindow && _buffer.push(_timestampProvider.now() + _windowTime);\n    }\n    this._trimBuffer();\n    super.next(value);\n  }\n\n  /** @internal */\n  protected _subscribe(subscriber: Subscriber<T>): Subscription {\n    this._throwIfClosed();\n    this._trimBuffer();\n\n    const subscription = this._innerSubscribe(subscriber);\n\n    const { _infiniteTimeWindow, _buffer } = this;\n    // We use a copy here, so reentrant code does not mutate our array while we're\n    // emitting it to a new subscriber.\n    const copy = _buffer.slice();\n    for (let i = 0; i < copy.length && !subscriber.closed; i += _infiniteTimeWindow ? 1 : 2) {\n      subscriber.next(copy[i] as T);\n    }\n\n    this._checkFinalizedStatuses(subscriber);\n\n    return subscription;\n  }\n\n  private _trimBuffer() {\n    const { _bufferSize, _timestampProvider, _buffer, _infiniteTimeWindow } = this;\n    // If we don't have an infinite buffer size, and we're over the length,\n    // use splice to truncate the old buffer values off. Note that we have to\n    // double the size for instances where we're not using an infinite time window\n    // because we're storing the values and the timestamps in the same array.\n    const adjustedBufferSize = (_infiniteTimeWindow ? 1 : 2) * _bufferSize;\n    _bufferSize < Infinity && adjustedBufferSize < _buffer.length && _buffer.splice(0, _buffer.length - adjustedBufferSize);\n\n    // Now, if we're not in an infinite time window, remove all values where the time is\n    // older than what is allowed.\n    if (!_infiniteTimeWindow) {\n      const now = _timestampProvider.now();\n      let last = 0;\n      // Search the array for the first timestamp that isn't expired and\n      // truncate the buffer up to that point.\n      for (let i = 1; i < _buffer.length && (_buffer[i] as number) <= now; i += 2) {\n        last = i;\n      }\n      last && _buffer.splice(0, last + 1);\n    }\n  }\n}\n", "import { Scheduler } from '../Scheduler';\nimport { Subscription } from '../Subscription';\nimport { SchedulerAction } from '../types';\n\n/**\n * A unit of work to be executed in a `scheduler`. An action is typically\n * created from within a {@link SchedulerLike} and an RxJS user does not need to concern\n * themselves about creating and manipulating an Action.\n *\n * ```ts\n * class Action<T> extends Subscription {\n *   new (scheduler: Scheduler, work: (state?: T) => void);\n *   schedule(state?: T, delay: number = 0): Subscription;\n * }\n * ```\n */\nexport class Action<T> extends Subscription {\n  constructor(scheduler: Scheduler, work: (this: SchedulerAction<T>, state?: T) => void) {\n    super();\n  }\n  /**\n   * Schedules this action on its parent {@link SchedulerLike} for execution. May be passed\n   * some context object, `state`. May happen at some point in the future,\n   * according to the `delay` parameter, if specified.\n   * @param state Some contextual data that the `work` function uses when called by the\n   * Scheduler.\n   * @param delay Time to wait before executing the work, where the time unit is implicit\n   * and defined by the Scheduler.\n   * @return A subscription in order to be able to unsubscribe the scheduled work.\n   */\n  public schedule(state?: T, delay: number = 0): Subscription {\n    return this;\n  }\n}\n", "import type { TimerHandle } from './timerHandle';\ntype SetIntervalFunction = (handler: () => void, timeout?: number, ...args: any[]) => TimerHandle;\ntype ClearIntervalFunction = (handle: TimerHandle) => void;\n\ninterface IntervalProvider {\n  setInterval: SetIntervalFunction;\n  clearInterval: ClearIntervalFunction;\n  delegate:\n    | {\n        setInterval: SetIntervalFunction;\n        clearInterval: ClearIntervalFunction;\n      }\n    | undefined;\n}\n\nexport const intervalProvider: IntervalProvider = {\n  // When accessing the delegate, use the variable rather than `this` so that\n  // the functions can be called without being bound to the provider.\n  setInterval(handler: () => void, timeout?: number, ...args) {\n    const { delegate } = intervalProvider;\n    if (delegate?.setInterval) {\n      return delegate.setInterval(handler, timeout, ...args);\n    }\n    return setInterval(handler, timeout, ...args);\n  },\n  clearInterval(handle) {\n    const { delegate } = intervalProvider;\n    return (delegate?.clearInterval || clearInterval)(handle as any);\n  },\n  delegate: undefined,\n};\n", "import { Action } from './Action';\nimport { SchedulerAction } from '../types';\nimport { Subscription } from '../Subscription';\nimport { AsyncScheduler } from './AsyncScheduler';\nimport { intervalProvider } from './intervalProvider';\nimport { arrRemove } from '../util/arrRemove';\nimport { TimerHandle } from './timerHandle';\n\nexport class AsyncAction<T> extends Action<T> {\n  public id: TimerHandle | undefined;\n  public state?: T;\n  // @ts-ignore: Property has no initializer and is not definitely assigned\n  public delay: number;\n  protected pending: boolean = false;\n\n  constructor(protected scheduler: AsyncScheduler, protected work: (this: SchedulerAction<T>, state?: T) => void) {\n    super(scheduler, work);\n  }\n\n  public schedule(state?: T, delay: number = 0): Subscription {\n    if (this.closed) {\n      return this;\n    }\n\n    // Always replace the current state with the new state.\n    this.state = state;\n\n    const id = this.id;\n    const scheduler = this.scheduler;\n\n    //\n    // Important implementation note:\n    //\n    // Actions only execute once by default, unless rescheduled from within the\n    // scheduled callback. This allows us to implement single and repeat\n    // actions via the same code path, without adding API surface area, as well\n    // as mimic traditional recursion but across asynchronous boundaries.\n    //\n    // However, JS runtimes and timers distinguish between intervals achieved by\n    // serial `setTimeout` calls vs. a single `setInterval` call. An interval of\n    // serial `setTimeout` calls can be individually delayed, which delays\n    // scheduling the next `setTimeout`, and so on. `setInterval` attempts to\n    // guarantee the interval callback will be invoked more precisely to the\n    // interval period, regardless of load.\n    //\n    // Therefore, we use `setInterval` to schedule single and repeat actions.\n    // If the action reschedules itself with the same delay, the interval is not\n    // canceled. If the action doesn't reschedule, or reschedules with a\n    // different delay, the interval will be canceled after scheduled callback\n    // execution.\n    //\n    if (id != null) {\n      this.id = this.recycleAsyncId(scheduler, id, delay);\n    }\n\n    // Set the pending flag indicating that this action has been scheduled, or\n    // has recursively rescheduled itself.\n    this.pending = true;\n\n    this.delay = delay;\n    // If this action has already an async Id, don't request a new one.\n    this.id = this.id ?? this.requestAsyncId(scheduler, this.id, delay);\n\n    return this;\n  }\n\n  protected requestAsyncId(scheduler: AsyncScheduler, _id?: TimerHandle, delay: number = 0): TimerHandle {\n    return intervalProvider.setInterval(scheduler.flush.bind(scheduler, this), delay);\n  }\n\n  protected recycleAsyncId(_scheduler: AsyncScheduler, id?: TimerHandle, delay: number | null = 0): TimerHandle | undefined {\n    // If this action is rescheduled with the same delay time, don't clear the interval id.\n    if (delay != null && this.delay === delay && this.pending === false) {\n      return id;\n    }\n    // Otherwise, if the action's delay time is different from the current delay,\n    // or the action has been rescheduled before it's executed, clear the interval id\n    if (id != null) {\n      intervalProvider.clearInterval(id);\n    }\n\n    return undefined;\n  }\n\n  /**\n   * Immediately executes this action and the `work` it contains.\n   */\n  public execute(state: T, delay: number): any {\n    if (this.closed) {\n      return new Error('executing a cancelled action');\n    }\n\n    this.pending = false;\n    const error = this._execute(state, delay);\n    if (error) {\n      return error;\n    } else if (this.pending === false && this.id != null) {\n      // Dequeue if the action didn't reschedule itself. Don't call\n      // unsubscribe(), because the action could reschedule later.\n      // For example:\n      // ```\n      // scheduler.schedule(function doWork(counter) {\n      //   /* ... I'm a busy worker bee ... */\n      //   var originalAction = this;\n      //   /* wait 100ms before rescheduling the action */\n      //   setTimeout(function () {\n      //     originalAction.schedule(counter + 1);\n      //   }, 100);\n      // }, 1000);\n      // ```\n      this.id = this.recycleAsyncId(this.scheduler, this.id, null);\n    }\n  }\n\n  protected _execute(state: T, _delay: number): any {\n    let errored: boolean = false;\n    let errorValue: any;\n    try {\n      this.work(state);\n    } catch (e) {\n      errored = true;\n      // HACK: Since code elsewhere is relying on the \"truthiness\" of the\n      // return here, we can't have it return \"\" or 0 or false.\n      // TODO: Clean this up when we refactor schedulers mid-version-8 or so.\n      errorValue = e ? e : new Error('Scheduled action threw falsy error');\n    }\n    if (errored) {\n      this.unsubscribe();\n      return errorValue;\n    }\n  }\n\n  unsubscribe() {\n    if (!this.closed) {\n      const { id, scheduler } = this;\n      const { actions } = scheduler;\n\n      this.work = this.state = this.scheduler = null!;\n      this.pending = false;\n\n      arrRemove(actions, this);\n      if (id != null) {\n        this.id = this.recycleAsyncId(scheduler, id, null);\n      }\n\n      this.delay = null!;\n      super.unsubscribe();\n    }\n  }\n}\n", "import { Action } from './scheduler/Action';\nimport { Subscription } from './Subscription';\nimport { SchedulerLike, SchedulerAction } from './types';\nimport { dateTimestampProvider } from './scheduler/dateTimestampProvider';\n\n/**\n * An execution context and a data structure to order tasks and schedule their\n * execution. Provides a notion of (potentially virtual) time, through the\n * `now()` getter method.\n *\n * Each unit of work in a Scheduler is called an `Action`.\n *\n * ```ts\n * class Scheduler {\n *   now(): number;\n *   schedule(work, delay?, state?): Subscription;\n * }\n * ```\n *\n * @deprecated Scheduler is an internal implementation detail of RxJS, and\n * should not be used directly. Rather, create your own class and implement\n * {@link SchedulerLike}. Will be made internal in v8.\n */\nexport class Scheduler implements SchedulerLike {\n  public static now: () => number = dateTimestampProvider.now;\n\n  constructor(private schedulerActionCtor: typeof Action, now: () => number = Scheduler.now) {\n    this.now = now;\n  }\n\n  /**\n   * A getter method that returns a number representing the current time\n   * (at the time this function was called) according to the scheduler's own\n   * internal clock.\n   * @return A number that represents the current time. May or may not\n   * have a relation to wall-clock time. May or may not refer to a time unit\n   * (e.g. milliseconds).\n   */\n  public now: () => number;\n\n  /**\n   * Schedules a function, `work`, for execution. May happen at some point in\n   * the future, according to the `delay` parameter, if specified. May be passed\n   * some context object, `state`, which will be passed to the `work` function.\n   *\n   * The given arguments will be processed an stored as an Action object in a\n   * queue of actions.\n   *\n   * @param work A function representing a task, or some unit of work to be\n   * executed by the Scheduler.\n   * @param delay Time to wait before executing the work, where the time unit is\n   * implicit and defined by the Scheduler itself.\n   * @param state Some contextual data that the `work` function uses when called\n   * by the Scheduler.\n   * @return A subscription in order to be able to unsubscribe the scheduled work.\n   */\n  public schedule<T>(work: (this: SchedulerAction<T>, state?: T) => void, delay: number = 0, state?: T): Subscription {\n    return new this.schedulerActionCtor<T>(this, work).schedule(state, delay);\n  }\n}\n", "import { Scheduler } from '../Scheduler';\nimport { Action } from './Action';\nimport { AsyncAction } from './AsyncAction';\nimport { TimerHandle } from './timerHandle';\n\nexport class AsyncScheduler extends Scheduler {\n  public actions: Array<AsyncAction<any>> = [];\n  /**\n   * A flag to indicate whether the Scheduler is currently executing a batch of\n   * queued actions.\n   * @internal\n   */\n  public _active: boolean = false;\n  /**\n   * An internal ID used to track the latest asynchronous task such as those\n   * coming from `setTimeout`, `setInterval`, `requestAnimationFrame`, and\n   * others.\n   * @internal\n   */\n  public _scheduled: TimerHandle | undefined;\n\n  constructor(SchedulerAction: typeof Action, now: () => number = Scheduler.now) {\n    super(SchedulerAction, now);\n  }\n\n  public flush(action: AsyncAction<any>): void {\n    const { actions } = this;\n\n    if (this._active) {\n      actions.push(action);\n      return;\n    }\n\n    let error: any;\n    this._active = true;\n\n    do {\n      if ((error = action.execute(action.state, action.delay))) {\n        break;\n      }\n    } while ((action = actions.shift()!)); // exhaust the scheduler queue\n\n    this._active = false;\n\n    if (error) {\n      while ((action = actions.shift()!)) {\n        action.unsubscribe();\n      }\n      throw error;\n    }\n  }\n}\n", "import { AsyncAction } from './AsyncAction';\nimport { AsyncScheduler } from './AsyncScheduler';\n\n/**\n *\n * Async Scheduler\n *\n * <span class=\"informal\">Schedule task as if you used setTimeout(task, duration)</span>\n *\n * `async` scheduler schedules tasks asynchronously, by putting them on the JavaScript\n * event loop queue. It is best used to delay tasks in time or to schedule tasks repeating\n * in intervals.\n *\n * If you just want to \"defer\" task, that is to perform it right after currently\n * executing synchronous code ends (commonly achieved by `setTimeout(deferredTask, 0)`),\n * better choice will be the {@link asapScheduler} scheduler.\n *\n * ## Examples\n * Use async scheduler to delay task\n * ```ts\n * import { asyncScheduler } from 'rxjs';\n *\n * const task = () => console.log('it works!');\n *\n * asyncScheduler.schedule(task, 2000);\n *\n * // After 2 seconds logs:\n * // \"it works!\"\n * ```\n *\n * Use async scheduler to repeat task in intervals\n * ```ts\n * import { asyncScheduler } from 'rxjs';\n *\n * function task(state) {\n *   console.log(state);\n *   this.schedule(state + 1, 1000); // `this` references currently executing Action,\n *                                   // which we reschedule with new state and delay\n * }\n *\n * asyncScheduler.schedule(task, 3000, 0);\n *\n * // Logs:\n * // 0 after 3s\n * // 1 after 4s\n * // 2 after 5s\n * // 3 after 6s\n * ```\n */\n\nexport const asyncScheduler = new AsyncScheduler(AsyncAction);\n\n/**\n * @deprecated Renamed to {@link asyncScheduler}. Will be removed in v8.\n */\nexport const async = asyncScheduler;\n", "import { AsyncAction } from './AsyncAction';\nimport { Subscription } from '../Subscription';\nimport { QueueScheduler } from './QueueScheduler';\nimport { SchedulerAction } from '../types';\nimport { TimerHandle } from './timerHandle';\n\nexport class QueueAction<T> extends AsyncAction<T> {\n  constructor(protected scheduler: QueueScheduler, protected work: (this: SchedulerAction<T>, state?: T) => void) {\n    super(scheduler, work);\n  }\n\n  public schedule(state?: T, delay: number = 0): Subscription {\n    if (delay > 0) {\n      return super.schedule(state, delay);\n    }\n    this.delay = delay;\n    this.state = state;\n    this.scheduler.flush(this);\n    return this;\n  }\n\n  public execute(state: T, delay: number): any {\n    return delay > 0 || this.closed ? super.execute(state, delay) : this._execute(state, delay);\n  }\n\n  protected requestAsyncId(scheduler: QueueScheduler, id?: TimerHandle, delay: number = 0): TimerHandle {\n    // If delay exists and is greater than 0, or if the delay is null (the\n    // action wasn't rescheduled) but was originally scheduled as an async\n    // action, then recycle as an async action.\n\n    if ((delay != null && delay > 0) || (delay == null && this.delay > 0)) {\n      return super.requestAsyncId(scheduler, id, delay);\n    }\n\n    // Otherwise flush the scheduler starting with this action.\n    scheduler.flush(this);\n\n    // HACK: In the past, this was returning `void`. However, `void` isn't a valid\n    // `TimerHandle`, and generally the return value here isn't really used. So the\n    // compromise is to return `0` which is both \"falsy\" and a valid `TimerHandle`,\n    // as opposed to refactoring every other instanceo of `requestAsyncId`.\n    return 0;\n  }\n}\n", "import { AsyncScheduler } from './AsyncScheduler';\n\nexport class QueueScheduler extends AsyncScheduler {\n}\n", "import { QueueAction } from './QueueAction';\nimport { QueueScheduler } from './QueueScheduler';\n\n/**\n *\n * Queue Scheduler\n *\n * <span class=\"informal\">Put every next task on a queue, instead of executing it immediately</span>\n *\n * `queue` scheduler, when used with delay, behaves the same as {@link asyncScheduler} scheduler.\n *\n * When used without delay, it schedules given task synchronously - executes it right when\n * it is scheduled. However when called recursively, that is when inside the scheduled task,\n * another task is scheduled with queue scheduler, instead of executing immediately as well,\n * that task will be put on a queue and wait for current one to finish.\n *\n * This means that when you execute task with `queue` scheduler, you are sure it will end\n * before any other task scheduled with that scheduler will start.\n *\n * ## Examples\n * Schedule recursively first, then do something\n * ```ts\n * import { queueScheduler } from 'rxjs';\n *\n * queueScheduler.schedule(() => {\n *   queueScheduler.schedule(() => console.log('second')); // will not happen now, but will be put on a queue\n *\n *   console.log('first');\n * });\n *\n * // Logs:\n * // \"first\"\n * // \"second\"\n * ```\n *\n * Reschedule itself recursively\n * ```ts\n * import { queueScheduler } from 'rxjs';\n *\n * queueScheduler.schedule(function(state) {\n *   if (state !== 0) {\n *     console.log('before', state);\n *     this.schedule(state - 1); // `this` references currently executing Action,\n *                               // which we reschedule with new state\n *     console.log('after', state);\n *   }\n * }, 0, 3);\n *\n * // In scheduler that runs recursively, you would expect:\n * // \"before\", 3\n * // \"before\", 2\n * // \"before\", 1\n * // \"after\", 1\n * // \"after\", 2\n * // \"after\", 3\n *\n * // But with queue it logs:\n * // \"before\", 3\n * // \"after\", 3\n * // \"before\", 2\n * // \"after\", 2\n * // \"before\", 1\n * // \"after\", 1\n * ```\n */\n\nexport const queueScheduler = new QueueScheduler(QueueAction);\n\n/**\n * @deprecated Renamed to {@link queueScheduler}. Will be removed in v8.\n */\nexport const queue = queueScheduler;\n", "import { AsyncAction } from './AsyncAction';\nimport { AnimationFrameScheduler } from './AnimationFrameScheduler';\nimport { SchedulerAction } from '../types';\nimport { animationFrameProvider } from './animationFrameProvider';\nimport { TimerHandle } from './timerHandle';\n\nexport class AnimationFrameAction<T> extends AsyncAction<T> {\n  constructor(protected scheduler: AnimationFrameScheduler, protected work: (this: SchedulerAction<T>, state?: T) => void) {\n    super(scheduler, work);\n  }\n\n  protected requestAsyncId(scheduler: AnimationFrameScheduler, id?: TimerHandle, delay: number = 0): TimerHandle {\n    // If delay is greater than 0, request as an async action.\n    if (delay !== null && delay > 0) {\n      return super.requestAsyncId(scheduler, id, delay);\n    }\n    // Push the action to the end of the scheduler queue.\n    scheduler.actions.push(this);\n    // If an animation frame has already been requested, don't request another\n    // one. If an animation frame hasn't been requested yet, request one. Return\n    // the current animation frame request id.\n    return scheduler._scheduled || (scheduler._scheduled = animationFrameProvider.requestAnimationFrame(() => scheduler.flush(undefined)));\n  }\n\n  protected recycleAsyncId(scheduler: AnimationFrameScheduler, id?: TimerHandle, delay: number = 0): TimerHandle | undefined {\n    // If delay exists and is greater than 0, or if the delay is null (the\n    // action wasn't rescheduled) but was originally scheduled as an async\n    // action, then recycle as an async action.\n    if (delay != null ? delay > 0 : this.delay > 0) {\n      return super.recycleAsyncId(scheduler, id, delay);\n    }\n    // If the scheduler queue has no remaining actions with the same async id,\n    // cancel the requested animation frame and set the scheduled flag to\n    // undefined so the next AnimationFrameAction will request its own.\n    const { actions } = scheduler;\n    if (id != null && id === scheduler._scheduled && actions[actions.length - 1]?.id !== id) {\n      animationFrameProvider.cancelAnimationFrame(id as number);\n      scheduler._scheduled = undefined;\n    }\n    // Return undefined so the action knows to request a new async id if it's rescheduled.\n    return undefined;\n  }\n}\n", "import { AsyncAction } from './AsyncAction';\nimport { AsyncScheduler } from './AsyncScheduler';\n\nexport class AnimationFrameScheduler extends AsyncScheduler {\n  public flush(action?: AsyncAction<any>): void {\n    this._active = true;\n    // The async id that effects a call to flush is stored in _scheduled.\n    // Before executing an action, it's necessary to check the action's async\n    // id to determine whether it's supposed to be executed in the current\n    // flush.\n    // Previous implementations of this method used a count to determine this,\n    // but that was unsound, as actions that are unsubscribed - i.e. cancelled -\n    // are removed from the actions array and that can shift actions that are\n    // scheduled to be executed in a subsequent flush into positions at which\n    // they are executed within the current flush.\n    let flushId;\n    if (action) {\n      flushId = action.id;\n    } else {\n      flushId = this._scheduled;\n      this._scheduled = undefined;\n    }\n\n    const { actions } = this;\n    let error: any;\n    action = action || actions.shift()!;\n\n    do {\n      if ((error = action.execute(action.state, action.delay))) {\n        break;\n      }\n    } while ((action = actions[0]) && action.id === flushId && actions.shift());\n\n    this._active = false;\n\n    if (error) {\n      while ((action = actions[0]) && action.id === flushId && actions.shift()) {\n        action.unsubscribe();\n      }\n      throw error;\n    }\n  }\n}\n", "import { AnimationFrameAction } from './AnimationFrameAction';\nimport { AnimationFrameScheduler } from './AnimationFrameScheduler';\n\n/**\n *\n * Animation Frame Scheduler\n *\n * <span class=\"informal\">Perform task when `window.requestAnimationFrame` would fire</span>\n *\n * When `animationFrame` scheduler is used with delay, it will fall back to {@link asyncScheduler} scheduler\n * behaviour.\n *\n * Without delay, `animationFrame` scheduler can be used to create smooth browser animations.\n * It makes sure scheduled task will happen just before next browser content repaint,\n * thus performing animations as efficiently as possible.\n *\n * ## Example\n * Schedule div height animation\n * ```ts\n * // html: <div style=\"background: #0ff;\"></div>\n * import { animationFrameScheduler } from 'rxjs';\n *\n * const div = document.querySelector('div');\n *\n * animationFrameScheduler.schedule(function(height) {\n *   div.style.height = height + \"px\";\n *\n *   this.schedule(height + 1);  // `this` references currently executing Action,\n *                               // which we reschedule with new state\n * }, 0, 0);\n *\n * // You will see a div element growing in height\n * ```\n */\n\nexport const animationFrameScheduler = new AnimationFrameScheduler(AnimationFrameAction);\n\n/**\n * @deprecated Renamed to {@link animationFrameScheduler}. Will be removed in v8.\n */\nexport const animationFrame = animationFrameScheduler;\n", "import { Observable } from '../Observable';\nimport { SchedulerLike } from '../types';\n\n/**\n * A simple Observable that emits no items to the Observer and immediately\n * emits a complete notification.\n *\n * <span class=\"informal\">Just emits 'complete', and nothing else.</span>\n *\n * ![](empty.png)\n *\n * A simple Observable that only emits the complete notification. It can be used\n * for composing with other Observables, such as in a {@link mergeMap}.\n *\n * ## Examples\n *\n * Log complete notification\n *\n * ```ts\n * import { EMPTY } from 'rxjs';\n *\n * EMPTY.subscribe({\n *   next: () => console.log('Next'),\n *   complete: () => console.log('Complete!')\n * });\n *\n * // Outputs\n * // Complete!\n * ```\n *\n * Emit the number 7, then complete\n *\n * ```ts\n * import { EMPTY, startWith } from 'rxjs';\n *\n * const result = EMPTY.pipe(startWith(7));\n * result.subscribe(x => console.log(x));\n *\n * // Outputs\n * // 7\n * ```\n *\n * Map and flatten only odd numbers to the sequence `'a'`, `'b'`, `'c'`\n *\n * ```ts\n * import { interval, mergeMap, of, EMPTY } from 'rxjs';\n *\n * const interval$ = interval(1000);\n * const result = interval$.pipe(\n *   mergeMap(x => x % 2 === 1 ? of('a', 'b', 'c') : EMPTY),\n * );\n * result.subscribe(x => console.log(x));\n *\n * // Results in the following to the console:\n * // x is equal to the count on the interval, e.g. (0, 1, 2, 3, ...)\n * // x will occur every 1000ms\n * // if x % 2 is equal to 1, print a, b, c (each on its own)\n * // if x % 2 is not equal to 1, nothing will be output\n * ```\n *\n * @see {@link Observable}\n * @see {@link NEVER}\n * @see {@link of}\n * @see {@link throwError}\n */\nexport const EMPTY = new Observable<never>((subscriber) => subscriber.complete());\n\n/**\n * @param scheduler A {@link SchedulerLike} to use for scheduling\n * the emission of the complete notification.\n * @deprecated Replaced with the {@link EMPTY} constant or {@link scheduled} (e.g. `scheduled([], scheduler)`). Will be removed in v8.\n */\nexport function empty(scheduler?: SchedulerLike) {\n  return scheduler ? emptyScheduled(scheduler) : EMPTY;\n}\n\nfunction emptyScheduled(scheduler: SchedulerLike) {\n  return new Observable<never>((subscriber) => scheduler.schedule(() => subscriber.complete()));\n}\n", "import { SchedulerLike } from '../types';\nimport { isFunction } from './isFunction';\n\nexport function isScheduler(value: any): value is SchedulerLike {\n  return value && isFunction(value.schedule);\n}\n", "import { SchedulerLike } from '../types';\nimport { isFunction } from './isFunction';\nimport { isScheduler } from './isScheduler';\n\nfunction last<T>(arr: T[]): T | undefined {\n  return arr[arr.length - 1];\n}\n\nexport function popResultSelector(args: any[]): ((...args: unknown[]) => unknown) | undefined {\n  return isFunction(last(args)) ? args.pop() : undefined;\n}\n\nexport function popScheduler(args: any[]): SchedulerLike | undefined {\n  return isScheduler(last(args)) ? args.pop() : undefined;\n}\n\nexport function popNumber(args: any[], defaultValue: number): number {\n  return typeof last(args) === 'number' ? args.pop()! : defaultValue;\n}\n", "export const isArrayLike = (<T>(x: any): x is ArrayLike<T> => x && typeof x.length === 'number' && typeof x !== 'function');", "import { isFunction } from \"./isFunction\";\n\n/**\n * Tests to see if the object is \"thennable\".\n * @param value the object to test\n */\nexport function isPromise(value: any): value is PromiseLike<any> {\n  return isFunction(value?.then);\n}\n", "import { InteropObservable } from '../types';\nimport { observable as Symbol_observable } from '../symbol/observable';\nimport { isFunction } from './isFunction';\n\n/** Identifies an input as being Observable (but not necessary an Rx Observable) */\nexport function isInteropObservable(input: any): input is InteropObservable<any> {\n  return isFunction(input[Symbol_observable]);\n}\n", "import { isFunction } from './isFunction';\n\nexport function isAsyncIterable<T>(obj: any): obj is AsyncIterable<T> {\n  return Symbol.asyncIterator && isFunction(obj?.[Symbol.asyncIterator]);\n}\n", "/**\n * Creates the TypeError to throw if an invalid object is passed to `from` or `scheduled`.\n * @param input The object that was passed.\n */\nexport function createInvalidObservableTypeError(input: any) {\n  // TODO: We should create error codes that can be looked up, so this can be less verbose.\n  return new TypeError(\n    `You provided ${\n      input !== null && typeof input === 'object' ? 'an invalid object' : `'${input}'`\n    } where a stream was expected. You can provide an Observable, Promise, ReadableStream, Array, AsyncIterable, or Iterable.`\n  );\n}\n", "export function getSymbolIterator(): symbol {\n  if (typeof Symbol !== 'function' || !Symbol.iterator) {\n    return '@@iterator' as any;\n  }\n\n  return Symbol.iterator;\n}\n\nexport const iterator = getSymbolIterator();\n", "import { iterator as Symbol_iterator } from '../symbol/iterator';\nimport { isFunction } from './isFunction';\n\n/** Identifies an input as being an Iterable */\nexport function isIterable(input: any): input is Iterable<any> {\n  return isFunction(input?.[Symbol_iterator]);\n}\n", "import { ReadableStreamLike } from '../types';\nimport { isFunction } from './isFunction';\n\nexport async function* readableStreamLikeToAsyncGenerator<T>(readableStream: ReadableStreamLike<T>): AsyncGenerator<T> {\n  const reader = readableStream.getReader();\n  try {\n    while (true) {\n      const { value, done } = await reader.read();\n      if (done) {\n        return;\n      }\n      yield value!;\n    }\n  } finally {\n    reader.releaseLock();\n  }\n}\n\nexport function isReadableStreamLike<T>(obj: any): obj is ReadableStreamLike<T> {\n  // We don't want to use instanceof checks because they would return\n  // false for instances from another Realm, like an <iframe>.\n  return isFunction(obj?.getReader);\n}\n", "import { isArrayLike } from '../util/isArrayLike';\nimport { isPromise } from '../util/isPromise';\nimport { Observable } from '../Observable';\nimport { ObservableInput, ObservedValueOf, ReadableStreamLike } from '../types';\nimport { isInteropObservable } from '../util/isInteropObservable';\nimport { isAsyncIterable } from '../util/isAsyncIterable';\nimport { createInvalidObservableTypeError } from '../util/throwUnobservableError';\nimport { isIterable } from '../util/isIterable';\nimport { isReadableStreamLike, readableStreamLikeToAsyncGenerator } from '../util/isReadableStreamLike';\nimport { Subscriber } from '../Subscriber';\nimport { isFunction } from '../util/isFunction';\nimport { reportUnhandledError } from '../util/reportUnhandledError';\nimport { observable as Symbol_observable } from '../symbol/observable';\n\nexport function innerFrom<O extends ObservableInput<any>>(input: O): Observable<ObservedValueOf<O>>;\nexport function innerFrom<T>(input: ObservableInput<T>): Observable<T> {\n  if (input instanceof Observable) {\n    return input;\n  }\n  if (input != null) {\n    if (isInteropObservable(input)) {\n      return fromInteropObservable(input);\n    }\n    if (isArrayLike(input)) {\n      return fromArrayLike(input);\n    }\n    if (isPromise(input)) {\n      return fromPromise(input);\n    }\n    if (isAsyncIterable(input)) {\n      return fromAsyncIterable(input);\n    }\n    if (isIterable(input)) {\n      return fromIterable(input);\n    }\n    if (isReadableStreamLike(input)) {\n      return fromReadableStreamLike(input);\n    }\n  }\n\n  throw createInvalidObservableTypeError(input);\n}\n\n/**\n * Creates an RxJS Observable from an object that implements `Symbol.observable`.\n * @param obj An object that properly implements `Symbol.observable`.\n */\nexport function fromInteropObservable<T>(obj: any) {\n  return new Observable((subscriber: Subscriber<T>) => {\n    const obs = obj[Symbol_observable]();\n    if (isFunction(obs.subscribe)) {\n      return obs.subscribe(subscriber);\n    }\n    // Should be caught by observable subscribe function error handling.\n    throw new TypeError('Provided object does not correctly implement Symbol.observable');\n  });\n}\n\n/**\n * Synchronously emits the values of an array like and completes.\n * This is exported because there are creation functions and operators that need to\n * make direct use of the same logic, and there's no reason to make them run through\n * `from` conditionals because we *know* they're dealing with an array.\n * @param array The array to emit values from\n */\nexport function fromArrayLike<T>(array: ArrayLike<T>) {\n  return new Observable((subscriber: Subscriber<T>) => {\n    // Loop over the array and emit each value. Note two things here:\n    // 1. We're making sure that the subscriber is not closed on each loop.\n    //    This is so we don't continue looping over a very large array after\n    //    something like a `take`, `takeWhile`, or other synchronous unsubscription\n    //    has already unsubscribed.\n    // 2. In this form, reentrant code can alter that array we're looping over.\n    //    This is a known issue, but considered an edge case. The alternative would\n    //    be to copy the array before executing the loop, but this has\n    //    performance implications.\n    for (let i = 0; i < array.length && !subscriber.closed; i++) {\n      subscriber.next(array[i]);\n    }\n    subscriber.complete();\n  });\n}\n\nexport function fromPromise<T>(promise: PromiseLike<T>) {\n  return new Observable((subscriber: Subscriber<T>) => {\n    promise\n      .then(\n        (value) => {\n          if (!subscriber.closed) {\n            subscriber.next(value);\n            subscriber.complete();\n          }\n        },\n        (err: any) => subscriber.error(err)\n      )\n      .then(null, reportUnhandledError);\n  });\n}\n\nexport function fromIterable<T>(iterable: Iterable<T>) {\n  return new Observable((subscriber: Subscriber<T>) => {\n    for (const value of iterable) {\n      subscriber.next(value);\n      if (subscriber.closed) {\n        return;\n      }\n    }\n    subscriber.complete();\n  });\n}\n\nexport function fromAsyncIterable<T>(asyncIterable: AsyncIterable<T>) {\n  return new Observable((subscriber: Subscriber<T>) => {\n    process(asyncIterable, subscriber).catch((err) => subscriber.error(err));\n  });\n}\n\nexport function fromReadableStreamLike<T>(readableStream: ReadableStreamLike<T>) {\n  return fromAsyncIterable(readableStreamLikeToAsyncGenerator(readableStream));\n}\n\nasync function process<T>(asyncIterable: AsyncIterable<T>, subscriber: Subscriber<T>) {\n  for await (const value of asyncIterable) {\n    subscriber.next(value);\n    // A side-effect may have closed our subscriber,\n    // check before the next iteration.\n    if (subscriber.closed) {\n      return;\n    }\n  }\n  subscriber.complete();\n}\n", "import { Subscription } from '../Subscription';\nimport { SchedulerAction, SchedulerLike } from '../types';\n\nexport function executeSchedule(\n  parentSubscription: Subscription,\n  scheduler: SchedulerLike,\n  work: () => void,\n  delay: number,\n  repeat: true\n): void;\nexport function executeSchedule(\n  parentSubscription: Subscription,\n  scheduler: SchedulerLike,\n  work: () => void,\n  delay?: number,\n  repeat?: false\n): Subscription;\n\nexport function executeSchedule(\n  parentSubscription: Subscription,\n  scheduler: SchedulerLike,\n  work: () => void,\n  delay = 0,\n  repeat = false\n): Subscription | void {\n  const scheduleSubscription = scheduler.schedule(function (this: SchedulerAction<any>) {\n    work();\n    if (repeat) {\n      parentSubscription.add(this.schedule(null, delay));\n    } else {\n      this.unsubscribe();\n    }\n  }, delay);\n\n  parentSubscription.add(scheduleSubscription);\n\n  if (!repeat) {\n    // Because user-land scheduler implementations are unlikely to properly reuse\n    // Actions for repeat scheduling, we can't trust that the returned subscription\n    // will control repeat subscription scenarios. So we're trying to avoid using them\n    // incorrectly within this library.\n    return scheduleSubscription;\n  }\n}\n", "/** @prettier */\nimport { MonoTypeOperatorFunction, SchedulerLike } from '../types';\nimport { executeSchedule } from '../util/executeSchedule';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Re-emits all notifications from source Observable with specified scheduler.\n *\n * <span class=\"informal\">Ensure a specific scheduler is used, from outside of an Observable.</span>\n *\n * `observeOn` is an operator that accepts a scheduler as a first parameter, which will be used to reschedule\n * notifications emitted by the source Observable. It might be useful, if you do not have control over\n * internal scheduler of a given Observable, but want to control when its values are emitted nevertheless.\n *\n * Returned Observable emits the same notifications (nexted values, complete and error events) as the source Observable,\n * but rescheduled with provided scheduler. Note that this doesn't mean that source Observables internal\n * scheduler will be replaced in any way. Original scheduler still will be used, but when the source Observable emits\n * notification, it will be immediately scheduled again - this time with scheduler passed to `observeOn`.\n * An anti-pattern would be calling `observeOn` on Observable that emits lots of values synchronously, to split\n * that emissions into asynchronous chunks. For this to happen, scheduler would have to be passed into the source\n * Observable directly (usually into the operator that creates it). `observeOn` simply delays notifications a\n * little bit more, to ensure that they are emitted at expected moments.\n *\n * As a matter of fact, `observeOn` accepts second parameter, which specifies in milliseconds with what delay notifications\n * will be emitted. The main difference between {@link delay} operator and `observeOn` is that `observeOn`\n * will delay all notifications - including error notifications - while `delay` will pass through error\n * from source Observable immediately when it is emitted. In general it is highly recommended to use `delay` operator\n * for any kind of delaying of values in the stream, while using `observeOn` to specify which scheduler should be used\n * for notification emissions in general.\n *\n * ## Example\n *\n * Ensure values in subscribe are called just before browser repaint\n *\n * ```ts\n * import { interval, observeOn, animationFrameScheduler } from 'rxjs';\n *\n * const someDiv = document.createElement('div');\n * someDiv.style.cssText = 'width: 200px;background: #09c';\n * document.body.appendChild(someDiv);\n * const intervals = interval(10);      // Intervals are scheduled\n *                                      // with async scheduler by default...\n * intervals.pipe(\n *   observeOn(animationFrameScheduler) // ...but we will observe on animationFrame\n * )                                    // scheduler to ensure smooth animation.\n * .subscribe(val => {\n *   someDiv.style.height = val + 'px';\n * });\n * ```\n *\n * @see {@link delay}\n *\n * @param scheduler Scheduler that will be used to reschedule notifications from source Observable.\n * @param delay Number of milliseconds that states with what delay every notification should be rescheduled.\n * @return A function that returns an Observable that emits the same\n * notifications as the source Observable, but with provided scheduler.\n */\nexport function observeOn<T>(scheduler: SchedulerLike, delay = 0): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => executeSchedule(subscriber, scheduler, () => subscriber.next(value), delay),\n        () => executeSchedule(subscriber, scheduler, () => subscriber.complete(), delay),\n        (err) => executeSchedule(subscriber, scheduler, () => subscriber.error(err), delay)\n      )\n    );\n  });\n}\n", "import { MonoTypeOperatorFunction, SchedulerLike } from '../types';\nimport { operate } from '../util/lift';\n\n/**\n * Asynchronously subscribes Observers to this Observable on the specified {@link SchedulerLike}.\n *\n * With `subscribeOn` you can decide what type of scheduler a specific Observable will be using when it is subscribed to.\n *\n * Schedulers control the speed and order of emissions to observers from an Observable stream.\n *\n * ![](subscribeOn.png)\n *\n * ## Example\n *\n * Given the following code:\n *\n * ```ts\n * import { of, merge } from 'rxjs';\n *\n * const a = of(1, 2, 3);\n * const b = of(4, 5, 6);\n *\n * merge(a, b).subscribe(console.log);\n *\n * // Outputs\n * // 1\n * // 2\n * // 3\n * // 4\n * // 5\n * // 6\n * ```\n *\n * Both Observable `a` and `b` will emit their values directly and synchronously once they are subscribed to.\n *\n * If we instead use the `subscribeOn` operator declaring that we want to use the {@link asyncScheduler} for values emitted by Observable `a`:\n *\n * ```ts\n * import { of, subscribeOn, asyncScheduler, merge } from 'rxjs';\n *\n * const a = of(1, 2, 3).pipe(subscribeOn(asyncScheduler));\n * const b = of(4, 5, 6);\n *\n * merge(a, b).subscribe(console.log);\n *\n * // Outputs\n * // 4\n * // 5\n * // 6\n * // 1\n * // 2\n * // 3\n * ```\n *\n * The reason for this is that Observable `b` emits its values directly and synchronously like before\n * but the emissions from `a` are scheduled on the event loop because we are now using the {@link asyncScheduler} for that specific Observable.\n *\n * @param scheduler The {@link SchedulerLike} to perform subscription actions on.\n * @param delay A delay to pass to the scheduler to delay subscriptions\n * @return A function that returns an Observable modified so that its\n * subscriptions happen on the specified {@link SchedulerLike}.\n */\nexport function subscribeOn<T>(scheduler: SchedulerLike, delay: number = 0): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    subscriber.add(scheduler.schedule(() => source.subscribe(subscriber), delay));\n  });\n}\n", "import { innerFrom } from '../observable/innerFrom';\nimport { observeOn } from '../operators/observeOn';\nimport { subscribeOn } from '../operators/subscribeOn';\nimport { InteropObservable, SchedulerLike } from '../types';\n\nexport function scheduleObservable<T>(input: InteropObservable<T>, scheduler: SchedulerLike) {\n  return innerFrom(input).pipe(subscribeOn(scheduler), observeOn(scheduler));\n}\n", "import { innerFrom } from '../observable/innerFrom';\nimport { observeOn } from '../operators/observeOn';\nimport { subscribeOn } from '../operators/subscribeOn';\nimport { SchedulerLike } from '../types';\n\nexport function schedulePromise<T>(input: PromiseLike<T>, scheduler: SchedulerLike) {\n  return innerFrom(input).pipe(subscribeOn(scheduler), observeOn(scheduler));\n}\n", "import { Observable } from '../Observable';\nimport { SchedulerLike } from '../types';\n\nexport function scheduleArray<T>(input: ArrayLike<T>, scheduler: SchedulerLike) {\n  return new Observable<T>((subscriber) => {\n    // The current array index.\n    let i = 0;\n    // Start iterating over the array like on a schedule.\n    return scheduler.schedule(function () {\n      if (i === input.length) {\n        // If we have hit the end of the array like in the\n        // previous job, we can complete.\n        subscriber.complete();\n      } else {\n        // Otherwise let's next the value at the current index,\n        // then increment our index.\n        subscriber.next(input[i++]);\n        // If the last emission didn't cause us to close the subscriber\n        // (via take or some side effect), reschedule the job and we'll\n        // make another pass.\n        if (!subscriber.closed) {\n          this.schedule();\n        }\n      }\n    });\n  });\n}\n", "import { Observable } from '../Observable';\nimport { SchedulerLike } from '../types';\nimport { iterator as Symbol_iterator } from '../symbol/iterator';\nimport { isFunction } from '../util/isFunction';\nimport { executeSchedule } from '../util/executeSchedule';\n\n/**\n * Used in {@link scheduled} to create an observable from an Iterable.\n * @param input The iterable to create an observable from\n * @param scheduler The scheduler to use\n */\nexport function scheduleIterable<T>(input: Iterable<T>, scheduler: SchedulerLike) {\n  return new Observable<T>((subscriber) => {\n    let iterator: Iterator<T, T>;\n\n    // Schedule the initial creation of the iterator from\n    // the iterable. This is so the code in the iterable is\n    // not called until the scheduled job fires.\n    executeSchedule(subscriber, scheduler, () => {\n      // Create the iterator.\n      iterator = (input as any)[Symbol_iterator]();\n\n      executeSchedule(\n        subscriber,\n        scheduler,\n        () => {\n          let value: T;\n          let done: boolean | undefined;\n          try {\n            // Pull the value out of the iterator\n            ({ value, done } = iterator.next());\n          } catch (err) {\n            // We got an error while pulling from the iterator\n            subscriber.error(err);\n            return;\n          }\n\n          if (done) {\n            // If it is \"done\" we just complete. This mimics the\n            // behavior of JavaScript's `for..of` consumption of\n            // iterables, which will not emit the value from an iterator\n            // result of `{ done: true: value: 'here' }`.\n            subscriber.complete();\n          } else {\n            // The iterable is not done, emit the value.\n            subscriber.next(value);\n          }\n        },\n        0,\n        true\n      );\n    });\n\n    // During finalization, if we see this iterator has a `return` method,\n    // then we know it is a Generator, and not just an Iterator. So we call\n    // the `return()` function. This will ensure that any `finally { }` blocks\n    // inside of the generator we can hit will be hit properly.\n    return () => isFunction(iterator?.return) && iterator.return();\n  });\n}\n", "import { SchedulerLike } from '../types';\nimport { Observable } from '../Observable';\nimport { executeSchedule } from '../util/executeSchedule';\n\nexport function scheduleAsyncIterable<T>(input: AsyncIterable<T>, scheduler: SchedulerLike) {\n  if (!input) {\n    throw new Error('Iterable cannot be null');\n  }\n  return new Observable<T>((subscriber) => {\n    executeSchedule(subscriber, scheduler, () => {\n      const iterator = input[Symbol.asyncIterator]();\n      executeSchedule(\n        subscriber,\n        scheduler,\n        () => {\n          iterator.next().then((result) => {\n            if (result.done) {\n              // This will remove the subscriptions from\n              // the parent subscription.\n              subscriber.complete();\n            } else {\n              subscriber.next(result.value);\n            }\n          });\n        },\n        0,\n        true\n      );\n    });\n  });\n}\n", "import { SchedulerLike, ReadableStreamLike } from '../types';\nimport { Observable } from '../Observable';\nimport { scheduleAsyncIterable } from './scheduleAsyncIterable';\nimport { readableStreamLikeToAsyncGenerator } from '../util/isReadableStreamLike';\n\nexport function scheduleReadableStreamLike<T>(input: ReadableStreamLike<T>, scheduler: SchedulerLike): Observable<T> {\n  return scheduleAsyncIterable(readableStreamLikeToAsyncGenerator(input), scheduler);\n}\n", "import { scheduleObservable } from './scheduleObservable';\nimport { schedulePromise } from './schedulePromise';\nimport { scheduleArray } from './scheduleArray';\nimport { scheduleIterable } from './scheduleIterable';\nimport { scheduleAsyncIterable } from './scheduleAsyncIterable';\nimport { isInteropObservable } from '../util/isInteropObservable';\nimport { isPromise } from '../util/isPromise';\nimport { isArrayLike } from '../util/isArrayLike';\nimport { isIterable } from '../util/isIterable';\nimport { ObservableInput, SchedulerLike } from '../types';\nimport { Observable } from '../Observable';\nimport { isAsyncIterable } from '../util/isAsyncIterable';\nimport { createInvalidObservableTypeError } from '../util/throwUnobservableError';\nimport { isReadableStreamLike } from '../util/isReadableStreamLike';\nimport { scheduleReadableStreamLike } from './scheduleReadableStreamLike';\n\n/**\n * Converts from a common {@link ObservableInput} type to an observable where subscription and emissions\n * are scheduled on the provided scheduler.\n *\n * @see {@link from}\n * @see {@link of}\n *\n * @param input The observable, array, promise, iterable, etc you would like to schedule\n * @param scheduler The scheduler to use to schedule the subscription and emissions from\n * the returned observable.\n */\nexport function scheduled<T>(input: ObservableInput<T>, scheduler: SchedulerLike): Observable<T> {\n  if (input != null) {\n    if (isInteropObservable(input)) {\n      return scheduleObservable(input, scheduler);\n    }\n    if (isArrayLike(input)) {\n      return scheduleArray(input, scheduler);\n    }\n    if (isPromise(input)) {\n      return schedulePromise(input, scheduler);\n    }\n    if (isAsyncIterable(input)) {\n      return scheduleAsyncIterable(input, scheduler);\n    }\n    if (isIterable(input)) {\n      return scheduleIterable(input, scheduler);\n    }\n    if (isReadableStreamLike(input)) {\n      return scheduleReadableStreamLike(input, scheduler);\n    }\n  }\n  throw createInvalidObservableTypeError(input);\n}\n", "import { Observable } from '../Observable';\nimport { ObservableInput, SchedulerLike, ObservedValueOf } from '../types';\nimport { scheduled } from '../scheduled/scheduled';\nimport { innerFrom } from './innerFrom';\n\nexport function from<O extends ObservableInput<any>>(input: O): Observable<ObservedValueOf<O>>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function from<O extends ObservableInput<any>>(input: O, scheduler: SchedulerLike | undefined): Observable<ObservedValueOf<O>>;\n\n/**\n * Creates an Observable from an Array, an array-like object, a Promise, an iterable object, or an Observable-like object.\n *\n * <span class=\"informal\">Converts almost anything to an Observable.</span>\n *\n * ![](from.png)\n *\n * `from` converts various other objects and data types into Observables. It also converts a Promise, an array-like, or an\n * <a href=\"https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Iteration_protocols#iterable\" target=\"_blank\">iterable</a>\n * object into an Observable that emits the items in that promise, array, or iterable. A String, in this context, is treated\n * as an array of characters. Observable-like objects (contains a function named with the ES2015 Symbol for Observable) can also be\n * converted through this operator.\n *\n * ## Examples\n *\n * Converts an array to an Observable\n *\n * ```ts\n * import { from } from 'rxjs';\n *\n * const array = [10, 20, 30];\n * const result = from(array);\n *\n * result.subscribe(x => console.log(x));\n *\n * // Logs:\n * // 10\n * // 20\n * // 30\n * ```\n *\n * Convert an infinite iterable (from a generator) to an Observable\n *\n * ```ts\n * import { from, take } from 'rxjs';\n *\n * function* generateDoubles(seed) {\n *    let i = seed;\n *    while (true) {\n *      yield i;\n *      i = 2 * i; // double it\n *    }\n * }\n *\n * const iterator = generateDoubles(3);\n * const result = from(iterator).pipe(take(10));\n *\n * result.subscribe(x => console.log(x));\n *\n * // Logs:\n * // 3\n * // 6\n * // 12\n * // 24\n * // 48\n * // 96\n * // 192\n * // 384\n * // 768\n * // 1536\n * ```\n *\n * With `asyncScheduler`\n *\n * ```ts\n * import { from, asyncScheduler } from 'rxjs';\n *\n * console.log('start');\n *\n * const array = [10, 20, 30];\n * const result = from(array, asyncScheduler);\n *\n * result.subscribe(x => console.log(x));\n *\n * console.log('end');\n *\n * // Logs:\n * // 'start'\n * // 'end'\n * // 10\n * // 20\n * // 30\n * ```\n *\n * @see {@link fromEvent}\n * @see {@link fromEventPattern}\n *\n * @param input A subscription object, a Promise, an Observable-like,\n * an Array, an iterable, or an array-like object to be converted.\n * @param scheduler An optional {@link SchedulerLike} on which to schedule the emission of values.\n * @return An Observable converted from {@link ObservableInput}.\n */\nexport function from<T>(input: ObservableInput<T>, scheduler?: SchedulerLike): Observable<T> {\n  return scheduler ? scheduled(input, scheduler) : innerFrom(input);\n}\n", "import { SchedulerLike, ValueFromArray } from '../types';\nimport { Observable } from '../Observable';\nimport { popScheduler } from '../util/args';\nimport { from } from './from';\n\n// Devs are more likely to pass null or undefined than they are a scheduler\n// without accompanying values. To make things easier for (naughty) devs who\n// use the `strictNullChecks: false` TypeScript compiler option, these\n// overloads with explicit null and undefined values are included.\n\nexport function of(value: null): Observable<null>;\nexport function of(value: undefined): Observable<undefined>;\n\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function of(scheduler: SchedulerLike): Observable<never>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function of<A extends readonly unknown[]>(...valuesAndScheduler: [...A, SchedulerLike]): Observable<ValueFromArray<A>>;\n\nexport function of(): Observable<never>;\n/** @deprecated Do not specify explicit type parameters. Signatures with type parameters that cannot be inferred will be removed in v8. */\nexport function of<T>(): Observable<T>;\nexport function of<T>(value: T): Observable<T>;\nexport function of<A extends readonly unknown[]>(...values: A): Observable<ValueFromArray<A>>;\n\n/**\n * Converts the arguments to an observable sequence.\n *\n * <span class=\"informal\">Each argument becomes a `next` notification.</span>\n *\n * ![](of.png)\n *\n * Unlike {@link from}, it does not do any flattening and emits each argument in whole\n * as a separate `next` notification.\n *\n * ## Examples\n *\n * Emit the values `10, 20, 30`\n *\n * ```ts\n * import { of } from 'rxjs';\n *\n * of(10, 20, 30)\n *   .subscribe({\n *     next: value => console.log('next:', value),\n *     error: err => console.log('error:', err),\n *     complete: () => console.log('the end'),\n *   });\n *\n * // Outputs\n * // next: 10\n * // next: 20\n * // next: 30\n * // the end\n * ```\n *\n * Emit the array `[1, 2, 3]`\n *\n * ```ts\n * import { of } from 'rxjs';\n *\n * of([1, 2, 3])\n *   .subscribe({\n *     next: value => console.log('next:', value),\n *     error: err => console.log('error:', err),\n *     complete: () => console.log('the end'),\n *   });\n *\n * // Outputs\n * // next: [1, 2, 3]\n * // the end\n * ```\n *\n * @see {@link from}\n * @see {@link range}\n *\n * @param args A comma separated list of arguments you want to be emitted.\n * @return An Observable that synchronously emits the arguments described\n * above and then immediately completes.\n */\nexport function of<T>(...args: Array<T | SchedulerLike>): Observable<T> {\n  const scheduler = popScheduler(args);\n  return from(args as T[], scheduler);\n}\n", "import { Observable } from '../Observable';\nimport { Subscriber } from '../Subscriber';\nimport { SchedulerLike } from '../types';\nimport { isFunction } from '../util/isFunction';\n\n/**\n * Creates an observable that will create an error instance and push it to the consumer as an error\n * immediately upon subscription.\n *\n * <span class=\"informal\">Just errors and does nothing else</span>\n *\n * ![](throw.png)\n *\n * This creation function is useful for creating an observable that will create an error and error every\n * time it is subscribed to. Generally, inside of most operators when you might want to return an errored\n * observable, this is unnecessary. In most cases, such as in the inner return of {@link concatMap},\n * {@link mergeMap}, {@link defer}, and many others, you can simply throw the error, and RxJS will pick\n * that up and notify the consumer of the error.\n *\n * ## Example\n *\n * Create a simple observable that will create a new error with a timestamp and log it\n * and the message every time you subscribe to it\n *\n * ```ts\n * import { throwError } from 'rxjs';\n *\n * let errorCount = 0;\n *\n * const errorWithTimestamp$ = throwError(() => {\n *   const error: any = new Error(`This is error number ${ ++errorCount }`);\n *   error.timestamp = Date.now();\n *   return error;\n * });\n *\n * errorWithTimestamp$.subscribe({\n *   error: err => console.log(err.timestamp, err.message)\n * });\n *\n * errorWithTimestamp$.subscribe({\n *   error: err => console.log(err.timestamp, err.message)\n * });\n *\n * // Logs the timestamp and a new error message for each subscription\n * ```\n *\n * ### Unnecessary usage\n *\n * Using `throwError` inside of an operator or creation function\n * with a callback, is usually not necessary\n *\n * ```ts\n * import { of, concatMap, timer, throwError } from 'rxjs';\n *\n * const delays$ = of(1000, 2000, Infinity, 3000);\n *\n * delays$.pipe(\n *   concatMap(ms => {\n *     if (ms < 10000) {\n *       return timer(ms);\n *     } else {\n *       // This is probably overkill.\n *       return throwError(() => new Error(`Invalid time ${ ms }`));\n *     }\n *   })\n * )\n * .subscribe({\n *   next: console.log,\n *   error: console.error\n * });\n * ```\n *\n * You can just throw the error instead\n *\n * ```ts\n * import { of, concatMap, timer } from 'rxjs';\n *\n * const delays$ = of(1000, 2000, Infinity, 3000);\n *\n * delays$.pipe(\n *   concatMap(ms => {\n *     if (ms < 10000) {\n *       return timer(ms);\n *     } else {\n *       // Cleaner and easier to read for most folks.\n *       throw new Error(`Invalid time ${ ms }`);\n *     }\n *   })\n * )\n * .subscribe({\n *   next: console.log,\n *   error: console.error\n * });\n * ```\n *\n * @param errorFactory A factory function that will create the error instance that is pushed.\n */\nexport function throwError(errorFactory: () => any): Observable<never>;\n\n/**\n * Returns an observable that will error with the specified error immediately upon subscription.\n *\n * @param error The error instance to emit\n * @deprecated Support for passing an error value will be removed in v8. Instead, pass a factory function to `throwError(() => new Error('test'))`. This is\n * because it will create the error at the moment it should be created and capture a more appropriate stack trace. If\n * for some reason you need to create the error ahead of time, you can still do that: `const err = new Error('test'); throwError(() => err);`.\n */\nexport function throwError(error: any): Observable<never>;\n\n/**\n * Notifies the consumer of an error using a given scheduler by scheduling it at delay `0` upon subscription.\n *\n * @param errorOrErrorFactory An error instance or error factory\n * @param scheduler A scheduler to use to schedule the error notification\n * @deprecated The `scheduler` parameter will be removed in v8.\n * Use `throwError` in combination with {@link observeOn}: `throwError(() => new Error('test')).pipe(observeOn(scheduler));`.\n * Details: https://rxjs.dev/deprecations/scheduler-argument\n */\nexport function throwError(errorOrErrorFactory: any, scheduler: SchedulerLike): Observable<never>;\n\nexport function throwError(errorOrErrorFactory: any, scheduler?: SchedulerLike): Observable<never> {\n  const errorFactory = isFunction(errorOrErrorFactory) ? errorOrErrorFactory : () => errorOrErrorFactory;\n  const init = (subscriber: Subscriber<never>) => subscriber.error(errorFactory());\n  return new Observable(scheduler ? (subscriber) => scheduler.schedule(init as any, 0, subscriber) : init);\n}\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface EmptyError extends Error {}\n\nexport interface EmptyErrorCtor {\n  /**\n   * @deprecated Internal implementation detail. Do not construct error instances.\n   * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n   */\n  new (): EmptyError;\n}\n\n/**\n * An error thrown when an Observable or a sequence was queried but has no\n * elements.\n *\n * @see {@link first}\n * @see {@link last}\n * @see {@link single}\n * @see {@link firstValueFrom}\n * @see {@link lastValueFrom}\n */\nexport const EmptyError: EmptyErrorCtor = createErrorClass(\n  (_super) =>\n    function EmptyErrorImpl(this: any) {\n      _super(this);\n      this.name = 'EmptyError';\n      this.message = 'no elements in sequence';\n    }\n);\n", "/**\n * Checks to see if a value is not only a `Date` object,\n * but a *valid* `Date` object that can be converted to a\n * number. For example, `new Date('blah')` is indeed an\n * `instanceof Date`, however it cannot be converted to a\n * number.\n */\nexport function isValidDate(value: any): value is Date {\n  return value instanceof Date && !isNaN(value as any);\n}\n", "import { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\nexport function map<T, R>(project: (value: T, index: number) => R): OperatorFunction<T, R>;\n/** @deprecated Use a closure instead of a `thisArg`. Signatures accepting a `thisArg` will be removed in v8. */\nexport function map<T, R, A>(project: (this: A, value: T, index: number) => R, thisArg: A): OperatorFunction<T, R>;\n\n/**\n * Applies a given `project` function to each value emitted by the source\n * Observable, and emits the resulting values as an Observable.\n *\n * <span class=\"informal\">Like [Array.prototype.map()](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Array/map),\n * it passes each source value through a transformation function to get\n * corresponding output values.</span>\n *\n * ![](map.png)\n *\n * Similar to the well known `Array.prototype.map` function, this operator\n * applies a projection to each value and emits that projection in the output\n * Observable.\n *\n * ## Example\n *\n * Map every click to the `clientX` position of that click\n *\n * ```ts\n * import { fromEvent, map } from 'rxjs';\n *\n * const clicks = fromEvent<PointerEvent>(document, 'click');\n * const positions = clicks.pipe(map(ev => ev.clientX));\n *\n * positions.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link mapTo}\n * @see {@link pluck}\n *\n * @param project The function to apply to each `value` emitted by the source\n * Observable. The `index` parameter is the number `i` for the i-th emission\n * that has happened since the subscription, starting from the number `0`.\n * @param thisArg An optional argument to define what `this` is in the\n * `project` function.\n * @return A function that returns an Observable that emits the values from the\n * source Observable transformed by the given `project` function.\n */\nexport function map<T, R>(project: (value: T, index: number) => R, thisArg?: any): OperatorFunction<T, R> {\n  return operate((source, subscriber) => {\n    // The index of the value from the source. Used with projection.\n    let index = 0;\n    // Subscribe to the source, all errors and completions are sent along\n    // to the consumer.\n    source.subscribe(\n      createOperatorSubscriber(subscriber, (value: T) => {\n        // Call the projection function with the appropriate this context,\n        // and send the resulting value to the consumer.\n        subscriber.next(project.call(thisArg, value, index++));\n      })\n    );\n  });\n}\n", "import { OperatorFunction } from \"../types\";\nimport { map } from \"../operators/map\";\n\nconst { isArray } = Array;\n\nfunction callOrApply<T, R>(fn: ((...values: T[]) => R), args: T|T[]): R {\n    return isArray(args) ? fn(...args) : fn(args);\n}\n\n/**\n * Used in several -- mostly deprecated -- situations where we need to \n * apply a list of arguments or a single argument to a result selector.\n */\nexport function mapOneOrManyArgs<T, R>(fn: ((...values: T[]) => R)): OperatorFunction<T|T[], R> {\n    return map(args => callOrApply(fn, args))\n}", "const { isArray } = Array;\nconst { getPrototypeOf, prototype: objectProto, keys: getKeys } = Object;\n\n/**\n * Used in functions where either a list of arguments, a single array of arguments, or a\n * dictionary of arguments can be returned. Returns an object with an `args` property with\n * the arguments in an array, if it is a dictionary, it will also return the `keys` in another\n * property.\n */\nexport function argsArgArrayOrObject<T, O extends Record<string, T>>(args: T[] | [O] | [T[]]): { args: T[]; keys: string[] | null } {\n  if (args.length === 1) {\n    const first = args[0];\n    if (isArray(first)) {\n      return { args: first, keys: null };\n    }\n    if (isPOJO(first)) {\n      const keys = getKeys(first);\n      return {\n        args: keys.map((key) => first[key]),\n        keys,\n      };\n    }\n  }\n\n  return { args: args as T[], keys: null };\n}\n\nfunction isPOJO(obj: any): obj is object {\n  return obj && typeof obj === 'object' && getPrototypeOf(obj) === objectProto;\n}\n", "export function createObject(keys: string[], values: any[]) {\n  return keys.reduce((result, key, i) => ((result[key] = values[i]), result), {} as any);\n}\n", "import { Observable } from '../Observable';\nimport { ObservableInput, SchedulerLike, ObservedValueOf, ObservableInputTuple } from '../types';\nimport { argsArgArrayOrObject } from '../util/argsArgArrayOrObject';\nimport { Subscriber } from '../Subscriber';\nimport { from } from './from';\nimport { identity } from '../util/identity';\nimport { Subscription } from '../Subscription';\nimport { mapOneOrManyArgs } from '../util/mapOneOrManyArgs';\nimport { popResultSelector, popScheduler } from '../util/args';\nimport { createObject } from '../util/createObject';\nimport { createOperatorSubscriber } from '../operators/OperatorSubscriber';\nimport { AnyCatcher } from '../AnyCatcher';\nimport { executeSchedule } from '../util/executeSchedule';\n\n// combineLatest(any)\n// We put this first because we need to catch cases where the user has supplied\n// _exactly `any`_ as the argument. Since `any` literally matches _anything_,\n// we don't want it to randomly hit one of the other type signatures below,\n// as we have no idea at build-time what type we should be returning when given an any.\n\n/**\n * You have passed `any` here, we can't figure out if it is\n * an array or an object, so you're getting `unknown`. Use better types.\n * @param arg Something typed as `any`\n */\nexport function combineLatest<T extends AnyCatcher>(arg: T): Observable<unknown>;\n\n// combineLatest([a, b, c])\nexport function combineLatest(sources: []): Observable<never>;\nexport function combineLatest<A extends readonly unknown[]>(sources: readonly [...ObservableInputTuple<A>]): Observable<A>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `combineLatestAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function combineLatest<A extends readonly unknown[], R>(\n  sources: readonly [...ObservableInputTuple<A>],\n  resultSelector: (...values: A) => R,\n  scheduler: SchedulerLike\n): Observable<R>;\nexport function combineLatest<A extends readonly unknown[], R>(\n  sources: readonly [...ObservableInputTuple<A>],\n  resultSelector: (...values: A) => R\n): Observable<R>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `combineLatestAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function combineLatest<A extends readonly unknown[]>(\n  sources: readonly [...ObservableInputTuple<A>],\n  scheduler: SchedulerLike\n): Observable<A>;\n\n// combineLatest(a, b, c)\n/** @deprecated Pass an array of sources instead. The rest-parameters signature will be removed in v8. Details: https://rxjs.dev/deprecations/array-argument */\nexport function combineLatest<A extends readonly unknown[]>(...sources: [...ObservableInputTuple<A>]): Observable<A>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `combineLatestAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function combineLatest<A extends readonly unknown[], R>(\n  ...sourcesAndResultSelectorAndScheduler: [...ObservableInputTuple<A>, (...values: A) => R, SchedulerLike]\n): Observable<R>;\n/** @deprecated Pass an array of sources instead. The rest-parameters signature will be removed in v8. Details: https://rxjs.dev/deprecations/array-argument */\nexport function combineLatest<A extends readonly unknown[], R>(\n  ...sourcesAndResultSelector: [...ObservableInputTuple<A>, (...values: A) => R]\n): Observable<R>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `combineLatestAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function combineLatest<A extends readonly unknown[]>(\n  ...sourcesAndScheduler: [...ObservableInputTuple<A>, SchedulerLike]\n): Observable<A>;\n\n// combineLatest({a, b, c})\nexport function combineLatest(sourcesObject: { [K in any]: never }): Observable<never>;\nexport function combineLatest<T extends Record<string, ObservableInput<any>>>(\n  sourcesObject: T\n): Observable<{ [K in keyof T]: ObservedValueOf<T[K]> }>;\n\n/**\n * Combines multiple Observables to create an Observable whose values are\n * calculated from the latest values of each of its input Observables.\n *\n * <span class=\"informal\">Whenever any input Observable emits a value, it\n * computes a formula using the latest values from all the inputs, then emits\n * the output of that formula.</span>\n *\n * ![](combineLatest.png)\n *\n * `combineLatest` combines the values from all the Observables passed in the\n * observables array. This is done by subscribing to each Observable in order and,\n * whenever any Observable emits, collecting an array of the most recent\n * values from each Observable. So if you pass `n` Observables to this operator,\n * the returned Observable will always emit an array of `n` values, in an order\n * corresponding to the order of the passed Observables (the value from the first Observable\n * will be at index 0 of the array and so on).\n *\n * Static version of `combineLatest` accepts an array of Observables. Note that an array of\n * Observables is a good choice, if you don't know beforehand how many Observables\n * you will combine. Passing an empty array will result in an Observable that\n * completes immediately.\n *\n * To ensure the output array always has the same length, `combineLatest` will\n * actually wait for all input Observables to emit at least once,\n * before it starts emitting results. This means if some Observable emits\n * values before other Observables started emitting, all these values but the last\n * will be lost. On the other hand, if some Observable does not emit a value but\n * completes, resulting Observable will complete at the same moment without\n * emitting anything, since it will now be impossible to include a value from the\n * completed Observable in the resulting array. Also, if some input Observable does\n * not emit any value and never completes, `combineLatest` will also never emit\n * and never complete, since, again, it will wait for all streams to emit some\n * value.\n *\n * If at least one Observable was passed to `combineLatest` and all passed Observables\n * emitted something, the resulting Observable will complete when all combined\n * streams complete. So even if some Observable completes, the result of\n * `combineLatest` will still emit values when other Observables do. In case\n * of a completed Observable, its value from now on will always be the last\n * emitted value. On the other hand, if any Observable errors, `combineLatest`\n * will error immediately as well, and all other Observables will be unsubscribed.\n *\n * ## Examples\n *\n * Combine two timer Observables\n *\n * ```ts\n * import { timer, combineLatest } from 'rxjs';\n *\n * const firstTimer = timer(0, 1000); // emit 0, 1, 2... after every second, starting from now\n * const secondTimer = timer(500, 1000); // emit 0, 1, 2... after every second, starting 0,5s from now\n * const combinedTimers = combineLatest([firstTimer, secondTimer]);\n * combinedTimers.subscribe(value => console.log(value));\n * // Logs\n * // [0, 0] after 0.5s\n * // [1, 0] after 1s\n * // [1, 1] after 1.5s\n * // [2, 1] after 2s\n * ```\n *\n * Combine a dictionary of Observables\n *\n * ```ts\n * import { of, delay, startWith, combineLatest } from 'rxjs';\n *\n * const observables = {\n *   a: of(1).pipe(delay(1000), startWith(0)),\n *   b: of(5).pipe(delay(5000), startWith(0)),\n *   c: of(10).pipe(delay(10000), startWith(0))\n * };\n * const combined = combineLatest(observables);\n * combined.subscribe(value => console.log(value));\n * // Logs\n * // { a: 0, b: 0, c: 0 } immediately\n * // { a: 1, b: 0, c: 0 } after 1s\n * // { a: 1, b: 5, c: 0 } after 5s\n * // { a: 1, b: 5, c: 10 } after 10s\n * ```\n *\n * Combine an array of Observables\n *\n * ```ts\n * import { of, delay, startWith, combineLatest } from 'rxjs';\n *\n * const observables = [1, 5, 10].map(\n *   n => of(n).pipe(\n *     delay(n * 1000), // emit 0 and then emit n after n seconds\n *     startWith(0)\n *   )\n * );\n * const combined = combineLatest(observables);\n * combined.subscribe(value => console.log(value));\n * // Logs\n * // [0, 0, 0] immediately\n * // [1, 0, 0] after 1s\n * // [1, 5, 0] after 5s\n * // [1, 5, 10] after 10s\n * ```\n *\n * Use map operator to dynamically calculate the Body-Mass Index\n *\n * ```ts\n * import { of, combineLatest, map } from 'rxjs';\n *\n * const weight = of(70, 72, 76, 79, 75);\n * const height = of(1.76, 1.77, 1.78);\n * const bmi = combineLatest([weight, height]).pipe(\n *   map(([w, h]) => w / (h * h)),\n * );\n * bmi.subscribe(x => console.log('BMI is ' + x));\n *\n * // With output to console:\n * // BMI is 24.212293388429753\n * // BMI is 23.93948099205209\n * // BMI is 23.671253629592222\n * ```\n *\n * @see {@link combineLatestAll}\n * @see {@link merge}\n * @see {@link withLatestFrom}\n *\n * @param args Any number of `ObservableInput`s provided either as an array or as an object\n * to combine with each other. If the last parameter is the function, it will be used to project the\n * values from the combined latest values into a new value on the output Observable.\n * @return An Observable of projected values from the most recent values from each `ObservableInput`,\n * or an array of the most recent values from each `ObservableInput`.\n */\nexport function combineLatest<O extends ObservableInput<any>, R>(...args: any[]): Observable<R> | Observable<ObservedValueOf<O>[]> {\n  const scheduler = popScheduler(args);\n  const resultSelector = popResultSelector(args);\n\n  const { args: observables, keys } = argsArgArrayOrObject(args);\n\n  if (observables.length === 0) {\n    // If no observables are passed, or someone has passed an empty array\n    // of observables, or even an empty object POJO, we need to just\n    // complete (EMPTY), but we have to honor the scheduler provided if any.\n    return from([], scheduler as any);\n  }\n\n  const result = new Observable<ObservedValueOf<O>[]>(\n    combineLatestInit(\n      observables as ObservableInput<ObservedValueOf<O>>[],\n      scheduler,\n      keys\n        ? // A handler for scrubbing the array of args into a dictionary.\n          (values) => createObject(keys, values)\n        : // A passthrough to just return the array\n          identity\n    )\n  );\n\n  return resultSelector ? (result.pipe(mapOneOrManyArgs(resultSelector)) as Observable<R>) : result;\n}\n\nexport function combineLatestInit(\n  observables: ObservableInput<any>[],\n  scheduler?: SchedulerLike,\n  valueTransform: (values: any[]) => any = identity\n) {\n  return (subscriber: Subscriber<any>) => {\n    // The outer subscription. We're capturing this in a function\n    // because we may have to schedule it.\n    maybeSchedule(\n      scheduler,\n      () => {\n        const { length } = observables;\n        // A store for the values each observable has emitted so far. We match observable to value on index.\n        const values = new Array(length);\n        // The number of currently active subscriptions, as they complete, we decrement this number to see if\n        // we are all done combining values, so we can complete the result.\n        let active = length;\n        // The number of inner sources that still haven't emitted the first value\n        // We need to track this because all sources need to emit one value in order\n        // to start emitting values.\n        let remainingFirstValues = length;\n        // The loop to kick off subscription. We're keying everything on index `i` to relate the observables passed\n        // in to the slot in the output array or the key in the array of keys in the output dictionary.\n        for (let i = 0; i < length; i++) {\n          maybeSchedule(\n            scheduler,\n            () => {\n              const source = from(observables[i], scheduler as any);\n              let hasFirstValue = false;\n              source.subscribe(\n                createOperatorSubscriber(\n                  subscriber,\n                  (value) => {\n                    // When we get a value, record it in our set of values.\n                    values[i] = value;\n                    if (!hasFirstValue) {\n                      // If this is our first value, record that.\n                      hasFirstValue = true;\n                      remainingFirstValues--;\n                    }\n                    if (!remainingFirstValues) {\n                      // We're not waiting for any more\n                      // first values, so we can emit!\n                      subscriber.next(valueTransform(values.slice()));\n                    }\n                  },\n                  () => {\n                    if (!--active) {\n                      // We only complete the result if we have no more active\n                      // inner observables.\n                      subscriber.complete();\n                    }\n                  }\n                )\n              );\n            },\n            subscriber\n          );\n        }\n      },\n      subscriber\n    );\n  };\n}\n\n/**\n * A small utility to handle the couple of locations where we want to schedule if a scheduler was provided,\n * but we don't if there was no scheduler.\n */\nfunction maybeSchedule(scheduler: SchedulerLike | undefined, execute: () => void, subscription: Subscription) {\n  if (scheduler) {\n    executeSchedule(subscription, scheduler, execute);\n  } else {\n    execute();\n  }\n}\n", "import { Observable } from '../Observable';\nimport { innerFrom } from '../observable/innerFrom';\nimport { Subscriber } from '../Subscriber';\nimport { ObservableInput, SchedulerLike } from '../types';\nimport { executeSchedule } from '../util/executeSchedule';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * A process embodying the general \"merge\" strategy. This is used in\n * `mergeMap` and `mergeScan` because the logic is otherwise nearly identical.\n * @param source The original source observable\n * @param subscriber The consumer subscriber\n * @param project The projection function to get our inner sources\n * @param concurrent The number of concurrent inner subscriptions\n * @param onBeforeNext Additional logic to apply before nexting to our consumer\n * @param expand If `true` this will perform an \"expand\" strategy, which differs only\n * in that it recurses, and the inner subscription must be schedule-able.\n * @param innerSubScheduler A scheduler to use to schedule inner subscriptions,\n * this is to support the expand strategy, mostly, and should be deprecated\n */\nexport function mergeInternals<T, R>(\n  source: Observable<T>,\n  subscriber: Subscriber<R>,\n  project: (value: T, index: number) => ObservableInput<R>,\n  concurrent: number,\n  onBeforeNext?: (innerValue: R) => void,\n  expand?: boolean,\n  innerSubScheduler?: SchedulerLike,\n  additionalFinalizer?: () => void\n) {\n  // Buffered values, in the event of going over our concurrency limit\n  const buffer: T[] = [];\n  // The number of active inner subscriptions.\n  let active = 0;\n  // An index to pass to our accumulator function\n  let index = 0;\n  // Whether or not the outer source has completed.\n  let isComplete = false;\n\n  /**\n   * Checks to see if we can complete our result or not.\n   */\n  const checkComplete = () => {\n    // If the outer has completed, and nothing is left in the buffer,\n    // and we don't have any active inner subscriptions, then we can\n    // Emit the state and complete.\n    if (isComplete && !buffer.length && !active) {\n      subscriber.complete();\n    }\n  };\n\n  // If we're under our concurrency limit, just start the inner subscription, otherwise buffer and wait.\n  const outerNext = (value: T) => (active < concurrent ? doInnerSub(value) : buffer.push(value));\n\n  const doInnerSub = (value: T) => {\n    // If we're expanding, we need to emit the outer values and the inner values\n    // as the inners will \"become outers\" in a way as they are recursively fed\n    // back to the projection mechanism.\n    expand && subscriber.next(value as any);\n\n    // Increment the number of active subscriptions so we can track it\n    // against our concurrency limit later.\n    active++;\n\n    // A flag used to show that the inner observable completed.\n    // This is checked during finalization to see if we should\n    // move to the next item in the buffer, if there is on.\n    let innerComplete = false;\n\n    // Start our inner subscription.\n    innerFrom(project(value, index++)).subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (innerValue) => {\n          // `mergeScan` has additional handling here. For example\n          // taking the inner value and updating state.\n          onBeforeNext?.(innerValue);\n\n          if (expand) {\n            // If we're expanding, then just recurse back to our outer\n            // handler. It will emit the value first thing.\n            outerNext(innerValue as any);\n          } else {\n            // Otherwise, emit the inner value.\n            subscriber.next(innerValue);\n          }\n        },\n        () => {\n          // Flag that we have completed, so we know to check the buffer\n          // during finalization.\n          innerComplete = true;\n        },\n        // Errors are passed to the destination.\n        undefined,\n        () => {\n          // During finalization, if the inner completed (it wasn't errored or\n          // cancelled), then we want to try the next item in the buffer if\n          // there is one.\n          if (innerComplete) {\n            // We have to wrap this in a try/catch because it happens during\n            // finalization, possibly asynchronously, and we want to pass\n            // any errors that happen (like in a projection function) to\n            // the outer Subscriber.\n            try {\n              // INNER SOURCE COMPLETE\n              // Decrement the active count to ensure that the next time\n              // we try to call `doInnerSub`, the number is accurate.\n              active--;\n              // If we have more values in the buffer, try to process those\n              // Note that this call will increment `active` ahead of the\n              // next conditional, if there were any more inner subscriptions\n              // to start.\n              while (buffer.length && active < concurrent) {\n                const bufferedValue = buffer.shift()!;\n                // Particularly for `expand`, we need to check to see if a scheduler was provided\n                // for when we want to start our inner subscription. Otherwise, we just start\n                // are next inner subscription.\n                if (innerSubScheduler) {\n                  executeSchedule(subscriber, innerSubScheduler, () => doInnerSub(bufferedValue));\n                } else {\n                  doInnerSub(bufferedValue);\n                }\n              }\n              // Check to see if we can complete, and complete if so.\n              checkComplete();\n            } catch (err) {\n              subscriber.error(err);\n            }\n          }\n        }\n      )\n    );\n  };\n\n  // Subscribe to our source observable.\n  source.subscribe(\n    createOperatorSubscriber(subscriber, outerNext, () => {\n      // Outer completed, make a note of it, and check to see if we can complete everything.\n      isComplete = true;\n      checkComplete();\n    })\n  );\n\n  // Additional finalization (for when the destination is torn down).\n  // Other finalization is added implicitly via subscription above.\n  return () => {\n    additionalFinalizer?.();\n  };\n}\n", "import { ObservableInput, OperatorFunction, ObservedValueOf } from '../types';\nimport { map } from './map';\nimport { innerFrom } from '../observable/innerFrom';\nimport { operate } from '../util/lift';\nimport { mergeInternals } from './mergeInternals';\nimport { isFunction } from '../util/isFunction';\n\n/* tslint:disable:max-line-length */\nexport function mergeMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  concurrent?: number\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function mergeMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector: undefined,\n  concurrent?: number\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function mergeMap<T, R, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector: (outerValue: T, innerValue: ObservedValueOf<O>, outerIndex: number, innerIndex: number) => R,\n  concurrent?: number\n): OperatorFunction<T, R>;\n/* tslint:enable:max-line-length */\n\n/**\n * Projects each source value to an Observable which is merged in the output\n * Observable.\n *\n * <span class=\"informal\">Maps each value to an Observable, then flattens all of\n * these inner Observables using {@link mergeAll}.</span>\n *\n * ![](mergeMap.png)\n *\n * Returns an Observable that emits items based on applying a function that you\n * supply to each item emitted by the source Observable, where that function\n * returns an Observable, and then merging those resulting Observables and\n * emitting the results of this merger.\n *\n * ## Example\n *\n * Map and flatten each letter to an Observable ticking every 1 second\n *\n * ```ts\n * import { of, mergeMap, interval, map } from 'rxjs';\n *\n * const letters = of('a', 'b', 'c');\n * const result = letters.pipe(\n *   mergeMap(x => interval(1000).pipe(map(i => x + i)))\n * );\n *\n * result.subscribe(x => console.log(x));\n *\n * // Results in the following:\n * // a0\n * // b0\n * // c0\n * // a1\n * // b1\n * // c1\n * // continues to list a, b, c every second with respective ascending integers\n * ```\n *\n * @see {@link concatMap}\n * @see {@link exhaustMap}\n * @see {@link merge}\n * @see {@link mergeAll}\n * @see {@link mergeMapTo}\n * @see {@link mergeScan}\n * @see {@link switchMap}\n *\n * @param project A function that, when applied to an item emitted by the source\n * Observable, returns an Observable.\n * @param concurrent Maximum number of `ObservableInput`s being subscribed to concurrently.\n * @return A function that returns an Observable that emits the result of\n * applying the projection function (and the optional deprecated\n * `resultSelector`) to each item emitted by the source Observable and merging\n * the results of the Observables obtained from this transformation.\n */\nexport function mergeMap<T, R, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector?: ((outerValue: T, innerValue: ObservedValueOf<O>, outerIndex: number, innerIndex: number) => R) | number,\n  concurrent: number = Infinity\n): OperatorFunction<T, ObservedValueOf<O> | R> {\n  if (isFunction(resultSelector)) {\n    // DEPRECATED PATH\n    return mergeMap((a, i) => map((b: any, ii: number) => resultSelector(a, b, i, ii))(innerFrom(project(a, i))), concurrent);\n  } else if (typeof resultSelector === 'number') {\n    concurrent = resultSelector;\n  }\n\n  return operate((source, subscriber) => mergeInternals(source, subscriber, project, concurrent));\n}\n", "import { mergeMap } from './mergeMap';\nimport { identity } from '../util/identity';\nimport { OperatorFunction, ObservableInput, ObservedValueOf } from '../types';\n\n/**\n * Converts a higher-order Observable into a first-order Observable which\n * concurrently delivers all values that are emitted on the inner Observables.\n *\n * <span class=\"informal\">Flattens an Observable-of-Observables.</span>\n *\n * ![](mergeAll.png)\n *\n * `mergeAll` subscribes to an Observable that emits Observables, also known as\n * a higher-order Observable. Each time it observes one of these emitted inner\n * Observables, it subscribes to that and delivers all the values from the\n * inner Observable on the output Observable. The output Observable only\n * completes once all inner Observables have completed. Any error delivered by\n * a inner Observable will be immediately emitted on the output Observable.\n *\n * ## Examples\n *\n * Spawn a new interval Observable for each click event, and blend their outputs as one Observable\n *\n * ```ts\n * import { fromEvent, map, interval, mergeAll } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const higherOrder = clicks.pipe(map(() => interval(1000)));\n * const firstOrder = higherOrder.pipe(mergeAll());\n *\n * firstOrder.subscribe(x => console.log(x));\n * ```\n *\n * Count from 0 to 9 every second for each click, but only allow 2 concurrent timers\n *\n * ```ts\n * import { fromEvent, map, interval, take, mergeAll } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const higherOrder = clicks.pipe(\n *   map(() => interval(1000).pipe(take(10)))\n * );\n * const firstOrder = higherOrder.pipe(mergeAll(2));\n *\n * firstOrder.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link combineLatestAll}\n * @see {@link concatAll}\n * @see {@link exhaustAll}\n * @see {@link merge}\n * @see {@link mergeMap}\n * @see {@link mergeMapTo}\n * @see {@link mergeScan}\n * @see {@link switchAll}\n * @see {@link switchMap}\n * @see {@link zipAll}\n *\n * @param concurrent Maximum number of inner Observables being subscribed to\n * concurrently.\n * @return A function that returns an Observable that emits values coming from\n * all the inner Observables emitted by the source Observable.\n */\nexport function mergeAll<O extends ObservableInput<any>>(concurrent: number = Infinity): OperatorFunction<O, ObservedValueOf<O>> {\n  return mergeMap(identity, concurrent);\n}\n", "import { mergeAll } from './mergeAll';\nimport { OperatorFunction, ObservableInput, ObservedValueOf } from '../types';\n\n/**\n * Converts a higher-order Observable into a first-order Observable by\n * concatenating the inner Observables in order.\n *\n * <span class=\"informal\">Flattens an Observable-of-Observables by putting one\n * inner Observable after the other.</span>\n *\n * ![](concatAll.svg)\n *\n * Joins every Observable emitted by the source (a higher-order Observable), in\n * a serial fashion. It subscribes to each inner Observable only after the\n * previous inner Observable has completed, and merges all of their values into\n * the returned observable.\n *\n * __Warning:__ If the source Observable emits Observables quickly and\n * endlessly, and the inner Observables it emits generally complete slower than\n * the source emits, you can run into memory issues as the incoming Observables\n * collect in an unbounded buffer.\n *\n * Note: `concatAll` is equivalent to `mergeAll` with concurrency parameter set\n * to `1`.\n *\n * ## Example\n *\n * For each click event, tick every second from 0 to 3, with no concurrency\n *\n * ```ts\n * import { fromEvent, map, interval, take, concatAll } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const higherOrder = clicks.pipe(\n *   map(() => interval(1000).pipe(take(4)))\n * );\n * const firstOrder = higherOrder.pipe(concatAll());\n * firstOrder.subscribe(x => console.log(x));\n *\n * // Results in the following:\n * // (results are not concurrent)\n * // For every click on the \"document\" it will emit values 0 to 3 spaced\n * // on a 1000ms interval\n * // one click = 1000ms-> 0 -1000ms-> 1 -1000ms-> 2 -1000ms-> 3\n * ```\n *\n * @see {@link combineLatestAll}\n * @see {@link concat}\n * @see {@link concatMap}\n * @see {@link concatMapTo}\n * @see {@link exhaustAll}\n * @see {@link mergeAll}\n * @see {@link switchAll}\n * @see {@link switchMap}\n * @see {@link zipAll}\n *\n * @return A function that returns an Observable emitting values from all the\n * inner Observables concatenated.\n */\nexport function concatAll<O extends ObservableInput<any>>(): OperatorFunction<O, ObservedValueOf<O>> {\n  return mergeAll(1);\n}\n", "import { Observable } from '../Observable';\nimport { ObservableInputTuple, SchedulerLike } from '../types';\nimport { concatAll } from '../operators/concatAll';\nimport { popScheduler } from '../util/args';\nimport { from } from './from';\n\nexport function concat<T extends readonly unknown[]>(...inputs: [...ObservableInputTuple<T>]): Observable<T[number]>;\nexport function concat<T extends readonly unknown[]>(\n  ...inputsAndScheduler: [...ObservableInputTuple<T>, SchedulerLike]\n): Observable<T[number]>;\n\n/**\n * Creates an output Observable which sequentially emits all values from the first given\n * Observable and then moves on to the next.\n *\n * <span class=\"informal\">Concatenates multiple Observables together by\n * sequentially emitting their values, one Observable after the other.</span>\n *\n * ![](concat.png)\n *\n * `concat` joins multiple Observables together, by subscribing to them one at a time and\n * merging their results into the output Observable. You can pass either an array of\n * Observables, or put them directly as arguments. Passing an empty array will result\n * in Observable that completes immediately.\n *\n * `concat` will subscribe to first input Observable and emit all its values, without\n * changing or affecting them in any way. When that Observable completes, it will\n * subscribe to then next Observable passed and, again, emit its values. This will be\n * repeated, until the operator runs out of Observables. When last input Observable completes,\n * `concat` will complete as well. At any given moment only one Observable passed to operator\n * emits values. If you would like to emit values from passed Observables concurrently, check out\n * {@link merge} instead, especially with optional `concurrent` parameter. As a matter of fact,\n * `concat` is an equivalent of `merge` operator with `concurrent` parameter set to `1`.\n *\n * Note that if some input Observable never completes, `concat` will also never complete\n * and Observables following the one that did not complete will never be subscribed. On the other\n * hand, if some Observable simply completes immediately after it is subscribed, it will be\n * invisible for `concat`, which will just move on to the next Observable.\n *\n * If any Observable in chain errors, instead of passing control to the next Observable,\n * `concat` will error immediately as well. Observables that would be subscribed after\n * the one that emitted error, never will.\n *\n * If you pass to `concat` the same Observable many times, its stream of values\n * will be \"replayed\" on every subscription, which means you can repeat given Observable\n * as many times as you like. If passing the same Observable to `concat` 1000 times becomes tedious,\n * you can always use {@link repeat}.\n *\n * ## Examples\n *\n * Concatenate a timer counting from 0 to 3 with a synchronous sequence from 1 to 10\n *\n * ```ts\n * import { interval, take, range, concat } from 'rxjs';\n *\n * const timer = interval(1000).pipe(take(4));\n * const sequence = range(1, 10);\n * const result = concat(timer, sequence);\n * result.subscribe(x => console.log(x));\n *\n * // results in:\n * // 0 -1000ms-> 1 -1000ms-> 2 -1000ms-> 3 -immediate-> 1 ... 10\n * ```\n *\n * Concatenate 3 Observables\n *\n * ```ts\n * import { interval, take, concat } from 'rxjs';\n *\n * const timer1 = interval(1000).pipe(take(10));\n * const timer2 = interval(2000).pipe(take(6));\n * const timer3 = interval(500).pipe(take(10));\n *\n * const result = concat(timer1, timer2, timer3);\n * result.subscribe(x => console.log(x));\n *\n * // results in the following:\n * // (Prints to console sequentially)\n * // -1000ms-> 0 -1000ms-> 1 -1000ms-> ... 9\n * // -2000ms-> 0 -2000ms-> 1 -2000ms-> ... 5\n * // -500ms-> 0 -500ms-> 1 -500ms-> ... 9\n * ```\n *\n * Concatenate the same Observable to repeat it\n *\n * ```ts\n * import { interval, take, concat } from 'rxjs';\n *\n * const timer = interval(1000).pipe(take(2));\n *\n * concat(timer, timer) // concatenating the same Observable!\n *   .subscribe({\n *     next: value => console.log(value),\n *     complete: () => console.log('...and it is done!')\n *   });\n *\n * // Logs:\n * // 0 after 1s\n * // 1 after 2s\n * // 0 after 3s\n * // 1 after 4s\n * // '...and it is done!' also after 4s\n * ```\n *\n * @see {@link concatAll}\n * @see {@link concatMap}\n * @see {@link concatMapTo}\n * @see {@link startWith}\n * @see {@link endWith}\n *\n * @param args `ObservableInput`s to concatenate.\n */\nexport function concat(...args: any[]): Observable<unknown> {\n  return concatAll()(from(args, popScheduler(args)));\n}\n", "import { Observable } from '../Observable';\nimport { ObservedValueOf, ObservableInput } from '../types';\nimport { innerFrom } from './innerFrom';\n\n/**\n * Creates an Observable that, on subscribe, calls an Observable factory to\n * make an Observable for each new Observer.\n *\n * <span class=\"informal\">Creates the Observable lazily, that is, only when it\n * is subscribed.\n * </span>\n *\n * ![](defer.png)\n *\n * `defer` allows you to create an Observable only when the Observer\n * subscribes. It waits until an Observer subscribes to it, calls the given\n * factory function to get an Observable -- where a factory function typically\n * generates a new Observable -- and subscribes the Observer to this Observable.\n * In case the factory function returns a falsy value, then EMPTY is used as\n * Observable instead. Last but not least, an exception during the factory\n * function call is transferred to the Observer by calling `error`.\n *\n * ## Example\n *\n * Subscribe to either an Observable of clicks or an Observable of interval, at random\n *\n * ```ts\n * import { defer, fromEvent, interval } from 'rxjs';\n *\n * const clicksOrInterval = defer(() => {\n *   return Math.random() > 0.5\n *     ? fromEvent(document, 'click')\n *     : interval(1000);\n * });\n * clicksOrInterval.subscribe(x => console.log(x));\n *\n * // Results in the following behavior:\n * // If the result of Math.random() is greater than 0.5 it will listen\n * // for clicks anywhere on the \"document\"; when document is clicked it\n * // will log a MouseEvent object to the console. If the result is less\n * // than 0.5 it will emit ascending numbers, one every second(1000ms).\n * ```\n *\n * @see {@link Observable}\n *\n * @param observableFactory The Observable factory function to invoke for each\n * Observer that subscribes to the output Observable. May also return any\n * `ObservableInput`, which will be converted on the fly to an Observable.\n * @return An Observable whose Observers' subscriptions trigger an invocation of the\n * given Observable factory function.\n */\nexport function defer<R extends ObservableInput<any>>(observableFactory: () => R): Observable<ObservedValueOf<R>> {\n  return new Observable<ObservedValueOf<R>>((subscriber) => {\n    innerFrom(observableFactory()).subscribe(subscriber);\n  });\n}\n", "import { innerFrom } from '../observable/innerFrom';\nimport { Observable } from '../Observable';\nimport { mergeMap } from '../operators/mergeMap';\nimport { isArrayLike } from '../util/isArrayLike';\nimport { isFunction } from '../util/isFunction';\nimport { mapOneOrManyArgs } from '../util/mapOneOrManyArgs';\n\n// These constants are used to create handler registry functions using array mapping below.\nconst nodeEventEmitterMethods = ['addListener', 'removeListener'] as const;\nconst eventTargetMethods = ['addEventListener', 'removeEventListener'] as const;\nconst jqueryMethods = ['on', 'off'] as const;\n\nexport interface NodeStyleEventEmitter {\n  addListener(eventName: string | symbol, handler: NodeEventHandler): this;\n  removeListener(eventName: string | symbol, handler: NodeEventHandler): this;\n}\n\nexport type NodeEventHandler = (...args: any[]) => void;\n\n// For APIs that implement `addListener` and `removeListener` methods that may\n// not use the same arguments or return EventEmitter values\n// such as React Native\nexport interface NodeCompatibleEventEmitter {\n  addListener(eventName: string, handler: NodeEventHandler): void | {};\n  removeListener(eventName: string, handler: NodeEventHandler): void | {};\n}\n\n// Use handler types like those in @types/jquery. See:\n// https://github.com/DefinitelyTyped/DefinitelyTyped/blob/847731ba1d7fa6db6b911c0e43aa0afe596e7723/types/jquery/misc.d.ts#L6395\nexport interface JQueryStyleEventEmitter<TContext, T> {\n  on(eventName: string, handler: (this: TContext, t: T, ...args: any[]) => any): void;\n  off(eventName: string, handler: (this: TContext, t: T, ...args: any[]) => any): void;\n}\n\nexport interface EventListenerObject<E> {\n  handleEvent(evt: E): void;\n}\n\nexport interface HasEventTargetAddRemove<E> {\n  addEventListener(\n    type: string,\n    listener: ((evt: E) => void) | EventListenerObject<E> | null,\n    options?: boolean | AddEventListenerOptions\n  ): void;\n  removeEventListener(\n    type: string,\n    listener: ((evt: E) => void) | EventListenerObject<E> | null,\n    options?: EventListenerOptions | boolean\n  ): void;\n}\n\nexport interface EventListenerOptions {\n  capture?: boolean;\n  passive?: boolean;\n  once?: boolean;\n}\n\nexport interface AddEventListenerOptions extends EventListenerOptions {\n  once?: boolean;\n  passive?: boolean;\n}\n\nexport function fromEvent<T>(target: HasEventTargetAddRemove<T> | ArrayLike<HasEventTargetAddRemove<T>>, eventName: string): Observable<T>;\nexport function fromEvent<T, R>(\n  target: HasEventTargetAddRemove<T> | ArrayLike<HasEventTargetAddRemove<T>>,\n  eventName: string,\n  resultSelector: (event: T) => R\n): Observable<R>;\nexport function fromEvent<T>(\n  target: HasEventTargetAddRemove<T> | ArrayLike<HasEventTargetAddRemove<T>>,\n  eventName: string,\n  options: EventListenerOptions\n): Observable<T>;\nexport function fromEvent<T, R>(\n  target: HasEventTargetAddRemove<T> | ArrayLike<HasEventTargetAddRemove<T>>,\n  eventName: string,\n  options: EventListenerOptions,\n  resultSelector: (event: T) => R\n): Observable<R>;\n\nexport function fromEvent(target: NodeStyleEventEmitter | ArrayLike<NodeStyleEventEmitter>, eventName: string): Observable<unknown>;\n/** @deprecated Do not specify explicit type parameters. Signatures with type parameters that cannot be inferred will be removed in v8. */\nexport function fromEvent<T>(target: NodeStyleEventEmitter | ArrayLike<NodeStyleEventEmitter>, eventName: string): Observable<T>;\nexport function fromEvent<R>(\n  target: NodeStyleEventEmitter | ArrayLike<NodeStyleEventEmitter>,\n  eventName: string,\n  resultSelector: (...args: any[]) => R\n): Observable<R>;\n\nexport function fromEvent(\n  target: NodeCompatibleEventEmitter | ArrayLike<NodeCompatibleEventEmitter>,\n  eventName: string\n): Observable<unknown>;\n/** @deprecated Do not specify explicit type parameters. Signatures with type parameters that cannot be inferred will be removed in v8. */\nexport function fromEvent<T>(target: NodeCompatibleEventEmitter | ArrayLike<NodeCompatibleEventEmitter>, eventName: string): Observable<T>;\nexport function fromEvent<R>(\n  target: NodeCompatibleEventEmitter | ArrayLike<NodeCompatibleEventEmitter>,\n  eventName: string,\n  resultSelector: (...args: any[]) => R\n): Observable<R>;\n\nexport function fromEvent<T>(\n  target: JQueryStyleEventEmitter<any, T> | ArrayLike<JQueryStyleEventEmitter<any, T>>,\n  eventName: string\n): Observable<T>;\nexport function fromEvent<T, R>(\n  target: JQueryStyleEventEmitter<any, T> | ArrayLike<JQueryStyleEventEmitter<any, T>>,\n  eventName: string,\n  resultSelector: (value: T, ...args: any[]) => R\n): Observable<R>;\n\n/**\n * Creates an Observable that emits events of a specific type coming from the\n * given event target.\n *\n * <span class=\"informal\">Creates an Observable from DOM events, or Node.js\n * EventEmitter events or others.</span>\n *\n * ![](fromEvent.png)\n *\n * `fromEvent` accepts as a first argument event target, which is an object with methods\n * for registering event handler functions. As a second argument it takes string that indicates\n * type of event we want to listen for. `fromEvent` supports selected types of event targets,\n * which are described in detail below. If your event target does not match any of the ones listed,\n * you should use {@link fromEventPattern}, which can be used on arbitrary APIs.\n * When it comes to APIs supported by `fromEvent`, their methods for adding and removing event\n * handler functions have different names, but they all accept a string describing event type\n * and function itself, which will be called whenever said event happens.\n *\n * Every time resulting Observable is subscribed, event handler function will be registered\n * to event target on given event type. When that event fires, value\n * passed as a first argument to registered function will be emitted by output Observable.\n * When Observable is unsubscribed, function will be unregistered from event target.\n *\n * Note that if event target calls registered function with more than one argument, second\n * and following arguments will not appear in resulting stream. In order to get access to them,\n * you can pass to `fromEvent` optional project function, which will be called with all arguments\n * passed to event handler. Output Observable will then emit value returned by project function,\n * instead of the usual value.\n *\n * Remember that event targets listed below are checked via duck typing. It means that\n * no matter what kind of object you have and no matter what environment you work in,\n * you can safely use `fromEvent` on that object if it exposes described methods (provided\n * of course they behave as was described above). So for example if Node.js library exposes\n * event target which has the same method names as DOM EventTarget, `fromEvent` is still\n * a good choice.\n *\n * If the API you use is more callback then event handler oriented (subscribed\n * callback function fires only once and thus there is no need to manually\n * unregister it), you should use {@link bindCallback} or {@link bindNodeCallback}\n * instead.\n *\n * `fromEvent` supports following types of event targets:\n *\n * **DOM EventTarget**\n *\n * This is an object with `addEventListener` and `removeEventListener` methods.\n *\n * In the browser, `addEventListener` accepts - apart from event type string and event\n * handler function arguments - optional third parameter, which is either an object or boolean,\n * both used for additional configuration how and when passed function will be called. When\n * `fromEvent` is used with event target of that type, you can provide this values\n * as third parameter as well.\n *\n * **Node.js EventEmitter**\n *\n * An object with `addListener` and `removeListener` methods.\n *\n * **JQuery-style event target**\n *\n * An object with `on` and `off` methods\n *\n * **DOM NodeList**\n *\n * List of DOM Nodes, returned for example by `document.querySelectorAll` or `Node.childNodes`.\n *\n * Although this collection is not event target in itself, `fromEvent` will iterate over all Nodes\n * it contains and install event handler function in every of them. When returned Observable\n * is unsubscribed, function will be removed from all Nodes.\n *\n * **DOM HtmlCollection**\n *\n * Just as in case of NodeList it is a collection of DOM nodes. Here as well event handler function is\n * installed and removed in each of elements.\n *\n *\n * ## Examples\n *\n * Emit clicks happening on the DOM document\n *\n * ```ts\n * import { fromEvent } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * clicks.subscribe(x => console.log(x));\n *\n * // Results in:\n * // MouseEvent object logged to console every time a click\n * // occurs on the document.\n * ```\n *\n * Use `addEventListener` with capture option\n *\n * ```ts\n * import { fromEvent } from 'rxjs';\n *\n * const div = document.createElement('div');\n * div.style.cssText = 'width: 200px; height: 200px; background: #09c;';\n * document.body.appendChild(div);\n *\n * // note optional configuration parameter which will be passed to addEventListener\n * const clicksInDocument = fromEvent(document, 'click', { capture: true });\n * const clicksInDiv = fromEvent(div, 'click');\n *\n * clicksInDocument.subscribe(() => console.log('document'));\n * clicksInDiv.subscribe(() => console.log('div'));\n *\n * // By default events bubble UP in DOM tree, so normally\n * // when we would click on div in document\n * // \"div\" would be logged first and then \"document\".\n * // Since we specified optional `capture` option, document\n * // will catch event when it goes DOWN DOM tree, so console\n * // will log \"document\" and then \"div\".\n * ```\n *\n * @see {@link bindCallback}\n * @see {@link bindNodeCallback}\n * @see {@link fromEventPattern}\n *\n * @param target The DOM EventTarget, Node.js EventEmitter, JQuery-like event target,\n * NodeList or HTMLCollection to attach the event handler to.\n * @param eventName The event name of interest, being emitted by the `target`.\n * @param options Options to pass through to the underlying `addListener`,\n * `addEventListener` or `on` functions.\n * @param resultSelector A mapping function used to transform events. It takes the\n * arguments from the event handler and should return a single value.\n * @return An Observable emitting events registered through `target`'s\n * listener handlers.\n */\nexport function fromEvent<T>(\n  target: any,\n  eventName: string,\n  options?: EventListenerOptions | ((...args: any[]) => T),\n  resultSelector?: (...args: any[]) => T\n): Observable<T> {\n  if (isFunction(options)) {\n    resultSelector = options;\n    options = undefined;\n  }\n  if (resultSelector) {\n    return fromEvent<T>(target, eventName, options as EventListenerOptions).pipe(mapOneOrManyArgs(resultSelector));\n  }\n\n  // Figure out our add and remove methods. In order to do this,\n  // we are going to analyze the target in a preferred order, if\n  // the target matches a given signature, we take the two \"add\" and \"remove\"\n  // method names and apply them to a map to create opposite versions of the\n  // same function. This is because they all operate in duplicate pairs,\n  // `addListener(name, handler)`, `removeListener(name, handler)`, for example.\n  // The call only differs by method name, as to whether or not you're adding or removing.\n  const [add, remove] =\n    // If it is an EventTarget, we need to use a slightly different method than the other two patterns.\n    isEventTarget(target)\n      ? eventTargetMethods.map((methodName) => (handler: any) => target[methodName](eventName, handler, options as EventListenerOptions))\n      : // In all other cases, the call pattern is identical with the exception of the method names.\n      isNodeStyleEventEmitter(target)\n      ? nodeEventEmitterMethods.map(toCommonHandlerRegistry(target, eventName))\n      : isJQueryStyleEventEmitter(target)\n      ? jqueryMethods.map(toCommonHandlerRegistry(target, eventName))\n      : [];\n\n  // If add is falsy, it's because we didn't match a pattern above.\n  // Check to see if it is an ArrayLike, because if it is, we want to\n  // try to apply fromEvent to all of it's items. We do this check last,\n  // because there are may be some types that are both ArrayLike *and* implement\n  // event registry points, and we'd rather delegate to that when possible.\n  if (!add) {\n    if (isArrayLike(target)) {\n      return mergeMap((subTarget: any) => fromEvent(subTarget, eventName, options as EventListenerOptions))(\n        innerFrom(target)\n      ) as Observable<T>;\n    }\n  }\n\n  // If add is falsy and we made it here, it's because we didn't\n  // match any valid target objects above.\n  if (!add) {\n    throw new TypeError('Invalid event target');\n  }\n\n  return new Observable<T>((subscriber) => {\n    // The handler we are going to register. Forwards the event object, by itself, or\n    // an array of arguments to the event handler, if there is more than one argument,\n    // to the consumer.\n    const handler = (...args: any[]) => subscriber.next(1 < args.length ? args : args[0]);\n    // Do the work of adding the handler to the target.\n    add(handler);\n    // When we finalize, we want to remove the handler and free up memory.\n    return () => remove!(handler);\n  });\n}\n\n/**\n * Used to create `add` and `remove` functions to register and unregister event handlers\n * from a target in the most common handler pattern, where there are only two arguments.\n * (e.g.  `on(name, fn)`, `off(name, fn)`, `addListener(name, fn)`, or `removeListener(name, fn)`)\n * @param target The target we're calling methods on\n * @param eventName The event name for the event we're creating register or unregister functions for\n */\nfunction toCommonHandlerRegistry(target: any, eventName: string) {\n  return (methodName: string) => (handler: any) => target[methodName](eventName, handler);\n}\n\n/**\n * Checks to see if the target implements the required node-style EventEmitter methods\n * for adding and removing event handlers.\n * @param target the object to check\n */\nfunction isNodeStyleEventEmitter(target: any): target is NodeStyleEventEmitter {\n  return isFunction(target.addListener) && isFunction(target.removeListener);\n}\n\n/**\n * Checks to see if the target implements the required jQuery-style EventEmitter methods\n * for adding and removing event handlers.\n * @param target the object to check\n */\nfunction isJQueryStyleEventEmitter(target: any): target is JQueryStyleEventEmitter<any, any> {\n  return isFunction(target.on) && isFunction(target.off);\n}\n\n/**\n * Checks to see if the target implements the required EventTarget methods\n * for adding and removing event handlers.\n * @param target the object to check\n */\nfunction isEventTarget(target: any): target is HasEventTargetAddRemove<any> {\n  return isFunction(target.addEventListener) && isFunction(target.removeEventListener);\n}\n", "import { Observable } from '../Observable';\nimport { isFunction } from '../util/isFunction';\nimport { NodeEventHandler } from './fromEvent';\nimport { mapOneOrManyArgs } from '../util/mapOneOrManyArgs';\n\n/* tslint:disable:max-line-length */\nexport function fromEventPattern<T>(\n  addHandler: (handler: NodeEventHandler) => any,\n  removeHandler?: (handler: NodeEventHandler, signal?: any) => void\n): Observable<T>;\nexport function fromEventPattern<T>(\n  addHandler: (handler: NodeEventHandler) => any,\n  removeHandler?: (handler: NodeEventHandler, signal?: any) => void,\n  resultSelector?: (...args: any[]) => T\n): Observable<T>;\n/* tslint:enable:max-line-length */\n\n/**\n * Creates an Observable from an arbitrary API for registering event handlers.\n *\n * <span class=\"informal\">When that method for adding event handler was something {@link fromEvent}\n * was not prepared for.</span>\n *\n * ![](fromEventPattern.png)\n *\n * `fromEventPattern` allows you to convert into an Observable any API that supports registering handler functions\n * for events. It is similar to {@link fromEvent}, but far\n * more flexible. In fact, all use cases of {@link fromEvent} could be easily handled by\n * `fromEventPattern` (although in slightly more verbose way).\n *\n * This operator accepts as a first argument an `addHandler` function, which will be injected with\n * handler parameter. That handler is actually an event handler function that you now can pass\n * to API expecting it. `addHandler` will be called whenever Observable\n * returned by the operator is subscribed, so registering handler in API will not\n * necessarily happen when `fromEventPattern` is called.\n *\n * After registration, every time an event that we listen to happens,\n * Observable returned by `fromEventPattern` will emit value that event handler\n * function was called with. Note that if event handler was called with more\n * than one argument, second and following arguments will not appear in the Observable.\n *\n * If API you are using allows to unregister event handlers as well, you can pass to `fromEventPattern`\n * another function - `removeHandler` - as a second parameter. It will be injected\n * with the same handler function as before, which now you can use to unregister\n * it from the API. `removeHandler` will be called when consumer of resulting Observable\n * unsubscribes from it.\n *\n * In some APIs unregistering is actually handled differently. Method registering an event handler\n * returns some kind of token, which is later used to identify which function should\n * be unregistered or it itself has method that unregisters event handler.\n * If that is the case with your API, make sure token returned\n * by registering method is returned by `addHandler`. Then it will be passed\n * as a second argument to `removeHandler`, where you will be able to use it.\n *\n * If you need access to all event handler parameters (not only the first one),\n * or you need to transform them in any way, you can call `fromEventPattern` with optional\n * third parameter - project function which will accept all arguments passed to\n * event handler when it is called. Whatever is returned from project function will appear on\n * resulting stream instead of usual event handlers first argument. This means\n * that default project can be thought of as function that takes its first parameter\n * and ignores the rest.\n *\n * ## Examples\n *\n * Emits clicks happening on the DOM document\n *\n * ```ts\n * import { fromEventPattern } from 'rxjs';\n *\n * function addClickHandler(handler) {\n *   document.addEventListener('click', handler);\n * }\n *\n * function removeClickHandler(handler) {\n *   document.removeEventListener('click', handler);\n * }\n *\n * const clicks = fromEventPattern(\n *   addClickHandler,\n *   removeClickHandler\n * );\n * clicks.subscribe(x => console.log(x));\n *\n * // Whenever you click anywhere in the browser, DOM MouseEvent\n * // object will be logged.\n * ```\n *\n * Use with API that returns cancellation token\n *\n * ```ts\n * import { fromEventPattern } from 'rxjs';\n *\n * const token = someAPI.registerEventHandler(function() {});\n * someAPI.unregisterEventHandler(token); // this APIs cancellation method accepts\n *                                        // not handler itself, but special token.\n *\n * const someAPIObservable = fromEventPattern(\n *   function(handler) { return someAPI.registerEventHandler(handler); }, // Note that we return the token here...\n *   function(handler, token) { someAPI.unregisterEventHandler(token); }  // ...to then use it here.\n * );\n * ```\n *\n * Use with project function\n *\n * ```ts\n * import { fromEventPattern } from 'rxjs';\n *\n * someAPI.registerEventHandler((eventType, eventMessage) => {\n *   console.log(eventType, eventMessage); // Logs 'EVENT_TYPE' 'EVENT_MESSAGE' to console.\n * });\n *\n * const someAPIObservable = fromEventPattern(\n *   handler => someAPI.registerEventHandler(handler),\n *   handler => someAPI.unregisterEventHandler(handler)\n *   (eventType, eventMessage) => eventType + ' --- ' + eventMessage // without that function only 'EVENT_TYPE'\n * );                                                                // would be emitted by the Observable\n *\n * someAPIObservable.subscribe(value => console.log(value));\n *\n * // Logs:\n * // 'EVENT_TYPE --- EVENT_MESSAGE'\n * ```\n *\n * @see {@link fromEvent}\n * @see {@link bindCallback}\n * @see {@link bindNodeCallback}\n *\n * @param addHandler A function that takes a `handler` function as argument and attaches it\n * somehow to the actual source of events.\n * @param removeHandler A function that takes a `handler` function as an argument and removes\n * it from the event source. If `addHandler` returns some kind of token, `removeHandler` function\n * will have it as a second parameter.\n * @param resultSelector A function to transform results. It takes the arguments from the event\n * handler and should return a single value.\n * @return Observable which, when an event happens, emits first parameter passed to registered\n * event handler. Alternatively it emits whatever project function returns at that moment.\n */\nexport function fromEventPattern<T>(\n  addHandler: (handler: NodeEventHandler) => any,\n  removeHandler?: (handler: NodeEventHandler, signal?: any) => void,\n  resultSelector?: (...args: any[]) => T\n): Observable<T | T[]> {\n  if (resultSelector) {\n    return fromEventPattern<T>(addHandler, removeHandler).pipe(mapOneOrManyArgs(resultSelector));\n  }\n\n  return new Observable<T | T[]>((subscriber) => {\n    const handler = (...e: T[]) => subscriber.next(e.length === 1 ? e[0] : e);\n    const retValue = addHandler(handler);\n    return isFunction(removeHandler) ? () => removeHandler(handler, retValue) : undefined;\n  });\n}\n", "import { Observable } from '../Observable';\nimport { SchedulerLike } from '../types';\nimport { async as asyncScheduler } from '../scheduler/async';\nimport { isScheduler } from '../util/isScheduler';\nimport { isValidDate } from '../util/isDate';\n\n/**\n * Creates an observable that will wait for a specified time period, or exact date, before\n * emitting the number 0.\n *\n * <span class=\"informal\">Used to emit a notification after a delay.</span>\n *\n * This observable is useful for creating delays in code, or racing against other values\n * for ad-hoc timeouts.\n *\n * The `delay` is specified by default in milliseconds, however providing a custom scheduler could\n * create a different behavior.\n *\n * ## Examples\n *\n * Wait 3 seconds and start another observable\n *\n * You might want to use `timer` to delay subscription to an\n * observable by a set amount of time. Here we use a timer with\n * {@link concatMapTo} or {@link concatMap} in order to wait\n * a few seconds and start a subscription to a source.\n *\n * ```ts\n * import { of, timer, concatMap } from 'rxjs';\n *\n * // This could be any observable\n * const source = of(1, 2, 3);\n *\n * timer(3000)\n *   .pipe(concatMap(() => source))\n *   .subscribe(console.log);\n * ```\n *\n * Take all values until the start of the next minute\n *\n * Using a `Date` as the trigger for the first emission, you can\n * do things like wait until midnight to fire an event, or in this case,\n * wait until a new minute starts (chosen so the example wouldn't take\n * too long to run) in order to stop watching a stream. Leveraging\n * {@link takeUntil}.\n *\n * ```ts\n * import { interval, takeUntil, timer } from 'rxjs';\n *\n * // Build a Date object that marks the\n * // next minute.\n * const currentDate = new Date();\n * const startOfNextMinute = new Date(\n *   currentDate.getFullYear(),\n *   currentDate.getMonth(),\n *   currentDate.getDate(),\n *   currentDate.getHours(),\n *   currentDate.getMinutes() + 1\n * );\n *\n * // This could be any observable stream\n * const source = interval(1000);\n *\n * const result = source.pipe(\n *   takeUntil(timer(startOfNextMinute))\n * );\n *\n * result.subscribe(console.log);\n * ```\n *\n * ### Known Limitations\n *\n * - The {@link asyncScheduler} uses `setTimeout` which has limitations for how far in the future it can be scheduled.\n *\n * - If a `scheduler` is provided that returns a timestamp other than an epoch from `now()`, and\n * a `Date` object is passed to the `dueTime` argument, the calculation for when the first emission\n * should occur will be incorrect. In this case, it would be best to do your own calculations\n * ahead of time, and pass a `number` in as the `dueTime`.\n *\n * @param due If a `number`, the amount of time in milliseconds to wait before emitting.\n * If a `Date`, the exact time at which to emit.\n * @param scheduler The scheduler to use to schedule the delay. Defaults to {@link asyncScheduler}.\n */\nexport function timer(due: number | Date, scheduler?: SchedulerLike): Observable<0>;\n\n/**\n * Creates an observable that starts an interval after a specified delay, emitting incrementing numbers -- starting at `0` --\n * on each interval after words.\n *\n * The `delay` and `intervalDuration` are specified by default in milliseconds, however providing a custom scheduler could\n * create a different behavior.\n *\n * ## Example\n *\n * ### Start an interval that starts right away\n *\n * Since {@link interval} waits for the passed delay before starting,\n * sometimes that's not ideal. You may want to start an interval immediately.\n * `timer` works well for this. Here we have both side-by-side so you can\n * see them in comparison.\n *\n * Note that this observable will never complete.\n *\n * ```ts\n * import { timer, interval } from 'rxjs';\n *\n * timer(0, 1000).subscribe(n => console.log('timer', n));\n * interval(1000).subscribe(n => console.log('interval', n));\n * ```\n *\n * ### Known Limitations\n *\n * - The {@link asyncScheduler} uses `setTimeout` which has limitations for how far in the future it can be scheduled.\n *\n * - If a `scheduler` is provided that returns a timestamp other than an epoch from `now()`, and\n * a `Date` object is passed to the `dueTime` argument, the calculation for when the first emission\n * should occur will be incorrect. In this case, it would be best to do your own calculations\n * ahead of time, and pass a `number` in as the `startDue`.\n * @param startDue If a `number`, is the time to wait before starting the interval.\n * If a `Date`, is the exact time at which to start the interval.\n * @param intervalDuration The delay between each value emitted in the interval. Passing a\n * negative number here will result in immediate completion after the first value is emitted, as though\n * no `intervalDuration` was passed at all.\n * @param scheduler The scheduler to use to schedule the delay. Defaults to {@link asyncScheduler}.\n */\nexport function timer(startDue: number | Date, intervalDuration: number, scheduler?: SchedulerLike): Observable<number>;\n\n/**\n * @deprecated The signature allowing `undefined` to be passed for `intervalDuration` will be removed in v8. Use the `timer(dueTime, scheduler?)` signature instead.\n */\nexport function timer(dueTime: number | Date, unused: undefined, scheduler?: SchedulerLike): Observable<0>;\n\nexport function timer(\n  dueTime: number | Date = 0,\n  intervalOrScheduler?: number | SchedulerLike,\n  scheduler: SchedulerLike = asyncScheduler\n): Observable<number> {\n  // Since negative intervalDuration is treated as though no\n  // interval was specified at all, we start with a negative number.\n  let intervalDuration = -1;\n\n  if (intervalOrScheduler != null) {\n    // If we have a second argument, and it's a scheduler,\n    // override the scheduler we had defaulted. Otherwise,\n    // it must be an interval.\n    if (isScheduler(intervalOrScheduler)) {\n      scheduler = intervalOrScheduler;\n    } else {\n      // Note that this *could* be negative, in which case\n      // it's like not passing an intervalDuration at all.\n      intervalDuration = intervalOrScheduler;\n    }\n  }\n\n  return new Observable((subscriber) => {\n    // If a valid date is passed, calculate how long to wait before\n    // executing the first value... otherwise, if it's a number just schedule\n    // that many milliseconds (or scheduler-specified unit size) in the future.\n    let due = isValidDate(dueTime) ? +dueTime - scheduler!.now() : dueTime;\n\n    if (due < 0) {\n      // Ensure we don't schedule in the future.\n      due = 0;\n    }\n\n    // The incrementing value we emit.\n    let n = 0;\n\n    // Start the timer.\n    return scheduler.schedule(function () {\n      if (!subscriber.closed) {\n        // Emit the next value and increment.\n        subscriber.next(n++);\n\n        if (0 <= intervalDuration) {\n          // If we have a interval after the initial timer,\n          // reschedule with the period.\n          this.schedule(undefined, intervalDuration);\n        } else {\n          // We didn't have an interval. So just complete.\n          subscriber.complete();\n        }\n      }\n    }, due);\n  });\n}\n", "import { Observable } from '../Observable';\nimport { ObservableInput, ObservableInputTuple, SchedulerLike } from '../types';\nimport { mergeAll } from '../operators/mergeAll';\nimport { innerFrom } from './innerFrom';\nimport { EMPTY } from './empty';\nimport { popNumber, popScheduler } from '../util/args';\nimport { from } from './from';\n\nexport function merge<A extends readonly unknown[]>(...sources: [...ObservableInputTuple<A>]): Observable<A[number]>;\nexport function merge<A extends readonly unknown[]>(...sourcesAndConcurrency: [...ObservableInputTuple<A>, number?]): Observable<A[number]>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `mergeAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function merge<A extends readonly unknown[]>(\n  ...sourcesAndScheduler: [...ObservableInputTuple<A>, SchedulerLike?]\n): Observable<A[number]>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `mergeAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function merge<A extends readonly unknown[]>(\n  ...sourcesAndConcurrencyAndScheduler: [...ObservableInputTuple<A>, number?, SchedulerLike?]\n): Observable<A[number]>;\n\n/**\n * Creates an output Observable which concurrently emits all values from every\n * given input Observable.\n *\n * <span class=\"informal\">Flattens multiple Observables together by blending\n * their values into one Observable.</span>\n *\n * ![](merge.png)\n *\n * `merge` subscribes to each given input Observable (as arguments), and simply\n * forwards (without doing any transformation) all the values from all the input\n * Observables to the output Observable. The output Observable only completes\n * once all input Observables have completed. Any error delivered by an input\n * Observable will be immediately emitted on the output Observable.\n *\n * ## Examples\n *\n * Merge together two Observables: 1s interval and clicks\n *\n * ```ts\n * import { merge, fromEvent, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const timer = interval(1000);\n * const clicksOrTimer = merge(clicks, timer);\n * clicksOrTimer.subscribe(x => console.log(x));\n *\n * // Results in the following:\n * // timer will emit ascending values, one every second(1000ms) to console\n * // clicks logs MouseEvents to console every time the \"document\" is clicked\n * // Since the two streams are merged you see these happening\n * // as they occur.\n * ```\n *\n * Merge together 3 Observables, but run only 2 concurrently\n *\n * ```ts\n * import { interval, take, merge } from 'rxjs';\n *\n * const timer1 = interval(1000).pipe(take(10));\n * const timer2 = interval(2000).pipe(take(6));\n * const timer3 = interval(500).pipe(take(10));\n *\n * const concurrent = 2; // the argument\n * const merged = merge(timer1, timer2, timer3, concurrent);\n * merged.subscribe(x => console.log(x));\n *\n * // Results in the following:\n * // - First timer1 and timer2 will run concurrently\n * // - timer1 will emit a value every 1000ms for 10 iterations\n * // - timer2 will emit a value every 2000ms for 6 iterations\n * // - after timer1 hits its max iteration, timer2 will\n * //   continue, and timer3 will start to run concurrently with timer2\n * // - when timer2 hits its max iteration it terminates, and\n * //   timer3 will continue to emit a value every 500ms until it is complete\n * ```\n *\n * @see {@link mergeAll}\n * @see {@link mergeMap}\n * @see {@link mergeMapTo}\n * @see {@link mergeScan}\n *\n * @param args `ObservableInput`s to merge together. If the last parameter\n * is of type number, `merge` will use it to limit number of concurrently\n * subscribed `ObservableInput`s. If the last parameter is {@link SchedulerLike},\n * it will be used for scheduling the emission of values.\n * @return An Observable that emits items that are the result of every input Observable.\n */\nexport function merge(...args: (ObservableInput<unknown> | number | SchedulerLike)[]): Observable<unknown> {\n  const scheduler = popScheduler(args);\n  const concurrent = popNumber(args, Infinity);\n  const sources = args as ObservableInput<unknown>[];\n  return !sources.length\n    ? // No source provided\n      EMPTY\n    : sources.length === 1\n    ? // One source? Just return it.\n      innerFrom(sources[0])\n    : // Merge all sources\n      mergeAll(concurrent)(from(sources, scheduler));\n}\n", "import { Observable } from '../Observable';\nimport { noop } from '../util/noop';\n\n/**\n * An Observable that emits no items to the Observer and never completes.\n *\n * ![](never.png)\n *\n * A simple Observable that emits neither values nor errors nor the completion\n * notification. It can be used for testing purposes or for composing with other\n * Observables. Please note that by never emitting a complete notification, this\n * Observable keeps the subscription from being disposed automatically.\n * Subscriptions need to be manually disposed.\n *\n * ##  Example\n *\n * Emit the number 7, then never emit anything else (not even complete)\n *\n * ```ts\n * import { NEVER, startWith } from 'rxjs';\n *\n * const info = () => console.log('Will not be called');\n *\n * const result = NEVER.pipe(startWith(7));\n * result.subscribe({\n *   next: x => console.log(x),\n *   error: info,\n *   complete: info\n * });\n * ```\n *\n * @see {@link Observable}\n * @see {@link EMPTY}\n * @see {@link of}\n * @see {@link throwError}\n */\nexport const NEVER = new Observable<never>(noop);\n\n/**\n * @deprecated Replaced with the {@link NEVER} constant. Will be removed in v8.\n */\nexport function never() {\n  return NEVER;\n}\n", "const { isArray } = Array;\n\n/**\n * Used in operators and functions that accept either a list of arguments, or an array of arguments\n * as a single argument.\n */\nexport function argsOrArgArray<T>(args: (T | T[])[]): T[] {\n  return args.length === 1 && isArray(args[0]) ? args[0] : (args as T[]);\n}\n", "import { OperatorFunction, MonoTypeOperatorFunction, TruthyTypesOf } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/** @deprecated Use a closure instead of a `thisArg`. Signatures accepting a `thisArg` will be removed in v8. */\nexport function filter<T, S extends T, A>(predicate: (this: A, value: T, index: number) => value is S, thisArg: A): OperatorFunction<T, S>;\nexport function filter<T, S extends T>(predicate: (value: T, index: number) => value is S): OperatorFunction<T, S>;\nexport function filter<T>(predicate: BooleanConstructor): OperatorFunction<T, TruthyTypesOf<T>>;\n/** @deprecated Use a closure instead of a `thisArg`. Signatures accepting a `thisArg` will be removed in v8. */\nexport function filter<T, A>(predicate: (this: A, value: T, index: number) => boolean, thisArg: A): MonoTypeOperatorFunction<T>;\nexport function filter<T>(predicate: (value: T, index: number) => boolean): MonoTypeOperatorFunction<T>;\n\n/**\n * Filter items emitted by the source Observable by only emitting those that\n * satisfy a specified predicate.\n *\n * <span class=\"informal\">Like\n * [Array.prototype.filter()](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Array/filter),\n * it only emits a value from the source if it passes a criterion function.</span>\n *\n * ![](filter.png)\n *\n * Similar to the well-known `Array.prototype.filter` method, this operator\n * takes values from the source Observable, passes them through a `predicate`\n * function and only emits those values that yielded `true`.\n *\n * ## Example\n *\n * Emit only click events whose target was a DIV element\n *\n * ```ts\n * import { fromEvent, filter } from 'rxjs';\n *\n * const div = document.createElement('div');\n * div.style.cssText = 'width: 200px; height: 200px; background: #09c;';\n * document.body.appendChild(div);\n *\n * const clicks = fromEvent(document, 'click');\n * const clicksOnDivs = clicks.pipe(filter(ev => (<HTMLElement>ev.target).tagName === 'DIV'));\n * clicksOnDivs.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link distinct}\n * @see {@link distinctUntilChanged}\n * @see {@link distinctUntilKeyChanged}\n * @see {@link ignoreElements}\n * @see {@link partition}\n * @see {@link skip}\n *\n * @param predicate A function that\n * evaluates each value emitted by the source Observable. If it returns `true`,\n * the value is emitted, if `false` the value is not passed to the output\n * Observable. The `index` parameter is the number `i` for the i-th source\n * emission that has happened since the subscription, starting from the number\n * `0`.\n * @param thisArg An optional argument to determine the value of `this`\n * in the `predicate` function.\n * @return A function that returns an Observable that emits items from the\n * source Observable that satisfy the specified `predicate`.\n */\nexport function filter<T>(predicate: (value: T, index: number) => boolean, thisArg?: any): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    // An index passed to our predicate function on each call.\n    let index = 0;\n\n    // Subscribe to the source, all errors and completions are\n    // forwarded to the consumer.\n    source.subscribe(\n      // Call the predicate with the appropriate `this` context,\n      // if the predicate returns `true`, then send the value\n      // to the consumer.\n      createOperatorSubscriber(subscriber, (value) => predicate.call(thisArg, value, index++) && subscriber.next(value))\n    );\n  });\n}\n", "import { Observable } from '../Observable';\nimport { ObservableInputTuple } from '../types';\nimport { innerFrom } from './innerFrom';\nimport { argsOrArgArray } from '../util/argsOrArgArray';\nimport { EMPTY } from './empty';\nimport { createOperatorSubscriber } from '../operators/OperatorSubscriber';\nimport { popResultSelector } from '../util/args';\n\nexport function zip<A extends readonly unknown[]>(sources: [...ObservableInputTuple<A>]): Observable<A>;\nexport function zip<A extends readonly unknown[], R>(\n  sources: [...ObservableInputTuple<A>],\n  resultSelector: (...values: A) => R\n): Observable<R>;\nexport function zip<A extends readonly unknown[]>(...sources: [...ObservableInputTuple<A>]): Observable<A>;\nexport function zip<A extends readonly unknown[], R>(\n  ...sourcesAndResultSelector: [...ObservableInputTuple<A>, (...values: A) => R]\n): Observable<R>;\n\n/**\n * Combines multiple Observables to create an Observable whose values are calculated from the values, in order, of each\n * of its input Observables.\n *\n * If the last parameter is a function, this function is used to compute the created value from the input values.\n * Otherwise, an array of the input values is returned.\n *\n * ## Example\n *\n * Combine age and name from different sources\n *\n * ```ts\n * import { of, zip, map } from 'rxjs';\n *\n * const age$ = of(27, 25, 29);\n * const name$ = of('Foo', 'Bar', 'Beer');\n * const isDev$ = of(true, true, false);\n *\n * zip(age$, name$, isDev$).pipe(\n *   map(([age, name, isDev]) => ({ age, name, isDev }))\n * )\n * .subscribe(x => console.log(x));\n *\n * // Outputs\n * // { age: 27, name: 'Foo', isDev: true }\n * // { age: 25, name: 'Bar', isDev: true }\n * // { age: 29, name: 'Beer', isDev: false }\n * ```\n *\n * @param args Any number of `ObservableInput`s provided either as an array or as an object\n * to combine with each other.\n * @return An Observable of array values of the values emitted at the same index from each\n * individual `ObservableInput`.\n */\nexport function zip(...args: unknown[]): Observable<unknown> {\n  const resultSelector = popResultSelector(args);\n\n  const sources = argsOrArgArray(args) as Observable<unknown>[];\n\n  return sources.length\n    ? new Observable<unknown[]>((subscriber) => {\n        // A collection of buffers of values from each source.\n        // Keyed by the same index with which the sources were passed in.\n        let buffers: unknown[][] = sources.map(() => []);\n\n        // An array of flags of whether or not the sources have completed.\n        // This is used to check to see if we should complete the result.\n        // Keyed by the same index with which the sources were passed in.\n        let completed = sources.map(() => false);\n\n        // When everything is done, release the arrays above.\n        subscriber.add(() => {\n          buffers = completed = null!;\n        });\n\n        // Loop over our sources and subscribe to each one. The index `i` is\n        // especially important here, because we use it in closures below to\n        // access the related buffers and completion properties\n        for (let sourceIndex = 0; !subscriber.closed && sourceIndex < sources.length; sourceIndex++) {\n          innerFrom(sources[sourceIndex]).subscribe(\n            createOperatorSubscriber(\n              subscriber,\n              (value) => {\n                buffers[sourceIndex].push(value);\n                // if every buffer has at least one value in it, then we\n                // can shift out the oldest value from each buffer and emit\n                // them as an array.\n                if (buffers.every((buffer) => buffer.length)) {\n                  const result: any = buffers.map((buffer) => buffer.shift()!);\n                  // Emit the array. If theres' a result selector, use that.\n                  subscriber.next(resultSelector ? resultSelector(...result) : result);\n                  // If any one of the sources is both complete and has an empty buffer\n                  // then we complete the result. This is because we cannot possibly have\n                  // any more values to zip together.\n                  if (buffers.some((buffer, i) => !buffer.length && completed[i])) {\n                    subscriber.complete();\n                  }\n                }\n              },\n              () => {\n                // This source completed. Mark it as complete so we can check it later\n                // if we have to.\n                completed[sourceIndex] = true;\n                // But, if this complete source has nothing in its buffer, then we\n                // can complete the result, because we can't possibly have any more\n                // values from this to zip together with the other values.\n                !buffers[sourceIndex].length && subscriber.complete();\n              }\n            )\n          );\n        }\n\n        // When everything is done, release the arrays above.\n        return () => {\n          buffers = completed = null!;\n        };\n      })\n    : EMPTY;\n}\n", "import { Subscriber } from '../Subscriber';\nimport { MonoTypeOperatorFunction, ObservableInput } from '../types';\n\nimport { operate } from '../util/lift';\nimport { innerFrom } from '../observable/innerFrom';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Ignores source values for a duration determined by another Observable, then\n * emits the most recent value from the source Observable, then repeats this\n * process.\n *\n * <span class=\"informal\">It's like {@link auditTime}, but the silencing\n * duration is determined by a second Observable.</span>\n *\n * ![](audit.svg)\n *\n * `audit` is similar to `throttle`, but emits the last value from the silenced\n * time window, instead of the first value. `audit` emits the most recent value\n * from the source Observable on the output Observable as soon as its internal\n * timer becomes disabled, and ignores source values while the timer is enabled.\n * Initially, the timer is disabled. As soon as the first source value arrives,\n * the timer is enabled by calling the `durationSelector` function with the\n * source value, which returns the \"duration\" Observable. When the duration\n * Observable emits a value, the timer is disabled, then the most\n * recent source value is emitted on the output Observable, and this process\n * repeats for the next source value.\n *\n * ## Example\n *\n * Emit clicks at a rate of at most one click per second\n *\n * ```ts\n * import { fromEvent, audit, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(audit(ev => interval(1000)));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link auditTime}\n * @see {@link debounce}\n * @see {@link delayWhen}\n * @see {@link sample}\n * @see {@link throttle}\n *\n * @param durationSelector A function\n * that receives a value from the source Observable, for computing the silencing\n * duration, returned as an Observable or a Promise.\n * @return A function that returns an Observable that performs rate-limiting of\n * emissions from the source Observable.\n */\nexport function audit<T>(durationSelector: (value: T) => ObservableInput<any>): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let hasValue = false;\n    let lastValue: T | null = null;\n    let durationSubscriber: Subscriber<any> | null = null;\n    let isComplete = false;\n\n    const endDuration = () => {\n      durationSubscriber?.unsubscribe();\n      durationSubscriber = null;\n      if (hasValue) {\n        hasValue = false;\n        const value = lastValue!;\n        lastValue = null;\n        subscriber.next(value);\n      }\n      isComplete && subscriber.complete();\n    };\n\n    const cleanupDuration = () => {\n      durationSubscriber = null;\n      isComplete && subscriber.complete();\n    };\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          hasValue = true;\n          lastValue = value;\n          if (!durationSubscriber) {\n            innerFrom(durationSelector(value)).subscribe(\n              (durationSubscriber = createOperatorSubscriber(subscriber, endDuration, cleanupDuration))\n            );\n          }\n        },\n        () => {\n          isComplete = true;\n          (!hasValue || !durationSubscriber || durationSubscriber.closed) && subscriber.complete();\n        }\n      )\n    );\n  });\n}\n", "import { asyncScheduler } from '../scheduler/async';\nimport { audit } from './audit';\nimport { timer } from '../observable/timer';\nimport { MonoTypeOperatorFunction, SchedulerLike } from '../types';\n\n/**\n * Ignores source values for `duration` milliseconds, then emits the most recent\n * value from the source Observable, then repeats this process.\n *\n * <span class=\"informal\">When it sees a source value, it ignores that plus\n * the next ones for `duration` milliseconds, and then it emits the most recent\n * value from the source.</span>\n *\n * ![](auditTime.png)\n *\n * `auditTime` is similar to `throttleTime`, but emits the last value from the\n * silenced time window, instead of the first value. `auditTime` emits the most\n * recent value from the source Observable on the output Observable as soon as\n * its internal timer becomes disabled, and ignores source values while the\n * timer is enabled. Initially, the timer is disabled. As soon as the first\n * source value arrives, the timer is enabled. After `duration` milliseconds (or\n * the time unit determined internally by the optional `scheduler`) has passed,\n * the timer is disabled, then the most recent source value is emitted on the\n * output Observable, and this process repeats for the next source value.\n * Optionally takes a {@link SchedulerLike} for managing timers.\n *\n * ## Example\n *\n * Emit clicks at a rate of at most one click per second\n *\n * ```ts\n * import { fromEvent, auditTime } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(auditTime(1000));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link audit}\n * @see {@link debounceTime}\n * @see {@link delay}\n * @see {@link sampleTime}\n * @see {@link throttleTime}\n *\n * @param duration Time to wait before emitting the most recent source value,\n * measured in milliseconds or the time unit determined internally by the\n * optional `scheduler`.\n * @param scheduler The {@link SchedulerLike} to use for managing the timers\n * that handle the rate-limiting behavior.\n * @return A function that returns an Observable that performs rate-limiting of\n * emissions from the source Observable.\n */\nexport function auditTime<T>(duration: number, scheduler: SchedulerLike = asyncScheduler): MonoTypeOperatorFunction<T> {\n  return audit(() => timer(duration, scheduler));\n}\n", "import { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { arrRemove } from '../util/arrRemove';\n\n/**\n * Buffers the source Observable values until the size hits the maximum\n * `bufferSize` given.\n *\n * <span class=\"informal\">Collects values from the past as an array, and emits\n * that array only when its size reaches `bufferSize`.</span>\n *\n * ![](bufferCount.png)\n *\n * Buffers a number of values from the source Observable by `bufferSize` then\n * emits the buffer and clears it, and starts a new buffer each\n * `startBufferEvery` values. If `startBufferEvery` is not provided or is\n * `null`, then new buffers are started immediately at the start of the source\n * and when each buffer closes and is emitted.\n *\n * ## Examples\n *\n * Emit the last two click events as an array\n *\n * ```ts\n * import { fromEvent, bufferCount } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const buffered = clicks.pipe(bufferCount(2));\n * buffered.subscribe(x => console.log(x));\n * ```\n *\n * On every click, emit the last two click events as an array\n *\n * ```ts\n * import { fromEvent, bufferCount } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const buffered = clicks.pipe(bufferCount(2, 1));\n * buffered.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link buffer}\n * @see {@link bufferTime}\n * @see {@link bufferToggle}\n * @see {@link bufferWhen}\n * @see {@link pairwise}\n * @see {@link windowCount}\n *\n * @param bufferSize The maximum size of the buffer emitted.\n * @param startBufferEvery Interval at which to start a new buffer.\n * For example if `startBufferEvery` is `2`, then a new buffer will be started\n * on every other value from the source. A new buffer is started at the\n * beginning of the source by default.\n * @return A function that returns an Observable of arrays of buffered values.\n */\nexport function bufferCount<T>(bufferSize: number, startBufferEvery: number | null = null): OperatorFunction<T, T[]> {\n  // If no `startBufferEvery` value was supplied, then we're\n  // opening and closing on the bufferSize itself.\n  startBufferEvery = startBufferEvery ?? bufferSize;\n\n  return operate((source, subscriber) => {\n    let buffers: T[][] = [];\n    let count = 0;\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          let toEmit: T[][] | null = null;\n\n          // Check to see if we need to start a buffer.\n          // This will start one at the first value, and then\n          // a new one every N after that.\n          if (count++ % startBufferEvery! === 0) {\n            buffers.push([]);\n          }\n\n          // Push our value into our active buffers.\n          for (const buffer of buffers) {\n            buffer.push(value);\n            // Check to see if we're over the bufferSize\n            // if we are, record it so we can emit it later.\n            // If we emitted it now and removed it, it would\n            // mutate the `buffers` array while we're looping\n            // over it.\n            if (bufferSize <= buffer.length) {\n              toEmit = toEmit ?? [];\n              toEmit.push(buffer);\n            }\n          }\n\n          if (toEmit) {\n            // We have found some buffers that are over the\n            // `bufferSize`. Emit them, and remove them from our\n            // buffers list.\n            for (const buffer of toEmit) {\n              arrRemove(buffers, buffer);\n              subscriber.next(buffer);\n            }\n          }\n        },\n        () => {\n          // When the source completes, emit all of our\n          // active buffers.\n          for (const buffer of buffers) {\n            subscriber.next(buffer);\n          }\n          subscriber.complete();\n        },\n        // Pass all errors through to consumer.\n        undefined,\n        () => {\n          // Clean up our memory when we finalize\n          buffers = null!;\n        }\n      )\n    );\n  });\n}\n", "import { Observable } from '../Observable';\n\nimport { ObservableInput, OperatorFunction, ObservedValueOf } from '../types';\nimport { Subscription } from '../Subscription';\nimport { innerFrom } from '../observable/innerFrom';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { operate } from '../util/lift';\n\nexport function catchError<T, O extends ObservableInput<any>>(\n  selector: (err: any, caught: Observable<T>) => O\n): OperatorFunction<T, T | ObservedValueOf<O>>;\n\n/**\n * Catches errors on the observable to be handled by returning a new observable or throwing an error.\n *\n * <span class=\"informal\">\n * It only listens to the error channel and ignores notifications.\n * Handles errors from the source observable, and maps them to a new observable.\n * The error may also be rethrown, or a new error can be thrown to emit an error from the result.\n * </span>\n *\n * ![](catch.png)\n *\n * This operator handles errors, but forwards along all other events to the resulting observable.\n * If the source observable terminates with an error, it will map that error to a new observable,\n * subscribe to it, and forward all of its events to the resulting observable.\n *\n * ## Examples\n *\n * Continue with a different Observable when there's an error\n *\n * ```ts\n * import { of, map, catchError } from 'rxjs';\n *\n * of(1, 2, 3, 4, 5)\n *   .pipe(\n *     map(n => {\n *       if (n === 4) {\n *         throw 'four!';\n *       }\n *       return n;\n *     }),\n *     catchError(err => of('I', 'II', 'III', 'IV', 'V'))\n *   )\n *   .subscribe(x => console.log(x));\n *   // 1, 2, 3, I, II, III, IV, V\n * ```\n *\n * Retry the caught source Observable again in case of error, similar to `retry()` operator\n *\n * ```ts\n * import { of, map, catchError, take } from 'rxjs';\n *\n * of(1, 2, 3, 4, 5)\n *   .pipe(\n *     map(n => {\n *       if (n === 4) {\n *         throw 'four!';\n *       }\n *       return n;\n *     }),\n *     catchError((err, caught) => caught),\n *     take(30)\n *   )\n *   .subscribe(x => console.log(x));\n *   // 1, 2, 3, 1, 2, 3, ...\n * ```\n *\n * Throw a new error when the source Observable throws an error\n *\n * ```ts\n * import { of, map, catchError } from 'rxjs';\n *\n * of(1, 2, 3, 4, 5)\n *   .pipe(\n *     map(n => {\n *       if (n === 4) {\n *         throw 'four!';\n *       }\n *       return n;\n *     }),\n *     catchError(err => {\n *       throw 'error in source. Details: ' + err;\n *     })\n *   )\n *   .subscribe({\n *     next: x => console.log(x),\n *     error: err => console.log(err)\n *   });\n *   // 1, 2, 3, error in source. Details: four!\n * ```\n *\n * @see {@link onErrorResumeNext}\n * @see {@link repeat}\n * @see {@link repeatWhen}\n * @see {@link retry }\n * @see {@link retryWhen}\n *\n * @param selector A function that takes as arguments `err`, which is the error, and `caught`, which\n * is the source observable, in case you'd like to \"retry\" that observable by returning it again.\n * Whatever observable is returned by the `selector` will be used to continue the observable chain.\n * @return A function that returns an Observable that originates from either\n * the source or the Observable returned by the `selector` function.\n */\nexport function catchError<T, O extends ObservableInput<any>>(\n  selector: (err: any, caught: Observable<T>) => O\n): OperatorFunction<T, T | ObservedValueOf<O>> {\n  return operate((source, subscriber) => {\n    let innerSub: Subscription | null = null;\n    let syncUnsub = false;\n    let handledResult: Observable<ObservedValueOf<O>>;\n\n    innerSub = source.subscribe(\n      createOperatorSubscriber(subscriber, undefined, undefined, (err) => {\n        handledResult = innerFrom(selector(err, catchError(selector)(source)));\n        if (innerSub) {\n          innerSub.unsubscribe();\n          innerSub = null;\n          handledResult.subscribe(subscriber);\n        } else {\n          // We don't have an innerSub yet, that means the error was synchronous\n          // because the subscribe call hasn't returned yet.\n          syncUnsub = true;\n        }\n      })\n    );\n\n    if (syncUnsub) {\n      // We have a synchronous error, we need to make sure to\n      // finalize right away. This ensures that callbacks in the `finalize` operator are called\n      // at the right time, and that finalization occurs at the expected\n      // time between the source error and the subscription to the\n      // next observable.\n      innerSub.unsubscribe();\n      innerSub = null;\n      handledResult!.subscribe(subscriber);\n    }\n  });\n}\n", "import { Observable } from '../Observable';\nimport { Subscriber } from '../Subscriber';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * A basic scan operation. This is used for `scan` and `reduce`.\n * @param accumulator The accumulator to use\n * @param seed The seed value for the state to accumulate\n * @param hasSeed Whether or not a seed was provided\n * @param emitOnNext Whether or not to emit the state on next\n * @param emitBeforeComplete Whether or not to emit the before completion\n */\n\nexport function scanInternals<V, A, S>(\n  accumulator: (acc: V | A | S, value: V, index: number) => A,\n  seed: S,\n  hasSeed: boolean,\n  emitOnNext: boolean,\n  emitBeforeComplete?: undefined | true\n) {\n  return (source: Observable<V>, subscriber: Subscriber<any>) => {\n    // Whether or not we have state yet. This will only be\n    // false before the first value arrives if we didn't get\n    // a seed value.\n    let hasState = hasSeed;\n    // The state that we're tracking, starting with the seed,\n    // if there is one, and then updated by the return value\n    // from the accumulator on each emission.\n    let state: any = seed;\n    // An index to pass to the accumulator function.\n    let index = 0;\n\n    // Subscribe to our source. All errors and completions are passed through.\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          // Always increment the index.\n          const i = index++;\n          // Set the state\n          state = hasState\n            ? // We already have state, so we can get the new state from the accumulator\n              accumulator(state, value, i)\n            : // We didn't have state yet, a seed value was not provided, so\n\n              // we set the state to the first value, and mark that we have state now\n              ((hasState = true), value);\n\n          // Maybe send it to the consumer.\n          emitOnNext && subscriber.next(state);\n        },\n        // If an onComplete was given, call it, otherwise\n        // just pass through the complete notification to the consumer.\n        emitBeforeComplete &&\n          (() => {\n            hasState && subscriber.next(state);\n            subscriber.complete();\n          })\n      )\n    );\n  };\n}\n", "import { combineLatestInit } from '../observable/combineLatest';\nimport { ObservableInput, ObservableInputTuple, OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { argsOrArgArray } from '../util/argsOrArgArray';\nimport { mapOneOrManyArgs } from '../util/mapOneOrManyArgs';\nimport { pipe } from '../util/pipe';\nimport { popResultSelector } from '../util/args';\n\n/** @deprecated Replaced with {@link combineLatestWith}. Will be removed in v8. */\nexport function combineLatest<T, A extends readonly unknown[], R>(\n  sources: [...ObservableInputTuple<A>],\n  project: (...values: [T, ...A]) => R\n): OperatorFunction<T, R>;\n/** @deprecated Replaced with {@link combineLatestWith}. Will be removed in v8. */\nexport function combineLatest<T, A extends readonly unknown[], R>(sources: [...ObservableInputTuple<A>]): OperatorFunction<T, [T, ...A]>;\n\n/** @deprecated Replaced with {@link combineLatestWith}. Will be removed in v8. */\nexport function combineLatest<T, A extends readonly unknown[], R>(\n  ...sourcesAndProject: [...ObservableInputTuple<A>, (...values: [T, ...A]) => R]\n): OperatorFunction<T, R>;\n/** @deprecated Replaced with {@link combineLatestWith}. Will be removed in v8. */\nexport function combineLatest<T, A extends readonly unknown[], R>(...sources: [...ObservableInputTuple<A>]): OperatorFunction<T, [T, ...A]>;\n\n/**\n * @deprecated Replaced with {@link combineLatestWith}. Will be removed in v8.\n */\nexport function combineLatest<T, R>(...args: (ObservableInput<any> | ((...values: any[]) => R))[]): OperatorFunction<T, unknown> {\n  const resultSelector = popResultSelector(args);\n  return resultSelector\n    ? pipe(combineLatest(...(args as Array<ObservableInput<any>>)), mapOneOrManyArgs(resultSelector))\n    : operate((source, subscriber) => {\n        combineLatestInit([source, ...argsOrArgArray(args)])(subscriber);\n      });\n}\n", "import { ObservableInputTuple, OperatorFunction, Cons } from '../types';\nimport { combineLatest } from './combineLatest';\n\n/**\n * Create an observable that combines the latest values from all passed observables and the source\n * into arrays and emits them.\n *\n * Returns an observable, that when subscribed to, will subscribe to the source observable and all\n * sources provided as arguments. Once all sources emit at least one value, all of the latest values\n * will be emitted as an array. After that, every time any source emits a value, all of the latest values\n * will be emitted as an array.\n *\n * This is a useful operator for eagerly calculating values based off of changed inputs.\n *\n * ## Example\n *\n * Simple concatenation of values from two inputs\n *\n * ```ts\n * import { fromEvent, combineLatestWith, map } from 'rxjs';\n *\n * // Setup: Add two inputs to the page\n * const input1 = document.createElement('input');\n * document.body.appendChild(input1);\n * const input2 = document.createElement('input');\n * document.body.appendChild(input2);\n *\n * // Get streams of changes\n * const input1Changes$ = fromEvent(input1, 'change');\n * const input2Changes$ = fromEvent(input2, 'change');\n *\n * // Combine the changes by adding them together\n * input1Changes$.pipe(\n *   combineLatestWith(input2Changes$),\n *   map(([e1, e2]) => (<HTMLInputElement>e1.target).value + ' - ' + (<HTMLInputElement>e2.target).value)\n * )\n * .subscribe(x => console.log(x));\n * ```\n *\n * @param otherSources the other sources to subscribe to.\n * @return A function that returns an Observable that emits the latest\n * emissions from both source and provided Observables.\n */\nexport function combineLatestWith<T, A extends readonly unknown[]>(\n  ...otherSources: [...ObservableInputTuple<A>]\n): OperatorFunction<T, Cons<T, A>> {\n  return combineLatest(...otherSources);\n}\n", "import { Subscriber } from '../Subscriber';\nimport { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\nimport { noop } from '../util/noop';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\n\n/**\n * Emits a notification from the source Observable only after a particular time span\n * determined by another Observable has passed without another source emission.\n *\n * <span class=\"informal\">It's like {@link debounceTime}, but the time span of\n * emission silence is determined by a second Observable.</span>\n *\n * ![](debounce.svg)\n *\n * `debounce` delays notifications emitted by the source Observable, but drops previous\n * pending delayed emissions if a new notification arrives on the source Observable.\n * This operator keeps track of the most recent notification from the source\n * Observable, and spawns a duration Observable by calling the\n * `durationSelector` function. The notification is emitted only when the duration\n * Observable emits a next notification, and if no other notification was emitted on\n * the source Observable since the duration Observable was spawned. If a new\n * notification appears before the duration Observable emits, the previous notification will\n * not be emitted and a new duration is scheduled from `durationSelector` is scheduled.\n * If the completing event happens during the scheduled duration the last cached notification\n * is emitted before the completion event is forwarded to the output observable.\n * If the error event happens during the scheduled duration or after it only the error event is\n * forwarded to the output observable. The cache notification is not emitted in this case.\n *\n * Like {@link debounceTime}, this is a rate-limiting operator, and also a\n * delay-like operator since output emissions do not necessarily occur at the\n * same time as they did on the source Observable.\n *\n * ## Example\n *\n * Emit the most recent click after a burst of clicks\n *\n * ```ts\n * import { fromEvent, scan, debounce, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(\n *   scan(i => ++i, 1),\n *   debounce(i => interval(200 * i))\n * );\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link audit}\n * @see {@link auditTime}\n * @see {@link debounceTime}\n * @see {@link delay}\n * @see {@link sample}\n * @see {@link sampleTime}\n * @see {@link throttle}\n * @see {@link throttleTime}\n *\n * @param durationSelector A function\n * that receives a value from the source Observable, for computing the timeout\n * duration for each source value, returned as an Observable or a Promise.\n * @return A function that returns an Observable that delays the emissions of\n * the source Observable by the specified duration Observable returned by\n * `durationSelector`, and may drop some values if they occur too frequently.\n */\nexport function debounce<T>(durationSelector: (value: T) => ObservableInput<any>): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let hasValue = false;\n    let lastValue: T | null = null;\n    // The subscriber/subscription for the current debounce, if there is one.\n    let durationSubscriber: Subscriber<any> | null = null;\n\n    const emit = () => {\n      // Unsubscribe any current debounce subscription we have,\n      // we only cared about the first notification from it, and we\n      // want to clean that subscription up as soon as possible.\n      durationSubscriber?.unsubscribe();\n      durationSubscriber = null;\n      if (hasValue) {\n        // We have a value! Free up memory first, then emit the value.\n        hasValue = false;\n        const value = lastValue!;\n        lastValue = null;\n        subscriber.next(value);\n      }\n    };\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value: T) => {\n          // Cancel any pending debounce duration. We don't\n          // need to null it out here yet tho, because we're just going\n          // to create another one in a few lines.\n          durationSubscriber?.unsubscribe();\n          hasValue = true;\n          lastValue = value;\n          // Capture our duration subscriber, so we can unsubscribe it when we're notified\n          // and we're going to emit the value.\n          durationSubscriber = createOperatorSubscriber(subscriber, emit, noop);\n          // Subscribe to the duration.\n          innerFrom(durationSelector(value)).subscribe(durationSubscriber);\n        },\n        () => {\n          // Source completed.\n          // Emit any pending debounced values then complete\n          emit();\n          subscriber.complete();\n        },\n        // Pass all errors through to consumer\n        undefined,\n        () => {\n          // Finalization.\n          lastValue = durationSubscriber = null;\n        }\n      )\n    );\n  });\n}\n", "import { asyncScheduler } from '../scheduler/async';\nimport { Subscription } from '../Subscription';\nimport { MonoTypeOperatorFunction, SchedulerAction, SchedulerLike } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Emits a notification from the source Observable only after a particular time span\n * has passed without another source emission.\n *\n * <span class=\"informal\">It's like {@link delay}, but passes only the most\n * recent notification from each burst of emissions.</span>\n *\n * ![](debounceTime.png)\n *\n * `debounceTime` delays notifications emitted by the source Observable, but drops\n * previous pending delayed emissions if a new notification arrives on the source\n * Observable. This operator keeps track of the most recent notification from the\n * source Observable, and emits that only when `dueTime` has passed\n * without any other notification appearing on the source Observable. If a new value\n * appears before `dueTime` silence occurs, the previous notification will be dropped\n * and will not be emitted and a new `dueTime` is scheduled.\n * If the completing event happens during `dueTime` the last cached notification\n * is emitted before the completion event is forwarded to the output observable.\n * If the error event happens during `dueTime` or after it only the error event is\n * forwarded to the output observable. The cache notification is not emitted in this case.\n *\n * This is a rate-limiting operator, because it is impossible for more than one\n * notification to be emitted in any time window of duration `dueTime`, but it is also\n * a delay-like operator since output emissions do not occur at the same time as\n * they did on the source Observable. Optionally takes a {@link SchedulerLike} for\n * managing timers.\n *\n * ## Example\n *\n * Emit the most recent click after a burst of clicks\n *\n * ```ts\n * import { fromEvent, debounceTime } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(debounceTime(1000));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link audit}\n * @see {@link auditTime}\n * @see {@link debounce}\n * @see {@link sample}\n * @see {@link sampleTime}\n * @see {@link throttle}\n * @see {@link throttleTime}\n *\n * @param dueTime The timeout duration in milliseconds (or the time unit determined\n * internally by the optional `scheduler`) for the window of time required to wait\n * for emission silence before emitting the most recent source value.\n * @param scheduler The {@link SchedulerLike} to use for managing the timers that\n * handle the timeout for each value.\n * @return A function that returns an Observable that delays the emissions of\n * the source Observable by the specified `dueTime`, and may drop some values\n * if they occur too frequently.\n */\nexport function debounceTime<T>(dueTime: number, scheduler: SchedulerLike = asyncScheduler): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let activeTask: Subscription | null = null;\n    let lastValue: T | null = null;\n    let lastTime: number | null = null;\n\n    const emit = () => {\n      if (activeTask) {\n        // We have a value! Free up memory first, then emit the value.\n        activeTask.unsubscribe();\n        activeTask = null;\n        const value = lastValue!;\n        lastValue = null;\n        subscriber.next(value);\n      }\n    };\n    function emitWhenIdle(this: SchedulerAction<unknown>) {\n      // This is called `dueTime` after the first value\n      // but we might have received new values during this window!\n\n      const targetTime = lastTime! + dueTime;\n      const now = scheduler.now();\n      if (now < targetTime) {\n        // On that case, re-schedule to the new target\n        activeTask = this.schedule(undefined, targetTime - now);\n        subscriber.add(activeTask);\n        return;\n      }\n\n      emit();\n    }\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value: T) => {\n          lastValue = value;\n          lastTime = scheduler.now();\n\n          // Only set up a task if it's not already up\n          if (!activeTask) {\n            activeTask = scheduler.schedule(emitWhenIdle, dueTime);\n            subscriber.add(activeTask);\n          }\n        },\n        () => {\n          // Source completed.\n          // Emit any pending debounced values then complete\n          emit();\n          subscriber.complete();\n        },\n        // Pass all errors through to consumer.\n        undefined,\n        () => {\n          // Finalization.\n          lastValue = activeTask = null;\n        }\n      )\n    );\n  });\n}\n", "import { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Emits a given value if the source Observable completes without emitting any\n * `next` value, otherwise mirrors the source Observable.\n *\n * <span class=\"informal\">If the source Observable turns out to be empty, then\n * this operator will emit a default value.</span>\n *\n * ![](defaultIfEmpty.png)\n *\n * `defaultIfEmpty` emits the values emitted by the source Observable or a\n * specified default value if the source Observable is empty (completes without\n * having emitted any `next` value).\n *\n * ## Example\n *\n * If no clicks happen in 5 seconds, then emit 'no clicks'\n *\n * ```ts\n * import { fromEvent, takeUntil, interval, defaultIfEmpty } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const clicksBeforeFive = clicks.pipe(takeUntil(interval(5000)));\n * const result = clicksBeforeFive.pipe(defaultIfEmpty('no clicks'));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link empty}\n * @see {@link last}\n *\n * @param defaultValue The default value used if the source\n * Observable is empty.\n * @return A function that returns an Observable that emits either the\n * specified `defaultValue` if the source Observable emits no items, or the\n * values emitted by the source Observable.\n */\nexport function defaultIfEmpty<T, R>(defaultValue: R): OperatorFunction<T, T | R> {\n  return operate((source, subscriber) => {\n    let hasValue = false;\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          hasValue = true;\n          subscriber.next(value);\n        },\n        () => {\n          if (!hasValue) {\n            subscriber.next(defaultValue!);\n          }\n          subscriber.complete();\n        }\n      )\n    );\n  });\n}\n", "import { MonoTypeOperatorFunction } from '../types';\nimport { EMPTY } from '../observable/empty';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Emits only the first `count` values emitted by the source Observable.\n *\n * <span class=\"informal\">Takes the first `count` values from the source, then\n * completes.</span>\n *\n * ![](take.png)\n *\n * `take` returns an Observable that emits only the first `count` values emitted\n * by the source Observable. If the source emits fewer than `count` values then\n * all of its values are emitted. After that, it completes, regardless if the\n * source completes.\n *\n * ## Example\n *\n * Take the first 5 seconds of an infinite 1-second interval Observable\n *\n * ```ts\n * import { interval, take } from 'rxjs';\n *\n * const intervalCount = interval(1000);\n * const takeFive = intervalCount.pipe(take(5));\n * takeFive.subscribe(x => console.log(x));\n *\n * // Logs:\n * // 0\n * // 1\n * // 2\n * // 3\n * // 4\n * ```\n *\n * @see {@link takeLast}\n * @see {@link takeUntil}\n * @see {@link takeWhile}\n * @see {@link skip}\n *\n * @param count The maximum number of `next` values to emit.\n * @return A function that returns an Observable that emits only the first\n * `count` values emitted by the source Observable, or all of the values from\n * the source if the source emits fewer than `count` values.\n */\nexport function take<T>(count: number): MonoTypeOperatorFunction<T> {\n  return count <= 0\n    ? // If we are taking no values, that's empty.\n      () => EMPTY\n    : operate((source, subscriber) => {\n        let seen = 0;\n        source.subscribe(\n          createOperatorSubscriber(subscriber, (value) => {\n            // Increment the number of values we have seen,\n            // then check it against the allowed count to see\n            // if we are still letting values through.\n            if (++seen <= count) {\n              subscriber.next(value);\n              // If we have met or passed our allowed count,\n              // we need to complete. We have to do <= here,\n              // because re-entrant code will increment `seen` twice.\n              if (count <= seen) {\n                subscriber.complete();\n              }\n            }\n          })\n        );\n      });\n}\n", "import { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { noop } from '../util/noop';\n\n/**\n * Ignores all items emitted by the source Observable and only passes calls of `complete` or `error`.\n *\n * ![](ignoreElements.png)\n *\n * The `ignoreElements` operator suppresses all items emitted by the source Observable,\n * but allows its termination notification (either `error` or `complete`) to pass through unchanged.\n *\n * If you do not care about the items being emitted by an Observable, but you do want to be notified\n * when it completes or when it terminates with an error, you can apply the `ignoreElements` operator\n * to the Observable, which will ensure that it will never call its observers\u2019 `next` handlers.\n *\n * ## Example\n *\n * Ignore all `next` emissions from the source\n *\n * ```ts\n * import { of, ignoreElements } from 'rxjs';\n *\n * of('you', 'talking', 'to', 'me')\n *   .pipe(ignoreElements())\n *   .subscribe({\n *     next: word => console.log(word),\n *     error: err => console.log('error:', err),\n *     complete: () => console.log('the end'),\n *   });\n *\n * // result:\n * // 'the end'\n * ```\n *\n * @return A function that returns an empty Observable that only calls\n * `complete` or `error`, based on which one is called by the source\n * Observable.\n */\nexport function ignoreElements(): OperatorFunction<unknown, never> {\n  return operate((source, subscriber) => {\n    source.subscribe(createOperatorSubscriber(subscriber, noop));\n  });\n}\n", "import { OperatorFunction } from '../types';\nimport { map } from './map';\n\n/** @deprecated To be removed in v9. Use {@link map} instead: `map(() => value)`. */\nexport function mapTo<R>(value: R): OperatorFunction<unknown, R>;\n/**\n * @deprecated Do not specify explicit type parameters. Signatures with type parameters\n * that cannot be inferred will be removed in v8. `mapTo` itself will be removed in v9,\n * use {@link map} instead: `map(() => value)`.\n * */\nexport function mapTo<T, R>(value: R): OperatorFunction<T, R>;\n\n/**\n * Emits the given constant value on the output Observable every time the source\n * Observable emits a value.\n *\n * <span class=\"informal\">Like {@link map}, but it maps every source value to\n * the same output value every time.</span>\n *\n * ![](mapTo.png)\n *\n * Takes a constant `value` as argument, and emits that whenever the source\n * Observable emits a value. In other words, ignores the actual source value,\n * and simply uses the emission moment to know when to emit the given `value`.\n *\n * ## Example\n *\n * Map every click to the string `'Hi'`\n *\n * ```ts\n * import { fromEvent, mapTo } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const greetings = clicks.pipe(mapTo('Hi'));\n *\n * greetings.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link map}\n *\n * @param value The value to map each source value to.\n * @return A function that returns an Observable that emits the given `value`\n * every time the source Observable emits.\n * @deprecated To be removed in v9. Use {@link map} instead: `map(() => value)`.\n */\nexport function mapTo<R>(value: R): OperatorFunction<unknown, R> {\n  return map(() => value);\n}\n", "import { Observable } from '../Observable';\nimport { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { concat } from '../observable/concat';\nimport { take } from './take';\nimport { ignoreElements } from './ignoreElements';\nimport { mapTo } from './mapTo';\nimport { mergeMap } from './mergeMap';\nimport { innerFrom } from '../observable/innerFrom';\n\n/** @deprecated The `subscriptionDelay` parameter will be removed in v8. */\nexport function delayWhen<T>(\n  delayDurationSelector: (value: T, index: number) => ObservableInput<any>,\n  subscriptionDelay: Observable<any>\n): MonoTypeOperatorFunction<T>;\nexport function delayWhen<T>(delayDurationSelector: (value: T, index: number) => ObservableInput<any>): MonoTypeOperatorFunction<T>;\n\n/**\n * Delays the emission of items from the source Observable by a given time span\n * determined by the emissions of another Observable.\n *\n * <span class=\"informal\">It's like {@link delay}, but the time span of the\n * delay duration is determined by a second Observable.</span>\n *\n * ![](delayWhen.png)\n *\n * `delayWhen` operator shifts each emitted value from the source Observable by\n * a time span determined by another Observable. When the source emits a value,\n * the `delayDurationSelector` function is called with the value emitted from\n * the source Observable as the first argument to the `delayDurationSelector`.\n * The `delayDurationSelector` function should return an {@link ObservableInput},\n * that is internally converted to an Observable that is called the \"duration\"\n * Observable.\n *\n * The source value is emitted on the output Observable only when the \"duration\"\n * Observable emits ({@link guide/glossary-and-semantics#next next}s) any value.\n * Upon that, the \"duration\" Observable gets unsubscribed.\n *\n * Before RxJS V7, the {@link guide/glossary-and-semantics#complete completion}\n * of the \"duration\" Observable would have been triggering the emission of the\n * source value to the output Observable, but with RxJS V7, this is not the case\n * anymore.\n *\n * Only next notifications (from the \"duration\" Observable) trigger values from\n * the source Observable to be passed to the output Observable. If the \"duration\"\n * Observable only emits the complete notification (without next), the value\n * emitted by the source Observable will never get to the output Observable - it\n * will be swallowed. If the \"duration\" Observable errors, the error will be\n * propagated to the output Observable.\n *\n * Optionally, `delayWhen` takes a second argument, `subscriptionDelay`, which\n * is an Observable. When `subscriptionDelay` emits its first value or\n * completes, the source Observable is subscribed to and starts behaving like\n * described in the previous paragraph. If `subscriptionDelay` is not provided,\n * `delayWhen` will subscribe to the source Observable as soon as the output\n * Observable is subscribed.\n *\n * ## Example\n *\n * Delay each click by a random amount of time, between 0 and 5 seconds\n *\n * ```ts\n * import { fromEvent, delayWhen, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const delayedClicks = clicks.pipe(\n *   delayWhen(() => interval(Math.random() * 5000))\n * );\n * delayedClicks.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link delay}\n * @see {@link throttle}\n * @see {@link throttleTime}\n * @see {@link debounce}\n * @see {@link debounceTime}\n * @see {@link sample}\n * @see {@link sampleTime}\n * @see {@link audit}\n * @see {@link auditTime}\n *\n * @param delayDurationSelector A function that returns an `ObservableInput` for\n * each `value` emitted by the source Observable, which is then used to delay the\n * emission of that `value` on the output Observable until the `ObservableInput`\n * returned from this function emits a next value. When called, beside `value`,\n * this function receives a zero-based `index` of the emission order.\n * @param subscriptionDelay An Observable that triggers the subscription to the\n * source Observable once it emits any value.\n * @return A function that returns an Observable that delays the emissions of\n * the source Observable by an amount of time specified by the Observable\n * returned by `delayDurationSelector`.\n */\nexport function delayWhen<T>(\n  delayDurationSelector: (value: T, index: number) => ObservableInput<any>,\n  subscriptionDelay?: Observable<any>\n): MonoTypeOperatorFunction<T> {\n  if (subscriptionDelay) {\n    // DEPRECATED PATH\n    return (source: Observable<T>) =>\n      concat(subscriptionDelay.pipe(take(1), ignoreElements()), source.pipe(delayWhen(delayDurationSelector)));\n  }\n\n  return mergeMap((value, index) => innerFrom(delayDurationSelector(value, index)).pipe(take(1), mapTo(value)));\n}\n", "import { asyncScheduler } from '../scheduler/async';\nimport { MonoTypeOperatorFunction, SchedulerLike } from '../types';\nimport { delayWhen } from './delayWhen';\nimport { timer } from '../observable/timer';\n\n/**\n * Delays the emission of items from the source Observable by a given timeout or\n * until a given Date.\n *\n * <span class=\"informal\">Time shifts each item by some specified amount of\n * milliseconds.</span>\n *\n * ![](delay.svg)\n *\n * If the delay argument is a Number, this operator time shifts the source\n * Observable by that amount of time expressed in milliseconds. The relative\n * time intervals between the values are preserved.\n *\n * If the delay argument is a Date, this operator time shifts the start of the\n * Observable execution until the given date occurs.\n *\n * ## Examples\n *\n * Delay each click by one second\n *\n * ```ts\n * import { fromEvent, delay } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const delayedClicks = clicks.pipe(delay(1000)); // each click emitted after 1 second\n * delayedClicks.subscribe(x => console.log(x));\n * ```\n *\n * Delay all clicks until a future date happens\n *\n * ```ts\n * import { fromEvent, delay } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const date = new Date('March 15, 2050 12:00:00'); // in the future\n * const delayedClicks = clicks.pipe(delay(date)); // click emitted only after that date\n * delayedClicks.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link delayWhen}\n * @see {@link throttle}\n * @see {@link throttleTime}\n * @see {@link debounce}\n * @see {@link debounceTime}\n * @see {@link sample}\n * @see {@link sampleTime}\n * @see {@link audit}\n * @see {@link auditTime}\n *\n * @param due The delay duration in milliseconds (a `number`) or a `Date` until\n * which the emission of the source items is delayed.\n * @param scheduler The {@link SchedulerLike} to use for managing the timers\n * that handle the time-shift for each item.\n * @return A function that returns an Observable that delays the emissions of\n * the source Observable by the specified timeout or Date.\n */\nexport function delay<T>(due: number | Date, scheduler: SchedulerLike = asyncScheduler): MonoTypeOperatorFunction<T> {\n  const duration = timer(due, scheduler);\n  return delayWhen(() => duration);\n}\n", "import { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { noop } from '../util/noop';\nimport { innerFrom } from '../observable/innerFrom';\n\n/**\n * Returns an Observable that emits all items emitted by the source Observable that are distinct by comparison from previous items.\n *\n * If a `keySelector` function is provided, then it will project each value from the source observable into a new value that it will\n * check for equality with previously projected values. If the `keySelector` function is not provided, it will use each value from the\n * source observable directly with an equality check against previous values.\n *\n * In JavaScript runtimes that support `Set`, this operator will use a `Set` to improve performance of the distinct value checking.\n *\n * In other runtimes, this operator will use a minimal implementation of `Set` that relies on an `Array` and `indexOf` under the\n * hood, so performance will degrade as more values are checked for distinction. Even in newer browsers, a long-running `distinct`\n * use might result in memory leaks. To help alleviate this in some scenarios, an optional `flushes` parameter is also provided so\n * that the internal `Set` can be \"flushed\", basically clearing it of values.\n *\n * ## Examples\n *\n * A simple example with numbers\n *\n * ```ts\n * import { of, distinct } from 'rxjs';\n *\n * of(1, 1, 2, 2, 2, 1, 2, 3, 4, 3, 2, 1)\n *   .pipe(distinct())\n *   .subscribe(x => console.log(x));\n *\n * // Outputs\n * // 1\n * // 2\n * // 3\n * // 4\n * ```\n *\n * An example using the `keySelector` function\n *\n * ```ts\n * import { of, distinct } from 'rxjs';\n *\n * of(\n *   { age: 4, name: 'Foo'},\n *   { age: 7, name: 'Bar'},\n *   { age: 5, name: 'Foo'}\n * )\n * .pipe(distinct(({ name }) => name))\n * .subscribe(x => console.log(x));\n *\n * // Outputs\n * // { age: 4, name: 'Foo' }\n * // { age: 7, name: 'Bar' }\n * ```\n * @see {@link distinctUntilChanged}\n * @see {@link distinctUntilKeyChanged}\n *\n * @param keySelector Optional `function` to select which value you want to check as distinct.\n * @param flushes Optional `ObservableInput` for flushing the internal HashSet of the operator.\n * @return A function that returns an Observable that emits items from the\n * source Observable with distinct values.\n */\nexport function distinct<T, K>(keySelector?: (value: T) => K, flushes?: ObservableInput<any>): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    const distinctKeys = new Set();\n    source.subscribe(\n      createOperatorSubscriber(subscriber, (value) => {\n        const key = keySelector ? keySelector(value) : value;\n        if (!distinctKeys.has(key)) {\n          distinctKeys.add(key);\n          subscriber.next(value);\n        }\n      })\n    );\n\n    flushes && innerFrom(flushes).subscribe(createOperatorSubscriber(subscriber, () => distinctKeys.clear(), noop));\n  });\n}\n", "import { MonoTypeOperatorFunction } from '../types';\nimport { identity } from '../util/identity';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\nexport function distinctUntilChanged<T>(comparator?: (previous: T, current: T) => boolean): MonoTypeOperatorFunction<T>;\nexport function distinctUntilChanged<T, K>(\n  comparator: (previous: K, current: K) => boolean,\n  keySelector: (value: T) => K\n): MonoTypeOperatorFunction<T>;\n\n/**\n * Returns a result {@link Observable} that emits all values pushed by the source observable if they\n * are distinct in comparison to the last value the result observable emitted.\n *\n * When provided without parameters or with the first parameter (`{@link distinctUntilChanged#comparator comparator}`),\n * it behaves like this:\n *\n * 1. It will always emit the first value from the source.\n * 2. For all subsequent values pushed by the source, they will be compared to the previously emitted values\n *    using the provided `comparator` or an `===` equality check.\n * 3. If the value pushed by the source is determined to be unequal by this check, that value is emitted and\n *    becomes the new \"previously emitted value\" internally.\n *\n * When the second parameter (`{@link distinctUntilChanged#keySelector keySelector}`) is provided, the behavior\n * changes:\n *\n * 1. It will always emit the first value from the source.\n * 2. The `keySelector` will be run against all values, including the first value.\n * 3. For all values after the first, the selected key will be compared against the key selected from\n *    the previously emitted value using the `comparator`.\n * 4. If the keys are determined to be unequal by this check, the value (not the key), is emitted\n *    and the selected key from that value is saved for future comparisons against other keys.\n *\n * ## Examples\n *\n * A very basic example with no `{@link distinctUntilChanged#comparator comparator}`. Note that `1` is emitted more than once,\n * because it's distinct in comparison to the _previously emitted_ value,\n * not in comparison to _all other emitted values_.\n *\n * ```ts\n * import { of, distinctUntilChanged } from 'rxjs';\n *\n * of(1, 1, 1, 2, 2, 2, 1, 1, 3, 3)\n *   .pipe(distinctUntilChanged())\n *   .subscribe(console.log);\n * // Logs: 1, 2, 1, 3\n * ```\n *\n * With a `{@link distinctUntilChanged#comparator comparator}`, you can do custom comparisons. Let's say\n * you only want to emit a value when all of its components have\n * changed:\n *\n * ```ts\n * import { of, distinctUntilChanged } from 'rxjs';\n *\n * const totallyDifferentBuilds$ = of(\n *   { engineVersion: '1.1.0', transmissionVersion: '1.2.0' },\n *   { engineVersion: '1.1.0', transmissionVersion: '1.4.0' },\n *   { engineVersion: '1.3.0', transmissionVersion: '1.4.0' },\n *   { engineVersion: '1.3.0', transmissionVersion: '1.5.0' },\n *   { engineVersion: '2.0.0', transmissionVersion: '1.5.0' }\n * ).pipe(\n *   distinctUntilChanged((prev, curr) => {\n *     return (\n *       prev.engineVersion === curr.engineVersion ||\n *       prev.transmissionVersion === curr.transmissionVersion\n *     );\n *   })\n * );\n *\n * totallyDifferentBuilds$.subscribe(console.log);\n *\n * // Logs:\n * // { engineVersion: '1.1.0', transmissionVersion: '1.2.0' }\n * // { engineVersion: '1.3.0', transmissionVersion: '1.4.0' }\n * // { engineVersion: '2.0.0', transmissionVersion: '1.5.0' }\n * ```\n *\n * You can also provide a custom `{@link distinctUntilChanged#comparator comparator}` to check that emitted\n * changes are only in one direction. Let's say you only want to get\n * the next record temperature:\n *\n * ```ts\n * import { of, distinctUntilChanged } from 'rxjs';\n *\n * const temps$ = of(30, 31, 20, 34, 33, 29, 35, 20);\n *\n * const recordHighs$ = temps$.pipe(\n *   distinctUntilChanged((prevHigh, temp) => {\n *     // If the current temp is less than\n *     // or the same as the previous record,\n *     // the record hasn't changed.\n *     return temp <= prevHigh;\n *   })\n * );\n *\n * recordHighs$.subscribe(console.log);\n * // Logs: 30, 31, 34, 35\n * ```\n *\n * Selecting update events only when the `updatedBy` field shows\n * the account changed hands.\n *\n * ```ts\n * import { of, distinctUntilChanged } from 'rxjs';\n *\n * // A stream of updates to a given account\n * const accountUpdates$ = of(\n *   { updatedBy: 'blesh', data: [] },\n *   { updatedBy: 'blesh', data: [] },\n *   { updatedBy: 'ncjamieson', data: [] },\n *   { updatedBy: 'ncjamieson', data: [] },\n *   { updatedBy: 'blesh', data: [] }\n * );\n *\n * // We only want the events where it changed hands\n * const changedHands$ = accountUpdates$.pipe(\n *   distinctUntilChanged(undefined, update => update.updatedBy)\n * );\n *\n * changedHands$.subscribe(console.log);\n * // Logs:\n * // { updatedBy: 'blesh', data: Array[0] }\n * // { updatedBy: 'ncjamieson', data: Array[0] }\n * // { updatedBy: 'blesh', data: Array[0] }\n * ```\n *\n * @see {@link distinct}\n * @see {@link distinctUntilKeyChanged}\n *\n * @param comparator A function used to compare the previous and current keys for\n * equality. Defaults to a `===` check.\n * @param keySelector Used to select a key value to be passed to the `comparator`.\n *\n * @return A function that returns an Observable that emits items from the\n * source Observable with distinct values.\n */\nexport function distinctUntilChanged<T, K>(\n  comparator?: (previous: K, current: K) => boolean,\n  keySelector: (value: T) => K = identity as (value: T) => K\n): MonoTypeOperatorFunction<T> {\n  // We've been allowing `null` do be passed as the `compare`, so we can't do\n  // a default value for the parameter, because that will only work\n  // for `undefined`.\n  comparator = comparator ?? defaultCompare;\n\n  return operate((source, subscriber) => {\n    // The previous key, used to compare against keys selected\n    // from new arrivals to determine \"distinctiveness\".\n    let previousKey: K;\n    // Whether or not this is the first value we've gotten.\n    let first = true;\n\n    source.subscribe(\n      createOperatorSubscriber(subscriber, (value) => {\n        // We always call the key selector.\n        const currentKey = keySelector(value);\n\n        // If it's the first value, we always emit it.\n        // Otherwise, we compare this key to the previous key, and\n        // if the comparer returns false, we emit.\n        if (first || !comparator!(previousKey, currentKey)) {\n          // Update our state *before* we emit the value\n          // as emission can be the source of re-entrant code\n          // in functional libraries like this. We only really\n          // need to do this if it's the first value, or if the\n          // key we're tracking in previous needs to change.\n          first = false;\n          previousKey = currentKey;\n\n          // Emit the value!\n          subscriber.next(value);\n        }\n      })\n    );\n  });\n}\n\nfunction defaultCompare(a: any, b: any) {\n  return a === b;\n}\n", "import { distinctUntilChanged } from './distinctUntilChanged';\nimport { MonoTypeOperatorFunction } from '../types';\n\nexport function distinctUntilKeyChanged<T>(key: keyof T): MonoTypeOperatorFunction<T>;\nexport function distinctUntilKeyChanged<T, K extends keyof T>(key: K, compare: (x: T[K], y: T[K]) => boolean): MonoTypeOperatorFunction<T>;\n\n/**\n * Returns an Observable that emits all items emitted by the source Observable that\n * are distinct by comparison from the previous item, using a property accessed by\n * using the key provided to check if the two items are distinct.\n *\n * If a comparator function is provided, then it will be called for each item to\n * test for whether that value should be emitted or not.\n *\n * If a comparator function is not provided, an equality check is used by default.\n *\n * ## Examples\n *\n * An example comparing the name of persons\n *\n * ```ts\n * import { of, distinctUntilKeyChanged } from 'rxjs';\n *\n * of(\n *   { age: 4, name: 'Foo' },\n *   { age: 7, name: 'Bar' },\n *   { age: 5, name: 'Foo' },\n *   { age: 6, name: 'Foo' }\n * ).pipe(\n *   distinctUntilKeyChanged('name')\n * )\n * .subscribe(x => console.log(x));\n *\n * // displays:\n * // { age: 4, name: 'Foo' }\n * // { age: 7, name: 'Bar' }\n * // { age: 5, name: 'Foo' }\n * ```\n *\n * An example comparing the first letters of the name\n *\n * ```ts\n * import { of, distinctUntilKeyChanged } from 'rxjs';\n *\n * of(\n *   { age: 4, name: 'Foo1' },\n *   { age: 7, name: 'Bar' },\n *   { age: 5, name: 'Foo2' },\n *   { age: 6, name: 'Foo3' }\n * ).pipe(\n *   distinctUntilKeyChanged('name', (x, y) => x.substring(0, 3) === y.substring(0, 3))\n * )\n * .subscribe(x => console.log(x));\n *\n * // displays:\n * // { age: 4, name: 'Foo1' }\n * // { age: 7, name: 'Bar' }\n * // { age: 5, name: 'Foo2' }\n * ```\n *\n * @see {@link distinct}\n * @see {@link distinctUntilChanged}\n *\n * @param key String key for object property lookup on each item.\n * @param compare Optional comparison function called to test if an item is distinct\n * from the previous item in the source.\n * @return A function that returns an Observable that emits items from the source\n * Observable with distinct values based on the key specified.\n */\nexport function distinctUntilKeyChanged<T, K extends keyof T>(\n  key: K,\n  compare?: (x: T[K], y: T[K]) => boolean\n): MonoTypeOperatorFunction<T> {\n  return distinctUntilChanged((x: T, y: T) => (compare ? compare(x[key], y[key]) : x[key] === y[key]));\n}\n", "import { EmptyError } from '../util/EmptyError';\nimport { MonoTypeOperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * If the source observable completes without emitting a value, it will emit\n * an error. The error will be created at that time by the optional\n * `errorFactory` argument, otherwise, the error will be {@link EmptyError}.\n *\n * ![](throwIfEmpty.png)\n *\n * ## Example\n *\n * Throw an error if the document wasn't clicked within 1 second\n *\n * ```ts\n * import { fromEvent, takeUntil, timer, throwIfEmpty } from 'rxjs';\n *\n * const click$ = fromEvent(document, 'click');\n *\n * click$.pipe(\n *   takeUntil(timer(1000)),\n *   throwIfEmpty(() => new Error('The document was not clicked within 1 second'))\n * )\n * .subscribe({\n *   next() {\n *    console.log('The document was clicked');\n *   },\n *   error(err) {\n *     console.error(err.message);\n *   }\n * });\n * ```\n *\n * @param errorFactory A factory function called to produce the\n * error to be thrown when the source observable completes without emitting a\n * value.\n * @return A function that returns an Observable that throws an error if the\n * source Observable completed without emitting.\n */\nexport function throwIfEmpty<T>(errorFactory: () => any = defaultErrorFactory): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let hasValue = false;\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          hasValue = true;\n          subscriber.next(value);\n        },\n        () => (hasValue ? subscriber.complete() : subscriber.error(errorFactory()))\n      )\n    );\n  });\n}\n\nfunction defaultErrorFactory() {\n  return new EmptyError();\n}\n", "/** prettier */\nimport { Observable } from '../Observable';\nimport { concat } from '../observable/concat';\nimport { of } from '../observable/of';\nimport { MonoTypeOperatorFunction, SchedulerLike, OperatorFunction, ValueFromArray } from '../types';\n\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `concatAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function endWith<T>(scheduler: SchedulerLike): MonoTypeOperatorFunction<T>;\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `concatAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function endWith<T, A extends unknown[] = T[]>(\n  ...valuesAndScheduler: [...A, SchedulerLike]\n): OperatorFunction<T, T | ValueFromArray<A>>;\n\nexport function endWith<T, A extends unknown[] = T[]>(...values: A): OperatorFunction<T, T | ValueFromArray<A>>;\n\n/**\n * Returns an observable that will emit all values from the source, then synchronously emit\n * the provided value(s) immediately after the source completes.\n *\n * NOTE: Passing a last argument of a Scheduler is _deprecated_, and may result in incorrect\n * types in TypeScript.\n *\n * This is useful for knowing when an observable ends. Particularly when paired with an\n * operator like {@link takeUntil}\n *\n * ![](endWith.png)\n *\n * ## Example\n *\n * Emit values to know when an interval starts and stops. The interval will\n * stop when a user clicks anywhere on the document.\n *\n * ```ts\n * import { interval, map, fromEvent, startWith, takeUntil, endWith } from 'rxjs';\n *\n * const ticker$ = interval(5000).pipe(\n *   map(() => 'tick')\n * );\n *\n * const documentClicks$ = fromEvent(document, 'click');\n *\n * ticker$.pipe(\n *   startWith('interval started'),\n *   takeUntil(documentClicks$),\n *   endWith('interval ended by click')\n * )\n * .subscribe(x => console.log(x));\n *\n * // Result (assuming a user clicks after 15 seconds)\n * // 'interval started'\n * // 'tick'\n * // 'tick'\n * // 'tick'\n * // 'interval ended by click'\n * ```\n *\n * @see {@link startWith}\n * @see {@link concat}\n * @see {@link takeUntil}\n *\n * @param values Items you want the modified Observable to emit last.\n * @return A function that returns an Observable that emits all values from the\n * source, then synchronously emits the provided value(s) immediately after the\n * source completes.\n */\nexport function endWith<T>(...values: Array<T | SchedulerLike>): MonoTypeOperatorFunction<T> {\n  return (source: Observable<T>) => concat(source, of(...values)) as Observable<T>;\n}\n", "import { Observable } from '../Observable';\nimport { Subscriber } from '../Subscriber';\nimport { ObservableInput, OperatorFunction, ObservedValueOf } from '../types';\nimport { map } from './map';\nimport { innerFrom } from '../observable/innerFrom';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/* tslint:disable:max-line-length */\nexport function exhaustMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function exhaustMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector: undefined\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function exhaustMap<T, I, R>(\n  project: (value: T, index: number) => ObservableInput<I>,\n  resultSelector: (outerValue: T, innerValue: I, outerIndex: number, innerIndex: number) => R\n): OperatorFunction<T, R>;\n/* tslint:enable:max-line-length */\n\n/**\n * Projects each source value to an Observable which is merged in the output\n * Observable only if the previous projected Observable has completed.\n *\n * <span class=\"informal\">Maps each value to an Observable, then flattens all of\n * these inner Observables using {@link exhaustAll}.</span>\n *\n * ![](exhaustMap.png)\n *\n * Returns an Observable that emits items based on applying a function that you\n * supply to each item emitted by the source Observable, where that function\n * returns an (so-called \"inner\") Observable. When it projects a source value to\n * an Observable, the output Observable begins emitting the items emitted by\n * that projected Observable. However, `exhaustMap` ignores every new projected\n * Observable if the previous projected Observable has not yet completed. Once\n * that one completes, it will accept and flatten the next projected Observable\n * and repeat this process.\n *\n * ## Example\n *\n * Run a finite timer for each click, only if there is no currently active timer\n *\n * ```ts\n * import { fromEvent, exhaustMap, interval, take } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(\n *   exhaustMap(() => interval(1000).pipe(take(5)))\n * );\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link concatMap}\n * @see {@link exhaust}\n * @see {@link mergeMap}\n * @see {@link switchMap}\n *\n * @param project A function that, when applied to an item emitted by the source\n * Observable, returns an Observable.\n * @return A function that returns an Observable containing projected\n * Observables of each item of the source, ignoring projected Observables that\n * start before their preceding Observable has completed.\n */\nexport function exhaustMap<T, R, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector?: (outerValue: T, innerValue: ObservedValueOf<O>, outerIndex: number, innerIndex: number) => R\n): OperatorFunction<T, ObservedValueOf<O> | R> {\n  if (resultSelector) {\n    // DEPRECATED PATH\n    return (source: Observable<T>) =>\n      source.pipe(exhaustMap((a, i) => innerFrom(project(a, i)).pipe(map((b: any, ii: any) => resultSelector(a, b, i, ii)))));\n  }\n  return operate((source, subscriber) => {\n    let index = 0;\n    let innerSub: Subscriber<T> | null = null;\n    let isComplete = false;\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (outerValue) => {\n          if (!innerSub) {\n            innerSub = createOperatorSubscriber(subscriber, undefined, () => {\n              innerSub = null;\n              isComplete && subscriber.complete();\n            });\n            innerFrom(project(outerValue, index++)).subscribe(innerSub);\n          }\n        },\n        () => {\n          isComplete = true;\n          !innerSub && subscriber.complete();\n        }\n      )\n    );\n  });\n}\n", "import { MonoTypeOperatorFunction } from '../types';\nimport { operate } from '../util/lift';\n\n/**\n * Returns an Observable that mirrors the source Observable, but will call a specified function when\n * the source terminates on complete or error.\n * The specified function will also be called when the subscriber explicitly unsubscribes.\n *\n * ## Examples\n *\n * Execute callback function when the observable completes\n *\n * ```ts\n * import { interval, take, finalize } from 'rxjs';\n *\n * // emit value in sequence every 1 second\n * const source = interval(1000);\n * const example = source.pipe(\n *   take(5), //take only the first 5 values\n *   finalize(() => console.log('Sequence complete')) // Execute when the observable completes\n * );\n * const subscribe = example.subscribe(val => console.log(val));\n *\n * // results:\n * // 0\n * // 1\n * // 2\n * // 3\n * // 4\n * // 'Sequence complete'\n * ```\n *\n * Execute callback function when the subscriber explicitly unsubscribes\n *\n * ```ts\n * import { interval, finalize, tap, noop, timer } from 'rxjs';\n *\n * const source = interval(100).pipe(\n *   finalize(() => console.log('[finalize] Called')),\n *   tap({\n *     next: () => console.log('[next] Called'),\n *     error: () => console.log('[error] Not called'),\n *     complete: () => console.log('[tap complete] Not called')\n *   })\n * );\n *\n * const sub = source.subscribe({\n *   next: x => console.log(x),\n *   error: noop,\n *   complete: () => console.log('[complete] Not called')\n * });\n *\n * timer(150).subscribe(() => sub.unsubscribe());\n *\n * // results:\n * // '[next] Called'\n * // 0\n * // '[finalize] Called'\n * ```\n *\n * @param callback Function to be called when source terminates.\n * @return A function that returns an Observable that mirrors the source, but\n * will call the specified function on termination.\n */\nexport function finalize<T>(callback: () => void): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    // TODO: This try/finally was only added for `useDeprecatedSynchronousErrorHandling`.\n    // REMOVE THIS WHEN THAT HOT GARBAGE IS REMOVED IN V8.\n    try {\n      source.subscribe(subscriber);\n    } finally {\n      subscriber.add(callback);\n    }\n  });\n}\n", "import { Observable } from '../Observable';\nimport { EmptyError } from '../util/EmptyError';\nimport { OperatorFunction, TruthyTypesOf } from '../types';\nimport { filter } from './filter';\nimport { take } from './take';\nimport { defaultIfEmpty } from './defaultIfEmpty';\nimport { throwIfEmpty } from './throwIfEmpty';\nimport { identity } from '../util/identity';\n\nexport function first<T, D = T>(predicate?: null, defaultValue?: D): OperatorFunction<T, T | D>;\nexport function first<T>(predicate: BooleanConstructor): OperatorFunction<T, TruthyTypesOf<T>>;\nexport function first<T, D>(predicate: BooleanConstructor, defaultValue: D): OperatorFunction<T, TruthyTypesOf<T> | D>;\nexport function first<T, S extends T>(\n  predicate: (value: T, index: number, source: Observable<T>) => value is S,\n  defaultValue?: S\n): OperatorFunction<T, S>;\nexport function first<T, S extends T, D>(\n  predicate: (value: T, index: number, source: Observable<T>) => value is S,\n  defaultValue: D\n): OperatorFunction<T, S | D>;\nexport function first<T, D = T>(\n  predicate: (value: T, index: number, source: Observable<T>) => boolean,\n  defaultValue?: D\n): OperatorFunction<T, T | D>;\n\n/**\n * Emits only the first value (or the first value that meets some condition)\n * emitted by the source Observable.\n *\n * <span class=\"informal\">Emits only the first value. Or emits only the first\n * value that passes some test.</span>\n *\n * ![](first.png)\n *\n * If called with no arguments, `first` emits the first value of the source\n * Observable, then completes. If called with a `predicate` function, `first`\n * emits the first value of the source that matches the specified condition. Emits an error\n * notification if `defaultValue` was not provided and a matching element is not found.\n *\n * ## Examples\n *\n * Emit only the first click that happens on the DOM\n *\n * ```ts\n * import { fromEvent, first } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(first());\n * result.subscribe(x => console.log(x));\n * ```\n *\n * Emits the first click that happens on a DIV\n *\n * ```ts\n * import { fromEvent, first } from 'rxjs';\n *\n * const div = document.createElement('div');\n * div.style.cssText = 'width: 200px; height: 200px; background: #09c;';\n * document.body.appendChild(div);\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(first(ev => (<HTMLElement>ev.target).tagName === 'DIV'));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link filter}\n * @see {@link find}\n * @see {@link take}\n * @see {@link last}\n *\n * @throws {EmptyError} Delivers an `EmptyError` to the Observer's `error`\n * callback if the Observable completes before any `next` notification was sent.\n * This is how `first()` is different from `take(1)` which completes instead.\n *\n * @param predicate An optional function called with each item to test for condition\n * matching.\n * @param defaultValue The default value emitted in case no valid value was found on\n * the source.\n * @return A function that returns an Observable that emits the first item that\n * matches the condition.\n */\nexport function first<T, D>(\n  predicate?: ((value: T, index: number, source: Observable<T>) => boolean) | null,\n  defaultValue?: D\n): OperatorFunction<T, T | D> {\n  const hasDefaultValue = arguments.length >= 2;\n  return (source: Observable<T>) =>\n    source.pipe(\n      predicate ? filter((v, i) => predicate(v, i, source)) : identity,\n      take(1),\n      hasDefaultValue ? defaultIfEmpty(defaultValue!) : throwIfEmpty(() => new EmptyError())\n    );\n}\n", "import { EMPTY } from '../observable/empty';\nimport { MonoTypeOperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * Waits for the source to complete, then emits the last N values from the source,\n * as specified by the `count` argument.\n *\n * ![](takeLast.png)\n *\n * `takeLast` results in an observable that will hold values up to `count` values in memory,\n * until the source completes. It then pushes all values in memory to the consumer, in the\n * order they were received from the source, then notifies the consumer that it is\n * complete.\n *\n * If for some reason the source completes before the `count` supplied to `takeLast` is reached,\n * all values received until that point are emitted, and then completion is notified.\n *\n * **Warning**: Using `takeLast` with an observable that never completes will result\n * in an observable that never emits a value.\n *\n * ## Example\n *\n * Take the last 3 values of an Observable with many values\n *\n * ```ts\n * import { range, takeLast } from 'rxjs';\n *\n * const many = range(1, 100);\n * const lastThree = many.pipe(takeLast(3));\n * lastThree.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link take}\n * @see {@link takeUntil}\n * @see {@link takeWhile}\n * @see {@link skip}\n *\n * @param count The maximum number of values to emit from the end of\n * the sequence of values emitted by the source Observable.\n * @return A function that returns an Observable that emits at most the last\n * `count` values emitted by the source Observable.\n */\nexport function takeLast<T>(count: number): MonoTypeOperatorFunction<T> {\n  return count <= 0\n    ? () => EMPTY\n    : operate((source, subscriber) => {\n        // This buffer will hold the values we are going to emit\n        // when the source completes. Since we only want to take the\n        // last N values, we can't emit until we're sure we're not getting\n        // any more values.\n        let buffer: T[] = [];\n        source.subscribe(\n          createOperatorSubscriber(\n            subscriber,\n            (value) => {\n              // Add the most recent value onto the end of our buffer.\n              buffer.push(value);\n              // If our buffer is now larger than the number of values we\n              // want to take, we remove the oldest value from the buffer.\n              count < buffer.length && buffer.shift();\n            },\n            () => {\n              // The source completed, we now know what are last values\n              // are, emit them in the order they were received.\n              for (const value of buffer) {\n                subscriber.next(value);\n              }\n              subscriber.complete();\n            },\n            // Errors are passed through to the consumer\n            undefined,\n            () => {\n              // During finalization release the values in our buffer.\n              buffer = null!;\n            }\n          )\n        );\n      });\n}\n", "import { ObservableInput, ObservableInputTuple, OperatorFunction, SchedulerLike } from '../types';\nimport { operate } from '../util/lift';\nimport { mergeAll } from './mergeAll';\nimport { popNumber, popScheduler } from '../util/args';\nimport { from } from '../observable/from';\n\n/** @deprecated Replaced with {@link mergeWith}. Will be removed in v8. */\nexport function merge<T, A extends readonly unknown[]>(...sources: [...ObservableInputTuple<A>]): OperatorFunction<T, T | A[number]>;\n/** @deprecated Replaced with {@link mergeWith}. Will be removed in v8. */\nexport function merge<T, A extends readonly unknown[]>(\n  ...sourcesAndConcurrency: [...ObservableInputTuple<A>, number]\n): OperatorFunction<T, T | A[number]>;\n/** @deprecated Replaced with {@link mergeWith}. Will be removed in v8. */\nexport function merge<T, A extends readonly unknown[]>(\n  ...sourcesAndScheduler: [...ObservableInputTuple<A>, SchedulerLike]\n): OperatorFunction<T, T | A[number]>;\n/** @deprecated Replaced with {@link mergeWith}. Will be removed in v8. */\nexport function merge<T, A extends readonly unknown[]>(\n  ...sourcesAndConcurrencyAndScheduler: [...ObservableInputTuple<A>, number, SchedulerLike]\n): OperatorFunction<T, T | A[number]>;\n\nexport function merge<T>(...args: unknown[]): OperatorFunction<T, unknown> {\n  const scheduler = popScheduler(args);\n  const concurrent = popNumber(args, Infinity);\n\n  return operate((source, subscriber) => {\n    mergeAll(concurrent)(from([source, ...(args as ObservableInput<T>[])], scheduler)).subscribe(subscriber);\n  });\n}\n", "import { ObservableInputTuple, OperatorFunction } from '../types';\nimport { merge } from './merge';\n\n/**\n * Merge the values from all observables to a single observable result.\n *\n * Creates an observable, that when subscribed to, subscribes to the source\n * observable, and all other sources provided as arguments. All values from\n * every source are emitted from the resulting subscription.\n *\n * When all sources complete, the resulting observable will complete.\n *\n * When any source errors, the resulting observable will error.\n *\n * ## Example\n *\n * Joining all outputs from multiple user input event streams\n *\n * ```ts\n * import { fromEvent, map, mergeWith } from 'rxjs';\n *\n * const clicks$ = fromEvent(document, 'click').pipe(map(() => 'click'));\n * const mousemoves$ = fromEvent(document, 'mousemove').pipe(map(() => 'mousemove'));\n * const dblclicks$ = fromEvent(document, 'dblclick').pipe(map(() => 'dblclick'));\n *\n * mousemoves$\n *   .pipe(mergeWith(clicks$, dblclicks$))\n *   .subscribe(x => console.log(x));\n *\n * // result (assuming user interactions)\n * // 'mousemove'\n * // 'mousemove'\n * // 'mousemove'\n * // 'click'\n * // 'click'\n * // 'dblclick'\n * ```\n *\n * @see {@link merge}\n *\n * @param otherSources the sources to combine the current source with.\n * @return A function that returns an Observable that merges the values from\n * all given Observables.\n */\nexport function mergeWith<T, A extends readonly unknown[]>(\n  ...otherSources: [...ObservableInputTuple<A>]\n): OperatorFunction<T, T | A[number]> {\n  return merge(...otherSources);\n}\n", "import { Subscription } from '../Subscription';\nimport { EMPTY } from '../observable/empty';\nimport { operate } from '../util/lift';\nimport { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\nimport { timer } from '../observable/timer';\n\nexport interface RepeatConfig {\n  /**\n   * The number of times to repeat the source. Defaults to `Infinity`.\n   */\n  count?: number;\n\n  /**\n   * If a `number`, will delay the repeat of the source by that number of milliseconds.\n   * If a function, it will provide the number of times the source has been subscribed to,\n   * and the return value should be a valid observable input that will notify when the source\n   * should be repeated. If the notifier observable is empty, the result will complete.\n   */\n  delay?: number | ((count: number) => ObservableInput<any>);\n}\n\n/**\n * Returns an Observable that will resubscribe to the source stream when the source stream completes.\n *\n * <span class=\"informal\">Repeats all values emitted on the source. It's like {@link retry}, but for non error cases.</span>\n *\n * ![](repeat.png)\n *\n * Repeat will output values from a source until the source completes, then it will resubscribe to the\n * source a specified number of times, with a specified delay. Repeat can be particularly useful in\n * combination with closing operators like {@link take}, {@link takeUntil}, {@link first}, or {@link takeWhile},\n * as it can be used to restart a source again from scratch.\n *\n * Repeat is very similar to {@link retry}, where {@link retry} will resubscribe to the source in the error case, but\n * `repeat` will resubscribe if the source completes.\n *\n * Note that `repeat` will _not_ catch errors. Use {@link retry} for that.\n *\n * - `repeat(0)` returns an empty observable\n * - `repeat()` will repeat forever\n * - `repeat({ delay: 200 })` will repeat forever, with a delay of 200ms between repetitions.\n * - `repeat({ count: 2, delay: 400 })` will repeat twice, with a delay of 400ms between repetitions.\n * - `repeat({ delay: (count) => timer(count * 1000) })` will repeat forever, but will have a delay that grows by one second for each repetition.\n *\n * ## Example\n *\n * Repeat a message stream\n *\n * ```ts\n * import { of, repeat } from 'rxjs';\n *\n * const source = of('Repeat message');\n * const result = source.pipe(repeat(3));\n *\n * result.subscribe(x => console.log(x));\n *\n * // Results\n * // 'Repeat message'\n * // 'Repeat message'\n * // 'Repeat message'\n * ```\n *\n * Repeat 3 values, 2 times\n *\n * ```ts\n * import { interval, take, repeat } from 'rxjs';\n *\n * const source = interval(1000);\n * const result = source.pipe(take(3), repeat(2));\n *\n * result.subscribe(x => console.log(x));\n *\n * // Results every second\n * // 0\n * // 1\n * // 2\n * // 0\n * // 1\n * // 2\n * ```\n *\n * Defining two complex repeats with delays on the same source.\n * Note that the second repeat cannot be called until the first\n * repeat as exhausted it's count.\n *\n * ```ts\n * import { defer, of, repeat } from 'rxjs';\n *\n * const source = defer(() => {\n *    return of(`Hello, it is ${new Date()}`)\n * });\n *\n * source.pipe(\n *    // Repeat 3 times with a delay of 1 second between repetitions\n *    repeat({\n *      count: 3,\n *      delay: 1000,\n *    }),\n *\n *    // *Then* repeat forever, but with an exponential step-back\n *    // maxing out at 1 minute.\n *    repeat({\n *      delay: (count) => timer(Math.min(60000, 2 ^ count * 1000))\n *    })\n * )\n * ```\n *\n * @see {@link repeatWhen}\n * @see {@link retry}\n *\n * @param countOrConfig Either the number of times the source Observable items are repeated\n * (a count of 0 will yield an empty Observable) or a {@link RepeatConfig} object.\n */\nexport function repeat<T>(countOrConfig?: number | RepeatConfig): MonoTypeOperatorFunction<T> {\n  let count = Infinity;\n  let delay: RepeatConfig['delay'];\n\n  if (countOrConfig != null) {\n    if (typeof countOrConfig === 'object') {\n      ({ count = Infinity, delay } = countOrConfig);\n    } else {\n      count = countOrConfig;\n    }\n  }\n\n  return count <= 0\n    ? () => EMPTY\n    : operate((source, subscriber) => {\n        let soFar = 0;\n        let sourceSub: Subscription | null;\n\n        const resubscribe = () => {\n          sourceSub?.unsubscribe();\n          sourceSub = null;\n          if (delay != null) {\n            const notifier = typeof delay === 'number' ? timer(delay) : innerFrom(delay(soFar));\n            const notifierSubscriber = createOperatorSubscriber(subscriber, () => {\n              notifierSubscriber.unsubscribe();\n              subscribeToSource();\n            });\n            notifier.subscribe(notifierSubscriber);\n          } else {\n            subscribeToSource();\n          }\n        };\n\n        const subscribeToSource = () => {\n          let syncUnsub = false;\n          sourceSub = source.subscribe(\n            createOperatorSubscriber(subscriber, undefined, () => {\n              if (++soFar < count) {\n                if (sourceSub) {\n                  resubscribe();\n                } else {\n                  syncUnsub = true;\n                }\n              } else {\n                subscriber.complete();\n              }\n            })\n          );\n\n          if (syncUnsub) {\n            resubscribe();\n          }\n        };\n\n        subscribeToSource();\n      });\n}\n", "import { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\nimport { scanInternals } from './scanInternals';\n\nexport function scan<V, A = V>(accumulator: (acc: A | V, value: V, index: number) => A): OperatorFunction<V, V | A>;\nexport function scan<V, A>(accumulator: (acc: A, value: V, index: number) => A, seed: A): OperatorFunction<V, A>;\nexport function scan<V, A, S>(accumulator: (acc: A | S, value: V, index: number) => A, seed: S): OperatorFunction<V, A>;\n\n// TODO: link to a \"redux pattern\" section in the guide (location TBD)\n\n/**\n * Useful for encapsulating and managing state. Applies an accumulator (or \"reducer function\")\n * to each value from the source after an initial state is established -- either via\n * a `seed` value (second argument), or from the first value from the source.\n *\n * <span class=\"informal\">It's like {@link reduce}, but emits the current\n * accumulation state after each update</span>\n *\n * ![](scan.png)\n *\n * This operator maintains an internal state and emits it after processing each value as follows:\n *\n * 1. First value arrives\n *   - If a `seed` value was supplied (as the second argument to `scan`), let `state = seed` and `value = firstValue`.\n *   - If NO `seed` value was supplied (no second argument), let `state = firstValue` and go to 3.\n * 2. Let `state = accumulator(state, value)`.\n *   - If an error is thrown by `accumulator`, notify the consumer of an error. The process ends.\n * 3. Emit `state`.\n * 4. Next value arrives, let `value = nextValue`, go to 2.\n *\n * ## Examples\n *\n * An average of previous numbers. This example shows how\n * not providing a `seed` can prime the stream with the\n * first value from the source.\n *\n * ```ts\n * import { of, scan, map } from 'rxjs';\n *\n * const numbers$ = of(1, 2, 3);\n *\n * numbers$\n *   .pipe(\n *     // Get the sum of the numbers coming in.\n *     scan((total, n) => total + n),\n *     // Get the average by dividing the sum by the total number\n *     // received so far (which is 1 more than the zero-based index).\n *     map((sum, index) => sum / (index + 1))\n *   )\n *   .subscribe(console.log);\n * ```\n *\n * The Fibonacci sequence. This example shows how you can use\n * a seed to prime accumulation process. Also... you know... Fibonacci.\n * So important to like, computers and stuff that its whiteboarded\n * in job interviews. Now you can show them the Rx version! (Please don't, haha)\n *\n * ```ts\n * import { interval, scan, map, startWith } from 'rxjs';\n *\n * const firstTwoFibs = [0, 1];\n * // An endless stream of Fibonacci numbers.\n * const fibonacci$ = interval(1000).pipe(\n *   // Scan to get the fibonacci numbers (after 0, 1)\n *   scan(([a, b]) => [b, a + b], firstTwoFibs),\n *   // Get the second number in the tuple, it's the one you calculated\n *   map(([, n]) => n),\n *   // Start with our first two digits :)\n *   startWith(...firstTwoFibs)\n * );\n *\n * fibonacci$.subscribe(console.log);\n * ```\n *\n * @see {@link expand}\n * @see {@link mergeScan}\n * @see {@link reduce}\n * @see {@link switchScan}\n *\n * @param accumulator A \"reducer function\". This will be called for each value after an initial state is\n * acquired.\n * @param seed The initial state. If this is not provided, the first value from the source will\n * be used as the initial state, and emitted without going through the accumulator. All subsequent values\n * will be processed by the accumulator function. If this is provided, all values will go through\n * the accumulator function.\n * @return A function that returns an Observable of the accumulated values.\n */\nexport function scan<V, A, S>(accumulator: (acc: V | A | S, value: V, index: number) => A, seed?: S): OperatorFunction<V, V | A> {\n  // providing a seed of `undefined` *should* be valid and trigger\n  // hasSeed! so don't use `seed !== undefined` checks!\n  // For this reason, we have to check it here at the original call site\n  // otherwise inside Operator/Subscriber we won't know if `undefined`\n  // means they didn't provide anything or if they literally provided `undefined`\n  return operate(scanInternals(accumulator, seed as S, arguments.length >= 2, true));\n}\n", "import { innerFrom } from '../observable/innerFrom';\nimport { Subject } from '../Subject';\nimport { SafeSubscriber } from '../Subscriber';\nimport { Subscription } from '../Subscription';\nimport { MonoTypeOperatorFunction, SubjectLike, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\n\nexport interface ShareConfig<T> {\n  /**\n   * The factory used to create the subject that will connect the source observable to\n   * multicast consumers.\n   */\n  connector?: () => SubjectLike<T>;\n  /**\n   * If `true`, the resulting observable will reset internal state on error from source and return to a \"cold\" state. This\n   * allows the resulting observable to be \"retried\" in the event of an error.\n   * If `false`, when an error comes from the source it will push the error into the connecting subject, and the subject\n   * will remain the connecting subject, meaning the resulting observable will not go \"cold\" again, and subsequent retries\n   * or resubscriptions will resubscribe to that same subject. In all cases, RxJS subjects will emit the same error again, however\n   * {@link ReplaySubject} will also push its buffered values before pushing the error.\n   * It is also possible to pass a notifier factory returning an `ObservableInput` instead which grants more fine-grained\n   * control over how and when the reset should happen. This allows behaviors like conditional or delayed resets.\n   */\n  resetOnError?: boolean | ((error: any) => ObservableInput<any>);\n  /**\n   * If `true`, the resulting observable will reset internal state on completion from source and return to a \"cold\" state. This\n   * allows the resulting observable to be \"repeated\" after it is done.\n   * If `false`, when the source completes, it will push the completion through the connecting subject, and the subject\n   * will remain the connecting subject, meaning the resulting observable will not go \"cold\" again, and subsequent repeats\n   * or resubscriptions will resubscribe to that same subject.\n   * It is also possible to pass a notifier factory returning an `ObservableInput` instead which grants more fine-grained\n   * control over how and when the reset should happen. This allows behaviors like conditional or delayed resets.\n   */\n  resetOnComplete?: boolean | (() => ObservableInput<any>);\n  /**\n   * If `true`, when the number of subscribers to the resulting observable reaches zero due to those subscribers unsubscribing, the\n   * internal state will be reset and the resulting observable will return to a \"cold\" state. This means that the next\n   * time the resulting observable is subscribed to, a new subject will be created and the source will be subscribed to\n   * again.\n   * If `false`, when the number of subscribers to the resulting observable reaches zero due to unsubscription, the subject\n   * will remain connected to the source, and new subscriptions to the result will be connected through that same subject.\n   * It is also possible to pass a notifier factory returning an `ObservableInput` instead which grants more fine-grained\n   * control over how and when the reset should happen. This allows behaviors like conditional or delayed resets.\n   */\n  resetOnRefCountZero?: boolean | (() => ObservableInput<any>);\n}\n\nexport function share<T>(): MonoTypeOperatorFunction<T>;\n\nexport function share<T>(options: ShareConfig<T>): MonoTypeOperatorFunction<T>;\n\n/**\n * Returns a new Observable that multicasts (shares) the original Observable. As long as there is at least one\n * Subscriber this Observable will be subscribed and emitting data. When all subscribers have unsubscribed it will\n * unsubscribe from the source Observable. Because the Observable is multicasting it makes the stream `hot`.\n * This is an alias for `multicast(() => new Subject()), refCount()`.\n *\n * The subscription to the underlying source Observable can be reset (unsubscribe and resubscribe for new subscribers),\n * if the subscriber count to the shared observable drops to 0, or if the source Observable errors or completes. It is\n * possible to use notifier factories for the resets to allow for behaviors like conditional or delayed resets. Please\n * note that resetting on error or complete of the source Observable does not behave like a transparent retry or restart\n * of the source because the error or complete will be forwarded to all subscribers and their subscription will be\n * closed. Only new subscribers after a reset on error or complete happened will cause a fresh subscription to the\n * source. To achieve transparent retries or restarts pipe the source through appropriate operators before sharing.\n *\n * ![](share.png)\n *\n * ## Example\n *\n * Generate new multicast Observable from the `source` Observable value\n *\n * ```ts\n * import { interval, tap, map, take, share } from 'rxjs';\n *\n * const source = interval(1000).pipe(\n *   tap(x => console.log('Processing: ', x)),\n *   map(x => x * x),\n *   take(6),\n *   share()\n * );\n *\n * source.subscribe(x => console.log('subscription 1: ', x));\n * source.subscribe(x => console.log('subscription 2: ', x));\n *\n * // Logs:\n * // Processing: 0\n * // subscription 1: 0\n * // subscription 2: 0\n * // Processing: 1\n * // subscription 1: 1\n * // subscription 2: 1\n * // Processing: 2\n * // subscription 1: 4\n * // subscription 2: 4\n * // Processing: 3\n * // subscription 1: 9\n * // subscription 2: 9\n * // Processing: 4\n * // subscription 1: 16\n * // subscription 2: 16\n * // Processing: 5\n * // subscription 1: 25\n * // subscription 2: 25\n * ```\n *\n * ## Example with notifier factory: Delayed reset\n *\n * ```ts\n * import { interval, take, share, timer } from 'rxjs';\n *\n * const source = interval(1000).pipe(\n *   take(3),\n *   share({\n *     resetOnRefCountZero: () => timer(1000)\n *   })\n * );\n *\n * const subscriptionOne = source.subscribe(x => console.log('subscription 1: ', x));\n * setTimeout(() => subscriptionOne.unsubscribe(), 1300);\n *\n * setTimeout(() => source.subscribe(x => console.log('subscription 2: ', x)), 1700);\n *\n * setTimeout(() => source.subscribe(x => console.log('subscription 3: ', x)), 5000);\n *\n * // Logs:\n * // subscription 1:  0\n * // (subscription 1 unsubscribes here)\n * // (subscription 2 subscribes here ~400ms later, source was not reset)\n * // subscription 2:  1\n * // subscription 2:  2\n * // (subscription 2 unsubscribes here)\n * // (subscription 3 subscribes here ~2000ms later, source did reset before)\n * // subscription 3:  0\n * // subscription 3:  1\n * // subscription 3:  2\n * ```\n *\n * @see {@link shareReplay}\n *\n * @return A function that returns an Observable that mirrors the source.\n */\nexport function share<T>(options: ShareConfig<T> = {}): MonoTypeOperatorFunction<T> {\n  const { connector = () => new Subject<T>(), resetOnError = true, resetOnComplete = true, resetOnRefCountZero = true } = options;\n  // It's necessary to use a wrapper here, as the _operator_ must be\n  // referentially transparent. Otherwise, it cannot be used in calls to the\n  // static `pipe` function - to create a partial pipeline.\n  //\n  // The _operator function_ - the function returned by the _operator_ - will\n  // not be referentially transparent - as it shares its source - but the\n  // _operator function_ is called when the complete pipeline is composed via a\n  // call to a source observable's `pipe` method - not when the static `pipe`\n  // function is called.\n  return (wrapperSource) => {\n    let connection: SafeSubscriber<T> | undefined;\n    let resetConnection: Subscription | undefined;\n    let subject: SubjectLike<T> | undefined;\n    let refCount = 0;\n    let hasCompleted = false;\n    let hasErrored = false;\n\n    const cancelReset = () => {\n      resetConnection?.unsubscribe();\n      resetConnection = undefined;\n    };\n    // Used to reset the internal state to a \"cold\"\n    // state, as though it had never been subscribed to.\n    const reset = () => {\n      cancelReset();\n      connection = subject = undefined;\n      hasCompleted = hasErrored = false;\n    };\n    const resetAndUnsubscribe = () => {\n      // We need to capture the connection before\n      // we reset (if we need to reset).\n      const conn = connection;\n      reset();\n      conn?.unsubscribe();\n    };\n\n    return operate<T, T>((source, subscriber) => {\n      refCount++;\n      if (!hasErrored && !hasCompleted) {\n        cancelReset();\n      }\n\n      // Create the subject if we don't have one yet. Grab a local reference to\n      // it as well, which avoids non-null assertions when using it and, if we\n      // connect to it now, then error/complete need a reference after it was\n      // reset.\n      const dest = (subject = subject ?? connector());\n\n      // Add the finalization directly to the subscriber - instead of returning it -\n      // so that the handling of the subscriber's unsubscription will be wired\n      // up _before_ the subscription to the source occurs. This is done so that\n      // the assignment to the source connection's `closed` property will be seen\n      // by synchronous firehose sources.\n      subscriber.add(() => {\n        refCount--;\n\n        // If we're resetting on refCount === 0, and it's 0, we only want to do\n        // that on \"unsubscribe\", really. Resetting on error or completion is a different\n        // configuration.\n        if (refCount === 0 && !hasErrored && !hasCompleted) {\n          resetConnection = handleReset(resetAndUnsubscribe, resetOnRefCountZero);\n        }\n      });\n\n      // The following line adds the subscription to the subscriber passed.\n      // Basically, `subscriber === dest.subscribe(subscriber)` is `true`.\n      dest.subscribe(subscriber);\n\n      if (\n        !connection &&\n        // Check this shareReplay is still activate - it can be reset to 0\n        // and be \"unsubscribed\" _before_ it actually subscribes.\n        // If we were to subscribe then, it'd leak and get stuck.\n        refCount > 0\n      ) {\n        // We need to create a subscriber here - rather than pass an observer and\n        // assign the returned subscription to connection - because it's possible\n        // for reentrant subscriptions to the shared observable to occur and in\n        // those situations we want connection to be already-assigned so that we\n        // don't create another connection to the source.\n        connection = new SafeSubscriber({\n          next: (value) => dest.next(value),\n          error: (err) => {\n            hasErrored = true;\n            cancelReset();\n            resetConnection = handleReset(reset, resetOnError, err);\n            dest.error(err);\n          },\n          complete: () => {\n            hasCompleted = true;\n            cancelReset();\n            resetConnection = handleReset(reset, resetOnComplete);\n            dest.complete();\n          },\n        });\n        innerFrom(source).subscribe(connection);\n      }\n    })(wrapperSource);\n  };\n}\n\nfunction handleReset<T extends unknown[] = never[]>(\n  reset: () => void,\n  on: boolean | ((...args: T) => ObservableInput<any>),\n  ...args: T\n): Subscription | undefined {\n  if (on === true) {\n    reset();\n    return;\n  }\n\n  if (on === false) {\n    return;\n  }\n\n  const onSubscriber = new SafeSubscriber({\n    next: () => {\n      onSubscriber.unsubscribe();\n      reset();\n    },\n  });\n\n  return innerFrom(on(...args)).subscribe(onSubscriber);\n}\n", "import { ReplaySubject } from '../ReplaySubject';\nimport { MonoTypeOperatorFunction, SchedulerLike } from '../types';\nimport { share } from './share';\n\nexport interface ShareReplayConfig {\n  bufferSize?: number;\n  windowTime?: number;\n  refCount: boolean;\n  scheduler?: SchedulerLike;\n}\n\nexport function shareReplay<T>(config: ShareReplayConfig): MonoTypeOperatorFunction<T>;\nexport function shareReplay<T>(bufferSize?: number, windowTime?: number, scheduler?: SchedulerLike): MonoTypeOperatorFunction<T>;\n\n/**\n * Share source and replay specified number of emissions on subscription.\n *\n * This operator is a specialization of `replay` that connects to a source observable\n * and multicasts through a `ReplaySubject` constructed with the specified arguments.\n * A successfully completed source will stay cached in the `shareReplay`ed observable forever,\n * but an errored source can be retried.\n *\n * ## Why use `shareReplay`?\n *\n * You generally want to use `shareReplay` when you have side-effects or taxing computations\n * that you do not wish to be executed amongst multiple subscribers.\n * It may also be valuable in situations where you know you will have late subscribers to\n * a stream that need access to previously emitted values.\n * This ability to replay values on subscription is what differentiates {@link share} and `shareReplay`.\n *\n * ## Reference counting\n *\n * By default `shareReplay` will use `refCount` of false, meaning that it will _not_ unsubscribe the\n * source when the reference counter drops to zero, i.e. the inner `ReplaySubject` will _not_ be unsubscribed\n * (and potentially run for ever).\n * This is the default as it is expected that `shareReplay` is often used to keep around expensive to setup\n * observables which we want to keep running instead of having to do the expensive setup again.\n *\n * As of RXJS version 6.4.0 a new overload signature was added to allow for manual control over what\n * happens when the operators internal reference counter drops to zero.\n * If `refCount` is true, the source will be unsubscribed from once the reference count drops to zero, i.e.\n * the inner `ReplaySubject` will be unsubscribed. All new subscribers will receive value emissions from a\n * new `ReplaySubject` which in turn will cause a new subscription to the source observable.\n *\n * ## Examples\n *\n * Example with a third subscriber coming late to the party\n *\n * ```ts\n * import { interval, take, shareReplay } from 'rxjs';\n *\n * const shared$ = interval(2000).pipe(\n *   take(6),\n *   shareReplay(3)\n * );\n *\n * shared$.subscribe(x => console.log('sub A: ', x));\n * shared$.subscribe(y => console.log('sub B: ', y));\n *\n * setTimeout(() => {\n *   shared$.subscribe(y => console.log('sub C: ', y));\n * }, 11000);\n *\n * // Logs:\n * // (after ~2000 ms)\n * // sub A: 0\n * // sub B: 0\n * // (after ~4000 ms)\n * // sub A: 1\n * // sub B: 1\n * // (after ~6000 ms)\n * // sub A: 2\n * // sub B: 2\n * // (after ~8000 ms)\n * // sub A: 3\n * // sub B: 3\n * // (after ~10000 ms)\n * // sub A: 4\n * // sub B: 4\n * // (after ~11000 ms, sub C gets the last 3 values)\n * // sub C: 2\n * // sub C: 3\n * // sub C: 4\n * // (after ~12000 ms)\n * // sub A: 5\n * // sub B: 5\n * // sub C: 5\n * ```\n *\n * Example for `refCount` usage\n *\n * ```ts\n * import { Observable, tap, interval, shareReplay, take } from 'rxjs';\n *\n * const log = <T>(name: string, source: Observable<T>) => source.pipe(\n *   tap({\n *     subscribe: () => console.log(`${ name }: subscribed`),\n *     next: value => console.log(`${ name }: ${ value }`),\n *     complete: () => console.log(`${ name }: completed`),\n *     finalize: () => console.log(`${ name }: unsubscribed`)\n *   })\n * );\n *\n * const obs$ = log('source', interval(1000));\n *\n * const shared$ = log('shared', obs$.pipe(\n *   shareReplay({ bufferSize: 1, refCount: true }),\n *   take(2)\n * ));\n *\n * shared$.subscribe(x => console.log('sub A: ', x));\n * shared$.subscribe(y => console.log('sub B: ', y));\n *\n * // PRINTS:\n * // shared: subscribed <-- reference count = 1\n * // source: subscribed\n * // shared: subscribed <-- reference count = 2\n * // source: 0\n * // shared: 0\n * // sub A: 0\n * // shared: 0\n * // sub B: 0\n * // source: 1\n * // shared: 1\n * // sub A: 1\n * // shared: completed <-- take(2) completes the subscription for sub A\n * // shared: unsubscribed <-- reference count = 1\n * // shared: 1\n * // sub B: 1\n * // shared: completed <-- take(2) completes the subscription for sub B\n * // shared: unsubscribed <-- reference count = 0\n * // source: unsubscribed <-- replaySubject unsubscribes from source observable because the reference count dropped to 0 and refCount is true\n *\n * // In case of refCount being false, the unsubscribe is never called on the source and the source would keep on emitting, even if no subscribers\n * // are listening.\n * // source: 2\n * // source: 3\n * // source: 4\n * // ...\n * ```\n *\n * @see {@link publish}\n * @see {@link share}\n * @see {@link publishReplay}\n *\n * @param configOrBufferSize Maximum element count of the replay buffer or {@link ShareReplayConfig configuration}\n * object.\n * @param windowTime Maximum time length of the replay buffer in milliseconds.\n * @param scheduler Scheduler where connected observers within the selector function\n * will be invoked on.\n * @return A function that returns an Observable sequence that contains the\n * elements of a sequence produced by multicasting the source sequence within a\n * selector function.\n */\nexport function shareReplay<T>(\n  configOrBufferSize?: ShareReplayConfig | number,\n  windowTime?: number,\n  scheduler?: SchedulerLike\n): MonoTypeOperatorFunction<T> {\n  let bufferSize: number;\n  let refCount = false;\n  if (configOrBufferSize && typeof configOrBufferSize === 'object') {\n    ({ bufferSize = Infinity, windowTime = Infinity, refCount = false, scheduler } = configOrBufferSize);\n  } else {\n    bufferSize = (configOrBufferSize ?? Infinity) as number;\n  }\n  return share<T>({\n    connector: () => new ReplaySubject(bufferSize, windowTime, scheduler),\n    resetOnError: true,\n    resetOnComplete: false,\n    resetOnRefCountZero: refCount,\n  });\n}\n", "import { MonoTypeOperatorFunction } from '../types';\nimport { filter } from './filter';\n\n/**\n * Returns an Observable that skips the first `count` items emitted by the source Observable.\n *\n * ![](skip.png)\n *\n * Skips the values until the sent notifications are equal or less than provided skip count. It raises\n * an error if skip count is equal or more than the actual number of emits and source raises an error.\n *\n * ## Example\n *\n * Skip the values before the emission\n *\n * ```ts\n * import { interval, skip } from 'rxjs';\n *\n * // emit every half second\n * const source = interval(500);\n * // skip the first 10 emitted values\n * const result = source.pipe(skip(10));\n *\n * result.subscribe(value => console.log(value));\n * // output: 10...11...12...13...\n * ```\n *\n * @see {@link last}\n * @see {@link skipWhile}\n * @see {@link skipUntil}\n * @see {@link skipLast}\n *\n * @param count The number of times, items emitted by source Observable should be skipped.\n * @return A function that returns an Observable that skips the first `count`\n * values emitted by the source Observable.\n */\nexport function skip<T>(count: number): MonoTypeOperatorFunction<T> {\n  return filter((_, index) => count <= index);\n}\n", "import { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\nimport { noop } from '../util/noop';\n\n/**\n * Returns an Observable that skips items emitted by the source Observable until a second Observable emits an item.\n *\n * The `skipUntil` operator causes the observable stream to skip the emission of values until the passed in observable\n * emits the first value. This can be particularly useful in combination with user interactions, responses of HTTP\n * requests or waiting for specific times to pass by.\n *\n * ![](skipUntil.png)\n *\n * Internally, the `skipUntil` operator subscribes to the passed in `notifier` `ObservableInput` (which gets converted\n * to an Observable) in order to recognize the emission of its first value. When `notifier` emits next, the operator\n * unsubscribes from it and starts emitting the values of the *source* observable until it completes or errors. It\n * will never let the *source* observable emit any values if the `notifier` completes or throws an error without\n * emitting a value before.\n *\n * ## Example\n *\n * In the following example, all emitted values of the interval observable are skipped until the user clicks anywhere\n * within the page\n *\n * ```ts\n * import { interval, fromEvent, skipUntil } from 'rxjs';\n *\n * const intervalObservable = interval(1000);\n * const click = fromEvent(document, 'click');\n *\n * const emitAfterClick = intervalObservable.pipe(\n *   skipUntil(click)\n * );\n * // clicked at 4.6s. output: 5...6...7...8........ or\n * // clicked at 7.3s. output: 8...9...10..11.......\n * emitAfterClick.subscribe(value => console.log(value));\n * ```\n *\n * @see {@link last}\n * @see {@link skip}\n * @see {@link skipWhile}\n * @see {@link skipLast}\n *\n * @param notifier An `ObservableInput` that has to emit an item before the source Observable elements begin to\n * be mirrored by the resulting Observable.\n * @return A function that returns an Observable that skips items from the\n * source Observable until the `notifier` Observable emits an item, then emits the\n * remaining items.\n */\nexport function skipUntil<T>(notifier: ObservableInput<any>): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let taking = false;\n\n    const skipSubscriber = createOperatorSubscriber(\n      subscriber,\n      () => {\n        skipSubscriber?.unsubscribe();\n        taking = true;\n      },\n      noop\n    );\n\n    innerFrom(notifier).subscribe(skipSubscriber);\n\n    source.subscribe(createOperatorSubscriber(subscriber, (value) => taking && subscriber.next(value)));\n  });\n}\n", "import { concat } from '../observable/concat';\nimport { OperatorFunction, SchedulerLike, ValueFromArray } from '../types';\nimport { popScheduler } from '../util/args';\nimport { operate } from '../util/lift';\n\n// Devs are more likely to pass null or undefined than they are a scheduler\n// without accompanying values. To make things easier for (naughty) devs who\n// use the `strictNullChecks: false` TypeScript compiler option, these\n// overloads with explicit null and undefined values are included.\n\nexport function startWith<T>(value: null): OperatorFunction<T, T | null>;\nexport function startWith<T>(value: undefined): OperatorFunction<T, T | undefined>;\n\n/** @deprecated The `scheduler` parameter will be removed in v8. Use `scheduled` and `concatAll`. Details: https://rxjs.dev/deprecations/scheduler-argument */\nexport function startWith<T, A extends readonly unknown[] = T[]>(\n  ...valuesAndScheduler: [...A, SchedulerLike]\n): OperatorFunction<T, T | ValueFromArray<A>>;\nexport function startWith<T, A extends readonly unknown[] = T[]>(...values: A): OperatorFunction<T, T | ValueFromArray<A>>;\n\n/**\n * Returns an observable that, at the moment of subscription, will synchronously emit all\n * values provided to this operator, then subscribe to the source and mirror all of its emissions\n * to subscribers.\n *\n * This is a useful way to know when subscription has occurred on an existing observable.\n *\n * <span class=\"informal\">First emits its arguments in order, and then any\n * emissions from the source.</span>\n *\n * ![](startWith.png)\n *\n * ## Examples\n *\n * Emit a value when a timer starts.\n *\n * ```ts\n * import { timer, map, startWith } from 'rxjs';\n *\n * timer(1000)\n *   .pipe(\n *     map(() => 'timer emit'),\n *     startWith('timer start')\n *   )\n *   .subscribe(x => console.log(x));\n *\n * // results:\n * // 'timer start'\n * // 'timer emit'\n * ```\n *\n * @param values Items you want the modified Observable to emit first.\n * @return A function that returns an Observable that synchronously emits\n * provided values before subscribing to the source Observable.\n *\n * @see {@link endWith}\n * @see {@link finalize}\n * @see {@link concat}\n */\nexport function startWith<T, D>(...values: D[]): OperatorFunction<T, T | D> {\n  const scheduler = popScheduler(values);\n  return operate((source, subscriber) => {\n    // Here we can't pass `undefined` as a scheduler, because if we did, the\n    // code inside of `concat` would be confused by the `undefined`, and treat it\n    // like an invalid observable. So we have to split it two different ways.\n    (scheduler ? concat(values, source, scheduler) : concat(values, source)).subscribe(subscriber);\n  });\n}\n", "import { Subscriber } from '../Subscriber';\nimport { ObservableInput, OperatorFunction, ObservedValueOf } from '../types';\nimport { innerFrom } from '../observable/innerFrom';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/* tslint:disable:max-line-length */\nexport function switchMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function switchMap<T, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector: undefined\n): OperatorFunction<T, ObservedValueOf<O>>;\n/** @deprecated The `resultSelector` parameter will be removed in v8. Use an inner `map` instead. Details: https://rxjs.dev/deprecations/resultSelector */\nexport function switchMap<T, R, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector: (outerValue: T, innerValue: ObservedValueOf<O>, outerIndex: number, innerIndex: number) => R\n): OperatorFunction<T, R>;\n/* tslint:enable:max-line-length */\n\n/**\n * Projects each source value to an Observable which is merged in the output\n * Observable, emitting values only from the most recently projected Observable.\n *\n * <span class=\"informal\">Maps each value to an Observable, then flattens all of\n * these inner Observables using {@link switchAll}.</span>\n *\n * ![](switchMap.png)\n *\n * Returns an Observable that emits items based on applying a function that you\n * supply to each item emitted by the source Observable, where that function\n * returns an (so-called \"inner\") Observable. Each time it observes one of these\n * inner Observables, the output Observable begins emitting the items emitted by\n * that inner Observable. When a new inner Observable is emitted, `switchMap`\n * stops emitting items from the earlier-emitted inner Observable and begins\n * emitting items from the new one. It continues to behave like this for\n * subsequent inner Observables.\n *\n * ## Example\n *\n * Generate new Observable according to source Observable values\n *\n * ```ts\n * import { of, switchMap } from 'rxjs';\n *\n * const switched = of(1, 2, 3).pipe(switchMap(x => of(x, x ** 2, x ** 3)));\n * switched.subscribe(x => console.log(x));\n * // outputs\n * // 1\n * // 1\n * // 1\n * // 2\n * // 4\n * // 8\n * // 3\n * // 9\n * // 27\n * ```\n *\n * Restart an interval Observable on every click event\n *\n * ```ts\n * import { fromEvent, switchMap, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(switchMap(() => interval(1000)));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link concatMap}\n * @see {@link exhaustMap}\n * @see {@link mergeMap}\n * @see {@link switchAll}\n * @see {@link switchMapTo}\n *\n * @param project A function that, when applied to an item emitted by the source\n * Observable, returns an Observable.\n * @return A function that returns an Observable that emits the result of\n * applying the projection function (and the optional deprecated\n * `resultSelector`) to each item emitted by the source Observable and taking\n * only the values from the most recently projected inner Observable.\n */\nexport function switchMap<T, R, O extends ObservableInput<any>>(\n  project: (value: T, index: number) => O,\n  resultSelector?: (outerValue: T, innerValue: ObservedValueOf<O>, outerIndex: number, innerIndex: number) => R\n): OperatorFunction<T, ObservedValueOf<O> | R> {\n  return operate((source, subscriber) => {\n    let innerSubscriber: Subscriber<ObservedValueOf<O>> | null = null;\n    let index = 0;\n    // Whether or not the source subscription has completed\n    let isComplete = false;\n\n    // We only complete the result if the source is complete AND we don't have an active inner subscription.\n    // This is called both when the source completes and when the inners complete.\n    const checkComplete = () => isComplete && !innerSubscriber && subscriber.complete();\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        (value) => {\n          // Cancel the previous inner subscription if there was one\n          innerSubscriber?.unsubscribe();\n          let innerIndex = 0;\n          const outerIndex = index++;\n          // Start the next inner subscription\n          innerFrom(project(value, outerIndex)).subscribe(\n            (innerSubscriber = createOperatorSubscriber(\n              subscriber,\n              // When we get a new inner value, next it through. Note that this is\n              // handling the deprecate result selector here. This is because with this architecture\n              // it ends up being smaller than using the map operator.\n              (innerValue) => subscriber.next(resultSelector ? resultSelector(value, innerValue, outerIndex, innerIndex++) : innerValue),\n              () => {\n                // The inner has completed. Null out the inner subscriber to\n                // free up memory and to signal that we have no inner subscription\n                // currently.\n                innerSubscriber = null!;\n                checkComplete();\n              }\n            ))\n          );\n        },\n        () => {\n          isComplete = true;\n          checkComplete();\n        }\n      )\n    );\n  });\n}\n", "import { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\nimport { noop } from '../util/noop';\n\n/**\n * Emits the values emitted by the source Observable until a `notifier`\n * Observable emits a value.\n *\n * <span class=\"informal\">Lets values pass until a second Observable,\n * `notifier`, emits a value. Then, it completes.</span>\n *\n * ![](takeUntil.png)\n *\n * `takeUntil` subscribes and begins mirroring the source Observable. It also\n * monitors a second Observable, `notifier` that you provide. If the `notifier`\n * emits a value, the output Observable stops mirroring the source Observable\n * and completes. If the `notifier` doesn't emit any value and completes\n * then `takeUntil` will pass all values.\n *\n * ## Example\n *\n * Tick every second until the first click happens\n *\n * ```ts\n * import { interval, fromEvent, takeUntil } from 'rxjs';\n *\n * const source = interval(1000);\n * const clicks = fromEvent(document, 'click');\n * const result = source.pipe(takeUntil(clicks));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link take}\n * @see {@link takeLast}\n * @see {@link takeWhile}\n * @see {@link skip}\n *\n * @param notifier The `ObservableInput` whose first emitted value will cause the output\n * Observable of `takeUntil` to stop emitting values from the source Observable.\n * @return A function that returns an Observable that emits the values from the\n * source Observable until `notifier` emits its first value.\n */\nexport function takeUntil<T>(notifier: ObservableInput<any>): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    innerFrom(notifier).subscribe(createOperatorSubscriber(subscriber, () => subscriber.complete(), noop));\n    !subscriber.closed && source.subscribe(subscriber);\n  });\n}\n", "import { OperatorFunction, MonoTypeOperatorFunction, TruthyTypesOf } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\nexport function takeWhile<T>(predicate: BooleanConstructor, inclusive: true): MonoTypeOperatorFunction<T>;\nexport function takeWhile<T>(predicate: BooleanConstructor, inclusive: false): OperatorFunction<T, TruthyTypesOf<T>>;\nexport function takeWhile<T>(predicate: BooleanConstructor): OperatorFunction<T, TruthyTypesOf<T>>;\nexport function takeWhile<T, S extends T>(predicate: (value: T, index: number) => value is S): OperatorFunction<T, S>;\nexport function takeWhile<T, S extends T>(predicate: (value: T, index: number) => value is S, inclusive: false): OperatorFunction<T, S>;\nexport function takeWhile<T>(predicate: (value: T, index: number) => boolean, inclusive?: boolean): MonoTypeOperatorFunction<T>;\n\n/**\n * Emits values emitted by the source Observable so long as each value satisfies\n * the given `predicate`, and then completes as soon as this `predicate` is not\n * satisfied.\n *\n * <span class=\"informal\">Takes values from the source only while they pass the\n * condition given. When the first value does not satisfy, it completes.</span>\n *\n * ![](takeWhile.png)\n *\n * `takeWhile` subscribes and begins mirroring the source Observable. Each value\n * emitted on the source is given to the `predicate` function which returns a\n * boolean, representing a condition to be satisfied by the source values. The\n * output Observable emits the source values until such time as the `predicate`\n * returns false, at which point `takeWhile` stops mirroring the source\n * Observable and completes the output Observable.\n *\n * ## Example\n *\n * Emit click events only while the clientX property is greater than 200\n *\n * ```ts\n * import { fromEvent, takeWhile } from 'rxjs';\n *\n * const clicks = fromEvent<PointerEvent>(document, 'click');\n * const result = clicks.pipe(takeWhile(ev => ev.clientX > 200));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link take}\n * @see {@link takeLast}\n * @see {@link takeUntil}\n * @see {@link skip}\n *\n * @param predicate A function that evaluates a value emitted by the source\n * Observable and returns a boolean. Also takes the (zero-based) index as the\n * second argument.\n * @param inclusive When set to `true` the value that caused `predicate` to\n * return `false` will also be emitted.\n * @return A function that returns an Observable that emits values from the\n * source Observable so long as each value satisfies the condition defined by\n * the `predicate`, then completes.\n */\nexport function takeWhile<T>(predicate: (value: T, index: number) => boolean, inclusive = false): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    let index = 0;\n    source.subscribe(\n      createOperatorSubscriber(subscriber, (value) => {\n        const result = predicate(value, index++);\n        (result || inclusive) && subscriber.next(value);\n        !result && subscriber.complete();\n      })\n    );\n  });\n}\n", "import { MonoTypeOperatorFunction, Observer } from '../types';\nimport { isFunction } from '../util/isFunction';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { identity } from '../util/identity';\n\n/**\n * An extension to the {@link Observer} interface used only by the {@link tap} operator.\n *\n * It provides a useful set of callbacks a user can register to do side-effects in\n * cases other than what the usual {@link Observer} callbacks are\n * ({@link guide/glossary-and-semantics#next next},\n * {@link guide/glossary-and-semantics#error error} and/or\n * {@link guide/glossary-and-semantics#complete complete}).\n *\n * ## Example\n *\n * ```ts\n * import { fromEvent, switchMap, tap, interval, take } from 'rxjs';\n *\n * const source$ = fromEvent(document, 'click');\n * const result$ = source$.pipe(\n *   switchMap((_, i) => i % 2 === 0\n *     ? fromEvent(document, 'mousemove').pipe(\n *         tap({\n *           subscribe: () => console.log('Subscribed to the mouse move events after click #' + i),\n *           unsubscribe: () => console.log('Mouse move events #' + i + ' unsubscribed'),\n *           finalize: () => console.log('Mouse move events #' + i + ' finalized')\n *         })\n *       )\n *     : interval(1_000).pipe(\n *         take(5),\n *         tap({\n *           subscribe: () => console.log('Subscribed to the 1-second interval events after click #' + i),\n *           unsubscribe: () => console.log('1-second interval events #' + i + ' unsubscribed'),\n *           finalize: () => console.log('1-second interval events #' + i + ' finalized')\n *         })\n *       )\n *   )\n * );\n *\n * const subscription = result$.subscribe({\n *   next: console.log\n * });\n *\n * setTimeout(() => {\n *   console.log('Unsubscribe after 60 seconds');\n *   subscription.unsubscribe();\n * }, 60_000);\n * ```\n */\nexport interface TapObserver<T> extends Observer<T> {\n  /**\n   * The callback that `tap` operator invokes at the moment when the source Observable\n   * gets subscribed to.\n   */\n  subscribe: () => void;\n  /**\n   * The callback that `tap` operator invokes when an explicit\n   * {@link guide/glossary-and-semantics#unsubscription unsubscribe} happens. It won't get invoked on\n   * `error` or `complete` events.\n   */\n  unsubscribe: () => void;\n  /**\n   * The callback that `tap` operator invokes when any kind of\n   * {@link guide/glossary-and-semantics#finalization finalization} happens - either when\n   * the source Observable `error`s or `complete`s or when it gets explicitly unsubscribed\n   * by the user. There is no difference in using this callback or the {@link finalize}\n   * operator, but if you're already using `tap` operator, you can use this callback\n   * instead. You'd get the same result in either case.\n   */\n  finalize: () => void;\n}\nexport function tap<T>(observerOrNext?: Partial<TapObserver<T>> | ((value: T) => void)): MonoTypeOperatorFunction<T>;\n/** @deprecated Instead of passing separate callback arguments, use an observer argument. Signatures taking separate callback arguments will be removed in v8. Details: https://rxjs.dev/deprecations/subscribe-arguments */\nexport function tap<T>(\n  next?: ((value: T) => void) | null,\n  error?: ((error: any) => void) | null,\n  complete?: (() => void) | null\n): MonoTypeOperatorFunction<T>;\n\n/**\n * Used to perform side-effects for notifications from the source observable\n *\n * <span class=\"informal\">Used when you want to affect outside state with a notification without altering the notification</span>\n *\n * ![](tap.png)\n *\n * Tap is designed to allow the developer a designated place to perform side effects. While you _could_ perform side-effects\n * inside of a `map` or a `mergeMap`, that would make their mapping functions impure, which isn't always a big deal, but will\n * make it so you can't do things like memoize those functions. The `tap` operator is designed solely for such side-effects to\n * help you remove side-effects from other operations.\n *\n * For any notification, next, error, or complete, `tap` will call the appropriate callback you have provided to it, via a function\n * reference, or a partial observer, then pass that notification down the stream.\n *\n * The observable returned by `tap` is an exact mirror of the source, with one exception: Any error that occurs -- synchronously -- in a handler\n * provided to `tap` will be emitted as an error from the returned observable.\n *\n * > Be careful! You can mutate objects as they pass through the `tap` operator's handlers.\n *\n * The most common use of `tap` is actually for debugging. You can place a `tap(console.log)` anywhere\n * in your observable `pipe`, log out the notifications as they are emitted by the source returned by the previous\n * operation.\n *\n * ## Examples\n *\n * Check a random number before it is handled. Below is an observable that will use a random number between 0 and 1,\n * and emit `'big'` or `'small'` depending on the size of that number. But we wanted to log what the original number\n * was, so we have added a `tap(console.log)`.\n *\n * ```ts\n * import { of, tap, map } from 'rxjs';\n *\n * of(Math.random()).pipe(\n *   tap(console.log),\n *   map(n => n > 0.5 ? 'big' : 'small')\n * ).subscribe(console.log);\n * ```\n *\n * Using `tap` to analyze a value and force an error. Below is an observable where in our system we only\n * want to emit numbers 3 or less we get from another source. We can force our observable to error\n * using `tap`.\n *\n * ```ts\n * import { of, tap } from 'rxjs';\n *\n * const source = of(1, 2, 3, 4, 5);\n *\n * source.pipe(\n *   tap(n => {\n *     if (n > 3) {\n *       throw new TypeError(`Value ${ n } is greater than 3`);\n *     }\n *   })\n * )\n * .subscribe({ next: console.log, error: err => console.log(err.message) });\n * ```\n *\n * We want to know when an observable completes before moving on to the next observable. The system\n * below will emit a random series of `'X'` characters from 3 different observables in sequence. The\n * only way we know when one observable completes and moves to the next one, in this case, is because\n * we have added a `tap` with the side effect of logging to console.\n *\n * ```ts\n * import { of, concatMap, interval, take, map, tap } from 'rxjs';\n *\n * of(1, 2, 3).pipe(\n *   concatMap(n => interval(1000).pipe(\n *     take(Math.round(Math.random() * 10)),\n *     map(() => 'X'),\n *     tap({ complete: () => console.log(`Done with ${ n }`) })\n *   ))\n * )\n * .subscribe(console.log);\n * ```\n *\n * @see {@link finalize}\n * @see {@link TapObserver}\n *\n * @param observerOrNext A next handler or partial observer\n * @param error An error handler\n * @param complete A completion handler\n * @return A function that returns an Observable identical to the source, but\n * runs the specified Observer or callback(s) for each item.\n */\nexport function tap<T>(\n  observerOrNext?: Partial<TapObserver<T>> | ((value: T) => void) | null,\n  error?: ((e: any) => void) | null,\n  complete?: (() => void) | null\n): MonoTypeOperatorFunction<T> {\n  // We have to check to see not only if next is a function,\n  // but if error or complete were passed. This is because someone\n  // could technically call tap like `tap(null, fn)` or `tap(null, null, fn)`.\n  const tapObserver =\n    isFunction(observerOrNext) || error || complete\n      ? // tslint:disable-next-line: no-object-literal-type-assertion\n        ({ next: observerOrNext as Exclude<typeof observerOrNext, Partial<TapObserver<T>>>, error, complete } as Partial<TapObserver<T>>)\n      : observerOrNext;\n\n  return tapObserver\n    ? operate((source, subscriber) => {\n        tapObserver.subscribe?.();\n        let isUnsub = true;\n        source.subscribe(\n          createOperatorSubscriber(\n            subscriber,\n            (value) => {\n              tapObserver.next?.(value);\n              subscriber.next(value);\n            },\n            () => {\n              isUnsub = false;\n              tapObserver.complete?.();\n              subscriber.complete();\n            },\n            (err) => {\n              isUnsub = false;\n              tapObserver.error?.(err);\n              subscriber.error(err);\n            },\n            () => {\n              if (isUnsub) {\n                tapObserver.unsubscribe?.();\n              }\n              tapObserver.finalize?.();\n            }\n          )\n        );\n      })\n    : // Tap was called with no valid tap observer or handler\n      // (e.g. `tap(null, null, null)` or `tap(null)` or `tap()`)\n      // so we're going to just mirror the source.\n      identity;\n}\n", "import { Subscription } from '../Subscription';\n\nimport { MonoTypeOperatorFunction, ObservableInput } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\n\n/**\n * An object interface used by {@link throttle} or {@link throttleTime} that ensure\n * configuration options of these operators.\n *\n * @see {@link throttle}\n * @see {@link throttleTime}\n */\nexport interface ThrottleConfig {\n  /**\n   * If `true`, the resulting Observable will emit the first value from the source\n   * Observable at the **start** of the \"throttling\" process (when starting an\n   * internal timer that prevents other emissions from the source to pass through).\n   * If `false`, it will not emit the first value from the source Observable at the\n   * start of the \"throttling\" process.\n   *\n   * If not provided, defaults to: `true`.\n   */\n  leading?: boolean;\n  /**\n   * If `true`, the resulting Observable will emit the last value from the source\n   * Observable at the **end** of the \"throttling\" process (when ending an internal\n   * timer that prevents other emissions from the source to pass through).\n   * If `false`, it will not emit the last value from the source Observable at the\n   * end of the \"throttling\" process.\n   *\n   * If not provided, defaults to: `false`.\n   */\n  trailing?: boolean;\n}\n\n/**\n * Emits a value from the source Observable, then ignores subsequent source\n * values for a duration determined by another Observable, then repeats this\n * process.\n *\n * <span class=\"informal\">It's like {@link throttleTime}, but the silencing\n * duration is determined by a second Observable.</span>\n *\n * ![](throttle.svg)\n *\n * `throttle` emits the source Observable values on the output Observable\n * when its internal timer is disabled, and ignores source values when the timer\n * is enabled. Initially, the timer is disabled. As soon as the first source\n * value arrives, it is forwarded to the output Observable, and then the timer\n * is enabled by calling the `durationSelector` function with the source value,\n * which returns the \"duration\" Observable. When the duration Observable emits a\n * value, the timer is disabled, and this process repeats for the\n * next source value.\n *\n * ## Example\n *\n * Emit clicks at a rate of at most one click per second\n *\n * ```ts\n * import { fromEvent, throttle, interval } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(throttle(() => interval(1000)));\n *\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link audit}\n * @see {@link debounce}\n * @see {@link delayWhen}\n * @see {@link sample}\n * @see {@link throttleTime}\n *\n * @param durationSelector A function that receives a value from the source\n * Observable, for computing the silencing duration for each source value,\n * returned as an `ObservableInput`.\n * @param config A configuration object to define `leading` and `trailing`\n * behavior. Defaults to `{ leading: true, trailing: false }`.\n * @return A function that returns an Observable that performs the throttle\n * operation to limit the rate of emissions from the source.\n */\nexport function throttle<T>(durationSelector: (value: T) => ObservableInput<any>, config?: ThrottleConfig): MonoTypeOperatorFunction<T> {\n  return operate((source, subscriber) => {\n    const { leading = true, trailing = false } = config ?? {};\n    let hasValue = false;\n    let sendValue: T | null = null;\n    let throttled: Subscription | null = null;\n    let isComplete = false;\n\n    const endThrottling = () => {\n      throttled?.unsubscribe();\n      throttled = null;\n      if (trailing) {\n        send();\n        isComplete && subscriber.complete();\n      }\n    };\n\n    const cleanupThrottling = () => {\n      throttled = null;\n      isComplete && subscriber.complete();\n    };\n\n    const startThrottle = (value: T) =>\n      (throttled = innerFrom(durationSelector(value)).subscribe(createOperatorSubscriber(subscriber, endThrottling, cleanupThrottling)));\n\n    const send = () => {\n      if (hasValue) {\n        // Ensure we clear out our value and hasValue flag\n        // before we emit, otherwise reentrant code can cause\n        // issues here.\n        hasValue = false;\n        const value = sendValue!;\n        sendValue = null;\n        // Emit the value.\n        subscriber.next(value);\n        !isComplete && startThrottle(value);\n      }\n    };\n\n    source.subscribe(\n      createOperatorSubscriber(\n        subscriber,\n        // Regarding the presence of throttled.closed in the following\n        // conditions, if a synchronous duration selector is specified - weird,\n        // but legal - an already-closed subscription will be assigned to\n        // throttled, so the subscription's closed property needs to be checked,\n        // too.\n        (value) => {\n          hasValue = true;\n          sendValue = value;\n          !(throttled && !throttled.closed) && (leading ? send() : startThrottle(value));\n        },\n        () => {\n          isComplete = true;\n          !(trailing && hasValue && throttled && !throttled.closed) && subscriber.complete();\n        }\n      )\n    );\n  });\n}\n", "import { asyncScheduler } from '../scheduler/async';\nimport { throttle, ThrottleConfig } from './throttle';\nimport { MonoTypeOperatorFunction, SchedulerLike } from '../types';\nimport { timer } from '../observable/timer';\n\n/**\n * Emits a value from the source Observable, then ignores subsequent source\n * values for `duration` milliseconds, then repeats this process.\n *\n * <span class=\"informal\">Lets a value pass, then ignores source values for the\n * next `duration` milliseconds.</span>\n *\n * ![](throttleTime.png)\n *\n * `throttleTime` emits the source Observable values on the output Observable\n * when its internal timer is disabled, and ignores source values when the timer\n * is enabled. Initially, the timer is disabled. As soon as the first source\n * value arrives, it is forwarded to the output Observable, and then the timer\n * is enabled. After `duration` milliseconds (or the time unit determined\n * internally by the optional `scheduler`) has passed, the timer is disabled,\n * and this process repeats for the next source value. Optionally takes a\n * {@link SchedulerLike} for managing timers.\n *\n * ## Examples\n *\n * ### Limit click rate\n *\n * Emit clicks at a rate of at most one click per second\n *\n * ```ts\n * import { fromEvent, throttleTime } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const result = clicks.pipe(throttleTime(1000));\n *\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link auditTime}\n * @see {@link debounceTime}\n * @see {@link delay}\n * @see {@link sampleTime}\n * @see {@link throttle}\n *\n * @param duration Time to wait before emitting another value after\n * emitting the last value, measured in milliseconds or the time unit determined\n * internally by the optional `scheduler`.\n * @param scheduler The {@link SchedulerLike} to use for\n * managing the timers that handle the throttling. Defaults to {@link asyncScheduler}.\n * @param config A configuration object to define `leading` and\n * `trailing` behavior. Defaults to `{ leading: true, trailing: false }`.\n * @return A function that returns an Observable that performs the throttle\n * operation to limit the rate of emissions from the source.\n */\nexport function throttleTime<T>(\n  duration: number,\n  scheduler: SchedulerLike = asyncScheduler,\n  config?: ThrottleConfig\n): MonoTypeOperatorFunction<T> {\n  const duration$ = timer(duration, scheduler);\n  return throttle(() => duration$, config);\n}\n", "import { OperatorFunction, ObservableInputTuple } from '../types';\nimport { operate } from '../util/lift';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\nimport { innerFrom } from '../observable/innerFrom';\nimport { identity } from '../util/identity';\nimport { noop } from '../util/noop';\nimport { popResultSelector } from '../util/args';\n\nexport function withLatestFrom<T, O extends unknown[]>(...inputs: [...ObservableInputTuple<O>]): OperatorFunction<T, [T, ...O]>;\n\nexport function withLatestFrom<T, O extends unknown[], R>(\n  ...inputs: [...ObservableInputTuple<O>, (...value: [T, ...O]) => R]\n): OperatorFunction<T, R>;\n\n/**\n * Combines the source Observable with other Observables to create an Observable\n * whose values are calculated from the latest values of each, only when the\n * source emits.\n *\n * <span class=\"informal\">Whenever the source Observable emits a value, it\n * computes a formula using that value plus the latest values from other input\n * Observables, then emits the output of that formula.</span>\n *\n * ![](withLatestFrom.png)\n *\n * `withLatestFrom` combines each value from the source Observable (the\n * instance) with the latest values from the other input Observables only when\n * the source emits a value, optionally using a `project` function to determine\n * the value to be emitted on the output Observable. All input Observables must\n * emit at least one value before the output Observable will emit a value.\n *\n * ## Example\n *\n * On every click event, emit an array with the latest timer event plus the click event\n *\n * ```ts\n * import { fromEvent, interval, withLatestFrom } from 'rxjs';\n *\n * const clicks = fromEvent(document, 'click');\n * const timer = interval(1000);\n * const result = clicks.pipe(withLatestFrom(timer));\n * result.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link combineLatest}\n *\n * @param inputs An input Observable to combine with the source Observable. More\n * than one input Observables may be given as argument. If the last parameter is\n * a function, it will be used as a projection function for combining values\n * together. When the function is called, it receives all values in order of the\n * Observables passed, where the first parameter is a value from the source\n * Observable. (e.g.\n * `a.pipe(withLatestFrom(b, c), map(([a1, b1, c1]) => a1 + b1 + c1))`). If this\n * is not passed, arrays will be emitted on the output Observable.\n * @return A function that returns an Observable of projected values from the\n * most recent values from each input Observable, or an array of the most\n * recent values from each input Observable.\n */\nexport function withLatestFrom<T, R>(...inputs: any[]): OperatorFunction<T, R | any[]> {\n  const project = popResultSelector(inputs) as ((...args: any[]) => R) | undefined;\n\n  return operate((source, subscriber) => {\n    const len = inputs.length;\n    const otherValues = new Array(len);\n    // An array of whether or not the other sources have emitted. Matched with them by index.\n    // TODO: At somepoint, we should investigate the performance implications here, and look\n    // into using a `Set()` and checking the `size` to see if we're ready.\n    let hasValue = inputs.map(() => false);\n    // Flipped true when we have at least one value from all other sources and\n    // we are ready to start emitting values.\n    let ready = false;\n\n    // Other sources. Note that here we are not checking `subscriber.closed`,\n    // this causes all inputs to be subscribed to, even if nothing can be emitted\n    // from them. This is an important distinction because subscription constitutes\n    // a side-effect.\n    for (let i = 0; i < len; i++) {\n      innerFrom(inputs[i]).subscribe(\n        createOperatorSubscriber(\n          subscriber,\n          (value) => {\n            otherValues[i] = value;\n            if (!ready && !hasValue[i]) {\n              // If we're not ready yet, flag to show this observable has emitted.\n              hasValue[i] = true;\n              // Intentionally terse code.\n              // If all of our other observables have emitted, set `ready` to `true`,\n              // so we know we can start emitting values, then clean up the `hasValue` array,\n              // because we don't need it anymore.\n              (ready = hasValue.every(identity)) && (hasValue = null!);\n            }\n          },\n          // Completing one of the other sources has\n          // no bearing on the completion of our result.\n          noop\n        )\n      );\n    }\n\n    // Source subscription\n    source.subscribe(\n      createOperatorSubscriber(subscriber, (value) => {\n        if (ready) {\n          // We have at least one value from the other sources. Go ahead and emit.\n          const values = [value, ...otherValues];\n          subscriber.next(project ? project(...values) : values);\n        }\n      })\n    );\n  });\n}\n", "import { zip as zipStatic } from '../observable/zip';\nimport { ObservableInput, ObservableInputTuple, OperatorFunction, Cons } from '../types';\nimport { operate } from '../util/lift';\n\n/** @deprecated Replaced with {@link zipWith}. Will be removed in v8. */\nexport function zip<T, A extends readonly unknown[]>(otherInputs: [...ObservableInputTuple<A>]): OperatorFunction<T, Cons<T, A>>;\n/** @deprecated Replaced with {@link zipWith}. Will be removed in v8. */\nexport function zip<T, A extends readonly unknown[], R>(\n  otherInputsAndProject: [...ObservableInputTuple<A>],\n  project: (...values: Cons<T, A>) => R\n): OperatorFunction<T, R>;\n/** @deprecated Replaced with {@link zipWith}. Will be removed in v8. */\nexport function zip<T, A extends readonly unknown[]>(...otherInputs: [...ObservableInputTuple<A>]): OperatorFunction<T, Cons<T, A>>;\n/** @deprecated Replaced with {@link zipWith}. Will be removed in v8. */\nexport function zip<T, A extends readonly unknown[], R>(\n  ...otherInputsAndProject: [...ObservableInputTuple<A>, (...values: Cons<T, A>) => R]\n): OperatorFunction<T, R>;\n\n/**\n * @deprecated Replaced with {@link zipWith}. Will be removed in v8.\n */\nexport function zip<T, R>(...sources: Array<ObservableInput<any> | ((...values: Array<any>) => R)>): OperatorFunction<T, any> {\n  return operate((source, subscriber) => {\n    zipStatic(source as ObservableInput<any>, ...(sources as Array<ObservableInput<any>>)).subscribe(subscriber);\n  });\n}\n", "import { ObservableInputTuple, OperatorFunction, Cons } from '../types';\nimport { zip } from './zip';\n\n/**\n * Subscribes to the source, and the observable inputs provided as arguments, and combines their values, by index, into arrays.\n *\n * What is meant by \"combine by index\": The first value from each will be made into a single array, then emitted,\n * then the second value from each will be combined into a single array and emitted, then the third value\n * from each will be combined into a single array and emitted, and so on.\n *\n * This will continue until it is no longer able to combine values of the same index into an array.\n *\n * After the last value from any one completed source is emitted in an array, the resulting observable will complete,\n * as there is no way to continue \"zipping\" values together by index.\n *\n * Use-cases for this operator are limited. There are memory concerns if one of the streams is emitting\n * values at a much faster rate than the others. Usage should likely be limited to streams that emit\n * at a similar pace, or finite streams of known length.\n *\n * In many cases, authors want `combineLatestWith` and not `zipWith`.\n *\n * @param otherInputs other observable inputs to collate values from.\n * @return A function that returns an Observable that emits items by index\n * combined from the source Observable and provided Observables, in form of an\n * array.\n */\nexport function zipWith<T, A extends readonly unknown[]>(...otherInputs: [...ObservableInputTuple<A>]): OperatorFunction<T, Cons<T, A>> {\n  return zip(...otherInputs);\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  ReplaySubject,\n  Subject,\n  fromEvent\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch document\n *\n * Documents are implemented as subjects, so all downstream observables are\n * automatically updated when a new document is emitted.\n *\n * @returns Document subject\n */\nexport function watchDocument(): Subject<Document> {\n  const document$ = new ReplaySubject<Document>(1)\n  fromEvent(document, \"DOMContentLoaded\", { once: true })\n    .subscribe(() => document$.next(document))\n\n  /* Return document */\n  return document$\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve all elements matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Elements\n */\nexport function getElements<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T][]\n\nexport function getElements<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T[]\n\nexport function getElements<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T[] {\n  return Array.from(node.querySelectorAll<T>(selector))\n}\n\n/**\n * Retrieve an element matching a query selector or throw a reference error\n *\n * Note that this function assumes that the element is present. If unsure if an\n * element is existent, use the `getOptionalElement` function instead.\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element\n */\nexport function getElement<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T]\n\nexport function getElement<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T\n\nexport function getElement<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T {\n  const el = getOptionalElement<T>(selector, node)\n  if (typeof el === \"undefined\")\n    throw new ReferenceError(\n      `Missing element: expected \"${selector}\" to be present`\n    )\n\n  /* Return element */\n  return el\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Retrieve an optional element matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element or nothing\n */\nexport function getOptionalElement<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T] | undefined\n\nexport function getOptionalElement<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T | undefined\n\nexport function getOptionalElement<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T | undefined {\n  return node.querySelector<T>(selector) || undefined\n}\n\n/**\n * Retrieve the currently active element\n *\n * @returns Element or nothing\n */\nexport function getActiveElement(): HTMLElement | undefined {\n  return (\n    document.activeElement?.shadowRoot?.activeElement as HTMLElement ??\n    document.activeElement as HTMLElement ??\n    undefined\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  debounceTime,\n  distinctUntilChanged,\n  fromEvent,\n  map,\n  merge,\n  shareReplay,\n  startWith\n} from \"rxjs\"\n\nimport { getActiveElement } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Focus observable\n *\n * Previously, this observer used `focus` and `blur` events to determine whether\n * an element is focused, but this doesn't work if there are focusable elements\n * within the elements itself. A better solutions are `focusin` and `focusout`\n * events, which bubble up the tree and allow for more fine-grained control.\n *\n * `debounceTime` is necessary, because when a focus change happens inside an\n * element, the observable would first emit `false` and then `true` again.\n */\nconst observer$ = merge(\n  fromEvent(document.body, \"focusin\"),\n  fromEvent(document.body, \"focusout\")\n)\n  .pipe(\n    debounceTime(1),\n    startWith(undefined),\n    map(() => getActiveElement() || document.body),\n    shareReplay(1)\n  )\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch element focus\n *\n * @param el - Element\n *\n * @returns Element focus observable\n */\nexport function watchElementFocus(\n  el: HTMLElement\n): Observable<boolean> {\n  return observer$\n    .pipe(\n      map(active => el.contains(active)),\n      distinctUntilChanged()\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  debounce,\n  defer,\n  fromEvent,\n  identity,\n  map,\n  merge,\n  startWith,\n  timer\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch element hover\n *\n * The second parameter allows to specify a timeout in milliseconds after which\n * the hover state will be reset to `false`. This is useful for tooltips which\n * should disappear after a certain amount of time, in order to allow the user\n * to move the cursor from the host to the tooltip.\n *\n * @param el - Element\n * @param timeout - Timeout\n *\n * @returns Element hover observable\n */\nexport function watchElementHover(\n  el: HTMLElement, timeout?: number\n): Observable<boolean> {\n  return defer(() => merge(\n    fromEvent(el, \"mouseenter\").pipe(map(() => true)),\n    fromEvent(el, \"mouseleave\").pipe(map(() => false))\n  )\n    .pipe(\n      timeout ? debounce(active => timer(+!active * timeout)) : identity,\n      startWith(el.matches(\":hover\"))\n    )\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { JSX as JSXInternal } from \"preact\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * HTML attributes\n */\ntype Attributes =\n  & JSXInternal.HTMLAttributes\n  & JSXInternal.SVGAttributes\n  & Record<string, any>\n\n/**\n * Child element\n */\ntype Child =\n  | ChildNode\n  | HTMLElement\n  | Text\n  | string\n  | number\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Append a child node to an element\n *\n * @param el - Element\n * @param child - Child node(s)\n */\nfunction appendChild(el: HTMLElement, child: Child | Child[]): void {\n\n  /* Handle primitive types (including raw HTML) */\n  if (typeof child === \"string\" || typeof child === \"number\") {\n    el.innerHTML += child.toString()\n\n  /* Handle nodes */\n  } else if (child instanceof Node) {\n    el.appendChild(child)\n\n  /* Handle nested children */\n  } else if (Array.isArray(child)) {\n    for (const node of child)\n      appendChild(el, node)\n  }\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * JSX factory\n *\n * @template T - Element type\n *\n * @param tag - HTML tag\n * @param attributes - HTML attributes\n * @param children - Child elements\n *\n * @returns Element\n */\nexport function h<T extends keyof HTMLElementTagNameMap>(\n  tag: T, attributes?: Attributes | null, ...children: Child[]\n): HTMLElementTagNameMap[T]\n\nexport function h<T extends h.JSX.Element>(\n  tag: string, attributes?: Attributes | null, ...children: Child[]\n): T\n\nexport function h<T extends h.JSX.Element>(\n  tag: string, attributes?: Attributes | null, ...children: Child[]\n): T {\n  const el = document.createElement(tag)\n\n  /* Set attributes, if any */\n  if (attributes)\n    for (const attr of Object.keys(attributes)) {\n      if (typeof attributes[attr] === \"undefined\")\n        continue\n\n      /* Set default attribute or boolean */\n      if (typeof attributes[attr] !== \"boolean\")\n        el.setAttribute(attr, attributes[attr])\n      else\n        el.setAttribute(attr, \"\")\n    }\n\n  /* Append child nodes */\n  for (const child of children)\n    appendChild(el, child)\n\n  /* Return element */\n  return el as T\n}\n\n/* ----------------------------------------------------------------------------\n * Namespace\n * ------------------------------------------------------------------------- */\n\nexport declare namespace h {\n  namespace JSX {\n    type Element = HTMLElement\n    type IntrinsicElements = JSXInternal.IntrinsicElements\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Round a number for display with repository facts\n *\n * This is a reverse-engineered version of GitHub's weird rounding algorithm\n * for stars, forks and all other numbers. While all numbers below `1,000` are\n * returned as-is, bigger numbers are converted to fixed numbers:\n *\n * - `1,049` => `1k`\n * - `1,050` => `1.1k`\n * - `1,949` => `1.9k`\n * - `1,950` => `2k`\n *\n * @param value - Original value\n *\n * @returns Rounded value\n */\nexport function round(value: number): string {\n  if (value > 999) {\n    const digits = +((value - 950) % 1000 > 99)\n    return `${((value + 0.000001) / 1000).toFixed(digits)}k`\n  } else {\n    return value.toString()\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  defer,\n  finalize,\n  fromEvent,\n  map,\n  merge,\n  switchMap,\n  take,\n  throwError\n} from \"rxjs\"\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create and load a `script` element\n *\n * This function returns an observable that will emit when the script was\n * successfully loaded, or throw an error if it wasn't.\n *\n * @param src - Script URL\n *\n * @returns Script observable\n */\nexport function watchScript(src: string): Observable<void> {\n  const script = h(\"script\", { src })\n  return defer(() => {\n    document.head.appendChild(script)\n    return merge(\n      fromEvent(script, \"load\"),\n      fromEvent(script, \"error\")\n        .pipe(\n          switchMap(() => (\n            throwError(() => new ReferenceError(`Invalid script: ${src}`))\n          ))\n        )\n    )\n      .pipe(\n        map(() => undefined),\n        finalize(() => document.head.removeChild(script)),\n        take(1)\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  NEVER,\n  Observable,\n  Subject,\n  defer,\n  filter,\n  finalize,\n  map,\n  merge,\n  of,\n  shareReplay,\n  startWith,\n  switchMap,\n  tap\n} from \"rxjs\"\n\nimport { watchScript } from \"../../../script\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Element offset\n */\nexport interface ElementSize {\n  width: number                        /* Element width */\n  height: number                       /* Element height */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Resize observer entry subject\n */\nconst entry$ = new Subject<ResizeObserverEntry>()\n\n/**\n * Resize observer observable\n *\n * This observable will create a `ResizeObserver` on the first subscription\n * and will automatically terminate it when there are no more subscribers.\n * It's quite important to centralize observation in a single `ResizeObserver`,\n * as the performance difference can be quite dramatic, as the link shows.\n *\n * If the browser doesn't have a `ResizeObserver` implementation available, a\n * polyfill is automatically downloaded from unpkg.com. This is also compatible\n * with the built-in privacy plugin, which will download the polyfill and put\n * it alongside the built site for self-hosting.\n *\n * @see https://bit.ly/3iIYfEm - Google Groups on performance\n */\nconst observer$ = defer(() => (\n  typeof ResizeObserver === \"undefined\"\n    ? watchScript(\"https://unpkg.com/resize-observer-polyfill\")\n    : of(undefined)\n))\n  .pipe(\n    map(() => new ResizeObserver(entries => (\n      entries.forEach(entry => entry$.next(entry))\n    ))),\n    switchMap(observer => merge(NEVER, of(observer)).pipe(\n      finalize(() => observer.disconnect())\n    )),\n    shareReplay(1)\n  )\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element size\n *\n * @param el - Element\n *\n * @returns Element size\n */\nexport function getElementSize(\n  el: HTMLElement\n): ElementSize {\n  return {\n    width:  el.offsetWidth,\n    height: el.offsetHeight\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element size\n *\n * This function returns an observable that subscribes to a single internal\n * instance of `ResizeObserver` upon subscription, and emit resize events until\n * termination. Note that this function should not be called with the same\n * element twice, as the first unsubscription will terminate observation.\n *\n * Sadly, we can't use the `DOMRect` objects returned by the observer, because\n * we need the emitted values to be consistent with `getElementSize`, which will\n * return the used values (rounded) and not actual values (unrounded). Thus, we\n * use the `offset*` properties. See the linked GitHub issue.\n *\n * @see https://bit.ly/3m0k3he - GitHub issue\n *\n * @param el - Element\n *\n * @returns Element size observable\n */\nexport function watchElementSize(\n  el: HTMLElement\n): Observable<ElementSize> {\n\n  // Compute target element - since inline elements cannot be observed by the\n  // current `ResizeObserver` implementation as provided by browsers, we need\n  // to determine the first containing parent element and use that one as a\n  // target, while we always compute the actual size from the element.\n  let target = el\n  while (target.clientWidth === 0)\n    if (target.parentElement)\n      target = target.parentElement\n    else\n      break\n\n  // Observe target element and recompute element size on resize - as described\n  // above, the target element is not necessarily the element of interest\n  return observer$.pipe(\n    tap(observer => observer.observe(target)),\n    switchMap(observer => entry$.pipe(\n      filter(entry => entry.target === target),\n      finalize(() => observer.unobserve(target))\n    )),\n    map(() => getElementSize(el)),\n    startWith(getElementSize(el))\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ElementSize } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element content size (= scroll width and height)\n *\n * @param el - Element\n *\n * @returns Element content size\n */\nexport function getElementContentSize(\n  el: HTMLElement\n): ElementSize {\n  return {\n    width:  el.scrollWidth,\n    height: el.scrollHeight\n  }\n}\n\n/**\n * Retrieve the overflowing container of an element, if any\n *\n * @param el - Element\n *\n * @returns Overflowing container or nothing\n */\nexport function getElementContainer(\n  el: HTMLElement\n): HTMLElement | undefined {\n  let parent = el.parentElement\n  while (parent)\n    if (\n      el.scrollWidth  <= parent.scrollWidth &&\n      el.scrollHeight <= parent.scrollHeight\n    )\n      parent = (el = parent).parentElement\n    else\n      break\n\n  /* Return overflowing container */\n  return parent ? el : undefined\n}\n\n/**\n * Retrieve all overflowing containers of an element, if any\n *\n * Note that this function has a slightly different behavior, so we should at\n * some point consider refactoring how overflowing containers are handled.\n *\n * @param el - Element\n *\n * @returns Overflowing containers\n */\nexport function getElementContainers(\n  el: HTMLElement\n): HTMLElement[] {\n  const containers: HTMLElement[] = []\n\n  // Walk up the DOM tree until we find an overflowing container\n  let parent = el.parentElement\n  while (parent) {\n    if (\n      el.clientWidth  > parent.clientWidth ||\n      el.clientHeight > parent.clientHeight\n    )\n      containers.push(parent)\n\n    // Continue with parent element\n    parent = (el = parent).parentElement\n  }\n\n  // If the page is short, the body might not be overflowing and there might be\n  // no other containers, which is why we need to make sure the body is present\n  if (containers.length === 0)\n    containers.push(document.documentElement)\n\n  // Return overflowing containers\n  return containers\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  animationFrameScheduler,\n  auditTime,\n  fromEvent,\n  map,\n  merge,\n  startWith\n} from \"rxjs\"\n\nimport { watchElementSize } from \"../../size\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Element offset\n */\nexport interface ElementOffset {\n  x: number                            /* Horizontal offset */\n  y: number                            /* Vertical offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element offset\n *\n * @param el - Element\n *\n * @returns Element offset\n */\nexport function getElementOffset(\n  el: HTMLElement\n): ElementOffset {\n  return {\n    x: el.offsetLeft,\n    y: el.offsetTop\n  }\n}\n\n/**\n * Retrieve absolute element offset\n *\n * @param el - Element\n *\n * @returns Element offset\n */\nexport function getElementOffsetAbsolute(\n  el: HTMLElement\n): ElementOffset {\n  const rect = el.getBoundingClientRect()\n  return {\n    x: rect.x + window.scrollX,\n    y: rect.y + window.scrollY\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element offset\n *\n * @param el - Element\n *\n * @returns Element offset observable\n */\nexport function watchElementOffset(\n  el: HTMLElement\n): Observable<ElementOffset> {\n  return merge(\n    fromEvent(window, \"load\"),\n    fromEvent(window, \"resize\")\n  )\n    .pipe(\n      auditTime(0, animationFrameScheduler),\n      map(() => getElementOffset(el)),\n      startWith(getElementOffset(el))\n    )\n}\n\n/**\n * Watch absolute element offset\n *\n * @param el - Element\n *\n * @returns Element offset observable\n */\nexport function watchElementOffsetAbsolute(\n  el: HTMLElement\n): Observable<ElementOffset> {\n  return merge(\n    watchElementOffset(el),\n    watchElementSize(document.body) // @todo find a better way for this\n  )\n    .pipe(\n      map(() => getElementOffsetAbsolute(el)),\n      startWith(getElementOffsetAbsolute(el))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  animationFrameScheduler,\n  auditTime,\n  fromEvent,\n  map,\n  merge,\n  startWith\n} from \"rxjs\"\n\nimport { ElementOffset } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element content offset (= scroll offset)\n *\n * @param el - Element\n *\n * @returns Element content offset\n */\nexport function getElementContentOffset(\n  el: HTMLElement\n): ElementOffset {\n  return {\n    x: el.scrollLeft,\n    y: el.scrollTop\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element content offset\n *\n * @param el - Element\n *\n * @returns Element content offset observable\n */\nexport function watchElementContentOffset(\n  el: HTMLElement\n): Observable<ElementOffset> {\n  return merge(\n    fromEvent(el, \"scroll\"),\n    fromEvent(window, \"scroll\"),\n    fromEvent(window, \"resize\")\n  )\n    .pipe(\n      auditTime(0, animationFrameScheduler),\n      map(() => getElementContentOffset(el)),\n      startWith(getElementContentOffset(el))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  NEVER,\n  Observable,\n  Subject,\n  defer,\n  distinctUntilChanged,\n  filter,\n  finalize,\n  map,\n  merge,\n  of,\n  shareReplay,\n  switchMap,\n  tap\n} from \"rxjs\"\n\nimport {\n  getElementContentSize,\n  getElementSize,\n  watchElementContentOffset\n} from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Intersection observer entry subject\n */\nconst entry$ = new Subject<IntersectionObserverEntry>()\n\n/**\n * Intersection observer observable\n *\n * This observable will create an `IntersectionObserver` on first subscription\n * and will automatically terminate it when there are no more subscribers.\n *\n * @see https://bit.ly/3iIYfEm - Google Groups on performance\n */\nconst observer$ = defer(() => of(\n  new IntersectionObserver(entries => {\n    for (const entry of entries)\n      entry$.next(entry)\n  }, {\n    threshold: 0\n  })\n))\n  .pipe(\n    switchMap(observer => merge(NEVER, of(observer))\n      .pipe(\n        finalize(() => observer.disconnect())\n      )\n    ),\n    shareReplay(1)\n  )\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch element visibility\n *\n * @param el - Element\n *\n * @returns Element visibility observable\n */\nexport function watchElementVisibility(\n  el: HTMLElement\n): Observable<boolean> {\n  return observer$\n    .pipe(\n      tap(observer => observer.observe(el)),\n      switchMap(observer => entry$\n        .pipe(\n          filter(({ target }) => target === el),\n          finalize(() => observer.unobserve(el)),\n          map(({ isIntersecting }) => isIntersecting)\n        )\n      )\n    )\n}\n\n/**\n * Watch element boundary\n *\n * This function returns an observable which emits whether the bottom content\n * boundary (= scroll offset) of an element is within a certain threshold.\n *\n * @param el - Element\n * @param threshold - Threshold\n *\n * @returns Element boundary observable\n */\nexport function watchElementBoundary(\n  el: HTMLElement, threshold = 16\n): Observable<boolean> {\n  return watchElementContentOffset(el)\n    .pipe(\n      map(({ y }) => {\n        const visible = getElementSize(el)\n        const content = getElementContentSize(el)\n        return y >= (\n          content.height - visible.height - threshold\n        )\n      }),\n      distinctUntilChanged()\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  fromEvent,\n  map,\n  startWith\n} from \"rxjs\"\n\nimport { getElement } from \"../element\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Toggle\n */\nexport type Toggle =\n  | \"drawer\"                           /* Toggle for drawer */\n  | \"search\"                           /* Toggle for search */\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Toggle map\n */\nconst toggles: Record<Toggle, HTMLInputElement> = {\n  drawer: getElement(\"[data-md-toggle=drawer]\"),\n  search: getElement(\"[data-md-toggle=search]\")\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve the value of a toggle\n *\n * @param name - Toggle\n *\n * @returns Toggle value\n */\nexport function getToggle(name: Toggle): boolean {\n  return toggles[name].checked\n}\n\n/**\n * Set toggle\n *\n * Simulating a click event seems to be the most cross-browser compatible way\n * of changing the value while also emitting a `change` event. Before, Material\n * used `CustomEvent` to programmatically change the value of a toggle, but this\n * is a much simpler and cleaner solution which doesn't require a polyfill.\n *\n * @param name - Toggle\n * @param value - Toggle value\n */\nexport function setToggle(name: Toggle, value: boolean): void {\n  if (toggles[name].checked !== value)\n    toggles[name].click()\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch toggle\n *\n * @param name - Toggle\n *\n * @returns Toggle value observable\n */\nexport function watchToggle(name: Toggle): Observable<boolean> {\n  const el = toggles[name]\n  return fromEvent(el, \"change\")\n    .pipe(\n      map(() => el.checked),\n      startWith(el.checked)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  filter,\n  fromEvent,\n  map,\n  merge,\n  share,\n  startWith,\n  switchMap\n} from \"rxjs\"\n\nimport { getActiveElement } from \"../element\"\nimport { getToggle } from \"../toggle\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Keyboard mode\n */\nexport type KeyboardMode =\n  | \"global\"                           /* Global */\n  | \"search\"                           /* Search is open */\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Keyboard\n */\nexport interface Keyboard {\n  mode: KeyboardMode                   /* Keyboard mode */\n  type: string                         /* Key type */\n  claim(): void                        /* Key claim */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Check whether an element may receive keyboard input\n *\n * @param el - Element\n * @param type - Key type\n *\n * @returns Test result\n */\nfunction isSusceptibleToKeyboard(\n  el: HTMLElement, type: string\n): boolean {\n  switch (el.constructor) {\n\n    /* Input elements */\n    case HTMLInputElement:\n      /* @ts-expect-error - omit unnecessary type cast */\n      if (el.type === \"radio\")\n        return /^Arrow/.test(type)\n      else\n        return true\n\n    /* Select element and textarea */\n    case HTMLSelectElement:\n    case HTMLTextAreaElement:\n      return true\n\n    /* Everything else */\n    default:\n      return el.isContentEditable\n  }\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch composition events\n *\n * @returns Composition observable\n */\nexport function watchComposition(): Observable<boolean> {\n  return merge(\n    fromEvent(window, \"compositionstart\").pipe(map(() => true)),\n    fromEvent(window, \"compositionend\").pipe(map(() => false))\n  )\n    .pipe(\n      startWith(false)\n    )\n}\n\n/**\n * Watch keyboard\n *\n * @returns Keyboard observable\n */\nexport function watchKeyboard(): Observable<Keyboard> {\n  const keyboard$ = fromEvent<KeyboardEvent>(window, \"keydown\")\n    .pipe(\n      filter(ev => !(ev.metaKey || ev.ctrlKey)),\n      map(ev => ({\n        mode: getToggle(\"search\") ? \"search\" : \"global\",\n        type: ev.key,\n        claim() {\n          ev.preventDefault()\n          ev.stopPropagation()\n        }\n      } as Keyboard)),\n      filter(({ mode, type }) => {\n        if (mode === \"global\") {\n          const active = getActiveElement()\n          if (typeof active !== \"undefined\")\n            return !isSusceptibleToKeyboard(active, type)\n        }\n        return true\n      }),\n      share()\n    )\n\n  /* Don't emit during composition events - see https://bit.ly/3te3Wl8 */\n  return watchComposition()\n    .pipe(\n      switchMap(active => !active ? keyboard$ : EMPTY)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Subject } from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve location\n *\n * This function returns a `URL` object (and not `Location`) to normalize the\n * typings across the application. Furthermore, locations need to be tracked\n * without setting them and `Location` is a singleton which represents the\n * current location.\n *\n * @returns URL\n */\nexport function getLocation(): URL {\n  return new URL(location.href)\n}\n\n/**\n * Set location\n *\n * If instant navigation is enabled, this function creates a temporary anchor\n * element, sets the `href` attribute, appends it to the body, clicks it, and\n * then removes it again. The event will bubble up the DOM and be intercepted\n * by the instant navigation event handlers.\n *\n * Note that we must append and remove the anchor element, or the event will\n * not bubble up the DOM, making it impossible to intercept it.\n *\n * @param url - URL to navigate to\n * @param navigate - Force navigation\n */\nexport function setLocation(\n  url: URL | HTMLLinkElement, navigate = false\n): void {\n  if (feature(\"navigation.instant\") && !navigate) {\n    const el = h(\"a\", { href: url.href })\n    document.body.appendChild(el)\n    el.click()\n    el.remove()\n\n  // If we're not using instant navigation, and the page should not be reloaded\n  // just instruct the browser to navigate to the given URL\n  } else {\n    location.href = url.href\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch location\n *\n * @returns Location subject\n */\nexport function watchLocation(): Subject<URL> {\n  return new Subject<URL>()\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  filter,\n  fromEvent,\n  map,\n  merge,\n  shareReplay,\n  startWith\n} from \"rxjs\"\n\nimport { getOptionalElement } from \"~/browser\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve location hash\n *\n * @returns Location hash\n */\nexport function getLocationHash(): string {\n  return location.hash.slice(1)\n}\n\n/**\n * Set location hash\n *\n * Setting a new fragment identifier via `location.hash` will have no effect\n * if the value doesn't change. When a new fragment identifier is set, we want\n * the browser to target the respective element at all times, which is why we\n * use this dirty little trick.\n *\n * @param hash - Location hash\n */\nexport function setLocationHash(hash: string): void {\n  const el = h(\"a\", { href: hash })\n  el.addEventListener(\"click\", ev => ev.stopPropagation())\n  el.click()\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch location hash\n *\n * @param location$ - Location observable\n *\n * @returns Location hash observable\n */\nexport function watchLocationHash(\n  location$: Observable<URL>\n): Observable<string> {\n  return merge(\n    fromEvent<HashChangeEvent>(window, \"hashchange\"),\n    location$\n  )\n    .pipe(\n      map(getLocationHash),\n      startWith(getLocationHash()),\n      filter(hash => hash.length > 0),\n      shareReplay(1)\n    )\n}\n\n/**\n * Watch location target\n *\n * @param location$ - Location observable\n *\n * @returns Location target observable\n */\nexport function watchLocationTarget(\n  location$: Observable<URL>\n): Observable<HTMLElement> {\n  return watchLocationHash(location$)\n    .pipe(\n      map(id => getOptionalElement(`[id=\"${id}\"]`)!),\n      filter(el => typeof el !== \"undefined\")\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  fromEvent,\n  fromEventPattern,\n  map,\n  merge,\n  startWith,\n  switchMap\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch media query\n *\n * Note that although `MediaQueryList.addListener` is deprecated we have to\n * use it, because it's the only way to ensure proper downward compatibility.\n *\n * @see https://bit.ly/3dUBH2m - GitHub issue\n *\n * @param query - Media query\n *\n * @returns Media observable\n */\nexport function watchMedia(query: string): Observable<boolean> {\n  const media = matchMedia(query)\n  return fromEventPattern<boolean>(next => (\n    media.addListener(() => next(media.matches))\n  ))\n    .pipe(\n      startWith(media.matches)\n    )\n}\n\n/**\n * Watch print mode\n *\n * @returns Print observable\n */\nexport function watchPrint(): Observable<boolean> {\n  const media = matchMedia(\"print\")\n  return merge(\n    fromEvent(window, \"beforeprint\").pipe(map(() => true)),\n    fromEvent(window, \"afterprint\").pipe(map(() => false))\n  )\n    .pipe(\n      startWith(media.matches)\n    )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Toggle an observable with a media observable\n *\n * @template T - Data type\n *\n * @param query$ - Media observable\n * @param factory - Observable factory\n *\n * @returns Toggled observable\n */\nexport function at<T>(\n  query$: Observable<boolean>, factory: () => Observable<T>\n): Observable<T> {\n  return query$\n    .pipe(\n      switchMap(active => active ? factory() : EMPTY)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  map,\n  shareReplay,\n  switchMap\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Options\n */\ninterface Options {\n  progress$?: Subject<number>          // Progress subject\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch the given URL\n *\n * This function returns an observable that emits the response as a blob and\n * completes, or emits an error if the request failed. The caller can cancel\n * the request by unsubscribing at any time, which will automatically abort\n * the inflight request and complete the observable.\n *\n * Note that we use `XMLHTTPRequest` not because we're nostalgic, but because\n * it's the only way to get progress events for downloads and also allow for\n * cancellation of requests, as the official Fetch API does not support this\n * yet, even though we're already in 2024.\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function request(\n  url: URL | string, options?: Options\n): Observable<Blob> {\n  return new Observable<Blob>(observer => {\n    const req = new XMLHttpRequest()\n    req.open(\"GET\", `${url}`)\n    req.responseType = \"blob\"\n\n    // Handle response\n    req.addEventListener(\"load\", () => {\n      if (req.status >= 200 && req.status < 300) {\n        observer.next(req.response)\n        observer.complete()\n\n      // Every response that is not in the 2xx range is considered an error\n      } else {\n        observer.error(new Error(req.statusText))\n      }\n    })\n\n    // Handle network errors\n    req.addEventListener(\"error\", () => {\n      observer.error(new Error(\"Network error\"))\n    })\n\n    // Handle aborted requests\n    req.addEventListener(\"abort\", () => {\n      observer.complete()\n    })\n\n    // Handle download progress\n    if (typeof options?.progress$ !== \"undefined\") {\n      req.addEventListener(\"progress\", event => {\n        if (event.lengthComputable) {\n          options.progress$!.next((event.loaded / event.total) * 100)\n\n        // Hack: Chromium doesn't report the total number of bytes if content\n        // is compressed, so we need this fallback - see https://t.ly/ZXofI\n        } else {\n          const length = req.getResponseHeader(\"Content-Length\") ?? 0\n          options.progress$!.next((event.loaded / +length) * 100)\n        }\n      })\n\n      // Immediately set progress to 5% to indicate that we're loading\n      options.progress$.next(5)\n    }\n\n    // Send request and automatically abort request upon unsubscription\n    req.send()\n    return () => req.abort()\n  })\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Fetch JSON from the given URL\n *\n * @template T - Data type\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function requestJSON<T>(\n  url: URL | string, options?: Options\n): Observable<T> {\n  return request(url, options)\n    .pipe(\n      switchMap(res => res.text()),\n      map(body => JSON.parse(body) as T),\n      shareReplay(1)\n    )\n}\n\n/**\n * Fetch HTML from the given URL\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function requestHTML(\n  url: URL | string, options?: Options\n): Observable<Document> {\n  const dom = new DOMParser()\n  return request(url, options)\n    .pipe(\n      switchMap(res => res.text()),\n      map(res => dom.parseFromString(res, \"text/html\")),\n      shareReplay(1)\n    )\n}\n\n/**\n * Fetch XML from the given URL\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function requestXML(\n  url: URL | string, options?: Options\n): Observable<Document> {\n  const dom = new DOMParser()\n  return request(url, options)\n    .pipe(\n      switchMap(res => res.text()),\n      map(res => dom.parseFromString(res, \"text/xml\")),\n      shareReplay(1)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  fromEvent,\n  map,\n  merge,\n  startWith\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport offset\n */\nexport interface ViewportOffset {\n  x: number                            /* Horizontal offset */\n  y: number                            /* Vertical offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve viewport offset\n *\n * On iOS Safari, viewport offset can be negative due to overflow scrolling.\n * As this may induce strange behaviors downstream, we'll just limit it to 0.\n *\n * @returns Viewport offset\n */\nexport function getViewportOffset(): ViewportOffset {\n  return {\n    x: Math.max(0, scrollX),\n    y: Math.max(0, scrollY)\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport offset\n *\n * @returns Viewport offset observable\n */\nexport function watchViewportOffset(): Observable<ViewportOffset> {\n  return merge(\n    fromEvent(window, \"scroll\", { passive: true }),\n    fromEvent(window, \"resize\", { passive: true })\n  )\n    .pipe(\n      map(getViewportOffset),\n      startWith(getViewportOffset())\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  fromEvent,\n  map,\n  startWith\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport size\n */\nexport interface ViewportSize {\n  width: number                        /* Viewport width */\n  height: number                       /* Viewport height */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve viewport size\n *\n * @returns Viewport size\n */\nexport function getViewportSize(): ViewportSize {\n  return {\n    width:  innerWidth,\n    height: innerHeight\n  }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport size\n *\n * @returns Viewport size observable\n */\nexport function watchViewportSize(): Observable<ViewportSize> {\n  return fromEvent(window, \"resize\", { passive: true })\n    .pipe(\n      map(getViewportSize),\n      startWith(getViewportSize())\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  combineLatest,\n  map,\n  shareReplay\n} from \"rxjs\"\n\nimport {\n  ViewportOffset,\n  watchViewportOffset\n} from \"../offset\"\nimport {\n  ViewportSize,\n  watchViewportSize\n} from \"../size\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport\n */\nexport interface Viewport {\n  offset: ViewportOffset               /* Viewport offset */\n  size: ViewportSize                   /* Viewport size */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport\n *\n * @returns Viewport observable\n */\nexport function watchViewport(): Observable<Viewport> {\n  return combineLatest([\n    watchViewportOffset(),\n    watchViewportSize()\n  ])\n    .pipe(\n      map(([offset, size]) => ({ offset, size })),\n      shareReplay(1)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  combineLatest,\n  distinctUntilKeyChanged,\n  map\n} from \"rxjs\"\n\nimport { Header } from \"~/components\"\n\nimport { getElementOffset } from \"../../element\"\nimport { Viewport } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport relative to element\n *\n * @param el - Element\n * @param options - Options\n *\n * @returns Viewport observable\n */\nexport function watchViewportAt(\n  el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable<Viewport> {\n  const size$ = viewport$\n    .pipe(\n      distinctUntilKeyChanged(\"size\")\n    )\n\n  /* Compute element offset */\n  const offset$ = combineLatest([size$, header$])\n    .pipe(\n      map(() => getElementOffset(el))\n    )\n\n  /* Compute relative viewport, return hot observable */\n  return combineLatest([header$, viewport$, offset$])\n    .pipe(\n      map(([{ height }, { offset, size }, { x, y }]) => ({\n        offset: {\n          x: offset.x - x,\n          y: offset.y - y + height\n        },\n        size\n      }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  endWith,\n  fromEvent,\n  ignoreElements,\n  mergeWith,\n  share,\n  takeUntil\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Worker message\n */\nexport interface WorkerMessage {\n  type: unknown                        /* Message type */\n  data?: unknown                       /* Message data */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create an observable for receiving from a web worker\n *\n * @template T - Data type\n *\n * @param worker - Web worker\n *\n * @returns Message observable\n */\nfunction recv<T>(worker: Worker): Observable<T> {\n  return fromEvent<MessageEvent<T>, T>(worker, \"message\", ev => ev.data)\n}\n\n/**\n * Create a subject for sending to a web worker\n *\n * @template T - Data type\n *\n * @param worker - Web worker\n *\n * @returns Message subject\n */\nfunction send<T>(worker: Worker): Subject<T> {\n  const send$ = new Subject<T>()\n  send$.subscribe(data => worker.postMessage(data))\n\n  /* Return message subject */\n  return send$\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a bidirectional communication channel to a web worker\n *\n * @template T - Data type\n *\n * @param url - Worker URL\n * @param worker - Worker\n *\n * @returns Worker subject\n */\nexport function watchWorker<T extends WorkerMessage>(\n  url: string, worker = new Worker(url)\n): Subject<T> {\n  const recv$ = recv<T>(worker)\n  const send$ = send<T>(worker)\n\n  /* Create worker subject and forward messages */\n  const worker$ = new Subject<T>()\n  worker$.subscribe(send$)\n\n  /* Return worker subject */\n  const done$ = send$.pipe(ignoreElements(), endWith(true))\n  return worker$\n    .pipe(\n      ignoreElements(),\n      mergeWith(recv$.pipe(takeUntil(done$))),\n      share()\n    ) as Subject<T>\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { getElement, getLocation } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Feature flag\n */\nexport type Flag =\n  | \"announce.dismiss\"                 /* Dismissable announcement bar */\n  | \"content.code.annotate\"            /* Code annotations */\n  | \"content.code.copy\"                /* Code copy button */\n  | \"content.code.select\"              /* Code selection */\n  | \"content.footnote.tooltips\"        /* Footnote tooltips */\n  | \"content.lazy\"                     /* Lazy content elements */\n  | \"content.tabs.link\"                /* Link content tabs */\n  | \"content.tooltips\"                 /* Tooltips */\n  | \"header.autohide\"                  /* Hide header */\n  | \"navigation.expand\"                /* Automatic expansion */\n  | \"navigation.indexes\"               /* Section pages */\n  | \"navigation.instant\"               /* Instant navigation */\n  | \"navigation.instant.prefetch\"      /* Instant navigation prefetching */\n  | \"navigation.instant.progress\"      /* Instant navigation progress */\n  | \"navigation.instant.preview\"       /* Instant preview */\n  | \"navigation.sections\"              /* Section navigation */\n  | \"navigation.tabs\"                  /* Tabs navigation */\n  | \"navigation.tabs.sticky\"           /* Tabs navigation (sticky) */\n  | \"navigation.top\"                   /* Back-to-top button */\n  | \"navigation.tracking\"              /* Anchor tracking */\n  | \"search.highlight\"                 /* Search highlighting */\n  | \"search.share\"                     /* Search sharing */\n  | \"search.suggest\"                   /* Search suggestions */\n  | \"toc.follow\"                       /* Following table of contents */\n  | \"toc.integrate\"                    /* Integrated table of contents */\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Translation\n */\nexport type Translation =\n  | \"clipboard.copy\"                   /* Copy to clipboard */\n  | \"clipboard.copied\"                 /* Copied to clipboard */\n  | \"search.result.placeholder\"        /* Type to start searching */\n  | \"search.result.none\"               /* No matching documents */\n  | \"search.result.one\"                /* 1 matching document */\n  | \"search.result.other\"              /* # matching documents */\n  | \"search.result.more.one\"           /* 1 more on this page */\n  | \"search.result.more.other\"         /* # more on this page */\n  | \"search.result.term.missing\"       /* Missing */\n  | \"select.version\"                   /* Version selector */\n\n/**\n * Translations\n */\nexport type Translations =\n  Record<Translation, string>\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Versioning\n */\nexport interface Versioning {\n  provider: \"mike\"                     /* Version provider */\n  default?: string | string[]          /* Default version */\n  alias?: boolean                      /* Show alias */\n}\n\n/**\n * Configuration\n */\nexport interface Config {\n  base: string                         /* Base URL */\n  features: Flag[]                     /* Feature flags */\n  translations: Translations           /* Translations */\n  search: string                       /* Search worker URL */\n  annotate?: Record<string, string[]>  /* Annotation mappings */\n  tags?: Record<string, string>        /* Tags mapping */\n  version?: Versioning                 /* Versioning */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve global configuration and make base URL absolute\n */\nconst script = getElement(\"#__config\")\nconst config: Config = JSON.parse(script.textContent!)\nconfig.base = `${new URL(config.base, getLocation())}`\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve global configuration\n *\n * @returns Global configuration\n */\nexport function configuration(): Config {\n  return config\n}\n\n/**\n * Check whether a feature flag is enabled\n *\n * @param flag - Feature flag\n *\n * @returns Test result\n */\nexport function feature(flag: Flag): boolean {\n  return config.features.includes(flag)\n}\n\n/**\n * Retrieve the translation for the given key\n *\n * @param key - Key to be translated\n * @param value - Positional value, if any\n *\n * @returns Translation\n */\nexport function translation(\n  key: Translation, value?: string | number\n): string {\n  return typeof value !== \"undefined\"\n    ? config.translations[key].replace(\"#\", value.toString())\n    : config.translations[key]\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { getElement, getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Component type\n */\nexport type ComponentType =\n  | \"announce\"                         /* Announcement bar */\n  | \"container\"                        /* Container */\n  | \"consent\"                          /* Consent */\n  | \"content\"                          /* Content */\n  | \"dialog\"                           /* Dialog */\n  | \"header\"                           /* Header */\n  | \"header-title\"                     /* Header title */\n  | \"header-topic\"                     /* Header topic */\n  | \"main\"                             /* Main area */\n  | \"outdated\"                         /* Version warning */\n  | \"palette\"                          /* Color palette */\n  | \"progress\"                         /* Progress indicator */\n  | \"search\"                           /* Search */\n  | \"search-query\"                     /* Search input */\n  | \"search-result\"                    /* Search results */\n  | \"search-share\"                     /* Search sharing */\n  | \"search-suggest\"                   /* Search suggestions */\n  | \"sidebar\"                          /* Sidebar */\n  | \"skip\"                             /* Skip link */\n  | \"source\"                           /* Repository information */\n  | \"tabs\"                             /* Navigation tabs */\n  | \"toc\"                              /* Table of contents */\n  | \"top\"                              /* Back-to-top button */\n\n/**\n * Component\n *\n * @template T - Component type\n * @template U - Reference type\n */\nexport type Component<\n  T extends {} = {},\n  U extends HTMLElement = HTMLElement\n> =\n  T & {\n    ref: U                             /* Component reference */\n  }\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Component type map\n */\ninterface ComponentTypeMap {\n  \"announce\": HTMLElement              /* Announcement bar */\n  \"container\": HTMLElement             /* Container */\n  \"consent\": HTMLElement               /* Consent */\n  \"content\": HTMLElement               /* Content */\n  \"dialog\": HTMLElement                /* Dialog */\n  \"header\": HTMLElement                /* Header */\n  \"header-title\": HTMLElement          /* Header title */\n  \"header-topic\": HTMLElement          /* Header topic */\n  \"main\": HTMLElement                  /* Main area */\n  \"outdated\": HTMLElement              /* Version warning */\n  \"palette\": HTMLElement               /* Color palette */\n  \"progress\": HTMLElement              /* Progress indicator */\n  \"search\": HTMLElement                /* Search */\n  \"search-query\": HTMLInputElement     /* Search input */\n  \"search-result\": HTMLElement         /* Search results */\n  \"search-share\": HTMLAnchorElement    /* Search sharing */\n  \"search-suggest\": HTMLElement        /* Search suggestions */\n  \"sidebar\": HTMLElement               /* Sidebar */\n  \"skip\": HTMLAnchorElement            /* Skip link */\n  \"source\": HTMLAnchorElement          /* Repository information */\n  \"tabs\": HTMLElement                  /* Navigation tabs */\n  \"toc\": HTMLElement                   /* Table of contents */\n  \"top\": HTMLAnchorElement             /* Back-to-top button */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve the element for a given component or throw a reference error\n *\n * @template T - Component type\n *\n * @param type - Component type\n * @param node - Node of reference\n *\n * @returns Element\n */\nexport function getComponentElement<T extends ComponentType>(\n  type: T, node: ParentNode = document\n): ComponentTypeMap[T] {\n  return getElement(`[data-md-component=${type}]`, node)\n}\n\n/**\n * Retrieve all elements for a given component\n *\n * @template T - Component type\n *\n * @param type - Component type\n * @param node - Node of reference\n *\n * @returns Elements\n */\nexport function getComponentElements<T extends ComponentType>(\n  type: T, node: ParentNode = document\n): ComponentTypeMap[T][] {\n  return getElements(`[data-md-component=${type}]`, node)\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  defer,\n  finalize,\n  fromEvent,\n  map,\n  tap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport { getElement } from \"~/browser\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Announcement bar\n */\nexport interface Announce {\n  hash: number                        /* Content hash */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch announcement bar\n *\n * @param el - Announcement bar element\n *\n * @returns Announcement bar observable\n */\nexport function watchAnnounce(\n  el: HTMLElement\n): Observable<Announce> {\n  const button = getElement(\".md-typeset > :first-child\", el)\n  return fromEvent(button, \"click\", { once: true })\n    .pipe(\n      map(() => getElement(\".md-typeset\", el)),\n      map(content => ({ hash: __md_hash(content.innerHTML) }))\n    )\n}\n\n/**\n * Mount announcement bar\n *\n * @param el - Announcement bar element\n *\n * @returns Announcement bar component observable\n */\nexport function mountAnnounce(\n  el: HTMLElement\n): Observable<Component<Announce>> {\n  if (!feature(\"announce.dismiss\") || !el.childElementCount)\n    return EMPTY\n\n  /* Support instant navigation - see https://t.ly/3FTme */\n  if (!el.hidden) {\n    const content = getElement(\".md-typeset\", el)\n    if (__md_hash(content.innerHTML) === __md_get(\"__announce\"))\n      el.hidden = true\n  }\n\n  /* Mount component on subscription */\n  return defer(() => {\n    const push$ = new Subject<Announce>()\n    push$.subscribe(({ hash }) => {\n      el.hidden = true\n\n      /* Persist preference in local storage */\n      __md_set<number>(\"__announce\", hash)\n    })\n\n    /* Create and return component */\n    return watchAnnounce(el)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  finalize,\n  map,\n  tap\n} from \"rxjs\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Consent\n */\nexport interface Consent {\n  hidden: boolean                      /* Consent is hidden */\n}\n\n/**\n * Consent defaults\n */\nexport interface ConsentDefaults {\n  analytics?: boolean                  /* Consent for Analytics */\n  github?: boolean                     /* Consent for GitHub */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  target$: Observable<HTMLElement>     /* Target observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch consent\n *\n * @param el - Consent element\n * @param options - Options\n *\n * @returns Consent observable\n */\nexport function watchConsent(\n  el: HTMLElement, { target$ }: WatchOptions\n): Observable<Consent> {\n  return target$\n    .pipe(\n      map(target => ({ hidden: target !== el }))\n    )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount consent\n *\n * @param el - Consent element\n * @param options - Options\n *\n * @returns Consent component observable\n */\nexport function mountConsent(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<Consent>> {\n  const internal$ = new Subject<Consent>()\n  internal$.subscribe(({ hidden }) => {\n    el.hidden = hidden\n  })\n\n  /* Create and return component */\n  return watchConsent(el, options)\n    .pipe(\n      tap(state => internal$.next(state)),\n      finalize(() => internal$.complete()),\n      map(state => ({ ref: el, ...state }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ComponentChild } from \"preact\"\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Tooltip style\n */\nexport type TooltipStyle =\n  | \"inline\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a tooltip\n *\n * @param id - Tooltip identifier\n * @param style - Tooltip style\n *\n * @returns Element\n */\nexport function renderTooltip(\n  id?: string, style?: TooltipStyle\n): HTMLElement {\n  if (style === \"inline\") { // @todo refactor control flow\n    return (\n      <div class=\"md-tooltip md-tooltip--inline\" id={id} role=\"tooltip\">\n        <div class=\"md-tooltip__inner md-typeset\"></div>\n      </div>\n    )\n  } else {\n    return (\n      <div class=\"md-tooltip\" id={id} role=\"tooltip\">\n        <div class=\"md-tooltip__inner md-typeset\"></div>\n      </div>\n    )\n  }\n}\n\n/**\n * Render a tooltip\n *\n * @param children - Child nodes\n *\n * @returns Element\n */\nexport function renderTooltip2(\n  ...children: ComponentChild[]\n): HTMLElement {\n  return (\n    <div class=\"md-tooltip2\" role=\"dialog\">\n      <div class=\"md-tooltip2__inner md-typeset\">\n        {children}\n      </div>\n    </div>\n  )\n}\n\n// @todo: rename\nexport function renderInlineTooltip2(\n  ...children: ComponentChild[]\n): HTMLElement {\n  return (\n    <div class=\"md-tooltip2\" role=\"tooltip\">\n      <div class=\"md-tooltip2__inner md-typeset\">\n        {children}\n      </div>\n    </div>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\nimport { renderTooltip } from \"../tooltip\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render an annotation\n *\n * @param id - Annotation identifier\n * @param prefix - Tooltip identifier prefix\n *\n * @returns Element\n */\nexport function renderAnnotation(\n  id: string | number, prefix?: string\n): HTMLElement {\n  prefix = prefix ? `${prefix}_annotation_${id}` : undefined\n\n  /* Render tooltip with anchor, if given */\n  if (prefix) {\n    const anchor = prefix ? `#${prefix}` : undefined\n    return (\n      <aside class=\"md-annotation\" tabIndex={0}>\n        {renderTooltip(prefix)}\n        <a href={anchor} class=\"md-annotation__index\" tabIndex={-1}>\n          <span data-md-annotation-id={id}></span>\n        </a>\n      </aside>\n    )\n  } else {\n    return (\n      <aside class=\"md-annotation\" tabIndex={0}>\n        {renderTooltip(prefix)}\n        <span class=\"md-annotation__index\" tabIndex={-1}>\n          <span data-md-annotation-id={id}></span>\n        </span>\n      </aside>\n    )\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { translation } from \"~/_\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a 'copy-to-clipboard' button\n *\n * @param id - Unique identifier\n *\n * @returns Element\n */\nexport function renderClipboardButton(id: string): HTMLElement {\n  return (\n    <button\n      class=\"md-code__button\"\n      title={translation(\"clipboard.copy\")}\n      data-clipboard-target={`#${id} > code`}\n      data-md-type=\"copy\"\n    ></button>\n  )\n}\n\nexport function renderSelectionButton(): HTMLElement {\n  return (\n    <button\n      class=\"md-code__button\"\n      title=\"Toggle line selection\"\n      data-md-type=\"select\"\n    ></button>\n  )\n}\n\nexport function renderCodeBlockNavigation() {\n  return (\n    <nav class=\"md-code__nav\"></nav>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\nimport { ComponentChild } from \"preact\"\n\nimport { configuration, feature, translation } from \"~/_\"\nimport { SearchItem } from \"~/integrations/search\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Render flag\n */\nconst enum Flag {\n  TEASER = 1,                          /* Render teaser */\n  PARENT = 2                           /* Render as parent */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper function\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a search document\n *\n * @param document - Search document\n * @param flag - Render flags\n *\n * @returns Element\n */\nfunction renderSearchDocument(\n  document: SearchItem, flag: Flag\n): HTMLElement {\n  const parent = flag & Flag.PARENT\n  const teaser = flag & Flag.TEASER\n\n  /* Render missing query terms */\n  const missing = Object.keys(document.terms)\n    .filter(key => !document.terms[key])\n    .reduce<ComponentChild[]>((list, key) => [\n      ...list, <del>{escapeHTML(key)}</del>, \" \"\n    ], [])\n    .slice(0, -1)\n\n  /* Assemble query string for highlighting */\n  const config = configuration()\n  const url = new URL(document.location, config.base)\n  if (feature(\"search.highlight\"))\n    url.searchParams.set(\"h\", Object.entries(document.terms)\n      .filter(([, match]) => match)\n      .reduce((highlight, [value]) => `${highlight} ${value}`.trim(), \"\")\n    )\n\n  /* Render article or section, depending on flags */\n  const { tags } = configuration()\n  return (\n    <a href={`${url}`} class=\"md-search-result__link\" tabIndex={-1}>\n      <article\n        class=\"md-search-result__article md-typeset\"\n        data-md-score={document.score.toFixed(2)}\n      >\n        {parent > 0 && <div class=\"md-search-result__icon md-icon\"></div>}\n        {parent > 0 && <h1>{document.title}</h1>}\n        {parent <= 0 && <h2>{document.title}</h2>}\n        {teaser > 0 && document.text.length > 0 &&\n          document.text\n        }\n        {document.tags && (\n          <nav class=\"md-tags\">\n            {document.tags.map(tag => {\n              const type = tags\n                ? tag in tags\n                  ? `md-tag-icon md-tag--${tags[tag]}`\n                  : \"md-tag-icon\"\n                : \"\"\n              return (\n                <span class={`md-tag ${type}`}>{tag}</span>\n              )\n            })}\n          </nav>\n        )}\n        {teaser > 0 && missing.length > 0 &&\n          <p class=\"md-search-result__terms\">\n            {translation(\"search.result.term.missing\")}: {...missing}\n          </p>\n        }\n      </article>\n    </a>\n  )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a search result\n *\n * @param result - Search result\n *\n * @returns Element\n */\nexport function renderSearchResultItem(\n  result: SearchItem[]\n): HTMLElement {\n  const threshold = result[0].score\n  const docs = [...result]\n\n  const config = configuration()\n\n  /* Find and extract parent article */\n  const parent = docs.findIndex(doc => {\n    const l = `${new URL(doc.location, config.base)}` // @todo hacky\n    return !l.includes(\"#\")\n  })\n  const [article] = docs.splice(parent, 1)\n\n  /* Determine last index above threshold */\n  let index = docs.findIndex(doc => doc.score < threshold)\n  if (index === -1)\n    index = docs.length\n\n  /* Partition sections */\n  const best = docs.slice(0, index)\n  const more = docs.slice(index)\n\n  /* Render children */\n  const children = [\n    renderSearchDocument(article, Flag.PARENT | +(!parent && index === 0)),\n    ...best.map(section => renderSearchDocument(section, Flag.TEASER)),\n    ...more.length ? [\n      <details class=\"md-search-result__more\">\n        <summary tabIndex={-1}>\n          <div>\n            {more.length > 0 && more.length === 1\n              ? translation(\"search.result.more.one\")\n              : translation(\"search.result.more.other\", more.length)\n            }\n          </div>\n        </summary>\n        {...more.map(section => renderSearchDocument(section, Flag.TEASER))}\n      </details>\n    ] : []\n  ]\n\n  /* Render search result */\n  return (\n    <li class=\"md-search-result__item\">\n      {children}\n    </li>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { SourceFacts } from \"~/components\"\nimport { h, round } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render repository facts\n *\n * @param facts - Repository facts\n *\n * @returns Element\n */\nexport function renderSourceFacts(facts: SourceFacts): HTMLElement {\n  return (\n    <ul class=\"md-source__facts\">\n      {Object.entries(facts).map(([key, value]) => (\n        <li class={`md-source__fact md-source__fact--${key}`}>\n          {typeof value === \"number\" ? round(value) : value}\n        </li>\n      ))}\n    </ul>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Tabbed control type\n */\ntype TabbedControlType =\n  | \"prev\"\n  | \"next\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render control for content tabs\n *\n * @param type - Control type\n *\n * @returns Element\n */\nexport function renderTabbedControl(\n  type: TabbedControlType\n): HTMLElement {\n  const classes = `tabbed-control tabbed-control--${type}`\n  return (\n    <div class={classes} hidden>\n      <button class=\"tabbed-button\" tabIndex={-1} aria-hidden=\"true\"></button>\n    </div>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a table inside a wrapper to improve scrolling on mobile\n *\n * @param table - Table element\n *\n * @returns Element\n */\nexport function renderTable(table: HTMLElement): HTMLElement {\n  return (\n    <div class=\"md-typeset__scrollwrap\">\n      <div class=\"md-typeset__table\">\n        {table}\n      </div>\n    </div>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { configuration, translation } from \"~/_\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Version properties\n */\nexport interface VersionProperties {\n  hidden?: boolean                     /* Version is hidden */\n}\n\n/**\n * Version\n */\nexport interface Version {\n  version: string                      /* Version identifier */\n  title: string                        /* Version title */\n  aliases: string[]                    /* Version aliases */\n  properties?: VersionProperties       /* Version properties */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a version\n *\n * @param version - Version\n *\n * @returns Element\n */\nfunction renderVersion(version: Version): HTMLElement {\n  const config = configuration()\n\n  /* Ensure trailing slash - see https://bit.ly/3rL5u3f */\n  const url = new URL(`../${version.version}/`, config.base)\n  return (\n    <li class=\"md-version__item\">\n      <a href={`${url}`} class=\"md-version__link\">\n        {version.title}\n        {config.version?.alias && version.aliases.length > 0 && (\n          <span class=\"md-version__alias\">\n            {version.aliases[0]}\n          </span>\n        )}\n      </a>\n    </li>\n  )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a version selector\n *\n * @param versions - Versions\n * @param active - Active version\n *\n * @returns Element\n */\nexport function renderVersionSelector(\n  versions: Version[], active: Version\n): HTMLElement {\n  const config = configuration()\n  versions = versions.filter(version => !version.properties?.hidden)\n  return (\n    <div class=\"md-version\">\n      <button\n        class=\"md-version__current\"\n        aria-label={translation(\"select.version\")}\n      >\n        {active.title}\n        {config.version?.alias && active.aliases.length > 0 && (\n          <span class=\"md-version__alias\">\n            {active.aliases[0]}\n          </span>\n        )}\n      </button>\n      <ul class=\"md-version__list\">\n        {versions.map(renderVersion)}\n      </ul>\n    </div>\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  BehaviorSubject,\n  EMPTY,\n  Observable,\n  Subject,\n  animationFrameScheduler,\n  combineLatest,\n  combineLatestWith,\n  debounce,\n  defer,\n  distinctUntilChanged,\n  endWith,\n  filter,\n  finalize,\n  first,\n  ignoreElements,\n  map,\n  mergeMap,\n  observeOn,\n  queueScheduler,\n  share,\n  startWith,\n  switchMap,\n  tap,\n  throttleTime,\n  timer,\n  withLatestFrom\n} from \"rxjs\"\n\nimport {\n  ElementOffset,\n  Viewport,\n  getElement,\n  getElementContainers,\n  getElementOffsetAbsolute,\n  getElementSize,\n  watchElementContentOffset,\n  watchElementFocus,\n  watchElementHover\n} from \"~/browser\"\nimport { renderInlineTooltip2 } from \"~/templates\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Tooltip\n */\nexport interface Tooltip {\n  active: boolean                      // Tooltip is active\n  offset: ElementOffset                // Tooltip offset\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dependencies\n */\ninterface Dependencies {\n  content$: Observable<HTMLElement>    // Tooltip content observable\n  viewport$: Observable<Viewport>      // Viewport observable\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Global sequence number for tooltips\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch tooltip\n *\n * This function tracks the tooltip host element, and deduces the active state\n * and offset of the tooltip from it. The active state is determined by whether\n * the host element is focused or hovered, and the offset is determined by the\n * host element's absolute position in the document.\n *\n * @param el - Tooltip host element\n * @param timeout - Timeout\n *\n * @returns Tooltip observable\n */\nexport function watchTooltip2(\n  el: HTMLElement, timeout = 250\n): Observable<Tooltip> {\n\n  // Compute whether tooltip should be shown - we need to watch both focus and\n  // hover events on the host element and emit if one of them is active. In case\n  // of a hover event, we keep the element visible for a short amount of time\n  // after the pointer left the host element for a better user experience.\n  const active$ =\n    combineLatest([\n      watchElementFocus(el),\n      watchElementHover(el, timeout)\n    ])\n      .pipe(\n        map(([focus, hover]) => focus || hover),\n        distinctUntilChanged()\n      )\n\n  // We need to determine all parent elements of the host element that are\n  // currently scrollable, as they might affect the position of the tooltip\n  // depending on their horizontal of vertical offset. We must track all of\n  // them and recompute the position of the tooltip if they change.\n  const offset$ =\n    defer(() => getElementContainers(el)).pipe(\n      mergeMap(watchElementContentOffset),\n      throttleTime(1),\n      // Note that we need to poll the value again if the active state changes,\n      // as otherwise the tooltip might be misplaced. This particularly happens\n      // when using third-party integrations like tablesort that change the\n      // position of elements \u2013 see https://t.ly/Y-V7X\n      combineLatestWith(active$),\n      map(() => getElementOffsetAbsolute(el)),\n    )\n\n  // Only track parent elements and compute offset of the tooltip host if the\n  // tooltip should be shown - we defer the computation of the offset until the\n  // tooltip becomes active for the first time. This is necessary, because we\n  // must also keep the tooltip active as long as it is focused or hovered.\n  return active$.pipe(\n    first(active => active),\n    switchMap(() => combineLatest([active$, offset$])),\n    map(([active, offset]) => ({ active, offset })),\n    share()\n  )\n}\n\n/**\n * Mount tooltip\n *\n * This function renders a tooltip with the content from the provided `content$`\n * observable as passed via the dependencies. If the returned element has a role\n * of type `dialog`, the tooltip is considered to be interactive, and rendered\n * either above or below the host element, depending on the available space.\n *\n * If the returned element has a role of type `tooltip`, the tooltip is always\n * rendered below the host element and considered to be non-interactive. This\n * allows us to reuse the same positioning logic for both interactive and\n * non-interactive tooltips, as it is largely the same.\n *\n * @param el - Tooltip host element\n * @param dependencies - Dependencies\n * @param timeout - Timeout @todo move into options\n *\n * @returns Tooltip component observable\n */\nexport function mountTooltip2(\n  el: HTMLElement, dependencies: Dependencies, timeout = 250\n): Observable<Component<Tooltip>> {\n  const { content$, viewport$ } = dependencies\n\n  // Compute unique tooltip id - this is necessary to associate the tooltip host\n  // element with the tooltip element for ARIA purposes\n  const id = `__tooltip2_${sequence++}`\n\n  // Create component on subscription\n  return defer(() => {\n    const push$ = new Subject<Tooltip>()\n\n    // Create subject to track tooltip presence and visibility - we use another\n    // purely internal subject to track the tooltip's presence and visibility,\n    // as the tooltip should be visible if the host element or tooltip itself\n    // is focused or hovered to allow for smooth pointer migration\n    const show$ = new BehaviorSubject(false)\n    push$.pipe(ignoreElements(), endWith(false))\n      .subscribe(show$)\n\n    // Create observable controlling tooltip element - we create and attach the\n    // tooltip only if it is actually present, in order to keep the number of\n    // elements low. We need to keep the tooltip visible for a short time after\n    // the pointer left the host element or tooltip itself. For this, we use an\n    // inner subscription to the tooltip observable, which we terminate when the\n    // tooltip should not be shown, automatically removing the element. Moreover\n    // we use the queue scheduler, which will schedule synchronously in case the\n    // tooltip should be shown, and asynchronously if it should be hidden.\n    const node$ = show$.pipe(\n      debounce(active => timer(+!active * 250, queueScheduler)),\n      distinctUntilChanged(),\n      switchMap(active => active ? content$ : EMPTY),\n      tap(node => node.id = id),\n      share()\n    )\n\n    // Compute tooltip presence and visibility - the tooltip should be shown if\n    // the host element or the tooltip itself is focused or hovered\n    combineLatest([\n      push$.pipe(map(({ active }) => active)),\n      node$.pipe(\n        switchMap(node => watchElementHover(node, 250)),\n        startWith(false)\n      )\n    ])\n      .pipe(map(states => states.some(active => active)))\n      .subscribe(show$)\n\n    // Compute tooltip origin - we need to compute the tooltip origin depending\n    // on the position of the host element, the viewport size, as well as the\n    // actual size of the tooltip, if positioned above. The tooltip must about\n    // to be rendered for this to be correct, which is why we do it here.\n    const origin$ = show$.pipe(\n      filter(active => active),\n      withLatestFrom(node$, viewport$),\n      map(([_, node, { size }]) => {\n        const host = el.getBoundingClientRect()\n        const x = host.width / 2\n\n        // If the tooltip is non-interactive, we always render it below the\n        // actual element because all operating systems do it that way\n        if (node.role === \"tooltip\") {\n          return { x, y: 8 + host.height }\n\n        // Otherwise, we determine where there is more space, and render the\n        // tooltip either above or below the host element\n        } else if (host.y >= size.height / 2) {\n          const { height } = getElementSize(node)\n          return { x, y: -16 - height }\n        } else {\n          return { x, y: +16 + host.height }\n        }\n      })\n    )\n\n    // Update tooltip position - we always need to update the position of the\n    // tooltip, as it might change depending on the viewport offset of the host\n    combineLatest([node$, push$, origin$])\n      .subscribe(([node, { offset }, origin]) => {\n        node.style.setProperty(\"--md-tooltip-host-x\", `${offset.x}px`)\n        node.style.setProperty(\"--md-tooltip-host-y\", `${offset.y}px`)\n\n        // Update tooltip origin - this is mainly set to determine the position\n        // of the tooltip tail, to show the direction it is originating from\n        node.style.setProperty(\"--md-tooltip-x\", `${origin.x}px`)\n        node.style.setProperty(\"--md-tooltip-y\", `${origin.y}px`)\n\n        // Update tooltip render location, i.e., whether the tooltip is shown\n        // above or below the host element, depending on the available space\n        node.classList.toggle(\"md-tooltip2--top\",    origin.y <  0)\n        node.classList.toggle(\"md-tooltip2--bottom\", origin.y >= 0)\n      })\n\n    // Update tooltip width - we only explicitly set the width of the tooltip\n    // if it is non-interactive, in case it should always be rendered centered\n    show$.pipe(\n      filter(active => active),\n      withLatestFrom(node$, (_, node) => node),\n      filter(node => node.role === \"tooltip\")\n    )\n      .subscribe(node => {\n        const size = getElementSize(getElement(\":scope > *\", node))\n\n        // Set tooltip width and remove tail by setting it to a width of zero -\n        // if authors want to keep the tail, we can move this to CSS later\n        node.style.setProperty(\"--md-tooltip-width\", `${size.width}px`)\n        node.style.setProperty(\"--md-tooltip-tail\",  `${0}px`)\n      })\n\n    // Update tooltip visibility - we defer to the next animation frame, because\n    // the tooltip must first be added to the document before we make it appear,\n    // or it will appear instantly without delay. Additionally, we need to keep\n    // the tooltip visible for a short time after the pointer left the host.\n    show$.pipe(\n      distinctUntilChanged(),\n      observeOn(animationFrameScheduler),\n      withLatestFrom(node$)\n    )\n      .subscribe(([active, node]) => {\n        node.classList.toggle(\"md-tooltip2--active\", active)\n      })\n\n    // Set up ARIA attributes when tooltip is visible\n    combineLatest([\n      show$.pipe(filter(active => active)),\n      node$\n    ])\n      .subscribe(([_, node]) => {\n        if (node.role === \"dialog\") {\n          el.setAttribute(\"aria-controls\", id)\n          el.setAttribute(\"aria-haspopup\", \"dialog\")\n        } else {\n          el.setAttribute(\"aria-describedby\", id)\n        }\n      })\n\n    // Remove ARIA attributes when tooltip is hidden\n    show$.pipe(filter(active => !active))\n      .subscribe(() => {\n        el.removeAttribute(\"aria-controls\")\n        el.removeAttribute(\"aria-describedby\")\n        el.removeAttribute(\"aria-haspopup\")\n      })\n\n    // Create and return component\n    return watchTooltip2(el, timeout)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n\n// ----------------------------------------------------------------------------\n\n/**\n * Mount inline tooltip\n *\n * @todo refactor this function\n *\n * @param el - Tooltip host element\n * @param dependencies - Dependencies\n * @param container - Container\n *\n * @returns Tooltip component observable\n */\nexport function mountInlineTooltip2(\n  el: HTMLElement, { viewport$ }: { viewport$: Observable<Viewport> },\n  container = document.body\n): Observable<Component<Tooltip>> {\n  return mountTooltip2(el, {\n    content$: new Observable<HTMLElement>(observer => {\n      const title = el.title\n      const node = renderInlineTooltip2(title)\n      observer.next(node)\n      el.removeAttribute(\"title\")\n      // Append tooltip and remove on unsubscription\n      container.append(node)\n      return () => {\n        node.remove()\n        el.setAttribute(\"title\", title)\n      }\n    }),\n    viewport$\n  }, 0)\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  animationFrameScheduler,\n  auditTime,\n  combineLatest,\n  debounceTime,\n  defer,\n  delay,\n  endWith,\n  filter,\n  finalize,\n  fromEvent,\n  ignoreElements,\n  map,\n  merge,\n  switchMap,\n  take,\n  takeUntil,\n  tap,\n  throttleTime,\n  withLatestFrom\n} from \"rxjs\"\n\nimport {\n  ElementOffset,\n  getActiveElement,\n  getElementSize,\n  watchElementContentOffset,\n  watchElementFocus,\n  watchElementOffset,\n  watchElementVisibility\n} from \"~/browser\"\n\nimport { Component } from \"../../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Annotation\n */\nexport interface Annotation {\n  active: boolean                      /* Annotation is active */\n  offset: ElementOffset                /* Annotation offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch annotation\n *\n * @param el - Annotation element\n * @param container - Containing element\n *\n * @returns Annotation observable\n */\nexport function watchAnnotation(\n  el: HTMLElement, container: HTMLElement\n): Observable<Annotation> {\n  const offset$ = defer(() => combineLatest([\n    watchElementOffset(el),\n    watchElementContentOffset(container)\n  ]))\n    .pipe(\n      map(([{ x, y }, scroll]): ElementOffset => {\n        const { width, height } = getElementSize(el)\n        return ({\n          x: x - scroll.x + width  / 2,\n          y: y - scroll.y + height / 2\n        })\n      })\n    )\n\n  /* Actively watch annotation on focus */\n  return watchElementFocus(el)\n    .pipe(\n      switchMap(active => offset$\n        .pipe(\n          map(offset => ({ active, offset })),\n          take(+!active || Infinity)\n        )\n      )\n    )\n}\n\n/**\n * Mount annotation\n *\n * @param el - Annotation element\n * @param container - Containing element\n * @param options - Options\n *\n * @returns Annotation component observable\n */\nexport function mountAnnotation(\n  el: HTMLElement, container: HTMLElement, { target$ }: MountOptions\n): Observable<Component<Annotation>> {\n  const [tooltip, index] = Array.from(el.children)\n\n  /* Mount component on subscription */\n  return defer(() => {\n    const push$ = new Subject<Annotation>()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n    push$.subscribe({\n\n      /* Handle emission */\n      next({ offset }) {\n        el.style.setProperty(\"--md-tooltip-x\", `${offset.x}px`)\n        el.style.setProperty(\"--md-tooltip-y\", `${offset.y}px`)\n      },\n\n      /* Handle complete */\n      complete() {\n        el.style.removeProperty(\"--md-tooltip-x\")\n        el.style.removeProperty(\"--md-tooltip-y\")\n      }\n    })\n\n    /* Start animation only when annotation is visible */\n    watchElementVisibility(el)\n      .pipe(\n        takeUntil(done$)\n      )\n        .subscribe(visible => {\n          el.toggleAttribute(\"data-md-visible\", visible)\n        })\n\n    /* Toggle tooltip presence to mitigate empty lines when copying */\n    merge(\n      push$.pipe(filter(({ active }) => active)),\n      push$.pipe(debounceTime(250), filter(({ active }) => !active))\n    )\n      .subscribe({\n\n        /* Handle emission */\n        next({ active }) {\n          if (active)\n            el.prepend(tooltip)\n          else\n            tooltip.remove()\n        },\n\n        /* Handle complete */\n        complete() {\n          el.prepend(tooltip)\n        }\n      })\n\n    /* Toggle tooltip visibility */\n    push$\n      .pipe(\n        auditTime(16, animationFrameScheduler)\n      )\n        .subscribe(({ active }) => {\n          tooltip.classList.toggle(\"md-tooltip--active\", active)\n        })\n\n    /* Track relative origin of tooltip */\n    push$\n      .pipe(\n        throttleTime(125, animationFrameScheduler),\n        filter(() => !!el.offsetParent),\n        map(() => el.offsetParent!.getBoundingClientRect()),\n        map(({ x }) => x)\n      )\n        .subscribe({\n\n          /* Handle emission */\n          next(origin) {\n            if (origin)\n              el.style.setProperty(\"--md-tooltip-0\", `${-origin}px`)\n            else\n              el.style.removeProperty(\"--md-tooltip-0\")\n          },\n\n          /* Handle complete */\n          complete() {\n            el.style.removeProperty(\"--md-tooltip-0\")\n          }\n        })\n\n    /* Allow to copy link without scrolling to anchor */\n    fromEvent<MouseEvent>(index, \"click\")\n      .pipe(\n        takeUntil(done$),\n        filter(ev => !(ev.metaKey || ev.ctrlKey))\n      )\n        .subscribe(ev => {\n          ev.stopPropagation()\n          ev.preventDefault()\n        })\n\n    /* Allow to open link in new tab or blur on close */\n    fromEvent<MouseEvent>(index, \"mousedown\")\n      .pipe(\n        takeUntil(done$),\n        withLatestFrom(push$)\n      )\n        .subscribe(([ev, { active }]) => {\n\n          /* Open in new tab */\n          if (ev.button !== 0 || ev.metaKey || ev.ctrlKey) {\n            ev.preventDefault()\n\n          /* Close annotation */\n          } else if (active) {\n            ev.preventDefault()\n\n            /* Focus parent annotation, if any */\n            const parent = el.parentElement!.closest(\".md-annotation\")\n            if (parent instanceof HTMLElement)\n              parent.focus()\n            else\n              getActiveElement()?.blur()\n          }\n        })\n\n    /* Open and focus annotation on location target */\n    target$\n      .pipe(\n        takeUntil(done$),\n        filter(target => target === tooltip),\n        delay(125)\n      )\n        .subscribe(() => el.focus())\n\n    /* Create and return component */\n    return watchAnnotation(el, container)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  defer,\n  endWith,\n  finalize,\n  ignoreElements,\n  merge,\n  share,\n  takeUntil\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n  getElement,\n  getElements,\n  getOptionalElement\n} from \"~/browser\"\nimport { renderAnnotation } from \"~/templates\"\n\nimport { Component } from \"../../../_\"\nimport {\n  Annotation,\n  mountAnnotation\n} from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n  print$: Observable<boolean>          /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Find all annotation hosts in the containing element\n *\n * @param container - Containing element\n *\n * @returns Annotation hosts\n */\nfunction findHosts(container: HTMLElement): HTMLElement[] {\n  const config = configuration()\n  if (container.tagName !== \"CODE\")\n    return [container]\n\n  /* Try to determine language of code block */\n  const selectors = [\".c\", \".c1\", \".cm\"]\n  if (config.annotate && typeof config.annotate === \"object\") {\n    const host = container.closest(\"[class|=language]\")\n    if (host) {\n\n      /* Extract language from class name */\n      for (const value of Array.from(host.classList)) {\n        if (!value.startsWith(\"language-\"))\n          continue\n\n        /* Obtain additional mappings, if any */\n        const [, language] = value.split(\"-\")\n        if (language in config.annotate)\n          selectors.push(...config.annotate[language])\n      }\n    }\n  }\n\n  /* Retrieve and return annotation hosts */\n  return getElements(selectors.join(\", \"), container)\n}\n\n/**\n * Find all annotation markers in the containing element\n *\n * @param container - Containing element\n *\n * @returns Annotation markers\n */\nfunction findMarkers(container: HTMLElement): Text[] {\n  const markers: Text[] = []\n  for (const el of findHosts(container)) {\n    const nodes: Text[] = []\n\n    /* Find all text nodes in current element */\n    const it = document.createNodeIterator(el, NodeFilter.SHOW_TEXT)\n    for (let node = it.nextNode(); node; node = it.nextNode())\n      nodes.push(node as Text)\n\n    /* Find all markers in each text node */\n    for (let text of nodes) {\n      let match: RegExpExecArray | null\n\n      /* Split text at marker and add to list */\n      while ((match = /(\\(\\d+\\))(!)?/.exec(text.textContent!))) {\n        const [, id, force] = match\n        if (typeof force === \"undefined\") {\n          const marker = text.splitText(match.index)\n          text = marker.splitText(id.length)\n          markers.push(marker)\n\n        /* Replace entire text with marker */\n        } else {\n          text.textContent = id\n          markers.push(text)\n          break\n        }\n      }\n    }\n  }\n  return markers\n}\n\n/**\n * Swap the child nodes of two elements\n *\n * @param source - Source element\n * @param target - Target element\n */\nfunction swap(source: HTMLElement, target: HTMLElement): void {\n  target.append(...Array.from(source.childNodes))\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount annotation list\n *\n * This function analyzes the containing code block and checks for markers\n * referring to elements in the given annotation list. If no markers are found,\n * the list is left untouched. Otherwise, list elements are rendered as\n * annotations inside the code block.\n *\n * @param el - Annotation list element\n * @param container - Containing element\n * @param options - Options\n *\n * @returns Annotation component observable\n */\nexport function mountAnnotationList(\n  el: HTMLElement, container: HTMLElement, { target$, print$ }: MountOptions\n): Observable<Component<Annotation>> {\n\n  /* Compute prefix for tooltip anchors */\n  const parent = container.closest(\"[id]\")\n  const prefix = parent?.id\n\n  /* Find and replace all markers with empty annotations */\n  const annotations = new Map<string, HTMLElement>()\n  for (const marker of findMarkers(container)) {\n    const [, id] = marker.textContent!.match(/\\((\\d+)\\)/)!\n    if (getOptionalElement(`:scope > li:nth-child(${id})`, el)) {\n      annotations.set(id, renderAnnotation(id, prefix))\n      marker.replaceWith(annotations.get(id)!)\n    }\n  }\n\n  /* Keep list if there are no annotations to render */\n  if (annotations.size === 0)\n    return EMPTY\n\n  /* Mount component on subscription */\n  return defer(() => {\n    const push$ = new Subject()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n\n    /* Retrieve container pairs for swapping */\n    const pairs: [HTMLElement, HTMLElement][] = []\n    for (const [id, annotation] of annotations)\n      pairs.push([\n        getElement(\".md-typeset\", annotation),\n        getElement(`:scope > li:nth-child(${id})`, el)\n      ])\n\n    /* Handle print mode - see https://bit.ly/3rgPdpt */\n    print$.pipe(takeUntil(done$))\n      .subscribe(active => {\n        el.hidden = !active\n\n        /* Add class to discern list element */\n        el.classList.toggle(\"md-annotation-list\", active)\n\n        /* Show annotations in code block or list (print) */\n        for (const [inner, child] of pairs)\n          if (!active)\n            swap(child, inner)\n          else\n            swap(inner, child)\n      })\n\n    /* Create and return component */\n    return merge(...[...annotations]\n      .map(([, annotation]) => (\n        mountAnnotation(annotation, container, { target$ })\n      ))\n    )\n      .pipe(\n        finalize(() => push$.complete()),\n        share()\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { EMPTY, Observable, defer } from \"rxjs\"\n\nimport { Component } from \"../../../_\"\nimport { Annotation } from \"../_\"\nimport { mountAnnotationList } from \"../list\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n  print$: Observable<boolean>          /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Find list element directly following a block\n *\n * @param el - Annotation block element\n *\n * @returns List element or nothing\n */\nfunction findList(el: HTMLElement): HTMLElement | undefined {\n  if (el.nextElementSibling) {\n    const sibling = el.nextElementSibling as HTMLElement\n    if (sibling.tagName === \"OL\")\n      return sibling\n\n    /* Skip empty paragraphs - see https://bit.ly/3r4ZJ2O */\n    else if (sibling.tagName === \"P\" && !sibling.children.length)\n      return findList(sibling)\n  }\n\n  /* Everything else */\n  return undefined\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount annotation block\n *\n * @param el - Annotation block element\n * @param options - Options\n *\n * @returns Annotation component observable\n */\nexport function mountAnnotationBlock(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<Annotation>> {\n  return defer(() => {\n    const list = findList(el)\n    return typeof list !== \"undefined\"\n      ? mountAnnotationList(list, el, options)\n      : EMPTY\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport ClipboardJS from \"clipboard\"\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  asyncScheduler,\n  defer,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  filter,\n  finalize,\n  from,\n  fromEvent,\n  map,\n  merge,\n  mergeMap,\n  mergeWith,\n  observeOn,\n  scan,\n  share,\n  shareReplay,\n  startWith,\n  switchMap,\n  take,\n  takeLast,\n  takeUntil,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  getElement,\n  getElementContentSize,\n  getElements,\n  getOptionalElement,\n  watchElementHover,\n  watchElementSize,\n  watchElementVisibility,\n  watchLocationHash\n} from \"~/browser\"\nimport {\n  Tooltip,\n  mountInlineTooltip2\n} from \"~/components/tooltip2\"\nimport {\n  renderClipboardButton,\n  renderCodeBlockNavigation,\n  renderSelectionButton\n} from \"~/templates\"\n\nimport { Component } from \"../../../_\"\nimport {\n  Annotation,\n  mountAnnotationList\n} from \"../../annotation\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Code block overflow\n */\nexport interface Overflow {\n  scrollable: boolean                  /* Code block overflows */\n}\n\n/**\n * Code block\n */\nexport type CodeBlock =\n  | Overflow\n  | Annotation\n  | Tooltip\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n  print$: Observable<boolean>          /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Global sequence number for code blocks\n */\nlet sequence = 0\n\n/**\n * Shift-key observable - @todo consolidate with keyboard observable\n */\nconst shift$ = merge(\n  fromEvent(window, \"keydown\").pipe(map(() => true)),\n  merge(\n    fromEvent(window, \"keyup\"),\n    fromEvent(window, \"contextmenu\")\n  )\n    .pipe(map(() => false))\n)\n  .pipe(\n    startWith(false),\n    shareReplay(1)\n  )\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Find list element directly following a code block\n *\n * @param el - Code block element\n *\n * @returns List element or nothing\n */\nfunction findList(el: HTMLElement): HTMLElement | undefined {\n  if (el.nextElementSibling) {\n    const sibling = el.nextElementSibling as HTMLElement\n    if (sibling.tagName === \"OL\")\n      return sibling\n\n    /* Skip empty paragraphs - see https://bit.ly/3r4ZJ2O */\n    else if (sibling.tagName === \"P\" && !sibling.children.length)\n      return findList(sibling)\n  }\n\n  /* Everything else */\n  return undefined\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch code block\n *\n * This function monitors size changes of the viewport, as well as switches of\n * content tabs with embedded code blocks, as both may trigger overflow.\n *\n * @param el - Code block element\n *\n * @returns Code block observable\n */\nexport function watchCodeBlock(\n  el: HTMLElement\n): Observable<Overflow> {\n  return watchElementSize(el)\n    .pipe(\n      map(({ width }) => {\n        const content = getElementContentSize(el)\n        return {\n          scrollable: content.width > width\n        }\n      }),\n      distinctUntilKeyChanged(\"scrollable\")\n    )\n}\n\n/**\n * Mount code block\n *\n * This function ensures that an overflowing code block is focusable through\n * keyboard, so it can be scrolled without a mouse to improve on accessibility.\n * Furthermore, if code annotations are enabled, they are mounted if and only\n * if the code block is currently visible, e.g., not in a hidden content tab.\n *\n * Note that code blocks may be mounted eagerly or lazily. If they're mounted\n * lazily (on first visibility), code annotation anchor links will not work,\n * as they are evaluated on initial page load, and code annotations in general\n * might feel a little bumpier.\n *\n * @param el - Code block element\n * @param options - Options\n *\n * @returns Code block and annotation component observable\n */\nexport function mountCodeBlock(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<CodeBlock>> {\n  const { matches: hover } = matchMedia(\"(hover)\")\n\n  /* Defer mounting of code block - see https://bit.ly/3vHVoVD */\n  const factory$ = defer(() => {\n    const push$ = new Subject<Overflow>()\n    const done$ = push$.pipe(takeLast(1))\n    push$.subscribe(({ scrollable }) => {\n      if (scrollable && hover)\n        el.setAttribute(\"tabindex\", \"0\")\n      else\n        el.removeAttribute(\"tabindex\")\n    })\n\n    // Code block sequence number\n    const buttons: HTMLElement[] = []\n    const parent = el.closest(\"pre\")!\n\n    // Check if there's a parent element with an id, and use that id, otherwise\n    // generate a new one. This is necessary to allow for authors to define\n    // unique ids for code blocks - see https://t.ly/q7UEq\n    const unique = parent.closest(\"[id]\")\n    const id = unique ? unique.id : sequence++\n    parent.id = `__code_${id}`\n\n    /* Handle code annotations and highlights */\n    const content$: Array<Observable<Component<CodeBlock>>> = []\n    const container = el.closest(\".highlight\")\n    if (container instanceof HTMLElement) {\n      const list = findList(container)\n\n      /* Mount code annotations, if enabled */\n      if (typeof list !== \"undefined\" && (\n        container.classList.contains(\"annotate\") ||\n        feature(\"content.code.annotate\")\n      )) {\n        const annotations$ = mountAnnotationList(list, el, options)\n        content$.push(\n          watchElementSize(container)\n            .pipe(\n              takeUntil(done$),\n              map(({ width, height }) => width && height),\n              distinctUntilChanged(),\n              switchMap(active => active ? annotations$ : EMPTY)\n            )\n        )\n      }\n    }\n\n    // @todo: refactor and move into separate component\n\n    /* Check if code block has line spans */\n    const spans = getElements(\":scope > span[id]\", el)\n    if (spans.length) {\n      el.classList.add(\"md-code__content\")\n\n      /* Mount code selection */\n      if (el.closest(\".select\") || (\n        feature(\"content.code.select\") && !el.closest(\".no-select\")\n      )) {\n        const base = +spans[0].id.split(\"-\").pop()!\n\n        /* Mount tooltip, if enabled */\n        const button = renderSelectionButton()\n        buttons.push(button)\n        if (feature(\"content.tooltips\"))\n          content$.push(mountInlineTooltip2(button, { viewport$ }))\n\n        /* Selection state */\n        const select$ = fromEvent(button, \"click\")\n          .pipe(\n            scan(active => !active, false),\n            tap(() => button.blur()),\n            share()\n          )\n\n        /* Toggle active selection state on button */\n        select$.subscribe(active => {\n          button.classList.toggle(\"md-code__button--active\", active)\n        })\n\n        /* Observable that monitors hovering */\n        const hover$ = from(spans)\n          .pipe(\n            mergeMap(span => watchElementHover(span)\n              .pipe(\n                map(active => [span, active] as const)\n              )\n            )\n          )\n\n        /* Trigger hover selection state based on state */\n        select$\n          .pipe(\n            switchMap(active => active ? hover$ : EMPTY)\n          )\n            .subscribe(([span, active]) => {\n              // @todo: don't mutate, but wrap everything in selection elements\n              const highlight = getOptionalElement(\".hll.select\", span)\n              if (highlight && !active) {\n                highlight.replaceWith(...Array.from(highlight.childNodes))\n              } else if (!highlight && active) {\n                const hll = document.createElement(\"span\")\n                hll.className = \"hll select\"\n                hll.append(...Array.from(span.childNodes).slice(1))\n                span.append(hll)\n              }\n            })\n\n        // @todo: use a single event handler and consolidate events\n        const click$ = from(spans)\n          .pipe(\n            mergeMap(span => fromEvent(span, \"mousedown\")\n              .pipe(\n                tap(ev => ev.preventDefault()),\n                map(() => span)\n              )\n            )\n          )\n\n        const range$ = select$\n          .pipe(\n            switchMap(active => active ? click$ : EMPTY),\n            withLatestFrom(shift$),\n            map(([span, shift]) => {\n\n              /* Determine focused line number */\n              const active = spans.indexOf(span) + base\n              if (shift === false) {\n                return [active, active] as const\n\n                /* Shift is pressed, so extend selection */\n              } else {\n                const range = getElements(\".hll\", el)\n                  .map(line => spans.indexOf(line.parentElement!) + base)\n\n                // Hack: this is a side effect, but we need to remove all ranges\n                // or rendering might look weird.\n                window.getSelection()?.removeAllRanges()\n\n                /* Return range */\n                return [\n                  Math.min(active, ...range),\n                  Math.max(active, ...range)\n                ] as const\n              }\n            })\n          )\n\n        // Currently, all mounted code blocks will receive this event. That#s\n        // not ideal, since we should handle this higher up the tree\n        const hash$ = watchLocationHash(EMPTY)\n          .pipe(\n            // @todo: make more resilient\n            filter(hash => hash.startsWith(`__codelineno-${id}-`))\n          )\n\n        hash$.subscribe(hash => {\n          const [, , line] = hash.split(\"-\")\n          const range = line.split(\":\").map(value => +value - base + 1)\n          if (range.length === 1)\n            range.push(range[0])\n\n          // remove all existing, then set range...\n          for (const span of getElements(\".hll:not(.select)\", el)) {\n            span.replaceWith(...Array.from(span.childNodes))\n          }\n\n          // set new range @todo move this into one block\n          const selection = spans.slice(range[0] - 1, range[1])\n          for (const span of selection) {\n            const hll = document.createElement(\"span\")\n            hll.className = \"hll\"\n            hll.append(...Array.from(span.childNodes).slice(1))\n            span.append(hll)\n          }\n        })\n\n        hash$.pipe(take(1), observeOn(asyncScheduler))\n          .subscribe(hash => {\n            if (hash.includes(\":\")) {\n              const anchor = document.getElementById(hash.split(\":\")[0])\n              if (anchor) {\n                // this is a hack - we will refactor anchor / targetting as one\n                // of the next big things when merging one of the next goals.\n                // we need to unify how offsets are computed for tooltips and\n                // make the whole experience smoother.\n                setTimeout(() => {\n                  let tmp = anchor\n                  let top = -(48 + 16)\n                  while (tmp !== document.body) {\n                    top += tmp.offsetTop\n                    tmp  = tmp.offsetParent as HTMLElement\n                  }\n                  window.scrollTo({ top })\n                }, 1)\n              }\n            }\n          })\n\n        /* Allow selection via anchor links */\n        const jump$ = from(\n          getElements(\"a[href^=\\\"#__codelineno\\\"]\", container!)\n        )\n          .pipe(\n            mergeMap(anchor => fromEvent(anchor, \"click\")\n              .pipe(\n                tap(ev => ev.preventDefault()),\n                map(() => anchor as HTMLAnchorElement)\n              )\n            )\n          )\n\n        /* Determine next highlighted lines */\n        const next$ = jump$\n          .pipe(\n            takeUntil(done$),\n            withLatestFrom(shift$),\n            map(([anchor, shift]) => {\n              const target = getElement(`[id=\"${anchor.hash.slice(1)}\"]`)\n\n              /* Determine focused line number */\n              const active = +target.parentElement!.id.split(\"-\").pop()!\n              if (shift === false) {\n                return [active, active] as const\n\n              /* Shift is pressed, so extend selection */\n              } else {\n                const range = getElements(\".hll\", el)\n                  .map(line => +line.parentElement!.id.split(\"-\").pop()!)\n\n                /* Return range */\n                return [\n                  Math.min(active, ...range),\n                  Math.max(active, ...range)\n                ] as const\n              }\n            })\n          )\n\n        // Push selection to URL\n        merge(range$, next$).subscribe(range => {\n          // @todo: improve resilience, so we're not dependent on class names\n          let hash = `#__codelineno-${id}-`\n          if (range[0] === range[1]) {\n            hash += range[0]\n          } else {\n            hash += `${range[0]}:${range[1]}`\n          }\n          history.replaceState({}, \"\", hash)\n          // @hack dispatch artificial hashchange event\n          window.dispatchEvent(new HashChangeEvent(\"hashchange\", {\n            newURL: window.location.origin + window.location.pathname + hash,\n            oldURL: window.location.href\n          }))\n        })\n      }\n    }\n\n    /* Render button for Clipboard.js integration */\n    if (ClipboardJS.isSupported()) {\n      if (el.closest(\".copy\") || (\n        feature(\"content.code.copy\") && !el.closest(\".no-copy\")\n      )) {\n\n        /* Mount tooltip, if enabled */\n        const button = renderClipboardButton(parent.id)\n        buttons.push(button)\n        if (feature(\"content.tooltips\"))\n          content$.push(mountInlineTooltip2(button, { viewport$ }))\n      }\n    }\n\n    // @hack Render code navigation and buttons\n    if (buttons.length) {\n      const nav = renderCodeBlockNavigation()\n      nav.append(...buttons)\n      parent.insertBefore(nav, el)\n    }\n\n    /* Create and return component */\n    return watchCodeBlock(el)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state })),\n        mergeWith(merge(...content$).pipe(\n          takeUntil(done$)\n        )),\n      )\n  })\n\n  /* Mount code block lazily */\n  if (feature(\"content.lazy\"))\n    return watchElementVisibility(el)\n      .pipe(\n        filter(visible => visible),\n        take(1),\n        switchMap(() => factory$)\n      )\n\n  /* Mount code block */\n  return factory$\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  defer,\n  filter,\n  finalize,\n  map,\n  merge,\n  tap\n} from \"rxjs\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Details\n */\nexport interface Details {\n  action: \"open\" | \"close\"             /* Details state */\n  reveal?: boolean                     /* Details is revealed */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n  print$: Observable<boolean>          /* Media print observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  target$: Observable<HTMLElement>     /* Location target observable */\n  print$: Observable<boolean>          /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch details\n *\n * @param el - Details element\n * @param options - Options\n *\n * @returns Details observable\n */\nexport function watchDetails(\n  el: HTMLDetailsElement, { target$, print$ }: WatchOptions\n): Observable<Details> {\n  let open = true\n  return merge(\n\n    /* Open and focus details on location target */\n    target$\n      .pipe(\n        map(target => target.closest(\"details:not([open])\")!),\n        filter(details => el === details),\n        map(() => ({\n          action: \"open\", reveal: true\n        }) as Details)\n      ),\n\n    /* Open details on print and close afterwards */\n    print$\n      .pipe(\n        filter(active => active || !open),\n        tap(() => open = el.open),\n        map(active => ({\n          action: active ? \"open\" : \"close\"\n        }) as Details)\n      )\n  )\n}\n\n/**\n * Mount details\n *\n * This function ensures that `details` tags are opened on anchor jumps and\n * prior to printing, so the whole content of the page is visible.\n *\n * @param el - Details element\n * @param options - Options\n *\n * @returns Details component observable\n */\nexport function mountDetails(\n  el: HTMLDetailsElement, options: MountOptions\n): Observable<Component<Details>> {\n  return defer(() => {\n    const push$ = new Subject<Details>()\n    push$.subscribe(({ action, reveal }) => {\n      el.toggleAttribute(\"open\", action === \"open\")\n      if (reveal)\n        el.scrollIntoView()\n    })\n\n    /* Create and return component */\n    return watchDetails(el, options)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  combineLatest,\n  distinctUntilChanged,\n  filter,\n  map,\n  of,\n  switchMap,\n  zip\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElements,\n  getOptionalElement,\n  requestHTML,\n  watchElementFocus,\n  watchElementHover\n} from \"~/browser\"\nimport { Sitemap } from \"~/integrations\"\nimport { renderTooltip2 } from \"~/templates\"\n\nimport { Component } from \"../../_\"\nimport { mountTooltip2 } from \"../../tooltip2\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Link\n */\nexport interface Link {}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dependencies\n */\ninterface Dependencies {\n  sitemap$: Observable<Sitemap>        // Sitemap observable\n  viewport$: Observable<Viewport>      // Viewport observable\n  target$: Observable<HTMLElement>     // Location target observable\n  print$: Observable<boolean>          // Media print observable\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Global sequence number for instant previews\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Extract elements until next heading\n *\n * @param headline - Heading\n *\n * @returns Elements until next heading\n */\nfunction extract(headline: HTMLElement): HTMLElement[] {\n  const newHeading = document.createElement(\"h3\")\n  newHeading.innerHTML = headline.innerHTML\n  const els = [newHeading]\n\n  //\n  let nextElement = headline.nextElementSibling\n  while (nextElement && !(nextElement instanceof HTMLHeadingElement)) {\n    // @ts-expect-error - fix once instant previews are stable\n    els.push(nextElement as HTMLElement)\n    nextElement = nextElement.nextElementSibling\n  }\n\n  //\n  return els\n}\n\n/**\n * Resolve relative URLs in the given document\n *\n * @todo deduplicate with resolution in instant navigation. This functoion also\n * adds the ability to resolve from a specific base URL, which is essential for\n * instant previews to work, so we should generalize this functionality the\n * next time we work on instant navigation.\n *\n * @param document - Document\n * @param base - Base URL\n *\n * @returns Document observable\n */\nfunction resolve(\n  document: Document, base: URL | string\n): Observable<Document> {\n\n  // Replace all links\n  for (const el of getElements(\"[href], [src]\", document))\n    for (const key of [\"href\", \"src\"]) {\n      const value = el.getAttribute(key)\n      if (value && !/^(?:[a-z]+:)?\\/\\//i.test(value)) {\n        // @ts-expect-error - trick: self-assign to resolve URL\n        el[key] = new URL(el.getAttribute(key), base).toString()\n        break\n      }\n    }\n\n  // Ensure ids are free of collisions (e.g. content tabs)\n  for (const el of getElements(\"[name^=__], [for]\", document))\n    for (const key of [\"id\", \"for\", \"name\"]) {\n      const value = el.getAttribute(key)\n      if (value) {\n        el.setAttribute(key, `${value}$preview_${sequence}`)\n      }\n    }\n\n  // Return document observable\n  sequence++\n  return of(document)\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount Link\n *\n * @param el - Link element\n * @param dependencies - Depenendencies\n *\n * @returns Link component observable\n */\nexport function mountLink(\n  el: HTMLElement, dependencies: Dependencies\n): Observable<Component<Link>> {\n  const { sitemap$ } = dependencies\n  if (!(el instanceof HTMLAnchorElement))\n    return EMPTY\n\n  //\n  if (!(\n    feature(\"navigation.instant.preview\") ||\n    el.hasAttribute(\"data-preview\")\n  ))\n    return EMPTY\n\n  // Remove title, as it will overlay the instant preview, and we want to give\n  // instant previews precedence over titles \u2013 see https://t.ly/o0_Rk\n  el.removeAttribute(\"title\")\n\n  const active$ =\n    combineLatest([\n      watchElementFocus(el),\n      watchElementHover(el)\n    ])\n      .pipe(\n        map(([focus, hover]) => focus || hover),\n        distinctUntilChanged(),\n        filter(active => active)\n      )\n\n  // @todo: this is taken from the handle function in instant loading - we\n  // should generalize this once instant loading becomes stable.\n  const elements$ = zip([sitemap$, active$]).pipe(\n    switchMap(([sitemap]) => {\n      const url = new URL(el.href)\n      url.search = url.hash = \"\"\n\n      //\n      if (!sitemap.has(`${url}`))\n        return EMPTY\n\n      //\n      return of(url)\n    }),\n    switchMap(url => requestHTML(url).pipe(\n      switchMap(doc => resolve(doc, url))\n    )),\n    switchMap(doc => {\n      const selector = el.hash\n        ? `article [id=\"${el.hash.slice(1)}\"]`\n        : \"article h1\"\n\n      //\n      const target = getOptionalElement(selector, doc)\n      if (typeof target === \"undefined\")\n        return EMPTY\n\n      //\n      return of(extract(target))\n    })\n  )\n\n  //\n  return elements$.pipe(\n    switchMap(els => {\n      const content$ = new Observable<HTMLElement>(observer => {\n        const node = renderTooltip2(...els)\n        observer.next(node)\n\n        //\n        document.body.append(node)\n        return () => node.remove()\n      })\n\n      //\n      return mountTooltip2(el, { content$,  ...dependencies })\n    })\n  )\n}\n", ".node circle,.node ellipse,.node path,.node polygon,.node rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}marker{fill:var(--md-mermaid-edge-color)!important}.edgeLabel .label rect{fill:#0000}.flowchartTitleText{fill:var(--md-mermaid-label-fg-color)}.label{color:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.label foreignObject{line-height:normal;overflow:visible}.label div .edgeLabel{color:var(--md-mermaid-label-fg-color)}.edgeLabel,.edgeLabel p,.label div .edgeLabel{background-color:var(--md-mermaid-label-bg-color)}.edgeLabel,.edgeLabel p{fill:var(--md-mermaid-label-bg-color);color:var(--md-mermaid-edge-color)}.edgePath .path,.flowchart-link{stroke:var(--md-mermaid-edge-color)}.edgePath .arrowheadPath{fill:var(--md-mermaid-edge-color);stroke:none}.cluster rect{fill:var(--md-default-fg-color--lightest);stroke:var(--md-default-fg-color--lighter)}.cluster span{color:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}g #flowchart-circleEnd,g #flowchart-circleStart,g #flowchart-crossEnd,g #flowchart-crossStart,g #flowchart-pointEnd,g #flowchart-pointStart{stroke:none}.classDiagramTitleText{fill:var(--md-mermaid-label-fg-color)}g.classGroup line,g.classGroup rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}g.classGroup text{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.classLabel .box{fill:var(--md-mermaid-label-bg-color);background-color:var(--md-mermaid-label-bg-color);opacity:1}.classLabel .label{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.node .divider{stroke:var(--md-mermaid-node-fg-color)}.relation{stroke:var(--md-mermaid-edge-color)}.cardinality{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.cardinality text{fill:inherit!important}defs marker.marker.composition.class path,defs marker.marker.dependency.class path,defs marker.marker.extension.class path{fill:var(--md-mermaid-edge-color)!important;stroke:var(--md-mermaid-edge-color)!important}defs marker.marker.aggregation.class path{fill:var(--md-mermaid-label-bg-color)!important;stroke:var(--md-mermaid-edge-color)!important}.statediagramTitleText{fill:var(--md-mermaid-label-fg-color)}g.stateGroup rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}g.stateGroup .state-title{fill:var(--md-mermaid-label-fg-color)!important;font-family:var(--md-mermaid-font-family)}g.stateGroup .composit{fill:var(--md-mermaid-label-bg-color)}.nodeLabel,.nodeLabel p{color:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}a .nodeLabel{text-decoration:underline}.node circle.state-end,.node circle.state-start,.start-state{fill:var(--md-mermaid-edge-color);stroke:none}.end-state-inner,.end-state-outer{fill:var(--md-mermaid-edge-color)}.end-state-inner,.node circle.state-end{stroke:var(--md-mermaid-label-bg-color)}.transition{stroke:var(--md-mermaid-edge-color)}[id^=state-fork] rect,[id^=state-join] rect{fill:var(--md-mermaid-edge-color)!important;stroke:none!important}.statediagram-cluster.statediagram-cluster .inner{fill:var(--md-default-bg-color)}.statediagram-cluster rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}.statediagram-state rect.divider{fill:var(--md-default-fg-color--lightest);stroke:var(--md-default-fg-color--lighter)}defs #statediagram-barbEnd{stroke:var(--md-mermaid-edge-color)}[id^=entity] path,[id^=entity] rect{fill:var(--md-default-bg-color)}.relationshipLine{stroke:var(--md-mermaid-edge-color)}defs .marker.oneOrMore.er *,defs .marker.onlyOne.er *,defs .marker.zeroOrMore.er *,defs .marker.zeroOrOne.er *{stroke:var(--md-mermaid-edge-color)!important}text:not([class]):last-child{fill:var(--md-mermaid-label-fg-color)}.actor{fill:var(--md-mermaid-sequence-actor-bg-color);stroke:var(--md-mermaid-sequence-actor-border-color)}text.actor>tspan{fill:var(--md-mermaid-sequence-actor-fg-color);font-family:var(--md-mermaid-font-family)}line{stroke:var(--md-mermaid-sequence-actor-line-color)}.actor-man circle,.actor-man line{fill:var(--md-mermaid-sequence-actorman-bg-color);stroke:var(--md-mermaid-sequence-actorman-line-color)}.messageLine0,.messageLine1{stroke:var(--md-mermaid-sequence-message-line-color)}.note{fill:var(--md-mermaid-sequence-note-bg-color);stroke:var(--md-mermaid-sequence-note-border-color)}.loopText,.loopText>tspan,.messageText,.noteText>tspan{stroke:none;font-family:var(--md-mermaid-font-family)!important}.messageText{fill:var(--md-mermaid-sequence-message-fg-color)}.loopText,.loopText>tspan{fill:var(--md-mermaid-sequence-loop-fg-color)}.noteText>tspan{fill:var(--md-mermaid-sequence-note-fg-color)}#arrowhead path{fill:var(--md-mermaid-sequence-message-line-color);stroke:none}.loopLine{fill:var(--md-mermaid-sequence-loop-bg-color);stroke:var(--md-mermaid-sequence-loop-border-color)}.labelBox{fill:var(--md-mermaid-sequence-label-bg-color);stroke:none}.labelText,.labelText>span{fill:var(--md-mermaid-sequence-label-fg-color);font-family:var(--md-mermaid-font-family)}.sequenceNumber{fill:var(--md-mermaid-sequence-number-fg-color)}rect.rect{fill:var(--md-mermaid-sequence-box-bg-color);stroke:none}rect.rect+text.text{fill:var(--md-mermaid-sequence-box-fg-color)}defs #sequencenumber{fill:var(--md-mermaid-sequence-number-bg-color)!important}", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  map,\n  of,\n  shareReplay,\n  tap\n} from \"rxjs\"\n\nimport { watchScript } from \"~/browser\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\nimport themeCSS from \"./index.css\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mermaid diagram\n */\nexport interface Mermaid {}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Mermaid instance observable\n */\nlet mermaid$: Observable<void>\n\n/**\n * Global sequence number for diagrams\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch Mermaid script\n *\n * @returns Mermaid scripts observable\n */\nfunction fetchScripts(): Observable<void> {\n  return typeof mermaid === \"undefined\" || mermaid instanceof Element\n    ? watchScript(\"https://unpkg.com/mermaid@11/dist/mermaid.min.js\")\n    : of(undefined)\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount Mermaid diagram\n *\n * @param el - Code block element\n *\n * @returns Mermaid diagram component observable\n */\nexport function mountMermaid(\n  el: HTMLElement\n): Observable<Component<Mermaid>> {\n  el.classList.remove(\"mermaid\") // Hack: mitigate https://bit.ly/3CiN6Du\n  mermaid$ ||= fetchScripts()\n    .pipe(\n      tap(() => mermaid.initialize({\n        startOnLoad: false,\n        themeCSS,\n        sequence: {\n          actorFontSize: \"16px\", // Hack: mitigate https://bit.ly/3y0NEi3\n          messageFontSize: \"16px\",\n          noteFontSize: \"16px\"\n        }\n      })),\n      map(() => undefined),\n      shareReplay(1)\n    )\n\n  /* Render diagram */\n  mermaid$.subscribe(async () => {\n    el.classList.add(\"mermaid\") // Hack: mitigate https://bit.ly/3CiN6Du\n    const id = `__mermaid_${sequence++}`\n\n    /* Create host element to replace code block */\n    const host = h(\"div\", { class: \"mermaid\" })\n    const text = el.textContent\n\n    /* Render and inject diagram */\n    const { svg, fn } = await mermaid.render(id, text)\n\n    /* Create a shadow root and inject diagram */\n    const shadow = host.attachShadow({ mode: \"closed\" })\n    shadow.innerHTML = svg\n\n    /* Replace code block with diagram and bind functions */\n    el.replaceWith(host)\n    fn?.(shadow)\n  })\n\n  /* Create and return component */\n  return mermaid$\n    .pipe(\n      map(() => ({ ref: el }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Observable, of } from \"rxjs\"\n\nimport { renderTable } from \"~/templates\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Data table\n */\nexport interface DataTable {}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Sentinel for replacement\n */\nconst sentinel = h(\"table\")\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount data table\n *\n * This function wraps a data table in another scrollable container, so it can\n * be smoothly scrolled on smaller screen sizes and won't break the layout.\n *\n * @param el - Data table element\n *\n * @returns Data table component observable\n */\nexport function mountDataTable(\n  el: HTMLElement\n): Observable<Component<DataTable>> {\n  el.replaceWith(sentinel)\n  sentinel.replaceWith(renderTable(el))\n\n  /* Create and return component */\n  return of({ ref: el })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  animationFrameScheduler,\n  asyncScheduler,\n  auditTime,\n  combineLatest,\n  defer,\n  endWith,\n  filter,\n  finalize,\n  fromEvent,\n  ignoreElements,\n  map,\n  merge,\n  skip,\n  startWith,\n  subscribeOn,\n  takeUntil,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElement,\n  getElementContentOffset,\n  getElementContentSize,\n  getElementOffset,\n  getElementSize,\n  getElements,\n  watchElementContentOffset,\n  watchElementSize,\n  watchElementVisibility\n} from \"~/browser\"\nimport { renderTabbedControl } from \"~/templates\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Content tabs\n */\nexport interface ContentTabs {\n  active: HTMLLabelElement             /* Active tab label */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  target$: Observable<HTMLElement>     /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch content tabs\n *\n * @param inputs - Content tabs input elements\n *\n * @returns Content tabs observable\n */\nexport function watchContentTabs(\n  inputs: HTMLInputElement[]\n): Observable<ContentTabs> {\n  const initial = inputs.find(input => input.checked) || inputs[0]\n  return merge(...inputs.map(input => fromEvent(input, \"change\")\n    .pipe(\n      map(() => getElement<HTMLLabelElement>(`label[for=\"${input.id}\"]`))\n    )\n  ))\n    .pipe(\n      startWith(getElement<HTMLLabelElement>(`label[for=\"${initial.id}\"]`)),\n      map(active => ({ active }))\n    )\n}\n\n/**\n * Mount content tabs\n *\n * @param el - Content tabs element\n * @param options - Options\n *\n * @returns Content tabs component observable\n */\nexport function mountContentTabs(\n  el: HTMLElement, { viewport$, target$ }: MountOptions\n): Observable<Component<ContentTabs>> {\n  const container = getElement(\".tabbed-labels\", el)\n  const inputs = getElements<HTMLInputElement>(\":scope > input\", el)\n\n  /* Render content tab previous button for pagination */\n  const prev = renderTabbedControl(\"prev\")\n  el.append(prev)\n\n  /* Render content tab next button for pagination */\n  const next = renderTabbedControl(\"next\")\n  el.append(next)\n\n  /* Mount component on subscription */\n  return defer(() => {\n    const push$ = new Subject<ContentTabs>()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n    combineLatest([push$, watchElementSize(el), watchElementVisibility(el)])\n      .pipe(\n        takeUntil(done$),\n        auditTime(1, animationFrameScheduler)\n      )\n        .subscribe({\n\n          /* Handle emission */\n          next([{ active }, size]) {\n            const offset = getElementOffset(active)\n            const { width } = getElementSize(active)\n\n            /* Set tab indicator offset and width */\n            el.style.setProperty(\"--md-indicator-x\", `${offset.x}px`)\n            el.style.setProperty(\"--md-indicator-width\", `${width}px`)\n\n            /* Scroll container to active content tab */\n            const content = getElementContentOffset(container)\n            if (\n              offset.x         < content.x              ||\n              offset.x + width > content.x + size.width\n            )\n              container.scrollTo({\n                left: Math.max(0, offset.x - 16),\n                behavior: \"smooth\"\n              })\n          },\n\n          /* Handle complete */\n          complete() {\n            el.style.removeProperty(\"--md-indicator-x\")\n            el.style.removeProperty(\"--md-indicator-width\")\n          }\n        })\n\n    /* Hide content tab buttons on borders */\n    combineLatest([\n      watchElementContentOffset(container),\n      watchElementSize(container)\n    ])\n      .pipe(\n        takeUntil(done$)\n      )\n        .subscribe(([offset, size]) => {\n          const content = getElementContentSize(container)\n          prev.hidden = offset.x < 16\n          next.hidden = offset.x > content.width - size.width - 16\n        })\n\n    /* Paginate content tab container on click */\n    merge(\n      fromEvent(prev, \"click\").pipe(map(() => -1)),\n      fromEvent(next, \"click\").pipe(map(() => +1))\n    )\n      .pipe(\n        takeUntil(done$)\n      )\n        .subscribe(direction => {\n          const { width } = getElementSize(container)\n          container.scrollBy({\n            left: width * direction,\n            behavior: \"smooth\"\n          })\n        })\n\n    /* Switch to content tab target */\n    target$\n      .pipe(\n        takeUntil(done$),\n        filter(input => inputs.includes(input as HTMLInputElement))\n      )\n        .subscribe(input => input.click())\n\n    /* Add link to each content tab label */\n    container.classList.add(\"tabbed-labels--linked\")\n    for (const input of inputs) {\n      const label = getElement<HTMLLabelElement>(`label[for=\"${input.id}\"]`)\n      label.replaceChildren(h(\"a\", {\n        href: `#${label.htmlFor}`,\n        tabIndex: -1\n      }, ...Array.from(label.childNodes)))\n\n      /* Allow to copy link without scrolling to anchor */\n      fromEvent<MouseEvent>(label.firstElementChild!, \"click\")\n        .pipe(\n          takeUntil(done$),\n          filter(ev => !(ev.metaKey || ev.ctrlKey)),\n          tap(ev => {\n            ev.preventDefault()\n            ev.stopPropagation()\n          })\n        )\n          // @todo we might need to remove the anchor link on complete\n          .subscribe(() => {\n            history.replaceState({}, \"\", `#${label.htmlFor}`)\n            label.click()\n          })\n    }\n\n    /* Set up linking of content tabs, if enabled */\n    if (feature(\"content.tabs.link\"))\n      push$.pipe(\n        skip(1),\n        withLatestFrom(viewport$)\n      )\n        .subscribe(([{ active }, { offset }]) => {\n          const tab = active.innerText.trim()\n          if (active.hasAttribute(\"data-md-switching\")) {\n            active.removeAttribute(\"data-md-switching\")\n\n          /* Determine viewport offset of active tab */\n          } else {\n            const y = el.offsetTop - offset.y\n\n            /* Passively activate other tabs */\n            for (const set of getElements(\"[data-tabs]\"))\n              for (const input of getElements<HTMLInputElement>(\n                \":scope > input\", set\n              )) {\n                const label = getElement(`label[for=\"${input.id}\"]`)\n                if (\n                  label !== active &&\n                  label.innerText.trim() === tab\n                ) {\n                  label.setAttribute(\"data-md-switching\", \"\")\n                  input.click()\n                  break\n                }\n              }\n\n            /* Bring active tab into view */\n            window.scrollTo({\n              top: el.offsetTop - y\n            })\n\n            /* Persist active tabs in local storage */\n            const tabs = __md_get<string[]>(\"__tabs\") || []\n            __md_set(\"__tabs\", [...new Set([tab, ...tabs])])\n          }\n        })\n\n    /* Pause media (audio, video) on switch - see https://bit.ly/3Bk6cel */\n    push$.pipe(takeUntil(done$))\n      .subscribe(() => {\n        // If the video or audio is visible, and has autoplay enabled, it will\n        // continue playing. If it's not visible, it is paused in any case\n        for (const media of getElements<HTMLAudioElement>(\"audio, video\", el)) {\n          if (media.offsetWidth && media.autoplay) {\n            media.play().catch(() => {}) // Just ignore errors\n          } else {\n            media.pause()\n          }\n        }\n      })\n\n    /* Create and return component */\n    return watchContentTabs(inputs)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n    .pipe(\n      subscribeOn(asyncScheduler)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Observable, merge } from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport { Viewport, getElements } from \"~/browser\"\nimport { Sitemap } from \"~/integrations\"\nimport { renderTooltip2 } from \"~/templates\"\n\nimport { Component } from \"../../_\"\nimport {\n  Tooltip,\n  mountInlineTooltip2,\n  mountTooltip2\n} from \"../../tooltip2\"\nimport {\n  Annotation,\n  mountAnnotationBlock\n} from \"../annotation\"\nimport {\n  CodeBlock,\n  mountCodeBlock\n} from \"../code\"\nimport {\n  Details,\n  mountDetails\n} from \"../details\"\nimport {\n  Link,\n  mountLink\n} from \"../link\"\nimport {\n  Mermaid,\n  mountMermaid\n} from \"../mermaid\"\nimport {\n  DataTable,\n  mountDataTable\n} from \"../table\"\nimport {\n  ContentTabs,\n  mountContentTabs\n} from \"../tabs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Content\n */\nexport type Content =\n  | Annotation\n  | CodeBlock\n  | ContentTabs\n  | DataTable\n  | Details\n  | Link\n  | Mermaid\n  | Tooltip\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dependencies\n */\ninterface Dependencies {\n  sitemap$: Observable<Sitemap>        // Sitemap observable\n  viewport$: Observable<Viewport>      // Viewport observable\n  target$: Observable<HTMLElement>     // Location target observable\n  print$: Observable<boolean>          // Media print observable\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount content\n *\n * This function mounts all components that are found in the content of the\n * actual article, including code blocks, data tables and details.\n *\n * @param el - Content element\n * @param dependencies - Dependencies\n *\n * @returns Content component observable\n */\nexport function mountContent(\n  el: HTMLElement, dependencies: Dependencies\n): Observable<Component<Content>> {\n  const { viewport$, target$, print$ } = dependencies\n  return merge(\n\n    // Annotations\n    ...getElements(\".annotate:not(.highlight)\", el)\n      .map(child => mountAnnotationBlock(child, { target$, print$ })),\n\n    // Code blocks\n    ...getElements(\"pre:not(.mermaid) > code\", el)\n      .map(child => mountCodeBlock(child, { target$, print$ })),\n\n    // Links\n    ...getElements(\"a\", el)\n      .map(child => mountLink(child, dependencies)),\n\n    // Mermaid diagrams\n    ...getElements(\"pre.mermaid\", el)\n      .map(child => mountMermaid(child)),\n\n    // Data tables\n    ...getElements(\"table:not([class])\", el)\n      .map(child => mountDataTable(child)),\n\n    // Details\n    ...getElements(\"details\", el)\n      .map(child => mountDetails(child, { target$, print$ })),\n\n    // Content tabs\n    ...getElements(\"[data-tabs]\", el)\n      .map(child => mountContentTabs(child, { viewport$, target$ })),\n\n    // Tooltips\n    ...getElements(\"[title]:not([data-preview])\", el)\n      .filter(() => feature(\"content.tooltips\"))\n      .map(child => mountInlineTooltip2(child, { viewport$ })),\n\n    // Footnotes\n    ...getElements(\".footnote-ref\", el)\n      .filter(() => feature(\"content.footnote.tooltips\"))\n      // move into specific function! mountTooltip is a low level primitive...\n      .map(child => mountTooltip2(child, {\n        content$: new Observable<HTMLElement>(observer => {\n          // @ts-ignore\n          const hash = new URL(child.href).hash.slice(1)\n          const arr = Array.from(document.getElementById(hash)!\n            // @ts-ignore\n            // eslint-disable-next-line\n            .cloneNode(true).children) as any\n          const node = renderTooltip2(...arr)\n          observer.next(node)\n\n          // Append tooltip and remove on unsubscription\n          document.body.append(node)\n          return () => node.remove()\n        }),\n        viewport$\n      }))\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  defer,\n  delay,\n  finalize,\n  map,\n  merge,\n  of,\n  switchMap,\n  tap\n} from \"rxjs\"\n\nimport { getElement } from \"~/browser\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dialog\n */\nexport interface Dialog {\n  message: string                      /* Dialog message */\n  active: boolean                      /* Dialog is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  alert$: Subject<string>              /* Alert subject */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  alert$: Subject<string>              /* Alert subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch dialog\n *\n * @param _el - Dialog element\n * @param options - Options\n *\n * @returns Dialog observable\n */\nexport function watchDialog(\n  _el: HTMLElement, { alert$ }: WatchOptions\n): Observable<Dialog> {\n  return alert$\n    .pipe(\n      switchMap(message => merge(\n        of(true),\n        of(false).pipe(delay(2000))\n      )\n        .pipe(\n          map(active => ({ message, active }))\n        )\n      )\n    )\n}\n\n/**\n * Mount dialog\n *\n * This function reveals the dialog in the right corner when a new alert is\n * emitted through the subject that is passed as part of the options.\n *\n * @param el - Dialog element\n * @param options - Options\n *\n * @returns Dialog component observable\n */\nexport function mountDialog(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<Dialog>> {\n  const inner = getElement(\".md-typeset\", el)\n  return defer(() => {\n    const push$ = new Subject<Dialog>()\n    push$.subscribe(({ message, active }) => {\n      el.classList.toggle(\"md-dialog--active\", active)\n      inner.textContent = message\n    })\n\n    /* Create and return component */\n    return watchDialog(el, options)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  animationFrameScheduler,\n  asyncScheduler,\n  auditTime,\n  combineLatest,\n  debounceTime,\n  defer,\n  distinctUntilChanged,\n  filter,\n  finalize,\n  map,\n  merge,\n  of,\n  subscribeOn,\n  tap,\n  throttleTime\n} from \"rxjs\"\n\nimport {\n  ElementOffset,\n  getElement,\n  getElementContainer,\n  getElementOffset,\n  getElementSize,\n  watchElementContentOffset,\n  watchElementFocus,\n  watchElementHover\n} from \"~/browser\"\nimport { renderTooltip } from \"~/templates\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Tooltip\n */\nexport interface Tooltip {\n  active: boolean                      /* Tooltip is active */\n  offset: ElementOffset                /* Tooltip offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Global sequence number for tooltips\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch tooltip\n *\n * This function will append the tooltip temporarily to compute its width,\n * which is necessary for correct centering, and then removing it again.\n *\n * @param el - Tooltip element\n * @param host - Host element\n *\n * @returns Tooltip observable\n */\nexport function watchTooltip(\n  el: HTMLElement, host: HTMLElement\n): Observable<Tooltip> {\n  document.body.append(el)\n\n  /* Compute width and remove tooltip immediately */\n  const { width } = getElementSize(el)\n  el.style.setProperty(\"--md-tooltip-width\", `${width}px`)\n  el.remove()\n\n  /* Retrieve and watch containing element */\n  const container = getElementContainer(host)\n  const scroll$ =\n    typeof container !== \"undefined\"\n      ? watchElementContentOffset(container)\n      : of({ x: 0, y: 0 })\n\n  /* Compute tooltip visibility */\n  const active$ = merge(\n    watchElementFocus(host),\n    watchElementHover(host)\n  )\n    .pipe(\n      distinctUntilChanged()\n    )\n\n  /* Compute tooltip offset */\n  return combineLatest([active$, scroll$])\n    .pipe(\n      map(([active, scroll]) => {\n        let { x, y } = getElementOffset(host)\n        const size = getElementSize(host)\n\n        /**\n         * Experimental: fix handling of tables - see https://bit.ly/3TQEj5O\n         *\n         * If this proves to be a viable fix, we should refactor tooltip\n         * positioning and somehow streamline the current process. This might\n         * also fix positioning for annotations inside tables, which is another\n         * limitation.\n         */\n        const table = host.closest(\"table\")\n        if (table && host.parentElement) {\n          x += table.offsetLeft + host.parentElement.offsetLeft\n          y += table.offsetTop  + host.parentElement.offsetTop\n        }\n        return {\n          active,\n          offset: {\n            x: x - scroll.x + size.width  / 2 - width / 2,\n            y: y - scroll.y + size.height + 8\n          }\n        }\n      })\n    )\n}\n\n/**\n * Mount tooltip\n *\n * @param el - Host element\n *\n * @returns Tooltip component observable\n */\nexport function mountTooltip(\n  el: HTMLElement\n): Observable<Component<Tooltip>> {\n  const title = el.title\n  if (!title.length)\n    return EMPTY\n\n  /* Render tooltip and set title from host element */\n  const id = `__tooltip_${sequence++}`\n  const tooltip = renderTooltip(id, \"inline\")\n  const typeset = getElement(\".md-typeset\", tooltip)\n  typeset.innerHTML = title\n\n  /* Mount component on subscription */\n  return defer(() => {\n    const push$ = new Subject<Tooltip>()\n    push$.subscribe({\n\n      /* Handle emission */\n      next({ offset }) {\n        tooltip.style.setProperty(\"--md-tooltip-x\", `${offset.x}px`)\n        tooltip.style.setProperty(\"--md-tooltip-y\", `${offset.y}px`)\n      },\n\n      /* Handle complete */\n      complete() {\n        tooltip.style.removeProperty(\"--md-tooltip-x\")\n        tooltip.style.removeProperty(\"--md-tooltip-y\")\n      }\n    })\n\n    /* Toggle tooltip presence to mitigate empty lines when copying */\n    merge(\n      push$.pipe(filter(({ active }) => active)),\n      push$.pipe(debounceTime(250), filter(({ active }) => !active))\n    )\n      .subscribe({\n\n        /* Handle emission */\n        next({ active }) {\n          if (active) {\n            el.insertAdjacentElement(\"afterend\", tooltip)\n            el.setAttribute(\"aria-describedby\", id)\n            el.removeAttribute(\"title\")\n          } else {\n            tooltip.remove()\n            el.removeAttribute(\"aria-describedby\")\n            el.setAttribute(\"title\", title)\n          }\n        },\n\n        /* Handle complete */\n        complete() {\n          tooltip.remove()\n          el.removeAttribute(\"aria-describedby\")\n          el.setAttribute(\"title\", title)\n        }\n      })\n\n    /* Toggle tooltip visibility */\n    push$\n      .pipe(\n        auditTime(16, animationFrameScheduler)\n      )\n        .subscribe(({ active }) => {\n          tooltip.classList.toggle(\"md-tooltip--active\", active)\n        })\n\n    // @todo - refactor positioning together with annotations \u2013 there are\n    // several things that overlap and are identical in handling\n\n    /* Track relative origin of tooltip */\n    push$\n      .pipe(\n        throttleTime(125, animationFrameScheduler),\n        filter(() => !!el.offsetParent),\n        map(() => el.offsetParent!.getBoundingClientRect()),\n        map(({ x }) => x)\n      )\n      .subscribe({\n\n        /* Handle emission */\n        next(origin) {\n          if (origin)\n            tooltip.style.setProperty(\"--md-tooltip-0\", `${-origin}px`)\n          else\n            tooltip.style.removeProperty(\"--md-tooltip-0\")\n        },\n\n        /* Handle complete */\n        complete() {\n          tooltip.style.removeProperty(\"--md-tooltip-0\")\n        }\n      })\n\n    /* Create and return component */\n    return watchTooltip(tooltip, el)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n    .pipe(\n      subscribeOn(asyncScheduler)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  bufferCount,\n  combineLatest,\n  combineLatestWith,\n  defer,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  endWith,\n  filter,\n  from,\n  ignoreElements,\n  map,\n  mergeMap,\n  mergeWith,\n  of,\n  shareReplay,\n  startWith,\n  switchMap,\n  takeUntil\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElements,\n  watchElementSize,\n  watchToggle\n} from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { Main } from \"../../main\"\nimport { Tooltip, mountTooltip } from \"../../tooltip\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Header\n */\nexport interface Header {\n  height: number                       /* Header visible height */\n  hidden: boolean                      /* Header is hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dependencies\n */\ninterface Dependencies {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n  main$: Observable<Main>              /* Main area observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Compute whether the header is hidden\n *\n * If the user scrolls past a certain threshold, the header can be hidden when\n * scrolling down, and shown when scrolling up.\n *\n * @param dependencies - Dependencies\n *\n * @returns Toggle observable\n */\nfunction isHidden(\n  { viewport$ }: Pick<Dependencies, \"viewport$\">\n): Observable<boolean> {\n  if (!feature(\"header.autohide\"))\n    return of(false)\n\n  /* Compute direction and turning point */\n  const direction$ = viewport$\n    .pipe(\n      map(({ offset: { y } }) => y),\n      bufferCount(2, 1),\n      map(([a, b]) => [a < b, b] as const),\n      distinctUntilKeyChanged(0)\n    )\n\n  /* Compute whether header should be hidden */\n  const hidden$ = combineLatest([viewport$, direction$])\n    .pipe(\n      filter(([{ offset }, [, y]]) => Math.abs(y - offset.y) > 100),\n      map(([, [direction]]) => direction),\n      distinctUntilChanged()\n    )\n\n  /* Compute threshold for hiding */\n  const search$ = watchToggle(\"search\")\n  return combineLatest([viewport$, search$])\n    .pipe(\n      map(([{ offset }, search]) => offset.y > 400 && !search),\n      distinctUntilChanged(),\n      switchMap(active => active ? hidden$ : of(false)),\n      startWith(false)\n    )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch header\n *\n * @param el - Header element\n * @param dependencies - Dependencies\n *\n * @returns Header observable\n */\nexport function watchHeader(\n  el: HTMLElement, dependencies: Pick<Dependencies, \"viewport$\">\n): Observable<Header> {\n  return defer(() => combineLatest([\n    watchElementSize(el),\n    isHidden(dependencies)\n  ]))\n    .pipe(\n      map(([{ height }, hidden]) => ({\n        height,\n        hidden\n      })),\n      distinctUntilChanged((a, b) => (\n        a.height === b.height &&\n        a.hidden === b.hidden\n      )),\n      shareReplay(1)\n    )\n}\n\n/**\n * Mount header\n *\n * This function manages the different states of the header, i.e. whether it's\n * hidden or rendered with a shadow. This depends heavily on the main area.\n *\n * @param el - Header element\n * @param dependencies - Dependencies\n *\n * @returns Header component observable\n */\nexport function mountHeader(\n  el: HTMLElement, { header$, main$ }: Dependencies\n): Observable<Component<Header | Tooltip>> {\n  return defer(() => {\n    const push$ = new Subject<Main>()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n    push$\n      .pipe(\n        distinctUntilKeyChanged(\"active\"),\n        combineLatestWith(header$)\n      )\n        .subscribe(([{ active }, { hidden }]) => {\n          el.classList.toggle(\"md-header--shadow\", active && !hidden)\n          el.hidden = hidden\n        })\n\n    /* Mount tooltips, if enabled */\n    const tooltips = from(getElements(\"[title]\", el))\n      .pipe(\n        filter(() => feature(\"content.tooltips\")),\n        mergeMap(child => mountTooltip(child))\n      )\n\n    /* Link to main area */\n    main$.subscribe(push$)\n\n    /* Create and return component */\n    return header$\n      .pipe(\n        takeUntil(done$),\n        map(state => ({ ref: el, ...state })),\n        mergeWith(tooltips.pipe(takeUntil(done$)))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  defer,\n  distinctUntilKeyChanged,\n  finalize,\n  map,\n  tap\n} from \"rxjs\"\n\nimport {\n  Viewport,\n  getElementSize,\n  getOptionalElement,\n  watchViewportAt\n} from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { Header } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Header\n */\nexport interface HeaderTitle {\n  active: boolean                      /* Header title is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch header title\n *\n * @param el - Heading element\n * @param options - Options\n *\n * @returns Header title observable\n */\nexport function watchHeaderTitle(\n  el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable<HeaderTitle> {\n  return watchViewportAt(el, { viewport$, header$ })\n    .pipe(\n      map(({ offset: { y } }) => {\n        const { height } = getElementSize(el)\n        return {\n          active: height > 0 && y >= height\n        }\n      }),\n      distinctUntilKeyChanged(\"active\")\n    )\n}\n\n/**\n * Mount header title\n *\n * This function swaps the header title from the site title to the title of the\n * current page when the user scrolls past the first headline.\n *\n * @param el - Header title element\n * @param options - Options\n *\n * @returns Header title component observable\n */\nexport function mountHeaderTitle(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<HeaderTitle>> {\n  return defer(() => {\n    const push$ = new Subject<HeaderTitle>()\n    push$.subscribe({\n\n      /* Handle emission */\n      next({ active }) {\n        el.classList.toggle(\"md-header__title--active\", active)\n      },\n\n      /* Handle complete */\n      complete() {\n        el.classList.remove(\"md-header__title--active\")\n      }\n    })\n\n    /* Obtain headline, if any */\n    const heading = getOptionalElement(\".md-content h1\")\n    if (typeof heading === \"undefined\")\n      return EMPTY\n\n    /* Create and return component */\n    return watchHeaderTitle(heading, options)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  combineLatest,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  map,\n  switchMap\n} from \"rxjs\"\n\nimport {\n  Viewport,\n  watchElementSize\n} from \"~/browser\"\n\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Main area\n */\nexport interface Main {\n  offset: number                       /* Main area top offset */\n  height: number                       /* Main area visible height */\n  active: boolean                      /* Main area is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch main area\n *\n * This function returns an observable that computes the visual parameters of\n * the main area which depends on the viewport vertical offset and height, as\n * well as the height of the header element, if the header is fixed.\n *\n * @param el - Main area element\n * @param options - Options\n *\n * @returns Main area observable\n */\nexport function watchMain(\n  el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable<Main> {\n\n  /* Compute necessary adjustment for header */\n  const adjust$ = header$\n    .pipe(\n      map(({ height }) => height),\n      distinctUntilChanged()\n    )\n\n  /* Compute the main area's top and bottom borders */\n  const border$ = adjust$\n    .pipe(\n      switchMap(() => watchElementSize(el)\n        .pipe(\n          map(({ height }) => ({\n            top:    el.offsetTop,\n            bottom: el.offsetTop + height\n          })),\n          distinctUntilKeyChanged(\"bottom\")\n        )\n      )\n    )\n\n  /* Compute the main area's offset, visible height and if we scrolled past */\n  return combineLatest([adjust$, border$, viewport$])\n    .pipe(\n      map(([header, { top, bottom }, { offset: { y }, size: { height } }]) => {\n        height = Math.max(0, height\n          - Math.max(0, top    - y,  header)\n          - Math.max(0, height + y - bottom)\n        )\n        return {\n          offset: top - header,\n          height,\n          active: top - header <= y\n        }\n      }),\n      distinctUntilChanged((a, b) => (\n        a.offset === b.offset &&\n        a.height === b.height &&\n        a.active === b.active\n      ))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  asyncScheduler,\n  defer,\n  filter,\n  finalize,\n  fromEvent,\n  map,\n  mergeMap,\n  observeOn,\n  of,\n  repeat,\n  shareReplay,\n  skip,\n  startWith,\n  takeUntil,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { getElements, watchMedia } from \"~/browser\"\nimport { h } from \"~/utilities\"\n\nimport {\n  Component,\n  getComponentElement\n} from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Palette colors\n */\nexport interface PaletteColor {\n  media?: string                       /* Media query */\n  scheme?: string                      /* Color scheme */\n  primary?: string                     /* Primary color */\n  accent?: string                      /* Accent color */\n}\n\n/**\n * Palette\n */\nexport interface Palette {\n  index: number                        /* Palette index */\n  color: PaletteColor                  /* Palette colors */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch color palette\n *\n * @param inputs - Color palette element\n *\n * @returns Color palette observable\n */\nexport function watchPalette(\n  inputs: HTMLInputElement[]\n): Observable<Palette> {\n  const current = __md_get<Palette>(\"__palette\") || {\n    index: inputs.findIndex(input => matchMedia(\n      input.getAttribute(\"data-md-color-media\")!\n    ).matches)\n  }\n\n  /* Emit changes in color palette */\n  const index = Math.max(0, Math.min(current.index, inputs.length - 1))\n  return of(...inputs)\n    .pipe(\n      mergeMap(input => fromEvent(input, \"change\").pipe(map(() => input))),\n      startWith(inputs[index]),\n      map(input => ({\n        index: inputs.indexOf(input),\n        color: {\n          media:   input.getAttribute(\"data-md-color-media\"),\n          scheme:  input.getAttribute(\"data-md-color-scheme\"),\n          primary: input.getAttribute(\"data-md-color-primary\"),\n          accent:  input.getAttribute(\"data-md-color-accent\")\n        }\n      } as Palette)),\n      shareReplay(1)\n    )\n}\n\n/**\n * Mount color palette\n *\n * @param el - Color palette element\n *\n * @returns Color palette component observable\n */\nexport function mountPalette(\n  el: HTMLElement\n): Observable<Component<Palette>> {\n  const inputs = getElements<HTMLInputElement>(\"input\", el)\n  const meta = h(\"meta\", { name: \"theme-color\" })\n  document.head.appendChild(meta)\n\n  // Add color scheme meta tag\n  const scheme = h(\"meta\", { name: \"color-scheme\" })\n  document.head.appendChild(scheme)\n\n  /* Mount component on subscription */\n  const media$ = watchMedia(\"(prefers-color-scheme: light)\")\n  return defer(() => {\n    const push$ = new Subject<Palette>()\n    push$.subscribe(palette => {\n      document.body.setAttribute(\"data-md-color-switching\", \"\")\n\n      /* Retrieve color palette for system preference */\n      if (palette.color.media === \"(prefers-color-scheme)\") {\n        const media = matchMedia(\"(prefers-color-scheme: light)\")\n        const input = document.querySelector(media.matches\n          ? \"[data-md-color-media='(prefers-color-scheme: light)']\"\n          : \"[data-md-color-media='(prefers-color-scheme: dark)']\"\n        )!\n\n        /* Retrieve colors for system preference */\n        palette.color.scheme  = input.getAttribute(\"data-md-color-scheme\")!\n        palette.color.primary = input.getAttribute(\"data-md-color-primary\")!\n        palette.color.accent  = input.getAttribute(\"data-md-color-accent\")!\n      }\n\n      /* Set color palette */\n      for (const [key, value] of Object.entries(palette.color))\n        document.body.setAttribute(`data-md-color-${key}`, value)\n\n      /* Set toggle visibility */\n      for (let index = 0; index < inputs.length; index++) {\n        const label = inputs[index].nextElementSibling\n        if (label instanceof HTMLElement)\n          label.hidden = palette.index !== index\n      }\n\n      /* Persist preference in local storage */\n      __md_set(\"__palette\", palette)\n    })\n\n    // Handle color switch on Enter or Space - see https://t.ly/YIhVj\n    fromEvent<KeyboardEvent>(el, \"keydown\").pipe(\n      filter(ev => ev.key === \"Enter\"),\n      withLatestFrom(push$, (_, palette) => palette)\n    )\n      .subscribe(({ index }) => {\n        index = (index + 1) % inputs.length\n        inputs[index].click()\n        inputs[index].focus()\n      })\n\n    /* Update theme-color meta tag */\n    push$\n      .pipe(\n        map(() => {\n          const header = getComponentElement(\"header\")\n          const style  = window.getComputedStyle(header)\n\n          // Set color scheme\n          scheme.content = style.colorScheme\n\n          /* Return color in hexadecimal format */\n          return style.backgroundColor.match(/\\d+/g)!\n            .map(value => (+value).toString(16).padStart(2, \"0\"))\n            .join(\"\")\n        })\n      )\n        .subscribe(color => meta.content = `#${color}`)\n\n    /* Revert transition durations after color switch */\n    push$.pipe(observeOn(asyncScheduler))\n      .subscribe(() => {\n        document.body.removeAttribute(\"data-md-color-switching\")\n      })\n\n    /* Create and return component */\n    return watchPalette(inputs)\n      .pipe(\n        takeUntil(media$.pipe(skip(1))),\n        repeat(),\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  defer,\n  finalize,\n  map,\n  tap\n} from \"rxjs\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Progress indicator\n */\nexport interface Progress {\n  value: number                        // Progress value\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  progress$: Subject<number>           // Progress subject\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount progress indicator\n *\n * @param el - Progress indicator element\n * @param options - Options\n *\n * @returns Progress indicator component observable\n */\nexport function mountProgress(\n  el: HTMLElement, { progress$ }: MountOptions\n): Observable<Component<Progress>> {\n\n  // Mount component on subscription\n  return defer(() => {\n    const push$ = new Subject<Progress>()\n    push$.subscribe(({ value }) => {\n      el.style.setProperty(\"--md-progress-value\", `${value}`)\n    })\n\n    // Create and return component\n    return progress$\n      .pipe(\n        tap(value => push$.next({ value })),\n        finalize(() => push$.complete()),\n        map(value => ({ ref: el, value }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  catchError,\n  map,\n  of,\n  share\n} from \"rxjs\"\n\nimport {\n  getElement,\n  getElements,\n  requestXML\n} from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Sitemap, i.e. a list of URLs\n */\nexport type Sitemap = Map<string, URL[]>\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Resolve URL to the given base URL\n *\n * When serving the site with instant navigation, MkDocs will set the hostname\n * to the value as specified in `dev_addr`, but the browser allows for several\n * hostnames to be used: `localhost`, `127.0.0.1` or even `0.0.0.0`, depending\n * on configuration. This function resolves the URL to the given hostname.\n *\n * @param url - URL\n * @param base - Base URL\n *\n * @returns Resolved URL\n */\nfunction resolve(url: URL, base: URL) {\n  url.protocol = base.protocol\n  url.hostname = base.hostname\n  return url\n}\n\n/**\n * Extract sitemap from document\n *\n * This function extracts the URLs and alternate links from the document, and\n * associates alternate links to the original URL as found in `loc`, allowing\n * the browser to navigate to the correct page when switching languages. The\n * format of the sitemap is expected to adhere to:\n *\n * ``` xml\n * <urlset>\n *   <url>\n *     <loc>...</loc>\n *     <xhtml:link rel=\"alternate\" hreflang=\"en\" href=\"...\"/>\n *     <xhtml:link rel=\"alternate\" hreflang=\"de\" href=\"...\"/>\n *     ...\n *   </url>\n *   ...\n * </urlset>\n * ```\n *\n * @param document - Document\n * @param base - Base URL\n *\n * @returns Sitemap\n */\nfunction extract(document: Document, base: URL): Sitemap {\n  const sitemap: Sitemap = new Map()\n  for (const el of getElements(\"url\", document)) {\n    const url = getElement(\"loc\", el)\n\n    // Create entry for location and add it to the list of links\n    const links = [resolve(new URL(url.textContent!), base)]\n    sitemap.set(`${links[0]}`, links)\n\n    // Attach alternate links to current entry\n    for (const link of getElements(\"[rel=alternate]\", el)) {\n      const href = link.getAttribute(\"href\")\n      if (href != null)\n        links.push(resolve(new URL(href), base))\n    }\n  }\n\n  // Return sitemap\n  return sitemap\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch the sitemap for the given base URL\n *\n * If a network or parsing error occurs, we just default to an empty sitemap,\n * which means the caller should fall back to regular navigation.\n *\n * @param base - Base URL\n *\n * @returns Sitemap observable\n */\nexport function fetchSitemap(base: URL | string): Observable<Sitemap> {\n  return requestXML(new URL(\"sitemap.xml\", base))\n    .pipe(\n      map(document => extract(document, new URL(base))),\n      catchError(() => of(new Map())),\n      share()\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  catchError,\n  filter,\n  fromEvent,\n  map,\n  mergeMap,\n  of,\n  switchMap\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n  getElements,\n  getLocation,\n  setLocation\n} from \"~/browser\"\n\nimport { Sitemap, fetchSitemap } from \"../sitemap\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n  document$: Observable<Document>      /* Document subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up alternate version navigation\n *\n * @param options - Options\n */\nexport function setupAlternate(\n  { document$ }: SetupOptions\n): void {\n  const alternate = new Map<string, Sitemap>()\n\n  // Fetch sitemaps for all discovered alternate versions\n  document$\n    .pipe(\n      switchMap(() => getElements<HTMLLinkElement>(\"link[rel=alternate]\")),\n      map(el => new URL(el.href)),\n      filter(url => !alternate.has(url.toString())),\n      mergeMap(url => fetchSitemap(url)\n        .pipe(\n          map(sitemap => [url, sitemap] as const),\n          catchError(() => EMPTY)\n        )\n      )\n    )\n\n      // Persist fully qualified URL, because alternate versions may be on\n      // entirely different domains, but as long a proper cross-origin policy\n      // is set, we can still navigate to them. Also, remove the trailing slash\n      // to normalize the URL\n      .subscribe(([url, sitemap]) => {\n        alternate.set(url.toString().replace(/\\/$/, \"\"), sitemap)\n      })\n\n  // Intercept alternate navigation - when refactoring instant navigation later,\n  // we should provide a single stream of events that we all subscribe to, and\n  // from which we implement version and alternate language navigation\n  fromEvent<MouseEvent>(document.body, \"click\")\n    .pipe(\n      filter(ev => !ev.metaKey && !ev.ctrlKey),\n      switchMap(ev => {\n        if (ev.target instanceof Element) {\n          const el = ev.target.closest(\"a\")\n\n          // Now, we need to check whether the navigation target is an alternate\n          // version. If so, we need to prevent the default navigation behavior\n          // and instead navigate to the correct page, if we can resolve it.\n          if (el && !el.target) {\n            const result = [...alternate].find(([url]) => (\n              el.href.startsWith(`${url}/`)\n            ))\n\n            // Check, that we got a sitemap at least, so we know that we either\n            // navigate on the current site, or to an alternate site\n            if (typeof result === \"undefined\")\n              return EMPTY\n\n            // Check that we go to and alternate site\n            const [url, sitemap] = result\n            const location = getLocation()\n            if (location.href.startsWith(url))\n              return EMPTY\n\n            // Isolate the part to which we navigate and check if it's in the\n            // sitemap that we resolved earlier @todo: refactor this, as the\n            // semantics slightly changed due to the new sitemap resolution\n            // implementation, which normalizes all URLs.\n            const config = configuration()\n            let path = location.href.replace(config.base, \"\")\n            path = `${url}/${path}`\n            const target = sitemap.has(path.split(\"#\")[0])\n              ? new URL(path, config.base)\n              : new URL(url)\n\n            // Steal navigation and navigate to the correct page\n            ev.preventDefault()\n            return of(target)\n          }\n        }\n        return EMPTY\n      })\n    )\n    .subscribe(url => setLocation(url, true))\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport ClipboardJS from \"clipboard\"\nimport {\n  Observable,\n  Subject,\n  map,\n  tap\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport { getElement } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n  alert$: Subject<string>              /* Alert subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Extract text to copy\n *\n * @param el - HTML element\n *\n * @returns Extracted text\n */\nfunction extract(el: HTMLElement): string {\n  el.setAttribute(\"data-md-copying\", \"\")\n  const copy = el.closest(\"[data-copy]\")\n  const text = copy\n    ? copy.getAttribute(\"data-copy\")!\n    : el.innerText\n  el.removeAttribute(\"data-md-copying\")\n  return text.trimEnd()\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up Clipboard.js integration\n *\n * @param options - Options\n */\nexport function setupClipboardJS(\n  { alert$ }: SetupOptions\n): void {\n  if (ClipboardJS.isSupported()) {\n    new Observable<ClipboardJS.Event>(subscriber => {\n      new ClipboardJS(\"[data-clipboard-target], [data-clipboard-text]\", {\n        text: el => (\n          el.getAttribute(\"data-clipboard-text\")! ||\n          extract(getElement(\n            el.getAttribute(\"data-clipboard-target\")!\n          ))\n        )\n      })\n        .on(\"success\", ev => subscriber.next(ev))\n    })\n      .pipe(\n        tap(ev => {\n          const trigger = ev.trigger as HTMLElement\n          trigger.focus()\n        }),\n        map(() => translation(\"clipboard.copied\"))\n      )\n        .subscribe(alert$)\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  catchError,\n  combineLatestWith,\n  concat,\n  debounceTime,\n  distinct,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  endWith,\n  exhaustMap,\n  fromEvent,\n  ignoreElements,\n  map,\n  merge,\n  of,\n  share,\n  switchMap,\n  take,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElements,\n  getLocation,\n  getOptionalElement,\n  requestHTML,\n  setLocation,\n  setLocationHash\n} from \"~/browser\"\nimport { getComponentElement } from \"~/components\"\n\nimport { Sitemap } from \"../sitemap\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n  sitemap$: Observable<Sitemap>        // Sitemap observable\n  location$: Subject<URL>              // Location subject\n  viewport$: Observable<Viewport>      // Viewport observable\n  progress$: Subject<number>           // Progress subject\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Handle clicks on internal URLs while skipping external URLs\n *\n * @param ev - Mouse event\n * @param sitemap - Sitemap\n *\n * @returns Anchor observable\n */\nfunction handle(\n  ev: MouseEvent, sitemap: Sitemap\n): Observable<HTMLAnchorElement> {\n  if (!(ev.target instanceof Element))\n    return EMPTY\n\n  // Skip, as target is not within a link - clicks on non-link elements are\n  // also captured, which we need to exclude from processing\n  const el = ev.target.closest(\"a\")\n  if (el === null)\n    return EMPTY\n\n  // Skip, as link opens in new window - we now know we have captured a click\n  // on a link, but the link either has a `target` property defined, or the\n  // user pressed the `meta` or `ctrl` key to open it in a new window. Thus,\n  // we need to filter this event as well.\n  if (el.target || ev.metaKey || ev.ctrlKey)\n    return EMPTY\n\n  // Next, we must check if the URL is relevant for us, i.e., if it's an\n  // internal link to a page that is managed by MkDocs. Only then we can be\n  // sure that the structure of the page to be loaded adheres to the current\n  // document structure and can subsequently be injected into it without doing\n  // a full reload. For this reason, we must canonicalize the URL by removing\n  // all search parameters and hash fragments.\n  const url = new URL(el.href)\n  url.search = url.hash = \"\"\n\n  // Skip, if URL is not included in the sitemap - this could be the case when\n  // linking between versions or languages, or to another page that the author\n  // included as part of the build, but that is not managed by MkDocs. In that\n  // case we must not continue with instant navigation.\n  if (!sitemap.has(`${url}`))\n    return EMPTY\n\n  // We now know that we have a link to an internal page, so we prevent the\n  // browser from navigation and emit the URL for instant navigation. Note that\n  // this also includes anchor links, which means we need to implement anchor\n  // positioning ourselves. The reason for this is that if we wouldn't manage\n  // anchor links as well, scroll restoration will not work correctly (e.g.\n  // following an anchor link and scrolling).\n  ev.preventDefault()\n  return of(el)\n}\n\n/**\n * Create a map of head elements for lookup and replacement\n *\n * @param document - Document\n *\n * @returns Tag map\n */\nfunction head(document: Document): Map<string, HTMLElement> {\n  const tags = new Map<string, HTMLElement>()\n  for (const el of getElements(\":scope > *\", document.head))\n    tags.set(el.outerHTML, el)\n\n  // Return tag map\n  return tags\n}\n\n/**\n * Resolve relative URLs in the given document\n *\n * This function resolves relative `href` and `src` attributes, which can belong\n * to all sorts of tags, like meta tags, links, images, scripts and more.\n *\n * @param document - Document\n *\n * @returns Document observable\n */\nfunction resolve(document: Document): Observable<Document> {\n  for (const el of getElements(\"[href], [src]\", document))\n    for (const key of [\"href\", \"src\"]) {\n      const value = el.getAttribute(key)\n      if (value && !/^(?:[a-z]+:)?\\/\\//i.test(value)) {\n        // @ts-expect-error - trick: self-assign to resolve URL\n        el[key] = el[key]\n        break\n      }\n    }\n\n  // Return document observable\n  return of(document)\n}\n\n/**\n * Inject the contents of a document into the current one\n *\n * @param next - Next document\n *\n * @returns Document observable\n */\nfunction inject(next: Document): Observable<Document> {\n  for (const selector of [\n    \"[data-md-component=announce]\",\n    \"[data-md-component=container]\",\n    \"[data-md-component=header-topic]\",\n    \"[data-md-component=outdated]\",\n    \"[data-md-component=logo]\",\n    \"[data-md-component=skip]\",\n    ...feature(\"navigation.tabs.sticky\")\n      ? [\"[data-md-component=tabs]\"]\n      : []\n  ]) {\n    const source = getOptionalElement(selector)\n    const target = getOptionalElement(selector, next)\n    if (\n      typeof source !== \"undefined\" &&\n      typeof target !== \"undefined\"\n    ) {\n      source.replaceWith(target)\n    }\n  }\n\n  // Update meta tags\n  const tags = head(document)\n  for (const [html, el] of head(next))\n    if (tags.has(html))\n      tags.delete(html)\n    else\n      document.head.appendChild(el)\n\n  // Remove meta tags that are not present in the new document\n  for (const el of tags.values()) {\n    const name = el.getAttribute(\"name\")\n    // @todo - find a better way to handle attributes we add dynamically in\n    // other components without mounting components on every navigation, as\n    // this might impact overall performance - see https://t.ly/ehp_O\n    if (name !== \"theme-color\" && name !== \"color-scheme\")\n      el.remove()\n  }\n\n  // After components and meta tags were replaced, re-evaluate scripts\n  // that were provided by the author as part of Markdown files\n  const container = getComponentElement(\"container\")\n  return concat(getElements(\"script\", container))\n    .pipe(\n      switchMap(el => {\n        const script = next.createElement(\"script\")\n        if (el.src) {\n          for (const name of el.getAttributeNames())\n            script.setAttribute(name, el.getAttribute(name)!)\n          el.replaceWith(script)\n\n          // Complete when script is loaded\n          return new Observable(observer => {\n            script.onload = () => observer.complete()\n          })\n\n        // Complete immediately\n        } else {\n          script.textContent = el.textContent\n          el.replaceWith(script)\n          return EMPTY\n        }\n      }),\n      ignoreElements(),\n      endWith(document)\n    )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up instant navigation\n *\n * This is a heavily orchestrated operation - see inline comments to learn how\n * this works with Material for MkDocs, and how you can hook into it.\n *\n * @param options - Options\n *\n * @returns Document observable\n */\nexport function setupInstantNavigation(\n  { sitemap$, location$, viewport$, progress$ }: SetupOptions\n): Observable<Document> {\n  if (location.protocol === \"file:\")\n    return EMPTY\n\n  // Since we might be on a slow connection, the user might trigger multiple\n  // instant navigation events that overlap. MkDocs produces relative URLs for\n  // all internal links, which becomes a problem in this case, because we need\n  // to change the base URL the moment the user clicks a link that should be\n  // intercepted in order to be consistent with popstate, which means that the\n  // base URL would now be incorrect when resolving another relative link from\n  // the same site. For this reason we always resolve all relative links to\n  // absolute links, so we can be sure this never happens.\n  of(document)\n    .subscribe(resolve)\n\n  // --------------------------------------------------------------------------\n  // Navigation interception\n  // --------------------------------------------------------------------------\n\n  // Intercept navigation - to keep the number of event listeners down we use\n  // the fact that uncaptured events bubble up to the body. This has the nice\n  // property that we don't need to detach and then re-attach event listeners\n  // when the document is replaced after a navigation event.\n  const instant$ =\n    fromEvent<MouseEvent>(document.body, \"click\")\n      .pipe(\n        combineLatestWith(sitemap$),\n        switchMap(([ev, sitemap]) => handle(ev, sitemap)),\n        map(({ href }) => new URL(href)),\n        share()\n      )\n\n  // Intercept history change events, e.g. when the user uses the browser's\n  // back or forward buttons, and emit new location for fetching and parsing\n  const history$ =\n    fromEvent<PopStateEvent>(window, \"popstate\")\n      .pipe(\n        map(getLocation),\n        share()\n      )\n\n  // While it would be better UX to defer navigation events until the document\n  // is fully fetched and parsed, we must schedule it here to synchronize with\n  // popstate events, as they are emitted immediately. Moreover we need to\n  // store the current viewport offset for scroll restoration later on.\n  instant$.pipe(withLatestFrom(viewport$))\n    .subscribe(([url, { offset }]) => {\n      history.replaceState(offset, \"\")\n      history.pushState(null, \"\", url)\n    })\n\n  // Emit URLs that should be fetched via instant navigation on location subject\n  // which was passed into this function. The state of instant navigation can be\n  // intercepted by other parts of the application, which can synchronously back\n  // up or restore state before or after instant navigation happens.\n  merge(instant$, history$)\n    .subscribe(location$)\n\n  // --------------------------------------------------------------------------\n  // Fetching and parsing\n  // --------------------------------------------------------------------------\n\n  // Fetch document - we deduplicate requests to the same location, so we don't\n  // end up with multiple requests for the same page. We use `switchMap`, since\n  // we want to cancel the previous request when a new one is triggered, which\n  // is automatically handled by the observable returned by `request`. This is\n  // essential to ensure a good user experience, as we don't want to load pages\n  // that are not needed anymore, e.g., when the user clicks multiple links in\n  // quick succession or on slow connections. If the request fails for some\n  // reason, we fall back and use regular navigation, forcing a reload.\n  const document$ =\n    location$.pipe(\n      distinctUntilKeyChanged(\"pathname\"),\n      switchMap(url => requestHTML(url, { progress$ })\n        .pipe(\n          catchError(() => {\n            setLocation(url, true)\n            return EMPTY\n          })\n        )\n      ),\n\n      // The document was successfully fetched and parsed, so we can inject its\n      // contents into the currently active document\n      switchMap(resolve),\n      switchMap(inject),\n      share()\n    )\n\n  // --------------------------------------------------------------------------\n  // Scroll restoration\n  // --------------------------------------------------------------------------\n\n  // Handle scroll restoration - we must restore the viewport offset after the\n  // document has been fetched and injected, and every time the user clicks an\n  // anchor that leads to an element on the same page, which might also happen\n  // when the user uses the back or forward button.\n  merge(\n    document$.pipe(withLatestFrom(location$, (_, url) => url)),\n\n    // Handle instant navigation events that are triggered by the user clicking\n    // on an anchor link with a hash fragment different from the current one, as\n    // well as from popstate events, which are emitted when the user navigates\n    // back and forth between pages.\n    document$.pipe(\n      switchMap(() => location$),\n      distinctUntilKeyChanged(\"hash\"),\n    ),\n\n    // Handle instant navigation events that are triggered by the user clicking\n    // on an anchor link with the same hash fragment as the current one in the\n    // URL. It is essential that we only intercept those from instant navigation\n    // events and not from history change events, or we'll end up in and endless\n    // loop. The top-level history entry must be removed, as it will be replaced\n    // with a new one, which would otherwise lead to a duplicate entry.\n    location$.pipe(\n      distinctUntilChanged((a, b) => (\n        a.pathname === b.pathname &&\n        a.hash     === b.hash\n      )),\n      switchMap(() => instant$),\n      tap(() => history.back())\n    )\n  )\n    .subscribe(url => {\n\n      // Check if the current history entry has a state, which happens when the\n      // user presses the back or forward button to visit a page we've already\n      // seen. If there's no state, it means a new page was visited and we must\n      // scroll to the top, unless an anchor is given.\n      if (history.state !== null || !url.hash) {\n        window.scrollTo(0, history.state?.y ?? 0)\n      } else {\n        history.scrollRestoration = \"auto\"\n        setLocationHash(url.hash)\n        history.scrollRestoration = \"manual\"\n      }\n    })\n\n  // Disable scroll restoration when an instant navigation event occurs, so the\n  // browser does not immediately set the viewport offset to the prior history\n  // entry, scrolling to the position on the same page, which would look odd.\n  // Instead, we manually restore the position once the page has loaded.\n  location$.subscribe(() => {\n    history.scrollRestoration = \"manual\"\n  })\n\n  // Enable scroll restoration before window unloads - this is essential to\n  // ensure that full reloads (F5) restore the viewport offset correctly. If\n  // only popstate events wouldn't reset the viewport offset prior to their\n  // emission, we could just reset this in popstate. Meh.\n  fromEvent(window, \"beforeunload\")\n    .subscribe(() => {\n      history.scrollRestoration = \"auto\"\n    })\n\n  // Track viewport offset, so we can restore it when the user navigates back\n  // and forth between pages. Note that this must be debounced and cannot be\n  // done in popstate, as popstate has already removed the entry from the\n  // history, which means it is too late.\n  viewport$.pipe(\n    distinctUntilKeyChanged(\"offset\"),\n    debounceTime(100)\n  )\n    .subscribe(({ offset }) => {\n      history.replaceState(offset, \"\")\n    })\n\n  // --------------------------------------------------------------------------\n  // Navigation prefetching\n  // --------------------------------------------------------------------------\n\n  // If prefetching is enabled, prefetch pages for links that would trigger\n  // inter-site navigation on mouse events - this should improve performance,\n  // since pages will be cached. Note that we exhaust map URLs, so we ensure\n  // that loading is properly debounced and we don't fill caches up to quickly.\n  if (feature(\"navigation.instant.prefetch\"))\n    merge(\n      fromEvent<MouseEvent>(document.body, \"mousemove\"),\n      fromEvent<MouseEvent>(document.body, \"focusin\")\n    )\n      .pipe(\n        combineLatestWith(sitemap$),\n        switchMap(([ev, sitemap]) => handle(ev, sitemap)),\n        debounceTime(25),\n        distinct(({ href }) => href),\n        exhaustMap(href => {\n          const link = document.createElement(\"link\")\n          link.rel = \"prefetch\"\n          link.href = href.toString()\n\n          // Instruct browser to prefetch link by adding a link tag of type\n          // prefetch to the head, and remove it again once the page was loaded\n          document.head.appendChild(link)\n          return fromEvent(link, \"load\")\n            .pipe(\n              map(() => link),\n              take(1)\n            )\n        })\n      )\n        .subscribe(link => link.remove())\n\n  // Return document observable\n  return document$\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchConfig } from \"../config\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlight function\n *\n * @param value - Value\n *\n * @returns Highlighted value\n */\nexport type SearchHighlightFn = (value: string) => string\n\n/**\n * Search highlight factory function\n *\n * @param query - Query value\n *\n * @returns Search highlight function\n */\nexport type SearchHighlightFactoryFn = (query: string) => SearchHighlightFn\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search highlighter\n *\n * @param config - Search configuration\n *\n * @returns Search highlight factory function\n */\nexport function setupSearchHighlighter(\n  config: SearchConfig\n): SearchHighlightFactoryFn {\n  // Hack: temporarily remove pure lookaheads and lookbehinds\n  const regex = config.separator.split(\"|\").map(term => {\n    const temp = term.replace(/(\\(\\?[!=<][^)]+\\))/g, \"\")\n    return temp.length === 0 ? \"\uFFFD\" : term\n  })\n    .join(\"|\")\n\n  const separator = new RegExp(regex, \"img\")\n  const highlight = (_: unknown, data: string, term: string) => {\n    return `${data}<mark data-md-highlight>${term}</mark>`\n  }\n\n  /* Return factory function */\n  return (query: string) => {\n    query = query\n      .replace(/[\\s*+\\-:~^]+/g, \" \")\n      .replace(/&/g, \"&amp;\")\n      .trim()\n\n    /* Create search term match expression */\n    const match = new RegExp(`(^|${config.separator}|)(${\n      query\n        .replace(/[|\\\\{}()[\\]^$+*?.-]/g, \"\\\\$&\")\n        .replace(separator, \"|\")\n    })`, \"img\")\n\n    /* Highlight string value */\n    return value => escapeHTML(value)\n      .replace(match, highlight)\n      .replace(/<\\/mark>(\\s+)<mark[^>]*>/img, \"$1\")\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { SearchResult } from \"../../_\"\nimport { SearchIndex } from \"../../config\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search message type\n */\nexport const enum SearchMessageType {\n  SETUP,                               /* Search index setup */\n  READY,                               /* Search index ready */\n  QUERY,                               /* Search query */\n  RESULT                               /* Search results */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Message containing the data necessary to setup the search index\n */\nexport interface SearchSetupMessage {\n  type: SearchMessageType.SETUP        /* Message type */\n  data: SearchIndex                    /* Message data */\n}\n\n/**\n * Message indicating the search index is ready\n */\nexport interface SearchReadyMessage {\n  type: SearchMessageType.READY        /* Message type */\n}\n\n/**\n * Message containing a search query\n */\nexport interface SearchQueryMessage {\n  type: SearchMessageType.QUERY        /* Message type */\n  data: string                         /* Message data */\n}\n\n/**\n * Message containing results for a search query\n */\nexport interface SearchResultMessage {\n  type: SearchMessageType.RESULT       /* Message type */\n  data: SearchResult                   /* Message data */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Message exchanged with the search worker\n */\nexport type SearchMessage =\n  | SearchSetupMessage\n  | SearchReadyMessage\n  | SearchQueryMessage\n  | SearchResultMessage\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Type guard for search ready messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchReadyMessage(\n  message: SearchMessage\n): message is SearchReadyMessage {\n  return message.type === SearchMessageType.READY\n}\n\n/**\n * Type guard for search result messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchResultMessage(\n  message: SearchMessage\n): message is SearchResultMessage {\n  return message.type === SearchMessageType.RESULT\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  ObservableInput,\n  Subject,\n  first,\n  merge,\n  of,\n  switchMap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport { watchToggle, watchWorker } from \"~/browser\"\n\nimport { SearchIndex } from \"../../config\"\nimport {\n  SearchMessage,\n  SearchMessageType\n} from \"../message\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up search worker\n *\n * This function creates and initializes a web worker that is used for search,\n * so that the user interface doesn't freeze. In general, the application does\n * not care how search is implemented, as long as the web worker conforms to\n * the format expected by the application as defined in `SearchMessage`. This\n * allows the author to implement custom search functionality, by providing a\n * custom web worker via configuration.\n *\n * Material for MkDocs' built-in search implementation makes use of Lunr.js, an\n * efficient and fast implementation for client-side search. Leveraging a tiny\n * iframe-based web worker shim, search is even supported for the `file://`\n * protocol, enabling search for local non-hosted builds.\n *\n * If the protocol is `file://`, search initialization is deferred to mitigate\n * freezing, as it's now synchronous by design - see https://bit.ly/3C521EO\n *\n * @see https://bit.ly/3igvtQv - How to implement custom search\n *\n * @param url - Worker URL\n * @param index$ - Search index observable input\n *\n * @returns Search worker\n */\nexport function setupSearchWorker(\n  url: string, index$: ObservableInput<SearchIndex>\n): Subject<SearchMessage> {\n  const worker$ = watchWorker<SearchMessage>(url)\n  merge(\n    of(location.protocol !== \"file:\"),\n    watchToggle(\"search\")\n  )\n    .pipe(\n      first(active => active),\n      switchMap(() => index$)\n    )\n      .subscribe(({ config, docs }) => worker$.next({\n        type: SearchMessageType.SETUP,\n        data: {\n          config,\n          docs,\n          options: {\n            suggest: feature(\"search.suggest\")\n          }\n        }\n      }))\n\n  /* Return search worker */\n  return worker$\n}\n", "import { Sitemap } from \"../../sitemap\"\n\n/** See docstring for `selectedVersionCorrespondingURL` for the meaning of these fields. */\ntype CorrespondingURLParams = {\n  selectedVersionSitemap: Sitemap\n  selectedVersionBaseURL: URL\n  currentLocation: URL\n  currentBaseURL: string\n}\n\n/**\n * Choose a URL to navigate to when the user chooses a version in the version\n * selector.\n *\n * The parameters in `params` are named as follows, in order to make it clearer\n * which parameter means what when invoking the function:\n *\n *  - selectedVersionSitemap: Sitemap - as obtained by fetchSitemap from `${selectedVersionBaseURL}/sitemap.xml`\n *\n *  - selectedVersionBaseURL: URL - usually `${currentBaseURL}/../selectedVersion`\n *\n *  - currentLocation: URL - current web browser location\n *\n *  - currentBaseURL: string - as obtained from `config.base`\n *\n * @param params - arguments with the meanings explained above.\n * @returns the URL to navigate to or null if we can't be sure that the\n * corresponding page to the current page exists in the selected version\n */\nexport function selectedVersionCorrespondingURL(\n  params: CorrespondingURLParams\n): URL | undefined {\n  const {selectedVersionSitemap,\n    selectedVersionBaseURL,\n    currentLocation,\n    currentBaseURL} = params\n  const current_path = safeURLParse(currentBaseURL)?.pathname\n  if (current_path === undefined) {\n    return\n  }\n  const currentRelativePath = stripPrefix(currentLocation.pathname, current_path)\n  if (currentRelativePath === undefined) {\n    return\n  }\n  const sitemapCommonPrefix = shortestCommonPrefix(selectedVersionSitemap.keys())\n  if (!selectedVersionSitemap.has(sitemapCommonPrefix)) {\n    // We could also check that `commonSitemapPrefix` ends in the canonical version,\n    // similarly to https://github.com/squidfunk/mkdocs-material/pull/7227. However,\n    // I don't believe that Mike/MkDocs ever generate sitemaps where it would matter\n    return\n  }\n\n  const potentialSitemapURL = safeURLParse(currentRelativePath, sitemapCommonPrefix)\n  if (!potentialSitemapURL || !selectedVersionSitemap.has(potentialSitemapURL.href)) {\n    return\n  }\n\n  const result = safeURLParse(currentRelativePath, selectedVersionBaseURL)\n  if (!result) {\n    return\n  }\n  result.hash = currentLocation.hash\n  result.search = currentLocation.search\n  return result\n}\n\n/**\n * A version of `new URL` that never throws. A polyfill for URL.parse() which is\n * not yet ubuquitous.\n *\n * @param url - passed to `new URL` constructor\n * @param base - passed to `new URL` constructor\n *\n * @returns `new URL(url, base)` or undefined if the URL is invalid.\n */\nfunction safeURLParse(url: string|URL, base?: string|URL): URL | undefined {\n  try {\n    return new URL(url, base)\n  } catch {\n    return\n  }\n}\n\n// Basic string manipulation\n\n/** Strip a given prefix from a function\n *\n * @param s - string\n * @param prefix - prefix to strip\n *\n * @returns either the string with the prefix stripped or undefined if the\n * string did not begin with the prefix.\n */\nexport function stripPrefix(s: string, prefix: string): string | undefined {\n  if (s.startsWith(prefix)) {\n    return s.slice(prefix.length)\n  }\n  return undefined\n}\n\n/** Find the length of the longest common prefix of two strings\n *\n * @param s1 - first string\n * @param s2 - second string\n *\n * @returns - the length of the longest common prefix of the two strings.\n */\nfunction commonPrefixLen(s1: string, s2: string): number {\n  const max = Math.min(s1.length, s2.length)\n  let result\n  for (result = 0; result < max; ++result) {\n    if (s1[result] !== s2[result]) {\n      break\n    }\n  }\n  return result\n}\n\n/** Find the longest common prefix of any number of strings\n *\n * @param strs - an iterable of strings\n *\n * @returns the longest common prefix of all the strings\n */\nexport function shortestCommonPrefix(strs: Iterable<string>): string {\n  let result  // Undefined if no iterations happened\n  for (const s of strs) {\n    if (result === undefined) {\n      result = s\n    } else {\n      result = result.slice(0, commonPrefixLen(result, s))\n    }\n  }\n  return result ?? \"\"\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Subject,\n  catchError,\n  combineLatest,\n  filter,\n  fromEvent,\n  map,\n  of,\n  switchMap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n  getElement,\n  getLocation,\n  requestJSON,\n  setLocation\n} from \"~/browser\"\nimport { getComponentElements } from \"~/components\"\nimport {\n  Version,\n  renderVersionSelector\n} from \"~/templates\"\n\nimport { fetchSitemap } from \"../sitemap\"\n\nimport { selectedVersionCorrespondingURL } from \"./findurl\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n  document$: Subject<Document>         /* Document subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up version selector\n *\n * @param options - Options\n */\nexport function setupVersionSelector(\n  { document$ }: SetupOptions\n): void {\n  const config = configuration()\n  const versions$ = requestJSON<Version[]>(\n    new URL(\"../versions.json\", config.base)\n  )\n    .pipe(\n      catchError(() => EMPTY) // @todo refactor instant loading\n    )\n\n  /* Determine current version */\n  const current$ = versions$\n    .pipe(\n      map(versions => {\n        const [, current] = config.base.match(/([^/]+)\\/?$/)!\n        return versions.find(({ version, aliases }) => (\n          version === current || aliases.includes(current)\n        )) || versions[0]\n      })\n    )\n\n  /* Intercept inter-version navigation */\n  versions$\n    .pipe(\n      map(versions => new Map(versions.map(version => [\n        `${new URL(`../${version.version}/`, config.base)}`,\n        version\n      ]))),\n      switchMap(urls => fromEvent<MouseEvent>(document.body, \"click\")\n        .pipe(\n          filter(ev => !ev.metaKey && !ev.ctrlKey),\n          withLatestFrom(current$),\n          switchMap(([ev, current]) => {\n            if (ev.target instanceof Element) {\n              const el = ev.target.closest(\"a\")\n              if (el && !el.target && urls.has(el.href)) {\n                const url = el.href\n                // This is a temporary hack to detect if a version inside the\n                // version selector or on another part of the site was clicked.\n                // If we're inside the version selector, we definitely want to\n                // find the same page, as we might have different deployments\n                // due to aliases. However, if we're outside the version\n                // selector, we must abort here, because we might otherwise\n                // interfere with instant navigation. We need to refactor this\n                // at some point together with instant navigation.\n                //\n                // See https://github.com/squidfunk/mkdocs-material/issues/4012\n                if (!ev.target.closest(\".md-version\")) {\n                  const version = urls.get(url)!\n                  if (version === current)\n                    return EMPTY\n                }\n                ev.preventDefault()\n                return of(new URL(url))\n              }\n            }\n            return EMPTY\n          }),\n          switchMap(selectedVersionBaseURL => {\n            return fetchSitemap(selectedVersionBaseURL).pipe(\n              map(\n                sitemap =>\n                  selectedVersionCorrespondingURL({\n                    selectedVersionSitemap: sitemap,\n                    selectedVersionBaseURL,\n                    currentLocation: getLocation(),\n                    currentBaseURL: config.base\n                  }) ?? selectedVersionBaseURL,\n              ),\n            )\n          })\n        )\n      )\n    )\n      .subscribe(url => setLocation(url, true))\n\n  /* Render version selector and warning */\n  combineLatest([versions$, current$])\n    .subscribe(([versions, current]) => {\n      const topic = getElement(\".md-header__topic\")\n      topic.appendChild(renderVersionSelector(versions, current))\n    })\n\n  /* Integrate outdated version banner with instant navigation */\n  document$.pipe(switchMap(() => current$))\n    .subscribe(current => {\n\n      // Always scope outdate version banner to the base URL of the site\n      const base = new URL(config.base)\n\n      /* Check if version state was already determined */\n      let outdated = __md_get(\"__outdated\", sessionStorage, base)\n      if (outdated === null) {\n        outdated = true\n\n        /* Obtain and normalize default versions */\n        let ignored = config.version?.default || \"latest\"\n        if (!Array.isArray(ignored))\n          ignored = [ignored]\n\n        /* Check if version is considered a default */\n        main: for (const ignore of ignored)\n          for (const version of current.aliases.concat(current.version))\n            if (new RegExp(ignore, \"i\").test(version)) {\n              outdated = false\n              break main\n            }\n\n        /* Persist version state in session storage */\n        __md_set(\"__outdated\", outdated, sessionStorage, base)\n      }\n\n      /* Unhide outdated version banner */\n      if (outdated)\n        for (const warning of getComponentElements(\"outdated\"))\n          warning.hidden = false\n    })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  combineLatest,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  endWith,\n  finalize,\n  first,\n  fromEvent,\n  ignoreElements,\n  map,\n  merge,\n  shareReplay,\n  takeUntil,\n  tap\n} from \"rxjs\"\n\nimport {\n  getElement,\n  getLocation,\n  setToggle,\n  watchElementFocus,\n  watchToggle\n} from \"~/browser\"\nimport {\n  SearchMessage,\n  SearchMessageType,\n  isSearchReadyMessage\n} from \"~/integrations\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search query\n */\nexport interface SearchQuery {\n  value: string                        /* Query value */\n  focus: boolean                       /* Query focus */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  worker$: Subject<SearchMessage>      /* Search worker */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  worker$: Subject<SearchMessage>      /* Search worker */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch search query\n *\n * Note that the focus event which triggers re-reading the current query value\n * is delayed by `1ms` so the input's empty state is allowed to propagate.\n *\n * @param el - Search query element\n * @param options - Options\n *\n * @returns Search query observable\n */\nexport function watchSearchQuery(\n  el: HTMLInputElement, { worker$ }: WatchOptions\n): Observable<SearchQuery> {\n\n  /* Support search deep linking */\n  const { searchParams } = getLocation()\n  if (searchParams.has(\"q\")) {\n    setToggle(\"search\", true)\n\n    /* Set query from parameter */\n    el.value = searchParams.get(\"q\")!\n    el.focus()\n\n    /* Remove query parameter on close */\n    watchToggle(\"search\")\n      .pipe(\n        first(active => !active)\n      )\n        .subscribe(() => {\n          const url = getLocation()\n          url.searchParams.delete(\"q\")\n          history.replaceState({}, \"\", `${url}`)\n        })\n  }\n\n  /* Intercept focus and input events */\n  const focus$ = watchElementFocus(el)\n  const value$ = merge(\n    worker$.pipe(first(isSearchReadyMessage)),\n    fromEvent(el, \"keyup\"),\n    focus$\n  )\n    .pipe(\n      map(() => el.value),\n      distinctUntilChanged()\n    )\n\n  /* Combine into single observable */\n  return combineLatest([value$, focus$])\n    .pipe(\n      map(([value, focus]) => ({ value, focus })),\n      shareReplay(1)\n    )\n}\n\n/**\n * Mount search query\n *\n * @param el - Search query element\n * @param options - Options\n *\n * @returns Search query component observable\n */\nexport function mountSearchQuery(\n  el: HTMLInputElement, { worker$ }: MountOptions\n): Observable<Component<SearchQuery, HTMLInputElement>> {\n  const push$ = new Subject<SearchQuery>()\n  const done$ = push$.pipe(ignoreElements(), endWith(true))\n\n  /* Handle value change */\n  combineLatest([\n    worker$.pipe(first(isSearchReadyMessage)),\n    push$\n  ], (_, query) => query)\n    .pipe(\n      distinctUntilKeyChanged(\"value\")\n    )\n      .subscribe(({ value }) => worker$.next({\n        type: SearchMessageType.QUERY,\n        data: value\n      }))\n\n  /* Handle focus change */\n  push$\n    .pipe(\n      distinctUntilKeyChanged(\"focus\")\n    )\n      .subscribe(({ focus }) => {\n        if (focus)\n          setToggle(\"search\", focus)\n      })\n\n  /* Handle reset */\n  fromEvent(el.form!, \"reset\")\n    .pipe(\n      takeUntil(done$)\n    )\n      .subscribe(() => el.focus())\n\n  // Focus search query on label click - note that this is necessary to bring\n  // up the keyboard on iOS and other mobile platforms, as the search dialog is\n  // not visible at first, and programatically focusing an input element must\n  // be triggered by a user interaction - see https://t.ly/Cb30n\n  const label = getElement(\"header [for=__search]\")\n  fromEvent(label, \"click\")\n    .subscribe(() => el.focus())\n\n  /* Create and return component */\n  return watchSearchQuery(el, { worker$ })\n    .pipe(\n      tap(state => push$.next(state)),\n      finalize(() => push$.complete()),\n      map(state => ({ ref: el, ...state })),\n      shareReplay(1)\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  bufferCount,\n  filter,\n  finalize,\n  first,\n  fromEvent,\n  map,\n  merge,\n  mergeMap,\n  of,\n  share,\n  skipUntil,\n  switchMap,\n  takeUntil,\n  tap,\n  withLatestFrom,\n  zipWith\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport {\n  getElement,\n  getOptionalElement,\n  watchElementBoundary,\n  watchToggle\n} from \"~/browser\"\nimport {\n  SearchMessage,\n  SearchResult,\n  isSearchReadyMessage,\n  isSearchResultMessage\n} from \"~/integrations\"\nimport { renderSearchResultItem } from \"~/templates\"\nimport { round } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\nimport { SearchQuery } from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  query$: Observable<SearchQuery>      /* Search query observable */\n  worker$: Subject<SearchMessage>      /* Search worker */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search result list\n *\n * This function performs a lazy rendering of the search results, depending on\n * the vertical offset of the search result container.\n *\n * @param el - Search result list element\n * @param options - Options\n *\n * @returns Search result list component observable\n */\nexport function mountSearchResult(\n  el: HTMLElement, { worker$, query$ }: MountOptions\n): Observable<Component<SearchResult>> {\n  const push$ = new Subject<SearchResult>()\n  const boundary$ = watchElementBoundary(el.parentElement!)\n    .pipe(\n      filter(Boolean)\n    )\n\n  /* Retrieve container */\n  const container = el.parentElement!\n\n  /* Retrieve nested components */\n  const meta = getElement(\":scope > :first-child\", el)\n  const list = getElement(\":scope > :last-child\", el)\n\n  /* Reveal to accessibility tree \u2013 see https://bit.ly/3iAA7t8 */\n  watchToggle(\"search\")\n    .subscribe(active => {\n      list.setAttribute(\"role\", active ? \"list\" : \"presentation\")\n      list.hidden = !active\n    })\n\n  /* Update search result metadata */\n  push$\n    .pipe(\n      withLatestFrom(query$),\n      skipUntil(worker$.pipe(first(isSearchReadyMessage)))\n    )\n      .subscribe(([{ items }, { value }]) => {\n        switch (items.length) {\n\n          /* No results */\n          case 0:\n            meta.textContent = value.length\n              ? translation(\"search.result.none\")\n              : translation(\"search.result.placeholder\")\n            break\n\n          /* One result */\n          case 1:\n            meta.textContent = translation(\"search.result.one\")\n            break\n\n          /* Multiple result */\n          default:\n            const count = round(items.length)\n            meta.textContent = translation(\"search.result.other\", count)\n        }\n      })\n\n  /* Render search result item */\n  const render$ = push$\n    .pipe(\n      tap(() => list.innerHTML = \"\"),\n      switchMap(({ items }) => merge(\n        of(...items.slice(0, 10)),\n        of(...items.slice(10))\n          .pipe(\n            bufferCount(4),\n            zipWith(boundary$),\n            switchMap(([chunk]) => chunk)\n          )\n      )),\n      map(renderSearchResultItem),\n      share()\n    )\n\n  /* Update search result list */\n  render$.subscribe(item => list.appendChild(item))\n  render$\n    .pipe(\n      mergeMap(item => {\n        const details = getOptionalElement(\"details\", item)\n        if (typeof details === \"undefined\")\n          return EMPTY\n\n        /* Keep position of details element stable */\n        return fromEvent(details, \"toggle\")\n          .pipe(\n            takeUntil(push$),\n            map(() => details)\n          )\n      })\n    )\n      .subscribe(details => {\n        if (\n          details.open === false &&\n          details.offsetTop <= container.scrollTop\n        )\n          container.scrollTo({ top: details.offsetTop })\n      })\n\n  /* Filter search result message */\n  const result$ = worker$\n    .pipe(\n      filter(isSearchResultMessage),\n      map(({ data }) => data)\n    )\n\n  /* Create and return component */\n  return result$\n    .pipe(\n      tap(state => push$.next(state)),\n      finalize(() => push$.complete()),\n      map(state => ({ ref: el, ...state }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  endWith,\n  finalize,\n  fromEvent,\n  ignoreElements,\n  map,\n  takeUntil,\n  tap\n} from \"rxjs\"\n\nimport { getLocation } from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { SearchQuery } from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search sharing\n */\nexport interface SearchShare {\n  url: URL                             /* Deep link for sharing */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  query$: Observable<SearchQuery>      /* Search query observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  query$: Observable<SearchQuery>      /* Search query observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search sharing\n *\n * @param _el - Search sharing element\n * @param options - Options\n *\n * @returns Search sharing observable\n */\nexport function watchSearchShare(\n  _el: HTMLElement, { query$ }: WatchOptions\n): Observable<SearchShare> {\n  return query$\n    .pipe(\n      map(({ value }) => {\n        const url = getLocation()\n        url.hash = \"\"\n\n        /* Compute readable query strings */\n        value = value\n          .replace(/\\s+/g, \"+\")        /* Collapse whitespace */\n          .replace(/&/g, \"%26\")        /* Escape '&' character */\n          .replace(/=/g, \"%3D\")        /* Escape '=' character */\n\n        /* Replace query string */\n        url.search = `q=${value}`\n        return { url }\n      })\n    )\n}\n\n/**\n * Mount search sharing\n *\n * @param el - Search sharing element\n * @param options - Options\n *\n * @returns Search sharing component observable\n */\nexport function mountSearchShare(\n  el: HTMLAnchorElement, options: MountOptions\n): Observable<Component<SearchShare>> {\n  const push$ = new Subject<SearchShare>()\n  const done$ = push$.pipe(ignoreElements(), endWith(true))\n  push$.subscribe(({ url }) => {\n    el.setAttribute(\"data-clipboard-text\", el.href)\n    el.href = `${url}`\n  })\n\n  /* Prevent following of link */\n  fromEvent(el, \"click\")\n    .pipe(\n      takeUntil(done$)\n    )\n      .subscribe(ev => ev.preventDefault())\n\n  /* Create and return component */\n  return watchSearchShare(el, options)\n    .pipe(\n      tap(state => push$.next(state)),\n      finalize(() => push$.complete()),\n      map(state => ({ ref: el, ...state }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  asyncScheduler,\n  combineLatestWith,\n  distinctUntilChanged,\n  filter,\n  finalize,\n  fromEvent,\n  map,\n  merge,\n  observeOn,\n  tap\n} from \"rxjs\"\n\nimport { Keyboard } from \"~/browser\"\nimport {\n  SearchMessage,\n  SearchResult,\n  isSearchResultMessage\n} from \"~/integrations\"\n\nimport { Component, getComponentElement } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search suggestions\n */\nexport interface SearchSuggest {}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  keyboard$: Observable<Keyboard>      /* Keyboard observable */\n  worker$: Subject<SearchMessage>      /* Search worker */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search suggestions\n *\n * This function will perform a lazy rendering of the search results, depending\n * on the vertical offset of the search result container.\n *\n * @param el - Search result list element\n * @param options - Options\n *\n * @returns Search result list component observable\n */\nexport function mountSearchSuggest(\n  el: HTMLElement, { worker$, keyboard$ }: MountOptions\n): Observable<Component<SearchSuggest>> {\n  const push$ = new Subject<SearchResult>()\n\n  /* Retrieve query component and track all changes */\n  const query  = getComponentElement(\"search-query\")\n  const query$ = merge(\n    fromEvent(query, \"keydown\"),\n    fromEvent(query, \"focus\")\n  )\n    .pipe(\n      observeOn(asyncScheduler),\n      map(() => query.value),\n      distinctUntilChanged(),\n    )\n\n  /* Update search suggestions */\n  push$\n    .pipe(\n      combineLatestWith(query$),\n      map(([{ suggest }, value]) => {\n        const words = value.split(/([\\s-]+)/)\n        if (suggest?.length && words[words.length - 1]) {\n          const last = suggest[suggest.length - 1]\n          if (last.startsWith(words[words.length - 1]))\n            words[words.length - 1] = last\n        } else {\n          words.length = 0\n        }\n        return words\n      })\n    )\n      .subscribe(words => el.innerHTML = words\n        .join(\"\")\n        .replace(/\\s/g, \"&nbsp;\")\n      )\n\n  /* Set up search keyboard handlers */\n  keyboard$\n    .pipe(\n      filter(({ mode }) => mode === \"search\")\n    )\n      .subscribe(key => {\n        switch (key.type) {\n\n          /* Right arrow: accept current suggestion */\n          case \"ArrowRight\":\n            if (\n              el.innerText.length &&\n              query.selectionStart === query.value.length\n            )\n              query.value = el.innerText\n            break\n        }\n      })\n\n  /* Filter search result message */\n  const result$ = worker$\n    .pipe(\n      filter(isSearchResultMessage),\n      map(({ data }) => data)\n    )\n\n  /* Create and return component */\n  return result$\n    .pipe(\n      tap(state => push$.next(state)),\n      finalize(() => push$.complete()),\n      map(() => ({ ref: el }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  NEVER,\n  Observable,\n  ObservableInput,\n  filter,\n  fromEvent,\n  merge,\n  mergeWith\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n  Keyboard,\n  getActiveElement,\n  getElements,\n  setToggle\n} from \"~/browser\"\nimport {\n  SearchIndex,\n  SearchResult,\n  setupSearchWorker\n} from \"~/integrations\"\n\nimport {\n  Component,\n  getComponentElement,\n  getComponentElements\n} from \"../../_\"\nimport {\n  SearchQuery,\n  mountSearchQuery\n} from \"../query\"\nimport { mountSearchResult } from \"../result\"\nimport {\n  SearchShare,\n  mountSearchShare\n} from \"../share\"\nimport {\n  SearchSuggest,\n  mountSearchSuggest\n} from \"../suggest\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search\n */\nexport type Search =\n  | SearchQuery\n  | SearchResult\n  | SearchShare\n  | SearchSuggest\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  index$: ObservableInput<SearchIndex> /* Search index observable */\n  keyboard$: Observable<Keyboard>      /* Keyboard observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search\n *\n * This function sets up the search functionality, including the underlying\n * web worker and all keyboard bindings.\n *\n * @param el - Search element\n * @param options - Options\n *\n * @returns Search component observable\n */\nexport function mountSearch(\n  el: HTMLElement, { index$, keyboard$ }: MountOptions\n): Observable<Component<Search>> {\n  const config = configuration()\n  try {\n    const worker$ = setupSearchWorker(config.search, index$)\n\n    /* Retrieve query and result components */\n    const query  = getComponentElement(\"search-query\", el)\n    const result = getComponentElement(\"search-result\", el)\n\n    /* Always close search on result selection */\n    fromEvent<PointerEvent>(el, \"click\")\n      .pipe(\n        filter(({ target }) => (\n          target instanceof Element && !!target.closest(\"a\")\n        ))\n      )\n        .subscribe(() => setToggle(\"search\", false))\n\n    /* Set up search keyboard handlers */\n    keyboard$\n      .pipe(\n        filter(({ mode }) => mode === \"search\")\n      )\n        .subscribe(key => {\n          const active = getActiveElement()\n          switch (key.type) {\n\n            /* Enter: go to first (best) result */\n            case \"Enter\":\n              if (active === query) {\n                const anchors = new Map<HTMLAnchorElement, number>()\n                for (const anchor of getElements<HTMLAnchorElement>(\n                  \":first-child [href]\", result\n                )) {\n                  const article = anchor.firstElementChild!\n                  anchors.set(anchor, parseFloat(\n                    article.getAttribute(\"data-md-score\")!\n                  ))\n                }\n\n                /* Go to result with highest score, if any */\n                if (anchors.size) {\n                  const [[best]] = [...anchors].sort(([, a], [, b]) => b - a)\n                  best.click()\n                }\n\n                /* Otherwise omit form submission */\n                key.claim()\n              }\n              break\n\n            /* Escape or Tab: close search */\n            case \"Escape\":\n            case \"Tab\":\n              setToggle(\"search\", false)\n              query.blur()\n              break\n\n            /* Vertical arrows: select previous or next search result */\n            case \"ArrowUp\":\n            case \"ArrowDown\":\n              if (typeof active === \"undefined\") {\n                query.focus()\n              } else {\n                const els = [query, ...getElements(\n                  \":not(details) > [href], summary, details[open] [href]\",\n                  result\n                )]\n                const i = Math.max(0, (\n                  Math.max(0, els.indexOf(active)) + els.length + (\n                    key.type === \"ArrowUp\" ? -1 : +1\n                  )\n                ) % els.length)\n                els[i].focus()\n              }\n\n              /* Prevent scrolling of page */\n              key.claim()\n              break\n\n            /* All other keys: hand to search query */\n            default:\n              if (query !== getActiveElement())\n                query.focus()\n          }\n        })\n\n    /* Set up global keyboard handlers */\n    keyboard$\n      .pipe(\n        filter(({ mode }) => mode === \"global\")\n      )\n        .subscribe(key => {\n          switch (key.type) {\n\n            /* Open search and select query */\n            case \"f\":\n            case \"s\":\n            case \"/\":\n              query.focus()\n              query.select()\n\n              /* Prevent scrolling of page */\n              key.claim()\n              break\n          }\n        })\n\n    /* Create and return component */\n    const query$ = mountSearchQuery(query, { worker$ })\n    return merge(\n      query$,\n      mountSearchResult(result, { worker$, query$ })\n    )\n      .pipe(\n        mergeWith(\n\n          /* Search sharing */\n          ...getComponentElements(\"search-share\", el)\n            .map(child => mountSearchShare(child, { query$ })),\n\n          /* Search suggestions */\n          ...getComponentElements(\"search-suggest\", el)\n            .map(child => mountSearchSuggest(child, { worker$, keyboard$ }))\n        )\n      )\n\n  /* Gracefully handle broken search */\n  } catch (err) {\n    el.hidden = true\n    return NEVER\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  ObservableInput,\n  combineLatest,\n  filter,\n  map,\n  startWith\n} from \"rxjs\"\n\nimport { getLocation } from \"~/browser\"\nimport {\n  SearchIndex,\n  setupSearchHighlighter\n} from \"~/integrations\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlighting\n */\nexport interface SearchHighlight {\n  nodes: Map<ChildNode, string>        /* Map of replacements */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  index$: ObservableInput<SearchIndex> /* Search index observable */\n  location$: Observable<URL>           /* Location observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search highlighting\n *\n * @param el - Content element\n * @param options - Options\n *\n * @returns Search highlighting component observable\n */\nexport function mountSearchHiglight(\n  el: HTMLElement, { index$, location$ }: MountOptions\n): Observable<Component<SearchHighlight>> {\n  return combineLatest([\n    index$,\n    location$\n      .pipe(\n        startWith(getLocation()),\n        filter(url => !!url.searchParams.get(\"h\"))\n      )\n  ])\n    .pipe(\n      map(([index, url]) => setupSearchHighlighter(index.config)(\n        url.searchParams.get(\"h\")!\n      )),\n      map(fn => {\n        const nodes = new Map<ChildNode, string>()\n\n        /* Traverse text nodes and collect matches */\n        const it = document.createNodeIterator(el, NodeFilter.SHOW_TEXT)\n        for (let node = it.nextNode(); node; node = it.nextNode()) {\n          if (node.parentElement?.offsetHeight) {\n            const original = node.textContent!\n            const replaced = fn(original)\n            if (replaced.length > original.length)\n              nodes.set(node as ChildNode, replaced)\n          }\n        }\n\n        /* Replace original nodes with matches */\n        for (const [node, text] of nodes) {\n          const { childNodes } = h(\"span\", null, text)\n          node.replaceWith(...Array.from(childNodes))\n        }\n\n        /* Return component */\n        return { ref: el, nodes }\n      })\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  animationFrameScheduler,\n  asyncScheduler,\n  auditTime,\n  combineLatest,\n  defer,\n  distinctUntilChanged,\n  endWith,\n  finalize,\n  first,\n  from,\n  fromEvent,\n  ignoreElements,\n  map,\n  mergeMap,\n  observeOn,\n  takeUntil,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElement,\n  getElementOffset,\n  getElementSize,\n  getElements\n} from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\nimport { mountInlineTooltip2 } from \"../tooltip2\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Sidebar\n */\nexport interface Sidebar {\n  height: number                       /* Sidebar height */\n  locked: boolean                      /* Sidebar is locked */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  main$: Observable<Main>              /* Main area observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n  main$: Observable<Main>              /* Main area observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch sidebar\n *\n * This function returns an observable that computes the visual parameters of\n * the sidebar which depends on the vertical viewport offset, as well as the\n * height of the main area. When the page is scrolled beyond the header, the\n * sidebar is locked and fills the remaining space.\n *\n * @param el - Sidebar element\n * @param options - Options\n *\n * @returns Sidebar observable\n */\nexport function watchSidebar(\n  el: HTMLElement, { viewport$, main$ }: WatchOptions\n): Observable<Sidebar> {\n  const parent = el.closest<HTMLElement>(\".md-grid\")!\n  const adjust =\n    parent.offsetTop -\n    parent.parentElement!.offsetTop\n\n  /* Compute the sidebar's available height and if it should be locked */\n  return combineLatest([main$, viewport$])\n    .pipe(\n      map(([{ offset, height }, { offset: { y } }]) => {\n        height = height\n          + Math.min(adjust, Math.max(0, y - offset))\n          - adjust\n        return {\n          height,\n          locked: y >= offset + adjust\n        }\n      }),\n      distinctUntilChanged((a, b) => (\n        a.height === b.height &&\n        a.locked === b.locked\n      ))\n    )\n}\n\n/**\n * Mount sidebar\n *\n * This function doesn't set the height of the actual sidebar, but of its first\n * child \u2013 the `.md-sidebar__scrollwrap` element in order to mitigiate jittery\n * sidebars when the footer is scrolled into view. At some point we switched\n * from `absolute` / `fixed` positioning to `sticky` positioning, significantly\n * reducing jitter in some browsers (respectively Firefox and Safari) when\n * scrolling from the top. However, top-aligned sticky positioning means that\n * the sidebar snaps to the bottom when the end of the container is reached.\n * This is what leads to the mentioned jitter, as the sidebar's height may be\n * updated too slowly.\n *\n * This behaviour can be mitigiated by setting the height of the sidebar to `0`\n * while preserving the padding, and the height on its first element.\n *\n * @param el - Sidebar element\n * @param options - Options\n *\n * @returns Sidebar component observable\n */\nexport function mountSidebar(\n  el: HTMLElement, { header$, ...options }: MountOptions\n): Observable<Component<Sidebar>> {\n  const inner = getElement(\".md-sidebar__scrollwrap\", el)\n  const { y } = getElementOffset(inner)\n  return defer(() => {\n    const push$ = new Subject<Sidebar>()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n    const next$ = push$\n      .pipe(\n        auditTime(0, animationFrameScheduler)\n      )\n\n    /* Update sidebar height and offset */\n    next$.pipe(withLatestFrom(header$))\n      .subscribe({\n\n        /* Handle emission */\n        next([{ height }, { height: offset }]) {\n          inner.style.height = `${height - 2 * y}px`\n          el.style.top       = `${offset}px`\n        },\n\n        /* Handle complete */\n        complete() {\n          inner.style.height = \"\"\n          el.style.top       = \"\"\n        }\n      })\n\n    /* Bring active item into view on initial load */\n    next$.pipe(first())\n      .subscribe(() => {\n        for (const item of getElements(\".md-nav__link--active[href]\", el)) {\n          if (!item.clientHeight) // skip invisible toc in left sidebar\n            continue\n          const container = item.closest<HTMLElement>(\".md-sidebar__scrollwrap\")!\n          if (typeof container !== \"undefined\") {\n            const offset = item.offsetTop - container.offsetTop\n            const { height } = getElementSize(container)\n            container.scrollTo({\n              top: offset - height / 2\n            })\n          }\n        }\n      })\n\n    /* Handle accessibility for expandable items, see https://bit.ly/3jaod9p */\n    from(getElements<HTMLLabelElement>(\"label[tabindex]\", el))\n      .pipe(\n        mergeMap(label => fromEvent(label, \"click\")\n          .pipe(\n            observeOn(asyncScheduler),\n            map(() => label),\n            takeUntil(done$)\n          )\n        )\n      )\n        .subscribe(label => {\n          const input = getElement<HTMLInputElement>(`[id=\"${label.htmlFor}\"]`)\n          const nav = getElement(`[aria-labelledby=\"${label.id}\"]`)\n          nav.setAttribute(\"aria-expanded\", `${input.checked}`)\n        })\n\n    // Mount abbreviation tooltips\n    if (feature(\"content.tooltips\"))\n      from(getElements(\"abbr[title]\", el))\n        .pipe(\n          mergeMap(child => mountInlineTooltip2(child, { viewport$ })),\n          takeUntil(done$)\n        )\n          .subscribe()\n\n    /* Create and return component */\n    return watchSidebar(el, options)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Repo, User } from \"github-types\"\nimport {\n  EMPTY,\n  Observable,\n  catchError,\n  defaultIfEmpty,\n  map,\n  zip\n} from \"rxjs\"\n\nimport { requestJSON } from \"~/browser\"\n\nimport { SourceFacts } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * GitHub release (partial)\n */\ninterface Release {\n  tag_name: string                     /* Tag name */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch GitHub repository facts\n *\n * @param user - GitHub user or organization\n * @param repo - GitHub repository\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFactsFromGitHub(\n  user: string, repo?: string\n): Observable<SourceFacts> {\n  if (typeof repo !== \"undefined\") {\n    const url = `https://api.github.com/repos/${user}/${repo}`\n    return zip(\n\n      /* Fetch version */\n      requestJSON<Release>(`${url}/releases/latest`)\n        .pipe(\n          catchError(() => EMPTY), // @todo refactor instant loading\n          map(release => ({\n            version: release.tag_name\n          })),\n          defaultIfEmpty({})\n        ),\n\n      /* Fetch stars and forks */\n      requestJSON<Repo>(url)\n        .pipe(\n          catchError(() => EMPTY), // @todo refactor instant loading\n          map(info => ({\n            stars: info.stargazers_count,\n            forks: info.forks_count\n          })),\n          defaultIfEmpty({})\n        )\n    )\n      .pipe(\n        map(([release, info]) => ({ ...release, ...info }))\n      )\n\n  /* User or organization */\n  } else {\n    const url = `https://api.github.com/users/${user}`\n    return requestJSON<User>(url)\n      .pipe(\n        map(info => ({\n          repositories: info.public_repos\n        })),\n        defaultIfEmpty({})\n      )\n  }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ProjectSchema } from \"gitlab\"\nimport {\n  EMPTY,\n  Observable,\n  catchError,\n  defaultIfEmpty,\n  map,\n  zip\n} from \"rxjs\"\n\nimport { requestJSON } from \"~/browser\"\n\nimport { SourceFacts } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * GitLab release (partial)\n */\ninterface Release { // @todo remove and use the ReleaseSchema type instead after switching from gitlab to @gitbeaker/rest\n  tag_name: string                     /* Tag name */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch GitLab repository facts\n *\n * @param base - GitLab base\n * @param project - GitLab project\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFactsFromGitLab(\n  base: string, project: string\n): Observable<SourceFacts> {\n  const url = `https://${base}/api/v4/projects/${encodeURIComponent(project)}`\n  return zip(\n\n    /* Fetch version */\n    requestJSON<Release>(`${url}/releases/permalink/latest`)\n      .pipe(\n        catchError(() => EMPTY), // @todo refactor instant loading\n        map(({ tag_name }) => ({\n          version: tag_name\n        })),\n        defaultIfEmpty({})\n      ),\n\n    /* Fetch stars and forks */\n    requestJSON<ProjectSchema>(url)\n      .pipe(\n        catchError(() => EMPTY), // @todo refactor instant loading\n        map(({ star_count, forks_count }) => ({\n          stars: star_count,\n          forks: forks_count\n        })),\n        defaultIfEmpty({})\n      )\n  )\n    .pipe(\n      map(([release, info]) => ({ ...release, ...info }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { EMPTY, Observable } from \"rxjs\"\n\nimport { fetchSourceFactsFromGitHub } from \"../github\"\nimport { fetchSourceFactsFromGitLab } from \"../gitlab\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository facts for repositories\n */\nexport interface RepositoryFacts {\n  stars?: number                       /* Number of stars */\n  forks?: number                       /* Number of forks */\n  version?: string                     /* Latest version */\n}\n\n/**\n * Repository facts for organizations\n */\nexport interface OrganizationFacts {\n  repositories?: number                /* Number of repositories */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Repository facts\n */\nexport type SourceFacts =\n  | RepositoryFacts\n  | OrganizationFacts\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch repository facts\n *\n * @param url - Repository URL\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFacts(\n  url: string\n): Observable<SourceFacts> {\n\n  /* Try to match GitHub repository */\n  let match = url.match(/^.+github\\.com\\/([^/]+)\\/?([^/]+)?/i)\n  if (match) {\n    const [, user, repo] = match\n    return fetchSourceFactsFromGitHub(user, repo)\n  }\n\n  /* Try to match GitLab repository */\n  match = url.match(/^.+?([^/]*gitlab[^/]+)\\/(.+?)\\/?$/i)\n  if (match) {\n    const [, base, slug] = match\n    return fetchSourceFactsFromGitLab(base, slug)\n  }\n\n  /* Fallback */\n  return EMPTY\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  Subject,\n  catchError,\n  defer,\n  filter,\n  finalize,\n  map,\n  of,\n  shareReplay,\n  tap\n} from \"rxjs\"\n\nimport { getElement } from \"~/browser\"\nimport { ConsentDefaults } from \"~/components/consent\"\nimport { renderSourceFacts } from \"~/templates\"\n\nimport {\n  Component,\n  getComponentElements\n} from \"../../_\"\nimport {\n  SourceFacts,\n  fetchSourceFacts\n} from \"../facts\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository information\n */\nexport interface Source {\n  facts: SourceFacts                   /* Repository facts */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository information observable\n */\nlet fetch$: Observable<Source>\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch repository information\n *\n * This function tries to read the repository facts from session storage, and\n * if unsuccessful, fetches them from the underlying provider.\n *\n * @param el - Repository information element\n *\n * @returns Repository information observable\n */\nexport function watchSource(\n  el: HTMLAnchorElement\n): Observable<Source> {\n  return fetch$ ||= defer(() => {\n    const cached = __md_get<SourceFacts>(\"__source\", sessionStorage)\n    if (cached) {\n      return of(cached)\n    } else {\n\n      /* Check if consent is configured and was given */\n      const els = getComponentElements(\"consent\")\n      if (els.length) {\n        const consent = __md_get<ConsentDefaults>(\"__consent\")\n        if (!(consent && consent.github))\n          return EMPTY\n      }\n\n      /* Fetch repository facts */\n      return fetchSourceFacts(el.href)\n        .pipe(\n          tap(facts => __md_set(\"__source\", facts, sessionStorage))\n        )\n    }\n  })\n    .pipe(\n      catchError(() => EMPTY),\n      filter(facts => Object.keys(facts).length > 0),\n      map(facts => ({ facts })),\n      shareReplay(1)\n    )\n}\n\n/**\n * Mount repository information\n *\n * @param el - Repository information element\n *\n * @returns Repository information component observable\n */\nexport function mountSource(\n  el: HTMLAnchorElement\n): Observable<Component<Source>> {\n  const inner = getElement(\":scope > :last-child\", el)\n  return defer(() => {\n    const push$ = new Subject<Source>()\n    push$.subscribe(({ facts }) => {\n      inner.appendChild(renderSourceFacts(facts))\n      inner.classList.add(\"md-source__repository--active\")\n    })\n\n    /* Create and return component */\n    return watchSource(el)\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  defer,\n  distinctUntilKeyChanged,\n  finalize,\n  map,\n  of,\n  switchMap,\n  tap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  watchElementSize,\n  watchViewportAt\n} from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Navigation tabs\n */\nexport interface Tabs {\n  hidden: boolean                      /* Navigation tabs are hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch navigation tabs\n *\n * @param el - Navigation tabs element\n * @param options - Options\n *\n * @returns Navigation tabs observable\n */\nexport function watchTabs(\n  el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable<Tabs> {\n  return watchElementSize(document.body)\n    .pipe(\n      switchMap(() => watchViewportAt(el, { header$, viewport$ })),\n      map(({ offset: { y } }) => {\n        return {\n          hidden: y >= 10\n        }\n      }),\n      distinctUntilKeyChanged(\"hidden\")\n    )\n}\n\n/**\n * Mount navigation tabs\n *\n * This function hides the navigation tabs when scrolling past the threshold\n * and makes them reappear in a nice CSS animation when scrolling back up.\n *\n * @param el - Navigation tabs element\n * @param options - Options\n *\n * @returns Navigation tabs component observable\n */\nexport function mountTabs(\n  el: HTMLElement, options: MountOptions\n): Observable<Component<Tabs>> {\n  return defer(() => {\n    const push$ = new Subject<Tabs>()\n    push$.subscribe({\n\n      /* Handle emission */\n      next({ hidden }) {\n        el.hidden = hidden\n      },\n\n      /* Handle complete */\n      complete() {\n        el.hidden = false\n      }\n    })\n\n    /* Create and return component */\n    return (\n      feature(\"navigation.tabs.sticky\")\n        ? of({ hidden: false })\n        : watchTabs(el, options)\n    )\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  asyncScheduler,\n  bufferCount,\n  combineLatestWith,\n  debounceTime,\n  defer,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  endWith,\n  filter,\n  finalize,\n  ignoreElements,\n  map,\n  merge,\n  observeOn,\n  of,\n  repeat,\n  scan,\n  share,\n  skip,\n  startWith,\n  switchMap,\n  takeUntil,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElement,\n  getElementContainer,\n  getElementSize,\n  getElements,\n  getLocation,\n  getOptionalElement,\n  watchElementSize\n} from \"~/browser\"\n\nimport {\n  Component,\n  getComponentElement\n} from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Table of contents\n */\nexport interface TableOfContents {\n  prev: HTMLAnchorElement[][]          /* Anchors (previous) */\n  next: HTMLAnchorElement[][]          /* Anchors (next) */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n  main$: Observable<Main>              /* Main area observable */\n  target$: Observable<HTMLElement>     /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch table of contents\n *\n * This is effectively a scroll spy implementation which will account for the\n * fixed header and automatically re-calculate anchor offsets when the viewport\n * is resized. The returned observable will only emit if the table of contents\n * needs to be repainted.\n *\n * This implementation tracks an anchor element's entire path starting from its\n * level up to the top-most anchor element, e.g. `[h3, h2, h1]`. Although the\n * Material theme currently doesn't make use of this information, it enables\n * the styling of the entire hierarchy through customization.\n *\n * Note that the current anchor is the last item of the `prev` anchor list.\n *\n * @param el - Table of contents element\n * @param options - Options\n *\n * @returns Table of contents observable\n */\nexport function watchTableOfContents(\n  el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable<TableOfContents> {\n  const table = new Map<HTMLAnchorElement, HTMLElement>()\n\n  /* Compute anchor-to-target mapping */\n  const anchors = getElements<HTMLAnchorElement>(\".md-nav__link\", el)\n  for (const anchor of anchors) {\n    const id = decodeURIComponent(anchor.hash.substring(1))\n    const target = getOptionalElement(`[id=\"${id}\"]`)\n    if (typeof target !== \"undefined\")\n      table.set(anchor, target)\n  }\n\n  /* Compute necessary adjustment for header */\n  const adjust$ = header$\n    .pipe(\n      distinctUntilKeyChanged(\"height\"),\n      map(({ height }) => {\n        const main = getComponentElement(\"main\")\n        const grid = getElement(\":scope > :first-child\", main)\n        return height + 0.8 * (\n          grid.offsetTop -\n          main.offsetTop\n        )\n      }),\n      share()\n    )\n\n  /* Compute partition of previous and next anchors */\n  const partition$ = watchElementSize(document.body)\n    .pipe(\n      distinctUntilKeyChanged(\"height\"),\n\n      /* Build index to map anchor paths to vertical offsets */\n      switchMap(body => defer(() => {\n        let path: HTMLAnchorElement[] = []\n        return of([...table].reduce((index, [anchor, target]) => {\n          while (path.length) {\n            const last = table.get(path[path.length - 1])!\n            if (last.tagName >= target.tagName) {\n              path.pop()\n            } else {\n              break\n            }\n          }\n\n          /* If the current anchor is hidden, continue with its parent */\n          let offset = target.offsetTop\n          while (!offset && target.parentElement) {\n            target = target.parentElement\n            offset = target.offsetTop\n          }\n\n          /* Fix anchor offsets in tables - see https://bit.ly/3CUFOcn */\n          let parent = target.offsetParent as HTMLElement\n          for (; parent; parent = parent.offsetParent as HTMLElement)\n            offset += parent.offsetTop\n\n          /* Map reversed anchor path to vertical offset */\n          return index.set(\n            [...path = [...path, anchor]].reverse(),\n            offset\n          )\n        }, new Map<HTMLAnchorElement[], number>()))\n      })\n        .pipe(\n\n          /* Sort index by vertical offset (see https://bit.ly/30z6QSO) */\n          map(index => new Map([...index].sort(([, a], [, b]) => a - b))),\n          combineLatestWith(adjust$),\n\n          /* Re-compute partition when viewport offset changes */\n          switchMap(([index, adjust]) => viewport$\n            .pipe(\n              scan(([prev, next], { offset: { y }, size }) => {\n                const last = y + size.height >= Math.floor(body.height)\n\n                /* Look forward */\n                while (next.length) {\n                  const [, offset] = next[0]\n                  if (offset - adjust < y || last) {\n                    prev = [...prev, next.shift()!]\n                  } else {\n                    break\n                  }\n                }\n\n                /* Look backward */\n                while (prev.length) {\n                  const [, offset] = prev[prev.length - 1]\n                  if (offset - adjust >= y && !last) {\n                    next = [prev.pop()!, ...next]\n                  } else {\n                    break\n                  }\n                }\n\n                /* Return partition */\n                return [prev, next]\n              }, [[], [...index]]),\n              distinctUntilChanged((a, b) => (\n                a[0] === b[0] &&\n                a[1] === b[1]\n              ))\n            )\n          )\n        )\n      )\n    )\n\n  /* Compute and return anchor list migrations */\n  return partition$\n    .pipe(\n      map(([prev, next]) => ({\n        prev: prev.map(([path]) => path),\n        next: next.map(([path]) => path)\n      })),\n\n      /* Extract anchor list migrations */\n      startWith({ prev: [], next: [] }),\n      bufferCount(2, 1),\n      map(([a, b]) => {\n\n        /* Moving down */\n        if (a.prev.length < b.prev.length) {\n          return {\n            prev: b.prev.slice(Math.max(0, a.prev.length - 1), b.prev.length),\n            next: []\n          }\n\n        /* Moving up */\n        } else {\n          return {\n            prev: b.prev.slice(-1),\n            next: b.next.slice(0, b.next.length - a.next.length)\n          }\n        }\n      })\n    )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount table of contents\n *\n * @param el - Table of contents element\n * @param options - Options\n *\n * @returns Table of contents component observable\n */\nexport function mountTableOfContents(\n  el: HTMLElement, { viewport$, header$, main$, target$ }: MountOptions\n): Observable<Component<TableOfContents>> {\n  return defer(() => {\n    const push$ = new Subject<TableOfContents>()\n    const done$ = push$.pipe(ignoreElements(), endWith(true))\n    push$.subscribe(({ prev, next }) => {\n\n      /* Look forward */\n      for (const [anchor] of next) {\n        anchor.classList.remove(\"md-nav__link--passed\")\n        anchor.classList.remove(\"md-nav__link--active\")\n      }\n\n      /* Look backward */\n      for (const [index, [anchor]] of prev.entries()) {\n        anchor.classList.add(\"md-nav__link--passed\")\n        anchor.classList.toggle(\n          \"md-nav__link--active\",\n          index === prev.length - 1\n        )\n      }\n    })\n\n    /* Set up following, if enabled */\n    if (feature(\"toc.follow\")) {\n\n      /* Toggle smooth scrolling only for anchor clicks */\n      const smooth$ = merge(\n        viewport$.pipe(debounceTime(1), map(() => undefined)),\n        viewport$.pipe(debounceTime(250), map(() => \"smooth\" as const))\n      )\n\n      /* Bring active anchor into view */ // @todo: refactor\n      push$\n        .pipe(\n          filter(({ prev }) => prev.length > 0),\n          combineLatestWith(main$.pipe(observeOn(asyncScheduler))),\n          withLatestFrom(smooth$)\n        )\n          .subscribe(([[{ prev }], behavior]) => {\n            const [anchor] = prev[prev.length - 1]\n            if (anchor.offsetHeight) {\n\n              /* Retrieve overflowing container and scroll */\n              const container = getElementContainer(anchor)\n              if (typeof container !== \"undefined\") {\n                const offset = anchor.offsetTop - container.offsetTop\n                const { height } = getElementSize(container)\n                container.scrollTo({\n                  top: offset - height / 2,\n                  behavior\n                })\n              }\n            }\n          })\n    }\n\n    /* Set up anchor tracking, if enabled */\n    if (feature(\"navigation.tracking\"))\n      viewport$\n        .pipe(\n          takeUntil(done$),\n          distinctUntilKeyChanged(\"offset\"),\n          debounceTime(250),\n          skip(1),\n          takeUntil(target$.pipe(skip(1))),\n          repeat({ delay: 250 }),\n          withLatestFrom(push$)\n        )\n          .subscribe(([, { prev }]) => {\n            const url = getLocation()\n\n            /* Set hash fragment to active anchor */\n            const anchor = prev[prev.length - 1]\n            if (anchor && anchor.length) {\n              const [active] = anchor\n              const { hash } = new URL(active.href)\n              if (url.hash !== hash) {\n                url.hash = hash\n                history.replaceState({}, \"\", `${url}`)\n              }\n\n            /* Reset anchor when at the top */\n            } else {\n              url.hash = \"\"\n              history.replaceState({}, \"\", `${url}`)\n            }\n          })\n\n    /* Create and return component */\n    return watchTableOfContents(el, { viewport$, header$ })\n      .pipe(\n        tap(state => push$.next(state)),\n        finalize(() => push$.complete()),\n        map(state => ({ ref: el, ...state }))\n      )\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  Subject,\n  bufferCount,\n  combineLatest,\n  distinctUntilChanged,\n  distinctUntilKeyChanged,\n  endWith,\n  finalize,\n  fromEvent,\n  ignoreElements,\n  map,\n  repeat,\n  skip,\n  takeUntil,\n  tap\n} from \"rxjs\"\n\nimport { Viewport } from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Back-to-top button\n */\nexport interface BackToTop {\n  hidden: boolean                      /* Back-to-top button is hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  main$: Observable<Main>              /* Main area observable */\n  target$: Observable<HTMLElement>     /* Location target observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  header$: Observable<Header>          /* Header observable */\n  main$: Observable<Main>              /* Main area observable */\n  target$: Observable<HTMLElement>     /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch back-to-top\n *\n * @param _el - Back-to-top element\n * @param options - Options\n *\n * @returns Back-to-top observable\n */\nexport function watchBackToTop(\n  _el: HTMLElement, { viewport$, main$, target$ }: WatchOptions\n): Observable<BackToTop> {\n\n  /* Compute direction */\n  const direction$ = viewport$\n    .pipe(\n      map(({ offset: { y } }) => y),\n      bufferCount(2, 1),\n      map(([a, b]) => a > b && b > 0),\n      distinctUntilChanged()\n    )\n\n  /* Compute whether main area is active */\n  const active$ = main$\n    .pipe(\n      map(({ active }) => active)\n    )\n\n  /* Compute threshold for hiding */\n  return combineLatest([active$, direction$])\n    .pipe(\n      map(([active, direction]) => !(active && direction)),\n      distinctUntilChanged(),\n      takeUntil(target$.pipe(skip(1))),\n      endWith(true),\n      repeat({ delay: 250 }),\n      map(hidden => ({ hidden }))\n    )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount back-to-top\n *\n * @param el - Back-to-top element\n * @param options - Options\n *\n * @returns Back-to-top component observable\n */\nexport function mountBackToTop(\n  el: HTMLElement, { viewport$, header$, main$, target$ }: MountOptions\n): Observable<Component<BackToTop>> {\n  const push$ = new Subject<BackToTop>()\n  const done$ = push$.pipe(ignoreElements(), endWith(true))\n  push$.subscribe({\n\n    /* Handle emission */\n    next({ hidden }) {\n      el.hidden = hidden\n      if (hidden) {\n        el.setAttribute(\"tabindex\", \"-1\")\n        el.blur()\n      } else {\n        el.removeAttribute(\"tabindex\")\n      }\n    },\n\n    /* Handle complete */\n    complete() {\n      el.style.top = \"\"\n      el.hidden = true\n      el.removeAttribute(\"tabindex\")\n    }\n  })\n\n  /* Watch header height */\n  header$\n    .pipe(\n      takeUntil(done$),\n      distinctUntilKeyChanged(\"height\")\n    )\n      .subscribe(({ height }) => {\n        el.style.top = `${height + 16}px`\n      })\n\n  /* Go back to top */\n  fromEvent(el, \"click\")\n    .subscribe(ev => {\n      ev.preventDefault()\n      window.scrollTo({ top: 0 })\n    })\n\n  /* Create and return component */\n  return watchBackToTop(el, { viewport$, main$, target$ })\n    .pipe(\n      tap(state => push$.next(state)),\n      finalize(() => push$.complete()),\n      map(state => ({ ref: el, ...state }))\n    )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  EMPTY,\n  Observable,\n  filter,\n  finalize,\n  map,\n  mergeMap,\n  skip,\n  switchMap,\n  take,\n  takeUntil\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n  Viewport,\n  getElements,\n  watchElementVisibility\n} from \"~/browser\"\nimport { mountInlineTooltip2 } from \"~/components/tooltip2\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n  document$: Observable<Document>      /* Document observable */\n  viewport$: Observable<Viewport>      /* Viewport observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch ellipsis\n *\n * This function will fetch all elements that are shortened with ellipsis, and\n * filter those which are visible. Once they become visible, they stay in that\n * state, even though they may be hidden again. This optimization is necessary\n * to reduce pressure on the browser, with elements fading in and out of view.\n *\n * @param options - Options\n */\nexport function patchEllipsis(\n  { document$, viewport$ }: PatchOptions\n): void {\n  document$\n    .pipe(\n      switchMap(() => getElements(\".md-ellipsis\")),\n      mergeMap(el => watchElementVisibility(el)\n        .pipe(\n          takeUntil(document$.pipe(skip(1))),\n          filter(visible => visible),\n          map(() => el),\n          take(1)\n        )\n      ),\n      filter(el => el.offsetWidth < el.scrollWidth),\n      mergeMap(el => {\n        const text = el.innerText\n        const host = el.closest(\"a\") || el\n        host.title = text\n\n        // Do not mount improved tooltip if feature is disabled\n        if (!feature(\"content.tooltips\"))\n          return EMPTY\n\n        /* Mount tooltip */\n        return mountInlineTooltip2(host, { viewport$ })\n          .pipe(\n            takeUntil(document$.pipe(skip(1))),\n            finalize(() => host.removeAttribute(\"title\"))\n          )\n      })\n    )\n      .subscribe()\n\n  // @todo move this outside of here and fix memleaks\n  if (feature(\"content.tooltips\"))\n    document$\n      .pipe(\n        switchMap(() => getElements(\".md-status\")),\n        mergeMap(el => mountInlineTooltip2(el, { viewport$ }))\n      )\n        .subscribe()\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  fromEvent,\n  map,\n  mergeMap,\n  switchMap,\n  takeWhile,\n  tap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n  document$: Observable<Document>      /* Document observable */\n  tablet$: Observable<boolean>         /* Media tablet observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch indeterminate checkboxes\n *\n * This function replaces the indeterminate \"pseudo state\" with the actual\n * indeterminate state, which is used to keep navigation always expanded.\n *\n * @param options - Options\n */\nexport function patchIndeterminate(\n  { document$, tablet$ }: PatchOptions\n): void {\n  document$\n    .pipe(\n      switchMap(() => getElements<HTMLInputElement>(\n        \".md-toggle--indeterminate\"\n      )),\n      tap(el => {\n        el.indeterminate = true\n        el.checked = false\n      }),\n      mergeMap(el => fromEvent(el, \"change\")\n        .pipe(\n          takeWhile(() => el.classList.contains(\"md-toggle--indeterminate\")),\n          map(() => el)\n        )\n      ),\n      withLatestFrom(tablet$)\n    )\n      .subscribe(([el, tablet]) => {\n        el.classList.remove(\"md-toggle--indeterminate\")\n        if (tablet)\n          el.checked = false\n      })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  filter,\n  fromEvent,\n  map,\n  mergeMap,\n  switchMap,\n  tap\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n  document$: Observable<Document>      /* Document observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Check whether the given device is an Apple device\n *\n * @returns Test result\n */\nfunction isAppleDevice(): boolean {\n  return /(iPad|iPhone|iPod)/.test(navigator.userAgent)\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch all elements with `data-md-scrollfix` attributes\n *\n * This is a year-old patch which ensures that overflow scrolling works at the\n * top and bottom of containers on iOS by ensuring a `1px` scroll offset upon\n * the start of a touch event.\n *\n * @see https://bit.ly/2SCtAOO - Original source\n *\n * @param options - Options\n */\nexport function patchScrollfix(\n  { document$ }: PatchOptions\n): void {\n  document$\n    .pipe(\n      switchMap(() => getElements(\"[data-md-scrollfix]\")),\n      tap(el => el.removeAttribute(\"data-md-scrollfix\")),\n      filter(isAppleDevice),\n      mergeMap(el => fromEvent(el, \"touchstart\")\n        .pipe(\n          map(() => el)\n        )\n      )\n    )\n      .subscribe(el => {\n        const top = el.scrollTop\n\n        /* We're at the top of the container */\n        if (top === 0) {\n          el.scrollTop = 1\n\n        /* We're at the bottom of the container */\n        } else if (top + el.offsetHeight === el.scrollHeight) {\n          el.scrollTop = top - 1\n        }\n      })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  Observable,\n  combineLatest,\n  delay,\n  map,\n  of,\n  switchMap,\n  withLatestFrom\n} from \"rxjs\"\n\nimport {\n  Viewport,\n  watchToggle\n} from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n  viewport$: Observable<Viewport>      /* Viewport observable */\n  tablet$: Observable<boolean>         /* Media tablet observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch the document body to lock when search is open\n *\n * For mobile and tablet viewports, the search is rendered full screen, which\n * leads to scroll leaking when at the top or bottom of the search result. This\n * function locks the body when the search is in full screen mode, and restores\n * the scroll position when leaving.\n *\n * @param options - Options\n */\nexport function patchScrolllock(\n  { viewport$, tablet$ }: PatchOptions\n): void {\n  combineLatest([watchToggle(\"search\"), tablet$])\n    .pipe(\n      map(([active, tablet]) => active && !tablet),\n      switchMap(active => of(active)\n        .pipe(\n          delay(active ? 400 : 100)\n        )\n      ),\n      withLatestFrom(viewport$)\n    )\n      .subscribe(([active, { offset: { y }}]) => {\n        if (active) {\n          document.body.setAttribute(\"data-md-scrolllock\", \"\")\n          document.body.style.top = `-${y}px`\n        } else {\n          const value = -1 * parseInt(document.body.style.top, 10)\n          document.body.removeAttribute(\"data-md-scrolllock\")\n          document.body.style.top = \"\"\n          if (value)\n            window.scrollTo(0, value)\n        }\n      })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Polyfills\n * ------------------------------------------------------------------------- */\n\n/* Polyfill `Object.entries` */\nif (!Object.entries)\n  Object.entries = function (obj: object) {\n    const data: [string, string][] = []\n    for (const key of Object.keys(obj))\n      // @ts-expect-error - ignore property access warning\n      data.push([key, obj[key]])\n\n    /* Return entries */\n    return data\n  }\n\n/* Polyfill `Object.values` */\nif (!Object.values)\n  Object.values = function (obj: object) {\n    const data: string[] = []\n    for (const key of Object.keys(obj))\n      // @ts-expect-error - ignore property access warning\n      data.push(obj[key])\n\n    /* Return values */\n    return data\n  }\n\n/* ------------------------------------------------------------------------- */\n\n/* Polyfills for `Element` */\nif (typeof Element !== \"undefined\") {\n\n  /* Polyfill `Element.scrollTo` */\n  if (!Element.prototype.scrollTo)\n    Element.prototype.scrollTo = function (\n      x?: ScrollToOptions | number, y?: number\n    ): void {\n      if (typeof x === \"object\") {\n        this.scrollLeft = x.left!\n        this.scrollTop = x.top!\n      } else {\n        this.scrollLeft = x!\n        this.scrollTop = y!\n      }\n    }\n\n  /* Polyfill `Element.replaceWith` */\n  if (!Element.prototype.replaceWith)\n    Element.prototype.replaceWith = function (\n      ...nodes: Array<string | Node>\n    ): void {\n      const parent = this.parentNode\n      if (parent) {\n        if (nodes.length === 0)\n          parent.removeChild(this)\n\n        /* Replace children and create text nodes */\n        for (let i = nodes.length - 1; i >= 0; i--) {\n          let node = nodes[i]\n          if (typeof node === \"string\")\n            node = document.createTextNode(node)\n          else if (node.parentNode)\n            node.parentNode.removeChild(node)\n\n          /* Replace child or insert before previous sibling */\n          if (!i)\n            parent.replaceChild(node, this)\n          else\n            parent.insertBefore(this.previousSibling!, node)\n        }\n      }\n    }\n}\n"],
+  "mappings": 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+}
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.ar.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.ar.min.js
new file mode 100644
index 0000000..9b06c26
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.ar.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.da.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.da.min.js
new file mode 100644
index 0000000..b9d8509
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.da.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Danish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.da=function(){this.pipeline.reset(),this.pipeline.add(e.da.trimmer,e.da.stopWordFilter,e.da.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.da.stemmer))},e.da.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.da.trimmer=e.trimmerSupport.generateTrimmer(e.da.wordCharacters),e.Pipeline.registerFunction(e.da.trimmer,"trimmer-da"),e.da.stemmer=function(){var r=e.stemmerSupport.Among,i=e.stemmerSupport.SnowballProgram,n=new function(){function e(){var e,r=f.cursor+3;if(d=f.limit,0<=r&&r<=f.limit){for(a=r;;){if(e=f.cursor,f.in_grouping(w,97,248)){f.cursor=e;break}if(f.cursor=e,e>=f.limit)return;f.cursor++}for(;!f.out_grouping(w,97,248);){if(f.cursor>=f.limit)return;f.cursor++}d=f.cursor,d<a&&(d=a)}}function n(){var e,r;if(f.cursor>=d&&(r=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,e=f.find_among_b(c,32),f.limit_backward=r,e))switch(f.bra=f.cursor,e){case 1:f.slice_del();break;case 2:f.in_grouping_b(p,97,229)&&f.slice_del()}}function t(){var e,r=f.limit-f.cursor;f.cursor>=d&&(e=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,f.find_among_b(l,4)?(f.bra=f.cursor,f.limit_backward=e,f.cursor=f.limit-r,f.cursor>f.limit_backward&&(f.cursor--,f.bra=f.cursor,f.slice_del())):f.limit_backward=e)}function s(){var e,r,i,n=f.limit-f.cursor;if(f.ket=f.cursor,f.eq_s_b(2,"st")&&(f.bra=f.cursor,f.eq_s_b(2,"ig")&&f.slice_del()),f.cursor=f.limit-n,f.cursor>=d&&(r=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,e=f.find_among_b(m,5),f.limit_backward=r,e))switch(f.bra=f.cursor,e){case 1:f.slice_del(),i=f.limit-f.cursor,t(),f.cursor=f.limit-i;break;case 2:f.slice_from("løs")}}function o(){var e;f.cursor>=d&&(e=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,f.out_grouping_b(w,97,248)?(f.bra=f.cursor,u=f.slice_to(u),f.limit_backward=e,f.eq_v_b(u)&&f.slice_del()):f.limit_backward=e)}var a,d,u,c=[new r("hed",-1,1),new r("ethed",0,1),new r("ered",-1,1),new r("e",-1,1),new r("erede",3,1),new r("ende",3,1),new r("erende",5,1),new r("ene",3,1),new r("erne",3,1),new r("ere",3,1),new r("en",-1,1),new r("heden",10,1),new r("eren",10,1),new r("er",-1,1),new r("heder",13,1),new r("erer",13,1),new r("s",-1,2),new r("heds",16,1),new r("es",16,1),new r("endes",18,1),new r("erendes",19,1),new r("enes",18,1),new r("ernes",18,1),new r("eres",18,1),new r("ens",16,1),new r("hedens",24,1),new r("erens",24,1),new r("ers",16,1),new r("ets",16,1),new r("erets",28,1),new r("et",-1,1),new r("eret",30,1)],l=[new r("gd",-1,-1),new r("dt",-1,-1),new r("gt",-1,-1),new r("kt",-1,-1)],m=[new r("ig",-1,1),new r("lig",0,1),new r("elig",1,1),new r("els",-1,1),new r("løst",-1,2)],w=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,48,0,128],p=[239,254,42,3,0,0,0,0,0,0,0,0,0,0,0,0,16],f=new i;this.setCurrent=function(e){f.setCurrent(e)},this.getCurrent=function(){return f.getCurrent()},this.stem=function(){var r=f.cursor;return e(),f.limit_backward=r,f.cursor=f.limit,n(),f.cursor=f.limit,t(),f.cursor=f.limit,s(),f.cursor=f.limit,o(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return n.setCurrent(e),n.stem(),n.getCurrent()}):(n.setCurrent(e),n.stem(),n.getCurrent())}}(),e.Pipeline.registerFunction(e.da.stemmer,"stemmer-da"),e.da.stopWordFilter=e.generateStopWordFilter("ad af alle alt anden at blev blive bliver da de dem den denne der deres det dette dig din disse dog du efter eller en end er et for fra ham han hans har havde have hende hendes her hos hun hvad hvis hvor i ikke ind jeg jer jo kunne man mange med meget men mig min mine mit mod ned noget nogle nu når og også om op os over på selv sig sin sine sit skal skulle som sådan thi til ud under var vi vil ville vor være været".split(" ")),e.Pipeline.registerFunction(e.da.stopWordFilter,"stopWordFilter-da")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.de.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.de.min.js
new file mode 100644
index 0000000..f3b5c10
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.de.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `German` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.de=function(){this.pipeline.reset(),this.pipeline.add(e.de.trimmer,e.de.stopWordFilter,e.de.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.de.stemmer))},e.de.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.de.trimmer=e.trimmerSupport.generateTrimmer(e.de.wordCharacters),e.Pipeline.registerFunction(e.de.trimmer,"trimmer-de"),e.de.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,i=new function(){function e(e,r,n){return!(!v.eq_s(1,e)||(v.ket=v.cursor,!v.in_grouping(p,97,252)))&&(v.slice_from(r),v.cursor=n,!0)}function i(){for(var r,n,i,s,t=v.cursor;;)if(r=v.cursor,v.bra=r,v.eq_s(1,"ß"))v.ket=v.cursor,v.slice_from("ss");else{if(r>=v.limit)break;v.cursor=r+1}for(v.cursor=t;;)for(n=v.cursor;;){if(i=v.cursor,v.in_grouping(p,97,252)){if(s=v.cursor,v.bra=s,e("u","U",i))break;if(v.cursor=s,e("y","Y",i))break}if(i>=v.limit)return void(v.cursor=n);v.cursor=i+1}}function s(){for(;!v.in_grouping(p,97,252);){if(v.cursor>=v.limit)return!0;v.cursor++}for(;!v.out_grouping(p,97,252);){if(v.cursor>=v.limit)return!0;v.cursor++}return!1}function t(){m=v.limit,l=m;var e=v.cursor+3;0<=e&&e<=v.limit&&(d=e,s()||(m=v.cursor,m<d&&(m=d),s()||(l=v.cursor)))}function o(){for(var e,r;;){if(r=v.cursor,v.bra=r,!(e=v.find_among(h,6)))return;switch(v.ket=v.cursor,e){case 1:v.slice_from("y");break;case 2:case 5:v.slice_from("u");break;case 3:v.slice_from("a");break;case 4:v.slice_from("o");break;case 6:if(v.cursor>=v.limit)return;v.cursor++}}}function c(){return m<=v.cursor}function u(){return l<=v.cursor}function a(){var e,r,n,i,s=v.limit-v.cursor;if(v.ket=v.cursor,(e=v.find_among_b(w,7))&&(v.bra=v.cursor,c()))switch(e){case 1:v.slice_del();break;case 2:v.slice_del(),v.ket=v.cursor,v.eq_s_b(1,"s")&&(v.bra=v.cursor,v.eq_s_b(3,"nis")&&v.slice_del());break;case 3:v.in_grouping_b(g,98,116)&&v.slice_del()}if(v.cursor=v.limit-s,v.ket=v.cursor,(e=v.find_among_b(f,4))&&(v.bra=v.cursor,c()))switch(e){case 1:v.slice_del();break;case 2:if(v.in_grouping_b(k,98,116)){var t=v.cursor-3;v.limit_backward<=t&&t<=v.limit&&(v.cursor=t,v.slice_del())}}if(v.cursor=v.limit-s,v.ket=v.cursor,(e=v.find_among_b(_,8))&&(v.bra=v.cursor,u()))switch(e){case 1:v.slice_del(),v.ket=v.cursor,v.eq_s_b(2,"ig")&&(v.bra=v.cursor,r=v.limit-v.cursor,v.eq_s_b(1,"e")||(v.cursor=v.limit-r,u()&&v.slice_del()));break;case 2:n=v.limit-v.cursor,v.eq_s_b(1,"e")||(v.cursor=v.limit-n,v.slice_del());break;case 3:if(v.slice_del(),v.ket=v.cursor,i=v.limit-v.cursor,!v.eq_s_b(2,"er")&&(v.cursor=v.limit-i,!v.eq_s_b(2,"en")))break;v.bra=v.cursor,c()&&v.slice_del();break;case 4:v.slice_del(),v.ket=v.cursor,e=v.find_among_b(b,2),e&&(v.bra=v.cursor,u()&&1==e&&v.slice_del())}}var d,l,m,h=[new r("",-1,6),new r("U",0,2),new r("Y",0,1),new r("ä",0,3),new r("ö",0,4),new r("ü",0,5)],w=[new r("e",-1,2),new r("em",-1,1),new r("en",-1,2),new r("ern",-1,1),new r("er",-1,1),new r("s",-1,3),new r("es",5,2)],f=[new r("en",-1,1),new r("er",-1,1),new r("st",-1,2),new r("est",2,1)],b=[new r("ig",-1,1),new r("lich",-1,1)],_=[new r("end",-1,1),new r("ig",-1,2),new r("ung",-1,1),new r("lich",-1,3),new r("isch",-1,2),new r("ik",-1,2),new r("heit",-1,3),new r("keit",-1,4)],p=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,8,0,32,8],g=[117,30,5],k=[117,30,4],v=new n;this.setCurrent=function(e){v.setCurrent(e)},this.getCurrent=function(){return v.getCurrent()},this.stem=function(){var e=v.cursor;return i(),v.cursor=e,t(),v.limit_backward=e,v.cursor=v.limit,a(),v.cursor=v.limit_backward,o(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return i.setCurrent(e),i.stem(),i.getCurrent()}):(i.setCurrent(e),i.stem(),i.getCurrent())}}(),e.Pipeline.registerFunction(e.de.stemmer,"stemmer-de"),e.de.stopWordFilter=e.generateStopWordFilter("aber alle allem allen aller alles als also am an ander andere anderem anderen anderer anderes anderm andern anderr anders auch auf aus bei bin bis bist da damit dann das dasselbe dazu daß dein deine deinem deinen deiner deines dem demselben den denn denselben der derer derselbe derselben des desselben dessen dich die dies diese dieselbe dieselben diesem diesen dieser dieses dir doch dort du durch ein eine einem einen einer eines einig einige einigem einigen einiger einiges einmal er es etwas euch euer eure eurem euren eurer eures für gegen gewesen hab habe haben hat hatte hatten hier hin hinter ich ihm ihn ihnen ihr ihre ihrem ihren ihrer ihres im in indem ins ist jede jedem jeden jeder jedes jene jenem jenen jener jenes jetzt kann kein keine keinem keinen keiner keines können könnte machen man manche manchem manchen mancher manches mein meine meinem meinen meiner meines mich mir mit muss musste nach nicht nichts noch nun nur ob oder ohne sehr sein seine seinem seinen seiner seines selbst sich sie sind so solche solchem solchen solcher solches soll sollte sondern sonst um und uns unse unsem unsen unser unses unter viel vom von vor war waren warst was weg weil weiter welche welchem welchen welcher welches wenn werde werden wie wieder will wir wird wirst wo wollen wollte während würde würden zu zum zur zwar zwischen über".split(" ")),e.Pipeline.registerFunction(e.de.stopWordFilter,"stopWordFilter-de")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.du.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.du.min.js
new file mode 100644
index 0000000..49a0f3f
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.du.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Dutch` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");console.warn('[Lunr Languages] Please use the "nl" instead of the "du". The "nl" code is the standard code for Dutch language, and "du" will be removed in the next major versions.'),e.du=function(){this.pipeline.reset(),this.pipeline.add(e.du.trimmer,e.du.stopWordFilter,e.du.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.du.stemmer))},e.du.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.du.trimmer=e.trimmerSupport.generateTrimmer(e.du.wordCharacters),e.Pipeline.registerFunction(e.du.trimmer,"trimmer-du"),e.du.stemmer=function(){var r=e.stemmerSupport.Among,i=e.stemmerSupport.SnowballProgram,n=new function(){function e(){for(var e,r,i,o=C.cursor;;){if(C.bra=C.cursor,e=C.find_among(b,11))switch(C.ket=C.cursor,e){case 1:C.slice_from("a");continue;case 2:C.slice_from("e");continue;case 3:C.slice_from("i");continue;case 4:C.slice_from("o");continue;case 5:C.slice_from("u");continue;case 6:if(C.cursor>=C.limit)break;C.cursor++;continue}break}for(C.cursor=o,C.bra=o,C.eq_s(1,"y")?(C.ket=C.cursor,C.slice_from("Y")):C.cursor=o;;)if(r=C.cursor,C.in_grouping(q,97,232)){if(i=C.cursor,C.bra=i,C.eq_s(1,"i"))C.ket=C.cursor,C.in_grouping(q,97,232)&&(C.slice_from("I"),C.cursor=r);else if(C.cursor=i,C.eq_s(1,"y"))C.ket=C.cursor,C.slice_from("Y"),C.cursor=r;else if(n(r))break}else if(n(r))break}function n(e){return C.cursor=e,e>=C.limit||(C.cursor++,!1)}function o(){_=C.limit,f=_,t()||(_=C.cursor,_<3&&(_=3),t()||(f=C.cursor))}function t(){for(;!C.in_grouping(q,97,232);){if(C.cursor>=C.limit)return!0;C.cursor++}for(;!C.out_grouping(q,97,232);){if(C.cursor>=C.limit)return!0;C.cursor++}return!1}function s(){for(var e;;)if(C.bra=C.cursor,e=C.find_among(p,3))switch(C.ket=C.cursor,e){case 1:C.slice_from("y");break;case 2:C.slice_from("i");break;case 3:if(C.cursor>=C.limit)return;C.cursor++}}function u(){return _<=C.cursor}function c(){return f<=C.cursor}function a(){var e=C.limit-C.cursor;C.find_among_b(g,3)&&(C.cursor=C.limit-e,C.ket=C.cursor,C.cursor>C.limit_backward&&(C.cursor--,C.bra=C.cursor,C.slice_del()))}function l(){var e;w=!1,C.ket=C.cursor,C.eq_s_b(1,"e")&&(C.bra=C.cursor,u()&&(e=C.limit-C.cursor,C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-e,C.slice_del(),w=!0,a())))}function m(){var e;u()&&(e=C.limit-C.cursor,C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-e,C.eq_s_b(3,"gem")||(C.cursor=C.limit-e,C.slice_del(),a())))}function d(){var e,r,i,n,o,t,s=C.limit-C.cursor;if(C.ket=C.cursor,e=C.find_among_b(h,5))switch(C.bra=C.cursor,e){case 1:u()&&C.slice_from("heid");break;case 2:m();break;case 3:u()&&C.out_grouping_b(z,97,232)&&C.slice_del()}if(C.cursor=C.limit-s,l(),C.cursor=C.limit-s,C.ket=C.cursor,C.eq_s_b(4,"heid")&&(C.bra=C.cursor,c()&&(r=C.limit-C.cursor,C.eq_s_b(1,"c")||(C.cursor=C.limit-r,C.slice_del(),C.ket=C.cursor,C.eq_s_b(2,"en")&&(C.bra=C.cursor,m())))),C.cursor=C.limit-s,C.ket=C.cursor,e=C.find_among_b(k,6))switch(C.bra=C.cursor,e){case 1:if(c()){if(C.slice_del(),i=C.limit-C.cursor,C.ket=C.cursor,C.eq_s_b(2,"ig")&&(C.bra=C.cursor,c()&&(n=C.limit-C.cursor,!C.eq_s_b(1,"e")))){C.cursor=C.limit-n,C.slice_del();break}C.cursor=C.limit-i,a()}break;case 2:c()&&(o=C.limit-C.cursor,C.eq_s_b(1,"e")||(C.cursor=C.limit-o,C.slice_del()));break;case 3:c()&&(C.slice_del(),l());break;case 4:c()&&C.slice_del();break;case 5:c()&&w&&C.slice_del()}C.cursor=C.limit-s,C.out_grouping_b(j,73,232)&&(t=C.limit-C.cursor,C.find_among_b(v,4)&&C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-t,C.ket=C.cursor,C.cursor>C.limit_backward&&(C.cursor--,C.bra=C.cursor,C.slice_del())))}var f,_,w,b=[new r("",-1,6),new r("á",0,1),new r("ä",0,1),new r("é",0,2),new r("ë",0,2),new r("í",0,3),new r("ï",0,3),new r("ó",0,4),new r("ö",0,4),new r("ú",0,5),new r("ü",0,5)],p=[new r("",-1,3),new r("I",0,2),new r("Y",0,1)],g=[new r("dd",-1,-1),new r("kk",-1,-1),new r("tt",-1,-1)],h=[new r("ene",-1,2),new r("se",-1,3),new r("en",-1,2),new r("heden",2,1),new r("s",-1,3)],k=[new r("end",-1,1),new r("ig",-1,2),new r("ing",-1,1),new r("lijk",-1,3),new r("baar",-1,4),new r("bar",-1,5)],v=[new r("aa",-1,-1),new r("ee",-1,-1),new r("oo",-1,-1),new r("uu",-1,-1)],q=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],j=[1,0,0,17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],z=[17,67,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],C=new i;this.setCurrent=function(e){C.setCurrent(e)},this.getCurrent=function(){return C.getCurrent()},this.stem=function(){var r=C.cursor;return e(),C.cursor=r,o(),C.limit_backward=r,C.cursor=C.limit,d(),C.cursor=C.limit_backward,s(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return n.setCurrent(e),n.stem(),n.getCurrent()}):(n.setCurrent(e),n.stem(),n.getCurrent())}}(),e.Pipeline.registerFunction(e.du.stemmer,"stemmer-du"),e.du.stopWordFilter=e.generateStopWordFilter(" aan al alles als altijd andere ben bij daar dan dat de der deze die dit doch doen door dus een eens en er ge geen geweest haar had heb hebben heeft hem het hier hij hoe hun iemand iets ik in is ja je kan kon kunnen maar me meer men met mij mijn moet na naar niet niets nog nu of om omdat onder ons ook op over reeds te tegen toch toen tot u uit uw van veel voor want waren was wat werd wezen wie wil worden wordt zal ze zelf zich zij zijn zo zonder zou".split(" ")),e.Pipeline.registerFunction(e.du.stopWordFilter,"stopWordFilter-du")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.el.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.el.min.js
new file mode 100644
index 0000000..ace017b
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.el.min.js
@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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null!==o&&(s=o[1]+l[o[2]]),null!==(o=/^(.+?)(ΑΔΕΣ|ΑΔΩΝ)$/.exec(s))&&(s=o[1],/(ΟΚ|ΜΑΜ|ΜΑΝ|ΜΠΑΜΠ|ΠΑΤΕΡ|ΓΙΑΓΙ|ΝΤΑΝΤ|ΚΥΡ|ΘΕΙ|ΠΕΘΕΡ|ΜΟΥΣΑΜ|ΚΑΠΛΑΜ|ΠΑΡ|ΨΑΡ|ΤΖΟΥΡ|ΤΑΜΠΟΥΡ|ΓΑΛΑΤ|ΦΑΦΛΑΤ)$/.test(o[1])||(s+="ΑΔ")),null!==(o=/^(.+?)(ΕΔΕΣ|ΕΔΩΝ)$/.exec(s))&&(s=o[1],/(ΟΠ|ΙΠ|ΕΜΠ|ΥΠ|ΓΗΠ|ΔΑΠ|ΚΡΑΣΠ|ΜΙΛ)$/.test(o[1])&&(s+="ΕΔ")),null!==(o=/^(.+?)(ΟΥΔΕΣ|ΟΥΔΩΝ)$/.exec(s))&&(s=o[1],/(ΑΡΚ|ΚΑΛΙΑΚ|ΠΕΤΑΛ|ΛΙΧ|ΠΛΕΞ|ΣΚ|Σ|ΦΛ|ΦΡ|ΒΕΛ|ΛΟΥΛ|ΧΝ|ΣΠ|ΤΡΑΓ|ΦΕ)$/.test(o[1])&&(s+="ΟΥΔ")),null!==(o=/^(.+?)(ΕΩΣ|ΕΩΝ|ΕΑΣ|ΕΑ)$/.exec(s))&&(s=o[1],/^(Θ|Δ|ΕΛ|ΓΑΛ|Ν|Π|ΙΔ|ΠΑΡ|ΣΤΕΡ|ΟΡΦ|ΑΝΔΡ|ΑΝΤΡ)$/.test(o[1])&&(s+="Ε")),null!==(o=/^(.+?)(ΕΙΟ|ΕΙΟΣ|ΕΙΟΙ|ΕΙΑ|ΕΙΑΣ|ΕΙΕΣ|ΕΙΟΥ|ΕΙΟΥΣ|ΕΙΩΝ)$/.exec(s))&&o[1].length>4&&(s=o[1]),null!==(o=/^(.+?)(ΙΟΥΣ|ΙΑΣ|ΙΕΣ|ΙΟΣ|ΙΟΥ|ΙΟΙ|ΙΩΝ|ΙΟΝ|ΙΑ|ΙΟ)$/.exec(s))&&(s=o[1],(t(s)||s.length<2||/^(ΑΓ|ΑΓΓΕΛ|ΑΓΡ|ΑΕΡ|ΑΘΛ|ΑΚΟΥΣ|ΑΞ|ΑΣ|Β|ΒΙΒΛ|ΒΥΤ|Γ|ΓΙΑΓ|ΓΩΝ|Δ|ΔΑΝ|ΔΗΛ|ΔΗΜ|ΔΟΚΙΜ|ΕΛ|ΖΑΧΑΡ|ΗΛ|ΗΠ|ΙΔ|ΙΣΚ|ΙΣΤ|ΙΟΝ|ΙΩΝ|ΚΙΜΩΛ|ΚΟΛΟΝ|ΚΟΡ|ΚΤΗΡ|ΚΥΡ|ΛΑΓ|ΛΟΓ|ΜΑΓ|ΜΠΑΝ|ΜΠΡ|ΝΑΥΤ|ΝΟΤ|ΟΠΑΛ|ΟΞ|ΟΡ|ΟΣ|ΠΑΝΑΓ|ΠΑΤΡ|ΠΗΛ|ΠΗΝ|ΠΛΑΙΣ|ΠΟΝΤ|ΡΑΔ|ΡΟΔ|ΣΚ|ΣΚΟΡΠ|ΣΟΥΝ|ΣΠΑΝ|ΣΤΑΔ|ΣΥΡ|ΤΗΛ|ΤΙΜ|ΤΟΚ|ΤΟΠ|ΤΡΟΧ|ΦΙΛ|ΦΩΤ|Χ|ΧΙΛ|ΧΡΩΜ|ΧΩΡ)$/.test(o[1]))&&(s+="Ι"),/^(ΠΑΛ)$/.test(o[1])&&(s+="ΑΙ")),null!==(o=/^(.+?)(ΙΚΟΣ|ΙΚΟΝ|ΙΚΕΙΣ|ΙΚΟΙ|ΙΚΕΣ|ΙΚΟΥΣ|ΙΚΗ|ΙΚΗΣ|ΙΚΟ|ΙΚΑ|ΙΚΟΥ|ΙΚΩΝ|ΙΚΩΣ)$/.exec(s))&&(s=o[1],(t(s)||/^(ΑΔ|ΑΛ|ΑΜΑΝ|ΑΜΕΡ|ΑΜΜΟΧΑΛ|ΑΝΗΘ|ΑΝΤΙΔ|ΑΠΛ|ΑΤΤ|ΑΦΡ|ΒΑΣ|ΒΡΩΜ|ΓΕΝ|ΓΕΡ|Δ|ΔΙΚΑΝ|ΔΥΤ|ΕΙΔ|ΕΝΔ|ΕΞΩΔ|ΗΘ|ΘΕΤ|ΚΑΛΛΙΝ|ΚΑΛΠ|ΚΑΤΑΔ|ΚΟΥΖΙΝ|ΚΡ|ΚΩΔ|ΛΟΓ|Μ|ΜΕΡ|ΜΟΝΑΔ|ΜΟΥΛ|ΜΟΥΣ|ΜΠΑΓΙΑΤ|ΜΠΑΝ|ΜΠΟΛ|ΜΠΟΣ|ΜΥΣΤ|Ν|ΝΙΤ|ΞΙΚ|ΟΠΤ|ΠΑΝ|ΠΕΤΣ|ΠΙΚΑΝΤ|ΠΙΤΣ|ΠΛΑΣΤ|ΠΛΙΑΤΣ|ΠΟΝΤ|ΠΟΣΤΕΛΝ|ΠΡΩΤΟΔ|ΣΕΡΤ|ΣΗΜΑΝΤ|ΣΤΑΤ|ΣΥΝΑΔ|ΣΥΝΟΜΗΛ|ΤΕΛ|ΤΕΧΝ|ΤΡΟΠ|ΤΣΑΜ|ΥΠΟΔ|Φ|ΦΙΛΟΝ|ΦΥΛΟΔ|ΦΥΣ|ΧΑΣ)$/.test(o[1])||/(ΦΟΙΝ)$/.test(o[1]))&&(s+="ΙΚ")),"ΑΓΑΜΕ"===s&&(s="ΑΓΑΜ"),null!==(o=/^(.+?)(ΑΓΑΜΕ|ΗΣΑΜΕ|ΟΥΣΑΜΕ|ΗΚΑΜΕ|ΗΘΗΚΑΜΕ)$/.exec(s))&&(s=o[1]),null!==(o=/^(.+?)(ΑΜΕ)$/.exec(s))&&(s=o[1],/^(ΑΝΑΠ|ΑΠΟΘ|ΑΠΟΚ|ΑΠΟΣΤ|ΒΟΥΒ|ΞΕΘ|ΟΥΛ|ΠΕΘ|ΠΙΚΡ|ΠΟΤ|ΣΙΧ|Χ)$/.test(o[1])&&(s+="ΑΜ")),null!==(o=/^(.+?)(ΑΓΑΝΕ|ΗΣΑΝΕ|ΟΥΣΑΝΕ|ΙΟΝΤΑΝΕ|ΙΟΤΑΝΕ|ΙΟΥΝΤΑΝΕ|ΟΝΤΑΝΕ|ΟΤΑΝΕ|ΟΥΝΤΑΝΕ|ΗΚΑΝΕ|ΗΘΗΚΑΝΕ)$/.exec(s))&&(s=o[1],/^(ΤΡ|ΤΣ)$/.test(o[1])&&(s+="ΑΓΑΝ")),null!==(o=/^(.+?)(ΑΝΕ)$/.exec(s))&&(s=o[1],(r(s)||/^(ΒΕΤΕΡ|ΒΟΥΛΚ|ΒΡΑΧΜ|Γ|ΔΡΑΔΟΥΜ|Θ|ΚΑΛΠΟΥΖ|ΚΑΣΤΕΛ|ΚΟΡΜΟΡ|ΛΑΟΠΛ|ΜΩΑΜΕΘ|Μ|ΜΟΥΣΟΥΛΜΑΝ|ΟΥΛ|Π|ΠΕΛΕΚ|ΠΛ|ΠΟΛΙΣ|ΠΟΡΤΟΛ|ΣΑΡΑΚΑΤΣ|ΣΟΥΛΤ|ΤΣΑΡΛΑΤ|ΟΡΦ|ΤΣΙΓΓ|ΤΣΟΠ|ΦΩΤΟΣΤΕΦ|Χ|ΨΥΧΟΠΛ|ΑΓ|ΟΡΦ|ΓΑΛ|ΓΕΡ|ΔΕΚ|ΔΙΠΛ|ΑΜΕΡΙΚΑΝ|ΟΥΡ|ΠΙΘ|ΠΟΥΡΙΤ|Σ|ΖΩΝΤ|ΙΚ|ΚΑΣΤ|ΚΟΠ|ΛΙΧ|ΛΟΥΘΗΡ|ΜΑΙΝΤ|ΜΕΛ|ΣΙΓ|ΣΠ|ΣΤΕΓ|ΤΡΑΓ|ΤΣΑΓ|Φ|ΕΡ|ΑΔΑΠ|ΑΘΙΓΓ|ΑΜΗΧ|ΑΝΙΚ|ΑΝΟΡΓ|ΑΠΗΓ|ΑΠΙΘ|ΑΤΣΙΓΓ|ΒΑΣ|ΒΑΣΚ|ΒΑΘΥΓΑΛ|ΒΙΟΜΗΧ|ΒΡΑΧΥΚ|ΔΙΑΤ|ΔΙΑΦ|ΕΝΟΡΓ|ΘΥΣ|ΚΑΠΝΟΒΙΟΜΗΧ|ΚΑΤΑΓΑΛ|ΚΛΙΒ|ΚΟΙΛΑΡΦ|ΛΙΒ|ΜΕΓΛΟΒΙΟΜΗΧ|ΜΙΚΡΟΒΙΟΜΗΧ|ΝΤΑΒ|ΞΗΡΟΚΛΙΒ|ΟΛΙΓΟΔΑΜ|ΟΛΟΓΑΛ|ΠΕΝΤΑΡΦ|ΠΕΡΗΦ|ΠΕΡΙΤΡ|ΠΛΑΤ|ΠΟΛΥΔΑΠ|ΠΟΛΥΜΗΧ|ΣΤΕΦ|ΤΑΒ|ΤΕΤ|ΥΠΕΡΗΦ|ΥΠΟΚΟΠ|ΧΑΜΗΛΟΔΑΠ|ΨΗΛΟΤΑΒ)$/.test(o[1]))&&(s+="ΑΝ")),null!==(o=/^(.+?)(ΗΣΕΤΕ)$/.exec(s))&&(s=o[1]),null!==(o=/^(.+?)(ΕΤΕ)$/.exec(s))&&(s=o[1],(r(s)||/(ΟΔ|ΑΙΡ|ΦΟΡ|ΤΑΘ|ΔΙΑΘ|ΣΧ|ΕΝΔ|ΕΥΡ|ΤΙΘ|ΥΠΕΡΘ|ΡΑΘ|ΕΝΘ|ΡΟΘ|ΣΘ|ΠΥΡ|ΑΙΝ|ΣΥΝΔ|ΣΥΝ|ΣΥΝΘ|ΧΩΡ|ΠΟΝ|ΒΡ|ΚΑΘ|ΕΥΘ|ΕΚΘ|ΝΕΤ|ΡΟΝ|ΑΡΚ|ΒΑΡ|ΒΟΛ|ΩΦΕΛ)$/.test(o[1])||/^(ΑΒΑΡ|ΒΕΝ|ΕΝΑΡ|ΑΒΡ|ΑΔ|ΑΘ|ΑΝ|ΑΠΛ|ΒΑΡΟΝ|ΝΤΡ|ΣΚ|ΚΟΠ|ΜΠΟΡ|ΝΙΦ|ΠΑΓ|ΠΑΡΑΚΑΛ|ΣΕΡΠ|ΣΚΕΛ|ΣΥΡΦ|ΤΟΚ|Υ|Δ|ΕΜ|ΘΑΡΡ|Θ)$/.test(o[1]))&&(s+="ΕΤ")),null!==(o=/^(.+?)(ΟΝΤΑΣ|ΩΝΤΑΣ)$/.exec(s))&&(s=o[1],/^ΑΡΧ$/.test(o[1])&&(s+="ΟΝΤ"),/ΚΡΕ$/.test(o[1])&&(s+="ΩΝΤ")),null!==(o=/^(.+?)(ΟΜΑΣΤΕ|ΙΟΜΑΣΤΕ)$/.exec(s))&&(s=o[1],/^ΟΝ$/.test(o[1])&&(s+="ΟΜΑΣΤ")),null!==(o=/^(.+?)(ΙΕΣΤΕ)$/.exec(s))&&(s=o[1],/^(Π|ΑΠ|ΣΥΜΠ|ΑΣΥΜΠ|ΑΚΑΤΑΠ|ΑΜΕΤΑΜΦ)$/.test(o[1])&&(s+="ΙΕΣΤ")),null!==(o=/^(.+?)(ΕΣΤΕ)$/.exec(s))&&(s=o[1],/^(ΑΛ|ΑΡ|ΕΚΤΕΛ|Ζ|Μ|Ξ|ΠΑΡΑΚΑΛ|ΠΡΟ|ΝΙΣ)$/.test(o[1])&&(s+="ΕΣΤ")),null!==(o=/^(.+?)(ΗΘΗΚΑ|ΗΘΗΚΕΣ|ΗΘΗΚΕ)$/.exec(s))&&(s=o[1]),null!==(o=/^(.+?)(ΗΚΑ|ΗΚΕΣ|ΗΚΕ)$/.exec(s))&&(s=o[1],(/(ΣΚΩΛ|ΣΚΟΥΛ|ΝΑΡΘ|ΣΦ|ΟΘ|ΠΙΘ)$/.test(o[1])||/^(ΔΙΑΘ|Θ|ΠΑΡΑΚΑΤΑΘ|ΠΡΟΣΘ|ΣΥΝΘ)$/.test(o[1]))&&(s+="ΗΚ")),null!==(o=/^(.+?)(ΟΥΣΑ|ΟΥΣΕΣ|ΟΥΣΕ)$/.exec(s))&&(s=o[1],(t(s)||/^(ΦΑΡΜΑΚ|ΧΑΔ|ΑΓΚ|ΑΝΑΡΡ|ΒΡΟΜ|ΕΚΛΙΠ|ΛΑΜΠΙΔ|ΛΕΧ|Μ|ΠΑΤ|Ρ|Λ|ΜΕΔ|ΜΕΣΑΖ|ΥΠΟΤΕΙΝ|ΑΜ|ΑΙΘ|ΑΝΗΚ|ΔΕΣΠΟΖ|ΕΝΔΙΑΦΕΡ)$/.test(o[1])||/(ΠΟΔΑΡ|ΒΛΕΠ|ΠΑΝΤΑΧ|ΦΡΥΔ|ΜΑΝΤΙΛ|ΜΑΛΛ|ΚΥΜΑΤ|ΛΑΧ|ΛΗΓ|ΦΑΓ|ΟΜ|ΠΡΩΤ)$/.test(o[1]))&&(s+="ΟΥΣ")),null!==(o=/^(.+?)(ΑΓΑ|ΑΓΕΣ|ΑΓΕ)$/.exec(s))&&(s=o[1],(/^(ΑΒΑΣΤ|ΠΟΛΥΦ|ΑΔΗΦ|ΠΑΜΦ|Ρ|ΑΣΠ|ΑΦ|ΑΜΑΛ|ΑΜΑΛΛΙ|ΑΝΥΣΤ|ΑΠΕΡ|ΑΣΠΑΡ|ΑΧΑΡ|ΔΕΡΒΕΝ|ΔΡΟΣΟΠ|ΞΕΦ|ΝΕΟΠ|ΝΟΜΟΤ|ΟΛΟΠ|ΟΜΟΤ|ΠΡΟΣΤ|ΠΡΟΣΩΠΟΠ|ΣΥΜΠ|ΣΥΝΤ|Τ|ΥΠΟΤ|ΧΑΡ|ΑΕΙΠ|ΑΙΜΟΣΤ|ΑΝΥΠ|ΑΠΟΤ|ΑΡΤΙΠ|ΔΙΑΤ|ΕΝ|ΕΠΙΤ|ΚΡΟΚΑΛΟΠ|ΣΙΔΗΡΟΠ|Λ|ΝΑΥ|ΟΥΛΑΜ|ΟΥΡ|Π|ΤΡ|Μ)$/.test(o[1])||/(ΟΦ|ΠΕΛ|ΧΟΡΤ|ΛΛ|ΣΦ|ΡΠ|ΦΡ|ΠΡ|ΛΟΧ|ΣΜΗΝ)$/.test(o[1])&&!/^(ΨΟΦ|ΝΑΥΛΟΧ)$/.test(o[1])||/(ΚΟΛΛ)$/.test(o[1]))&&(s+="ΑΓ")),null!==(o=/^(.+?)(ΗΣΕ|ΗΣΟΥ|ΗΣΑ)$/.exec(s))&&(s=o[1],/^(Ν|ΧΕΡΣΟΝ|ΔΩΔΕΚΑΝ|ΕΡΗΜΟΝ|ΜΕΓΑΛΟΝ|ΕΠΤΑΝ|Ι)$/.test(o[1])&&(s+="ΗΣ")),null!==(o=/^(.+?)(ΗΣΤΕ)$/.exec(s))&&(s=o[1],/^(ΑΣΒ|ΣΒ|ΑΧΡ|ΧΡ|ΑΠΛ|ΑΕΙΜΝ|ΔΥΣΧΡ|ΕΥΧΡ|ΚΟΙΝΟΧΡ|ΠΑΛΙΜΨ)$/.test(o[1])&&(s+="ΗΣΤ")),null!==(o=/^(.+?)(ΟΥΝΕ|ΗΣΟΥΝΕ|ΗΘΟΥΝΕ)$/.exec(s))&&(s=o[1],/^(Ν|Ρ|ΣΠΙ|ΣΤΡΑΒΟΜΟΥΤΣ|ΚΑΚΟΜΟΥΤΣ|ΕΞΩΝ)$/.test(o[1])&&(s+="ΟΥΝ")),null!==(o=/^(.+?)(ΟΥΜΕ|ΗΣΟΥΜΕ|ΗΘΟΥΜΕ)$/.exec(s))&&(s=o[1],/^(ΠΑΡΑΣΟΥΣ|Φ|Χ|ΩΡΙΟΠΛ|ΑΖ|ΑΛΛΟΣΟΥΣ|ΑΣΟΥΣ)$/.test(o[1])&&(s+="ΟΥΜ")),null!=(o=/^(.+?)(ΜΑΤΟΙ|ΜΑΤΟΥΣ|ΜΑΤΟ|ΜΑΤΑ|ΜΑΤΩΣ|ΜΑΤΩΝ|ΜΑΤΟΣ|ΜΑΤΕΣ|ΜΑΤΗ|ΜΑΤΗΣ|ΜΑΤΟΥ)$/.exec(s))&&(s=o[1]+"Μ",/^(ΓΡΑΜ)$/.test(o[1])?s+="Α":/^(ΓΕ|ΣΤΑ)$/.test(o[1])&&(s+="ΑΤ")),null!==(o=/^(.+?)(ΟΥΑ)$/.exec(s))&&(s=o[1]+"ΟΥ"),n.length===s.length&&null!==(o=/^(.+?)(Α|ΑΓΑΤΕ|ΑΓΑΝ|ΑΕΙ|ΑΜΑΙ|ΑΝ|ΑΣ|ΑΣΑΙ|ΑΤΑΙ|ΑΩ|Ε|ΕΙ|ΕΙΣ|ΕΙΤΕ|ΕΣΑΙ|ΕΣ|ΕΤΑΙ|Ι|ΙΕΜΑΙ|ΙΕΜΑΣΤΕ|ΙΕΤΑΙ|ΙΕΣΑΙ|ΙΕΣΑΣΤΕ|ΙΟΜΑΣΤΑΝ|ΙΟΜΟΥΝ|ΙΟΜΟΥΝΑ|ΙΟΝΤΑΝ|ΙΟΝΤΟΥΣΑΝ|ΙΟΣΑΣΤΑΝ|ΙΟΣΑΣΤΕ|ΙΟΣΟΥΝ|ΙΟΣΟΥΝΑ|ΙΟΤΑΝ|ΙΟΥΜΑ|ΙΟΥΜΑΣΤΕ|ΙΟΥΝΤΑΙ|ΙΟΥΝΤΑΝ|Η|ΗΔΕΣ|ΗΔΩΝ|ΗΘΕΙ|ΗΘΕΙΣ|ΗΘΕΙΤΕ|ΗΘΗΚΑΤΕ|ΗΘΗΚΑΝ|ΗΘΟΥΝ|ΗΘΩ|ΗΚΑΤΕ|ΗΚΑΝ|ΗΣ|ΗΣΑΝ|ΗΣΑΤΕ|ΗΣΕΙ|ΗΣΕΣ|ΗΣΟΥΝ|ΗΣΩ|Ο|ΟΙ|ΟΜΑΙ|ΟΜΑΣΤΑΝ|ΟΜΟΥΝ|ΟΜΟΥΝΑ|ΟΝΤΑΙ|ΟΝΤΑΝ|ΟΝΤΟΥΣΑΝ|ΟΣ|ΟΣΑΣΤΑΝ|ΟΣΑΣΤΕ|ΟΣΟΥΝ|ΟΣΟΥΝΑ|ΟΤΑΝ|ΟΥ|ΟΥΜΑΙ|ΟΥΜΑΣΤΕ|ΟΥΝ|ΟΥΝΤΑΙ|ΟΥΝΤΑΝ|ΟΥΣ|ΟΥΣΑΝ|ΟΥΣΑΤΕ|Υ||ΥΑ|ΥΣ|Ω|ΩΝ|ΟΙΣ)$/.exec(s))&&(s=o[1]),null!=(o=/^(.+?)(ΕΣΤΕΡ|ΕΣΤΑΤ|ΟΤΕΡ|ΟΤΑΤ|ΥΤΕΡ|ΥΤΑΤ|ΩΤΕΡ|ΩΤΑΤ)$/.exec(s))&&(/^(ΕΞ|ΕΣ|ΑΝ|ΚΑΤ|Κ|ΠΡ)$/.test(o[1])||(s=o[1]),/^(ΚΑ|Μ|ΕΛΕ|ΛΕ|ΔΕ)$/.test(o[1])&&(s+="ΥΤ")),s}var 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t.update(function(t){for(var r="",n=0;n<t.length;n++)r+=e[t.charAt(n)]||t.charAt(n);return r});for(var r="",n=0;n<t.length;n++)r+=e[t.charAt(n)]||t.charAt(n);return r}}(),e.Pipeline.registerFunction(e.el.normilizer,"normilizer-el")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.es.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.es.min.js
new file mode 100644
index 0000000..2989d34
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.es.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Spanish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,s){"function"==typeof define&&define.amd?define(s):"object"==typeof exports?module.exports=s():s()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.fi.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.fi.min.js
new file mode 100644
index 0000000..29f5dfc
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.fi.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Finnish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(i,e){"function"==typeof define&&define.amd?define(e):"object"==typeof exports?module.exports=e():e()(i.lunr)}(this,function(){return function(i){if(void 0===i)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===i.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.fr.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.fr.min.js
new file mode 100644
index 0000000..68cd009
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.fr.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `French` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.he.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.he.min.js
new file mode 100644
index 0000000..b863d3e
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.he.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.he=function(){this.pipeline.reset(),this.pipeline.add(e.he.trimmer,e.he.stopWordFilter,e.he.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.he.stemmer))},e.he.wordCharacters="֑-״א-תa-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.he.trimmer=e.trimmerSupport.generateTrimmer(e.he.wordCharacters),e.Pipeline.registerFunction(e.he.trimmer,"trimmer-he"),e.he.stemmer=function(){var e=this;return e.result=!1,e.preRemoved=!1,e.sufRemoved=!1,e.pre={pre1:"ה ו י ת",pre2:"ב כ ל מ ש כש",pre3:"הב הכ הל המ הש בש לכ",pre4:"וב וכ ול ומ וש",pre5:"מה שה כל",pre6:"מב מכ מל ממ מש",pre7:"בה בו בי בת כה כו כי כת לה לו לי לת",pre8:"ובה ובו ובי ובת וכה וכו וכי וכת ולה ולו ולי ולת"},e.suf={suf1:"ך כ ם ן נ",suf2:"ים ות וך וכ ום ון ונ הם הן יכ יך ינ ים",suf3:"תי תך תכ תם תן תנ",suf4:"ותי ותך ותכ ותם ותן ותנ",suf5:"נו כם כן הם הן",suf6:"ונו וכם וכן והם והן",suf7:"תכם תכן תנו תהם תהן",suf8:"הוא היא הם הן אני אתה את אנו אתם אתן",suf9:"ני נו כי כו כם כן תי תך תכ תם תן",suf10:"י ך כ ם ן נ ת"},e.patterns=JSON.parse('{"hebrewPatterns": [{"pt1": [{"c": "ה", "l": 0}]}, {"pt2": [{"c": "ו", "l": 0}]}, {"pt3": [{"c": "י", "l": 0}]}, {"pt4": [{"c": "ת", "l": 0}]}, {"pt5": [{"c": "מ", "l": 0}]}, {"pt6": [{"c": "ל", "l": 0}]}, {"pt7": [{"c": "ב", "l": 0}]}, {"pt8": [{"c": "כ", "l": 0}]}, {"pt9": [{"c": "ש", "l": 0}]}, {"pt10": [{"c": "כש", "l": 0}]}, {"pt11": [{"c": "בה", "l": 0}]}, {"pt12": [{"c": "וב", "l": 0}]}, {"pt13": [{"c": "וכ", "l": 0}]}, {"pt14": [{"c": "ול", "l": 0}]}, {"pt15": [{"c": "ומ", "l": 0}]}, {"pt16": [{"c": "וש", "l": 0}]}, {"pt17": [{"c": "הב", "l": 0}]}, {"pt18": [{"c": "הכ", "l": 0}]}, {"pt19": [{"c": "הל", "l": 0}]}, {"pt20": [{"c": "המ", "l": 0}]}, {"pt21": [{"c": "הש", "l": 0}]}, {"pt22": [{"c": "מה", "l": 0}]}, {"pt23": [{"c": "שה", "l": 0}]}, {"pt24": [{"c": "כל", "l": 0}]}]}'),e.execArray=["cleanWord","removeDiacritics","removeStopWords","normalizeHebrewCharacters"],e.stem=function(){var r=0;for(e.result=!1,e.preRemoved=!1,e.sufRemoved=!1;r<e.execArray.length&&1!=e.result;)e.result=e[e.execArray[r]](),r++},e.setCurrent=function(r){e.word=r},e.getCurrent=function(){return e.word},e.cleanWord=function(){return!!new RegExp("[^֑-״א-ת]").test("")},e.removeDiacritics=function(){var r=new RegExp("[ְ-ֿ]","g");return e.word=e.word.replace(r,""),!1},e.removeStopWords=function(){if("אבל או אולי אותו אותי אותך אותם אותן אותנו אז אחר אחרות אחרי אחריכן אחרים אחרת אי איזה איך אין איפה אל אלה אלו אם אנחנו אני אף אפשר את אתה אתכם אתכן אתם אתן באיזה באיזו בגלל בין בלבד בעבור בעזרת בכל בכן בלי במידה במקום שבו ברוב בשביל בשעה ש בתוך גם דרך הוא היא היה היי היכן היתה היתי הם הן הנה הסיבה שבגללה הרי ואילו ואת זאת זה זות יהיה יוכל יוכלו יותר מדי יכול יכולה יכולות יכולים יכל יכלה יכלו יש כאן כאשר כולם כולן כזה כי כיצד כך כל כלל כמו כן כפי כש לא לאו לאיזותך לאן לבין לה להיות להם להן לו לזה לזות לי לך לכם לכן למה למעלה למעלה מ למטה למטה מ למעט למקום שבו למרות לנו לעבר לעיכן לפיכך לפני מאד מאחורי מאיזו סיבה מאין מאיפה מבלי מבעד מדוע מה מהיכן מול מחוץ מי מידע מכאן מכל מכן מלבד מן מנין מסוגל מעט מעטים מעל מצד מקום בו מתחת מתי נגד נגר נו עד עז על עלי עליו עליה עליהם עליך עלינו עם עצמה עצמהם עצמהן עצמו עצמי עצמם עצמן עצמנו פה רק שוב של שלה שלהם שלהן שלו שלי שלך שלכה שלכם שלכן שלנו שם תהיה תחת".split(" ").indexOf(e.word)>=0)return!0},e.normalizeHebrewCharacters=function(){return e.word=e.word.replace("ך","כ"),e.word=e.word.replace("ם","מ"),e.word=e.word.replace("ן","נ"),e.word=e.word.replace("ף","פ"),e.word=e.word.replace("ץ","צ"),!1},function(r){return"function"==typeof r.update?r.update(function(r){return e.setCurrent(r),e.stem(),e.getCurrent()}):(e.setCurrent(r),e.stem(),e.getCurrent())}}(),e.Pipeline.registerFunction(e.he.stemmer,"stemmer-he"),e.he.stopWordFilter=e.generateStopWordFilter("אבל או אולי אותו אותי אותך אותם אותן אותנו אז אחר אחרות אחרי אחריכן אחרים אחרת אי איזה איך אין איפה אל אלה אלו אם אנחנו אני אף אפשר את אתה אתכם אתכן אתם אתן באיזה באיזו בגלל בין בלבד בעבור בעזרת בכל בכן בלי במידה במקום שבו ברוב בשביל בשעה ש בתוך גם דרך הוא היא היה היי היכן היתה היתי הם הן הנה הסיבה שבגללה הרי ואילו ואת זאת זה זות יהיה יוכל יוכלו יותר מדי יכול יכולה יכולות יכולים יכל יכלה יכלו יש כאן כאשר כולם כולן כזה כי כיצד כך כל כלל כמו כן כפי כש לא לאו לאיזותך לאן לבין לה להיות להם להן לו לזה לזות לי לך לכם לכן למה למעלה למעלה מ למטה למטה מ למעט למקום שבו למרות לנו לעבר לעיכן לפיכך לפני מאד מאחורי מאיזו סיבה מאין מאיפה מבלי מבעד מדוע מה מהיכן מול מחוץ מי מידע מכאן מכל מכן מלבד מן מנין מסוגל מעט מעטים מעל מצד מקום בו מתחת מתי נגד נגר נו עד עז על עלי עליו עליה עליהם עליך עלינו עם עצמה עצמהם עצמהן עצמו עצמי עצמם עצמן עצמנו פה רק שוב של שלה שלהם שלהן שלו שלי שלך שלכה שלכם שלכן שלנו שם תהיה תחת".split(" ")),e.Pipeline.registerFunction(e.he.stopWordFilter,"stopWordFilter-he")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.hi.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.hi.min.js
new file mode 100644
index 0000000..7dbc414
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.hi.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hi=function(){this.pipeline.reset(),this.pipeline.add(e.hi.trimmer,e.hi.stopWordFilter,e.hi.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.hi.stemmer))},e.hi.wordCharacters="ऀ-ःऄ-एऐ-टठ-यर-िी-ॏॐ-य़ॠ-९॰-ॿa-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.hi.trimmer=e.trimmerSupport.generateTrimmer(e.hi.wordCharacters),e.Pipeline.registerFunction(e.hi.trimmer,"trimmer-hi"),e.hi.stopWordFilter=e.generateStopWordFilter("अत अपना अपनी अपने अभी अंदर आदि आप इत्यादि इन इनका इन्हीं इन्हें इन्हों इस इसका इसकी इसके इसमें इसी इसे उन उनका उनकी उनके उनको उन्हीं उन्हें उन्हों उस उसके उसी उसे एक एवं एस ऐसे और कई कर करता करते करना करने करें कहते कहा का काफ़ी कि कितना किन्हें किन्हों किया किर किस किसी किसे की कुछ कुल के को कोई कौन कौनसा गया घर जब जहाँ जा जितना जिन जिन्हें जिन्हों जिस जिसे जीधर जैसा जैसे जो तक तब तरह तिन तिन्हें तिन्हों तिस तिसे तो था थी थे दबारा दिया दुसरा दूसरे दो द्वारा न नके नहीं ना निहायत नीचे ने पर पहले पूरा पे फिर बनी बही बहुत बाद बाला बिलकुल भी भीतर मगर मानो मे में यदि यह यहाँ यही या यिह ये रखें रहा रहे ऱ्वासा लिए लिये लेकिन व वग़ैरह वर्ग वह वहाँ वहीं वाले वुह वे वो सकता सकते सबसे सभी साथ साबुत साभ सारा से सो संग ही हुआ हुई हुए है हैं हो होता होती होते होना होने".split(" ")),e.hi.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.hi.tokenizer=function(i){if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var t=i.toString().toLowerCase().replace(/^\s+/,"");return r.cut(t).split("|")},e.Pipeline.registerFunction(e.hi.stemmer,"stemmer-hi"),e.Pipeline.registerFunction(e.hi.stopWordFilter,"stopWordFilter-hi")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.hu.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.hu.min.js
new file mode 100644
index 0000000..ed9d909
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.hu.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Hungarian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,n){"function"==typeof define&&define.amd?define(n):"object"==typeof exports?module.exports=n():n()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hu=function(){this.pipeline.reset(),this.pipeline.add(e.hu.trimmer,e.hu.stopWordFilter,e.hu.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.hu.stemmer))},e.hu.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.hu.trimmer=e.trimmerSupport.generateTrimmer(e.hu.wordCharacters),e.Pipeline.registerFunction(e.hu.trimmer,"trimmer-hu"),e.hu.stemmer=function(){var n=e.stemmerSupport.Among,r=e.stemmerSupport.SnowballProgram,i=new function(){function e(){var e,n=L.cursor;if(d=L.limit,L.in_grouping(W,97,252))for(;;){if(e=L.cursor,L.out_grouping(W,97,252))return L.cursor=e,L.find_among(g,8)||(L.cursor=e,e<L.limit&&L.cursor++),void(d=L.cursor);if(L.cursor=e,e>=L.limit)return void(d=e);L.cursor++}if(L.cursor=n,L.out_grouping(W,97,252)){for(;!L.in_grouping(W,97,252);){if(L.cursor>=L.limit)return;L.cursor++}d=L.cursor}}function i(){return d<=L.cursor}function a(){var e;if(L.ket=L.cursor,(e=L.find_among_b(h,2))&&(L.bra=L.cursor,i()))switch(e){case 1:L.slice_from("a");break;case 2:L.slice_from("e")}}function t(){var e=L.limit-L.cursor;return!!L.find_among_b(p,23)&&(L.cursor=L.limit-e,!0)}function s(){if(L.cursor>L.limit_backward){L.cursor--,L.ket=L.cursor;var e=L.cursor-1;L.limit_backward<=e&&e<=L.limit&&(L.cursor=e,L.bra=e,L.slice_del())}}function c(){var e;if(L.ket=L.cursor,(e=L.find_among_b(_,2))&&(L.bra=L.cursor,i())){if((1==e||2==e)&&!t())return;L.slice_del(),s()}}function o(){L.ket=L.cursor,L.find_among_b(v,44)&&(L.bra=L.cursor,i()&&(L.slice_del(),a()))}function w(){var e;if(L.ket=L.cursor,(e=L.find_among_b(z,3))&&(L.bra=L.cursor,i()))switch(e){case 1:L.slice_from("e");break;case 2:case 3:L.slice_from("a")}}function l(){var e;if(L.ket=L.cursor,(e=L.find_among_b(y,6))&&(L.bra=L.cursor,i()))switch(e){case 1:case 2:L.slice_del();break;case 3:L.slice_from("a");break;case 4:L.slice_from("e")}}function u(){var e;if(L.ket=L.cursor,(e=L.find_among_b(j,2))&&(L.bra=L.cursor,i())){if((1==e||2==e)&&!t())return;L.slice_del(),s()}}function m(){var e;if(L.ket=L.cursor,(e=L.find_among_b(C,7))&&(L.bra=L.cursor,i()))switch(e){case 1:L.slice_from("a");break;case 2:L.slice_from("e");break;case 3:case 4:case 5:case 6:case 7:L.slice_del()}}function k(){var e;if(L.ket=L.cursor,(e=L.find_among_b(P,12))&&(L.bra=L.cursor,i()))switch(e){case 1:case 4:case 7:case 9:L.slice_del();break;case 2:case 5:case 8:L.slice_from("e");break;case 3:case 6:L.slice_from("a")}}function f(){var e;if(L.ket=L.cursor,(e=L.find_among_b(F,31))&&(L.bra=L.cursor,i()))switch(e){case 1:case 4:case 7:case 8:case 9:case 12:case 13:case 16:case 17:case 18:L.slice_del();break;case 2:case 5:case 10:case 14:case 19:L.slice_from("a");break;case 3:case 6:case 11:case 15:case 20:L.slice_from("e")}}function b(){var e;if(L.ket=L.cursor,(e=L.find_among_b(S,42))&&(L.bra=L.cursor,i()))switch(e){case 1:case 4:case 5:case 6:case 9:case 10:case 11:case 14:case 15:case 16:case 17:case 20:case 21:case 24:case 25:case 26:case 29:L.slice_del();break;case 2:case 7:case 12:case 18:case 22:case 27:L.slice_from("a");break;case 3:case 8:case 13:case 19:case 23:case 28:L.slice_from("e")}}var d,g=[new n("cs",-1,-1),new n("dzs",-1,-1),new n("gy",-1,-1),new n("ly",-1,-1),new n("ny",-1,-1),new n("sz",-1,-1),new n("ty",-1,-1),new n("zs",-1,-1)],h=[new n("á",-1,1),new n("é",-1,2)],p=[new n("bb",-1,-1),new n("cc",-1,-1),new n("dd",-1,-1),new n("ff",-1,-1),new n("gg",-1,-1),new n("jj",-1,-1),new n("kk",-1,-1),new n("ll",-1,-1),new n("mm",-1,-1),new n("nn",-1,-1),new n("pp",-1,-1),new n("rr",-1,-1),new n("ccs",-1,-1),new n("ss",-1,-1),new n("zzs",-1,-1),new n("tt",-1,-1),new n("vv",-1,-1),new n("ggy",-1,-1),new n("lly",-1,-1),new n("nny",-1,-1),new n("tty",-1,-1),new n("ssz",-1,-1),new n("zz",-1,-1)],_=[new n("al",-1,1),new n("el",-1,2)],v=[new n("ba",-1,-1),new n("ra",-1,-1),new n("be",-1,-1),new n("re",-1,-1),new n("ig",-1,-1),new n("nak",-1,-1),new n("nek",-1,-1),new n("val",-1,-1),new n("vel",-1,-1),new n("ul",-1,-1),new n("nál",-1,-1),new n("nél",-1,-1),new n("ból",-1,-1),new n("ról",-1,-1),new n("tól",-1,-1),new n("bõl",-1,-1),new n("rõl",-1,-1),new n("tõl",-1,-1),new n("ül",-1,-1),new n("n",-1,-1),new n("an",19,-1),new n("ban",20,-1),new n("en",19,-1),new n("ben",22,-1),new n("képpen",22,-1),new n("on",19,-1),new n("ön",19,-1),new n("képp",-1,-1),new n("kor",-1,-1),new n("t",-1,-1),new n("at",29,-1),new n("et",29,-1),new n("ként",29,-1),new n("anként",32,-1),new n("enként",32,-1),new n("onként",32,-1),new n("ot",29,-1),new n("ért",29,-1),new n("öt",29,-1),new n("hez",-1,-1),new n("hoz",-1,-1),new n("höz",-1,-1),new n("vá",-1,-1),new n("vé",-1,-1)],z=[new n("án",-1,2),new n("én",-1,1),new n("ánként",-1,3)],y=[new n("stul",-1,2),new n("astul",0,1),new n("ástul",0,3),new n("stül",-1,2),new n("estül",3,1),new n("éstül",3,4)],j=[new n("á",-1,1),new n("é",-1,2)],C=[new n("k",-1,7),new n("ak",0,4),new n("ek",0,6),new n("ok",0,5),new 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keressünk keresztül ki kívül között közül legalább legyen lehet lehetett lenne lenni lesz lett maga magát majd majd meg mellett mely melyek mert mi mikor milyen minden mindenki mindent mindig mint mintha mit mivel miért most már más másik még míg nagy nagyobb nagyon ne nekem neki nem nincs néha néhány nélkül olyan ott pedig persze rá s saját sem semmi sok sokat sokkal szemben szerint szinte számára talán tehát teljes tovább továbbá több ugyanis utolsó után utána vagy vagyis vagyok valaki valami valamint való van vannak vele vissza viszont volna volt voltak voltam voltunk által általában át én éppen és így õ õk õket össze úgy új újabb újra".split(" ")),e.Pipeline.registerFunction(e.hu.stopWordFilter,"stopWordFilter-hu")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.hy.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.hy.min.js
new file mode 100644
index 0000000..b37f792
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.hy.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hy=function(){this.pipeline.reset(),this.pipeline.add(e.hy.trimmer,e.hy.stopWordFilter)},e.hy.wordCharacters="[A-Za-z԰-֏ff-ﭏ]",e.hy.trimmer=e.trimmerSupport.generateTrimmer(e.hy.wordCharacters),e.Pipeline.registerFunction(e.hy.trimmer,"trimmer-hy"),e.hy.stopWordFilter=e.generateStopWordFilter("դու և եք էիր էիք հետո նաև նրանք որը վրա է որ պիտի են այս մեջ ն իր ու ի այդ որոնք այն կամ էր մի ես համար այլ իսկ էին ենք հետ ին թ էինք մենք նրա նա դուք եմ էի ըստ որպես ում".split(" ")),e.Pipeline.registerFunction(e.hy.stopWordFilter,"stopWordFilter-hy"),e.hy.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}(),e.Pipeline.registerFunction(e.hy.stemmer,"stemmer-hy")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.it.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.it.min.js
new file mode 100644
index 0000000..344b6a3
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.it.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Italian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
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r("evo",-1,1),new r("ivo",-1,1),new r("ar",-1,1),new r("ir",-1,1),new r("erà",-1,1),new r("irà",-1,1),new r("erò",-1,1),new r("irò",-1,1)],L=[17,65,16,0,0,0,0,0,0,0,0,0,0,0,0,128,128,8,2,1],y=[17,65,0,0,0,0,0,0,0,0,0,0,0,0,0,128,128,8,2],U=[17],x=new n;this.setCurrent=function(e){x.setCurrent(e)},this.getCurrent=function(){return x.getCurrent()},this.stem=function(){var e=x.cursor;return i(),x.cursor=e,u(),x.limit_backward=e,x.cursor=x.limit,f(),x.cursor=x.limit,v()||(x.cursor=x.limit,b()),x.cursor=x.limit,_(),x.cursor=x.limit_backward,c(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return i.setCurrent(e),i.stem(),i.getCurrent()}):(i.setCurrent(e),i.stem(),i.getCurrent())}}(),e.Pipeline.registerFunction(e.it.stemmer,"stemmer-it"),e.it.stopWordFilter=e.generateStopWordFilter("a abbia abbiamo abbiano abbiate ad agl agli ai al all alla alle allo anche avemmo avendo avesse avessero avessi avessimo aveste avesti avete aveva avevamo avevano avevate avevi avevo avrai avranno avrebbe avrebbero avrei avremmo avremo avreste avresti avrete avrà avrò avuta avute avuti avuto c che chi ci coi col come con contro cui da dagl dagli dai dal dall dalla dalle dallo degl degli dei del dell della delle dello di dov dove e ebbe ebbero ebbi ed era erano eravamo eravate eri ero essendo faccia facciamo facciano facciate faccio facemmo facendo facesse facessero facessi facessimo faceste facesti faceva facevamo facevano facevate facevi facevo fai fanno farai faranno farebbe farebbero farei faremmo faremo fareste faresti farete farà farò fece fecero feci fosse fossero fossi fossimo foste fosti fu fui fummo furono gli ha hai hanno ho i il in io l la le lei li lo loro lui ma mi mia mie miei mio ne negl negli nei nel nell nella nelle nello noi non nostra nostre nostri nostro o per perché più quale quanta quante quanti quanto quella quelle quelli quello questa queste questi questo sarai saranno sarebbe sarebbero sarei saremmo saremo sareste saresti sarete sarà sarò se sei si sia siamo siano siate siete sono sta stai stando stanno starai staranno starebbe starebbero starei staremmo staremo stareste staresti starete starà starò stava stavamo stavano stavate stavi stavo stemmo stesse stessero stessi stessimo steste stesti stette stettero stetti stia stiamo stiano stiate sto su sua sue sugl sugli sui sul sull sulla sulle sullo suo suoi ti tra tu tua tue tuo tuoi tutti tutto un una uno vi voi vostra vostre vostri vostro è".split(" ")),e.Pipeline.registerFunction(e.it.stopWordFilter,"stopWordFilter-it")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.ja.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.ja.min.js
new file mode 100644
index 0000000..5f254eb
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.ja.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var r="2"==e.version[0];e.ja=function(){this.pipeline.reset(),this.pipeline.add(e.ja.trimmer,e.ja.stopWordFilter,e.ja.stemmer),r?this.tokenizer=e.ja.tokenizer:(e.tokenizer&&(e.tokenizer=e.ja.tokenizer),this.tokenizerFn&&(this.tokenizerFn=e.ja.tokenizer))};var t=new e.TinySegmenter;e.ja.tokenizer=function(i){var n,o,s,p,a,u,m,l,c,f;if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(t){return r?new e.Token(t.toLowerCase()):t.toLowerCase()});for(o=i.toString().toLowerCase().replace(/^\s+/,""),n=o.length-1;n>=0;n--)if(/\S/.test(o.charAt(n))){o=o.substring(0,n+1);break}for(a=[],s=o.length,c=0,l=0;c<=s;c++)if(u=o.charAt(c),m=c-l,u.match(/\s/)||c==s){if(m>0)for(p=t.segment(o.slice(l,c)).filter(function(e){return!!e}),f=l,n=0;n<p.length;n++)r?a.push(new e.Token(p[n],{position:[f,p[n].length],index:a.length})):a.push(p[n]),f+=p[n].length;l=c+1}return a},e.ja.stemmer=function(){return function(e){return e}}(),e.Pipeline.registerFunction(e.ja.stemmer,"stemmer-ja"),e.ja.wordCharacters="一二三四五六七八九十百千万億兆一-龠々〆ヵヶぁ-んァ-ヴーｱ-ﾝﾞa-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.ja.trimmer=e.trimmerSupport.generateTrimmer(e.ja.wordCharacters),e.Pipeline.registerFunction(e.ja.trimmer,"trimmer-ja"),e.ja.stopWordFilter=e.generateStopWordFilter("これ それ あれ この その あの ここ そこ あそこ こちら どこ だれ なに なん 何 私 貴方 貴方方 我々 私達 あの人 あのかた 彼女 彼 です あります おります います は が の に を で え から まで より も どの と し それで しかし".split(" ")),e.Pipeline.registerFunction(e.ja.stopWordFilter,"stopWordFilter-ja"),e.jp=e.ja,e.Pipeline.registerFunction(e.jp.stemmer,"stemmer-jp"),e.Pipeline.registerFunction(e.jp.trimmer,"trimmer-jp"),e.Pipeline.registerFunction(e.jp.stopWordFilter,"stopWordFilter-jp")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.jp.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.jp.min.js
new file mode 100644
index 0000000..c055eba
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.jp.min.js
@@ -0,0 +1 @@
+module.exports=require("./lunr.ja");
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.kn.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.kn.min.js
new file mode 100644
index 0000000..1cef9be
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.kn.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.kn=function(){this.pipeline.reset(),this.pipeline.add(e.kn.trimmer,e.kn.stopWordFilter,e.kn.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.kn.stemmer))},e.kn.wordCharacters="ಀ-಄ಅ-ಔಕ-ಹಾ-ೌ಼-ಽೕ-ೖೝ-ೞೠ-ೡೢ-ೣ೤೥೦-೯ೱ-ೳ",e.kn.trimmer=e.trimmerSupport.generateTrimmer(e.kn.wordCharacters),e.Pipeline.registerFunction(e.kn.trimmer,"trimmer-kn"),e.kn.stopWordFilter=e.generateStopWordFilter("ಮತ್ತು ಈ ಒಂದು ರಲ್ಲಿ ಹಾಗೂ ಎಂದು ಅಥವಾ ಇದು ರ ಅವರು ಎಂಬ ಮೇಲೆ ಅವರ ತನ್ನ ಆದರೆ ತಮ್ಮ ನಂತರ ಮೂಲಕ ಹೆಚ್ಚು ನ ಆ ಕೆಲವು ಅನೇಕ ಎರಡು ಹಾಗು ಪ್ರಮುಖ ಇದನ್ನು ಇದರ ಸುಮಾರು ಅದರ ಅದು ಮೊದಲ ಬಗ್ಗೆ ನಲ್ಲಿ ರಂದು ಇತರ ಅತ್ಯಂತ ಹೆಚ್ಚಿನ ಸಹ ಸಾಮಾನ್ಯವಾಗಿ ನೇ ಹಲವಾರು ಹೊಸ ದಿ ಕಡಿಮೆ ಯಾವುದೇ ಹೊಂದಿದೆ ದೊಡ್ಡ ಅನ್ನು ಇವರು ಪ್ರಕಾರ ಇದೆ ಮಾತ್ರ ಕೂಡ ಇಲ್ಲಿ ಎಲ್ಲಾ ವಿವಿಧ ಅದನ್ನು ಹಲವು ರಿಂದ ಕೇವಲ ದ ದಕ್ಷಿಣ ಗೆ ಅವನ ಅತಿ ನೆಯ ಬಹಳ ಕೆಲಸ ಎಲ್ಲ ಪ್ರತಿ ಇತ್ಯಾದಿ ಇವು ಬೇರೆ ಹೀಗೆ ನಡುವೆ ಇದಕ್ಕೆ ಎಸ್ ಇವರ ಮೊದಲು ಶ್ರೀ ಮಾಡುವ ಇದರಲ್ಲಿ ರೀತಿಯ ಮಾಡಿದ ಕಾಲ ಅಲ್ಲಿ ಮಾಡಲು ಅದೇ ಈಗ ಅವು ಗಳು ಎ ಎಂಬುದು ಅವನು ಅಂದರೆ ಅವರಿಗೆ ಇರುವ ವಿಶೇಷ ಮುಂದೆ ಅವುಗಳ ಮುಂತಾದ ಮೂಲ ಬಿ ಮೀ ಒಂದೇ ಇನ್ನೂ ಹೆಚ್ಚಾಗಿ ಮಾಡಿ ಅವರನ್ನು ಇದೇ ಯ ರೀತಿಯಲ್ಲಿ ಜೊತೆ ಅದರಲ್ಲಿ ಮಾಡಿದರು ನಡೆದ ಆಗ ಮತ್ತೆ ಪೂರ್ವ ಆತ ಬಂದ ಯಾವ ಒಟ್ಟು ಇತರೆ ಹಿಂದೆ ಪ್ರಮಾಣದ ಗಳನ್ನು ಕುರಿತು ಯು ಆದ್ದರಿಂದ ಅಲ್ಲದೆ ನಗರದ ಮೇಲಿನ ಏಕೆಂದರೆ ರಷ್ಟು ಎಂಬುದನ್ನು ಬಾರಿ ಎಂದರೆ ಹಿಂದಿನ ಆದರೂ ಆದ ಸಂಬಂಧಿಸಿದ ಮತ್ತೊಂದು ಸಿ ಆತನ ".split(" ")),e.kn.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.kn.tokenizer=function(t){if(!arguments.length||null==t||void 0==t)return[];if(Array.isArray(t))return t.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var n=t.toString().toLowerCase().replace(/^\s+/,"");return r.cut(n).split("|")},e.Pipeline.registerFunction(e.kn.stemmer,"stemmer-kn"),e.Pipeline.registerFunction(e.kn.stopWordFilter,"stopWordFilter-kn")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.ko.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.ko.min.js
new file mode 100644
index 0000000..eaf9dab
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.ko.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.ko=function(){this.pipeline.reset(),this.pipeline.add(e.ko.trimmer,e.ko.stopWordFilter)},e.ko.wordCharacters="[A-Za-z가-힣]",e.ko.trimmer=e.trimmerSupport.generateTrimmer(e.ko.wordCharacters),e.Pipeline.registerFunction(e.ko.trimmer,"trimmer-ko"),e.ko.stopWordFilter=e.generateStopWordFilter("아 휴 아이구 아이쿠 아이고 어 나 우리 저희 따라 의해 을 를 에 의 가 으로 로 에게 뿐이다 의거하여 근거하여 입각하여 기준으로 예하면 예를 들면 예를 들자면 저 소인 소생 저희 지말고 하지마 하지마라 다른 물론 또한 그리고 비길수 없다 해서는 안된다 뿐만 아니라 만이 아니다 만은 아니다 막론하고 관계없이 그치지 않다 그러나 그런데 하지만 든간에 논하지 않다 따지지 않다 설사 비록 더라도 아니면 만 못하다 하는 편이 낫다 불문하고 향하여 향해서 향하다 쪽으로 틈타 이용하여 타다 오르다 제외하고 이 외에 이 밖에 하여야 비로소 한다면 몰라도 외에도 이곳 여기 부터 기점으로 따라서 할 생각이다 하려고하다 이리하여 그리하여 그렇게 함으로써 하지만 일때 할때 앞에서 중에서 보는데서 으로써 로써 까지 해야한다 일것이다 반드시 할줄알다 할수있다 할수있어 임에 틀림없다 한다면 등 등등 제 겨우 단지 다만 할뿐 딩동 댕그 대해서 대하여 대하면 훨씬 얼마나 얼마만큼 얼마큼 남짓 여 얼마간 약간 다소 좀 조금 다수 몇 얼마 지만 하물며 또한 그러나 그렇지만 하지만 이외에도 대해 말하자면 뿐이다 다음에 반대로 반대로 말하자면 이와 반대로 바꾸어서 말하면 바꾸어서 한다면 만약 그렇지않으면 까악 툭 딱 삐걱거리다 보드득 비걱거리다 꽈당 응당 해야한다 에 가서 각 각각 여러분 각종 각자 제각기 하도록하다 와 과 그러므로 그래서 고로 한 까닭에 하기 때문에 거니와 이지만 대하여 관하여 관한 과연 실로 아니나다를가 생각한대로 진짜로 한적이있다 하곤하였다 하 하하 허허 아하 거바 와 오 왜 어째서 무엇때문에 어찌 하겠는가 무슨 어디 어느곳 더군다나 하물며 더욱이는 어느때 언제 야 이봐 어이 여보시오 흐흐 흥 휴 헉헉 헐떡헐떡 영차 여차 어기여차 끙끙 아야 앗 아야 콸콸 졸졸 좍좍 뚝뚝 주룩주룩 솨 우르르 그래도 또 그리고 바꾸어말하면 바꾸어말하자면 혹은 혹시 답다 및 그에 따르는 때가 되어 즉 지든지 설령 가령 하더라도 할지라도 일지라도 지든지 몇 거의 하마터면 인젠 이젠 된바에야 된이상 만큼\t어찌됏든 그위에 게다가 점에서 보아 비추어 보아 고려하면 하게될것이다 일것이다 비교적 좀 보다더 비하면 시키다 하게하다 할만하다 의해서 연이서 이어서 잇따라 뒤따라 뒤이어 결국 의지하여 기대여 통하여 자마자 더욱더 불구하고 얼마든지 마음대로 주저하지 않고 곧 즉시 바로 당장 하자마자 밖에 안된다 하면된다 그래 그렇지 요컨대 다시 말하자면 바꿔 말하면 즉 구체적으로 말하자면 시작하여 시초에 이상 허 헉 허걱 바와같이 해도좋다 해도된다 게다가 더구나 하물며 와르르 팍 퍽 펄렁 동안 이래 하고있었다 이었다 에서 로부터 까지 예하면 했어요 해요 함께 같이 더불어 마저 마저도 양자 모두 습니다 가까스로 하려고하다 즈음하여 다른 다른 방면으로 해봐요 습니까 했어요 말할것도 없고 무릎쓰고 개의치않고 하는것만 못하다 하는것이 낫다 매 매번 들 모 어느것 어느 로써 갖고말하자면 어디 어느쪽 어느것 어느해 어느 년도 라 해도 언젠가 어떤것 어느것 저기 저쪽 저것 그때 그럼 그러면 요만한걸 그래 그때 저것만큼 그저 이르기까지 할 줄 안다 할 힘이 있다 너 너희 당신 어찌 설마 차라리 할지언정 할지라도 할망정 할지언정 구토하다 게우다 토하다 메쓰겁다 옆사람 퉤 쳇 의거하여 근거하여 의해 따라 힘입어 그 다음 버금 두번째로 기타 첫번째로 나머지는 그중에서 견지에서 형식으로 쓰여 입장에서 위해서 단지 의해되다 하도록시키다 뿐만아니라 반대로 전후 전자 앞의것 잠시 잠깐 하면서 그렇지만 다음에 그러한즉 그런즉 남들 아무거나 어찌하든지 같다 비슷하다 예컨대 이럴정도로 어떻게 만약 만일 위에서 서술한바와같이 인 듯하다 하지 않는다면 만약에 무엇 무슨 어느 어떤 아래윗 조차 한데 그럼에도 불구하고 여전히 심지어 까지도 조차도 하지 않도록 않기 위하여 때 시각 무렵 시간 동안 어때 어떠한 하여금 네 예 우선 누구 누가 알겠는가 아무도 줄은모른다 줄은 몰랏다 하는 김에 겸사겸사 하는바 그런 까닭에 한 이유는 그러니 그러니까 때문에 그 너희 그들 너희들 타인 것 것들 너 위하여 공동으로 동시에 하기 위하여 어찌하여 무엇때문에 붕붕 윙윙 나 우리 엉엉 휘익 윙윙 오호 아하 어쨋든 만 못하다\t하기보다는 차라리 하는 편이 낫다 흐흐 놀라다 상대적으로 말하자면 마치 아니라면 쉿 그렇지 않으면 그렇지 않다면 안 그러면 아니었다면 하든지 아니면 이라면 좋아 알았어 하는것도 그만이다 어쩔수 없다 하나 일 일반적으로 일단 한켠으로는 오자마자 이렇게되면 이와같다면 전부 한마디 한항목 근거로 하기에 아울러 하지 않도록 않기 위해서 이르기까지 이 되다 로 인하여 까닭으로 이유만으로 이로 인하여 그래서 이 때문에 그러므로 그런 까닭에 알 수 있다 결론을 낼 수 있다 으로 인하여 있다 어떤것 관계가 있다 관련이 있다 연관되다 어떤것들 에 대해 이리하여 그리하여 여부 하기보다는 하느니 하면 할수록 운운 이러이러하다 하구나 하도다 다시말하면 다음으로 에 있다 에 달려 있다 우리 우리들 오히려 하기는한데 어떻게 어떻해 어찌됏어 어때 어째서 본대로 자 이 이쪽 여기 이것 이번 이렇게말하자면 이런 이러한 이와 같은 요만큼 요만한 것 얼마 안 되는 것 이만큼 이 정도의 이렇게 많은 것 이와 같다 이때 이렇구나 것과 같이 끼익 삐걱 따위 와 같은 사람들 부류의 사람들 왜냐하면 중의하나 오직 오로지 에 한하다 하기만 하면 도착하다 까지 미치다 도달하다 정도에 이르다 할 지경이다 결과에 이르다 관해서는 여러분 하고 있다 한 후 혼자 자기 자기집 자신 우에 종합한것과같이 총적으로 보면 총적으로 말하면 총적으로 대로 하다 으로서 참 그만이다 할 따름이다 쿵 탕탕 쾅쾅 둥둥 봐 봐라 아이야 아니 와아 응 아이 참나 년 월 일 령 영 일 이 삼 사 오 육 륙 칠 팔 구 이천육 이천칠 이천팔 이천구 하나 둘 셋 넷 다섯 여섯 일곱 여덟 아홉 령 영".split(" ")),e.Pipeline.registerFunction(e.ko.stopWordFilter,"stopWordFilter-ko"),e.ko.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}(),e.Pipeline.registerFunction(e.ko.stemmer,"stemmer-ko")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.multi.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.multi.min.js
new file mode 100644
index 0000000..7debad0
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.multi.min.js
@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){e.multiLanguage=function(){for(var t=Array.prototype.slice.call(arguments),i=t.join("-"),r="",n=[],s=[],p=0;p<t.length;++p)"en"==t[p]?(r+="\\w",n.unshift(e.stopWordFilter),n.push(e.stemmer),s.push(e.stemmer)):(r+=e[t[p]].wordCharacters,e[t[p]].stopWordFilter&&n.unshift(e[t[p]].stopWordFilter),e[t[p]].stemmer&&(n.push(e[t[p]].stemmer),s.push(e[t[p]].stemmer)));var o=e.trimmerSupport.generateTrimmer(r);return e.Pipeline.registerFunction(o,"lunr-multi-trimmer-"+i),n.unshift(o),function(){this.pipeline.reset(),this.pipeline.add.apply(this.pipeline,n),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add.apply(this.searchPipeline,s))}}}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.nl.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.nl.min.js
new file mode 100644
index 0000000..c4a2535
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.nl.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Dutch` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(r,e){"function"==typeof define&&define.amd?define(e):"object"==typeof exports?module.exports=e():e()(r.lunr)}(this,function(){return function(r){if(void 0===r)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===r.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");r.nl=function(){this.pipeline.reset(),this.pipeline.add(r.nl.trimmer,r.nl.stopWordFilter,r.nl.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(r.nl.stemmer))},r.nl.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",r.nl.trimmer=r.trimmerSupport.generateTrimmer(r.nl.wordCharacters),r.Pipeline.registerFunction(r.nl.trimmer,"trimmer-nl"),r.nl.stemmer=function(){var e=r.stemmerSupport.Among,i=r.stemmerSupport.SnowballProgram,n=new function(){function r(){for(var r,e,i,o=C.cursor;;){if(C.bra=C.cursor,r=C.find_among(b,11))switch(C.ket=C.cursor,r){case 1:C.slice_from("a");continue;case 2:C.slice_from("e");continue;case 3:C.slice_from("i");continue;case 4:C.slice_from("o");continue;case 5:C.slice_from("u");continue;case 6:if(C.cursor>=C.limit)break;C.cursor++;continue}break}for(C.cursor=o,C.bra=o,C.eq_s(1,"y")?(C.ket=C.cursor,C.slice_from("Y")):C.cursor=o;;)if(e=C.cursor,C.in_grouping(q,97,232)){if(i=C.cursor,C.bra=i,C.eq_s(1,"i"))C.ket=C.cursor,C.in_grouping(q,97,232)&&(C.slice_from("I"),C.cursor=e);else if(C.cursor=i,C.eq_s(1,"y"))C.ket=C.cursor,C.slice_from("Y"),C.cursor=e;else if(n(e))break}else if(n(e))break}function n(r){return C.cursor=r,r>=C.limit||(C.cursor++,!1)}function o(){_=C.limit,d=_,t()||(_=C.cursor,_<3&&(_=3),t()||(d=C.cursor))}function t(){for(;!C.in_grouping(q,97,232);){if(C.cursor>=C.limit)return!0;C.cursor++}for(;!C.out_grouping(q,97,232);){if(C.cursor>=C.limit)return!0;C.cursor++}return!1}function s(){for(var r;;)if(C.bra=C.cursor,r=C.find_among(p,3))switch(C.ket=C.cursor,r){case 1:C.slice_from("y");break;case 2:C.slice_from("i");break;case 3:if(C.cursor>=C.limit)return;C.cursor++}}function u(){return _<=C.cursor}function c(){return d<=C.cursor}function a(){var r=C.limit-C.cursor;C.find_among_b(g,3)&&(C.cursor=C.limit-r,C.ket=C.cursor,C.cursor>C.limit_backward&&(C.cursor--,C.bra=C.cursor,C.slice_del()))}function l(){var r;w=!1,C.ket=C.cursor,C.eq_s_b(1,"e")&&(C.bra=C.cursor,u()&&(r=C.limit-C.cursor,C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-r,C.slice_del(),w=!0,a())))}function m(){var r;u()&&(r=C.limit-C.cursor,C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-r,C.eq_s_b(3,"gem")||(C.cursor=C.limit-r,C.slice_del(),a())))}function f(){var r,e,i,n,o,t,s=C.limit-C.cursor;if(C.ket=C.cursor,r=C.find_among_b(h,5))switch(C.bra=C.cursor,r){case 1:u()&&C.slice_from("heid");break;case 2:m();break;case 3:u()&&C.out_grouping_b(j,97,232)&&C.slice_del()}if(C.cursor=C.limit-s,l(),C.cursor=C.limit-s,C.ket=C.cursor,C.eq_s_b(4,"heid")&&(C.bra=C.cursor,c()&&(e=C.limit-C.cursor,C.eq_s_b(1,"c")||(C.cursor=C.limit-e,C.slice_del(),C.ket=C.cursor,C.eq_s_b(2,"en")&&(C.bra=C.cursor,m())))),C.cursor=C.limit-s,C.ket=C.cursor,r=C.find_among_b(k,6))switch(C.bra=C.cursor,r){case 1:if(c()){if(C.slice_del(),i=C.limit-C.cursor,C.ket=C.cursor,C.eq_s_b(2,"ig")&&(C.bra=C.cursor,c()&&(n=C.limit-C.cursor,!C.eq_s_b(1,"e")))){C.cursor=C.limit-n,C.slice_del();break}C.cursor=C.limit-i,a()}break;case 2:c()&&(o=C.limit-C.cursor,C.eq_s_b(1,"e")||(C.cursor=C.limit-o,C.slice_del()));break;case 3:c()&&(C.slice_del(),l());break;case 4:c()&&C.slice_del();break;case 5:c()&&w&&C.slice_del()}C.cursor=C.limit-s,C.out_grouping_b(z,73,232)&&(t=C.limit-C.cursor,C.find_among_b(v,4)&&C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-t,C.ket=C.cursor,C.cursor>C.limit_backward&&(C.cursor--,C.bra=C.cursor,C.slice_del())))}var d,_,w,b=[new e("",-1,6),new e("á",0,1),new e("ä",0,1),new e("é",0,2),new e("ë",0,2),new e("í",0,3),new e("ï",0,3),new e("ó",0,4),new e("ö",0,4),new e("ú",0,5),new e("ü",0,5)],p=[new e("",-1,3),new e("I",0,2),new e("Y",0,1)],g=[new e("dd",-1,-1),new e("kk",-1,-1),new e("tt",-1,-1)],h=[new e("ene",-1,2),new e("se",-1,3),new e("en",-1,2),new e("heden",2,1),new e("s",-1,3)],k=[new e("end",-1,1),new e("ig",-1,2),new e("ing",-1,1),new e("lijk",-1,3),new e("baar",-1,4),new e("bar",-1,5)],v=[new e("aa",-1,-1),new e("ee",-1,-1),new e("oo",-1,-1),new e("uu",-1,-1)],q=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],z=[1,0,0,17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],j=[17,67,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],C=new i;this.setCurrent=function(r){C.setCurrent(r)},this.getCurrent=function(){return C.getCurrent()},this.stem=function(){var e=C.cursor;return r(),C.cursor=e,o(),C.limit_backward=e,C.cursor=C.limit,f(),C.cursor=C.limit_backward,s(),!0}};return function(r){return"function"==typeof r.update?r.update(function(r){return n.setCurrent(r),n.stem(),n.getCurrent()}):(n.setCurrent(r),n.stem(),n.getCurrent())}}(),r.Pipeline.registerFunction(r.nl.stemmer,"stemmer-nl"),r.nl.stopWordFilter=r.generateStopWordFilter(" aan al alles als altijd andere ben bij daar dan dat de der deze die dit doch doen door dus een eens en er ge geen geweest haar had heb hebben heeft hem het hier hij hoe hun iemand iets ik in is ja je kan kon kunnen maar me meer men met mij mijn moet na naar niet niets nog nu of om omdat onder ons ook op over reeds te tegen toch toen tot u uit uw van veel voor want waren was wat werd wezen wie wil worden wordt zal ze zelf zich zij zijn zo zonder zou".split(" ")),r.Pipeline.registerFunction(r.nl.stopWordFilter,"stopWordFilter-nl")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.no.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.no.min.js
new file mode 100644
index 0000000..92bc7e4
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.no.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Norwegian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.no=function(){this.pipeline.reset(),this.pipeline.add(e.no.trimmer,e.no.stopWordFilter,e.no.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.no.stemmer))},e.no.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.no.trimmer=e.trimmerSupport.generateTrimmer(e.no.wordCharacters),e.Pipeline.registerFunction(e.no.trimmer,"trimmer-no"),e.no.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,i=new function(){function e(){var e,r=w.cursor+3;if(a=w.limit,0<=r||r<=w.limit){for(s=r;;){if(e=w.cursor,w.in_grouping(d,97,248)){w.cursor=e;break}if(e>=w.limit)return;w.cursor=e+1}for(;!w.out_grouping(d,97,248);){if(w.cursor>=w.limit)return;w.cursor++}a=w.cursor,a<s&&(a=s)}}function i(){var e,r,n;if(w.cursor>=a&&(r=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,e=w.find_among_b(m,29),w.limit_backward=r,e))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:n=w.limit-w.cursor,w.in_grouping_b(c,98,122)?w.slice_del():(w.cursor=w.limit-n,w.eq_s_b(1,"k")&&w.out_grouping_b(d,97,248)&&w.slice_del());break;case 3:w.slice_from("er")}}function t(){var e,r=w.limit-w.cursor;w.cursor>=a&&(e=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,w.find_among_b(u,2)?(w.bra=w.cursor,w.limit_backward=e,w.cursor=w.limit-r,w.cursor>w.limit_backward&&(w.cursor--,w.bra=w.cursor,w.slice_del())):w.limit_backward=e)}function o(){var e,r;w.cursor>=a&&(r=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,e=w.find_among_b(l,11),e?(w.bra=w.cursor,w.limit_backward=r,1==e&&w.slice_del()):w.limit_backward=r)}var s,a,m=[new r("a",-1,1),new r("e",-1,1),new r("ede",1,1),new r("ande",1,1),new r("ende",1,1),new r("ane",1,1),new r("ene",1,1),new r("hetene",6,1),new r("erte",1,3),new r("en",-1,1),new r("heten",9,1),new r("ar",-1,1),new r("er",-1,1),new r("heter",12,1),new r("s",-1,2),new r("as",14,1),new r("es",14,1),new r("edes",16,1),new r("endes",16,1),new r("enes",16,1),new r("hetenes",19,1),new r("ens",14,1),new r("hetens",21,1),new r("ers",14,1),new r("ets",14,1),new r("et",-1,1),new r("het",25,1),new r("ert",-1,3),new r("ast",-1,1)],u=[new r("dt",-1,-1),new r("vt",-1,-1)],l=[new r("leg",-1,1),new r("eleg",0,1),new r("ig",-1,1),new r("eig",2,1),new r("lig",2,1),new r("elig",4,1),new r("els",-1,1),new r("lov",-1,1),new r("elov",7,1),new r("slov",7,1),new r("hetslov",9,1)],d=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,48,0,128],c=[119,125,149,1],w=new n;this.setCurrent=function(e){w.setCurrent(e)},this.getCurrent=function(){return w.getCurrent()},this.stem=function(){var r=w.cursor;return e(),w.limit_backward=r,w.cursor=w.limit,i(),w.cursor=w.limit,t(),w.cursor=w.limit,o(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return i.setCurrent(e),i.stem(),i.getCurrent()}):(i.setCurrent(e),i.stem(),i.getCurrent())}}(),e.Pipeline.registerFunction(e.no.stemmer,"stemmer-no"),e.no.stopWordFilter=e.generateStopWordFilter("alle at av bare begge ble blei bli blir blitt både båe da de deg dei deim deira deires dem den denne der dere deres det dette di din disse ditt du dykk dykkar då eg ein eit eitt eller elles en enn er et ett etter for fordi fra før ha hadde han hans har hennar henne hennes her hjå ho hoe honom hoss hossen hun hva hvem hver hvilke hvilken hvis hvor hvordan hvorfor i ikke ikkje ikkje ingen ingi inkje inn inni ja jeg kan kom korleis korso kun kunne kva kvar kvarhelst kven kvi kvifor man mange me med medan meg meget mellom men mi min mine mitt mot mykje ned no noe noen noka noko nokon nokor nokre nå når og også om opp oss over på samme seg selv si si sia sidan siden sin sine sitt sjøl skal skulle slik so som som somme somt så sånn til um upp ut uten var vart varte ved vere verte vi vil ville vore vors vort vår være være vært å".split(" ")),e.Pipeline.registerFunction(e.no.stopWordFilter,"stopWordFilter-no")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.pt.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.pt.min.js
new file mode 100644
index 0000000..6c16996
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.pt.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Portuguese` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.ro.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.ro.min.js
new file mode 100644
index 0000000..7277140
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.ro.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Romanian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,i){"function"==typeof define&&define.amd?define(i):"object"==typeof exports?module.exports=i():i()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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dă ea ei el ele eram este eu eşti face fata fi fie fiecare fii fim fiu fiţi frumos fără graţie halbă iar ieri la le li lor lui lângă lîngă mai mea mei mele mereu meu mi mie mine mult multă mulţi mulţumesc mâine mîine mă ne nevoie nici nicăieri nimeni nimeri nimic nişte noastre noastră noi noroc nostru nouă noştri nu opt ori oricare orice oricine oricum oricând oricât oricînd oricît oriunde patra patru patrulea pe pentru peste pic poate pot prea prima primul prin puţin puţina puţină până pînă rog sa sale sau se spate spre sub sunt suntem sunteţi sută sînt sîntem sînteţi să săi său ta tale te timp tine toate toată tot totuşi toţi trei treia treilea tu tăi tău un una unde undeva unei uneia unele uneori unii unor unora unu unui unuia unul vi voastre voastră voi vostru vouă voştri vreme vreo vreun vă zece zero zi zice îi îl îmi împotriva în  înainte înaintea încotro încât încît între întrucât întrucît îţi ăla ălea ăsta ăstea ăştia şapte şase şi ştiu ţi ţie".split(" 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\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.ru.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.ru.min.js
new file mode 100644
index 0000000..186cc48
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.ru.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Russian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,n){"function"==typeof define&&define.amd?define(n):"object"==typeof exports?module.exports=n():n()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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n("ость",-1,1)],q=[new n("ейше",-1,1),new n("н",-1,2),new n("ейш",-1,1),new n("ь",-1,3)],S=[33,65,8,232],W=new r;this.setCurrent=function(e){W.setCurrent(e)},this.getCurrent=function(){return W.getCurrent()},this.stem=function(){return w(),W.cursor=W.limit,!(W.cursor<b)&&(W.limit_backward=b,o()||(W.cursor=W.limit,f()||(W.cursor=W.limit),m()||(W.cursor=W.limit,l()||(W.cursor=W.limit,a()))),W.cursor=W.limit,W.ket=W.cursor,W.eq_s_b(1,"и")?(W.bra=W.cursor,W.slice_del()):W.cursor=W.limit,p(),W.cursor=W.limit,d(),!0)}};return function(e){return"function"==typeof e.update?e.update(function(e){return t.setCurrent(e),t.stem(),t.getCurrent()}):(t.setCurrent(e),t.stem(),t.getCurrent())}}(),e.Pipeline.registerFunction(e.ru.stemmer,"stemmer-ru"),e.ru.stopWordFilter=e.generateStopWordFilter("алло без близко более больше будем будет будете будешь будто буду будут будь бы бывает бывь был была были было быть в важная важное важные важный вам вами вас ваш ваша ваше ваши вверх вдали вдруг ведь везде весь вниз внизу во вокруг вон восемнадцатый восемнадцать восемь восьмой вот впрочем времени время все всегда всего всем всеми всему всех всею всю всюду вся всё второй вы г где говорил говорит год года году да давно даже далеко дальше даром два двадцатый двадцать две двенадцатый двенадцать двух девятнадцатый девятнадцать девятый девять действительно дел день десятый десять для до довольно долго должно другая другие других друго другое другой е его ее ей ему если есть еще ещё ею её ж же жизнь за занят занята занято заняты затем зато зачем здесь значит и из или им именно иметь ими имя иногда их к каждая каждое каждые каждый кажется как какая какой кем когда кого ком кому конечно которая которого которой которые который которых кроме кругом кто куда лет ли лишь лучше люди м мало между меля менее меньше меня миллионов мимо мира мне много многочисленная многочисленное многочисленные многочисленный мной мною мог могут мож может можно можхо мои мой мор мочь моя моё мы на наверху над надо назад наиболее наконец нам нами нас начала наш наша наше наши не него недавно недалеко нее ней нельзя нем немного нему непрерывно нередко несколько нет нею неё ни нибудь ниже низко никогда никуда ними них ничего но ну нужно нх о об оба обычно один одиннадцатый одиннадцать однажды однако одного одной около он она они оно опять особенно от отовсюду отсюда очень первый перед по под пожалуйста позже пока пор пора после посреди потом потому почему почти прекрасно при про просто против процентов пятнадцатый пятнадцать пятый пять раз разве рано раньше рядом с сам сама сами самим самими самих само самого самой самом самому саму свое своего своей свои своих свою сеаой себе себя сегодня седьмой сейчас семнадцатый семнадцать семь сих сказал сказала сказать сколько слишком сначала снова со собой собою совсем спасибо стал суть т та так такая также такие такое такой там твой твоя твоё те тебе тебя тем теми теперь тех то тобой тобою тогда того тоже только том тому тот тою третий три тринадцатый тринадцать ту туда тут ты тысяч у уж уже уметь хорошо хотеть хоть хотя хочешь часто чаще чего человек чем чему через четвертый четыре четырнадцатый четырнадцать что чтоб чтобы чуть шестнадцатый шестнадцать шестой шесть эта эти этим этими этих это этого этой этом этому этот эту я \ufeffа".split(" ")),e.Pipeline.registerFunction(e.ru.stopWordFilter,"stopWordFilter-ru")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.sa.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.sa.min.js
new file mode 100644
index 0000000..50ee564
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.sa.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.sa=function(){this.pipeline.reset(),this.pipeline.add(e.sa.trimmer,e.sa.stopWordFilter,e.sa.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.sa.stemmer))},e.sa.wordCharacters="ऀ-ःऄ-एऐ-टठ-यर-िी-ॏॐ-य़ॠ-९॰-ॿ꣠-꣱ꣲ-ꣷ꣸-ꣻ꣼-ꣽꣾ-ꣿᆰ0-ᆰ9",e.sa.trimmer=e.trimmerSupport.generateTrimmer(e.sa.wordCharacters),e.Pipeline.registerFunction(e.sa.trimmer,"trimmer-sa"),e.sa.stopWordFilter=e.generateStopWordFilter('तथा अयम्‌ एकम्‌ इत्यस्मिन्‌ तथा तत्‌ वा अयम्‌ इत्यस्य ते आहूत उपरि तेषाम्‌  किन्तु तेषाम्‌ तदा इत्यनेन अधिकः इत्यस्य तत्‌ केचन बहवः द्वि तथा महत्वपूर्णः अयम्‌ अस्य  विषये अयं अस्ति तत्‌ प्रथमः विषये इत्युपरि इत्युपरि इतर अधिकतमः अधिकः अपि सामान्यतया ठ इतरेतर नूतनम्‌ द  न्यूनम्‌ कश्चित्‌ वा विशालः द  सः अस्ति तदनुसारम् तत्र अस्ति केवलम्‌ अपि अत्र सर्वे विविधाः तत्‌ बहवः यतः इदानीम्‌ द  दक्षिण इत्यस्मै तस्य उपरि नथ अतीव कार्यम्‌ सर्वे एकैकम्‌ इत्यादि। एते सन्ति  उत इत्थम्‌ मध्ये एतदर्थं . स कस्य प्रथमः श्री. करोति अस्मिन् प्रकारः निर्मिता कालः तत्र कर्तुं  समान अधुना ते सन्ति स एकः अस्ति सः अर्थात् तेषां कृते . स्थितम्  विशेषः अग्रिम तेषाम्‌ समान स्रोतः ख म समान इदानीमपि अधिकतया करोतु ते समान इत्यस्य वीथी सह यस्मिन्  कृतवान्‌ धृतः तदा पुनः पूर्वं सः आगतः किम्‌ कुल इतर पुरा  मात्रा स विषये उ अतएव अपि नगरस्य  उपरि यतः प्रतिशतं  कतरः कालः साधनानि भूत तथापि जात सम्बन्धि अन्यत्‌ ग अतः अस्माकं स्वकीयाः अस्माकं इदानीं अन्तः इत्यादयः भवन्तः इत्यादयः एते एताः तस्य अस्य इदम् एते तेषां तेषां तेषां तान् तेषां तेषां तेषां समानः सः एकः च तादृशाः बहवः अन्ये च वदन्ति यत् कियत् कस्मै  कस्मै  यस्मै  यस्मै  यस्मै  यस्मै न अतिनीचः किन्तु प्रथमं सम्पूर्णतया  ततः चिरकालानन्तरं पुस्तकं सम्पूर्णतया अन्तः  किन्तु अत्र वा इह इव श्रद्धाय अवशिष्यते  परन्तु अन्ये वर्गाः सन्ति ते सन्ति शक्नुवन्ति सर्वे मिलित्वा सर्वे एकत्र"'.split(" ")),e.sa.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.sa.tokenizer=function(t){if(!arguments.length||null==t||void 0==t)return[];if(Array.isArray(t))return t.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var i=t.toString().toLowerCase().replace(/^\s+/,"");return r.cut(i).split("|")},e.Pipeline.registerFunction(e.sa.stemmer,"stemmer-sa"),e.Pipeline.registerFunction(e.sa.stopWordFilter,"stopWordFilter-sa")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.stemmer.support.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.stemmer.support.min.js
new file mode 100644
index 0000000..abd4475
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.stemmer.support.min.js
@@ -0,0 +1 @@
+!function(r,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(r.lunr)}(this,function(){return function(r){r.stemmerSupport={Among:function(r,t,i,s){if(this.toCharArray=function(r){for(var t=r.length,i=new Array(t),s=0;s<t;s++)i[s]=r.charCodeAt(s);return i},!r&&""!=r||!t&&0!=t||!i)throw"Bad Among initialisation: s:"+r+", substring_i: "+t+", result: "+i;this.s_size=r.length,this.s=this.toCharArray(r),this.substring_i=t,this.result=i,this.method=s},SnowballProgram:function(){var r;return{bra:0,ket:0,limit:0,cursor:0,limit_backward:0,setCurrent:function(t){r=t,this.cursor=0,this.limit=t.length,this.limit_backward=0,this.bra=this.cursor,this.ket=this.limit},getCurrent:function(){var t=r;return r=null,t},in_grouping:function(t,i,s){if(this.cursor<this.limit){var e=r.charCodeAt(this.cursor);if(e<=s&&e>=i&&(e-=i,t[e>>3]&1<<(7&e)))return this.cursor++,!0}return!1},in_grouping_b:function(t,i,s){if(this.cursor>this.limit_backward){var e=r.charCodeAt(this.cursor-1);if(e<=s&&e>=i&&(e-=i,t[e>>3]&1<<(7&e)))return this.cursor--,!0}return!1},out_grouping:function(t,i,s){if(this.cursor<this.limit){var e=r.charCodeAt(this.cursor);if(e>s||e<i)return this.cursor++,!0;if(e-=i,!(t[e>>3]&1<<(7&e)))return this.cursor++,!0}return!1},out_grouping_b:function(t,i,s){if(this.cursor>this.limit_backward){var e=r.charCodeAt(this.cursor-1);if(e>s||e<i)return this.cursor--,!0;if(e-=i,!(t[e>>3]&1<<(7&e)))return this.cursor--,!0}return!1},eq_s:function(t,i){if(this.limit-this.cursor<t)return!1;for(var s=0;s<t;s++)if(r.charCodeAt(this.cursor+s)!=i.charCodeAt(s))return!1;return this.cursor+=t,!0},eq_s_b:function(t,i){if(this.cursor-this.limit_backward<t)return!1;for(var s=0;s<t;s++)if(r.charCodeAt(this.cursor-t+s)!=i.charCodeAt(s))return!1;return this.cursor-=t,!0},find_among:function(t,i){for(var s=0,e=i,n=this.cursor,u=this.limit,o=0,h=0,c=!1;;){for(var a=s+(e-s>>1),f=0,l=o<h?o:h,_=t[a],m=l;m<_.s_size;m++){if(n+l==u){f=-1;break}if(f=r.charCodeAt(n+l)-_.s[m])break;l++}if(f<0?(e=a,h=l):(s=a,o=l),e-s<=1){if(s>0||e==s||c)break;c=!0}}for(;;){var _=t[s];if(o>=_.s_size){if(this.cursor=n+_.s_size,!_.method)return _.result;var b=_.method();if(this.cursor=n+_.s_size,b)return _.result}if((s=_.substring_i)<0)return 0}},find_among_b:function(t,i){for(var s=0,e=i,n=this.cursor,u=this.limit_backward,o=0,h=0,c=!1;;){for(var a=s+(e-s>>1),f=0,l=o<h?o:h,_=t[a],m=_.s_size-1-l;m>=0;m--){if(n-l==u){f=-1;break}if(f=r.charCodeAt(n-1-l)-_.s[m])break;l++}if(f<0?(e=a,h=l):(s=a,o=l),e-s<=1){if(s>0||e==s||c)break;c=!0}}for(;;){var _=t[s];if(o>=_.s_size){if(this.cursor=n-_.s_size,!_.method)return _.result;var b=_.method();if(this.cursor=n-_.s_size,b)return _.result}if((s=_.substring_i)<0)return 0}},replace_s:function(t,i,s){var e=s.length-(i-t),n=r.substring(0,t),u=r.substring(i);return r=n+s+u,this.limit+=e,this.cursor>=i?this.cursor+=e:this.cursor>t&&(this.cursor=t),e},slice_check:function(){if(this.bra<0||this.bra>this.ket||this.ket>this.limit||this.limit>r.length)throw"faulty slice operation"},slice_from:function(r){this.slice_check(),this.replace_s(this.bra,this.ket,r)},slice_del:function(){this.slice_from("")},insert:function(r,t,i){var s=this.replace_s(r,t,i);r<=this.bra&&(this.bra+=s),r<=this.ket&&(this.ket+=s)},slice_to:function(){return this.slice_check(),r.substring(this.bra,this.ket)},eq_v_b:function(r){return this.eq_s_b(r.length,r)}}}},r.trimmerSupport={generateTrimmer:function(r){var t=new RegExp("^[^"+r+"]+"),i=new RegExp("[^"+r+"]+$");return function(r){return"function"==typeof r.update?r.update(function(r){return r.replace(t,"").replace(i,"")}):r.replace(t,"").replace(i,"")}}}}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.sv.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.sv.min.js
new file mode 100644
index 0000000..3e5eb64
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.sv.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Swedish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.sv=function(){this.pipeline.reset(),this.pipeline.add(e.sv.trimmer,e.sv.stopWordFilter,e.sv.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.sv.stemmer))},e.sv.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.sv.trimmer=e.trimmerSupport.generateTrimmer(e.sv.wordCharacters),e.Pipeline.registerFunction(e.sv.trimmer,"trimmer-sv"),e.sv.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,t=new function(){function e(){var e,r=w.cursor+3;if(o=w.limit,0<=r||r<=w.limit){for(a=r;;){if(e=w.cursor,w.in_grouping(l,97,246)){w.cursor=e;break}if(w.cursor=e,w.cursor>=w.limit)return;w.cursor++}for(;!w.out_grouping(l,97,246);){if(w.cursor>=w.limit)return;w.cursor++}o=w.cursor,o<a&&(o=a)}}function t(){var e,r=w.limit_backward;if(w.cursor>=o&&(w.limit_backward=o,w.cursor=w.limit,w.ket=w.cursor,e=w.find_among_b(u,37),w.limit_backward=r,e))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:w.in_grouping_b(d,98,121)&&w.slice_del()}}function i(){var e=w.limit_backward;w.cursor>=o&&(w.limit_backward=o,w.cursor=w.limit,w.find_among_b(c,7)&&(w.cursor=w.limit,w.ket=w.cursor,w.cursor>w.limit_backward&&(w.bra=--w.cursor,w.slice_del())),w.limit_backward=e)}function s(){var e,r;if(w.cursor>=o){if(r=w.limit_backward,w.limit_backward=o,w.cursor=w.limit,w.ket=w.cursor,e=w.find_among_b(m,5))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:w.slice_from("lös");break;case 3:w.slice_from("full")}w.limit_backward=r}}var a,o,u=[new r("a",-1,1),new r("arna",0,1),new r("erna",0,1),new r("heterna",2,1),new r("orna",0,1),new r("ad",-1,1),new r("e",-1,1),new r("ade",6,1),new r("ande",6,1),new r("arne",6,1),new r("are",6,1),new r("aste",6,1),new r("en",-1,1),new r("anden",12,1),new r("aren",12,1),new r("heten",12,1),new r("ern",-1,1),new r("ar",-1,1),new r("er",-1,1),new r("heter",18,1),new r("or",-1,1),new r("s",-1,2),new r("as",21,1),new r("arnas",22,1),new r("ernas",22,1),new r("ornas",22,1),new r("es",21,1),new r("ades",26,1),new r("andes",26,1),new r("ens",21,1),new r("arens",29,1),new r("hetens",29,1),new r("erns",21,1),new r("at",-1,1),new r("andet",-1,1),new r("het",-1,1),new r("ast",-1,1)],c=[new r("dd",-1,-1),new r("gd",-1,-1),new r("nn",-1,-1),new r("dt",-1,-1),new r("gt",-1,-1),new r("kt",-1,-1),new r("tt",-1,-1)],m=[new r("ig",-1,1),new r("lig",0,1),new r("els",-1,1),new r("fullt",-1,3),new r("löst",-1,2)],l=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,24,0,32],d=[119,127,149],w=new n;this.setCurrent=function(e){w.setCurrent(e)},this.getCurrent=function(){return w.getCurrent()},this.stem=function(){var r=w.cursor;return e(),w.limit_backward=r,w.cursor=w.limit,t(),w.cursor=w.limit,i(),w.cursor=w.limit,s(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return t.setCurrent(e),t.stem(),t.getCurrent()}):(t.setCurrent(e),t.stem(),t.getCurrent())}}(),e.Pipeline.registerFunction(e.sv.stemmer,"stemmer-sv"),e.sv.stopWordFilter=e.generateStopWordFilter("alla allt att av blev bli blir blivit de dem den denna deras dess dessa det detta dig din dina ditt du där då efter ej eller en er era ert ett från för ha hade han hans har henne hennes hon honom hur här i icke ingen inom inte jag ju kan kunde man med mellan men mig min mina mitt mot mycket ni nu när någon något några och om oss på samma sedan sig sin sina sitta själv skulle som så sådan sådana sådant till under upp ut utan vad var vara varför varit varje vars vart vem vi vid vilka vilkas vilken vilket vår våra vårt än är åt över".split(" ")),e.Pipeline.registerFunction(e.sv.stopWordFilter,"stopWordFilter-sv")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.ta.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.ta.min.js
new file mode 100644
index 0000000..a644bed
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.ta.min.js
@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.ta=function(){this.pipeline.reset(),this.pipeline.add(e.ta.trimmer,e.ta.stopWordFilter,e.ta.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.ta.stemmer))},e.ta.wordCharacters="஀-உஊ-ஏஐ-ஙச-ட஠-னப-யர-ஹ஺-ிீ-௉ொ-௏ௐ-௙௚-௟௠-௩௪-௯௰-௹௺-௿a-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.ta.trimmer=e.trimmerSupport.generateTrimmer(e.ta.wordCharacters),e.Pipeline.registerFunction(e.ta.trimmer,"trimmer-ta"),e.ta.stopWordFilter=e.generateStopWordFilter("அங்கு அங்கே அது அதை அந்த அவர் அவர்கள் அவள் அவன் அவை ஆக ஆகவே ஆகையால் ஆதலால் ஆதலினால் ஆனாலும் ஆனால் இங்கு இங்கே இது இதை இந்த இப்படி இவர் இவர்கள் இவள் இவன் இவை இவ்வளவு உனக்கு உனது உன் உன்னால் எங்கு எங்கே எது எதை எந்த எப்படி எவர் எவர்கள் எவள் எவன் எவை எவ்வளவு எனக்கு எனது எனவே என் என்ன என்னால் ஏது ஏன் தனது தன்னால் தானே தான் நாங்கள் நாம் நான் நீ நீங்கள்".split(" ")),e.ta.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var t=e.wordcut;t.init(),e.ta.tokenizer=function(r){if(!arguments.length||null==r||void 0==r)return[];if(Array.isArray(r))return r.map(function(t){return isLunr2?new e.Token(t.toLowerCase()):t.toLowerCase()});var i=r.toString().toLowerCase().replace(/^\s+/,"");return t.cut(i).split("|")},e.Pipeline.registerFunction(e.ta.stemmer,"stemmer-ta"),e.Pipeline.registerFunction(e.ta.stopWordFilter,"stopWordFilter-ta")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.te.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.te.min.js
new file mode 100644
index 0000000..9fa7a93
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.te.min.js
@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.te=function(){this.pipeline.reset(),this.pipeline.add(e.te.trimmer,e.te.stopWordFilter,e.te.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.te.stemmer))},e.te.wordCharacters="ఀ-ఄఅ-ఔక-హా-ౌౕ-ౖౘ-ౚౠ-ౡౢ-ౣ౦-౯౸-౿఼ఽ్ౝ౷౤౥",e.te.trimmer=e.trimmerSupport.generateTrimmer(e.te.wordCharacters),e.Pipeline.registerFunction(e.te.trimmer,"trimmer-te"),e.te.stopWordFilter=e.generateStopWordFilter("అందరూ అందుబాటులో అడగండి అడగడం అడ్డంగా అనుగుణంగా అనుమతించు అనుమతిస్తుంది అయితే ఇప్పటికే ఉన్నారు ఎక్కడైనా ఎప్పుడు ఎవరైనా ఎవరో ఏ ఏదైనా ఏమైనప్పటికి ఒక ఒకరు కనిపిస్తాయి కాదు కూడా గా గురించి చుట్టూ చేయగలిగింది తగిన తర్వాత దాదాపు దూరంగా నిజంగా పై ప్రకారం ప్రక్కన మధ్య మరియు మరొక మళ్ళీ మాత్రమే మెచ్చుకో వద్ద వెంట వేరుగా వ్యతిరేకంగా సంబంధం".split(" ")),e.te.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var t=e.wordcut;t.init(),e.te.tokenizer=function(r){if(!arguments.length||null==r||void 0==r)return[];if(Array.isArray(r))return r.map(function(t){return isLunr2?new e.Token(t.toLowerCase()):t.toLowerCase()});var i=r.toString().toLowerCase().replace(/^\s+/,"");return t.cut(i).split("|")},e.Pipeline.registerFunction(e.te.stemmer,"stemmer-te"),e.Pipeline.registerFunction(e.te.stopWordFilter,"stopWordFilter-te")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.th.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.th.min.js
new file mode 100644
index 0000000..dee3aac
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.th.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var r="2"==e.version[0];e.th=function(){this.pipeline.reset(),this.pipeline.add(e.th.trimmer),r?this.tokenizer=e.th.tokenizer:(e.tokenizer&&(e.tokenizer=e.th.tokenizer),this.tokenizerFn&&(this.tokenizerFn=e.th.tokenizer))},e.th.wordCharacters="[฀-๿]",e.th.trimmer=e.trimmerSupport.generateTrimmer(e.th.wordCharacters),e.Pipeline.registerFunction(e.th.trimmer,"trimmer-th");var t=e.wordcut;t.init(),e.th.tokenizer=function(i){if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(t){return r?new e.Token(t):t});var n=i.toString().replace(/^\s+/,"");return t.cut(n).split("|")}}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.tr.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.tr.min.js
new file mode 100644
index 0000000..563f6ec
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.tr.min.js
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Turkish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(r,i){"function"==typeof define&&define.amd?define(i):"object"==typeof exports?module.exports=i():i()(r.lunr)}(this,function(){return function(r){if(void 0===r)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===r.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");r.tr=function(){this.pipeline.reset(),this.pipeline.add(r.tr.trimmer,r.tr.stopWordFilter,r.tr.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(r.tr.stemmer))},r.tr.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",r.tr.trimmer=r.trimmerSupport.generateTrimmer(r.tr.wordCharacters),r.Pipeline.registerFunction(r.tr.trimmer,"trimmer-tr"),r.tr.stemmer=function(){var i=r.stemmerSupport.Among,e=r.stemmerSupport.SnowballProgram,n=new function(){function r(r,i,e){for(;;){var n=Dr.limit-Dr.cursor;if(Dr.in_grouping_b(r,i,e)){Dr.cursor=Dr.limit-n;break}if(Dr.cursor=Dr.limit-n,Dr.cursor<=Dr.limit_backward)return!1;Dr.cursor--}return!0}function n(){var i,e;i=Dr.limit-Dr.cursor,r(Wr,97,305);for(var n=0;n<Br.length;n++){e=Dr.limit-Dr.cursor;var t=Br[n];if(Dr.eq_s_b(1,t[0])&&r(t[1],t[2],t[3]))return Dr.cursor=Dr.limit-i,!0;Dr.cursor=Dr.limit-e}return Dr.cursor=Dr.limit-e,!(!Dr.eq_s_b(1,"ü")||!r(Zr,246,252))&&(Dr.cursor=Dr.limit-i,!0)}function t(r,i){var e,n=Dr.limit-Dr.cursor;return r()&&(Dr.cursor=Dr.limit-n,Dr.cursor>Dr.limit_backward&&(Dr.cursor--,e=Dr.limit-Dr.cursor,i()))?(Dr.cursor=Dr.limit-e,!0):(Dr.cursor=Dr.limit-n,r()?(Dr.cursor=Dr.limit-n,!1):(Dr.cursor=Dr.limit-n,!(Dr.cursor<=Dr.limit_backward)&&(Dr.cursor--,!!i()&&(Dr.cursor=Dr.limit-n,!0))))}function u(r){return t(r,function(){return Dr.in_grouping_b(Wr,97,305)})}function o(){return u(function(){return Dr.eq_s_b(1,"n")})}function s(){return u(function(){return Dr.eq_s_b(1,"s")})}function c(){return u(function(){return Dr.eq_s_b(1,"y")})}function l(){return t(function(){return Dr.in_grouping_b(Lr,105,305)},function(){return Dr.out_grouping_b(Wr,97,305)})}function a(){return Dr.find_among_b(ur,10)&&l()}function m(){return n()&&Dr.in_grouping_b(Lr,105,305)&&s()}function d(){return Dr.find_among_b(or,2)}function f(){return n()&&Dr.in_grouping_b(Lr,105,305)&&c()}function b(){return n()&&Dr.find_among_b(sr,4)}function w(){return n()&&Dr.find_among_b(cr,4)&&o()}function _(){return n()&&Dr.find_among_b(lr,2)&&c()}function k(){return n()&&Dr.find_among_b(ar,2)}function p(){return n()&&Dr.find_among_b(mr,4)}function g(){return n()&&Dr.find_among_b(dr,2)}function y(){return n()&&Dr.find_among_b(fr,4)}function z(){return n()&&Dr.find_among_b(br,2)}function v(){return n()&&Dr.find_among_b(wr,2)&&c()}function h(){return Dr.eq_s_b(2,"ki")}function q(){return n()&&Dr.find_among_b(_r,2)&&o()}function C(){return n()&&Dr.find_among_b(kr,4)&&c()}function P(){return n()&&Dr.find_among_b(pr,4)}function F(){return n()&&Dr.find_among_b(gr,4)&&c()}function S(){return Dr.find_among_b(yr,4)}function W(){return n()&&Dr.find_among_b(zr,2)}function L(){return n()&&Dr.find_among_b(vr,4)}function x(){return n()&&Dr.find_among_b(hr,8)}function A(){return Dr.find_among_b(qr,2)}function E(){return n()&&Dr.find_among_b(Cr,32)&&c()}function j(){return Dr.find_among_b(Pr,8)&&c()}function T(){return n()&&Dr.find_among_b(Fr,4)&&c()}function Z(){return Dr.eq_s_b(3,"ken")&&c()}function B(){var r=Dr.limit-Dr.cursor;return!(T()||(Dr.cursor=Dr.limit-r,E()||(Dr.cursor=Dr.limit-r,j()||(Dr.cursor=Dr.limit-r,Z()))))}function D(){if(A()){var r=Dr.limit-Dr.cursor;if(S()||(Dr.cursor=Dr.limit-r,W()||(Dr.cursor=Dr.limit-r,C()||(Dr.cursor=Dr.limit-r,P()||(Dr.cursor=Dr.limit-r,F()||(Dr.cursor=Dr.limit-r))))),T())return!1}return!0}function G(){if(W()){Dr.bra=Dr.cursor,Dr.slice_del();var r=Dr.limit-Dr.cursor;return Dr.ket=Dr.cursor,x()||(Dr.cursor=Dr.limit-r,E()||(Dr.cursor=Dr.limit-r,j()||(Dr.cursor=Dr.limit-r,T()||(Dr.cursor=Dr.limit-r)))),nr=!1,!1}return!0}function H(){if(!L())return!0;var r=Dr.limit-Dr.cursor;return!E()&&(Dr.cursor=Dr.limit-r,!j())}function I(){var 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Dr.bra=Dr.cursor,Dr.slice_del(),i=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,W()?(Dr.bra=Dr.cursor,Dr.slice_del(),K()):(Dr.cursor=Dr.limit-i,a()&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()))),!0;if(Dr.cursor=Dr.limit-r,w()){if(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,e=Dr.limit-Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else{if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,!a()&&(Dr.cursor=Dr.limit-e,!m()&&(Dr.cursor=Dr.limit-e,!K())))return!0;Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())}return!0}if(Dr.cursor=Dr.limit-r,g()){if(n=Dr.limit-Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else if(Dr.cursor=Dr.limit-n,m())Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K());else if(Dr.cursor=Dr.limit-n,!K())return!1;return!0}}return!1}function M(r){if(Dr.ket=Dr.cursor,!g()&&(Dr.cursor=Dr.limit-r,!k()))return!1;var i=Dr.limit-Dr.cursor;if(d())Dr.bra=Dr.cursor,Dr.slice_del();else if(Dr.cursor=Dr.limit-i,m())Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K());else if(Dr.cursor=Dr.limit-i,!K())return!1;return!0}function N(r){if(Dr.ket=Dr.cursor,!z()&&(Dr.cursor=Dr.limit-r,!b()))return!1;var i=Dr.limit-Dr.cursor;return!(!m()&&(Dr.cursor=Dr.limit-i,!d()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()),!0)}function O(){var r,i=Dr.limit-Dr.cursor;return Dr.ket=Dr.cursor,!(!w()&&(Dr.cursor=Dr.limit-i,!v()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),r=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,!(!W()||(Dr.bra=Dr.cursor,Dr.slice_del(),!K()))||(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!(a()||(Dr.cursor=Dr.limit-r,m()||(Dr.cursor=Dr.limit-r,K())))||(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()),!0)))}function Q(){var r,i,e=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,!p()&&(Dr.cursor=Dr.limit-e,!f()&&(Dr.cursor=Dr.limit-e,!_())))return!1;if(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,r=Dr.limit-Dr.cursor,a())Dr.bra=Dr.cursor,Dr.slice_del(),i=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,W()||(Dr.cursor=Dr.limit-i);else if(Dr.cursor=Dr.limit-r,!W())return!0;return Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,K(),!0}function R(){var r,i,e=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,W())return Dr.bra=Dr.cursor,Dr.slice_del(),void K();if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,q())if(Dr.bra=Dr.cursor,Dr.slice_del(),r=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else{if(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!a()&&(Dr.cursor=Dr.limit-r,!m())){if(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!W())return;if(Dr.bra=Dr.cursor,Dr.slice_del(),!K())return}Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())}else if(Dr.cursor=Dr.limit-e,!M(e)&&(Dr.cursor=Dr.limit-e,!N(e))){if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,y())return Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,i=Dr.limit-Dr.cursor,void(a()?(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())):(Dr.cursor=Dr.limit-i,W()?(Dr.bra=Dr.cursor,Dr.slice_del(),K()):(Dr.cursor=Dr.limit-i,K())));if(Dr.cursor=Dr.limit-e,!O()){if(Dr.cursor=Dr.limit-e,d())return Dr.bra=Dr.cursor,void Dr.slice_del();Dr.cursor=Dr.limit-e,K()||(Dr.cursor=Dr.limit-e,Q()||(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,(a()||(Dr.cursor=Dr.limit-e,m()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()))))}}}function U(){var r;if(Dr.ket=Dr.cursor,r=Dr.find_among_b(Sr,4))switch(Dr.bra=Dr.cursor,r){case 1:Dr.slice_from("p");break;case 2:Dr.slice_from("ç");break;case 3:Dr.slice_from("t");break;case 4:Dr.slice_from("k")}}function V(){for(;;){var r=Dr.limit-Dr.cursor;if(Dr.in_grouping_b(Wr,97,305)){Dr.cursor=Dr.limit-r;break}if(Dr.cursor=Dr.limit-r,Dr.cursor<=Dr.limit_backward)return!1;Dr.cursor--}return!0}function X(r,i,e){if(Dr.cursor=Dr.limit-r,V()){var n=Dr.limit-Dr.cursor;if(!Dr.eq_s_b(1,i)&&(Dr.cursor=Dr.limit-n,!Dr.eq_s_b(1,e)))return!0;Dr.cursor=Dr.limit-r;var t=Dr.cursor;return Dr.insert(Dr.cursor,Dr.cursor,e),Dr.cursor=t,!1}return!0}function Y(){var r=Dr.limit-Dr.cursor;(Dr.eq_s_b(1,"d")||(Dr.cursor=Dr.limit-r,Dr.eq_s_b(1,"g")))&&X(r,"a","ı")&&X(r,"e","i")&&X(r,"o","u")&&X(r,"ö","ü")}function $(){for(var r,i=Dr.cursor,e=2;;){for(r=Dr.cursor;!Dr.in_grouping(Wr,97,305);){if(Dr.cursor>=Dr.limit)return Dr.cursor=r,!(e>0)&&(Dr.cursor=i,!0);Dr.cursor++}e--}}function rr(r,i,e){for(;!Dr.eq_s(i,e);){if(Dr.cursor>=Dr.limit)return!0;Dr.cursor++}return(tr=i)!=Dr.limit||(Dr.cursor=r,!1)}function ir(){var r=Dr.cursor;return!rr(r,2,"ad")||(Dr.cursor=r,!rr(r,5,"soyad"))}function er(){var r=Dr.cursor;return!ir()&&(Dr.limit_backward=r,Dr.cursor=Dr.limit,Y(),Dr.cursor=Dr.limit,U(),!0)}var nr,tr,ur=[new i("m",-1,-1),new i("n",-1,-1),new i("miz",-1,-1),new i("niz",-1,-1),new i("muz",-1,-1),new i("nuz",-1,-1),new i("müz",-1,-1),new i("nüz",-1,-1),new i("mız",-1,-1),new i("nız",-1,-1)],or=[new i("leri",-1,-1),new i("ları",-1,-1)],sr=[new i("ni",-1,-1),new i("nu",-1,-1),new i("nü",-1,-1),new i("nı",-1,-1)],cr=[new i("in",-1,-1),new i("un",-1,-1),new i("ün",-1,-1),new i("ın",-1,-1)],lr=[new i("a",-1,-1),new i("e",-1,-1)],ar=[new i("na",-1,-1),new i("ne",-1,-1)],mr=[new i("da",-1,-1),new i("ta",-1,-1),new i("de",-1,-1),new i("te",-1,-1)],dr=[new i("nda",-1,-1),new i("nde",-1,-1)],fr=[new i("dan",-1,-1),new i("tan",-1,-1),new i("den",-1,-1),new i("ten",-1,-1)],br=[new i("ndan",-1,-1),new i("nden",-1,-1)],wr=[new i("la",-1,-1),new i("le",-1,-1)],_r=[new i("ca",-1,-1),new i("ce",-1,-1)],kr=[new i("im",-1,-1),new i("um",-1,-1),new i("üm",-1,-1),new i("ım",-1,-1)],pr=[new i("sin",-1,-1),new i("sun",-1,-1),new i("sün",-1,-1),new i("sın",-1,-1)],gr=[new i("iz",-1,-1),new i("uz",-1,-1),new i("üz",-1,-1),new i("ız",-1,-1)],yr=[new i("siniz",-1,-1),new i("sunuz",-1,-1),new i("sünüz",-1,-1),new i("sınız",-1,-1)],zr=[new i("lar",-1,-1),new i("ler",-1,-1)],vr=[new i("niz",-1,-1),new i("nuz",-1,-1),new i("nüz",-1,-1),new i("nız",-1,-1)],hr=[new i("dir",-1,-1),new i("tir",-1,-1),new i("dur",-1,-1),new i("tur",-1,-1),new i("dür",-1,-1),new i("tür",-1,-1),new i("dır",-1,-1),new i("tır",-1,-1)],qr=[new i("casına",-1,-1),new i("cesine",-1,-1)],Cr=[new i("di",-1,-1),new i("ti",-1,-1),new i("dik",-1,-1),new i("tik",-1,-1),new i("duk",-1,-1),new i("tuk",-1,-1),new i("dük",-1,-1),new i("tük",-1,-1),new i("dık",-1,-1),new i("tık",-1,-1),new i("dim",-1,-1),new i("tim",-1,-1),new i("dum",-1,-1),new i("tum",-1,-1),new i("düm",-1,-1),new i("tüm",-1,-1),new i("dım",-1,-1),new i("tım",-1,-1),new i("din",-1,-1),new i("tin",-1,-1),new i("dun",-1,-1),new i("tun",-1,-1),new i("dün",-1,-1),new i("tün",-1,-1),new i("dın",-1,-1),new i("tın",-1,-1),new i("du",-1,-1),new i("tu",-1,-1),new i("dü",-1,-1),new i("tü",-1,-1),new i("dı",-1,-1),new i("tı",-1,-1)],Pr=[new i("sa",-1,-1),new i("se",-1,-1),new i("sak",-1,-1),new i("sek",-1,-1),new i("sam",-1,-1),new i("sem",-1,-1),new i("san",-1,-1),new i("sen",-1,-1)],Fr=[new i("miş",-1,-1),new i("muş",-1,-1),new i("müş",-1,-1),new i("mış",-1,-1)],Sr=[new i("b",-1,1),new i("c",-1,2),new i("d",-1,3),new i("ğ",-1,4)],Wr=[17,65,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,32,8,0,0,0,0,0,0,1],Lr=[1,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0,0,0,0,0,0,1],xr=[1,64,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1],Ar=[17,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,130],Er=[1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1],jr=[17],Tr=[65],Zr=[65],Br=[["a",xr,97,305],["e",Ar,101,252],["ı",Er,97,305],["i",jr,101,105],["o",Tr,111,117],["ö",Zr,246,252],["u",Tr,111,117]],Dr=new e;this.setCurrent=function(r){Dr.setCurrent(r)},this.getCurrent=function(){return Dr.getCurrent()},this.stem=function(){return!!($()&&(Dr.limit_backward=Dr.cursor,Dr.cursor=Dr.limit,J(),Dr.cursor=Dr.limit,nr&&(R(),Dr.cursor=Dr.limit_backward,er())))}};return function(r){return"function"==typeof r.update?r.update(function(r){return n.setCurrent(r),n.stem(),n.getCurrent()}):(n.setCurrent(r),n.stem(),n.getCurrent())}}(),r.Pipeline.registerFunction(r.tr.stemmer,"stemmer-tr"),r.tr.stopWordFilter=r.generateStopWordFilter("acaba altmış altı ama ancak arada aslında ayrıca bana bazı belki ben benden beni benim beri beş bile bin bir biri birkaç birkez birçok birşey birşeyi biz bizden bize bizi bizim bu buna bunda bundan bunlar bunları bunların bunu bunun burada böyle böylece da daha dahi de defa değil diye diğer doksan dokuz dolayı dolayısıyla dört edecek eden ederek edilecek ediliyor edilmesi ediyor elli en etmesi etti ettiği ettiğini eğer gibi göre halen hangi hatta hem henüz hep hepsi her herhangi herkesin hiç hiçbir iki ile ilgili ise itibaren itibariyle için işte kadar karşın katrilyon kendi kendilerine kendini kendisi kendisine kendisini kez ki kim kimden kime kimi kimse kırk milyar milyon mu mü mı nasıl ne neden nedenle nerde nerede nereye niye niçin o olan olarak oldu olduklarını olduğu olduğunu olmadı olmadığı olmak olması olmayan olmaz olsa olsun olup olur olursa oluyor on ona ondan onlar onlardan onları onların onu onun otuz oysa pek rağmen sadece sanki sekiz seksen sen senden seni senin siz sizden sizi sizin tarafından trilyon tüm var vardı ve veya ya yani yapacak yapmak yaptı yaptıkları yaptığı yaptığını yapılan yapılması yapıyor yedi yerine yetmiş yine yirmi yoksa yüz zaten çok çünkü öyle üzere üç şey şeyden şeyi şeyler şu şuna şunda şundan şunları şunu şöyle".split(" ")),r.Pipeline.registerFunction(r.tr.stopWordFilter,"stopWordFilter-tr")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.vi.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.vi.min.js
new file mode 100644
index 0000000..22aed28
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.vi.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.vi=function(){this.pipeline.reset(),this.pipeline.add(e.vi.stopWordFilter,e.vi.trimmer)},e.vi.wordCharacters="[A-Za-ẓ̀͐́͑̉̃̓ÂâÊêÔôĂ-ăĐ-đƠ-ơƯ-ư]",e.vi.trimmer=e.trimmerSupport.generateTrimmer(e.vi.wordCharacters),e.Pipeline.registerFunction(e.vi.trimmer,"trimmer-vi"),e.vi.stopWordFilter=e.generateStopWordFilter("là cái nhưng mà".split(" "))}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/min/lunr.zh.min.js b/docs/htmls/assets/javascripts/lunr/min/lunr.zh.min.js
new file mode 100644
index 0000000..fda66e9
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/min/lunr.zh.min.js
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r(require("@node-rs/jieba")):r()(e.lunr)}(this,function(e){return function(r,t){if(void 0===r)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===r.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var i="2"==r.version[0];r.zh=function(){this.pipeline.reset(),this.pipeline.add(r.zh.trimmer,r.zh.stopWordFilter,r.zh.stemmer),i?this.tokenizer=r.zh.tokenizer:(r.tokenizer&&(r.tokenizer=r.zh.tokenizer),this.tokenizerFn&&(this.tokenizerFn=r.zh.tokenizer))},r.zh.tokenizer=function(n){if(!arguments.length||null==n||void 0==n)return[];if(Array.isArray(n))return n.map(function(e){return i?new r.Token(e.toLowerCase()):e.toLowerCase()});t&&e.load(t);var o=n.toString().trim().toLowerCase(),s=[];e.cut(o,!0).forEach(function(e){s=s.concat(e.split(" "))}),s=s.filter(function(e){return!!e});var u=0;return s.map(function(e,t){if(i){var n=o.indexOf(e,u),s={};return s.position=[n,e.length],s.index=t,u=n,new r.Token(e,s)}return e})},r.zh.wordCharacters="\\w一-龥",r.zh.trimmer=r.trimmerSupport.generateTrimmer(r.zh.wordCharacters),r.Pipeline.registerFunction(r.zh.trimmer,"trimmer-zh"),r.zh.stemmer=function(){return function(e){return e}}(),r.Pipeline.registerFunction(r.zh.stemmer,"stemmer-zh"),r.zh.stopWordFilter=r.generateStopWordFilter("的 一 不 在 人 有 是 为 為 以 于 於 上 他 而 后 後 之 来 來 及 了 因 下 可 到 由 这 這 与 與 也 此 但 并 並 个 個 其 已 无 無 小 我 们 們 起 最 再 今 去 好 只 又 或 很 亦 某 把 那 你 乃 它 吧 被 比 别 趁 当 當 从 從 得 打 凡 儿 兒 尔 爾 该 該 各 给 給 跟 和 何 还 還 即 几 幾 既 看 据 據 距 靠 啦 另 么 麽 每 嘛 拿 哪 您 凭 憑 且 却 卻 让 讓 仍 啥 如 若 使 谁 誰 虽 雖 随 隨 同 所 她 哇 嗡 往 些 向 沿 哟 喲 用 咱 则 則 怎 曾 至 致 着 著 诸 諸 自".split(" ")),r.Pipeline.registerFunction(r.zh.stopWordFilter,"stopWordFilter-zh")}});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/tinyseg.js b/docs/htmls/assets/javascripts/lunr/tinyseg.js
new file mode 100644
index 0000000..167fa6d
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/tinyseg.js
@@ -0,0 +1,206 @@
+/**
+ * export the module via AMD, CommonJS or as a browser global
+ * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js
+ */
+;(function (root, factory) {
+    if (typeof define === 'function' && define.amd) {
+        // AMD. Register as an anonymous module.
+        define(factory)
+    } else if (typeof exports === 'object') {
+        /**
+         * Node. Does not work with strict CommonJS, but
+         * only CommonJS-like environments that support module.exports,
+         * like Node.
+         */
+        module.exports = factory()
+    } else {
+        // Browser globals (root is window)
+        factory()(root.lunr);
+    }
+}(this, function () {
+    /**
+     * Just return a value to define the module export.
+     * This example returns an object, but the module
+     * can return a function as the exported value.
+     */
+
+    return function(lunr) {
+        // TinySegmenter 0.1 -- Super compact Japanese tokenizer in Javascript
+        // (c) 2008 Taku Kudo <taku@chasen.org>
+        // TinySegmenter is freely distributable under the terms of a new BSD licence.
+        // For details, see http://chasen.org/~taku/software/TinySegmenter/LICENCE.txt
+
+        function TinySegmenter() {
+          var patterns = {
+            "[一二三四五六七八九十百千万億兆]":"M",
+            "[一-龠々〆ヵヶ]":"H",
+            "[ぁ-ん]":"I",
+            "[ァ-ヴーｱ-ﾝﾞｰ]":"K",
+            "[a-zA-Zａ-ｚＡ-Ｚ]":"A",
+            "[0-9０-９]":"N"
+          }
+          this.chartype_ = [];
+          for (var i in patterns) {
+            var regexp = new RegExp(i);
+            this.chartype_.push([regexp, patterns[i]]);
+          }
+
+          this.BIAS__ = -332
+          this.BC1__ = {"HH":6,"II":2461,"KH":406,"OH":-1378};
+          this.BC2__ = {"AA":-3267,"AI":2744,"AN":-878,"HH":-4070,"HM":-1711,"HN":4012,"HO":3761,"IA":1327,"IH":-1184,"II":-1332,"IK":1721,"IO":5492,"KI":3831,"KK":-8741,"MH":-3132,"MK":3334,"OO":-2920};
+          this.BC3__ = {"HH":996,"HI":626,"HK":-721,"HN":-1307,"HO":-836,"IH":-301,"KK":2762,"MK":1079,"MM":4034,"OA":-1652,"OH":266};
+          this.BP1__ = {"BB":295,"OB":304,"OO":-125,"UB":352};
+          this.BP2__ = {"BO":60,"OO":-1762};
+          this.BQ1__ = {"BHH":1150,"BHM":1521,"BII":-1158,"BIM":886,"BMH":1208,"BNH":449,"BOH":-91,"BOO":-2597,"OHI":451,"OIH":-296,"OKA":1851,"OKH":-1020,"OKK":904,"OOO":2965};
+          this.BQ2__ = {"BHH":118,"BHI":-1159,"BHM":466,"BIH":-919,"BKK":-1720,"BKO":864,"OHH":-1139,"OHM":-181,"OIH":153,"UHI":-1146};
+          this.BQ3__ = {"BHH":-792,"BHI":2664,"BII":-299,"BKI":419,"BMH":937,"BMM":8335,"BNN":998,"BOH":775,"OHH":2174,"OHM":439,"OII":280,"OKH":1798,"OKI":-793,"OKO":-2242,"OMH":-2402,"OOO":11699};
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+            if (str.match(this.chartype_[i][0])) {
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+        TinySegmenter.prototype.ts_ = function(v) {
+          if (v) { return v; }
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+        TinySegmenter.prototype.segment = function(input) {
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+          for (var i = 4; i < seg.length - 3; ++i) {
+            var score = this.BIAS__;
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+            var c5 = ctype[i+1];
+            var c6 = ctype[i+2];
+            score += this.ts_(this.UP1__[p1]);
+            score += this.ts_(this.UP2__[p2]);
+            score += this.ts_(this.UP3__[p3]);
+            score += this.ts_(this.BP1__[p1 + p2]);
+            score += this.ts_(this.BP2__[p2 + p3]);
+            score += this.ts_(this.UW1__[w1]);
+            score += this.ts_(this.UW2__[w2]);
+            score += this.ts_(this.UW3__[w3]);
+            score += this.ts_(this.UW4__[w4]);
+            score += this.ts_(this.UW5__[w5]);
+            score += this.ts_(this.UW6__[w6]);
+            score += this.ts_(this.BW1__[w2 + w3]);
+            score += this.ts_(this.BW2__[w3 + w4]);
+            score += this.ts_(this.BW3__[w4 + w5]);
+            score += this.ts_(this.TW1__[w1 + w2 + w3]);
+            score += this.ts_(this.TW2__[w2 + w3 + w4]);
+            score += this.ts_(this.TW3__[w3 + w4 + w5]);
+            score += this.ts_(this.TW4__[w4 + w5 + w6]);
+            score += this.ts_(this.UC1__[c1]);
+            score += this.ts_(this.UC2__[c2]);
+            score += this.ts_(this.UC3__[c3]);
+            score += this.ts_(this.UC4__[c4]);
+            score += this.ts_(this.UC5__[c5]);
+            score += this.ts_(this.UC6__[c6]);
+            score += this.ts_(this.BC1__[c2 + c3]);
+            score += this.ts_(this.BC2__[c3 + c4]);
+            score += this.ts_(this.BC3__[c4 + c5]);
+            score += this.ts_(this.TC1__[c1 + c2 + c3]);
+            score += this.ts_(this.TC2__[c2 + c3 + c4]);
+            score += this.ts_(this.TC3__[c3 + c4 + c5]);
+            score += this.ts_(this.TC4__[c4 + c5 + c6]);
+        //  score += this.ts_(this.TC5__[c4 + c5 + c6]);    
+            score += this.ts_(this.UQ1__[p1 + c1]);
+            score += this.ts_(this.UQ2__[p2 + c2]);
+            score += this.ts_(this.UQ3__[p3 + c3]);
+            score += this.ts_(this.BQ1__[p2 + c2 + c3]);
+            score += this.ts_(this.BQ2__[p2 + c3 + c4]);
+            score += this.ts_(this.BQ3__[p3 + c2 + c3]);
+            score += this.ts_(this.BQ4__[p3 + c3 + c4]);
+            score += this.ts_(this.TQ1__[p2 + c1 + c2 + c3]);
+            score += this.ts_(this.TQ2__[p2 + c2 + c3 + c4]);
+            score += this.ts_(this.TQ3__[p3 + c1 + c2 + c3]);
+            score += this.ts_(this.TQ4__[p3 + c2 + c3 + c4]);
+            var p = "O";
+            if (score > 0) {
+              result.push(word);
+              word = "";
+              p = "B";
+            }
+            p1 = p2;
+            p2 = p3;
+            p3 = p;
+            word += seg[i];
+          }
+          result.push(word);
+
+          return result;
+        }
+
+        lunr.TinySegmenter = TinySegmenter;
+    };
+
+}));
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/lunr/wordcut.js b/docs/htmls/assets/javascripts/lunr/wordcut.js
new file mode 100644
index 0000000..0d898c9
--- /dev/null
+++ b/docs/htmls/assets/javascripts/lunr/wordcut.js
@@ -0,0 +1,6708 @@
+(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}(g.lunr || (g.lunr = {})).wordcut = f()}})(function(){var define,module,exports;return (function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s})({1:[function(require,module,exports){
+var _ = require("underscore");
+
+var Acceptors = {
+  creators: null,
+  current: null,
+  tag: null,
+
+  init: function() {
+    this.creators = [];
+    this.current = [];
+    this.tag = {};
+  },
+
+  reset: function() {
+    this.current = [];
+    this.tag = {}
+  },
+
+  transit: function(ch) {
+    var self = this;
+
+    self.creators.forEach(function(creator) {
+      var acceptor = creator.createAcceptor(self.tag);
+      if (acceptor) 
+        self.current.push(acceptor);
+    });
+    
+    var _current = [];
+    self.tag = {};
+
+    for (var i = 0; i < self.current.length; i++) {
+      var _acceptor = self.current[i]
+        , acceptor = _acceptor.transit(ch);
+      
+      if (!acceptor.isError) {
+        _current.push(acceptor);
+        self.tag[acceptor.tag] = acceptor;
+      }
+    }
+    self.current = _current;
+
+  },
+
+  getFinalAcceptors: function() {    
+    return this.current.filter(function(acceptor) {
+      return acceptor.isFinal;
+    });
+  }
+};
+
+module.exports = function() {
+  var acceptors = _.clone(Acceptors);
+  acceptors.init();
+  return acceptors;
+};
+
+},{"underscore":25}],2:[function(require,module,exports){
+(function (__dirname){
+
+var LEFT = 0;
+var RIGHT = 1;
+var path = require("path");
+var glob = require("glob");
+
+var WordcutDict = {
+
+
+  init: function (dictPathFile, withDefault, words) {
+    withDefault = withDefault || false
+    var defaultDict = path.normalize(__dirname + "/..") + "/data/tdict-*.txt";
+    this.dict=[]
+    var dictPathIsDefined = dictPathFile !== undefined
+    var dictPath = (withDefault || !dictPathIsDefined) ? [defaultDict]: [];
+    var dictPathFile = dictPathFile || defaultDict
+
+    if(dictPathIsDefined){
+      if (Array.isArray(dictPathFile)) {
+        dictPath.concat.apply(dictPath, dictPathFile);
+      } else {
+        dictPath.push(dictPathFile)
+      }
+    }
+
+    this.addFiles(dictPath, false)
+
+    if(words!==undefined){
+      this.addWords(words, false)
+    }
+    this.finalizeDict();
+  },
+
+  addWords: function(words, finalize){
+    finalize = finalize===undefined || finalize;
+    this.dict.push.apply(this.dict, words)
+    if(finalize){
+      this.finalizeDict();
+    }
+  },
+
+  finalizeDict: function(){
+    this.dict = this.sortuniq(this.dict);
+  },
+
+  addFiles: function(files, finalize){
+    finalize = finalize===undefined || finalize;
+    
+    for (var i = 0; i < 1; i++) {
+      var words = "ก.ก.\nก.ก.น.\nก.ข.ค.\nก.ค.\nก.จ.\nก.ช.น.\nก.ฌ.\nก.ต.\nก.ต.ง.\nก.ต.ช.\nก.ตร.\nก.ท.\nก.น.ช.\nก.บช.\nก.บถ.\nก.ป.ส.\nก.พ.\nก.ม.\nก.ย.\nก.ร.\nก.ล.ต.\nก.ว.\nก.ศ.ว.\nก.ส.ท.\nก.ส.ธ.\nก.ส.อ.\nก.อ.\nกก.ตชด.\nกก.ตร.น.\nกก.ภ.จว.\nกก.รสช.\nกกบ.ขส.ทบ.\nกกล.รพน.\nกง.กห.\nกง.ทบ.\nกง.ทร.\nกซข.ป.\nกซม.ป.\nกทม.กรุงเทพมหานคร\nกบ.ทบ.\nกป.สป.\nกพ.ทบ.\nกพ.ทร.\nกพ.ทหาร\nกร.ทบ.\nกรป.กลาง\nกรอ.พอ.\nกศ.ด.\nกศ.บ.\nกศ.บป.\nกศ.ม.\nกษ.ด.\nกษ.บ.\nกษ.ม.\nกส.ด.\nกส.ทบ.\nกส.บ.\nกส.ม.\nกอ.ปค.\nกอ.รพน.\nกอ.รมน.\nกอ.รสต.\nข.ต.ว.\nขว.ทบ.\nขว.ทร.\nขว.ทหาร\nขส.ทบ.\nขส.ทร.\nขส.ทอ.\nค.ด.\nค.บ.\nค.พ.ศ.\nค.ม.\nค.ร.น.\nค.ร.ฟ.\nค.ร.ม.\nค.ศ.\nค.อ.ด.\nค.อ.บ.\nค.อ.ม.\nคศ.ด.\nคศ.บ.\nคศ.ม.\nง.ด.\nจ.จ.\nจ.จ.จ.\nจ.ช.\nจ.ต.\nจ.ท.\nจ.ป.ร.\nจ.ม.\nจ.ศ.\nจ.ส.ต.\nจ.ส.ท.\nจ.ส.อ.\nจ.อ.\nจ.อ.ร.\nจ.๑๘\nจก.ธน.\nจก.สน.\nช.ค.\nช.ค.บ.\nช.พ.ค.\nช.ส.\nช.ส.ค.\nฌ.ป.ค.\nฌ.ศ.ร.\nฌ.ส.อ.\nฐท.สห.\nด.ช.\nด.ญ.\nด.ต.\nด.ศ.ค.\nด.ศ.ร.\nดย.ทร.\nต.ก.\nต.ค.\nต.จ.\nต.จ.ว.\nต.ช.\nต.ต.\nต.บ.\nต.ม.\nต.ร.\nต.ศ.ร.\nต.ห.\nต.อ.\nต.อ.จ.\nตร.กม.\nตร.ซม.\nตร.ต.\nตร.ทล.\nตร.น.\nตร.ปม.\nตร.ภ.\nตร.ม.\nตร.รฟ.\nตร.ว.\nตร.ส.\nตร.สข.\nท.จ.\nท.จ.ว.\nท.ช.\nท.ญ.\nท.ด.\nท.ท.ท.\nท.ทบ.\nท.บ.\nท.พ.\nท.ม.\nท.ศ.\nทก.ด.\nทก.บ.\nทก.ม.\nทส.ปช.\nทส.รมว.กห.\nทุ.ส.นิ.ม.\nธ.ก.ส.\nธ.ค.\nธ.ญ\nธ.บ.\nน.ช.\nน.ญ.\nน.ด.\nน.ต.\nน.ท.\nน.น.\nน.บ.\nน.บ.ท.\nน.ป.ท.\nน.พ.\nน.ม.\nน.ร.\nน.ว.\nน.ศ.\nน.ส.\nน.ส.พ.\nน.ส.๓\nน.สพ.\nน.อ.\nนปพ.ภ.\nนศ.ด.\nนศ.บ.\nนศ.ม.\nบ.ก.\nบ.ข.ส.\nบ.ช.\nบ.ด.ท.\nบ.ตร.\nบ.ภ.\nบ.ม.\nบก.จร.\nบก.ตชด.\nบก.ตม.\nบก.ทล.\nบก.น.\nบก.ป.\nบก.ปค.\nบก.ปม.\nบก.ภ.เขต\nบก.รน.\nบก.รฟ.\nบก.ร้อย.ตชด.\nบก.ส.\nบกข.ป.\nบจพ.ป.\nบช.ก.\nบช.ด.\nบช.ตชด.\nบช.น.\nบช.บ.\nบช.ปส.\nบช.ภ.\nบช.ม.\nบชท.ป.\nบชน.ป.\nบชส.ป.\nบธ.ด.\nบธ.บ.\nบธ.ม.\nบนท.ป.\nบนอ.ป.\nบปช.ป.\nป.กท.\nป.กศ.\nป.กศ.สูง\nป.จ.\nป.จ.ว.\nป.ช.\nป.ธ.\nป.ป.\nป.ป.ก.\nป.ป.ช.\nป.ป.ป.\nป.ป.ร.\nป.ป.ส.\nป.พ.\nป.พ.พ.\nป.พย.\nป.ม.\nป.ม.ก.\nป.ม.ช.\nป.ม.ธ.\nป.ม.ศ.\nป.ม.อ.\nป.ร.ร.๔\nป.ร.ร.๕\nป.ร.ร.๖\nป.ล.\nป.ว.พ.\nป.วิ.อ.\nป.ส.ส.\nป.อ.\nป.อ.ร.ส.\nป.๑\nปม.วส.\nปอ.พ.\nผกก.ภ.\nผช.ผอ.\nผต.มท.\nผบ.ตร.\nผบ.ทบ.\nผบ.ทร.\nผบ.ทสส.\nผบ.ทอ.\nผบก.น.\nผบก.ป.\nผบก.ปค.\nผบก.ปม.\nผบก.ภ.\nผบช.ก.\nผบช.ตชด.\nผบช.น.\nผบช.ภ.\nผว.กทม.\nผอ.ปจ.\nพ.ก.ง.\nพ.กศ.\nพ.ข.ต.\nพ.ค.\nพ.ค.ช.\nพ.ค.ว.\nพ.ค.ศ.\nพ.จ.ต.\nพ.จ.ท.\nพ.จ.อ.\nพ.ช.\nพ.ช.ค.\nพ.ด.\nพ.ต.\nพ.ต.ต.\nพ.ต.ท.\nพ.ต.อ.\nพ.ต.อ.พิเศษ\nพ.ท.\nพ.บ.\nพ.ป.\nพ.ภ.ม.\nพ.ม.\nพ.ม.ช.\nพ.ย.\nพ.ร.ก.\nพ.ร.ฎ.\nพ.ร.ต.\nพ.ร.ธ.\nพ.ร.บ.\nพ.ศ.\nพ.ศ.บ.\nพ.ส.ร.\nพ.ส.ล.\nพ.อ.\nพ.อ.ต.\nพ.อ.ท.\nพ.อ.พิเศษ\nพ.อ.อ.\nพณ.ด.\nพณ.บ.\nพณ.ม.\nพธ.ด.\nพธ.บ.\nพธ.ม.\nพบ.ด.\nพบ.บ.\nพบ.ม.\nพย.ด.\nพย.บ.\nพย.ม.\nพล.จ.\nพล.ต.\nพล.ต.จ.\nพล.ต.ต.\nพล.ต.ท.\nพล.ต.อ.\nพล.ท.\nพล.ปตอ.\nพล.ม.\nพล.ม.๒\nพล.ร.จ.\nพล.ร.ต.\nพล.ร.ท.\nพล.ร.อ.\nพล.อ.\nพล.อ.จ.\nพล.อ.ต.\nพล.อ.ท.\nพล.อ.อ.\nพลา.ทร.\nพศ.ด.\nพศ.บ.\nพศ.ม.\nพอ.สว.\nภ.ง.ด.\nภ.ง.ด.๙\nภ.ด.\nภ.บ.\nภ.บ.ท.๕\nภ.ป.ร.\nภ.พ.\nภ.ม.\nภ.สถ.บ.\nม.ค.\nม.จ.\nม.ป.ท.\nม.ป.ป.\nม.ป.พ.\nม.ร.ว.\nม.ศ.\nม.อ.\nม.อ.ปัตตานี\nมิ.ย.\nมี.ค.\nยศ.ทบ.\nยศ.ทร.\nยศ.ทอ.\nร.ง.\nร.ด.\nร.ต.\nร.ต.ต.\nร.ต.ท.\nร.ต.อ.\nร.ท.\nร.น.\nร.บ.\nร.พ.\nร.ฟ.ล.\nร.ย.ล.\nร.ย.ส.ท.\nร.ล.\nร.ศ.\nร.ส.พ.\nร.อ.\nรป.ม.\nรร.จปร.\nรร.จอ.\nรร.ชท.\nรร.ตท.\nรร.นร.\nรร.นรต.\nรร.นอ.\nล.ญ.\nล.ว.\nลส.ชบ.\nว.ค.\nว.ฉ.\nว.ช.\nว.ด.ป.\nว.ป.ถ.\nวท.บ.\nศ.บ.\nศ.ป.ก.\nศ.ศ.ป.\nศฝร.ภ.\nศศ.บ.\nศษ.บ.\nศส.บ.\nส.ก.\nส.ก.ศ.ท.\nส.ค.\nส.ค.1\nส.ค.ร.\nส.ค.ส.\nส.ต.\nส.ต.ต.\nส.ต.ท.\nส.ต.อ.\nส.ท.\nส.ทร.\nส.ป.ช.\nส.ป.ส.ท.\nส.ป.อ.\nส.ร.\nส.ล.น.\nส.ว.\nส.ว.ท.\nส.ว.ส.ท.\nส.ส.\nส.ส.ท.\nส.ส.ร.\nส.ห.\nส.อ.\nสถ.บ.\nสนง.สสอ.\nสพ.ญ.\nสพ.บ.\nสว.จร.\nสว.ธร.\nสว.ส.\nสว.สป.\nสว.สส.\nสว.อก.\nสส.บ.\nสุ.จิ.ปุ.ลิ.\nห.ร.ม.\nอ.ก.ค.\nอ.ก.จ.\nอ.จ.\nอ.ช.พ.\nอ.ตร.\nอ.บ.\nอ.ส.ท.\nอ.ส.ม.ท.\nอ.ส.ย.\nอ.อ.ป.\nอส.รด.\nอุ.อา.ก.ส.\nฮ.จ.\nฮ.ท.\nฮ.ฝ.\nฮ.ล.\nฮ.ศ.\nเม.ย.\n\nกรีนิช\nกลันตัน\nกัลกัตตา\nกัวลาลัมเปอร์\nกัศมีร์\nกาฐมาณฑุ\nโกลกาตา\nควิเบก\nคอนเนตทิคัต\nคาบูล\nคุชราต\nคุนหมิง\nเคนตักกี\nเคนทักกี\nเคมบริดจ์\nแคชเมียร์\nแคนซัส\nแคนเบอร์รา\nแคโรไลนา\nแคลิฟอร์เนีย\nโคเปนเฮเกน\nโคลัมโบ\nโคโลราโด\nไครสต์เชิร์ช\nไคโร\nจาการ์ตา\nจำปาศักดิ์\nเจนไน\nเจนีวา\nเจ้อเจียง\nฉงชิ่ง\nเฉิงตู\nชานตง\nชิคาโก\nเชนไน\nเชอร์โนบิล\nซัปโปโร\nซานมารีโน\nซาบาห์\nซาราเยโว\nซาราวัก\nซิดนีย์\nซีอาน\nซีแอตเทิล\nซูริก\nซูริค\nเซเชลส์\nเซนได\nเซี่ยงไฮ้\nโซเฟีย\nโซล\nโซโลมอน\nไซ่ง่อน\nไซบีเรีย\nดัลลัส\nดาโคตา\nดานัง\nดีทรอยต์\nดูไบ\nเดนเวอร์\nเดลาแวร์\nเดียนเบียนฟู\nโดเวอร์\nโดฮา\nไดฟุกุ\nไดฟูกุ\nตรังกานู\nตริโปลี\nตูวาลู\nเตหะราน\nโตเกียว\nโตรอนโต\nทมิฬนาฑู\nทริโปลี\nทิเบต\nเทกซัส\nเท็กซัส\nเทนเนสซี\nเทลอาวีฟ\nแทสเมเนีย\nโทรอนโต\nไทเป\nธากา\nนางาซากิ\nนาริตะ\nนิวเจอร์ซีย์\nนิวเดลี\nนิวยอร์ก\nนิวยอร์ค\nนิวแฮมป์เชียร์\nเนบราสกา\nเนแบรสกา\nเนวาดา\nบรัสเซลส์\nบราซิเลีย\nบอมเบย์\nบอสตัน\nบังกาลอร์\nบังคาลอร์\nบูคาเรสต์\nบูดาเปสต์\nเบงกาซี\nเบนกาซี\nเบรุต\nเบลเกรด\nเบอร์ลิน\nแบกแดด\nปอยเปต\nปะลิส\nปะหัง\nปักกิ่ง\nปัญจาบ\nปัฏนา\nปารีส\nปีนัง\nเประ\nเปียงยาง\nพนมเปญ\nพระตะบอง\nพะโค\nพะสิม\nพาราณสี\nพิหารี\nเพนซิลวาเนีย\nเพนซิลเวเนีย\nฟรานซ์\nฟลอริดา\nฟิลาเดลเฟีย\nฟุกุชิมะ\nฟุกุชิมา\nฟุกุโอกะ\nฟูกูโอกะ\nแฟรงก์เฟิร์ต\nมอสโก\nมะนิลา\nมะละแหม่ง\nมัณฑะเลย์\nมัทราส\nมาดริด\nมิชิแกน\nมินนิโซตา\nมิยางิ\nมิลาน\nมิวนิก\nมิสซูรี\nมุมไบ\nเมน\nเมลเบิร์น\nเมาะตะมะ\nเมาะลำเลิง\nแมนจูเรีย\nแมนเชสเตอร์\nแมนฮัตตัน\nแมริแลนด์\nแมรีแลนด์\nแมสซาชูเซตส์\nยะไข่\nย่างกุ้ง\nยูทาห์\nยูนนาน\nเยรูซาเล็ม\nโยโกฮามา\nริยาด\nรีโอเดจาเนโร\nโรดไอแลนด์\nลอนดอน\nลอสแองเจลิส\nลาปาซ\nลาสเวกัส\nลิสบอน\nลุยเซียนา\nโลซาน\nโลซานน์\nวอชิงตัน\nวอร์ซอ\nวิสคอนซิน\nเวนิส\nเวลส์\nเวอร์จิเนีย\nเวอร์มอนต์\nเวียงจันทน์\nเวียนนา\nแวนคูเวอร์\nไวโอมิง\nสกอตแลนด์\nสก็อตแลนด์\nสตอกโฮล์ม\nสลังงอร์\nเสฉวน\nเสียมราฐ\nเสียมเรียบ\nหงสา\nหงสาวดี\nหนานไห่\nหลวงพระบาง\nหูเป่ย\nหูเป่ย์\nหูหนาน\nเหอเป่ย\nเหอเป่ย์\nเหอหนาน\nอชันตา\nอลาสกา\nอวันตี\nออริกอน\nออสโล\nอะแลสกา\nอัตตะปือ\nอัมมาน\nอัมสเตอร์ดัม\nอัสสัม\nอาบูดาบี\nอาร์คันซอ\nอินเดียนา\nอิบารากิ\nอิลลินอยส์\nอิสตันบูล\nอิสลามาบัด\nอุรุมชี\nอูลานบาตอร์\nเอดินบะระ\nเอเธนส์\nแอตแลนตา\nแอริโซนา\nแอลเจียร์\nโอคลาโฮมา\nโอค็อตสค์\nโอกินาวา\nโอซากา\nโอริสสา\nโอเรกอน\nโอไฮโอ\nไอดาโฮ\nไอโอวา\nฮอนโนลูลู\nฮานอย\nฮาเนดะ\nฮาราเร\nฮาวาย\nฮิโรชิมา\nฮุสตัน\nเฮลซิงกิ\n\nมกรา\nกุมภา\nมีนา\nเมษา\nพฤษภา\nมิถุนา\nกรกฎา\nสิงหา\nกันยา\nตุลา\nพฤศจิกา\nธันวา\nเอ\nบี\nซี\nดี\nอี\nเอฟ\nจี\nเอช\nไอ\nเจ\nเค\nแอล\nเอ็ม\nเอ็น\nโอ\nพี\nคิว\nอาร์\nเอส\nที\nยู\nวี\nดับเบิล\nดับบลิว\nเอ็กซ์\nเอ๊กซ์\nวาย\nแซด\nแอลฟา\nแอลฟ่า\nเบตา\nเบต้า\nแกมมา\nแกมม่า\nเดลตา\nเดลต้า\nโอเมกา\nโอเมก้า\nเมกะ\nกิกะ\nนาโน\nไมโคร\n\nกรรมาชน\nกรอบรูป\nกระดี๊กระด๊า\nกระบับ\nกราวนด์\nกรีน\nกรุ๊ป\nกฤษณ์\nกลาส\nก๊วน\nกษัตริยา\nกษัตริยาธิราช\nก่อนหน้า\nกะบับ\nกับดัก\nกัมมันตะ\nก๊าก\nก๋ากั่น\nกาญจน์\nกาญจนาภิเษก\nกามิกาเซ่\nการันตี\nกาหลิบ\nกิฟท์\nกิมจิ\nกีวี\nกึ๊ก\nกึ๋ย\nกุนซือ\nกุมภาพันธ์\nกู๋\nเกจิ\nเกมส์\nเกย์\nเกรด\nเกรย์\nเกสต์เฮาส์\nเก๊ะ\nเก๋ากี้\nเกิร์ล\nแกงค์\nแกรนด์\nแกสโซฮอล์\nแก๊สโซฮอล์\nโกเต็กซ์\nโกลด์\nโกะ\nโก๊ะ\nไกด์\nขั้นตอน\nเขวี้ยง\nคณาญาติ\nครัวซอง\nครัวซองต์\nคร่ำครวญ\nครีเอทีฟ\nครูเสด\nคลับ\nคลาสสิก\nคลิตอริส\nคลิป\nความหมาย\nควิก\nควีน\nคองเกรส\nคอนซูเมอร์\nคอนเซปต์\nคอนเซ็ปต์\nคอนโด\nคอนโดมิเนียม\nคอนเทนเนอร์\nคอนแทค\nคอนแท็ค\nคอนโทรล\nคอนเฟิร์ม\nคอปเตอร์\nคอมพ์\nคอมเพล็กซ์\nคอมมอนส์\nคอมเมนท์\nคอมเมนต์\nคอร์ป\nคอร์ปอเรชั่น\nคอร์รัปชัน\nคอร์รัปชั่น\nคอรัปชัน\nคอรัปชั่น\nคอร์ส\nคอลเล็กชั่น\nคอลัมน์\nคอลัมนิสต์\nคัตเอาต์\nคันคาก\nคันถธุระ\nคันธาระ\nคันยิ\nคัสตาร์ด\nคาราโอเกะ\nคีตกวี\nคีตปฏิภาณ\nคีตราชัน\nคาปูชิโน\nคามิคาเซ่\nคาเฟ่\nคาร์\nคาร์โก้\nคาราเมล\nคาแรกเตอร์\nคาแร็กเตอร์\nคาแรคเตอร์\nคาแร็คเตอร์\nคาวบอย\nคาสิโน\nคิกขุ\nคิวบิก\nคูลเลอร์\nเคบับ\nเครป\nเคลม\nเคลียร์\nเคลื่อนย้าย\nเคส\nเคอร์ฟิว\nแคชเชียร์\nแคทวอล์ค\nแคนดิเดต\nแคนตาลูป\nแคนยอน\nแคนู\nแคป\nแคมป์\nแคมปัส\nแคมเปญ\nแคร์\nแครกเกอร์\nแคร็กเกอร์\nแครอท\nแคสต์\nแคสติง\nแคสติ้ง\nโค้ก\nโค้ช\nโคโยตี\nโคโยตี้\nโครนา\nโคอะล่า\nโคอาลา\nโคอาล่า\nไคลแมกซ์\nไคลแม็กซ์\nงั้น\nง่าว\nงี้\nเง็ง\nโง่เขลา\nไง\nจตุคาม\nจ๊อกกี้\nจอหงวน\nจังโก้\nจัมโบ้\nจ๊าบ\nจารกรรม\nจารชน\nจิ๊ก\nจิ๊กโก๋\nจิ๊กซอว์\nจิตพิสัย\nจิตเภท\nจีดีพี\nจึ๊ก\nจุ๊ย\nจูน\nจูเนียร์\nเจ๊\nเจได\nเจ็ต\nเจล\nเจ๊าะแจ๊ะ\nเจี๊ยว\nแจ็กเก็ต\nแจ๊กเก็ต\nแจ็กพอต\nแจ็กพ็อต\nแจ๊กพอต\nแจ๊กพ็อต\nแจม\nแจ๊ส\nโจ๋\nฉลุย\nเฉิ่ม\nชนะเลิศ\nช็อค\nช็อต\nช็อป\nช็อปปิ้ง\nช็อปเปอร์\nชะโนด\nชัตเตอร์\nชัวร์\nชาร์จ\nชาร์ต\nชาร์ป\nชินบัญชร\nชิฟฟอน\nชีส\nชีอะห์\nเช็ก\nเช็งเม้ง\nเชฟ\nเชลียร์\nเชอร์รี่\nแชเชือน\nแช่แข็ง\nแชมป์\nแชมปิยอง\nแชมเปญ\nแชมเปี้ยน\nแชมพู\nโชว์รูม\nโชห่วย\nใช้งาน\nไชน่า\nซ้อ\nซอมบี้\nซะ\nซังเต\nซันตาคลอส\nซัพพลาย\nซัพพลายเออร์\nซัมเมอร์\nซากุระ\nซาดิสต์\nซาดิสม์\nซาตาน\nซานตาคลอส\nซาฟารี\nซาบะ\nซามูไร\nซาร์\nซาร์ดีน\nซาเล้ง\nซิง\nซิ่ง\nซิงเกิล\nซิตี\nซิตี้\nซินโดรม\nซิม\nซิ้ม\nซิมโฟนี\nซิมโฟนี่\nซิลเวอร์\nซี้\nซี้ซั้ว\nซีดาน\nซีน\nซีนีเพล็กซ์\nซีเนียร์\nซีร็อกซ์\nซีรีส์\nซีเรียส\nซีอีโอ\nซื่อบื้อ\nซุนหนี่\nซุปเปอร์\nซูชิ\nซูเปอร์\nซูม\nซูโม่\nซูเอี๋ย\nซูฮก\nเซ็กซ์\nเซ็กซี่\nเซ็กส์\nเซนเซอร์\nเซ็นเซอร์\nเซนเตอร์\nเซ็นเตอร์\nเซ็นทรัล\nเซนส์\nเซ่นไหว้\nเซฟตี้\nเซรามิก\nเซลส์\nเซลส์แมน\nเซอร์\nเซอร์ไพรส์\nเซอร์วิส\nเซาท์\nเซี้ยว\nแซ็ก\nแซกโซโฟน\nแซ็กโซโฟน\nแซนด์วิช\nแซมบ้า\nแซลมอน\nแซว\nโซเชียล\nโซน\nโซนี่\nโซลาร์\nโซโล\nโซโล่\nญาณทัสสนะ\nดยุก\nดยุค\nดร็อป\nดรัมเมเยอร์\nดรามา\nดราม่า\nดอกเตอร์\nด็อกเตอร์\nดัมพ์\nดั๊มพ์\nดาวน์\nดิกชันนารี\nดิสเครดิต\nดีกรี\nดีเจ\nดีไซน์\nดีไซน์เนอร์\nดีไซเนอร์\nดีเบต\nดีพาร์ตเมนต์\nดีพาร์ตเมนท์\nดีพาร์ทเมนต์\nดีพาร์ทเมนท์\nดีมานด์\nดีล\nดีลเลอร์\nดีเลย์\nเดชานุภาพ\nเดบิต\nเดโม\nเดย์\nเด้อ\nเดอะ\nเด๊ะ\nเดี้ยง\nเดี๊ยะ\nแดนซ์\nแดนเซอร์\nแดรี่\nโดนัท\nโดมิโน\nโดรายากิ\nไดเอ็ต\nตถตา\nตนเอง\nตรวจทาน\nตรวจสอบ\nตอกย้ำ\nต๊อง\nต่อยอด\nต่อรอง\nตะหงิด\nตังค์\nตันเถียน\nตัวตน\nตัวเอง\nตาปรือ\nต้าอ่วย\nติงต๊อง\nติ๋ม\nติ่มซำ\nติว\nติวเตอร์\nตี๋\nตื้บ\nตุ๊ก\nตุ๊กตุ๊ก\nตุ๊ด\nตุ๋ย\nตู้เซฟ\nเต๊ะ\nเตี๊ยม\nแตงกวา\nแตงโม\nแต๋ว\nโต๋เต๋\nโต๊ะจีน\nไตรมาส\nถ่ายทำ\nถูกต้อง\nทงคัตสึ\nทริป\nทรู\nทอม\nท็อป\nทอร์นาโด\nทอล์ค\nทักซิโด\nทันตกรรม\nทันตแพทยศาสตร์\nทับซ้อน\nทัวร์\nทัวร์นาเมนต์\nทัวร์นาเมนท์\nทัวริสต์\nทาเลนต์\nทาวน์\nทาวน์เฮาส์\nทำงาน\nทิป\nทิพยสมบัติ\nทิวลิป\nทีรามิสุ\nทีวี\nทูน่า\nเท็กซ์\nเทค\nเทคโน\nเทคโนแครต\nเทควันโด\nเทป\nเทรด\nเทรนด์\nเทรนเนอร์\nเทรลเลอร์\nเทรลเล่อร์\nเทเลกราฟ\nเทวบัญชา\nเทวบุตร\nเทวา\nเทวาธิราช\nเทโวโรหนะ\nเทอร์โบ\nเที่ยงคืน\nเที่ยงวัน\nเทียมทาน\nแทกติค\nแทคติค\nแทงกั๊ก\nแทงโก้\nโทมาฮอก\nโทมาฮอว์ก\nโทมาฮอว์ค\nโทร\nโทรโข่ง\nไทม์\nไทยแลนด์\nไทเฮา\nธรรมา\nธรรมาภิบาล\nธัมโม\nธีม\nธุรกรรม\nธุหร่ำ\nเธค\nนพมาศ\nนรีแพทย์\nน็อก\nน็อค\nน้องใหม่\nนอมินี\nนอร์ท\nน่ะ\nนางแบบ\nนาฏยศาลา\nนายแบบ\nนายพราน\nนินจา\nนิรันดร์\nนิว\nนิวส์\nนู้ด\nเนอะ\nเนิร์สเซอรี\nเนิร์สเซอรี่\nเนี้ยบ\nโนติส\nไนท์\nไนน์\nบรรพชน\nบร็อกโคลี\nบร็อคโคลี\nบรา\nบริกร\nบริวเวอรี่ส์\nบลอนด์\nบลูเบอร์รี\nบลูเบอร์รี่\nบ๊วย\nบอกซ์\nบ็อกซ์\nบ๊อกซ์\nบอดี้\nบอนด์\nบ๊อบ\nบอมบ์\nบ๋อย\nบอยคอต\nบอยคอตต์\nบอร์ด\nบังเกอร์\nบัตเตอร์\nบัลลาสต์\nบัส\nบาบูน\nบาร์บีคิว\nบาร์บี้\nบาลานซ์\nบิ๊ก\nบิล\nบึม\nบึ้ม\nบุญคุณ\nบุ๋น\nบุปผา\nบู๊\nบูชิโด\nบูติก\nบูติค\nบูม\nเบเกอรี่\nเบญจมบพิตร\nเบตาดีน\nเบนโตะ\nเบนโล\nเบบี้\nเบลอ\nเบอร์เกอร์\nเบอร์รี\nเบิร์ด\nเบิร์น\nแบ็กโฮ\nแบคโฮ\nแบด\nแบต\nแบนเนอร์\nแบรนด์\nแบล็ก\nแบล็ค\nไบโอ\nโบกี้\nโบตั๋น\nโบ้ย\nโบรกเกอร์\nโบรชัวร์\nโบว์\nโบว์ลิ่ง\nไบเบิล\nปฏิสัมพันธ์\nป๊อก\nปอดแหก\nป๊อป\nป๋อหลอ\nปักขคณนา\nปัจเจกชน\nปัจฉิมนิเทศ\nป๊า\nป๋า\nป่าไม้\nปาร์ตี้\nปาสกาล\nปาสคาล\nปาสเตอร์\nปิกอัพ\nปิ๊ง\nปิโตรเคมี\nปิยมิตร\nปึ้ก\nปูอัด\nเปโซ\nเป็นไง\nเปปเปอร์มินต์\nเปเปอร์\nเปราะบาง\nเป๊ะ\nเป่ายิงฉุบ\nเป่ายิ้งฉุบ\nเปียโน\nแป้ก\nแป๋ว\nแป๊ะเจี๊ยะ\nโปร\nโปรเจกต์\nโปรเจ็กต์\nโปรเจกเตอร์\nโปรเจ็กเตอร์\nโปรเจคท์\nโปรเจ็คท์\nโปรดักชั่น\nโปรดิวเซอร์\nโปรโมชั่น\nโปรโมต\nโปรโมเตอร์\nโปรโมท\nโปลิศ\nโปสเตอร์\nผลไม้\nผลักดัน\nผ้าห่ม\nผิดพลาด\nผู้นำ\nแผดเผา\nเฝอ\nพงษ์\nพริตตี้\nพรีเซนต์\nพรีเซ็นเตอร์\nพรีเมียม\nพรีเมียร์\nพฤหัส\nพล็อต\nพลาซ่า\nพลานุภาพ\nพ่อค้า\nพอเพียง\nพะเรอ\nพันธกิจ\nพันธุวิศวกรรม\nพาร์\nพาร์ตเนอร์\nพาร์ทเนอร์\nพาวเวอร์\nพาสเจอร์ไรส์\nพาสตา\nพาสต้า\nพาสปอร์ต\nพาเหรด\nพิซซ่า\nพีเรียด\nพุดดิ้ง\nพุทธภูมิ\nพุทธศตวรรษ\nพุทโธ\nพูล\nเพทนาการ\nเพนกวิน\nเพนตากอน\nเพรส\nเพรียวบาง\nเพลซ\nเพลท\nเพลย์บอย\nเพียบแปร้\nเพียว\nเพาเวอร์\nแพกเกจ\nแพ็ค\nแพตเทิร์น\nแพทเทิร์น\nแพทยสภา\nแพนงเชิญ\nแพนดา\nแพนด้า\nแพลน\nโพลล์\nโพลารอยด์\nโพสต์\nไพลิน\nฟยอร์ด\nฟรังก์\nฟรุต\nฟลอร์\nฟลุก\nฟลุค\nฟลุต\nฟลุท\nฟอยล์\nฟอร์ม\nฟันด์\nฟาวล์\nฟาสต์ฟู้ด\nฟินิกซ์\nฟิวเจอร์\nฟีด\nฟีเวอร์\nฟุตบาท\nเฟรช\nเฟรชชี่\nเฟรม\nเฟมินิสต์\nเฟส\nเฟอร์นิเจอร์\nเฟอร์รี่\nเฟิร์ม\nเฟี้ยวฟ้าว\nแฟกซ์\nแฟ็กซ์\nแฟนซี\nแฟนตาซี\nแฟ้บ\nแฟร์\nแฟรนไชส์\nแฟรี\nแฟรี่\nแฟลช\nแฟล็ต\nโฟน\nโฟม\nโฟล์ค\nไฟต์\nไฟแนนซ์\nไฟลต์\nไฟลท์\nภควัทคีตา\nภควัมบดี\nภควัมปติ\nภคันทลาพาธ\nภววิสัย\nภารตะ\nภูมิทัศน์\nม้ง\nมวลชน\nมยุราภิรมย์\nมลภาวะ\nมหภาค\nมหาอุปราชา\nมอคคา\nมอคค่า\nมอนสเตอร์\nม็อบ\nมอบตัว\nมอยส์เจอไรเซอร์\nมอลล์\nมะกัน\nมั้ง\nมัฟฟิน\nมั้ย\nม้านั่ง\nมาเฟีย\nมาม่า\nมายองเนส\nมายาคติ\nมาร์ก\nมาร์เก็ต\nมาร์เก็ตติ้ง\nมาร์ค\nมาร์จิน\nมาร์ช\nมาร์ต\nมาร์ท\nมาราธอน\nม้าหินอ่อน\nมินต์\nมินท์\nมินิ\nมิลค์\nมิวสิค\nมิสซัง\nมิสไซล์\nมิสเตอร์\nมือถือ\nมุมมอง\nเมคอัพ\nเมจิก\nเมจิค\nเมทัล\nเมเปิล\nเมาท์\nเมี่ยงคำ\nแมกกาซีน\nแม็กกาซีน\nแมคเคอเรล\nแม่ค้า\nแมชชีน\nแมชีน\nแมนชั่น\nแมมบ้า\nแมมโบ้\nโมจิ\nโมเดล\nโมเดิร์น\nโมเต็ล\nโมโนเรล\nโมหจริต\nไมค์\nไมเกรน\nยนตรกรรม\nยอมรับ\nยะเยือก\nยังไง\nยากูซ่า\nยาวี\nยิม\nยิว\nยุวทูต\nยูโทเปีย\nยูโร\nยูวี\nเยน\nเยลลี่\nเย้ว\nเยอบีรา\nเยอบีร่า\nเยอร์บีรา\nเยอร์บีร่า\nแยมโรล\nโยเกิร์ต\nโยโย่\nรวมมิตร\nร็อค\nร็อคเก็ต\nรองรับ\nรอมฎอน\nรอยัลตี้\nระโงก\nรันเวย์\nรัม\nรากหญ้า\nราชบัณฑิตยสถาน\nราชานุญาต\nราชานุสาวรีย์\nรามเทพ\nรามาธิบดี\nรามายณะ\nราเม็ง\nราเมน\nรายชื่อ\nราสเบอร์รี\nริกเตอร์\nริคเตอร์\nรีไซเคิล\nรีดไถ\nรีทัช\nรีเทิร์น\nรีไทร์\nรีแบรนด์\nรีพอร์ท\nรีโมต\nรีโมท\nรีวิว\nรีสอร์ต\nรีสอร์ท\nรีเสิร์ช\nรุมบ้า\nรุสโซ\nรูบิก\nรูบิค\nเรซิน\nเรซิ่น\nเรดิโอ\nเรต\nเรตติ้ง\nแรงใจ\nแรงดูด\nแรงผลัก\nแรลลี\nแรลลี่\nโรดแมป\nโรเนียว\nโรแมนติก\nโรแมนติค\nโรล\nโรลออน\nไรเฟิล\nล็อกเกอร์\nลอจิสติกส์\nล็อต\nล็อบบี้\nลอร์ด\nล้มเหลว\nละติน\nละอ่อน\nลาซานญ่า\nลาติน\nลาเต้\nลานีญา\nลามะ\nลิมิต\nลิมูซีน\nลิสต์\nลีก\nลีด\nลีดเดอร์\nลีเมอร์\nลีลาวดี\nลุค\nลูกชาย\nลูกสาว\nเลกเชอร์\nเลคเชอร์\nเลดี้\nเลสเบี้ยน\nเลิฟ\nแลนด์\nแล็บ\nโลโก้\nโลชั่น\nไลท์\nไลน์\nไลฟ์\nวนาราม\nวราราม\nวโรกาส\nว้อดก้า\nวอเตอร์\nวอฟเฟิล\nว้อย\nวอร์ม\nวอร์มอัพ\nวอร์รูม\nวอล์ก\nวอล์ค\nวอลซ์\nวอลนัต\nวอลนัท\nวอลล์\nว่ะ\nวันเวย์\nวัสสา\nวาซาบิ\nวาทกรรม\nวาทะ\nวานิลลา\nวานิลา\nวาฟเฟิล\nวาริชศาสตร์\nว้าว\nวัคค์\nวัจนะ\nวาไรตี้\nวิก\nวิดีโอ\nวิทย์\nวิน\nวิป\nวิปปิ้ง\nวิภัชภาค\nวิว\nวิลล์\nวิลเลจ\nวีเจ\nวีซ่า\nวีดิทัศน์\nวีน\nวีไอพี\nวืด\nเวณิกา\nเวเฟอร์\nเวสต์\nเวอร์\nเวิร์ก\nเวิร์กช็อป\nเวิร์ค\nเวิร์ลด์\nเวิลด์\nแวมไพร์\nไวกิ้ง\nไวเบรเตอร์\nไวอะกร้า\nไวอากร้า\nศากยบุตร\nศิรินทร์\nศิลปวัฒนธรรม\nศิลปากร\nศิวิไลซ์\nศึกษาศาสตร์\nสกรัม\nสกาย\nสกู๊ป\nสเกตช์\nสเก็ตช์\nสคริปต์\nสแควร์\nสงบสุข\nสจ๊วต\nสตรอเบอร์รี\nสตรอเบอรี\nสตรอว์เบอร์รี\nสตริง\nสต็อก\nสต๊อก\nสต็อค\nสต๊อค\nสตอรี\nสตาร์\nสตาร์ท\nสติกเกอร์\nสติ๊กเกอร์\nสตีล\nสตูดิโอ\nสเตชัน\nสเตชั่น\nสเตเดียม\nสเตนเลส\nสเต็ป\nสเตย์\nสเตริโอ\nสเตอริโอ\nสแตนดาร์ด\nสแตนเลส\nสโตน\nสโตร์\nสไตรค์\nสไตล์\nสถาปัตย์\nสไนเปอร์\nสปอต\nสป็อต\nสปอนเซอร์\nสปอร์ต\nสปา\nสปาย\nสปิริต\nสเปก\nสเปค\nสไปเดอร์\nสมณพราหมณ์\nสมาพันธ์\nสมิติเวช\nสโรชา\nสลัม\nสแล็ก\nสโลแกน\nสโลว์\nสไลด์\nสวีท\nสหรัฐ\nสหัชญาณ\nสหัสวรรษ\nสะกอม\nสะเด่า\nสะบึม\nสะบึมส์\nสะออน\nสังโฆ\nสะโหลสะเหล\nสันทนาการ\nสัมนา\nสามช่า\nสามแยก\nสารขัณฑ์\nสี่แยก\nสึนามิ\nสุนทรีย์\nสุริยยาตร\nสุริยยาตร์\nสุหนี่\nเสกสรรค์\nเสพติด\nเสือโคร่ง\nหงวน\nหน่อมแน้ม\nหมวย\nหมั่นโถว\nหม่านโถว\nหมายปอง\nหมิง\nหยวน\nหลวงตา\nหลวงปู่\nหลวงพี่\nหล่อฮังก้วย\nหลินจือ\nห่วย\nเห็นด้วย\nเหมย\nเห่ย\nเหี่ยวย่น\nแหม็บ\nแหวว\nโหงว\nโหงวเฮ้ง\nโหลน\nโหลยโท่ย\nไหง\nไหร่\nอพาร์ตเมนต์\nอพาร์ตเมนท์\nอพาร์ทเมนต์\nอพาร์ทเมนท์\nอมาตยาธิปไตย\nอยุติธรรม\nอริยสงฆ์\nอ่วม\nอวอร์ด\nออกแบบ\nออดิชั่น\nออดิทอเรียม\nออเดอร์\nออโต้\nออทิสติก\nอ่อนด้อย\nออฟ\nออยล์\nออร์แกน\nออร์แกนิก\nออร์แกนิค\nออร์เดอร์\nออรัล\nออสซี่\nอะ\nอัตลักษณ์\nอัตวิสัย\nอันเดอร์\nอันตรกิริยา\nอัลตรา\nอัลไซเมอร์\nอัลบัม\nอัลบั้ม\nอัลมอนด์\nอาข่า\nอาโนเนะ\nอาฟเตอร์\nอาร์ติสต์\nอาร์พีจี\nอาว์\nอาสวะ\nอิกัวนา\nอินดอร์\nอินดัสตรีส์\nอินเตอร์\nอิ่มแปร้\nอิมพีเรียล\nอิเล็กทริก\nอิเล็กทริค\nอิเลียด\nอิสรชน\nอิเหนา\nอิออน\nอีแต๋น\nอีโรติก\nอีเวนท์\nอีสต์\nอีสเตอร์\nอึ๊บ\nอึ้ม\nอึ๋ม\nอึมครึม\nอุด้ง\nอุตสาหการ\nอุเทน\nอุปการคุณ\nอุปทาน\nอุปนายก\nอุปนายิกา\nอุปสงค์\nอุปัทวเหตุ\nอุรังคธาตุ\nอูคูเลเล่\nอู้ฟู่\nเอ๋\nเอ็กซ์โป\nเอ็กซ์เพรส\nเอ็กโซเซต์\nเอ็กโซเซ่ต์\nเอเซีย\nเอ็นจีโอ\nเอ็นเตอร์เทน\nเอนทรานซ์\nเอ็นทรานซ์\nเอฟเฟ็กต์\nเอเยนต์\nเอลนีโญ\nเอสเปรสโซ\nเอสเพรสโซ\nเอ๋อ\nเอาต์\nเอาท์\nเอาท์ดอร์\nเอ๊าะ\nแอ็กชั่น\nแอ็คชั่น\nแอคทีฟ\nแอดมิชชั่น\nแอดมิสชัน\nแอนด์\nแอ๊บแบ๊ว\nแอปเปิล\nแอปเปิ้ล\nแอปพริคอท\nแอพพริคอท\nแอพริคอต\nแอร์\nแอโรบิก\nแอโรบิค\nแอลมอนด์\nแอสเตอร์\nโอเค\nโอเปอเรเตอร์\nโอเปร่า\nโอเพ่น\nโอ้ย\nโอยัวะ\nโอรสาธิราช\nโอเลี้ยง\nโอวัลติน\nโอเวอร์\nไอซ์\nไอซียู\nไอดอล\nไอเดีย\nไอติม\nฮวงจุ้ย\nฮ่องเต้\nฮองเฮา\nฮอต\nฮ็อต\nฮอตดอก\nฮ็อตด็อก\nฮันนีมูน\nฮัม\nฮัลโลวีน\nฮัลโหล\nฮากกา\nฮาร์ด\nฮาราคีรี\nฮาลาล\nฮาโลวีน\nฮิ\nฮิต\nฮิบรู\nฮิปโป\nฮิปฮอป\nฮีโร่\nฮูลาฮูป\nฮูล่าฮูป\nเฮฟวี\nเฮฟวี่\nเฮอร์ริเคน\nเฮีย\nแฮนด์\nแฮปปี้\nแฮมเบอร์เกอร์\nโฮป\nโฮม\nโฮลดิงส์\nโฮลวีต\nโฮสเตส\nไฮกุ\nไฮแจ็ค\nไฮโซ\nไฮเทค\nไฮบริด\nไฮเปอร์\nไฮไลต์\nไฮไลท์\nไฮเวย์\nไฮสคูล\nไฮเอนด์\n\nกรีซ\nกัมพูชา\nกัวเตมาลา\nกาตาร์\nกานา\nกาบอง\nกายอานา\nกินี\nเกรนาดีนส์\nเกรเนดา\nเกาหลี\nแกมเบีย\nโกตดิวัวร์\nคองโก\nคอโมโรส\nคอสตาริกา\nคาซัคสถาน\nคิตส์\nคิริบาตี\nคิริบาส\nคิวบา\nคีร์กีซสถาน\nคูเวต\nเคนยา\nเคปเวิร์ด\nเคย์แมน\nแคนาดา\nแคเมอรูน\nโครเอเชีย\nโคลอมเบีย\nจอร์เจีย\nจอร์แดน\nจาเมกา\nจิบูตี\nจีน\nชาด\nชิลี\nเช็ก\nซามัว\nซาอุ\nซิมบับเว\nซีเรีย\nซูดาน\nซูรินาเม\nเซนต์\nเซเนกัล\nเซอร์เบีย\nเซาตูเม\nเซียร์รา\nแซมเบีย\nโซมาเลีย\nโซเวียต\nไซปรัส\nญี่ปุ่น\nดารุสซาลาม\nเดนมาร์ก\nโดมินิกัน\nโดมินิกา\nตรินิแดด\nตองกา\nติมอร์\nตุรกี\nตูนิเซีย\nเติร์กเมนิสถาน\nโตโก\nโตเบโก\nไต้หวัน\nทาจิกิสถาน\nแทนซาเนีย\nนอร์เวย์\nนามิเบีย\nนาอูรู\nนิการากัว\nนิวซีแลนด์\nเนเธอร์แลนด์\nเนปาล\nเนวิส\nไนจีเรีย\nไนเจอร์\nบราซิล\nบริติช\nบริเตน\nบรูไน\nบอตสวานา\nบอสเนีย\nบังกลาเทศ\nบังคลาเทศ\nบัลแกเรีย\nบาร์บูดา\nบาร์เบโดส\nบาห์เรน\nบาฮามาส\nบิสเซา\nบุรุนดี\nบูร์กินาฟาโซ\nเบนิน\nเบลเยียม\nเบลารุส\nเบลีซ\nเบอร์มิวดา\nโบลิเวีย\nปรินซิปี\nปากีสถาน\nปานามา\nปาปัวนิวกินี\nปารากวัย\nปาเลสไตน์\nปาเลา\nเปรู\nเปอร์เซีย\nเปอร์โตริโก\nโปรตุเกส\nโปแลนด์\nฝรั่งเศส\nพม่า\nฟิจิ\nฟินแลนด์\nฟิลิปปินส์\nเฟรนช์\nภูฏาน\nภูฐาน\nมองโกเลีย\nมอนเตเนโกร\nมอนแทนา\nมอริเชียส\nมอริเตเนีย\nมอลโดวา\nมอลตา\nมัลดีฟส์\nมาเก๊า\nมาซิโดเนีย\nมาดากัสการ์\nมาร์แชลล์\nมาลาวี\nมาลี\nมาเลเซีย\nเม็กซิโก\nเมียนมาร์\nโมซัมบิก\nโมนาโก\nโมนาโค\nโมร็อกโก\nไมโครนีเซีย\nยูกันดา\nยูโกสลาเวีย\nยูเครน\nเยเมน\nเยอรมนี\nรวันดา\nรัสเซีย\nโรมาเนีย\nลักเซมเบิร์ก\nลัตเวีย\nลาว\nลิกเตนสไตน์\nลิทัวเนีย\nลิเบีย\nลีโอน\nลูเซีย\nเลโซโท\nเลบานอน\nเลสเต\nไลบีเรีย\nวาติกัน\nวานูอาตู\nวินเซนต์\nเวเนซุเอลา\nเวียดนาม\nศรีลังกา\nสเปน\nสโลวะเกีย\nสโลวัก\nสโลวีเนีย\nสวาซิแลนด์\nสวิตเซอร์แลนด์\nสวีเดน\nสหรัฐ\nสหราชอาณาจักร\nสิกขิม\nสิงคโปร์\nอเมริกา\nออสเตรเลีย\nออสเตรีย\nอันดอร์รา\nอัฟกานิสถาน\nอาเซอร์ไบจาน\nอาร์เจนตินา\nอาร์เมเนีย\nอาระเบีย\nอิเควทอเรียล\nอิตาลี\nอินเดีย\nอินโดนีเซีย\nอิรัก\nอิสราเอล\nอิหร่าน\nอียิปต์\nอุซเบกิสถาน\nอุรุกวัย\nเอกวาดอร์\nเอธิโอเปีย\nเอมิเรตส์\nเอริเทรีย\nเอลซัลวาดอร์\nเอสโตเนีย\nแองโกลา\nแอนติกา\nแอลจีเรีย\nแอลเบเนีย\nโอมาน\nไอซ์แลนด์\nไอร์แลนด์\nฮ่องกง\nฮอนดูรัส\nฮังการี\nเฮติ\nเฮอร์เซโกวีนา\n\nกระบี่\nกรุงเทพ\nกาญจนบุรี\nกาฬสินธุ์\nกำแพงเพชร\nขอนแก่น\nจันทบุรี\nฉะเชิงเทรา\nชลบุรี\nชัยนาท\nชัยภูมิ\nชุมพร\nเชียงราย\nเชียงใหม่\nตรัง\nตราด\nตาก\nนครนายก\nนครปฐม\nนครพนม\nนครราชสีมา\nนครศรีธรรมราช\nนครสวรรค์\nนนทบุรี\nนราธิวาส\nน่าน\nบึงกาฬ\nบุรีรัมย์\nปทุมธานี\nประจวบคีรีขันธ์\nปราจีนบุรี\nปัตตานี\nพะเยา\nพังงา\nพัทลุง\nพิจิตร\nพิษณุโลก\nเพชรบุรี\nเพชรบูรณ์\nแพร่\nภูเก็ต\nมหาสารคาม\nมุกดาหาร\nแม่ฮ่องสอน\nยโสธร\nยะลา\nร้อยเอ็ด\nระนอง\nระยอง\nราชบุรี\nลพบุรี\nลำปาง\nลำพูน\nเลย\nศรีสะเกษ\nสกลนคร\nสงขลา\nสตูล\nสมุทรปราการ\nสมุทรสงคราม\nสมุทรสาคร\nสระแก้ว\nสระบุรี\nสิงห์บุรี\nสุโขทัย\nสุพรรณบุรี\nสุราษฎร์\nสุราษฎร์ธานี\nสุรินทร์\nหนองคาย\nหนองบัวลำภู\nอยุธยา\nอ่างทอง\nอำนาจเจริญ\nอุดรธานี\nอุตรดิตถ์\nอุทัยธานี\nอุบลราชธานี\nกันทรลักษ์\nจตุจักร\nไชยา\nซีคอน\nดอนเมือง\nถลาง\nไทรโยค\nธนบุรี\nธัญบุรี\nบางกอก\nบางปะกง\nบางระจัน\nปะทิว\nปาย\nพญาไท\nพัฒน์พงษ์\nพัทยา\nพารากอน\nภูมิซรอล\nรัตนาธิเบศร์\nรังสิต\nลันตา\nลาดพร้าว\nวโรรส\nวิภาวดี\nสตึก\nสมุย\nสัตหีบ\nสิมิลัน\nสุขุมวิท\nสุไหง\nเสลภูมิ\nอังรีดูนังต์\nอ่างขาง\nอินทนนท์\nเอ็มโพเรียม\n\nคิวชู\nแคริบเบียน\nแคสเปียน\nดานูบ\nตะนาวศรี\nนอร์วีเจียน\nนิโคบาร์\nเนรัญชรา\nไนล์\nบอร์เนียว\nบอลติก\nเบงกอล\nปิง\nแปซิฟิก\nมะละกา\nมินดาเนา\nมิสซิสซิปปี\nเมดิเตอร์เรเนียน\nเมโสโปเตเมีย\nยมุนา\nยุโรป\nยูเรเชีย\nยูเรเซีย\nแยงซี\nแยงซีเกียง\nสแกนดิเนเวีย\nสะโตง\nสาละวิน\nสุมาตรา\nสุเอซ\nอะเมซอน\nอันดามัน\nอัลไต\nอาร์กติก\nอาหรับ\nอินโดจีน\nอิรวดี\nอิระวดี\nอีเจียน\nอุษาคเณย์\nอูราล\nเอเชีย\nเอเดรียติก\nเอเวอเรสต์\nแอตแลนติก\nแอนตาร์กติก\nแอนตาร์กติกา\nแอฟริกา\nโอลิมปัส\nไอโอเนียน\nฮวงโห\nฮอกไกโด\nฮอนชู\n\nกบิลพัสดุ์\nกุสินารา\nโกลิยะ\nโกสัมพี\nโคตรบอง\nโคตรบูรณ์\nตองอู\nทรอย\nทวารวดี\nทวาราวดี\nเทวทหะ\nไทรบุรี\nนาลันทา\nไบแซนไทน์\nปรัสเซีย\nปัลลวะ\nปาฏลีบุตร\nพุทธคยา\nมถุรา\nมายัน\nมิถิลา\nราชคฤห์\nล้านช้าง\nล้านนา\nลุมพินี\nวัชชี\nเวสาลี\nสารนาถ\nสาวัตถี\nหริภุญชัย\nอโยธยา\nออตโตมัน\nอังวะ\nอินทปัตถ์\nอุชเชนี\n\nกราฟิก\nกราฟิกส์\nกราฟิค\nกริด\nกิกะไบต์\nกูเกิล\nกูเกิ้ล\nเกตเวย์\nโกลบอล\nคลัสเตอร์\nคลาส\nคลิก\nคลิปอาร์ต\nคอนโซล\nคอนเทนต์\nคอมพิวติ้ง\nคอมไพล์\nคอมไพเลอร์\nคอมมูนิเคชั่น\nคอร์\nคีย์\nคีย์บอร์ด\nเครือข่าย\nเคอร์เซอร์\nเคอร์เนล\nแคช\nแคมฟรอก\nแคมฟร็อก\nแคร็ก\nโค้ด\nจาวา\nจีพีเอส\nชิป\nชิพ\nเชลล์\nแช็ต\nแชนเนล\nแชนแนล\nซ็อกเก็ต\nซอฟต์แวร์\nซอฟท์แวร์\nซอร์ส\nซัพพอร์ต\nซัพพอร์ท\nซีดี\nซีดีรอม\nซีเนอร์\nเซิร์ฟเวอร์\nโซลูชัน\nโซลูชั่น\nไซต์\nไซเบอร์\nทรานแซกชัน\nทรานแซกชั่น\nทรานแซ็กชัน\nทรานแซ็กชั่น\nทรานแซคชัน\nทรานแซคชั่น\nทรานแซ็คชัน\nทรานแซ็คชั่น\nทวิตเตอร์\nทวีต\nทัชแพด\nเทมเพลต\nเทอร์มินัล\nแท็ก\nแท็บ\nแทบเล็ต\nโทรจัน\nเน็ต\nเน็ตบุ๊ก\nเน็ตบุค\nเน็ตบุ๊ค\nเน็ตเวิร์ก\nเน็ตเวิร์ค\nโน้ตบุ๊ก\nโน้ตบุค\nโน้ตบุ๊ค\nดอส\nดาวน์เกรด\nดาวน์โหลด\nดิจิตอล\nดิจิทัล\nดีบั๊ก\nดีวีดี\nดีไวซ์\nเดเบียน\nเดลไฟ\nเดสก์ท็อป\nโดเมน\nไดรว์\nไดรเวอร์\nไดเรกทอรี\nไดโอด\nเทเลคอม\nบล็อกเกอร์\nบรอดแบนด์\nบราวเซอร์\nบลูทูท\nบลูทูธ\nบลูเรย์\nบั๊ก\nบัฟเฟอร์\nบิต\nบิท\nบูต\nเบราว์เซอร์\nแบนด์วิดท์\nไบต์\nไบนารี\nโปรแกรมเมอร์\nโปรเซส\nโปรเซสเซอร์\nโปรโตคอล\nพร็อกซี\nพอร์ต\nพอร์ท\nพาเนล\nพาร์ทิชัน\nพารามิเตอร์\nพาสเวิร์ด\nพิกเซล\nเพจ\nเพจเจอร์\nแพกเก็ต\nแพตช์\nแพลตฟอร์ม\nโพรเซส\nโพรเซสเซอร์\nโพรโทคอล\nไพธอน\nฟล็อปส์\nฟอนต์\nฟอร์แมต\nฟอร์เวิร์ด\nฟอรัม\nฟีเจอร์\nเฟซบุ๊ก\nเฟิร์มแวร์\nแฟล็ก\nโฟลเดอร์\nไฟร์ฟอกซ์\nไฟร์วอลล์\nไฟล์\nมอดูล\nมอนิเตอร์\nมัลติ\nมัลติทัช\nมัลติเพล็กซ์\nมัลแวร์\nมาสเตอร์\nมีเดีย\nเมนู\nเมมโมรี\nเมล\nเมาส์\nแมค\nโมดูล\nโมเด็ม\nโมบาย\nโมบายล์\nโมไบล์\nไมโครซอฟท์\nยูนิกซ์\nยูนิโคด\nยูนิโค้ด\nริงโทน\nรีเฟรช\nรีเลย์\nเราเตอร์\nเรียลไทม์\nลิงก์\nลินุกซ์\nลีนุกซ์\nลูป\nเลเยอร์\nแล็ปท็อป\nไลเซนส์\nไลบรารี\nวิกิ\nวิกิพีเดีย\nวินโดวส์\nวินโดว์ส\nเว็บ\nเวอร์ชวล\nเวอร์ชัน\nเวอร์ชั่น\nเวิร์กสเตชัน\nเวิร์กสเตชั่น\nเวิร์คสเตชัน\nเวิร์คสเตชั่น\nเวิร์ด\nเวิร์ม\nไวแมกซ์\nสกรีน\nสแกน\nสแกนเนอร์\nสแต็ก\nสนิฟเฟอร์\nสปายแวร์\nสเปซ\nสแปม\nสมาร์ท\nสล็อต\nเสิร์ช\nโหลด\nออนไลน์\nออปติก\nออปติคอล\nออปติคัล\nออฟไลน์\nออราเคิล\nอัพเกรด\nอัพเดต\nอัพโหลด\nอัปเกรด\nอัปเดต\nอัปโหลด\nอัลกอริทึม\nอาร์กิวเมนต์\nอินเตอร์เน็ต\nอินทิเกรเตอร์\nอินเทอร์เน็ต\nอินเทอร์เฟซ\nอินเทล\nอินพุต\nอินพุท\nอีเมล\nอีเมล์\nอูบุนตู\nอูบันตู\nเอนจิน\nเอ็นจิน\nเอาต์พุต\nเอาต์พุท\nเอาท์พุต\nเอาท์พุท\nแอนะล็อก\nแอนิเมชัน\nแอนิเมชั่น\nแอปพลิเคชัน\nแอปพลิเคชั่น\nแอพพลิเคชัน\nแอพพลิเคชั่น\nแอสเซมบลี\nแอสเซมเบลอร์\nโอเพน\nไอคอน\nไอซี\nไอพอด\nไอพ็อด\nไอแพด\nไอโฟน\nฮับ\nฮาร์ดดิสก์\nฮาร์ดแวร์\nแฮกเกอร์\nแฮ็กเกอร์\nแฮนด์เฮลด์\nโฮสต์\n\nกรีก\nกัณณาฑ\nกัศมีรี\nคันจิ\nคาตาคานะ\nคุชราตี\nคุรุมุขี\nซีริลลิก\nซูลู\nเซลติก\nเซิร์บ\nตากาล็อก\nเตลุคู\nเติร์ก\nทราวิฑ\nเบงกาลี\nปัญจาบี\nพินอิน\nมลยาฬัม\nมองโกล\nมาราฐี\nมาเลย์\nเม็กซิกัน\nแมนจู\nแมนดาริน\nไมถิลี\nเยอรมัน\nรัสเซียน\nสวาฮิลี\nสวิส\nสินธี\nอูรดู\nอัสสมี\nอารบิก\nอิตาเลียน\nอุยกูร์\nแอฟริกัน\nโอริยา\nไอริช\nฮันกึล\nฮินดี\nฮิรางานะ\nฮีบรู\n\nกรีนพีซ\nกรือเซะ\nกวนอิม\nกวนอู\nกัดดาฟี\nกัลยาณวัตร\nกัสสปะ\nกาลิเลโอ\nกินเนส\nกุมภกรรณ\nกูเตนเบิร์ก\nเกตส์\nเกษมณี\nโกณฑัญญะ\nขงเบ้ง\nคริสโตเฟอร์\nคองคอร์ด\nคอลเกต\nคานธี\nคาเบรียล\nคาร์ฟูร์\nคาร์สัน\nคาราบาว\nคาสิโอ\nคิริน\nคุนลุ้น\nคูโบต้า\nเครมลิน\nแคทรีนา\nโคตมะ\nโคตมี\nโคลัมบัส\nไคฟง\nไครสเลอร์\nง้อไบ๊\nจตุพร\nจ็อบส์\nจอห์น\nจิ้น\nจิม\nจิ๋ม\nจิว\nจุฬาภรณ์\nจุฬาลงกรณ์\nเจมส์\nแจ็กสัน\nโจเซฟ\nโจว\nชมัยมรุเชฐ\nชมัยมรุเชษฐ์\nชเวดากอง\nชาร์ลส์\nชินราช\nชินวัตร\nชุนชิว\nเช็ง\nเชตวัน\nเชฟรอน\nเชฟโรเลต\nเชลซี\nไชยานุชิต\nซ่ง\nซังฮี้\nซัดดัม\nซันซิล\nซัมซุง\nซัวเจ๋ง\nซินหัว\nซีซาร์\nซีแพค\nซูซาน\nซูซูกิ\nซูบารุ\nเซ็นทารา\nเซเวน\nเซเว่น\nโซฟิเทล\nโซยุซ\nโซยูซ\nณัฐวุฒิ\nดาร์ลี่\nดาวโจนส์\nดิสนีย์\nดีแทค\nดูปองท์\nเดโมแครต\nเดลล์\nเดลินิวส์\nเดวิด\nแดวู\nโดนัลด์\nโดราเอมอน\nโดเรมอน\nต๋อง\nตั๊กม้อ\nตากสิน\nตาเมือน\nตาลีบัน\nตูน\nเตมีย์\nโต๋\nโตชิบา\nโตโยต้า\nถังซัมจั๋ง\nถังซำจั๋ง\nทรพา\nทราเวล\nทรูมูฟ\nทีปังกร\nเทปโก\nเทพรัตน\nเทวทัต\nเทสโก้\nโทมัส\nไททานิก\nไททานิค\nไทยรัฐ\nธีออส\nนครินทรา\nนโปเลียน\nนพดล\nนราดูร\nนเรนทร\nนอสตราดามุส\nนาซา\nนาซ่า\nนาซี\nนาโต\nนาโต้\nนาลแก\nนิคอน\nนิโคลัส\nนิด้า\nนินเทนโด\nนิปปอน\nนิวตัน\nนิสสัน\nเนคเทค\nเนชั่น\nเนชันแนล\nเนชั่นแนล\nเนวิน\nเนสเล่\nเนสาด\nแนท\nแนสแดค\nโนเกีย\nโนเบล\nโนเวลล์\nโนโวเทล\nไนเม็กซ์\nบรอดเวย์\nบรัดเลย์\nบรู๊ซ\nบัลเมอร์\nบารัก\nบารัค\nบู๊ตึ๊ง\nเบญกาย\nเบนซ์\nเบ็นซ์\nเบนจามิน\nโบตัน\nไบโอเทค\nประชาธิปัตย์\nปวีณา\nปอเต็กตึ๊ง\nปอเต๊กตึ๊ง\nป่อเต็กตึ๊ง\nปัตตะโชติ\nปารุสก์\nปีเตอร์\nปูติน\nเป๊ปซี่\nเป้ย\nเปอร์โยต์\nเปาบุ้นจิ้น\nโปเกมอน\nโป๊ยก่าย\nพรหมทัต\nพลาโต\nพอลล่า\nพานาโซนิค\nพานาโซนิก\nพิทยานุกูล\nพิมพิสาร\nเพนแทกซ์\nเพลโต\nไพโอเนียร์\nฟรอยด์\nฟรังซิส\nฟรานซิส\nฟลอเรนซ์\nฟอร์ด\nฟิลิปส์\nฟูจิ\nแฟซ่า\nโฟร์โมสต์\nภูมิพล\nภูริทัต\nมงฟอร์ต\nมณโฑ\nมติชน\nมหิตลาธิเบศร\nมโหสถ\nมัจฉานุ\nมาร์กาเร็ต\nมาร์ติน\nมาสด้า\nมิตซูบิชิ\nมิราเคิล\nมุสโสลินี\nเม้ง\nเมจิ\nเมอร์ซีเดส\nเมอร์เซเดส\nแมกซ์เวลล์\nแมกไซไซ\nแมคอินทอช\nแมชีนเนอรี่\nโมคคัลลานะ\nโมโตโรลา\nโมโตโรล่า\nโมเนีย\nไมเคิล\nไมยราพณ์\nยโสธรา\nยะโฮวา\nยะโฮวาห์\nยามาฮ่า\nยาเวห์\nยาฮู\nยูนิเซฟ\nยูเนสโก\nยูไล\nเยโฮวาห์\nรอยเตอร์\nรอยัล\nรัชดา\nรัสปูติน\nราฟาเอล\nรามาวตาร\nราเมศวร\nราหุล\nริชาร์ด\nรีพับลิกัน\nรูนีย์\nเรนโบว์\nแรมโบ้\nโรตารี\nโรนัลโด\nโรนัลโด้\nโรบินสัน\nโรเบิร์ต\nล็อกซเล่ย์\nลิงคอล์น\nลิจฉวี\nลิไท\nลิไทย\nลินคอล์น\nลิเวอร์พูล\nเลโนโว\nเลียดก๊ก\nโลตัส\nวชิราลงกรณ์\nวลาดิเมียร์\nวอลล์สตรีท\nวาเลนไทน์\nวิกตอเรีย\nวิทยานุสรณ์\nวิทยายน\nวิมเบิลดัน\nวิลเลียม\nวีระ\nวุฒิชัย\nเวียดกง\nไวตามิลค์\nศกุนตลา\nศรีวิชัย\nศิริพงษ์\nศิริราช\nศุภชลาศัย\nสดกก๊อกธม\nสดายุ\nสตาลิน\nสตีฟ\nสแตนฟอร์ด\nสวรินทิรา\nสังกัจจายน์\nสาทิตย์\nสารีบุตร\nสิริกิติ์\nสิรินธร\nสิหิงค์\nสีวลี\nสีหนุ\nสีหมุนี\nสีหโมนี\nสุครีพ\nสุทโธทนะ\nสุเทพ\nสุนทราภรณ์\nสุนีย์\nสุรนารี\nสุรยุทธ์\nสุริยาสน์\nเส้าหลิน\nโสกราตีส\nโสภิต\nหนุมาน\nหลินฮุ่ย\nหลุยส์\nเห้งเจีย\nไหหม่า\nองคต\nองคุลิมาล\nอชาตศัตรู\nอดุลยเดช\nอพอลโล\nอริสโตเติล\nอริสมันต์\nอลิซาเบธ\nอ๋อม\nออร์คิด\nออสการ์\nอะพอลโล\nอับราฮัม\nอั้ม\nอัลกออิดะห์\nอัลคาเทล\nอัลจาซีราห์\nอัลเฟรด\nอัลเลาะห์\nอัสซุส\nอัสสชิ\nอัสสัมชัญ\nอาเซม\nอาเซ็ม\nอาเซียน\nอาฟต้า\nอาร์เซนอล\nอินทรชิต\nอินทราทิตย์\nอีซูซุ\nอีเลฟเวน\nอีเลฟเว่น\nอุณรุท\nอุบลรัตน์\nอุบาลี\nอุ๋ย\nเอกทัศน์\nเอเซอร์\nเอ็ดเวิร์ด\nเอดิสัน\nเอแบค\nเอลิซาเบธ\nเอสพลานาด\nเอสพลานาร์ด\nแอคคอร์\nแอคคอร์ด\nแองเจลิน่า\nแอตแลนติส\nแอน\nแอ๋ม\nแอมบาสซาเดอร์\nแอมบาสเดอร์\nแอมเวย์\nแอ๋ว\nโอดีสซีย์\nโอเดียน\nโอบามา\nโอรสาราม\nโอลิมเปีย\nโออิชิ\nไอน์สไตน์\nฮอนด้า\nฮอปกินส์\nฮอลลีวูด\nฮอลลีวู้ด\nฮานามิ\nฮามาส\nฮิตเลอร์\nฮิตาชิ\nฮุนเซน\nฮุนเซ็น\nฮุนได\nฮุสเซ็น\nเฮนรี\nเฮนรี่\nเฮเลน\nโฮจิมินห์\nโฮปเวลล์\nโฮเมอร์\n\nกลีเซอรีน\nกำทอน\nแกนีมีด\nครอส\nคริสตัล\nคลอโรพลาสต์\nคลอไรด์\nควอนตัม\nคอนดักเตอร์\nคอปเปอร์\nคอลลาเจน\nคอเลสเตอรอล\nคอสมิก\nคูลอมบ์\nเคอราติน\nแคโรทีน\nแคสสินี\nโครมาโทกราฟี\nไคโตซาน\nจีโนม\nจุลชีววิทยา\nชิคุนกุนยา\nซัลฟิวริก\nซัลเฟต\nซัลไฟด์\nซิงค์\nซิริอุส\nซิลิกา\nซิลิเกต\nซิลิโคน\nซีเทน\nซีเวิร์ต\nเซ็กเตอร์\nเซ็กเมนต์\nเซมิ\nโซนาร์\nไซบอร์ก\nดอปเปลอร์\nดอปเพลอร์\nไดนามิก\nไดนามิกส์\nไดนามิค\nไดนามิคส์\nไดออกไซด์\nทรานส์\nทามิฟลู\nเทฟลอน\nเทสโทสเตอโรน\nเทอร์โม\nแทนนิน\nไททัน\nไทฟอยด์\nไทรอยด์\nธาลัสซีเมีย\nเนกาตีฟ\nโนวา\nบอแรกซ์\nโบทอกซ์\nโบท็อกซ์\nไบโอติน\nปฏิยานุพันธ์\nโปรเจสเตอโรน\nพอลิเมอร์\nพันธุศาสตร์\nพัลซาร์\nพาร์กินสัน\nพาราเซตามอล\nพาราโบลา\nเพอร์ออกไซด์\nโพรเจสเทอโรน\nโพลาไรซ์\nโพลิเมอร์\nโพลีเอทิลีน\nไพรเมต\nฟลาโวนอยด์\nฟลูออเรสเซนซ์\nฟลูออไรด์\nฟอสซิล\nฟิชชัน\nฟิวชัน\nฟีโรโมน\nไฟเบอร์\nมอนอกไซด์\nมิราจ\nเมตริกซ์\nเมทริกซ์\nเมลานิน\nเมลามีน\nโมเมนตัม\nไมโตคอนเดรีย\nไมโทคอนเดรีย\nยีสต์\nยูริก\nยูเรีย\nรูมาตอยด์\nวีก้า\nเวกเตอร์\nเวก้า\nเวสิเคิล\nโวลต์\nสเกล\nสเกลาร์\nสเต็ม\nสเตียรอยด์\nสปีชีส์\nสเปิร์ม\nสัมพัทธภาพ\nสุริยจักรวาล\nออกเทน\nออโรรา\nออโรร่า\nอะคริลิก\nอะครีลิก\nอะซีติก\nอะซีโตน\nอะมิโน\nอะลูมินา\nอันโดรเมดา\nอัลคาไลน์\nอัลตราซาวด์\nอัลตราซาวนด์\nอัลลอยด์\nอินทิกรัล\nอินทิเกรต\nอีโบลา\nอีโบล่า\nเอ็กซ์โพเนนเชียล\nเอทานอล\nเอทิลีน\nเอนโทรปี\nเอสเตอร์\nเอสโตรเจน\nเอสโทรเจน\nแอนดรอยด์\nแอนแทร็กซ์\nแอมพลิจูด\nแอมโมเนียม\nแอลกอฮอลิซึม\nแอสพาร์แตม\nโอเซลทามิเวียร์\nฮับเบิล\nฮิวมัส\nไฮดรอกไซด์\nไฮดรอลิก\nไฮโดรลิก\nไฮเพอร์โบลา\n\nกงเต็ก\nกฎุมพี\nกฏ\nกฏหมาย\nกบฎ\nกราไฟต์\nก๊อปปี้\nกะทะ\nกังวาล\nกุฎฐัง\nกุฏุมพี\nฃวด\nคฑา\nคลินิค\nคลีนิก\nคลีนิค\nคาทอลิค\nคึ่นฉ่าย\nแคตตาล็อก\nโควต้า\nฅน\nจุมพฎ\nช็อคโกแลต\nแซ่ด\nดัทช์\nทนง\nทรมาณ\nทราก\nทะแยง\nทิฏฐิ\nบล็อค\nบ๊องแบ๊ว\nบัลเล่ต์\nเบรค\nแบงค์\nปรากฎ\nปัคคหะ\nปาฏิโมกข์\nปิติ\nปิรามิด\nโปรเตสแตนท์\nพนิช\nพยักเพยิด\nพริ้ว\nพลูโตเนียม\nพากษ์\nเฟิร์น\nยากี้\nเยภุยยสิกา\nรุสเซีย\nฤาษี\nล็อค\nล็อคเกอร์\nวันทยาหัตถ์\nวานิช\nวิญญาน\nวิศิษฐ์\nศรีษะ\nสเปกโทรสโคป\nสฤษฎ์\nสลิ่ม\nสัตตสดก\nสาราณียากร\nสุกี้\nสุกี้ยากี้\nสูญญากาศ\nหยอมแหยม\nหยอย\nหล่ะ\nอะดรีนาลีน\nอะหลั่ย\nอัตคัต\nอัฟริกา\nอานิสงค์\nอาฟริกา\nอิริยาบท\nอิเลคโทรนิคส์\nอีรุงตุงนัง\nอุตรายัน\nอุลตรา\nอุลตร้า\nโอกาศ\n\nกกหู\nกงการ\nกงจักร\nกฎเกณฑ์\nกฎบัตร\nกฎหมาย\nกฎหมู่\nกดขี่\nกดดัน\nก้นกบ\nก้นบึ้ง\nก้นปล่อง\nกนิษฐภคินี\nกนิษฐภาดา\nกรงเล็บ\nกรมการ\nกรมท่า\nกรมธรรม์\nกรมนา\nกรมวัง\nกรรมกร\nกรรมการ\nกรรมฐาน\nกรรมบถ\nกรรมพันธุ์\nกรรมวิธี\nกรรมสิทธิ์\nกระจกเงา\nกระจกตา\nกระจกนูน\nกระจกเว้า\nกระจอกชวา\nกระจอกเทศ\nกระจ้อยร่อย\nกระจับบก\nกระจับปิ้ง\nกระจับปี่\nกระโชกโฮกฮาก\nกระดานดำ\nกระดานหก\nกระดาษแก้ว\nกระดาษไข\nกระดาษทราย\nกระดาษสา\nกระดูกงู\nกระทาชาย\nกระเท่เร่\nกระบวนการ\nกระบองเพชร\nกระผีกริ้น\nกระยาทิพย์\nกระยาสารท\nกระยาหาร\nกระสอบทราย\nกระสุนปืน\nกระแสจิต\nกระแสน้ำ\nกระแสลม\nกรับคู่\nกรับพวง\nกรับเสภา\nกราดเกรี้ยว\nกราวรูด\nกริ่งเกรง\nกรีฑาสถาน\nกรีดกราย\nกรี๊ดกร๊าด\nกลไก\nกลบท\nกลเม็ด\nกลยุทธ์\nกลวิธี\nกลศาสตร์\nกลอักษร\nกลบเกลื่อน\nกลมกล่อม\nกลมกลืน\nกลมเกลียว\nกล้วยแขก\nกล้วยไม้\nกล่องเสียง\nกล่อมเกลา\nกล่อมเกลี้ยง\nกลัดกลุ้ม\nกลัดมัน\nกลั่นกรอง\nกลั่นแกล้ง\nกลับกลอก\nกลางคน\nกลางคัน\nกลางค่ำ\nกลางคืน\nกลางแจ้ง\nกลางแปลง\nกลางวัน\nกลาดเกลื่อน\nกล่าวขวัญ\nกล่าวโทษ\nกล่าวหา\nกล้ำกราย\nกล้ำกลืน\nกลิ้งกลอก\nกลิ้งเกลือก\nกลิ่นอาย\nกลียุค\nกวดขัน\nกวัดแกว่ง\nกวัดไกว\nกวีนิพนธ์\nก่อกวน\nก่อการ\nก่อตั้ง\nก่อสร้าง\nก่อหวอด\nก้อร่อก้อติก\nกองกลาง\nกองเกิน\nกองโจร\nกองทัพ\nกองทุน\nกองพล\nกองพัน\nกองฟอน\nกองร้อย\nกองหนุน\nกอบโกย\nกะเกณฑ์\nกะบังลม\nกักกัน\nกักขัง\nกักตัว\nกักตุน\nกัณฑ์เทศน์\nกัดฟัน\nกันชน\nกันท่า\nกันสาด\nกันเอง\nกับแกล้ม\nกับข้าว\nกับระเบิด\nกากเพชร\nกากหมู\nกาชาด\nกาญจนาภิเษก\nก้านคอ\nกาฝาก\nก้ามกราม\nกามกิจ\nกามคุณ\nกามเทพ\nกามโรค\nก้ามปู\nกายกรรม\nกายบริหาร\nกายภาพ\nกายวิภาค\nกายสิทธิ์\nก่ายกอง\nการคลัง\nการเงิน\nการบ้าน\nการเปรียญ\nการเมือง\nการเรือน\nการละเล่น\nกาลกิริยา\nกาลเทศะ\nก้าวก่าย\nก้าวร้าว\nก้าวหน้า\nกาสาวพัสตร์\nกาฬพฤกษ์\nกาฬโรค\nกำปั้น\nกำมือ\nกำแพงขาว\nกำลังใจ\nกำลังม้า\nกี่งอำเภอ\nกิจกรรม\nกิจการ\nกิจวัตร\nกิจจะลักษณะ\nกิตติคุณ\nกิตติศัพท์\nกินขาด\nกินใจ\nกินดอง\nกินโต๊ะ\nกินแบ่ง\nกินเปล่า\nกินเลี้ยง\nกินเส้น\nกินแหนง\nกิโลกรัม\nกิโลเมตร\nกิโลลิตร\nกิโลเฮิรตซ์\nกีดกัน\nกีดกั้น\nกีดขวาง\nกึกก้อง\nกึกกัก\nกึกกือ\nกึ่งกลาง\nกุกกัก\nกุ๊กกิ๊ก\nกุ้งฝอย\nกุ้งมังกร\nกุ้งแห้ง\nกุ้งเต้น\nกุ้งยิง\nกุญแจผี\nกุญแจมือ\nกุญแจเลื่อน\nกุญแจเสียง\nกุลธิดา\nกุลบุตร\nกุลสตรี\nกู้ยืม\nเก้งก้าง\nเก็บกวาด\nเก็บเกี่ยว\nเก็บงำ\nเก็บตก\nเกรงกลัว\nเกรงใจ\nเกรงขาม\nเกรียงไกร\nเกรียมกรม\nเกรี้ยวกราด\nเกล็ดเลือด\nเกลี้ยกล่อม\nเกลี้ยงเกลา\nเกลือกกลั้ว\nเกลือกกลิ้ง\nเกลื่อนกล่น\nเกลื่อนกลาด\nเกศธาตุ\nเกษตรกร\nเกษตรกรรม\nเกษตรศาสตร์\nเกษมสันต์\nเกษียรสมุทร\nเก้อเขิน\nเกาะแกะ\nเกี่ยงงอน\nเกียจคร้าน\nเกียรติคุณ\nเกียรตินิยม\nเกียรติประวัติ\nเกียรติภูมิ\nเกียรติยศ\nเกียรติศักดิ์\nเกียรติมุข\nเกี่ยวข้อง\nเกี่ยวดอง\nเกี่ยวพัน\nเกี่ยวโยง\nเกี้ยวพาน\nเกี้ยวพาราสี\nแก่แดด\nแก้ขัด\nแก้ไข\nแก้ตัว\nแก้เผ็ด\nแก้ลำ\nแกงคั่ว\nแกงจืด\nแกงบวด\nแกงป่า\nแกงเผ็ด\nแกงส้ม\nแก่งแย่ง\nแก่นแก้ว\nแก่นสาร\nแก้วตา\nแก้วหู\nแกว่งกวัด\nแกว่งไกว\nแกะรอย\nโก้เก๋\nโกรธเกรี้ยว\nโกรธขึ้ง\nไก่เขี่ย\nไก่ชน\nไก่บ้าน\nไก่ป่า\nไก่ฟ้า\nไกล่เกลี่ย\nขจัดขจาย\nขนเพชร\nขนสัตว์\nขนหนู\nขนส่ง\nขนมจีน\nขบขัน\nขบวนการ\nข่มขี่\nข่มขู่\nข่มขืน\nข่มเหง\nขมหิน\nขมิ้นชัน\nขมุบขมิบ\nขยะแขยง\nขยักขย่อน\nขยักขย้อน\nขยับขยาย\nขยับเขยื้อน\nขวดโหล\nขวยเขิน\nขวัญใจ\nขวัญตา\nขวัญอ่อน\nขวากหนาม\nขวางโลก\nของ้าว\nขอสับ\nขอขมา\nขอทาน\nขอโทษ\nขอร้อง\nขออภัย\nข้อเขียน\nข้อความ\nข้อเท็จจริง\nของกลาง\nของขวัญ\nของแข็ง\nของชำ\nของลับ\nของเล่น\nของว่าง\nของเหลว\nของไหล\nของไหว้\nข้องใจ\nข้องแวะ\nขอบข่าย\nขอบเขต\nขอบคุณ\nขอบใจ\nขอบพระคุณ\nข้อมูล\nข้อแม้\nข้อหา\nข้อสังเกต\nขัดข้อง\nขัดขืน\nขัดเขิน\nขัดจังหวะ\nขัดดอก\nขัดแตะ\nขัดยอก\nขัดแย้ง\nขัดสมาธิ\nขันหมาก\nขันอาสา\nขับขี่\nขับเคี่ยว\nขั้วโลก\nขาจร\nขาประจำ\nข้าราชการ\nข้าศึก\nข้าหลวง\nขาดแคลน\nขาดใจ\nขาดตอน\nขาดตัว\nขาดทุน\nขาดเหลือ\nขายหน้า\nข่าวกรอง\nข่าวคราว\nข่าวล่า\nข่าวลือ\nข่าวสาร\nข้าวเกรียบ\nข้าวแกง\nข้าวของ\nข้าวจี่\nข้าวเจ้า\nข้าวซอย\nข้าวต้ม\nข้าวตอก\nข้าวตัง\nข้าวแตน\nข้าวทิพย์\nข้าวบิณฑ์\nข้าวเปลือก\nข้าวโพด\nข้าวฟ่าง\nข้าวเม่า\nข้าวสวย\nข้าวสาร\nข้าวเหนียว\nข้าวหมาก\nข้าวหลาม\nขี้เกียจ\nขี้ข้า\nขี้ครอก\nขี้คร้าน\nขี้คุก\nขี้ไคล\nขี้เซา\nขีดขั้น\nขีดคร่อม\nขีดคั่น\nขีดฆ่า\nขี้ตา\nขี้ตืด\nขี้เถ้า\nขี้ทูด\nขี้ปะติ๋ว\nขี้ผึ้ง\nขี้มูก\nขี้ยา\nขี้แย\nขี้ริ้ว\nขี้เรื้อน\nขี้เล็บ\nขี้หู\nขี้หน้า\nขี้เหนียว\nขี้เหล็ก\nขี้เหร่\nขึงขัง\nขึงพืด\nขึ้งโกรธ\nขึ้นใจ\nขึ้นชื่อ\nขึ้นมือ\nขืนใจ\nขื่นขม\nขุดคุ้ย\nขุนทอง\nขุนนาง\nขุนพล\nขุนศึก\nขุนหลวง\nขูดรีด\nเข็มกลัด\nเข็มขัด\nเข้มข้น\nเข้มแข็ง\nเข้มงวด\nเข็มทิศ\nเข็มหมุด\nเข้าขา\nเข้าเค้า\nเข้าใจ\nเข้าชื่อ\nเข้าตัว\nเข้าถึง\nเข้าทรง\nเข้าท่า\nเข้าที\nเข้าเนื้อ\nเข้าเล่ม\nเขียวเสวย\nเขียวหวาน\nแขกเต้า\nแข็งกร้าว\nแข็งกล้า\nแข็งแกร่ง\nแข็งข้อ\nแข็งขัน\nแข่งขัน\nแข็งใจ\nแข็งตัว\nแข็งเมือง\nแข็งแรง\nแขวนลอย\nโขกสับ\nโขยกเขยก\nไขข้อ\nไขควง\nไขมัน\nไข่มุก\nไขว่ห้าง\nไขสันหลัง\nไขสือ\nไข่เค็ม\nไข่เยี่ยวม้า\nไข่หงส์\nไข่เหี้ย\nคงกระพัน\nคงตัว\nคงทน\nคงที่\nคชลักษณ์\nคชสาร\nคชสีห์\nคชราช\nคณิตศาสตร์\nคดเคี้ยว\nคติธรรม\nคติพจน์\nคนกลาง\nคนไข้\nคนใช้\nคนทรง\nคบไฟ\nคบเพลิง\nคบค้า\nคบคิด\nคบหา\nคมคาย\nครบครัน\nครบถ้วน\nครอบครอง\nครอบคลุม\nครอบครัว\nครอบงำ\nครอบจักรวาล\nคริสตกาล\nคริสตจักร\nคริสต์มาส\nคริสต์ศตวรรษ\nคริสต์ศักราช\nคริสตัง\nคริสเตียน\nครุกรรม\nครุภัณฑ์\nครุศาสตร์\nครุฑพ่าห์\nครุ่นคิด\nคลอเคลีย\nคล่องแคล่ว\nคล่องตัว\nคล่องมือ\nคลั่งไคล้\nคลาคล่ำ\nคลาไคล\nคลาดเคลื่อน\nคลาดแคล้ว\nคลี่คลาย\nคลึงเคล้น\nคลึงเคล้า\nคลื่นไส้\nคลื่นเหียน\nคลุกคลี\nคลุกคลาน\nคลุมเครือ\nคลุมโปง\nคลุ้มคลั่ง\nควงสว่าน\nควบคุม\nควบคู่\nควบแน่น\nควันหลง\nความคิด\nความหลัง\nความเห็น\nคอหอย\nคอห่าน\nคอแห้ง\nค่อนขอด\nค่อนแคะ\nค้อนควัก\nคั่งค้าง\nคั่งแค้น\nคัดค้าน\nคัดง้าง\nคัดท้าย\nคัดเลือก\nคันจาม\nคันฉ่อง\nคันฉาย\nคันชัก\nคันชั่ง\nคันไถ\nคันนา\nคันเร่ง\nคับขัน\nคับคั่ง\nคับแค้น\nคับแคบ\nคางทูม\nคางหมู\nค้างคืน\nค้างปี\nคาดคั้น\nคาดเชือก\nคาดโทษ\nคาดหมาย\nคานหาม\nคาบเกี่ยว\nคาบศิลา\nคาบสมุทร\nคำขาด\nคำนำ\nคิดค้น\nคืนดี\nคืนตัว\nคุกเข่า\nคุณค่า\nคุณชาย\nคุณธรรม\nคุณนาย\nคุณภาพ\nคุณลักษณะ\nคุณวุฒิ\nคุณศัพท์\nคุณสมบัติ\nคุณหญิง\nคุณากร\nคุณูปการ\nคุโณปการ\nคุมเชิง\nคุ้มกัน\nคุยเขื่อง\nคุยโต\nคุ้ยเขี่ย\nคุ้มครอง\nคู่กรณี\nคู่กัด\nคู่ขา\nคู่แข่ง\nคู่ครอง\nคู่ควร\nคู่คิด\nคู่คี่\nคู่ใจ\nคู่ชีพ\nคู่ชีวิต\nคู่บารมี\nคู่บุญ\nคู่ปรปักษ์\nคู่ปรับ\nคู่ผสม\nคู่มือ\nคู่รัก\nคู่ลำดับ\nคู่สาย\nคู่หมั้น\nคู่หู\nคู่อริ\nคู่อาฆาต\nเคมีภัณฑ์\nเคยตัว\nเคร่งขรึม\nเคร่งครัด\nเคร่งเครียด\nเครดิตฟองซิเอร์\nเครื่องกล\nเครื่องกัณฑ์\nเครื่องแกง\nเครื่องเขิน\nเครื่องครัว\nเครื่องเคียง\nเครื่องเงิน\nเครื่องจักร\nเครื่องเซ่น\nเครื่องดนตรี\nเครื่องต้น\nเครื่องทุ่นแรง\nเครื่องเทศ\nเครื่องใน\nเครื่องบิน\nเครื่องบูชา\nเครื่องแบบ\nเครื่องประดับ\nเครื่องปรุง\nเครื่องปรุงรส\nเครื่องมือ\nเครื่องยนต์\nเครื่องร่อน\nเครื่องราง\nเครื่องเรือน\nเครื่องล่าง\nเครื่องเล่น\nเครื่องสาย\nเครื่องสำอาง\nเครื่องสุกำศพ\nเครื่องหมาย\nเครือรัฐ\nเคลียคลอ\nเคลื่อนที่\nเคลื่อนไหว\nเคลือบแคลง\nเคลือบแฝง\nเคลือบฟัน\nเคว้งคว้าง\nเคหสถาน\nเค้าโครง\nเคียดแค้น\nเคี่ยวเข็ญ\nเคี้ยวเอื้อง\nเคืองขุ่น\nโคนม\nโคบาล\nโคมูตร\nโคมลอย\nโครงการ\nโครงเรื่อง\nโครงงาน\nโครงสร้าง\nโครมคราม\nโคลงเคลง\nฆ้องกระแต\nฆ้องชัย\nฆ้องวง\nฆ้องหุ่ย\nฆ้องเหม่ง\nฆ้องโหม่ง\nฆาตกร\nฆาตกรรม\nฆานประสาท\nงงงวย\nงงงัน\nงดเว้น\nงบดุล\nงบประมาณ\nงมโข่ง\nงมงาย\nง่วงงุน\nง่วงเหงา\nงอหาย\nง้องอน\nงอนง้อ\nงอมแงม\nงาช้าง\nง่าเงย\nงานการ\nง่ายดาย\nงึมงำ\nเงินเดือน\nเงินตรา\nเงินยวง\nเงียบกริบ\nเงียบเชียบ\nเงียบเหงา\nเงื่องหงอย\nเงื่อนไข\nเงื่อนงำ\nเงื่อนเวลา\nเงื้อมมือ\nแง่งอน\nจงใจ\nจงรัก\nจดจ่อ\nจดจำ\nจดหมาย\nจดหมายเหตุ\nจรจัด\nจรรยาบรรณ\nจริงจัง\nจริงใจ\nจอมขวัญ\nจอมใจ\nจอมทัพ\nจอมปลวก\nจอมพล\nจ๊ะเอ๋\nจักสาน\nจักรพรรดิ\nจักรภพ\nจักรยาน\nจักรยานยนต์\nจักรราศี\nจักรวรรดิ\nจักรวรรดินิยม\nจักรวาล\nจังหนับ\nจัดการ\nจัดจ้าน\nจัดเจน\nจัดแจง\nจัดตั้ง\nจัดสรร\nจับกุม\nจับจด\nจับเจ่า\nจ่าหน้า\nจาตุทสี\nจาตุมหาราช\nจาตุมหาราชิก\nจาตุมหาราชิกา\nจาตุรงคสันนิบาต\nจาตุรราชการ\nจานเชิง\nจานบิน\nจานผี\nจานเสียง\nจาบจ้วง\nจำเป็น\nจำพรรษา\nจำวัด\nจ้ำจี้จ้ำไช\nจำเลาะตา\nจิงโจ้น้ำ\nจิตใจ\nจิตตภาวนา\nจิตตัง\nจิตตานุปัสสนา\nจิตนิยม\nจิตบำบัด\nจิตแพทย์\nจิตวิสัย\nจิตรกร\nจิตรกรรม\nจิตรลดา\nจิตวิทยา\nจิตเวช\nจิตเวชศาสตร์\nจินตกวี\nจินตนา\nจินตนาการ\nจินตภาพ\nจุฑามณี\nจุฑามาศ\nจุฑารัตน์\nจุนเจือ\nจุ้นจ้าน\nจุลชีพ\nจุลชีวัน\nจุลชีวิน\nจุลทรรศน์\nจุลภาค\nจุลวรรค\nจุลศักราช\nจุลสาร\nจุลินทรีย์\nจุฬามณี\nจุฬาลักษณ์\nเจตคติ\nเจตจำนง\nเจตนารมณ์\nเจตภูต\nเจริญพร\nเจ้ากรม\nเจ้ากรรม\nเจ้าของ\nเจ้าขา\nเจ้าข้า\nเจ้าคณะ\nเจ้าค่ะ\nเจ้าจอม\nเจ้าชู้\nเจ้าตัว\nเจ้าถิ่น\nเจ้าท่า\nเจ้าที่\nเจ้าทุกข์\nเจ้านาย\nเจ้าเนื้อ\nเจ้าบ้าน\nเจ้าบ่าว\nเจ้าประคุณ\nเจ้าประคู้น\nเจ้าพนักงาน\nเจ้าพระคุณ\nเจ้าพระยา\nเจ้าพ่อ\nเจ้าพายุ\nเจ้าฟ้า\nเจ้าภาพ\nเจ้ามือ\nเจ้าแม่\nเจ้าเรือน\nเจ้าสังกัด\nเจ้าสัว\nเจ้าสาว\nเจ้าหน้าที่\nเจ้าหนี้\nเจ้าอาวาส\nเจาะจง\nเจือจาง\nเจือจาน\nเจือปน\nเจื้อยแจ้ว\nแจกจ่าย\nแจ่มแจ้ง\nแจ่มใส\nโจงกระเบน\nโจมตี\nโจรกรรม\nโจรสลัด\nใจความ\nใจคอ\nฉกฉวย\nฉกชิง\nฉลองได\nฉ้อฉล\nฉัตรมงคล\nฉันทลักษณ์\nฉายาลักษณ์\nฉิบหาย\nฉุกเฉิน\nฉุกละหุก\nฉุนเฉียว\nฉุปศาสตร์\nเฉไฉ\nเฉยเมย\nเฉาโฉด\nเฉิดฉัน\nเฉิดฉาย\nเฉิดฉิน\nเฉียบขาด\nเฉียบพลัน\nเฉียบแหลม\nเฉื่อยชา\nแฉะแบะ\nโฉดเฉา\nโฉมงาม\nโฉมฉาย\nโฉมเฉลา\nโฉมตรู\nโฉมยง\nโฉมศรี\nโฉมหน้า\nชดช้อย\nชดเชย\nชดใช้\nชนบท\nชนินทร์\nชนกกรรม\nชนมพรรษา\nชนมายุ\nชมเชย\nชมพูทวีป\nชมพูนท\nชมพูนุท\nชราธรรม\nชราภาพ\nชลจร\nชลธาร\nชลธี\nชลนัยน์\nชลนา\nชลเนตร\nชลประทาน\nชลมารค\nชลาธาร\nชลาลัย\nชลาศัย\nชลาสินธุ์\nชโลทร\nช่วงชิง\nช่วงใช้\nชวนชม\nชวนหัว\nช่วยเหลือ\nช่อฟ้า\nช่อม่วง\nชอกช้ำ\nช่องเขา\nช่องแคบ\nช่องไฟ\nช่องว่าง\nช้องนาง\nชอบกล\nชอบใจ\nชอบธรรม\nชอบพอ\nชักโครก\nชักเงา\nชักจูง\nชักชวน\nชักนำ\nชักเนื้อ\nชักพระ\nชักเย่อ\nชักใย\nชั่งใจ\nชังฆวิหาร\nชัดเจน\nชั้นเชิง\nชั่วคน\nชั่วคราว\nชั่วช้า\nชั่วโมง\nชั่วแล่น\nชาเย็น\nช้านาน\nช่างเครื่อง\nช่างฝีมือ\nช่างฟิต\nช่างไฟ\nช้างน้ำ\nช้างเผือก\nช้างพลาย\nช้างพัง\nช้างสาร\nช้างสีดอ\nชาติธรรม\nชาตินิยม\nชาติพันธุ์\nชาติพันธุ์วิทยา\nชาติภูมิ\nชานชาลา\nชายชาตรี\nชายคา\nชายฝั่ง\nชายทะเล\nชาวเล\nชาววัง\nช้ำใจ\nช้ำชอก\nชิงชัง\nชิงพลบ\nชินชา\nชินบุตร\nชิ้นเอก\nชิมลาง\nชีเปลือย\nชี้ขาด\nชี้แจง\nชี้นำ\nชี้แนะ\nชี้ฟ้า\nชีพจร\nชีพิตักษัย\nชื่นชม\nชื่นบาน\nชื่นมื่น\nชื่อย่อ\nชื่อรอง\nชื่อเล่น\nชื่อเสียง\nชุกชุม\nชุติมา\nชุบตัว\nชุบเลี้ยง\nชุมชน\nชุมทาง\nชุมสาย\nชุ่มใจ\nชุ่มชื่น\nชุ่มชื้น\nชุมนุมชน\nชูชีพ\nชูโรง\nชู้สาว\nเชยชม\nเชลยศักดิ์\nเชลยศึก\nเช่าซื้อ\nเช้าตรู่\nเช้ามืด\nเชิงกราน\nเชิงกล\nเชิงชั้น\nเชิงชาย\nเชิงซ้อน\nเชิงเดียว\nเชิงเดี่ยว\nเชิงตะกอน\nเชิงเทิน\nเชิงมุม\nเชิดชู\nเชิงอรรถ\nเชี่ยนหมาก\nเชี่ยวชาญ\nเชื่องช้า\nเชื่อใจ\nเชื่อถือ\nเชื่อฟัง\nเชื่อมือ\nเชื้อชาติ\nเชื้อเพลิง\nเชื้อไฟ\nเชื้อโรค\nเชื้อสาย\nเชื้อเชิญ\nเชื่องช้า\nเชือนแช\nเชื่อวัน\nแช่เย็น\nแช่อิ่ม\nแช่มช้อย\nแช่มชื่น\nโชกโชน\nโชติช่วง\nโชติรส\nใช้สอย\nซบเซา\nซมซาน\nซวนเซ\nซอกซอน\nซอกแซก\nซ่องสุม\nซ่องเสพ\nซ่องแซ่ง\nซ่อนรูป\nซ่อนเร้น\nซ่อนหา\nซ่อนกลิ่น\nซ่อนทราย\nซ่อมแซม\nซักค้าน\nซักซ้อม\nซักไซ้\nซักฟอก\nซักแห้ง\nซังกะตาย\nซังตาย\nซัดเซ\nซัดทอด\nซับซ้อน\nซับใน\nซับพระพักตร์\nซากศพ\nซ่านเซ็น\nซ้ำซ้อน\nซ้ำซาก\nซ้ำเติม\nซ้ำร้าย\nซี่โครง\nซีดเซียว\nซึมกะทือ\nซึมซาบ\nซึมเซา\nซึมทราบ\nซึมเศร้า\nซื่อตรง\nซื่อสัตย์\nซื้อขาย\nซุกซน\nซุกซ่อน\nซุบซิบ\nซู่ซ่า\nเซซัง\nเซ่อซ่า\nแซ่ซ้อง\nโซดาไฟ\nญาณทัสนะ\nญาณวิทยา\nญาณศาสตร์\nญาติกา\nฐานราก\nดกดื่น\nดงดิบ\nดลใจ\nดลบันดาล\nดวงแก้ว\nดวงใจ\nดวงเดือน\nดวงตรา\nดวงตา\nดวงสมร\nดอกจัน\nดอกจิก\nดอกบัว\nดอกเบี้ย\nดอกฟ้า\nดอกไม้\nดอกยาง\nดอกเล็บ\nดอกทอง\nดอกสร้อย\nดองยา\nดักคอ\nดักฟัง\nดังนั้น\nดังนี้\nดังหนึ่ง\nดั้งเดิม\nดัดจริต\nดัดแปลง\nดันทุรัง\nดับขันธ์\nดับจิต\nดับชีพ\nด่าทอ\nด่างทับทิม\nด่างพร้อย\nดาดฟ้า\nดาราศาสตร์\nดาลเดือด\nดาวกระจาย\nดาวเคราะห์\nดาวตก\nดาวเทียม\nดาวรุ่ง\nดาวเรือง\nดาวฤกษ์\nดาวหาง\nดาวเหนือ\nดาษดื่น\nดินขาว\nดินดาน\nดินดำ\nดินประสิว\nดินปืน\nดินระเบิด\nดินสอ\nดินสอพอง\nดิ้นรน\nดิบดี\nดีเกลือ\nดีใจ\nดีซ่าน\nดีดัก\nดีเดือด\nดีฝ่อ\nดีดดิ้น\nดึกดำบรรพ์\nดึกดื่น\nดึงดัน\nดึงดูด\nดื่มด่ำ\nดื้อด้าน\nดื้อดึง\nดื้อแพ่ง\nดื้อยา\nดื้อรั้น\nดุดัน\nดุเดือด\nดุร้าย\nดุลการค้า\nดุลพินิจ\nดุลภาค\nดุลยพินิจ\nดุลยภาพ\nดุษฎีนิพนธ์\nดุษฎีบัณฑิต\nดุษณีภาพ\nดูแคลน\nดูถูก\nดูดาย\nดูเบา\nดูแล\nดูหมิ่น\nดูเหมือน\nดูดดื่ม\nเด็ดขาด\nเด็ดดวง\nเด็ดเดี่ยว\nเดนตาย\nเดาสวด\nเดาสุ่ม\nเดินทาง\nเดินสะพัด\nเดินสาย\nเดินเหิน\nเดิมพัน\nเดียงสา\nเดียดฉันท์\nเดียวกัน\nเดียวดาย\nเดี๋ยวเดียว\nเดี๋ยวนี้\nเดือดดาล\nเดือดร้อน\nเดือนมืด\nเดือนหงาย\nแดดาล\nแดดิ้น\nแดกดัน\nโด่เด่\nโด่งดัง\nโดดเดี่ยว\nโดยสาร\nได้การ\nได้แก่\nได้ใจ\nได้ที\nได้ยิน\nได้เสีย\nตกเขียว\nตกค้าง\nตกใจ\nตกต่ำ\nตกแต่ง\nตกทอด\nตกฟาก\nตกมัน\nตกยาก\nตกลง\nตกหล่น\nต้นขั้ว\nต้นคิด\nต้นฉบับ\nต้นตอ\nต้นตำรับ\nต้นทุน\nต้นแบบ\nต้นเพลิง\nต้นมือ\nต้นไม้\nต้นร่าง\nต้นเรื่อง\nต้นสังกัด\nต้นหน\nต้นเหตุ\nตบตา\nตบแต่ง\nตบแผละ\nตบมือ\nต้มข่า\nต้มโคล้ง\nต้มยำ\nต้มส้ม\nตรมตรอม\nตรรกวิทยา\nตรรกศาสตร์\nตรวจการ\nตรวจการณ์\nตรวจตรา\nตระบัดสัตย์\nตรัสรู้\nตราตั้ง\nตราบาป\nตรายาง\nตราสาร\nตริตรอง\nตรีกฏุก\nตรีกาย\nตรีโกณ\nตรีโกณมิติ\nตรีคูณ\nตรีทูต\nตรีปิฎก\nตรีภพ\nตรีมูรติ\nตรึกตรอง\nตรึงตรา\nตรุษจีน\nตฤณชาติ\nตฤณมัย\nตลกบาตร\nตลบตะแลง\nตลบหลัง\nตลาดนัด\nตลาดน้ำ\nตลาดมืด\nตลาดสด\nต่อตี\nต่อเติม\nต่อว่า\nต่อสู้\nต่อกร\nต่อต้าน\nต่อแย้ง\nต้องการ\nต้องโทษ\nต้องหา\nต้อนรับ\nตอบโต้\nตอบแทน\nต่อยหอย\nตะพาบน้ำ\nตักตวง\nตักบาตร\nตั้งเข็ม\nตั้งไข่\nตั้งเค้า\nตั้งแง่\nตั้งใจ\nตั้งต้น\nตั้งแต่\nตั้งท้อง\nตัดขาด\nตัดใจ\nตัดเชือก\nตัดตอน\nตัดทอน\nตัดบท\nตัดพ้อ\nตัดรอน\nตัดสิน\nตับเต่า\nตับแลบ\nตับอ่อน\nตัวกลาง\nตัวการ\nตัวเก็ง\nตัวดี\nตัวตั้ง\nตัวเต็ง\nตัวถัง\nตัวแทน\nตัวประกอบ\nตัวประกัน\nตัวแปร\nตัวผู้\nตัวพิมพ์\nตัวเมีย\nตัวยืน\nตัวเลข\nตัวอย่าง\nตั๋วเงิน\nตั๋วแลกเงิน\nตากล้อง\nตาไก่\nตาข่าย\nตาชั่ง\nตาตุ่ม\nตาทวด\nตาปลา\nตาราง\nต่างหาก\nต้านทาน\nตามใจ\nตายใจ\nตายซาก\nตายด้าน\nตายตัว\nตายทั้งกลม\nตายห่า\nตายโหง\nตาลปัตร\nต่ำช้า\nต่ำต้อย\nตำส้ม\nติเตียน\nติณชาติ\nติดขัด\nติดใจ\nติดต่อ\nติดตั้ง\nติดตาม\nติดตื้น\nติดพัน\nติดลม\nติดอ่าง\nตีเกลียว\nตีขลุม\nตีความ\nตีคู่\nตีจาก\nตีตื้น\nตีแผ่\nตีรวน\nตีลังกา\nตีวง\nตีเสมอ\nตีนกา\nตีนคู้\nตีนจก\nตีนตะขาบ\nตีนผี\nตีนเหยียด\nตึกแถว\nตึกระฟ้า\nตึงเครียด\nตึงตัง\nตื้นตัน\nตื่นตัว\nตื่นตูม\nตื่นเต้น\nตุ๊ต๊ะ\nตุ้บตั้บ\nตุ้มหู\nตุลาการ\nตุลาคม\nตู้นิรภัย\nตูมตาม\nตู้เสบียง\nเตโชธาตุ\nเตร็ดเตร่\nเต้นรำ\nเตาแก๊ส\nเตาผิง\nเตาฟู่\nเตาไฟ\nเตารีด\nเตาสูบ\nเต่าทอง\nเต้ารับ\nเต้าส่วน\nเต้าเสียบ\nเต้าหู้ยี้\nแต่ละ\nแตกคอ\nแตกคอก\nแตกฉาน\nแตกดับ\nแตกตื่น\nแตกพาน\nแตกแยก\nแตกร้าว\nแตกหัก\nแต่งงาน\nแต่งตั้ง\nแต้มคู\nแต้มต่อ\nแตรงอน\nแตรเดี่ยว\nแตรฝรั่ง\nแตรฟันฟาร์\nแตรวง\nโต้ตอบ\nโต้เถียง\nโต้แย้ง\nโต๊ะหมู่\nโต๊ะอิหม่าม\nใต้ถุน\nไต้ก๋ง\nไต่คู้\nไต่เต้า\nไต่ถาม\nไต้ฝุ่น\nไตรจักร\nไตรจีวร\nไตรตรึงษ์\nไตรทวาร\nไตรปิฎก\nไตรเพท\nไตรภพ\nไตรภูมิ\nไตรภาคี\nไตรยางศ์\nไตรรงค์\nไตรรัตน์\nไตรลักษณ์\nไตรโลก\nไตรสรณคมน์\nไตรสิกขา\nไต่สวน\nถกเถียง\nถดถอย\nถนัดถนี่\nถนิมสร้อย\nถมถืด\nถมเถ\nถมไป\nถลากไถล\nถ้วนถี่\nถ้วยฟู\nถ่องแท้\nถอดถอน\nถ้อยคำ\nถ้อยแถลง\nถากถาง\nถ่านไฟฉาย\nถ่านหิน\nถามไถ่\nถ่ายทอด\nถ่ายทุกข์\nถ่ายเท\nถาวรวัตถุ\nถ้ำมอง\nถี่ถ้วน\nถึงใจ\nถูกใจ\nถูกชะตา\nเถรวาท\nเถ้าแก่\nเถ้าแก่เนี้ย\nแถมพก\nแถลงการณ์\nไถ่ถอน\nไถ่ถาม\nทดแทน\nทดรอง\nทดลอง\nทดสอบ\nทนทาน\nทนายความ\nทบทวน\nทแยงมุม\nทรงกลด\nทรงเครื่อง\nทรงเจ้า\nทรัพย์สิน\nทรามชม\nทรามเชย\nทรามวัย\nทรามสงวน\nทรามสวาท\nทรุดโทรม\nทฤษฎีบท\nท้วงติง\nท่วมท้น\nทวาทศ\nทวาทศมาส\nทวาบรยุค\nทวารบาล\nทวิบถ\nทวิบท\nทวิบาท\nทวิภาค\nทวิภาคี\nทวีคูณ\nทศกัณฐ์\nทศชาติ\nทศทิศ\nทศนิยม\nทศพร\nทศพล\nทศพิธราชธรรม\nทศมาส\nทศวรรษ\nท่อไอเสีย\nท้อถอย\nท้อแท้\nทองขาว\nทองคำ\nทองคำขาว\nทองคำเปลว\nทองเค\nทองแดง\nทองบรอนซ์\nทองม้วน\nทองย้อย\nทองสัมฤทธิ์\nทองหยอด\nทองหยิบ\nทองเหลือง\nทองเอก\nท่องเที่ยว\nท้องตรา\nท้องถิ่น\nท้องที่\nท้องน้อย\nท้องร่อง\nท้องเรื่อง\nทอดมัน\nทอดทิ้ง\nทอดน่อง\nทอดยอด\nทอดหุ่ย\nทอยกอง\nทะเบียนบ้าน\nทะเลทราย\nทะเลสาบ\nทะเลหลวง\nทักขิณาวัฏ\nทักท้วง\nทักทาย\nทักษิณาวรรต\nทักษิณาทาน\nทักษิณานุประทาน\nทั้งกลม\nทั้งคน\nทั้งดุ้น\nทั้งที\nทั้งนั้น\nทั้งนี้\nทั้งปวง\nทั้งผอง\nทั้งเพ\nทั้งมวล\nทั้งสิ้น\nทั้งหมด\nทั้งหลาย\nทัณฑ์บน\nทัดทาน\nทัดเทียม\nทันควัน\nทันใจ\nทันใด\nทันตา\nทันสมัย\nทันที\nทับถม\nทับทรวง\nทับศัพท์\nทั่วถึง\nทั่วไป\nท่าทาง\nท่าที\nท้าทาย\nทางการ\nทางข้าม\nทางด่วน\nทางเท้า\nทางโท\nทางใน\nทางผ่าน\nทางม้าลาย\nทางหลวง\nทางออก\nทางเอก\nทานกัณฑ์\nทานตะวัน\nท่านชาย\nทานบารมี\nท่านผู้หญิง\nท่านหญิง\nทาบทาม\nท้ายทอย\nทารุณกรรม\nทำคลอด\nทำใจ\nทำซ้ำ\nทำท่า\nทำที\nทำแท้ง\nทำโทษ\nทำบาป\nทำบุญ\nทำพิษ\nทำฟัน\nทำร้าย\nทำวัตร\nทำสาว\nทำเสน่ห์\nทำหมัน\nทำให้\nทิ้งขว้าง\nทิ้งทวน\nทิ้งท้าย\nทินกร\nทิพจักขุ\nทิพโสต\nทิพยจักษุ\nทิพยญาณ\nทิพยเนตร\nทิพยรส\nทิพากร\nทิ่มตำ\nทิ่มแทง\nทิวากร\nทิวากาล\nทิศทาง\nทีเด็ด\nทีท่า\nทีนี้\nทีหลัง\nทีฆนิกาย\nทีฆสระ\nที่ดิน\nที่นอน\nที่นั่ง\nที่ปรึกษา\nที่พึ่ง\nที่มั่น\nที่ราบ\nที่ว่าการ\nที่สุด\nที่หมาย\nที่ไหน\nทุกที\nทุกเมื่อ\nทุกข์สุข\nทุนทรัพย์\nทุนนิยม\nทุนรอน\nทุนสำรอง\nทุ่มเถียง\nทุ่มเท\nทูนหัว\nทูลกระหม่อม\nเทกระจาด\nเทครัว\nเทพเจ้า\nเทพดา\nเทพธิดา\nเทพนม\nเทพนิยม\nเทพนิยาย\nเทพบุตร\nเทพสังหรณ์\nเทศกาล\nเทศนาโวหาร\nเทศบัญญัติ\nเทศบาล\nเทศมนตรี\nเทห์ฟากฟ้า\nเท่ากับ\nเท่าใด\nเท่าตัว\nเท่าทัน\nเท่าทุน\nเท่าเทียม\nเท่านั้น\nเท่าไร\nเท้าช้าง\nเทิดทูน\nเที่ยงตรง\nเที่ยงแท้\nเที่ยงธรรม\nเทียนชนวน\nเทียนพรรษา\nเทียบเคียง\nเทียบเท่า\nเทือกเขา\nเทือกเถา\nแท็งก์น้ำ\nแท่นพิมพ์\nแท่นมณฑล\nแท่นหมึก\nแทรกซอน\nแทรกซ้อน\nแทรกซึม\nแทรกแซง\nแทะโลม\nไทยดำ\nไทยทาน\nไทยธรรม\nไทยน้อย\nไทยใหญ่\nธงชัย\nธงชาติ\nธงทิว\nธรณีวิทยา\nธรณีสงฆ์\nธรรมกาย\nธรรมการ\nธรรมเกษตร\nธรรมขันธ์\nธรรมคุณ\nธรรมจรรยา\nธรรมจริยา\nธรรมจักร\nธรรมจักษุ\nธรรมจาคะ\nธรรมจารี\nธรรมชาติ\nธรรมดา\nธรรมเนียม\nธรรมราชา\nธรรมศาสตร์\nธรรมสภา\nธรรมสังเวช\nธัญพืช\nธารพระกร\nธีรภาพ\nธีรราช\nนกเขา\nนกต่อ\nนกยูง\nนกรู้\nนกหวีด\nนครบาล\nนครรัฐ\nนงคราญ\nนงนุช\nนงพะงา\nนงเยาว์\nนงราม\nนงลักษณ์\nนบนอบ\nนพเก้า\nนพคุณ\nนพเคราะห์\nนพปฎล\nนพพล\nนพรัตน์\nนพศก\nนพศูล\nนมข้น\nนมผง\nนมไม้\nนมนาน\nนมหนู\nนมแมว\nนรีเวช\nนรีเวชวิทยา\nนวดฟั้น\nนวยนาด\nนวลระหง\nนวลลออ\nนวลละออง\nนวลจันทร์\nนอกครู\nนอกคอก\nนอกจาก\nนอกใจ\nนอกชาน\nนอกรีต\nนอกเหนือ\nนองเนือง\nนองเลือด\nนอนก้น\nนอนใจ\nนอบนบ\nนอนเล่น\nนอบน้อม\nน้อมนำ\nน้อยใจ\nน้อยหน้า\nนักการ\nนักการเมือง\nนักกีฬา\nนักข่าว\nนักท่องเที่ยว\nนักเทศน์\nนักโทษ\nนักธรรม\nนักบวช\nนักบิน\nนักบุญ\nนักปราชญ์\nนักพรต\nนักรบ\nนักเรียน\nนักเลง\nนักวิชาการ\nนักศึกษา\nนักสิทธิ์\nนักสืบ\nนักหนา\nนั่งเทียน\nนั่งร้าน\nนัดแนะ\nนัดหมาย\nนั่นแหละ\nนั่นเอง\nนับถือ\nนับประสา\nนัยน์ตา\nนาดำ\nนาปรัง\nนาปี\nนาสวน\nนาหว่าน\nนาคบาศ\nนาคปรก\nนาคราช\nนางกวัก\nนางกำนัล\nนางงาม\nนางใน\nนางบำเรอ\nนางแบบ\nนางพญา\nนางฟ้า\nนางไม้\nนางโลม\nนางสาว\nนางห้าม\nนางเอก\nนาฏกรรม\nนาฏดนตรี\nนาฏศิลป์\nนานนม\nน่านน้ำ\nน่านฟ้า\nนามกร\nนามธรรม\nนามไธย\nนามบัตร\nนามปากกา\nนามแฝง\nนามสกุล\nนามสงเคราะห์\nนามสมญา\nนายทะเบียน\nนายท่า\nนายท้าย\nนายทุน\nนายประกัน\nนายหน้า\nนายอำเภอ\nนารายณ์หัตถ์\nนารีผล\nนาวิกโยธิน\nนำจับ\nนำพา\nนำทาง\nนำร่อง\nนำสืบ\nนำแสดง\nน้ำกรด\nน้ำกาม\nน้ำเกลือ\nน้ำข้าว\nน้ำแข็ง\nน้ำแข็งไส\nน้ำแข็งแห้ง\nน้ำครำ\nน้ำคร่ำ\nน้ำค้าง\nน้ำค้างแข็ง\nน้ำคาวปลา\nน้ำคำ\nน้ำเค็ม\nน้ำเคย\nน้ำเงิน\nน้ำเงี้ยว\nน้ำจัณฑ์\nน้ำจิ้ม\nน้ำใจ\nน้ำเชื้อ\nน้ำเชื่อม\nน้ำซาวข้าว\nน้ำดอกไม้\nน้ำดี\nน้ำตก\nน้ำตา\nน้ำตาล\nน้ำท่า\nน้ำนม\nน้ำนวล\nน้ำบาดาล\nน้ำประสานทอง\nน้ำประปา\nน้ำปลา\nน้ำป่า\nน้ำผึ้ง\nน้ำพริก\nน้ำพริกเผา\nน้ำพี้\nน้ำพุ\nน้ำมนต์\nน้ำมนตร์\nน้ำมัน\nน้ำมือ\nน้ำมูก\nน้ำเมา\nน้ำย่อย\nน้ำยา\nน้ำรัก\nน้ำแร่\nน้ำลาย\nน้ำเลี้ยง\nน้ำสต๊อก\nน้ำส้ม\nน้ำส้มสายชู\nน้ำสังข์\nน้ำสาบาน\nน้ำเสียง\nน้ำหนวก\nน้ำหนอง\nน้ำหนัก\nน้ำหน้า\nน้ำหนึ่ง\nน้ำหมึก\nน้ำหอม\nน้ำเหลือง\nน้ำอบ\nน้ำอ้อย\nน้ำอัดลม\nนิ่งเฉย\nนิจศีล\nนิดเดียว\nนิดหน่อย\nนิติกร\nนิติกรรม\nนิติธรรม\nนิตินัย\nนิติบัญญัติ\nนิติบุคคล\nนิติภาวะ\nนิติวิทยาศาสตร์\nนิติเวช\nนิติเวชศาสตร์\nนิติศาสตร์\nนิเทศศาสตร์\nนิ่มนวล\nนิรุกติศาสตร์\nนิเวศวิทยา\nนิศากร\nนิศากาล\nนิศาชล\nนิศารัตน์\nนี่แน่ะ\nนี่แหละ\nนี่เอง\nนึกคิด\nนุงถุง\nนุ่งห่ม\nนุ่มนวล\nนุ่มนิ่ม\nเนตรนารี\nเนติบัณฑิต\nเนยเทียม\nเนยใส\nเนิ่นนาน\nเนิบนาบ\nเนื้อความ\nเนื้อคู่\nเนื้อเค็ม\nเนื้องอก\nเนื้อตัว\nเนื้อตาย\nเนื้อที่\nเนื้อแท้\nเนื้อเปื่อย\nเนื้อผ้า\nเนื้อเพลง\nเนื้อไม้\nเนื้อเยื่อ\nเนื้อร้อง\nเนื้อร้าย\nเนื้อเรื่อง\nเนื้อหา\nเนืองนอง\nเนืองนิตย์\nเนืองแน่น\nแน่ใจ\nแน่ชัด\nแน่แท้\nแน่นอน\nแน่นิ่ง\nแน่แน่ว\nแน่นแฟ้น\nแน่นหนา\nแนบเนียน\nแนบแน่น\nแนวคิด\nแนวทาง\nแนวโน้ม\nแนวป่า\nแนวรบ\nแนวร่วม\nแนวหน้า\nแนวหลัง\nแน่วแน่\nแนะนำ\nแนะแนว\nโน้มน้าว\nในหลวง\nบกพร่อง\nบงกช\nบงการ\nบดบัง\nบทกลอน\nบทกวี\nบทความ\nบทคัดย่อ\nบทเฉพาะกาล\nบทนำ\nบทบัญญัติ\nบทบาท\nบทประพันธ์\nบทเพลง\nบทร้อง\nบทเรียน\nบทลงโทษ\nบทสนทนา\nบทอัศจรรย์\nบทจร\nบทบงสุ์\nบทมาลย์\nบทรัช\nบทเรศ\nบทวลัญช์\nบนบาน\nบรมครู\nบรมธาตุ\nบรมบพิตร\nบรมวงศานุวงศ์\nบรมอัฐิ\nบรรณพิภพ\nบรรณศาลา\nบรรณาการ\nบรรณาธิการ\nบรรณานุกรม\nบรรณารักษ์\nบรรณารักษศาสตร์\nบรรดามี\nบรรดาศักดิ์\nบรรทัดฐาน\nบรรพบุรุษ\nบรรลัยกัลป์\nบรรลัยจักร\nบริคณห์สนธิ\nบวงสรวง\nบ่วงบาศ\nบ้วนพระโอษฐ์\nบ่อเกิด\nบอกกล่าว\nบอกบท\nบอกบุญ\nบอกใบ้\nบอกปัด\nบ้องกัญชา\nบ้องตื้น\nบ้องไฟ\nบ้องหู\nบอดสี\nบ่อนทำลาย\nบอบช้ำ\nบอบบาง\nบอบแบบ\nบังโกลน\nบังโคลน\nบังใบ\nบั้งไฟ\nบังคับการ\nบังคับบัญชา\nบัญชาการ\nบัณฑุกัมพล\nบัดดล\nบัดเดี๋ยว\nบัดนั้น\nบัดนี้\nบัดสีบัดเถลิง\nบัตรเครดิต\nบัตรพลี\nบัตรสนเท่ห์\nบัตรสินเชื่อ\nบั่นทอน\nบั้นท้าย\nบั้นปลาย\nบั้นพระองค์\nบั้นเอว\nบันไดลิง\nบันไดเลื่อน\nบันเทิงคดี\nบัวลอย\nบัวบก\nบ้าจี้\nบ้าดีเดือด\nบ้าน้ำลาย\nบ้าบิ่น\nบ้าระห่ำ\nบ้าเลือด\nบ้าหอบฟาง\nบากบั่น\nบากหน้า\nบางตา\nบางเบา\nบางที\nบาดเจ็บ\nบาดแผล\nบาดหมาง\nบาตรใหญ่\nบาทบงกช\nบาทบงสุ์\nบาทบริจาริกา\nบาทวิถี\nบานเกล็ด\nบานตะเกียง\nบานตะไท\nบานเบอะ\nบานปลาย\nบานแผละ\nบานพับ\nบ้านจัดสรร\nบ้านช่อง\nบ้านนอก\nบ้านพัก\nบ้านเมือง\nบ้านรับรอง\nบ้านเรือน\nบาปกรรม\nบายศรี\nบ่ายเบี่ยง\nบ่ายหน้า\nบ่าวไพร่\nบิดเบี้ยว\nบิดเบือน\nบิดพลิ้ว\nบี้แบน\nบีบคั้น\nบีบรัด\nบึ้งตึง\nบึ้งบูด\nบุกบั่น\nบุกเบิก\nบุกรุก\nบุคลิกภาพ\nบุคลิกลักษณะ\nบุญธรรม\nบุญนิธิ\nบุญฤทธิ์\nบุบสลาย\nบุ้ยใบ้\nบุรุษเพศ\nบุหงารำไป\nบู้บี้\nบูชายัญ\nบูดบึ้ง\nบูดเบี้ยว\nเบาความ\nเบาใจ\nเบาบาง\nเบาปัญญา\nเบามือ\nเบาแรง\nเบาสมอง\nเบาหวาน\nเบาโหวง\nเบ้าตา\nเบาะแส\nเบิกความ\nเบิกบาน\nเบี้ยล่าง\nเบี้ยเลี้ยง\nเบี้ยหวัด\nเบี่ยงบ่าย\nเบียดบัง\nเบียดเบียน\nเบียดเสียด\nเบื้องต้น\nเบื้องบน\nเบื้องหน้า\nเบื้องหลัง\nแบกะดิน\nแบเบาะ\nแบ่งเบา\nแบ่งปัน\nแบ่งแยก\nแบบฉบับ\nแบบแปลน\nแบบแผน\nแบบฝึกหัด\nแบบพิมพ์\nแบบสอบถาม\nแบบอย่าง\nแบะแฉะ\nแบะท่า\nโบแดง\nโบราณคดี\nโบราณวัตถุ\nโบราณสถาน\nใบขับขี่\nใบจอง\nใบตอง\nใบแทรก\nใบบอก\nใบบุญ\nใบเบิกทาง\nใบปลิว\nใบพัด\nใบโพ\nใบไม้\nใบระกา\nใบรับรอง\nใบลา\nใบเลี้ยง\nใบสั่ง\nใบสำคัญ\nใบสุทธิ\nใบเสร็จ\nใบหน้า\nใบอนุญาต\nใบระกา\nปกครอง\nปกคลุม\nปกป้อง\nปกปิด\nปฏิบัติการ\nปฏิบัติบูชา\nปฐพีวิทยา\nปฐมฌาน\nปฐมทัศน์\nปฐมเทศนา\nปฐมนิเทศ\nปฐมพยาบาล\nปฐมยาม\nปฐมฤกษ์\nปฐมวัย\nปฐมสมโพธิ\nปนเป\nป่นปี้\nปมเขื่อง\nปมเด่น\nปมด้อย\nปรนเปรอ\nปรบไก่\nปรบมือ\nปรสิตวิทยา\nประโปรย\nประพรม\nประกันชีวิต\nประกันภัย\nประจักษ์พยาน\nประจัญบาน\nประจันหน้า\nประจำการ\nประจำเดือน\nประจำเมือง\nประจำยาม\nประชดประชัน\nประชากร\nประชากรศาสตร์\nประชาคม\nประชาชน\nประชาราษฎร์\nประชาชาติ\nประชาชี\nประชาทัณฑ์\nประชาบาล\nประชาพิจารณ์\nประชาภิบาล\nประชามติ\nประชาสงเคราะห์\nประชาสัมพันธ์\nประดับประดา\nประดามี\nประดาน้ำ\nประเดี๋ยวเดียว\nประเดี๋ยวนี้\nประทับใจ\nประทุษร้าย\nประเทศราช\nประพาสต้น\nประเพณีนิยม\nประลัยกัลป์\nประวัติการณ์\nประวัติศาสตร์\nประสบการณ์\nประสบการณ์นิยม\nประสาทการ\nประสูติการ\nประสูติกาล\nประเส\nปรับทุกข์\nปรับโทษ\nปรับปรุง\nปรากฏการณ์\nปราดเปรียว\nปราดเปรื่อง\nปราบปราม\nปริญญาบัตร\nปรัยัติธรรม\nปรุโปร่ง\nปลงใจ\nปลงตก\nปลดทุกข์\nปลดปลง\nปลดปล่อย\nปลดเปลื้อง\nปลดระวาง\nปลดแอก\nปล้นสะดม\nปลอกกระสุน\nปลอกคอ\nปลอดโปร่ง\nปลอดภัย\nปลอมปน\nปลอมแปลง\nปลอบโยน\nปล่อยใจ\nปล่อยตัว\nปล่อยปละ\nปลั๊กไฟ\nปลากริม\nปลาเค็ม\nปลาจ่อม\nปลาเจ่า\nปลาแดก\nปลาตู้\nปลาทอง\nปลาร้า\nปลาส้ม\nปลาดาว\nปลาบิน\nปลาฝา\nปลาวาฬ\nปลาหมึก\nปลาบปลื้ม\nปลายข้าว\nปลายแถว\nปลายทาง\nปลิ้นปลอก\nปลิ้นปล้อน\nปลีกตัว\nปลีกย่อย\nปลุกใจ\nปลุกปล้ำ\nปลุกปั่น\nปลุกระดม\nปลุกเสก\nปลูกฝัง\nปลูกสร้าง\nปวดถ่วง\nปวดมวน\nปวดร้าว\nป่วนปั่น\nป่วยการ\nปอกลอก\nป้องกัน\nปักใจ\nปักดำ\nปักหลัก\nปัจเจกบุคคล\nปัจเจกพุทธะ\nปัจเจกโพธิ\nปัจฉิมชน\nปัจฉิมทิศ\nปัจฉิมภาค\nปัจฉิมยาม\nปัจฉิมลิขิต\nปัจฉิมวัย\nปัจฉิมวาจา\nปัญญาชน\nปัญญาวิมุติ\nปัญญาอ่อน\nปัดเป่า\nปันส่วน\nปั่นป่วน\nปั่นแปะ\nปั่นหัว\nปั้นจิ้ม\nปั้นเจ๋อ\nปั้นปึ่ง\nปั้นสิบ\nปั๊มน้ำมัน\nป่าช้า\nป่าชายเลน\nป่าดง\nป่าดงดิบ\nป่าดิบ\nป่าเถื่อน\nป่าเบญจพรรณ\nป่าละเมาะ\nปากกา\nปากขอ\nปากแข็ง\nปากคอ\nปากคำ\nปากคีบ\nปากจัด\nปากน้ำ\nปากเปล่า\nปากเสียง\nปานกลาง\nป่านนี้\nป้านลม\nป้ายสี\nป่าวร้อง\nปิดฉาก\nปิดบัง\nปิตุฆาต\nปิตุภูมิ\nปีมะโว้\nปีแสง\nปี่กลาง\nปี่ไฉน\nปี่ชวา\nปี่นอก\nปี่ใน\nปี่พาทย์\nปี่อ้อ\nปีกกา\nปีนเกลียว\nปีนป่าย\nปึกแผ่น\nปึงปัง\nปืนกล\nปืนครก\nปืนพก\nปืนยา\nปืนยาว\nปืนลม\nปืนเล็ก\nปืนเล็กยาว\nปืนสั้น\nปืนใหญ่\nปุบปับ\nปุ๊บปั๊บ\nปุ่มเปือก\nปุยฝ้าย\nปุ๋ยคอก\nปุ๋ยเคมี\nปุ๋ยวิทยาศาสตร์\nปุ๋ยหมัก\nปุ๋ยอินทรีย์\nปูจ๋า\nปูเสฉวน\nปู่เจ้า\nปู่ทวด\nปูนขาว\nปูนซีเมนต์\nปูนดิบ\nปูนแดง\nปูนปลาสเตอร์\nปูนปั้น\nเป็ดเทศ\nเป็ดน้ำ\nเป็นกลาง\nเป็นใจ\nเป็นต้น\nเป็นต่อ\nเป็นรอง\nเป็นไร\nเป็นลม\nเป็นห่วง\nเป็นอยู่\nเปรมปรีดิ์\nเปรอะเปื้อน\nเปรียบเทียบ\nเปรียบเปรย\nเปรี้ยวปาก\nเปรี้ยวหวาน\nเปรื่องปราด\nเปลญวน\nเปล่งปลั่ง\nเปล่าดาย\nเปล่าเปลี่ยว\nเปลี่ยนใจ\nเปลี่ยนตัว\nเปลี่ยนแปลง\nเปลี่ยนมือ\nเปลี่ยนหน้า\nเป๋อเหลอ\nเปะปะ\nเป่ากบ\nเป้านิ่ง\nเป้าหมาย\nเปิดฉาก\nเปิดเปิง\nเปิดโปง\nเปิดผนึก\nเปิดเผย\nเปียกปูน\nแป้งสาลี\nแป้งนวล\nแป้งเปียก\nแป้งมัน\nแป้งฝุ่น\nแป้งร่ำ\nแป้งสิงคโปร์\nแป้งหมี่\nแปดปน\nแปดเปื้อน\nแปรปรวน\nแปรผัน\nแปรพักตร์\nแปรรูป\nแปรอักษร\nแปลกปลอม\nแปะโป้ง\nโป้ปด\nโปร่งแสง\nโปร่งใส\nโปรดปราน\nโปรยทาน\nโปรยปราย\nโปโลน้ำ\nผกผัน\nผกากรอง\nผงขาว\nผงชูรส\nผงซักฟอก\nผงฟู\nผดุงครรภ์\nผมไฟ\nผลพลอยได้\nผลลัพธ์\nผลัดเปลี่ยน\nผลิตผล\nผลิตภัณฑ์\nผลุบโผล่\nผสมเทียม\nผสมผสาน\nผสมผเส\nผสมพันธุ์\nผสมโรง\nผสมเสร็จ\nผ่องแผ้ว\nผ่องใส\nผ่อนคลาย\nผ่อนชำระ\nผ่อนปรน\nผ่อนผัน\nผ่อนส่ง\nผอมโซ\nผอมแห้ง\nผักชี\nผักตบชวา\nผักบุ้ง\nผังเมือง\nผัดผ่อน\nผันแปร\nผันผวน\nผ่าตัด\nผ่าเผย\nผ่าหมาก\nผ่าเหล่า\nผ้าขนหนู\nผ้าขาวม้า\nผ้าขี้ริ้ว\nผ้าเช็ดตัว\nผ้าเช็ดปาก\nผ้าเช็ดมือ\nผ้าเช็ดหน้า\nผ้าดิบ\nผ้าต่วน\nผ้าไตร\nผ้าถุง\nผ้าแถบ\nผ้านวม\nผ้านุ่ง\nผ้าใบ\nผ้าป่า\nผ้าป่าน\nผ้าผ่อน\nผ้าพันคอ\nผ้าพันแผล\nผ้าแพร\nผ้าโพกหัว\nผ้ามัดหมี่\nผ้ายาง\nผ้าลูกไม้\nผ้าเหลือง\nผ้าอนามัย\nผ้าอ้อม\nผาดโผน\nผาติกรรม\nผิดหวัง\nผิวเผิน\nผิวพรรณ\nผิวหนัง\nผีกระสือ\nผีกระหัง\nผีกองกอย\nผีโขมด\nผีดิบ\nผีตองเหลือง\nผีถ้วยแก้ว\nผีแถน\nผีทะเล\nผีบุญ\nผีปอบ\nผีพุ่งไต้\nผีฟ้า\nผีเรือน\nผีสาง\nผีเสื้อ\nผีห่า\nผึ่งผาย\nผุดผ่อง\nผุดผาด\nผู้คน\nผู้คุม\nผู้จัดการ\nผู้ชาย\nผู้เชี่ยวชาญ\nผู้ดี\nผู้โดยสาร\nผู้ต้องขัง\nผู้ต้องหา\nผู้แทน\nผู้น้อย\nผู้บริโภค\nผู้บังคับบัญชา\nผู้ปกครอง\nผู้ประกอบการ\nผู้ป่วย\nผู้พิพากษา\nผู้เยาว์\nผู้ร้าย\nผู้วิเศษ\nผู้สื่อข่าว\nผู้เสียหาย\nผู้หญิง\nผู้ใหญ่\nผู้ใหญ่บ้าน\nผูกขวัญ\nผูกขาด\nผูกพัน\nผูกมัด\nเผชิญหน้า\nเผด็จการ\nเผด็จศึก\nเผยแผ่\nเผยแพร่\nเผละผละ\nเผ่าพันธุ์\nเผื่อแผ่\nแผงลอย\nแผนการ\nแผนงาน\nแผนที่\nแผนผัง\nแผนภาพ\nแผนภูมิ\nแผ่นดิน\nแผ่นเสียง\nแผ้วพาน\nโผงผาง\nฝนทอง\nฝอยทอง\nฝักแค\nฝักบัว\nฝักฝ่าย\nฝักใฝ่\nฝังใจ\nฝังหัว\nฝาชี\nฝาแฝด\nฝาละมี\nฝ่าพระบาท\nฝ่าฝืน\nฝ่าฟัน\nฝ้าฟาง\nฝากตัว\nฝากฝัง\nฝีดาษ\nฝีมะม่วง\nฝีจักร\nฝีเท้า\nฝีปาก\nฝีพาย\nฝีมือ\nฝีเย็บ\nฝึกงาน\nฝึกปรือ\nฝึกฝน\nฝึกสอน\nฝึกหัด\nฝืดเคือง\nใฝ่ฝัน\nพงพี\nพงศ์พันธุ์\nพญาโศก\nพญาไฟ\nพบปะ\nพบพาน\nพรสวรรค์\nพรมคด\nพรมแดน\nพรมมิ\nพรรคพวก\nพรรณราย\nพรวดพราด\nพรหมชาติ\nพรหมลิขิต\nพรหมโลก\nพรหมวิหาร\nพร้อมใจ\nพร้อมพรั่ง\nพร้อมเพรียง\nพร้อมมูล\nพร้อมสรรพ\nพร้อมหน้า\nพระครู\nพระคุณ\nพระเคราะห์\nพระเครื่อง\nพระเจ้า\nพระเจ้าอยู่หัว\nพระชายา\nพระทัย\nพระนาง\nพระนางเจ้า\nพระเป็นเจ้า\nพระผู้เป็นเจ้า\nพระพิมพ์\nพระพุทธเจ้า\nพระพุทธองค์\nพระภูมิ\nพระยา\nพระรอง\nพระสนม\nพระสนมเอก\nพระองค์\nพระองค์เจ้า\nพระเอก\nพรั่งพร้อม\nพรั่งพรู\nพรั่นพรึง\nพร่างพราว\nพรายน้ำ\nพรายแพรว\nพราวแพรว\nพร่ำพลอด\nพร่ำเพรื่อ\nพร่ำเพ้อ\nพริกไทย\nพริ้งพราย\nพริ้งเพรา\nพริ้งเพริศ\nพริบตา\nพริ้มพราย\nพริ้มเพรา\nพรุ่งนี้\nพฤติกรรม\nพฤติการณ์\nพฤตินัย\nพลการ\nพลขับ\nพลความ\nพลเมือง\nพลรบ\nพลร่ม\nพลเรือน\nพลโลก\nพลศึกษา\nพลบค่ำ\nพลอดรัก\nพลังงาน\nพลังเงียบ\nพลังจิต\nพลั้งปาก\nพลั้งเผลอ\nพลั้งพลาด\nพลัดถิ่น\nพลัดพราก\nพลาดท่า\nพลาดพลั้ง\nพลิกแพลง\nพลีกรรม\nพลุ่งพล่าน\nพวกพ้อง\nพวงมาลัย\nพวงมาลา\nพวงหรีด\nพวงคราม\nพวงชมพู\nพวงแสด\nพ่วงพี\nพวยน้ำ\nพวยพุ่ง\nพสกนิกร\nพหุคูณ\nพหุภาคี\nพหูพจน์\nพหูสูต\nพอควร\nพอใจ\nพอใช้\nพอใช้ได้\nพอดี\nพอตัว\nพอทำเนา\nพอประมาณ\nพอเพียง\nพอแรง\nพอสมควร\nพอเหมาะ\nพ่อขุน\nพ่อครัว\nพ่อตา\nพ่อบ้าน\nพ่อพันธุ์\nพ่อม่าย\nพ่อเมือง\nพ่อเลี้ยง\nพ่อสื่อ\nพอกพูน\nพ้องพาน\nพักผ่อน\nพักพิง\nพักฟื้น\nพักร้อน\nพักแรม\nพัดยศ\nพัดลม\nพันพัว\nพับฐาน\nพับเพียบ\nพัวพัน\nพาซื่อ\nพาดพิง\nพิณพาทย์\nพิธีกร\nพิธีกรรม\nพิธีการ\nพิธีรีตอง\nพิธีสาร\nพินัยกรรม\nพิมพ์เขียว\nพิมพ์ใจ\nพิมพ์ดีด\nพิษสง\nพี่น้อง\nพี่เบิ้ม\nพี่เลี้ยง\nพึงใจ\nพึงพอใจ\nพึ่งพา\nพึ่งพิง\nพืชพันธุ์\nพืชมงคล\nพื้นฐาน\nพื้นที่\nพื้นบ้าน\nพื้นเพ\nพื้นเมือง\nพื้นเสีย\nพุพอง\nพุทธกาล\nพุทธคุณ\nพุทธจักร\nพุทธเจดีย์\nพุทธฎีกา\nพุทธปฏิมา\nพุทธปฏิมากร\nพุทธมามกะ\nพุทธศักราช\nพุทธศาสนิกชน\nพุทธองค์\nพุทธชาด\nพุทธรักษา\nพุ่มพวง\nพุ่มไม้\nพู่กัน\nพูดจา\nเพ่งเล็ง\nเพดานบิน\nเพดานปาก\nเพริศพราย\nเพริศพริ้ง\nเพริศแพร้ว\nเพรียกพร้อง\nเพรียวลม\nเพลงเชิด\nเพลงยาว\nเพลิงกัลป์\nเพลินใจ\nเพลินตา\nเพลี่ยงพล้ำ\nเพ้อฝัน\nเพาะกาย\nเพาะชำ\nเพาะปลูก\nเพิกถอน\nเพิกเฉย\nเพิ่มเติม\nเพิ่มพูน\nเพียงตา\nเพียงพอ\nเพียบแประ\nเพียบพร้อม\nเพื่อนเกลอ\nเพื่อนตาย\nเพื่อนบ้าน\nเพื่อนฝูง\nเพื่อนยาก\nแพ้ท้อง\nแพร่หลาย\nแพร่งพราย\nแพรวพราว\nโพธิญาณ\nโพธิบัลลังก์\nโพธิสมภาร\nโพธิสัตว์\nโพ้นทะเล\nโพยภัย\nไพ่ตาย\nไพ่ป๊อก\nไพรวัน\nไพรสณฑ์\nไพรสัณฑ์\nไพร่พล\nไพร่ฟ้า\nไพร่สม\nไพร่ส่วย\nไพร่หลวง\nฟกช้ำ\nฟองเต้าหู้\nฟองน้ำ\nฟองมัน\nฟ้องกลับ\nฟ้องร้อง\nฟอนเฟะ\nฟักทอง\nฟัดเฟียด\nฟันดาบ\nฟันฝ่า\nฟันแท้\nฟันน้ำนม\nฟันปลา\nฟันฟาง\nฟันเฟือง\nฟันม้า\nฟันเลื่อย\nฟันหนู\nฟั่นเฝือ\nฟั่นเฟือน\nฟื้นตัว\nฟื้นฝอย\nฟื้นฟู\nฟุ้งซ่าน\nฟุ้งเฟ้อ\nฟุ้งเฟื่อง\nฟุตบอล\nฟูฟ่อง\nฟูเฟื่อง\nฟูมฟัก\nฟูมฟาย\nเฟะฟะ\nเฟื่องฟ้า\nเฟื่องฟุ้ง\nเฟื่องฟู\nไฟฉาย\nไฟแช็ก\nไฟธาตุ\nไฟฟ้า\nภัตกิจ\nภาคทัณฑ์\nภาคพื้น\nภาคเรียน\nภาคภูมิ\nภาพถ่าย\nภาพนิ่ง\nภาพประกอบ\nภาพพจน์\nภาพยนตร์\nภาพลวงตา\nภาพลักษณ์\nภายนอก\nภายใน\nภายหน้า\nภายหลัง\nภารกิจ\nภารธุระ\nภารโรง\nภารตวิทยา\nภาษาศาสตร์\nภาสกร\nภิญโญภาพ\nภินชาติ\nภูธร\nภูธเรศ\nภูบาล\nภูเบศ\nภูเบศวร์\nภูเขา\nภูเขาไฟ\nภูผา\nภูตคาม\nภูตบดี\nภูตรูป\nภูเตศวร\nภูมินทร์\nภูมิบาล\nภูมิประเทศ\nภูมิภาค\nภูมิรัฐศาสตร์\nภูมิลำเนา\nภูมิศาสตร์\nภูมิอากาศ\nภูมิธรรม\nภูมิปัญญา\nภูมิรู้\nภูมิใจ\nภูมิฐาน\nภูมิคุ้มกัน\nภูมิแพ้\nภูษาโยง\nเภทภัย\nเภสัชกร\nเภสัชกรรม\nเภสัชวิทยา\nเภสัชศาสตร์\nโภคทรัพย์\nโภคภัณฑ์\nโภชนากร\nโภชนาการ\nมกุฎราชกุมาร\nมงคลแฝด\nมงคลสูตร\nมงคลหัตถี\nมณเฑียรบาล\nมดดำ\nมดแดง\nมดเท็จ\nมดยอบ\nมดลูก\nมธุปายาส\nมธุรส\nมนเทียรบาล\nมนุษย์กบ\nมโนกรรม\nมโนคติ\nมโนทุจริต\nมโนธรรม\nมโนภาพ\nมโนมัย\nมโนรถ\nมโนรมย์\nมโนสุจริต\nมรรคนายก\nมรรคผล\nมฤคชาติ\nมฤคทายวัน\nมฤคราช\nมลทิน\nมลพิษ\nมลสาร\nมวกเหล็ก\nม้วนหน้า\nมวยไทย\nมวยปล้ำ\nมวยล้ม\nมวยวัด\nมวยสากล\nมวยหมู่\nมวลสาร\nมอคราม\nมอซอ\nมอหมึก\nมองเมียง\nมอบตัว\nมอบหมาย\nมอมเมา\nมะขามเทศ\nมะขามป้อม\nมะขามเปียก\nมะเขือเทศ\nมะเขือพวง\nมะพร้าวแก้ว\nมักคุ้น\nมักจี่\nมักง่าย\nมักน้อย\nมักมาก\nมักใหญ่\nมั่งคั่ง\nมั่งมี\nมัจจุราช\nมัชฌิมนิกาย\nมัชฌิมประเทศ\nมัชฌิมยาม\nมัชฌิมวัย\nมัดจำ\nมัดหมี่\nมัธยมกาล\nมัธยมศึกษา\nมันแกว\nมันเทศ\nมันฝรั่ง\nมันเปลว\nมันสมอง\nมั่นคง\nมั่นใจ\nมั่นหมาย\nมั่นเหมาะ\nมัวเมา\nมัวหมอง\nมั่วสุม\nม้าเทศ\nม้าน้ำ\nม้ามืด\nม้าเร็ว\nม้าล่อ\nม้าลาย\nมากมาย\nมาตรการ\nมาตรฐาน\nมาตราส่วน\nมาตุคาม\nมาตุฆาต\nมาตุภูมิ\nม่านตา\nม่านบังตา\nมายากร\nมายากล\nมายาการ\nมายาวี\nมารผจญ\nมารวิชัย\nมารสังคม\nมารหัวขน\nมาลาการ\nมิ่งขวัญ\nมิ่งมิตร\nมิจฉาจาร\nมิจฉาชีพ\nมิดชิด\nมิดเมี้ยน\nมิดหมี\nมิตรจิต\nมิตรภาพ\nมิตรสหาย\nมิน่า\nมีหน้า\nมีดโกน\nมีดดาบ\nมีดโต้\nมีดพก\nมีดพับ\nมีดสั้น\nมึนงง\nมึนชา\nมึนตึง\nมึนเมา\nมืดครึ้ม\nมืดมน\nมืดมัว\nมือจับ\nมือดี\nมือเติบ\nมือปืน\nมือเปล่า\nมือมืด\nมือสอง\nมือเสือ\nมือหนึ่ง\nมือใหม่\nมุกตลก\nมุขปาฐะ\nมุขมนตรี\nมุ่งมั่น\nมุ่งมาด\nมุ่งหน้า\nมุ่งหมาย\nมุ่งหวัง\nมุ้งลวด\nมุ้งสายบัว\nมุมก้ม\nมุมกลับ\nมุมเงย\nมุมฉาก\nมุมตรง\nมุมป้าน\nมุมมืด\nมุมแย้ง\nมุมสะท้อน\nมุมหักเห\nมุมแหลม\nมุสาวาท\nมูกเลือด\nมูกมัน\nมูกหลวง\nมูนดิน\nมูลฐาน\nมูลนาย\nมูลนิธิ\nมูลเหตุ\nมูลค่า\nมูลฝอย\nเม็ดเงิน\nเม็ดเลือด\nเม็ดโลหิต\nเม่นทะเล\nเมรุมาศ\nเมรุราช\nเมล์อากาศ\nเมาดิบ\nเมามัน\nเมามัว\nเมามาย\nเมินเฉย\nเมียน้อย\nเมียหลวง\nเมียงมอง\nเมี่ยงลาว\nเมี่ยงส้ม\nเมื่อกี้\nเมื่อตะกี้\nเมื่อใด\nเมื่อไร\nเมื่อไหร่\nเมื่อนั้น\nเมืองขึ้น\nเมืองท่า\nเมืองนอก\nเมืองหลวง\nเมื่อยขบ\nเมื่อยล้า\nแม่กอง\nแม่กุญแจ\nแม่คุณ\nแม่งาน\nแม่เจ้า\nแม่ชี\nแม่ทัพ\nแม่นม\nแม่น้ำ\nแม่บท\nแม่บ้าน\nแม่เบี้ย\nแม่พระ\nแม่พิมพ์\nแม่เพลง\nแม่มด\nแม่ม่าย\nแม่ไม้\nแม่ยก\nแม่ยาย\nแม่ร้าง\nแม่เรือน\nแม่แรง\nแม่เล้า\nแม่เลี้ยง\nแม่สี\nแม่สื่อ\nแม่เหล็ก\nแมงมุม\nแม่นยำ\nแมลงช้าง\nแมลงวัน\nแมลงปอ\nแมลงภู่\nแมลงเม่า\nแมวเซา\nแมวน้ำ\nแมวป่า\nแมวมอง\nไม้กลัด\nไม้กวาด\nไม้กางเขน\nไม้เกาหลัง\nไม้ขีดไฟ\nไม้จิ้มฟัน\nไม้เด็ด\nไม้ตาย\nไม้ตีพริก\nไม้ที\nไม้เท้า\nไม้บรรทัด\nไม้เมตร\nไม้ระแนง\nไม้เรียว\nไม้หมอน\nไม้อัด\nไม้จัตวา\nไม้ตรี\nไม้ไต่คู้\nไม้โท\nไม้ผัด\nไม้มลาย\nไม้ม้วน\nไม้ยมก\nไม้หน้า\nไม้หันอากาศ\nไม้เอก\nยกกลีบ\nยกครู\nยกเครื่อง\nยกเค้า\nยกทรง\nยกฟ้อง\nยกเมฆ\nยกยอ\nยกย่อง\nยกเลิก\nยกเว้น\nย่นย่อ\nยมทูต\nยมบาล\nยมราช\nยมโลก\nยวดยิ่ง\nยวดยาน\nยวนยี\nยวบยาบ\nย่อท้อ\nย่อส่วน\nย่อหน้า\nย่อหย่อน\nยอกย้อน\nยองใย\nย่องเบา\nย่องแย่ง\nยอดเยี่ยม\nยอดอก\nย้อนยอก\nย้อนรอย\nย้อนศร\nย้อนแสง\nย้อนหลัง\nยอบแยบ\nยอมความ\nย่อมเยา\nย่อยยับ\nยักยอก\nยักย้าย\nยักเยื้อง\nยัญกรรม\nยัญพิธี\nยัดเยียด\nยับเยิน\nยับยั้ง\nยั่วยวน\nยั่วยุ\nยั่วเย้า\nยากวาด\nยากันยุง\nยาเขียว\nยาใจ\nยาฉุน\nยาชา\nยาซัด\nยาดอง\nยาแดง\nยาถ่าย\nยาธาตุ\nยานัตถุ์\nยาเบื่อ\nยาโป๊\nยาแฝด\nยาพิษ\nยาระบาย\nยาสลบ\nยาสั่ง\nยาสีฟัน\nยาสูบ\nยาเส้น\nยาเสพติด\nยาหม่อง\nยาเหลือง\nย่าทวด\nย่านาง\nยากแค้น\nยากจน\nยากเย็น\nยากไร้\nยางนอก\nยางใน\nยางมะตอย\nยางมะตูม\nยางลบ\nยางสน\nยางอาย\nย่างกราย\nย่างเยื้อง\nย่างสด\nย่างสามขุม\nย่างเหยียบ\nยานเกราะ\nยานพาหนะ\nยานอวกาศ\nยานคาง\nยายทวด\nยาวเฟื้อย\nยาวยืด\nยาวเหยียด\nยำทวาย\nยำใหญ่\nยำเกรง\nยำเยง\nย่ำต๊อก\nย่ำยี\nย่ำแย่\nยิงเป้า\nยิ่งนัก\nยิ่งยวด\nยิ่งใหญ่\nยินดี\nยินยอม\nยินร้าย\nยิ้มกริ่ม\nยิ้มแฉ่ง\nยิ้มแต้\nยิ้มแป้น\nยิ้มเผล่\nยิ้มเยาะ\nยิ้มแย้ม\nยียวน\nยึดครอง\nยึดถือ\nยึดมั่น\nยึดเหนี่ยว\nยืดยาด\nยืดยาว\nยืดเยื้อ\nยืดหยุ่น\nยืดอก\nยืนกราน\nยืนต้น\nยืนพื้น\nยืนยง\nยืนยัน\nยืนหยัด\nยื้อยุด\nยุยง\nยุแยง\nยุแหย่\nยุคลบาท\nยุคเข็ญ\nยุคทอง\nยุคมืด\nยุ่งขิง\nยุ่งยาก\nยุ่งเหยิง\nยุติธรรม\nยุทธการ\nยุทธนาวี\nยุทธปัจจัย\nยุทธภัณฑ์\nยุทธภูมิ\nยุทธวิธี\nยุทธศาสตร์\nยุทธหัตถี\nยุทธนาการ\nยุทธนาธิการ\nยุบยับ\nยุบยิบ\nยุพราช\nยู่ยี่\nเย็นเจี๊ยบ\nเย็นใจ\nเย็นฉ่ำ\nเย็นเฉียบ\nเย็นชา\nเย็นชืด\nเย็นตา\nเย็นเยียบ\nเย็นเยือก\nเย็นวาบ\nเย็นวูบ\nเย็บกี่\nเย็บจักร\nเย็บด้าย\nเย้ยหยัน\nเย้าหยอก\nเยาะเย้ย\nเยี่ยมกราย\nเยี่ยมเยียน\nเยี่ยมเยือน\nเยี่ยมยอด\nเยื่อเคย\nเยื่อใย\nเยือกเย็น\nเยื้องกราย\nเยื้องยัก\nเยื้องย่าง\nแยกย้าย\nแยกแยะ\nแย่งชิง\nแยบคาย\nแยบยล\nแย้มพราย\nแย้มยิ้ม\nแย้มสรวล\nโยเย\nโย้เย้\nโยกโคลง\nโยกย้าย\nโยกโย้\nโยนกลอง\nใยหิน\nรกชัฏ\nรกร้าง\nรกเรี้ยว\nรกเรื้อ\nรกราก\nรงควัตถุ\nรชนีกร\nรถกระบะ\nรถเก๋ง\nรถเข็น\nรถแข่ง\nรถจักร\nรถจี๊ป\nรถตู้\nรถทัวร์\nรถบรรทุก\nรถพ่วง\nรถพยาบาล\nรถไฟ\nรถไฟฟ้า\nรถม้า\nรถเมล์\nรถยนต์\nรถราง\nรถลาก\nรถสปอร์ต\nรถสิบล้อ\nรบกวน\nรบรา\nรบเร้า\nรมดำ\nร่มเกล้า\nร่มชูชีพ\nร่มเย็น\nร่มรื่น\nร่วงโรย\nรวงผึ้ง\nรวงรัง\nรวดเร็ว\nรวนเร\nรวบยอด\nรวบรวม\nรวบรัด\nรวมพล\nรวมหัว\nร่วมใจ\nร่วมเพศ\nร่วมมือ\nร่วมรัก\nร่วมสมัย\nรวยริน\nรวยรื่น\nรสชาติ\nรสนิยม\nรองท้อง\nรองเท้า\nรองพื้น\nร่องน้ำ\nร่องรอย\nร้องขอ\nร้องทุกข์\nร้องเรียน\nร้องห่ม\nร้องไห้\nรองช้ำ\nรองทรง\nรอดชีวิต\nรอดตัว\nรอดตาย\nรอนแรม\nร่อนเร่\nร้อนใจ\nร้อนตัว\nร้อนรน\nร้อนรุ่ม\nร้อนวิชา\nร้อนอาสน์\nรอบจัด\nรอบเดือน\nรอบรู้\nรอยร้าว\nร่อยหรอ\nร้อยละ\nร้อยกรอง\nร้อยแก้ว\nร้อยหวาย\nระนาดทุ้ม\nระนาดเอก\nระเบิดขวด\nระเบิดมือ\nระเบียบการ\nรักใคร่\nรักษาการ\nรักษาการณ์\nรังไข่\nรังแตน\nรังนก\nรังผึ้ง\nรังเพลิง\nรังมด\nรังสรรค์\nรังสฤษฏ์\nรั้งรอ\nรังสีแพทย์\nรังสีวิทยา\nรัชกาล\nรัชทายาท\nรัชนีกร\nรัฐธรรมนูญ\nรัฐบาล\nรัฐบุรุษ\nรัฐประศาสน์\nรัฐประหาร\nรัฐพิธี\nรัฐมนตรี\nรัฐวิสาหกิจ\nรัฐศาสตร์\nรัฐสภา\nรัดกุม\nรัดเกล้า\nรัดตัว\nรัดประคด\nรัดรึง\nรัดรูป\nรัตติกาล\nรับขวัญ\nรับจ้าง\nรับช่วง\nรับใช้\nรับซื้อ\nรับทราบ\nรับประกัน\nรับประทาน\nรับปาก\nรับผิด\nรับผิดชอบ\nรับฟ้อง\nรับฟัง\nรับมือ\nรับรอง\nรับรู้\nรับสมัคร\nรับสั่ง\nรับหน้า\nรับเหมา\nรั่วไหล\nรามือ\nร่าเริง\nรากแก้ว\nรากขวัญ\nรากฐาน\nรากฟัน\nรากศัพท์\nรากเหง้า\nร่างกาย\nร่างแห\nร้างรา\nราชกรณียกิจ\nราชการ\nราชกิจ\nราชครู\nราชฐาน\nราชทัณฑ์\nราชทินนาม\nราชทูต\nราชธานี\nราชนาวี\nราชบัณฑิต\nราชบัลลังก์\nราชบาตร\nราชบุตร\nราชปะแตน\nราชภัฏ\nราชมัล\nราชยาน\nราชรถ\nราชลัญจกร\nราชเลขาธิการ\nราชเลขานุการ\nราชวงศ์\nราชวัติ\nราชสกุล\nราชสมบัติ\nราชสาส์น\nราชหัตถเลขา\nราชองครักษ์\nราชโองการ\nราชาคณะ\nราชาศัพท์\nราชินีนาถ\nร้านชำ\nร้านรวง\nราบคาบ\nราบรื่น\nราบเรียบ\nรายการ\nรายงาน\nรายจ่าย\nรายได้\nรายทาง\nรายรับ\nรายล้อม\nรายละเอียด\nรายวิชา\nร่ายยาว\nร่ายรำ\nร้ายกาจ\nร้ายแรง\nราวนม\nราวป่า\nร้าวฉาน\nร้าวราน\nรำพัด\nรำแพน\nรำวง\nร่ำไป\nร่ำร้อง\nร่ำเรียน\nร่ำไร\nร่ำลา\nร่ำไห้\nริเริ่ม\nริอ่าน\nริมฝีปาก\nริ้วรอย\nรีบร้อน\nรีบรุด\nรีบเร่ง\nรื่นรมย์\nรื่นเริง\nรื้อถอน\nรื้อฟื้น\nรุกฆาต\nรุกราน\nรุกล้ำ\nรุกไล่\nรุ่งขึ้น\nรุ่งแจ้ง\nรุ่งเช้า\nรุ่งเรือง\nรุ่งโรจน์\nรุ่งสว่าง\nรุ่งสาง\nรุ่งอรุณ\nรุจิเรข\nรุดหน้า\nรุนแรง\nรุมเร้า\nรุมล้อม\nรุ่มรวย\nรุ่มร้อน\nรุ่ยร่าย\nรู้แกว\nรู้ความ\nรู้คุณ\nรู้งาน\nรู้จัก\nรู้แจ้ง\nรู้ใจ\nรู้เชิง\nรู้ตัว\nรู้ทัน\nรู้เท่า\nรู้เรื่อง\nรู้สำนึก\nรู้สึก\nรู้เห็น\nรูปการณ์\nรูปโฉม\nรูปฌาน\nรูปถ่าย\nรูปทรง\nรูปธรรม\nรูปแบบ\nรูปพรรณ\nรูปพรหม\nรูปภพ\nรูปภาพ\nรูปร่าง\nรูปสมบัติ\nเร่ร่อน\nเร่งด่วน\nเร่งมือ\nเร่งรัด\nเร่งรีบ\nเร่งเร้า\nเร้นลับ\nเร่อร่า\nเร่าร้อน\nเราะราย\nเราะร้าย\nเริงใจ\nเริงรมย์\nเริดร้าง\nเริ่มต้น\nเริ่มแรก\nเรี่ยราด\nเรี่ยไร\nเรียกคืน\nเรียกตัว\nเรียกร้อง\nเรียกหา\nเรียบร้อย\nเรียงความ\nเรียงตัว\nเรียงเบอร์\nเรียงพิมพ์\nเรียงเม็ด\nเรียงราย\nเรียนรู้\nเรียบร้อย\nเรียบเรียง\nเรียบวุธ\nเรี่ยมเร้\nเรี่ยวแรง\nเรือกลไฟ\nเรือกอและ\nเรือกำปั่น\nเรือจ้าง\nเรือดำน้ำ\nเรือโดยสาร\nเรือตรวจการณ์\nเรือตังเก\nเรือธง\nเรือนำร่อง\nเรือบด\nเรือบิน\nเรือใบ\nเรือประมง\nเรือพ่วง\nเรือพิฆาต\nเรือยนต์\nเรือยาว\nเรือโยง\nเรือรบ\nเรือลากจูง\nเรือสำปั้น\nเรือสำเภา\nเรือหลวง\nเรือหางยาว\nเรืออีโปง\nเรือเอี้ยมจุ๊น\nเรื้อรัง\nเรือกสวน\nเรืองนาม\nเรืองรอง\nเรืองแสง\nเรื่องราว\nเรื่องสั้น\nเรือนแก้ว\nเรือนจำ\nเรือนเบี้ย\nเรือนแพ\nเรือนหอ\nเรื่อยเจื้อย\nเรื่อยเฉื่อย\nเรื่อยเปื่อย\nแรเงา\nแรกนา\nแรกนาขวัญ\nแรงงาน\nแรงดึงดูด\nแรงเทียน\nแรงม้า\nแรงเหวี่ยง\nแรมรอน\nแรมรา\nแรมโรย\nโรคจิต\nโรงครัว\nโรงงาน\nโรงเจ\nโรงเตี๊ยม\nโรงทาน\nโรงนา\nโรงพยาบาล\nโรงพัก\nโรงพิมพ์\nโรงเรียน\nโรงเรือน\nโรงแรม\nโรงเลี้ยง\nโรงเลื่อย\nโรงสี\nโรงสีข้าว\nโรงอาหาร\nโรมรัน\nโรยรา\nฤชากร\nฤดูกาล\nลงขัน\nลงแขก\nลงคอ\nลงตัว\nลงท้าย\nลงทุน\nลงโทษ\nลงพุง\nลงมือ\nลงรัก\nลงรอย\nลงแรง\nลงโรง\nลงเอย\nลดตัว\nลดละ\nลดเลี้ยว\nลดหย่อน\nลดหลั่น\nลนลาน\nล้นพ้น\nล้นหลาม\nล้นเหลือ\nลบล้าง\nลบเลือน\nลบหลู่\nลมกรด\nลมค้า\nลมงวง\nลมแดด\nลมทะเล\nลมบก\nลมบน\nลมบ้าหมู\nลมปราณ\nลมปาก\nลมพิษ\nลมว่าว\nลมเสีย\nลมหนาว\nลมหายใจ\nล่มจม\nล่มสลาย\nล้มละลาย\nล้มลุก\nล้มเลิก\nล่วงเกิน\nล่วงรู้\nล่วงละเมิด\nล่วงลับ\nล่วงล้ำ\nล่วงเลย\nล่วงหน้า\nลวดลาย\nลวดสปริง\nลวดหนาม\nล้วนแล้ว\nลหุโทษ\nล่อลวง\nล่อหลอก\nล่อแหลม\nล้อต๊อก\nล้อเลื่อน\nล้อเล่น\nล้อเลียน\nล้อหลอก\nลองเชิง\nลองดี\nลองภูมิ\nล่องหน\nลอดช่อง\nล่อนจ้อน\nลอบกัด\nล้อมวง\nลอยแก้ว\nลอยชาย\nลอยตัว\nลอยนวล\nลอยแพ\nลอยลำ\nละทิ้ง\nละเลย\nละเว้น\nละครนอก\nละครใน\nละครเพลง\nละครร้อง\nละครรำ\nละครลิง\nละครสัตว์\nละเอียดอ่อน\nลักไก่\nลักพา\nลักเพศ\nลักยิ้ม\nลักลอบ\nลักลั่น\nลักหลับ\nลัดเลาะ\nลับตา\nลับแล\nลับหลัง\nลาออก\nล่าช้า\nล่าทัพ\nล้าสมัย\nล้าหลัง\nลากข้าง\nล้างบาง\nล้างผลาญ\nลาดเขา\nลาดตระเวน\nลาดเท\nลาดยาง\nลานบิน\nลาภปาก\nลาภลอย\nลามปาม\nลามเลีย\nลายคราม\nลายเซ็น\nลายแทง\nลายน้ำ\nลายพร้อย\nลายมือ\nลายลักษณ์\nลายเส้น\nลำกล้อง\nลำแข้ง\nลำธาร\nลำแสง\nลำไส้\nลำตัด\nลำนำ\nล่ำสัน\nล้ำยุค\nล้ำสมัย\nล้ำลึก\nล้ำเลิศ\nล้ำเส้น\nล้ำหน้า\nลิงจุ่น\nลิงลม\nลิงโลด\nลิดรอน\nลิ้นไก่\nลิ้นชัก\nลิ้นปี่\nลิ้นควาย\nลิ้นงูเห่า\nลิ้นหมา\nลิบลับ\nลิบลิ่ว\nลิ่มเลือด\nลี้ภัย\nลี้ลับ\nลึกซึ้ง\nลึกลับ\nลึกล้ำ\nลืมตน\nลืมต้น\nลืมตัว\nลืมตา\nลืมเลือน\nลือชา\nลือชื่อ\nลือลั่น\nลุล่วง\nลุกลน\nลุกลาม\nลุกลี้ลุกลน\nลุกฮือ\nลุ่มน้ำ\nลุ่มลึก\nลุ่มหลง\nลุ่ทาง\nลูกกรง\nลูกกรอก\nลูกกรุง\nลูกกลอน\nลูกกลิ้ง\nลูกกวาด\nลูกกะจ๊อก\nลูกกุญแจ\nลูกเกด\nลูกแก้ว\nลูกขนไก่\nลูกข่าง\nลูกขุน\nลูกเขย\nลูกครึ่ง\nลูกคลื่น\nลูกความ\nลูกคอ\nลูกค้า\nลูกคิด\nลูกคู่\nลูกจ้าง\nลูกช้าง\nลูกชิด\nลูกชิ้น\nลูกชุบ\nลูกซอง\nลูกโซ่\nลูกดอก\nลูกดิ่ง\nลูกตะกั่ว\nลูกตุ้ม\nลูกเต้า\nลูกเต๋า\nลูกถ้วย\nลูกทุ่ง\nลูกเธอ\nลูกน้อง\nลูกน้ำ\nลูกนิมิต\nลูกบอล\nลูกบ้าน\nลูกบาศก์\nลูกบิด\nลูกเบี้ยว\nลูกประคบ\nลูกประคำ\nลูกปัด\nลูกปืน\nลูกโป่ง\nลูกผสม\nลูกผู้ชาย\nลูกผู้หญิง\nลูกพรรค\nลูกพี่\nลูกฟูก\nลูกไฟ\nลูกมือ\nลูกโม่\nลูกไม้\nลูกยาเธอ\nลูกรอก\nลูกรัง\nลูกเรือ\nลูกล้อ\nลูกลอย\nลูกเล่น\nลูกเลี้ยง\nลูกโลก\nลูกวัด\nลูกศร\nลูกศิษย์\nลูกสมุน\nลูกสะใภ้\nลูกสูบ\nลูกเสือ\nลูกหนัง\nลูกหนี้\nลูกหนู\nลูกหมาก\nลูกหลง\nลูกหลาน\nลูกหาบ\nลูกหิน\nลูกเห็บ\nลูกเหม็น\nลูกแหง่\nลูกอม\nลูกหม้อ\nลูบคม\nลูบคลำ\nลูบไล้\nเล็กน้อย\nเลขคณิต\nเลขผา\nเลขหมาย\nเล็ดลอด\nเล่นงาน\nเล่นแง่\nเล่นชู้\nเล่นตัว\nเล่นลิ้น\nเล่นหัว\nเลนส์นูน\nเลนส์เว้า\nเล็บครุฑ\nเลยเถิด\nเลศนัย\nเล่ห์กล\nเล่ห์เหลี่ยม\nเลอโฉม\nเลอมาน\nเลอเลิศ\nเลอสรวง\nเล่อล่า\nเลอะเลือน\nเล่าเรียน\nเล่าลือ\nเลาะลัด\nเลิกรา\nเลิกร้าง\nเลิกล้ม\nเลิศเลอ\nเลี้ยงชีพ\nเลี้ยงดู\nเลี้ยงต้อย\nเลียบเคียง\nเลี้ยวลด\nเลือกตั้ง\nเลือกเฟ้น\nเลือกสรร\nเลื่องลือ\nเลือดกำเดา\nเลือดเนื้อ\nเลือดฝาด\nเลือดเย็น\nเลือดร้อน\nเลือดหมู\nเลือดอุ่น\nเลือนราง\nเลื่อนเปื้อน\nเลื่อนลอย\nเลื่อมพราย\nเลื่อมใส\nเลื่อยฉลุ\nเลื่อยลันดา\nเลื่อยวงเดือน\nเลื้อยคลาน\nแลเหลียว\nแลกเปลี่ยน\nแล้วกัน\nและเล็ม\nโล่งใจ\nโล่งโถง\nโล่งอก\nโลดเต้น\nโลดโผน\nโลดลิ่ว\nโลดแล่น\nไล่ที่\nไล่เบี้ย\nไล่เลี่ย\nไล่เลียง\nไล่หลัง\nไล่ออก\nวกวน\nวงกบ\nวงกลม\nวงการ\nวงแขน\nวงเงิน\nวงจร\nวงนอก\nวงใน\nวงรี\nวงเล็บ\nวงเวียน\nวงแหวน\nวงศ์วาน\nวจีกรรม\nวจีเภท\nวจีภาค\nวนเวียน\nวอดวาย\nว็อบแว็บ\nวังวน\nวังหน้า\nวังหลวง\nวังหลัง\nวัดราษฎร์\nวัดวา\nวัดหลวง\nวัดผล\nวัดพื้น\nวัตถุนิยม\nวัตถุประสงค์\nวัตรปฏิบัติ\nวันโกน\nวันพระ\nวันเพ็ญ\nวัยรุ่น\nวัยวุฒิ\nว่ากล่าว\nว่าจ้าง\nว่าด้วย\nว่าที่\nวางก้าม\nวางใจ\nวางตัว\nวางตา\nวางโต\nวางท่า\nวางมวย\nวางมาด\nวางมือ\nวางวาย\nว่างเปล่า\nว่างเว้น\nวาดเขียน\nว่านเครือ\nวาบหวาม\nวายชนม์\nวายปราณ\nวายวาง\nวายวอด\nวายร้าย\nวายุภักษ์\nวาววับ\nวาววาม\nวาวแวว\nวาวแสง\nวิกฤตการณ์\nวิกฤติการณ์\nวิกฤตกาล\nวิกฤติกาล\nวิกลจริต\nวิงเวียน\nวิ่งเต้น\nวิ่งผลัด\nวิ่งรอก\nวิ่งราว\nวิจิตรศิลป์\nวิชาการ\nวิชาชีพ\nวิชาธร\nวิญญูชน\nวิดพื้น\nวิตกจริต\nวิถีทาง\nวิทยากร\nวิทยากล\nวิทยาการ\nวิทยาเขต\nวิทยาทาน\nวิทยาธร\nวิทยานิพนธ์\nวิทยาศาสตร์\nวิเทศสัมพันธ์\nวิธีการ\nวินัยธร\nวินัยปิฎก\nวินาศกรรม\nวินาศภัย\nวินาศสันตะโร\nวิภัชพยากรณ์\nวิภัชวาที\nวิไลวรรณ\nวิสัญญีแพทย์\nวิสัญญีภาพ\nวิสัญญีวิทยา\nวุฒิบัตร\nวุฒิสภา\nวุฒิสมาชิก\nวุ่นวาย\nวุ้นเส้น\nวูบวาบ\nเวจกุฎี\nเวจมรรค\nเวชกรรม\nเวชภัณฑ์\nเวชศาสตร์\nเวทมนตร์\nเวนคืน\nเวรกรรม\nเวฬุการ\nเวฬุวัน\nเว้าวอน\nเวิ้งว้าง\nเวียงวัง\nเวียนเทียน\nแว้งกัด\nแวดล้อม\nแวดวง\nแว่นขยาย\nแว่นแคว้น\nแว่นตา\nแวบวับ\nแววตา\nแวววาม\nแวววาว\nแวะเวียน\nโวยวาย\nไวไฟ\nไว้ใจ\nไว้ชื่อ\nไว้ตัว\nไว้ทุกข์\nไว้ลาย\nไว้หน้า\nไว้อาลัย\nศนิวาร\nศอกกลับ\nศอกกำ\nศอกกำมา\nศักดิ์ศรี\nศักดิ์สิทธิ์\nศารทวิษุวัติ\nศาลแขวง\nศาลจังหวัด\nศาลชั้นต้น\nศาลฎีกา\nศาลเตี้ย\nศาลทหาร\nศาลปกครอง\nศาลพระภูมิ\nศาลเพียงตา\nศาลแพ่ง\nศาลรัฐธรรมนูญ\nศาลแรงงาน\nศาลล้มละลาย\nศาลโลก\nศาลสูง\nศาลสูงสุด\nศาลอาญา\nศาลอุทธรณ์\nศาลากลาง\nศาลาดิน\nศาลาราย\nศาลาวัด\nศิลาฤกษ์\nศิลาแลง\nศิษย์เก่า\nศิษย์เอก\nศีลจุ่ม\nศีลธรรม\nศีลวัต\nศีลอด\nศูนย์กลาง\nศูนย์การค้า\nศูนย์ถ่วง\nศูนย์สูตร\nศูนย์หน้า\nเศร้าใจ\nเศร้าโศก\nเศร้าสร้อย\nเศร้าสลด\nเศร้าหมอง\nเศวตฉัตร\nเศษเกิน\nเศษซ้อน\nเศษวรรค\nเศษส่วน\nเศษเหล็ก\nโศกนาฏกรรม\nโศกศัลย์\nโศกเศร้า\nโศกสลด\nสกลโลก\nส่งเดช\nส่งท้าย\nส่งเสริม\nส่งเสีย\nส่งเสียง\nสงบเงียบ\nสงบเสงี่ยม\nสง่างาม\nสง่าราศี\nสดชื่น\nสดใส\nสตรีเพศ\nสติปัญญา\nสถลมารค\nสถานกงสุล\nสถานที่\nสถานทูต\nสถานการณ์\nสถานภาพ\nสถิติศาสตร์\nสนตะพาย\nสนใจ\nส้นตีน\nสนธิสัญญา\nสนนราคา\nสนับแข้ง\nสนับเพลา\nสนับมือ\nสนามบิน\nสนามเพลาะ\nสนิทสนม\nสนิมขุม\nสนิมสร้อย\nสนุกสนาน\nสบประมาท\nสบายใจ\nสภาพธรรม\nสมควร\nสมจริง\nสมใจ\nสมนัย\nสมน้ำหน้า\nสมประกอบ\nสมส่วน\nสมหวัง\nสมคบ\nสมทบ\nสมยอม\nสมรัก\nสมรู้\nสมสู่\nส้มฉุน\nส้มตำ\nส้มลิ้ม\nส้มกุ้ง\nส้มเช้า\nสมญานาม\nสมมติฐาน\nสมมุติฐาน\nสมมติเทพ\nสมรภูมิ\nสมัครใจ\nสมัยนิยม\nสมุทรศาสตร์\nสมุทรเสนา\nสยดสยอง\nสยองขวัญ\nสยามรัฐ\nสรรหา\nสรวมชีพ\nสรวลเส\nสร้อยเศร้า\nสร้างสรรค์\nสร้างเสริม\nสลดใจ\nสลบไสล\nสละสลวย\nสลาเหิน\nสลากภัต\nสวนครัว\nสวนป่า\nสวนสนุก\nสวนหย่อม\nส่วนกลาง\nส่วนเกิน\nส่วนตัว\nส่วนบุญ\nส่วนแบ่ง\nส่วนประกอบ\nส่วนพระองค์\nส่วนผสม\nส่วนรวม\nส่วนร่วม\nส่วนลด\nส่วนสัด\nสวมกอด\nสวมเขา\nสวมรอย\nสวยมภู\nสว่างไสว\nสวามิภักดิ์\nสวิงสวาย\nสสารนิยม\nส่อเสียด\nสอดคล้อง\nสอดแทรก\nสอดแนม\nสอบถาม\nสอบทาน\nสอบไล่\nสอบสวน\nส้อมเสียง\nสะสวย\nสะแกวัลย์\nสะแกแสง\nสะใจ\nสะเด็ดยาด\nสะเทือนใจ\nสะบัดช่อ\nสั่งสม\nสั่งสอน\nสั่งเสีย\nสังเกตการณ์\nสังคมนิยม\nสังคมวิทยา\nสังคมศาสตร์\nสังคมศึกษา\nสังคมสงเคราะห์\nสัญญาบัตร\nสัดส่วน\nสัตการ\nสัตบุรุษ\nสัตบริภัณฑ์\nสัตภัณฑ์\nสัตมหาสถาน\nสัตโลหะ\nสันเขา\nสันดอน\nสันหลัง\nสั่นเทา\nสั่นเทิ้ม\nสันติบาล\nสันติภาพ\nสันติวิธี\nสันติสุข\nสับเปลี่ยน\nสับสน\nสับหลีก\nสับหว่าง\nสัมมาคารวะ\nสัมมาชีพ\nส่าเหล้า\nสากกะเบือ\nสาทิสลักษณ์\nสาธุการ\nสาธุชน\nสาบเสือ\nสาปสรร\nสาปแช่ง\nสาปส่ง\nสามง่าม\nสามล้อ\nสามเหลี่ยม\nสามเวท\nสามัญชน\nสามัญสำนึก\nสายดิ่ง\nสายดิน\nสายตรวจ\nสายน้ำ\nสายบัว\nสายพาน\nสายฟ้า\nสายยาง\nสายยู\nสายใย\nสายรก\nสายรุ้ง\nสายล่อฟ้า\nสายลับ\nสายเลือด\nสายโลหิต\nสายวัด\nสายส่ง\nสายสวาท\nสายสะดือ\nสายสะพาย\nสายสัมพันธ์\nสายสิญจน์\nสายสืบ\nสายไหม\nสายอากาศ\nสายตา\nสายหยุด\nสารตรา\nสารประกอบ\nสารละลาย\nสารส้ม\nสารหนู\nสารทฤดู\nสาวใช้\nสาวน้อย\nสาวใหญ่\nสำนักงาน\nสำนักพิมพ์\nสำนักสงฆ์\nสำมะโนครัว\nสำเร็จรูป\nสิกขาบท\nสิงสถิต\nสิงสู่\nสิ่งก่อสร้าง\nสิ่งของ\nสิ่งปฏิกูล\nสิ่งพิมพ์\nสิ่งแวดล้อม\nสิ่งศักดิ์สิทธิ์\nสิทธิกร\nสิทธิ์ขาด\nสิทธิชัย\nสิทธิโชค\nสิทธิบัตร\nสินค้า\nสินจ้าง\nสินเชื่อ\nสินไถ่\nสินทรัพย์\nสินน้ำใจ\nสินบน\nสินแร่\nสินสมรส\nสินสอด\nสินไหม\nสิ้นเชิง\nสิ้นสุด\nสีผึ้ง\nสีลม\nสีชอล์ก\nสีถ่าน\nสีเทียน\nสีน้ำ\nสีน้ำมัน\nสีโปสเตอร์\nสีฝุ่น\nสี่เหลี่ยม\nสีหน้า\nสึกหรอ\nสืบทอด\nสืบค้น\nสืบสวน\nสืบสาว\nสืบเสาะ\nสื่อผสม\nสื่อมวลชน\nสื่อสาร\nสุกงอม\nสุกดิบ\nสุกปลั่ง\nสุกใส\nสุขนาฏกรรม\nสุขภัณฑ์\nสุขภาพ\nสุขลักษณะ\nสุขวิทยา\nสุขศาลา\nสุขศึกษา\nสุดท้าย\nสุตกวี\nสุนทรพจน์\nสุภาพชน\nสู่ขอ\nสู่รู้\nสู่สม\nสูงส่ง\nสูญเปล่า\nสูญสิ้น\nสูญเสีย\nสูญหาย\nเสสรวล\nเสแสร้ง\nเสกสรร\nเสถียรภาพ\nเส้นชัย\nเส้นตรง\nเส้นตาย\nเส้นทาง\nเส้นใย\nเส้นรุ้ง\nเส้นเลือด\nเส้นแวง\nเส้นสาย\nเส้นเสียง\nเส้นหมี่\nเส้นเอ็น\nเสบียงกรัง\nเสมอภาค\nเสมอหน้า\nเสมอเหมือน\nเสมียนตรา\nเสร็จสรรพ\nเสร็จสิ้น\nเสริมส่ง\nเสริมสร้าง\nเสริมสวย\nเสรีไทย\nเสรีธรรม\nเสรีนิยม\nเสรีภาพ\nเสาเข็ม\nเสาธง\nเสียใจ\nเสียเชิง\nเสียดาย\nเสียที\nเสียเที่ยว\nเสียเปรียบ\nเสียเปล่า\nเสียรู้\nเสียแรง\nเสียสละ\nเสียหลัก\nเสียหาย\nเสี่ยงทาย\nเสียดแทง\nเสียดแทรก\nเสียดสี\nเสี้ยนศึก\nเสี้ยนหนาม\nเสี้ยมสอน\nเสียวซ่าน\nเสียวไส้\nเสือดาว\nเสือดำ\nเสือปลา\nเสือป่า\nเสือไฟ\nเสื่อกก\nเสื่อกระจูด\nเสื่อน้ำมัน\nเสื่อลำแพน\nเสื้อกล้าม\nเสื้อกั๊ก\nเสื้อเกราะ\nเสื้อครุย\nเสื้อแสง\nเสื้อเมือง\nเสือกคลาน\nเสือกสน\nเสือกไส\nเสื่อมคลาย\nเสื่อมถอย\nเสื่อมทราม\nเสื่อมโทรม\nเสื่อมสลาย\nเสื่อมสูญ\nเสื่อมเสีย\nเสือหมอบ\nแสกหน้า\nแสดงออก\nแสเถา\nแสนกล\nแสนรู้\nแสร้งว่า\nใส่ความ\nใส่ไคล้\nใส่ใจ\nใส่ไฟ\nไส้กรอก\nไส้ไก่\nไส้ติ่ง\nไส้ศึก\nไส้อั่ว\nไส้เดือน\nไส้ตัน\nไสยเวท\nไสยศาสตร์\nหกล้ม\nหงส์หยก\nหงอนไก่\nหงอยก๋อย\nหงอยเหงา\nหงายท้อง\nหงายหลัง\nหงำเหงอะ\nหงำเหงือก\nหดหาย\nหดหู่\nหนทาง\nหนวกหู\nหน่วงเหนี่ยว\nหน่วยก้าน\nหน่อไม้\nหนองใน\nหนองแซง\nหนักข้อ\nหนักใจ\nหนักแน่น\nหนักหน่วง\nหนักหนา\nหนังกลับ\nหนังตะลุง\nหนังเรียด\nหนังสด\nหนังใหญ่\nหนังสือพิมพ์\nหนาแน่น\nหน้ากระดาน\nหน้ากาก\nหน้ากาฬ\nหน้าแข้ง\nหน้าจั่ว\nหน้าฉาน\nหน้าตัก\nหน้าตา\nหน้าต่าง\nหน้าท้อง\nหน้าทับ\nหน้าที่\nหน้าที่นั่ง\nหน้าบัน\nหน้าปัด\nหน้าผา\nหน้าผาก\nหน้าม้า\nหน้ามุข\nหน้าไม้\nหน้าเลือด\nหน้าอก\nหนามเตย\nหน่ายหนี\nหน่ายแหนง\nหนาวเหน็บ\nหนำใจ\nหนี้สิน\nหนี้ส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น\nกณิกนันต์\nกณิการ์\nกด\nกตเวทิตา\nกตเวที\nกตัญชลี\nกตัญญุตา\nกตัญญู\nกตาธิการ\nกตาภินิหาร\nกติกา\nกถา\nกถิกาจารย์\nกทลี\nกน\nก่น\nก้น\nกนก\nกนิษฐ์\nกนิษฐา\nกบ\nกบฏ\nกบดาน\nกบทู\nกบาล\nกบินทร์\nกบิล\nกบี่\nกบูร\nกเบนทร์\nกม\nก้ม\nกมณฑลาภิเษก\nกมณฑโลทก\nกมล\nกมลา\nกมลาศ\nกมลาสน์\nกมเลศ\nกมัณฑลุ\nกมุท\nกร\nกรกฎ\nกรกฎาคม\nกรกฏ\nกรง\nกรชกาย\nกรณฑ์\nกรณิการ์\nกรณี\nกรณีย์\nกรณียกิจ\nกรณียะ\nกรด\nกรน\nกรบ\nกรบูร\nกรพินธุ์\nกรม\nกรรกฎ\nกรรกศ\nกรรเกด\nกรรไกร\nกรรเจียก\nกรรชิง\nกรรเชียง\nกรรโชก\nกรรฐ์\nกรรฐา\nกรรณ\nกรรณา\nกรรณิกา\nกรรณิการ์\nกรรดิ\nกรรดิก\nกรรดึก\nกรรตุ\nกรรไตร\nกรรทบ\nกรรแทก\nกรรบิด\nกรรบูร\nกรรภิรมย์\nกรรม\nกรรม์\nกรรม์ภิรมย์\nกรรมชวาต\nกรรมัชวาต\nกรรมาชีพ\nกรรมาธิการ\nกรรมาร\nกรรษก\nกรรสะ\nกรรแสง\nกรวด\nกรวบ\nกรวม\nกร้วม\nกรวย\nกรวิก\nกรสาปน์\nกรสุทธิ์\nกรอ\nกร้อ\nกรอก\nกร็อกกร๋อย\nกรอกแกรก\nกรอง\nกรองกรอย\nกรอด\nกร่อน\nกรอบ\nกรอม\nกร่อย\nกระ\nกระกร\nกระกรุ่น\nกระกลับกลอก\nกระกี้\nกระเกรอก\nกระเกริก\nกระเกริ่น\nกระคน\nกระคาย\nกระงกกระเงิ่น\nกระง่องกระแง่ง\nกระง่อนกระแง่น\nกระเง้ากระงอด\nกระโงก\nกระจก\nกระจง\nกระจร\nกระจอก\nกระจองหง่อง\nกระจ๋องหง่อง\nกระจองอแง\nกระจ้อน\nกระจอนหู\nกระจ้อย\nกระจ๋อหวอ\nกระจะ\nกระจัก\nกระจัง\nกระจัด\nกระจับ\nกระจ่า\nกระจ่าง\nกระจาด\nกระจาน\nกระจาบ\nกระจาม\nกระจาย\nกระจาว\nกระจิก\nกระจิ๋ง\nกระจิด\nกระจิบ\nกระจิ๋ม\nกระจิริด\nกระจิ๋ว\nกระจี้\nกระจี๋\nกระจุก\nกระจุ๋งกระจิ๋ง\nกระจุบ\nกระจุ๊บ\nกระจุ๋มกระจิ๋ม\nกระจุย\nกระจู้\nกระจู๋กระจี๋\nกระจูด\nกระเจอะกระเจิง\nกระเจา\nกระเจ่า\nกระเจ้า\nกระเจาะ\nกระเจิง\nกระเจิดกระเจิง\nกระเจี้ยง\nกระเจี๊ยบ\nกระเจียว\nกระเจี๊ยว\nกระแจะ\nกระโจน\nกระโจม\nกระฉอก\nกระฉ่อน\nกระฉับกระเฉง\nกระฉิ่ง\nกระฉีก\nกระฉูด\nกระเฉก\nกระเฉด\nกระแฉก\nกระโฉกกระเฉก\nกระโฉม\nกระชดกระช้อย\nกระชอน\nกระชอมดอก\nกระช้อย\nกระชัง\nกระชั้น\nกระชับ\nกระชาก\nกระชาย\nกระชิง\nกระชิด\nกระชุ\nกระชุก\nกระชุ่มกระชวย\nกระเชอ\nกระเชา\nกระเช้า\nกระเชียง\nกระแชง\nกระแชะ\nกระโชก\nกระซ่องกระแซ่ง\nกระซับ\nกระซาบ\nกระซิก\nกระซิบ\nกระซี้\nกระซุง\nกระซุบกระซิบ\nกระซุ้ม\nกระซู่\nกระเซ็น\nกระเซอ\nกระเซอะกระเซอ\nกระเซอะกระเซิง\nกระเซ้า\nกระเซิง\nกระแซ\nกระแซะ\nกระโซกระเซ\nกระฎี\nกระฎุมพี\nกระดก\nกระด้ง\nกระดนโด่\nกระดวง\nกระดวน\nกระด้วมกระเดี้ยม\nกระดอ\nกระดอง\nกระดองหาย\nกระดอน\nกระดอม\nกระดักกระเดี้ย\nกระดังงัว\nกระดังงา\nกระดาก\nกระด้าง\nกระดางลาง\nกระดาด\nกระดาดขาว\nกระดาน\nกระดานพน\nกระดาษ\nกระดำกระด่าง\nกระดิก\nกระดิ่ง\nกระดิ้ง\nกระดิบ\nกระดี่\nกระดี้กระเดียม\nกระดึง\nกระดืบ\nกระดุ\nกระดุกกระดิก\nกระดุ้งกระดิ้ง\nกระดุบ\nกระดุบกระดิบ\nกระดุม\nกระดูก\nกระเดก\nกระเด้ง\nกระเด็น\nกระเด้า\nกระเดาะ\nกระเดิด\nกระเดี้ย\nกระเดียด\nกระเดือก\nกระเดื่อง\nกระแด็ก\nกระแด้ง\nกระแด้แร่\nกระแด่ว\nกระแดะ\nกระโดก\nกระโดง\nกระโดด\nกระโดน\nกระได\nกระตรับ\nกระตราก\nกระตรุด\nกระตรุม\nกระต้วมกระเตี้ยม\nกระต้อ\nกระต่องกระแต่ง\nกระต๊อบ\nกระต้อยตีวิด\nกระตัก\nกระตั้ว\nกระต่าย\nกระติก\nกระติ๊ด\nกระติบ\nกระตือรือร้น\nกระตุก\nกระตุ้งกระติ้ง\nกระตุ่น\nกระตุ้น\nกระตูบ\nกระเตง\nกระเต็น\nกระเตอะ\nกระเตาะ\nกระเตาะกระแตะ\nกระเตื้อง\nกระแต\nกระแตแต้แว้ด\nกระโตกกระตาก\nกระโตน\nกระถด\nกระถอบ\nกระถั่ว\nกระถาง\nกระถิก\nกระถิน\nกระเถิบ\nกระโถน\nกระทก\nกระทง\nกระทบ\nกระทรวง\nกระทอก\nกระท้อน\nกระท่อนกระแท่น\nกระท่อม\nกระท้อมกระแท้ม\nกระทะ\nกระทั่ง\nกระทั้น\nกระทา\nกระทาย\nกระทาสี\nกระทาหอง\nกระทำ\nกระทิกกระทวย\nกระทิง\nกระทึง\nกระทืบ\nกระทุ\nกระทุง\nกระทุ้ง\nกระทุ่ม\nกระทู้\nกระเท่\nกระเทียบ\nกระเทียม\nกระเทือน\nกระเทื้อม\nกระแทก\nกระแท่น\nกระแทะ\nกระไทชาย\nกระน่อง\nกระนั้น\nกระนี้\nกระแนะกระแหน\nกระโน้น\nกระไน\nกระบก\nกระบม\nกระบวน\nกระบวย\nกระบวร\nกระบอก\nกระบอง\nกระบะ\nกระบัด\nกระบั้วกระเบี้ย\nกระบ่า\nกระบ้า\nกระบาก\nกระบาย\nกระบาล\nกระบิ\nกระบิ้ง\nกระบิด\nกระบิล\nกระบี่\nกระบือ\nกระบุง\nกระบุ่มกระบ่าม\nกระบู้กระบี้\nกระบูน\nกระบูร\nกระเบง\nกระเบญ\nกระเบ็ดกระบวน\nกระเบน\nกระเบา\nกระเบิก\nกระเบียด\nกระเบียน\nกระเบื้อง\nกระแบก\nกระแบะ\nกระโบม\nกระปมกระปำ\nกระปมกระเปา\nกระปรอก\nกระปรอกว่าว\nกระปรี้กระเปร่า\nกระปอก\nกระป้อกระแป้\nกระป่อง\nกระป๋อง\nกระปอดกระแปด\nกระป๋อหลอ\nกระปั้วกระเปี้ย\nกระป่ำ\nกระปุก\nกระปุ๊กลุก\nกระปุ่ม\nกระปุ่มกระป่ำ\nกระปุ่มกระปิ่ม\nกระเป๋า\nกระเปาะ\nกระโปก\nกระโปรง\nกระผม\nกระผลีกระผลาม\nกระผาน\nกระผีก\nกระพรวน\nกระพริ้ม\nกระพอก\nกระพอง\nกระพ้อม\nกระพัก\nกระพัง\nกระพังเหิร\nกระพังโหม\nกระพัด\nกระพัตร\nกระพัน\nกระพั่น\nกระพา\nกระพาก\nกระพี้\nกระพือ\nกระพุ้ง\nกระพุ่ม\nกระเพาะ\nกระเพิง\nกระเพื่อม\nกระแพ้ง\nกระฟัดกระเฟียด\nกระฟูมกระฟาย\nกระมล\nกระมอบ\nกระมอมกระแมม\nกระมัง\nกระมัน\nกระมิดกระเมี้ยน\nกระมุท\nกระเมาะ\nกระย่อง\nกระย่องกระแย่ง\nกระย่อน\nกระย่อม\nกระยา\nกระยาง\nกระยาจก\nกระยาหงัน\nกระยิก\nกระยิ้มกระย่อง\nกระยึกกระยือ\nกระยืดกระยาด\nกระเย้อกระแหย่ง\nกระรอก\nกระเรียน\nกระโรกน้ำข้าว\nกระโรกใหญ่\nกระไร\nกระลด\nกระลบ\nกระลอก\nกระลอม\nกระละหล่ำ\nกระลัด\nกระลับ\nกระลัมพร\nกระลา\nกระลำ\nกระลำพัก\nกระลำพุก\nกระลิง\nกระลี\nกระลุมพาง\nกระลุมพุก\nกระลุมพู\nกระลูน\nกระลู่น์\nกระเล็น\nกระเลียด\nกระเลือก\nกระโลง\nกระวน\nกระวัด\nกระวาด\nกระวาน\nกระวาย\nกระวิน\nกระวี\nกระวีกระวาด\nกระวูดกระวาด\nกระเวน\nกระเวยกระวาย\nกระแวน\nกระโวยกระวาย\nกระษัย\nกระษาปณ์\nกระสง\nกระสบ\nกระสม\nกระสรวล\nกระสร้อย\nกระสวน\nกระสวย\nกระสอบ\nกระสะ\nกระสัง\nกระสัน\nกระสับกระส่าย\nกระสา\nกระสานติ์\nกระสาบ\nกระสาย\nกระสือ\nกระสุงกระสิง\nกระส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ทิง\nกากะเยีย\nกากี\nกาง\nก้าง\nกางเกง\nกางเขน\nก๊าซ\nกาซะลอง\nกาญจนา\nกาฐ\nกาด\nก๊าด\nกาน\nก่าน\nก้าน\nก๊าน\nกานดา\nกานต์\nกานน\nก้านพร้าว\nกานพลู\nกาน้า\nกาบ\nก้าบ\nกาบู\nกาพย์\nกาเฟอีน\nกาแฟ\nกาม\nก้าม\nกามารมณ์\nกามินี\nกาเมสุมิจฉาจาร\nกาย\nก่าย\nกาเยน\nการ\nการณ์\nการ์ด\nการ์ตูน\nการบูร\nการย์\nการวิก\nการเวก\nการะเกด\nการะบุหนิง\nการัณย์\nการันต์\nการางหัวขวาน\nการิตการก\nการิตวาจก\nการุญ\nการุณย์\nกาเรการ่อน\nกาล\nกาลกรรณี\nกาลกิณี\nกาลจักร\nกาลัญญุตา\nกาลัญญู\nกาลัด\nกาลานุกาล\nกาลิก\nกาลี\nกาแล\nกาแล็กซี\nกาแล็กโทส\nกาว\nก้าว\nกาววาว\nกาวาง\nกาแวน\nกาศิก\nกาษฐะ\nกาษา\nกาสร\nกาสะ\nกาสา\nกาสาร\nกาสาวะ\nกาสิโน\nกาหล\nกาหลง\nกาหลา\nกาเหว่า\nกาไหล่\nกาฬ\nกาฬาวก\nกาฮัง\nกำ\nก่ำ\nกำกวม\nกำกัด\nกำกับ\nก้ำกึ่ง\nกำกูน\nก้ำเกิน\nกำเกียง\nกำคูน\nกำจร\nกำจัด\nกำจาย\nกำชับ\nกำชำ\nกำซาบ\nกำซำ\nกำด้น\nกำดัด\nกำดาล\nกำเดา\nกำธร\nกำนล\nกำนัน\nกำนัล\nกำเนิด\nกำบัง\nก่ำบึ้ง\nกำเบ้อ\nกำปอ\nกำปั่น\nกำผลา\nกำพง\nกำพด\nกำพต\nกำพร้า\nกำพราก\nกำพวด\nกำพอง\nกำพืด\nกำพุด\nกำพู\nกำเพลิง\nกำแพง\nกำภู\nกำมลาศน์\nกำมเลศ\nกำมะถัน\nกำมะลอ\nกำมะหยี่\nกำมะหริด\nกำมังละการ\nกำมังวิลิต\nกำมัชพล\nกำยาน\nกำยำ\nกำรอ\nกำราบ\nกำราล\nกำเริบ\nกำไร\nกำลัง\nกำลุง\nกำเลา\nกำไล\nกำสรด\nกำสรวล\nกำหนด\nกำหนัด\nกำเหน็จ\nกำแหง\nกิก\nกิ๊ก\nกิ่ง\nกิ้งก่า\nกิ้งกือ\nกิ้งโครง\nกิจ\nกิจจะ\nกิจจา\nกิดาการ\nกิดาหยัน\nกิตติ\nกิตติมศักดิ์\nกิน\nกินนร\nกินปลี\nกินเปี้ยว\nกินริน\nกินรี\nกิ๊บ\nกิมตึ๋ง\nกิมิชาติ\nกิมิวิทยา\nกิโมโน\nกิโยตีน\nกิระ\nกิริณี\nกิรินท\nกิริเนศวร\nกิริยา\nกิเลน\nกิเลส\nกิโล\nกิโลมกะ\nกิ่ว\nกิ๋ว\nกี\nกี่\nกี้\nกี๊\nกี๋\nกีฏวิทยา\nกีด\nกีตาร์\nกีบ\nกีรติ\nกีฬา\nกึก\nกึง\nกึ่ง\nกึ๋น\nกุ\nกุก\nกุ๊ก\nกุกกุฏ\nกุกกุร\nกุกรรม\nกุ้ง\nกุงอน\nกุงาน\nกุโงก\nกุจี\nกุญแจ\nกุญชร\nกุฎ\nกุฎา\nกุฎี\nกุฎุมพี\nกุฏฐัง\nกุฏิ\nกุณฑ์\nกุณฑล\nกุณฑี\nกุณโฑ\nกุณาล\nกุณี\nกุด\nกุดัง\nกุดั่น\nกุดา\nกุทัณฑ์\nกุน\nกุ๊น\nกุนเชียง\nกุนที\nกุโนกามอ\nกุบ\nกุบกับ\nกุม\nกุ่ม\nกุมฝอย\nกุมภ์\nกุมภนิยา\nกุมภัณฑ์\nกุมภา\nกุมภิล\nกุมภีล์\nกุมเหง\nกุมาร\nกุมารา\nกุมารี\nกุมุท\nกุย\nกุ๊ย\nกุ๋ย\nกุยช่าย\nกุยเฮง\nกุรระ\nกุรุพินท์\nกุเรา\nกุล\nกุลา\nกุลาหล\nกุลี\nกุลีกุจอ\nกุเลา\nกุแล\nกุเวร\nกุศราช\nกุศล\nกุศโลบาย\nกุสุม\nกุสุมภ์\nกุสุมา\nกุสุมาลย์\nกุสุมิตลดาเวลลิตา\nกุหนี\nกุหนุง\nกุหร่า\nกุหล่า\nกุหลาบ\nกุแหละ\nกู\nกู่\nกู้\nกู๊ก\nกูฏ\nกูฏา\nกูณฑ์\nกูด\nกูบ\nกูปรี\nกูรมะ\nกูรมาวตาร\nเก\nเก้\nเก๊\nเก๋\nเกก\nเก๊ก\nเกกมะเหรก\nเก๊กฮวย\nเก้กัง\nเก็ง\nเก่ง\nเก้ง\nเก๋ง\nเกงกอย\nเก่งกาจ\nเกงเขง\nเก๋งเคง\nเก็จ\nเกจิอาจารย์\nเกชา\nเกณฑ์\nเกด\nเก็ด\nเกตุ\nเกน\nเก็บ\nเกม\nเกย\nเกยูร\nเกรง\nเกร็ง\nเกร็ด\nเกรน\nเกร่อ\nเกรอะ\nเกราะ\nเกริก\nเกริน\nเกริ่น\nเกรียก\nเกรียง\nเกรียด\nเกรียน\nเกรียบ\nเกรียม\nเกรียว\nเกรี้ยว\nเกเร\nเกล็ด\nเกลศ\nเกลอ\nเกลา\nเกล้า\nเกลาะ\nเกลี่ย\nเกลี้ย\nเกลียง\nเกลี้ยง\nเกลียด\nเกลียว\nเกลือ\nเกลื้อ\nเกลือก\nเกลื่อน\nเกลื้อน\nเกวัฏ\nเกวียน\nเกศ\nเกศว\nเกศวะ\nเกศา\nเกศินี\nเกศี\nเกษตร\nเกษม\nเกษียณ\nเกษียน\nเกษียร\nเกส\nเกสร\nเกสรี\nเกสา\nเกสี\nเก้อ\nเกอิชา\nเกะ\nเกะกะ\nเกา\nเก่า\nเก้า\nเก๋า\nเกาต์\nเกาทัณฑ์\nเกาบิล\nเกาลัด\nเกาลิน\nเกาไศย\nเกาหลี\nเกาเหลา\nเกาเหลียง\nเก้าอี้\nเกาะ\nเกิ้ง\nเกิด\nเกิน\nเกิบ\nเกีย\nเกียกกาย\nเกียง\nเกี่ยง\nเกี๋ยง\nเกียจ\nเกียด\nเกียน\nเกี้ยมไฉ่\nเกี้ยมอี๋\nเกียร์\nเกียรติ\nเกียรติ์\nเกี่ยว\nเกี้ยว\nเกี๊ยว\nเกี๊ยะ\nเกื้อ\nเกือก\nเกื้อกูล\nเกือบ\nแก\nแก่\nแก้\nแกง\nแก่ง\nแก้ง\nแก๊ง\nแกงได\nแกงแนง\nแกโดลิเนียม\nแกน\nแก่น\nแก๊ป\nแกม\nแก้ม\nแกมมา\nแกรก\nแกร่ง\nแกร็น\nแกรนิต\nแกรไฟต์\nแกร่ว\nแกระ\nแกล\nแกล้ง\nแกลน\nแกลบ\nแกล้ม\nแกลลอน\nแกลเลียม\nแกล้ว\nแกละ\nแกแล\nแกว\nแก้ว\nแกว่ง\nแก๊ส\nแกะ\nโก\nโก่\nโก้\nโก๋\nโกก\nโกกนุท\nโกกิลา\nโกโก้\nโกง\nโก่ง\nโกงกาง\nโก้งเก้ง\nโกงโก้\nโก้งโค้ง\nโกเชาว์\nโกญจนาท\nโกญจา\nโกฏิ\nโกฐ\nโกฐาส\nโกณะ\nโกดัง\nโกทัณฑ์\nโกน\nโก่น\nโก๋น\nโกมล\nโกมุท\nโกเมน\nโกเมศ\nโกย\nโกรก\nโกรกกราก\nโกรง\nโกร่ง\nโกร่งกร่าง\nโกรงเกรง\nโกร๋งเกร๋ง\nโกรญจ\nโกรต๋น\nโกรธ\nโกรธา\nโกร๋น\nโกรม\nโกรย\nโกรศ\nโกโรโกเต\nโกโรโกโรก\nโกโรโกโส\nโกลน\nโกลาหล\nโกไล\nโกวิท\nโกศ\nโกศล\nโกษม\nโกสน\nโกสัช\nโกสินทร์\nโกสีย์\nโกสุม\nโกไสย\nโกหก\nใกล้\nไก\nไก่\nไก๊\nไก๋\nไก่กอม\nไกพัล\nไกร\nไกรพ\nไกรลาส\nไกรศร\nไกรศรี\nไกรสร\nไกรสรี\nไกรสิทธิ\nไกล\nไกล่\nไกลาส\nไกว\nไกวัล\nขงจื๊อ\nขจร\nขจรจบ\nขจัด\nขจ่าง\nขจาย\nขจาว\nขจิต\nขจี\nขจุย\nขเจา\nขณะ\nขด\nขน\nข้น\nขนง\nขนด\nขนบ\nขนม\nขนอง\nขนอน\nขนอบ\nขนัด\nขนัน\nขนาก\nขนาง\nขนาด\nขนาน\nขนาบ\nขนาย\nขนำ\nขนิษฐ\nขนิษฐา\nขนุน\nขนุนนก\nขบ\nขบถ\nขบวน\nขบวร\nขม\nข่ม\nขมงโกรย\nขมวด\nขมวน\nขมอง\nขม่อม\nขมัง\nขมับ\nขมา\nขม้ำ\nขมิ้น\nขมิบ\nขมีขมัน\nขมึง\nขมึงทึง\nขมุ\nขมุกขมัว\nขมุบ\nขโมย\nขยด\nขยม\nขย่ม\nขยอก\nขยอง\nขย่อน\nขย้อน\nขยะ\nขยัก\nขยัน\nขยั้น\nขยับ\nขยาด\nขยาย\nขยำ\nขย้ำ\nขยิก\nขยิบ\nขยิ่ม\nขยี้\nขยุกขยิก\nขยุกขยุย\nขยุบ\nขยุบขยิบ\nขยุม\nขยุ้ม\nขยุย\nขรม\nขรรค์\nขรัว\nขริบ\nขรี\nขรึม\nขรุขระ\nขลบ\nขล้อ\nขลัง\nขลับ\nขลาด\nขลาย\nขลิบ\nขลุก\nขลุกขลัก\nขลุกขลิก\nขลุบ\nขลุม\nขลุ่ย\nขลู\nขลู่\nขวง\nข่วง\nขวด\nข่วน\nขวนขวาย\nขวบ\nขวย\nขวักไขว่\nขวัญ\nขวั้น\nขวับ\nขวับเขวียว\nขวา\nขวาก\nขวาง\nขว้าง\nขวาด\nขวาน\nขวายขวน\nขวาว\nขว้าว\nขวิด\nขอ\nข่อ\nข้อ\nของ\nข้อง\nขอด\nขอน\nข้อน\nขอบ\nขอม\nข่อย\nข้อย\nข่อยหยอง\nขะแจะ\nขะเน็ด\nขะมอมขะแมม\nขะมักเขม้น\nขะมุกขะมอม\nขะยิก\nขะยุก\nขะเย้อแขย่ง\nขัค\nขัง\nขังขอก\nขัช\nขัณฑสกร\nขัณฑสีมา\nขัด\nขัดมอน\nขัตติยมานะ\nขัน\nขั้น\nขันติ\nขันตี\nขันโตก\nขันที\nขันธ์\nขันธาวาร\nขับ\nขัว\nขั้ว\nขา\nข่า\nข้า\nขาก\nขาก๊วย\nขาง\nข่าง\nข้าง\nขาณุ\nขาด\nขาทนียะ\nขาน\nขาบ\nข้าพเจ้า\nขาม\nข่าม\nข้าม\nขาย\nข่าย\nขาล\nขาว\nข่าว\nข้าว\nข้าวอังกุลี\nขำ\nขิก\nขิง\nขิงแกลง\nขิงแครง\nขิด\nขิปสัทโท\nขิม\nขี่\nขี้\nขี้เข็บ\nขีณาสพ\nขีด\nขี้ตังนี\nขีปนาวุธ\nขี้ยอก\nขีระ\nขึง\nขึ้ง\nขึ้น\nขึ้นฉ่าย\nขืน\nขื่น\nขื่อ\nขุก\nขุด\nขุน\nขุ่น\nขุนเพ็ด\nขุม\nขุย\nขู่\nขูด\nเข\nเข้\nเขก\nเข็ง\nเข่ง\nเขจร\nเข็ญ\nเข็ด\nเขดา\nเขต\nเขน\nเข็น\nเข่น\nเขนง\nเขน็ด\nเขนย\nเขบ็จขบวน\nเขบ็ต\nเขม\nเข็ม\nเข้ม\nเข้มขาบ\nเขม็ง\nเขม็ดแขม่\nเขม่น\nเขม้น\nเขม้นขะมัก\nเขมร\nเขมา\nเขม่า\nเขมือบ\nเขย\nเขยก\nเขย่ง\nเขย้อแขย่ง\nเขย่า\nเขยิน\nเขยิบ\nเขยื้อน\nเขรอะ\nเขลง\nเขลอะ\nเขละ\nเขลา\nเขลาะ\nเขว\nเขษม\nเขฬะ\nเขะขะ\nเขา\nเข่า\nเข้า\nเขิง\nเขิน\nเขิบ\nเขี่ย\nเขียง\nเขียด\nเขียดตะปาด\nเขียน\nเขี่ยน\nเขียม\nเขียว\nเขี้ยว\nเขียะ\nเขือ\nเขือง\nเขื่อง\nเขื่อน\nเขือม\nแข\nแข้\nแขก\nแข็ง\nแข่ง\nแข้ง\nแขน\nแข่น\nแข้น\nแขนง\nแขม\nแขม็บ\nแขม่ว\nแขยง\nแขย่ง\nแขวก\nแขวง\nแขวน\nแขวะ\nโข\nโขก\nโขง\nโข่ง\nโขด\nโขดง\nโขน\nโขนง\nโขม\nโขมง\nโขมด\nโขยก\nโขยง\nโขย่ง\nโขยด\nโขลก\nโขลง\nโขลน\nโขษม\nไข\nไข่\nไข้\nไขว่\nไขว้\nคคนะ\nคคนัมพร\nคคนางค์\nคคนานต์\nคง\nคงคา\nคงไคย\nคช\nคชาชาติ\nคชาชีพ\nคชาธาร\nคชาภรณ์\nคณนา\nคณบดี\nคณะ\nคณาจารย์\nคณาธิการ\nคณาธิปไตย\nคณานับ\nคณิกา\nคณิต\nคเณศ\nคด\nคดี\nคติ\nคทา\nคน\nค้น\nคนทา\nคนทิสอ\nคนที\nคนโท\nคนธ์\nคันธ์\nคนธรรพ์\nคเนจร\nคบ\nคม\nคมน์\nคมนาการ\nคมนาคม\nคมิกภัต\nครก\nครบ\nครรชิต\nครรภ\nครรภ์\nครรลอง\nครรโลง\nครรไล\nครวญ\nครวี\nครหา\nครอก\nครอง\nครองแครง\nคร่อเงาะ\nคร่อเทียน\nครอบ\nคร่อม\nคระเมิม\nคระแลง\nคระไล\nคระแวง\nคระหน\nคระหวน\nคระหาย\nคระโหย\nครั่ง\nครั้ง\nครัดเคร่ง\nครัน\nครั่น\nครั้น\nครับ\nครัว\nครา\nคร่า\nคราก\nคราง\nคราญ\nคราด\nคร้าน\nคราบ\nคราม\nคร้าม\nครามครัน\nคราว\nคร่าว\nคราส\nครำ\nคร่ำ\nคร่ำเคร่ง\nคริปทอน\nคริสต์\nครีบ\nครีม\nครีษมายัน\nครึ\nครึกครื้น\nครึกโครม\nครึ่ง\nครึ่ด\nครึน\nครึ้ม\nครืด\nครืน\nครื้น\nครืนครั่น\nครื้นครั่น\nครื้นครึก\nครื้นเครง\nครือ\nครุ\nครุคระ\nครุฑ\nครุ่น\nครุมเครือ\nครุย\nครุวนา\nครู\nครู่\nครูด\nคฤโฆษ\nคฤนถ์\nคฤหบดี\nคฤหัสถ์\nคฤหาสน์\nคลวง\nคลอ\nคล้อ\nคลอก\nคลอง\nคล่อง\nคล้อง\nคลอด\nคลอน\nคล้อย\nคลอรีน\nคลอโรฟอร์ม\nคลอโรฟีลล์\nคละ\nคละคลุ้ง\nคลัก\nคลั่ก\nคลัง\nคลั่ง\nคลัตช์\nคลับคล้าย\nคลับคลา\nคลา\nคล้า\nคลางแคลง\nคลาด\nคลาน\nคลาย\nคล้าย\nคล้ายคลึง\nคล่าว\nคลำ\nคล่ำ\nคล้ำ\nคลิ้งโคลง\nคลิด\nคลินิก\nคลี\nคลี่\nคลึง\nคลื่น\nคลุก\nคลุ้ง\nคลุบ\nคลุม\nคลุ่ม\nคลุ้ม\nควง\nควณ\nควน\nควบ\nควย\nควร\nควัก\nควั่ก\nควั่งคว้าง\nควัน\nควั่น\nคว้า\nควาก\nคว้าง\nควาญ\nควาน\nคว้าน\nความ\nควาย\nคว่าว\nคว่ำ\nควินิน\nควิวคว่าง\nคหกรรม\nคหกรรมศาสตร์\nคหบดี\nคหัฐ\nคอ\nค้อ\nคอก\nค็อกคัส\nค็อกเทล\nคอเคซอยด์\nค่องอ้อย\nคอด\nคอแดง\nคอน\nค่อน\nค้อน\nคอนกรีต\nคอนเดนเซอร์\nคอนแวนต์\nคอนเสิร์ต\nคอม\nค่อม\nค้อม\nคอมพิวเตอร์\nคอมมานโด\nคอมมิวนิสต์\nคอย\nค่อย\nค้อย\nคอยล์\nคอร์ด\nคอแลน\nคอสติกโซดา\nคะ\nค่ะ\nคะไขว่\nคะค้อย\nคะคาน\nคะนน\nคะนอง\nคะน้า\nคะนึง\nคะเน\nคะเนงร้าย\nคะเน็ด\nคะแนน\nคะมำ\nคะยั้นคะยอ\nคะเยอ\nคัก\nคั่ก\nคัคนะ\nคัคนัมพร\nคัคนางค์\nคัคนานต์\nคั่ง\nคังไคย\nคัจฉ\nคัณฑมาลา\nคัณฑสูตร\nคัด\nคัดเค้า\nคัดมอน\nคัดเม็ง\nคัทลียา\nคัน\nคั่น\nคั้น\nคันถรจนาจารย์\nคันธกุฎี\nคันธมาทน์\nคันธารราษฎร์\nคับ\nคับค้อน\nคับคา\nคับแค\nคัพภ์\nคัมภีร์\nคัมภีรภาพ\nคัล\nคั่ว\nคา\nค่า\nค้า\nค่าคบ\nคาง\nค่าง\nค้าง\nคางคก\nค้างคาว\nคาด\nคาถา\nคาทอลิก\nคาน\nค้าน\nคาบ\nคาพยุต\nคาม\nคามวาสี\nคามณีย์\nคามภีร์\nคาย\nค่าย\nคาร์บอน\nคาร์บอเนต\nคาร์บอลิก\nคาร์บูเรเตอร์\nคาร์โบรันดัม\nคาร์โบไฮเดรต\nคารม\nคารวะ\nคาราเต้\nคาราวาน\nคาว\nค่าว\nค้าว\nคาวตอง\nคาวี\nคาวุต\nคาส\nคำ\nค่ำ\nค้ำ\nคำนวณ\nคำนวร\nคำนับ\nคำนัล\nคำนึง\nคำนูณ\nคำฝอย\nคำเพลิง\nคำรน\nคำรบ\nคำราม\nคำแสด\nคำแหง\nคำโอง\nคิก\nคิง\nคิด\nคิมหันต์\nคิรี\nคิลาน\nคิลานะ\nคิว\nคิ้ว\nคี่\nคีต\nคีบ\nคีม\nคีรี\nคีรีบูน\nคึก\nคึ่ก\nคึกคัก\nคืน\nคืบ\nคือ\nคุ\nคุก\nคุกกี้\nคุกคาม\nคุกพาทย์\nคุ้ง\nคุณ\nคุด\nคุดทะราด\nคุต\nคุตติ\nคุ่น\nคุ้น\nคุป\nคุปต์\nคุปติ\nคุม\nคุ่ม\nคุ้ม\nคุย\nคุ้ย\nคุยหฐาน\nคุยหประเทศ\nคุรุ\nคุลา\nคุลิก่า\nคุลีการ\nคุหา\nคู\nคู่\nคู้\nคูณ\nคูถ\nคูน\nคูปอง\nคูเรียม\nคูหา\nเค้ก\nเค้เก้\nเค้ง\nเคณฑะ\nเคด\nเค็ด\nเคน\nเค้น\nเคเบิล\nเค็ม\nเคมี\nเคย\nเครง\nเคร่ง\nเครงครา\nเครงครำ\nเครดิต\nเครน\nเครา\nเคร่า\nเคราหณี\nเคราะห์\nเครียด\nเครียว\nเครือ\nเครื่อง\nเคล้ง\nเคล็ด\nเคล้น\nเคล้า\nเคล่าคล่อง\nเคลิบเคลิ้ม\nเคลิ้ม\nเคลีย\nเคลื่อน\nเคลือบ\nเคว้ง\nเคหะ\nเคหา\nเคอะ\nเค้า\nเคาน์เตอร์\nเคารพ\nเคาะ\nเคาะแคะ\nเคียง\nเคียด\nเคียน\nเคียม\nเคี่ยม\nเคียร\nเคียว\nเคี่ยว\nเคี้ยว\nเคือง\nแค\nแค่\nแค้\nแคแล\nแคดเมียม\nแค็ตตาล็อก\nแคแตร\nแคโทด\nแคน\nแค่น\nแค้น\nแคบ\nแคบหมู\nแคปซูล\nแคม\nแคร่\nแครก\nแครง\nแคระ\nแคลคูลัส\nแคลง\nแคลเซียม\nแคลน\nแคล้ว\nแคล่วคล่อง\nแคลอรี\nแคลิฟอร์เนียม\nแคว\nแควก\nแคว้น\nแคแสด\nแคะ\nโค\nโคก\nโคเคน\nโค่ง\nโค้ง\nโคจร\nโคเซแคนต์\nโคไซน์\nโคตร\nโคแทนเจนต์\nโคธา\nโคน\nโค่น\nโคบอลต์\nโคปผกะ\nโคม\nโคม่า\nโครก\nโครกคราก\nโครง\nโคร่ง\nโคร่งคร่าง\nโครม\nโครเมียม\nโครโมโซม\nโคราช\nโครำ\nโคล\nโคลง\nโคลน\nโควตา\nโคออร์ดิเนต\nใคร\nใคร่\nใคร่ครวญ\nไค\nไค้\nไคร้\nไคร้เครือ\nไคล\nไคล้\nฆนะ\nฆราวาส\nฆ้อง\nฆ่า\nฆาต\nฆาน\nฆานินทรีย์\nเฆี่ยน\nโฆรวิส\nโฆษก\nโฆษณา\nโฆษะ\nโฆษ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nเฉ่ง\nเฉด\nเฉท\nเฉนียน\nเฉพาะ\nเฉย\nเฉลย\nเฉลว\nเฉลา\nเฉลิม\nเฉลี่ย\nเฉลียง\nเฉลี่ยง\nเฉลียบ\nเฉลียว\nเฉวียง\nเฉวียน\nเฉอะแฉะ\nเฉา\nเฉาก๊วย\nเฉาฮื้อ\nเฉาะ\nเฉิด\nเฉิบ\nเฉียง\nเฉียงพร้านางแอ\nเฉียด\nเฉียบ\nเฉียว\nเฉี่ยว\nเฉือน\nเฉื่อย\nแฉ\nแฉ่\nแฉก\nแฉง\nแฉ่ง\nแฉลบ\nแฉล้ม\nแฉะ\nโฉ\nโฉ่\nโฉเก\nโฉ่งฉ่าง\nโฉงเฉง\nโฉด\nโฉนด\nโฉบ\nโฉเบ๊\nโฉม\nโฉลก\nไฉน\nไฉไล\nชก\nชคัตตรัย\nชง\nชงโค\nชงฆ์\nชงฆา\nชงโลง\nชฎา\nชฎามังษี\nชฎามังสี\nชฎิล\nชด\nชน\nชนก\nชนนี\nชนม์\nชนวน\nชนะ\nชนัก\nชนา\nชนาง\nชนิด\nชเนตตี\nชบา\nชม\nชมดชม้อย\nชมนาด\nชมพู\nชมพู่\nชมรม\nชม้อย\nชม้าย\nชไม\nชยา\nชโย\nชรทึง\nชรริน\nชรอุ่ม\nชระล้ำ\nชระลุ\nชระอาบ\nชระเอม\nชรัด\nชรา\nชล\nชโลง\nชโลม\nช่วง\nชวด\nชวน\nชวย\nช่วย\nชวร\nชวลิต\nชวา\nชวาล\nชวาลา\nช่อ\nชอก\nช็อก\nช็อกโกเลต\nช็อกโกแลต\nชอง\nช่อง\nช้อง\nชองระอา\nชอน\nช่อน\nช้อน\nชอบ\nชอม\nช้อย\nชอล์ก\nชอ่ำ\nชอุ่ม\nชะ\nชะคราม\nชะงอก\nชะง่อน\nชะงัก\nชะงัด\nชะง้ำ\nชะงุ้ม\nชะเง้อ\nชะเงื้อม\nชะแง้\nชะโงก\nชะฉ่า\nชะช่อง\nชะชะ\nชะช้า\nชะโด\nชะตา\nชะต้า\nชะนี\nชะเนาะ\nชะเนียง\nชะพลู\nชะเพลิง\nชะมด\nชะมบ\nชะมวง\nชะมัง\nชะมัด\nชะแม่\nชะรอย\nชะลอ\nชะลอม\nชะล่า\nชะลาน\nชะลิน\nชะลูด\nชะเลง\nชะเลย\nชะแล็ก\nชะแลง\nชะวาก\nชะวาด\nชะเวิกชะวาก\nชะแวง\nชะอม\nชะอ้อน\nชะเอม\nชะโอน\nชัก\nชักคราม\nชักช้า\nชัง\nชั่ง\nชังคา\nชังฆ\nชัชวาล\nชัฏ\nชัด\nชัดช้า\nชัน\nชั้น\nชันกาด\nชันชี\nชันตุ\nชันนะตุ\nชันนุ\nชันโรง\nชันษา\nชันสูตร\nชัปนะ\nชัพ\nชัมพูนท\nชัย\nชัยพฤกษ์\nชัยภูมิ\nชัลลุกา\nชั่ว\nชั้ว\nชัวชม\nชา\nช้า\nชาคระ\nชาคริต\nชาคริยานุโยค\nช่าง\nช้าง\nช้าช่อน\nชาญ\nชาด\nชาดก\nชาต\nชาตบุษย์\nชาตรี\nชาตะ\nชาตา\nชาติ\nชาน\nชานุ\nช้าปี่\nชาปีไหน\nช้าแป้น\nช้าพลู\nชาม\nชามพูนท\nชามาดร\nชามาดา\nชามาตุ\nชาย\nชายา\nชาล\nชาลา\nชาลินี\nช้าเลือด\nชาว\nชาวี\nชำ\nช่ำ\nช้ำ\nชำงัด\nชำงาย\nช่ำชอง\nชำนะ\nชำนัญ\nชำนัน\nชำนาญ\nชำนิ\nชำเนียร\nชำมะนาด\nชำมะเลียง\nชำร่วย\nชำระ\nช้ำรั่ว\nชำรุด\nชำเรา\nชำเราะ\nชำแรก\nชำแระ\nชำเลือง\nชำแหละ\nชิ\nชิง\nชิ่ง\nชิงชัน\nชิงช้า\nชิงช้าชาลี\nชิงชี่\nชิงฮื้อ\nชิชะ\nชิชิ\nชิณณะ\nชิด\nชิเดนทรีย์\nชิต\nชิตินทรีย์\nชิน\nชิ้น\nชินโต\nชิโนรส\nชิม\nชิมแปนซี\nชิยา\nชิรณะ\nชิระ\nชิวหา\nชิสา\nชี\nชี่\nชี้\nชีปะขาว\nชีผะขาว\nชีผ้าขาว\nชีพ\nชีฟอง\nชีรณ\nชีระ\nชีวเคมี\nชีวประวัติ\nชีวภาพ\nชีววิทยา\nชีวะ\nชีวัน\nชีวา\nชีวาตม์\nชีวาลัย\nชีวิต\nชีวิตักษัย\nชีวิน\nชีวี\nชืด\nชื่น\nชื้น\nชื่อ\nชุก\nชุกชี\nชุ้ง\nชุณห\nชุด\nชุติ\nชุน\nชุบ\nชุม\nชุ่ม\nชุมนุม\nชุมพร\nชุมพา\nชุมแพรก\nชุมรุม\nชุมแสง\nชุมเห็ด\nชุ่ย\nชุลมุน\nชุลี\nชุษณะ\nชู\nชู้\nเช็ค\nเช้ง\nเช้งวับ\nเชงเลง\nเช็ด\nเชน\nเช่น\nเชย\nเชลง\nเชลย\nเชลแล็ก\nเชลียง\nเชวง\nเชษฐะ\nเชษฐา\nเชอ\nเช่า\nเช้า\nเชาว์\nเชาวน์\nเชิง\nเชิญ\nเชิด\nเชิ้ต\nเชียง\nเชี่ยน\nเชียบ\nเชี่ยม\nเชียร\nเชียร์\nเชียว\nเชี่ยว\nเชื่อ\nเชื้อ\nเชือก\nเชื่อง\nเชือด\nเชือน\nเชื่อม\nแช\nแช่\nแช่ง\nแชงมา\nแชบ๊วย\nแช่ม\nแชร์\nแชล่ม\nแชสซี\nแชะ\nโชก\nโชค\nโชงโลง\nโชดก\nโชดึก\nโชต\nโชตก\nโชติ\nโชติก\nโชน\nโชมโรม\nโชย\nโชยงการ\nโชยชาย\nโชยติส\nโชว์\nใช่\nใช้\nไช\nไชนะ\nไชย\nไชโย\nซก\nซ่ก\nซงดำ\nซ่งฮื้อ\nซด\nซน\nซ้น\nซบ\nซม\nซวดเซ\nซวน\nซวย\nซอ\nซอก\nซอง\nซ่อง\nซ้อง\nซองแมว\nซ้องแมว\nซอน\nซ่อน\nซ้อน\nซอม\nซ่อม\nซ้อม\nซอมซ่อ\nซอย\nซอส\nซัก\nซักส้าว\nซัง\nซั้ง\nซัด\nซับ\nซัลฟา\nซั้ว\nซา\nซ่า\nซาก\nซาง\nซ่าง\nซาด\nซาน\nซ่าน\nซาบซ่าน\nซาบซึ้ง\nซ่าโบะ\nซาแมเรียม\nซ้าย\nซาลาเปา\nซาว\nซ่าหริ่ม\nซำ\nซ้ำ\nซิ\nซี\nซิก\nซิกข์\nซิกซี้\nซิกแซ็ก\nซิการ์\nซิงโคนา\nซิ่น\nซินนามิก\nซินแส\nซิบ\nซิป\nซิฟิลิส\nซิลิคอน\nซิว\nซี่\nซีก\nซีเซียม\nซีด\nซี้ด\nซีนอน\nซีป่าย\nซีเมนต์\nซีเรียม\nซีลีเนียม\nซีอิ๊ว\nซึก\nซึง\nซึ่ง\nซึ้ง\nซึม\nซื่อ\nซื้อ\nซุก\nซุง\nซุน\nซุบ\nซุป\nซุ่ม\nซุ้ม\nซุ่มซ่าม\nซุย\nซู่\nซูโครส\nซูด\nซู้ด\nซูดซาด\nซูบ\nเซ\nเซ็ก\nเซแคนต์\nเซ็ง\nเซ่ง\nเซ้ง\nเซ็งแซ่\nเซต\nเซน\nเซ็น\nเซ่น\nเซนติกรัม\nเซนติเกรด\nเซนติเมตร\nเซนติลิตร\nเซปักตะกร้อ\nเซราะ\nเซรุ่ม\nเซลเซียส\nเซลล์\nเซลลูลอยด์\nเซลลูโลส\nเซ่อ\nเซอร์โคเนียม\nเซอะ\nเซา\nเซ้าซี้\nเซาะ\nเซิง\nเซิ้ง\nเซียน\nเซียบ\nเซียมซี\nเซียว\nเซี่ยว\nเซี่ยวกาง\nเซื่อง\nแซ\nแซ่\nแซ็กคาริน\nแซง\nแซงแซว\nแซด\nแซบ\nแซม\nแซยิด\nแซ่ว\nแซะ\nโซ\nโซ่\nโซก\nโซ่ง\nโซงโขดง\nโซเซ\nโซดา\nโซเดียม\nโซม\nโซรม\nโซลา\nไซ\nไซ้\nไซเกิล\nไซโคลน\nไซน์\nไซยาไนด์\nไซร้\nไซเรน\nไซโล\nฌาน\nฌาปน\nฌาปนกิจ\nฌาปนสถาน\nเฌอ\nเฌอเอม\nญวน\nญัตติ\nญาณ\nญาติ\nญานาซะฮ์\nญิบ\nญี่ปุ่น\nเญยธรรม\nไญยธรรม\nฎีกา\nฐกัด\nฐากูร\nฐาน\nฐานะ\nฐานันดร\nฐานานุกรม\nฐานานุรูป\nฐานานุศักดิ์\nฐานียะ\nฐาปน\nฐาปนา\nฐายี\nฐิต\nฐิติ\nฑาหก\nฑาหะ\nเฒ่า\nณรงค์\nเณร\nดก\nดง\nด้ง\nด้น\nดนโด่\nดนตรี\nดนัย\nดนุ\nดนู\nดบัสวิน\nดบัสวี\nดม\nดรงค์\nดรณี\nดรรชนี\nดราฟต์\nดรุณ\nดรุณี\nดล\nดวง\nด้วง\nดวด\nด่วน\nด้วน\nด้วย\nดอก\nดอง\nด่อง\nด้อง\nดองฉาย\nดองดึง\nดอด\nดอน\nด่อน\nดอม\nด้อม\nดอย\nด้อย\nดอลลาร์\nดะ\nดะโต๊ะ\nดะหมัง\nดัก\nดักดาน\nดักแด้\nดัง\nดั่ง\nดั้ง\nดัชนี\nดัด\nดัตช์\nดัน\nดั้น\nดับ\nดัมพ์\nดั้วเดี้ย\nดัสกร\nดา\nด่า\nดาก\nด่าง\nด้าง\nดาด\nดาน\nด่าน\nด้าน\nดาบ\nดาบส\nดาม\nด้าม\nด้ามจิ้ว\nดามพ์\nดาย\nด้าย\nดารกะ\nดารณี\nดารดาษ\nดาระ\nดารา\nดาล\nดาลัด\nดาว\nด่าว\nด้าว\nดาวดึงส์\nดาวบส\nดาษ\nดาษดา\nดำ\nด่ำ\nด้ำ\nดำกล\nดำเกิง\nดำแคง\nดำดง\nดำนาณ\nดำเนิน\nดำบล\nดำรง\nดำรวจ\nดำรัส\nดำริ\nดำรี\nดำรู\nดำฤษณา\nดำเลิง\nดิก\nดิ่ง\nดิฉัน\nดิฐ\nดิตถ์\nดิถี\nดิน\nดิ้น\nดิบ\nดิรัจฉาน\nดิลก\nดิ่ว\nดิ้ว\nดิ้วเดี้ยว\nดิษฐ์\nดิสโพรเซียม\nดี\nดีเซล\nดีด\nดีดีที\nดีบุก\nดีปลี\nดีเปรสชัน\nดีหมี\nดีหลี\nดึก\nดึง\nดึ่ง\nดึ่ม\nดื่น\nดื่ม\nดือ\nดื้อ\nดุ\nดุก\nดุกดิก\nดุกทะเล\nดุ้ง\nดุ้งดิ้ง\nดุจ\nดุด\nดุน\nดุ้น\nดุบ\nดุม\nดุ่ม\nดุ่ย\nดุรงค์\nดุริยะ\nดุริยางค์\nดุริยางคศาสตร์\nดุริยางคศิลป์\nดุล\nดุษฎี\nดุษณี\nดุษณีภาพ\nดุษิต\nดุสิต\nดุเหว่า\nดู\nดูกค่าง\nดูกร\nดูด\nดูรา\nดูแล\nเด\nเด่\nเดก\nเด็ก\nเดกซ์โทรส\nเดคากรัม\nเดคาเมตร\nเดคาลิตร\nเด้ง\nเด็จ\nเดช\nเดชน์\nเดชนะ\nเดชะ\nเดโช\nเดซิกรัม\nเดซิเมตร\nเดซิลิตร\nเด็ด\nเดน\nเด่น\nเดนมาร์ก\nเดรัจฉาน\nเด๋อ\nเด๋อด๋า\nเดา\nเด้า\nเดาะ\nเดิน\nเดิ่น\nเดิม\nเดียง\nเดียด\nเดียรดาษ\nเดียรถีย์\nเดียรัจฉาน\nเดียว\nเดี่ยว\nเดี๋ยว\nเดียะ\nเดื่อ\nเดือก\nเดื่อง\nเดือด\nเดือน\nเดือย\nแด\nแด่\nแดก\nแด็ก\nแดกงา\nแดกแด้\nแดง\nแดด\nแดน\nแด่น\nแด่ว\nแดะ\nแดะแด๋\nโด\nโด่\nโดกเดก\nโด่ง\nโดด\nโดน\nโดม\nโดมร\nโดย\nโดรณ\nใด\nได\nได้\nไดแซ็กคาไรด์\nไดนาโม\nไดนาไมต์\nไดโนเสาร์\nไดเรกตริกซ์\nตก\nต๊กโต\nตง\nต๋ง\nตงฉิน\nตงิด\nตงุ่น\nตด\nตติย\nตถาคต\nตน\nต้น\nตนัย\nตนุ\nตบ\nตบะ\nตปนียะ\nตม\nต้ม\nตมูก\nตยาคี\nตรง\nตรณี\nตรม\nตรรก\nตรรกะ\nตรลบ\nตรลอด\nตรลาด\nตรวจ\nตรวน\nตรอก\nตรอง\nตรอมใจ\nตรอมตรม\nตระ\nตระกล\nตระกวน\nตระกอง\nตระการ\nตระกูล\nตระคัร\nตระเตรียม\nตระนาว\nตระบก\nตระบอก\nตระบอง\nตระบัด\nตระบัน\nตระเบ็ง\nตระแบก\nตระแบง\nตระโบม\nตระพอง\nตระพัง\nตระลาการ\nตระวัน\nตระเว็ด\nตระเวน\nตระสัก\nตระหง่าน\nตระหนก\nตระหนัก\nตระหน่ำ\nตระหนี่\nตรัง\nตรังค์\nตรับ\nตรับฟัง\nตรัย\nตรัยตรึงศ์\nตรัส\nตรัสสา\nตรา\nตรากตรำ\nตราชู\nตราบ\nตราสัง\nตรำ\nตริ\nตริว\nตรี\nตรีปวาย\nตรีพิธพรรณ\nตรียัมปวาย\nตรึก\nตรึง\nตรุ\nตรุณ\nตรุณะ\nตรุษ\nตรู\nตรู่\nตฤณ\nตฤตีย\nตฤษณา\nตลก\nตลบ\nตลอด\nตลับ\nตลาด\nตลิ่ง\nตลึง\nตวง\nต่วน\nต้วมเตี้ยม\nตวัก\nตวัด\nตวาด\nตอ\nตอม่อ\nต่อ\nต้อ\nตอก\nต๊อก\nต๊อกต๋อย\nตอง\nต้อง\nตองกราย\nต้องเต\nตองแตก\nต่องแต่ง\nตองเหลือง\nตอด\nตอน\nต้อน\nตอบ\nตอเบา\nตอม\nต่อม\nต๋อม\nต่อย\nต้อย\nต้อยตริ่ง\nต้อยติ่ง\nต้อยตีวิด\nตอแย\nตอร์ปิโด\nต่อไส้\nตอแหล\nตะ\nตะกรน\nตะกร้อ\nตะกรัน\nตะกรับ\nตะกร้า\nตะกราม\nตะกรุด\nตะกรุม\nตะกรุมตะกราม\nตะกละ\nตะกลาม\nตะกวด\nตะกอ\nตะกอน\nตะกัง\nตะกั่ว\nตะกาง\nตะกาด\nตะกาย\nตะกาว\nตะกุกตะกัก\nตะกุย\nตะกู\nตะกูด\nตะเกียกตะกาย\nตะเกียง\nตะเกียบ\nตะแก\nตะแก่\nตะแกรง\nตะโก\nตะโก้\nตะโกก\nตะโกน\nตะโกรง\nตะโกรม\nตะไกร\nตะขบ\nตะขอ\nตะขาบ\nตะขิดตะขวง\nตะเข้\nตะเข็บ\nตะโขง\nตะคร้อ\nตะครอง\nตะครั่นตะครอ\nตะคร้ำ\nตะคริว\nตะคิว\nตะครุบ\nตะคอก\nตะคัน\nตะค้า\nตะคาก\nตะค้าน\nตะคุ่ม\nตะเครียว\nตะเคียว\nตะเคียน\nตะแคง\nตะไคร่\nตะไคร้\nตะเฆ่\nตะนอย\nตะนาว\nตะบม\nตะบอง\nตะบอย\nตะบัน\nตะบิ้ง\nตะบิด\nตะบิดตะบอย\nตะบี้ตะบัน\nตะบึง\nตะบูน\nตะเบ็ง\nตะเบ็งมาน\nตะเบ๊ะ\nตะแบก\nตะแบง\nตะโบม\nตะไบ\nตะปบ\nตะปลิง\nตะปิ้ง\nตะปุ่มตะป่ำ\nตะปู\nตะพง\nตะพด\nตะพอง\nตะพัก\nตะพัง\nตะพัด\nตะพั้น\nตะพาก\nตะพาน\nตะพาบ\nตะพาย\nตะพึด\nตะพึดตะพือ\nตะพุ่น\nตะเพรา\nตะเพิง\nตะเพิด\nตะเพียน\nตะโพก\nตะโพง\nตะโพน\nตะเภา\nตะใภ้\nตะม่อ\nตะมอย\nตะรังกะนู\nตะรังตังกวาง\nตะรังตังช้าง\nตะราง\nตะลอง\nตะลอน\nตะล่อม\nตะละ\nตะลาน\nตะลิงปลิง\nตะลิบ\nตะลีตะลาน\nตะลึง\nตะลึงพรึงเพริด\nตะลุง\nตะลุ่ม\nตะลุ่มนก\nตะลุมบอน\nตะลุ่มโปง\nตะลุมพอ\nตะลุมพุก\nตะลุย\nตะเลง\nตะแลงแกง\nตะไล\nตะวัน\nตะเวน\nตะหลิว\nตะหลุก\nตะหลุง\nตะแหง่ว\nตะแหมะแขะ\nตะโหงก\nตัก\nตักกะ\nตักเตือน\nตั๊กแตน\nตักษัย\nตัง\nตั่ง\nตั้ง\nตังเก\nตังฉ่าย\nตังเม\nตังวาย\nตังโอ๋\nตัจฉก\nตัจฉนี\nตัณฑุล\nตัณหา\nตัด\nตัน\nตันตระ\nตันติ\nตันหยง\nตับ\nตับปิ้ง\nตัว\nตั๋ว\nตัวจี๊ด\nตัวตืด\nตั้วโผ\nตั้วเหี่ย\nตา\nตาก\nตากวาง\nต่าง\nตาด\nตาน\nต่าน\nต้าน\nตานนกกด\nตานี\nตาบ\nตาม\nตามะแน\nตามิน\nตาย\nตาราไต\nตาล\nตาลุ\nต๋าว\nตาเสือ\nตาหนู\nตาฬ\nตำ\nต่ำ\nตำนาน\nตำบล\nตำแบ\nตำแย\nตำรวจ\nตำรับ\nตำรา\nตำรุ\nตำลึง\nตำเสา\nตำหนัก\nตำหนิ\nตำแหน่ง\nติ\nติก\nติ๊ก\nติกะ\nติกาหรัง\nติง\nติ่ง\nติ๋ง\nติ่งตั่ง\nติ๋งต่าง\nติงส\nติงสติ\nติณ\nติด\nติตติกะ\nติตติร\nติตถ\nติตถะ\nติถี\nติมิงคละ\nติรัจฉาน\nติลก\nติละ\nติ้ว\nตี\nตี่\nตีน\nตีบ\nตีรถะ\nตีระ\nตึ\nตึก\nตึ้ก\nตึ้กตั้ก\nตึง\nตึดตื๋อ\nตึ๊ดตื๋อ\nตืด\nตื่น\nตื้น\nตื้อ\nตื๊อ\nตื๋อ\nตุ\nตุ๊\nตุ๊กแก\nตุ๊กตา\nตุ๊กต่ำ\nตุกติก\nตุ๊กติ๊ก\nตุ๊กตุ่น\nตุ๊กตุ๋ย\nตุง\nตุ้งก่า\nตุ้งติ้ง\nตุ๊ดตู่\nตุน\nตุ่น\nตุ๋น\nตุนาหงัน\nตุบ\nตุ้บ\nตุ๊บป่อง\nตุปัดตุป่อง\nตุปัดตุเป๋\nตุ่ม\nตุ้ม\nตุ๋ม\nตุ้มกว้าว\nตุมกา\nตุ้มแซะ\nตุมตัง\nตุ้มเต๋น\nตุ้มปี่\nตุมพะ\nตุ่ย\nตุ้ย\nตุ๊ย\nตุ๋ยตุ่ย\nตุรคะ\nตุรงค์\nตุล\nตุลา\nตุหรัดตุเหร่\nตู\nตู่\nตู้\nตูก\nตูด\nตูบ\nตูม\nเต๊ก\nเต็ง\nเต่ง\nเตช\nเตโช\nเต้น\nเต็นท์\nเต็ม\nเตย\nเตร่\nเตร็ด\nเตรตา\nเตรียม\nเตรียมตรม\nเตละ\nเตลิด\nเตว็ด\nเต่อ\nเตอะ\nเตะ\nเตา\nเต่า\nเต้า\nเต๋า\nเต่าเกียด\nเต้าเจี้ยว\nเต้าทึง\nเต้าหู้\nเต้าฮวย\nเต๊าะ\nเตาะแตะ\nเติ่ง\nเติบ\nเติม\nเตี้ย\nเตียง\nเตียน\nเตียบ\nเตี๋ยม\nเตียรถ์\nเตียว\nเตี่ยว\nเตือน\nแต่\nแต้\nแตก\nแตง\nแต่ง\nแตงเม\nแต้จิ๋ว\nแตด\nแต๊ดแต๋\nแตน\nแต้ม\nแตร\nแตระ\nแต้ว\nแต้วแร้ว\nแต้วแล้ว\nแต่ว่า\nแต้แว้ด\nแตะ\nโต\nโต้\nโตก\nโต่ง\nโต้ง\nโตงเตง\nโตฎก\nโต๊ด\nโตน\nโตนด\nโต้โผ\nโตมร\nโตย\nโตรก\nโต๊ะ\nใต้\nไต\nไต่\nไต้\nไต๋\nไตร\nไตรกิศยา\nไตรดายุค\nไตร่ตรอง\nไตรย\nไต้หวัน\nถก\nถกล\nถงาด\nถด\nถนน\nถนอม\nถนัด\nถนัน\nถนำ\nถนิม\nถม\nถ่ม\nถมอ\nถมึงทึง\nถลก\nถลกบาตร\nถลน\nถล่ม\nถลอก\nถลัน\nถลา\nถลาก\nถลาย\nถลำ\nถลึงตา\nถลุง\nถ่วง\nถ้วน\nถ้วย\nถวัล\nถวัลย์\nถวาย\nถวิน\nถวิล\nถ่อ\nถ้อ\nถอก\nถอง\nถ่อง\nถ้อง\nถอด\nถอน\nถอบ\nถอบแถบ\nถ่อม\nถอย\nถ่อย\nถ้อย\nถะ\nถะถั่น\nถะมัดถะแมง\nถัก\nถัง\nถั่ง\nถัด\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นยา\nบิลเลียด\nบิวเรตต์\nบิสมัท\nบี้\nบีฑา\nบีตา\nบีบ\nบีเยศ\nบึก\nบึกบึน\nบึง\nบึ่ง\nบึ้ง\nบุ\nบุก\nบุคคล\nบุคลากร\nบุคลาธิษฐาน\nบุคลิก\nบุง\nบุ่ง\nบุ้ง\nบุ้งกี๋\nบุญ\nบุญญาธิการ\nบุญญานุภาพ\nบุญญาภินิหาร\nบุญญาภิสังขาร\nบุณฑริก\nบุณมี\nบุณย์\nบุตร\nบุตรี\nบุถุชน\nบุทคล\nบุนนาค\nบุบ\nบุบบิบ\nบุปผชาติ\nบุพกรรม\nบุพการี\nบุพกิจ\nบุพชาติ\nบุพทักษิณ\nบุพนิมิต\nบุพบท\nบุพพาจารย์\nบุพเพสันนิวาส\nบุพโพ\nบุ๋ม\nบุ่มบ่าม\nบุ้ย\nบุรณะ\nบุรพทิศ\nบุรพบท\nบุรพาจารย์\nบูรพาจารย์\nบุระ\nบุราณ\nบุรินทร์\nบุริมทิศ\nบุริมพรรษา\nบุริมสิทธิ\nบุรี\nบุรุษ\nบุโรทั่ง\nบุษกร\nบุษบก\nบุษบง\nบุษบัน\nบุษบา\nบุษบามินตรา\nบุษปราค\nบุษปะ\nบุษย์\nบุษย์น้ำทอง\nบุษยมาส\nบุษยะ\nบุษราคัม\nบุหงัน\nบุหงา\nบุหรง\nบุหรี่\nบุหลัน\nบู่\nบู้\nบูชนียสถาน\nบูชา\nบูชิต\nบูด\nบูดู\nบูร\nบูรณ์\nบูรณภาพ\nบูรณมี\nบูรณะ\nบูรณาการ\nบูรพ์\nบูรพะ\nบูรพา\nเบ้\nเบ่ง\nเบ๊จี๋\nเบญกานี\nเบญจกัลยาณี\nเบญจกามคุณ\nเบญจขันธ์\nเบญจดุริยางค์\nเบญจธรรม\nเบญจบรรพต\nเบญจพรรณ\nเบญจเพส\nเบญจมาศ\nเบญจรงค์\nเบญจศก\nเบญจศีล\nเบญจะ\nเบญจา\nเบญจางค์\nเบญจางคประดิษฐ์\nเบญญา\nเบญพาด\nเบ็ด\nเบ็ดเตล็ด\nเบ็ดเสร็จ\nเบน\nเบนซิน\nเบรก\nเบริลเลียม\nเบส\nเบ้อ\nเบอร์\nเบอร์คีเลียม\nเบ้อเร่อ\nเบ้อเร่อเท่อ\nเบ้อเริ่ม\nเบ้อเริ่มเทิ่ม\nเบอะ\nเบอะบะ\nเบะ\nเบา\nเบ้า\nเบาราณ\nเบาะ\nเบิก\nเบิ่ง\nเบี้ย\nเบี่ยง\nเบียด\nเบียน\nเบียร์\nเบี้ยว\nเบือ\nเบื่อ\nเบื้อ\nเบื้อง\nเบือน\nแบ\nแบ้\nแบก\nแบคทีเรีย\nแบ่ง\nแบงก์\nแบดมินตัน\nแบตเตอรี่\nแบน\nแบนโจ\nแบบ\nแบ็บ\nแบเรียม\nแบหลา\nแบะ\nโบ\nโบ้\nโบ๋\nโบก\nโบกขรณี\nโบกขรพรรษ\nโบชุก\nโบต\nโบนัส\nโบ๊เบ๊\nโบย\nโบรมีน\nโบรอน\nโบราณ\nโบสถ์\nใบ\nใบ้\nไบ่\nปก\nปกติ\nปกรณ์\nปกรณัม\nปกิณกะ\nปกีรณัม\nปโกฏิ\nปง\nป่ง\nปงช้าง\nปฎล\nปฏัก\nปฏิกรณ์\nปฏิกรรม\nปฏิการะ\nปฏิกิริยา\nปฏิกูล\nปฏิคม\nปฏิคหิต\nปฏิคาหก\nปฏิฆะ\nปฏิชีวนะ\nปฏิญญา\nปฏิญาณ\nปฏิทิน\nปฏิบถ\nปฏิบัติ\nปฏิปทา\nปฏิปักษ์\nปฏิปัน\nปฏิปุจฉาพยากรณ์\nปฏิปุจฉาวาที\nปฏิพัทธ์\nปฏิพากย์\nปฏิภาค\nปฏิภาณ\nปฏิมา\nปฏิมากร\nปฏิยุทธ์\nปฏิรพ\nปฏิรูป\nปฏิโลม\nปฏิวัติ\nปฏิวาต\nปฏิวาท\nปฏิเวธ\nปฏิสนธิ\nปฏิสวะ\nปฏิสังขรณ์\nปฏิสันถาร\nปฏิสัมภิทา\nปฏิเสธ\nปฐพี\nปฐม\nปฐวี\nปณต\nปณาม\nปณิธาน\nปณิธิ\nปณีต\nปด\nปดิวรัดา\nปติ\nปถพี\nปถมัง\nปถวี\nปทัฏฐาน\nปทัสถาน\nปทานุกรม\nปทีป\nปทุม\nปน\nป่น\nปนัดดา\nปปัญจะ\nปม\nปรนัย\nปรปักษ์\nปรโลก\nปรวาที\nปรก\nปรกติ\nปรง\nปรตยักษ์\nปรน\nปรนนิบัติ\nปรนิมมิตวสวัตดี\nปรบ\nปรปักษ์\nปรมัตถ์\nปรมาจารย์\nปรมาณู\nปรมาภิไธย\nปรมาภิเษก\nปรมินทร์\nบรเมนทร์\nปรเมศวร์\nปรเมษฐ์\nปรวด\nปรวนแปร\nปรศุ\nปรสิต\nปร๋อ\nปรองดอง\nปรอด\nปรอท\nปรอย\nประ\nประกบ\nประกฤต\nประกฤติ\nประกล\nประกวด\nประกวดประขัน\nประกอบ\nประกัน\nประกับ\nประกาย\nประกายพรึก\nประการ\nประกาศ\nประกาศนียบัตร\nประกาศิต\nประกำ\nประกิด\nประกิต\nประคด\nประคนธรรพ\nประคนธรรพ์\nประคบ\nประคบประหงม\nประคอง\nประคับประคอง\nประคัลภ์\nประคำ\nประคิ่น\nประคุณ\nประเคน\nประเคราะห์\nประโคน\nประโคนธรรพ\nประโคนธรรพ์\nประโคม\nประจง\nประจญ\nประจบ\nประจบประแจง\nประจวบ\nประจ๋อประแจ๋\nประจักษ์\nประจักษนิยม\nประจัญ\nประจัน\nประจาก\nประจาค\nประจาน\nประจำ\nประจิม\nประจิ้มประเจ๋อ\nประจุ\nประจุคมน์\nประจุบัน\nประเจก\nประเจิด\nประเจิดประเจ้อ\nประเจียด\nประแจ\nประชด\nประชน\nประชวม\nประชวร\nประชัน\nประชา\nประชาธิปไตย\nประชิด\nประชี\nประชุม\nประเชิญ\nประณต\nประณม\nประณาม\nประณิธาน\nประณิธิ\nประณีต\nประณุท\nประดง\nประดน\nประดวน\nประดอน\nประดอย\nประดัก\nประดักประเดิด\nประดัง\nประดับ\nประดา\nประดาก\nประดาป\nประดาษ\nประดิชญา\nประดิดประดอย\nประดิทิน\nประดิษฐ์\nประดิษฐกรรม\nประดิษฐาน\nประดุง\nประดุจ\nประดู่\nประเด\nประเด็น\nประเดิม\nประเดียง\nประเดี๋ยว\nประเดี๋ยวประด๋าว\nประแดง\nประแดะ\nประโดง\nประโดย\nประตง\nประตัก\nประตาป\nประติชญา\nประติญาณ\nประติทิน\nประติมากร\nประติมากรรม\nประติรพ\nประตู\nประถม\nประถมจินดา\nประทม\nประท้วง\nประทวน\nประทักษ์\nประทักษิณ\nประทัง\nประทัด\nประทับ\nประทาน\nประทาย\nประทาศี\nประทิน\nประทิ่น\nประทีป\nประทุฐ\nประทุน\nประทุษ\nประทุษฐ์\nประเทศ\nประเทา\nประเทียด\nประเทียบ\nประเทือง\nประธาน\nประธานาธิบดี\nประนม\nประนอ\nประนอม\nประนัง\nประนัปดา\nประนีประนอม\nประปราน\nประปราย\nประปา\nประเปรี้ยง\nประเปรียว\nประพจน์\nประพนธ์\nประพรม\nประพฤติ\nประพฤทธิ์\nประพัด\nประพัทธ์\nประพันธ์\nประพาต\nประพาส\nประพาสมหรณพ\nประพาฬ\nประพิณ\nประพิมพ์ประพาย\nประพุทธ์\nประเพณี\nประโพธ\nประไพ\nประไพร\nประภพ\nประภัสสร\nประภา\nประภาคาร\nประภาพ\nประภาษ\nประภาส\nประเภท\nประมง\nประมวล\nประมาณ\nประมาท\nประมุข\nประมุท\nประมูล\nประเมิน\nประโมง\nประโมทย์\nประยงค์\nประยุกต์\nประยุทธ์\nประยุร\nประยูร\nประโยค\nประโยชน์\nประโรหิต\nประลมพ์\nประลอง\nประลัย\nประลาต\nประลาย\nประลุ\nประเล่ห์\nประเล้าประโลม\nประโลม\nประวรรต\nประวรรตน์\nประวัติ\nประวาล\nประวาลปัทม์\nประวาส\nประวิง\nประวิช\nประวิตร\nประวิน\nประวีณ\nประเวณี\nประเวศ\nประเวศน์\nประศม\nประศาสน์\nประศุ\nประสก\nประสงค์\nประสบ\nประสพ\nประสม\nประสะ\nประสัก\nประสันนาการ\nประสัยห์\nประสา\nประสาท\nประสาธน์\nประสาน\nประสาร\nประสิทธิ์\nประสิทธิผล\nประสิทธิภาพ\nประสีประสา\nประสูต\nประสูติ\nประเสบัน\nประเสบันอากง\nประเสริฐ\nประหนึ่ง\nประหม่า\nประหยัด\nประหลาด\nประหล่ำ\nประหวัด\nประหวั่น\nประหัตประหาร\nประหาณ\nประหาร\nประเหล\nประเหส\nประไหมสุหรี\nประอบ\nประอร\nปรัก\nปรักปรำ\nปรักมะ\nปรัง\nปรัชญา\nปรัตถจริยา\nปรัตยุบัน\nปรัน\nปรับ\nปรัมปรา\nปรัศจิม\nปรัศนา\nปรัศนี\nปรัศว์\nปรัสสบท\nปร่า\nปรากฏ\nปรากรม\nปรากฤต\nปราการ\nปราง\nปรางค์\nปราจีน\nปราชญ์\nปราชญา\nปราชัย\nปราณ\nปราณี\nปราด\nปราน\nปรานี\nปราบ\nปราบดาภิเษก\nปราปต์\nปราม\nปรามาส\nปราโมช\nปราโมทย์\nปราย\nปรารถนา\nปรารภ\nปรารมภ์\nปราศ\nปราศจาก\nปราศรัย\nปราษณี\nปราษาณ\nปราสัย\nปราสาท\nปรำ\nปริ\nปริก\nปริกขาร\nปริกรรม\nปริกัป\nปริคณห์\nปริจาค\nปริจาริกา\nปริเฉท\nปริชน\nปริซึม\nปริญญา\nปริณาม\nปริณายก\nปริต\nปริตตะ\nปริตโตทก\nปริตร\nปริทรรศน์\nปริทัยหัคคี\nปริทัศน์\nปริเทพ\nปริเทวะ\nปรินิพพาน\nปริบ\nปริบท\nปริปันถ์\nปริพนธ์\nปริพัตร\nปริพันธ์\nปริพาชก\nปริภัณฑ์\nปริภาษ\nปริภูมิ\nปริโภค\nปริ่ม\nปริมณฑล\nปริมาณ\nปริมาตร\nปริยัติ\nปริยานุช\nปริยาย\nปริเยศ\nปริโยสาน\nปริวรรต\nปริวัตร\nปริวาร\nปริวาส\nปริวิตก\nปริเวณ\nปริศนา\nปริษัท\nปริสัญญู\nปริสุทธิ\nปริหาน\nปริหาร\nปรี่\nปรีชญา\nปรีชา\nปรี๊ด\nปรีดา\nปรีดิ\nปรีดิ์\nปรีดี\nปรีติ\nปรียะ\nปรียา\nปรึก\nปรึกษา\nปรึง\nปรือ\nปรื๋อ\nปรุ\nปรุง\nปรู\nปรู๋\nปรูด\nปรู๊ด\nปรู๊ดปร๊าด\nปรู๊ฟ\nปฤงคพ\nปฤจฉา\nปฤษฎางค์\nปฤษฐ\nปลก\nปลกเปลี้ย\nปลง\nปล่ง\nปลด\nปล้น\nปลวก\nปลอก\nปล่อง\nปล้อง\nปลอด\nปล้อน\nปลอบ\nปลอม\nปล่อย\nปละ\nปลัก\nปลั๊ก\nปลัง\nปลั่ง\nปลัด\nปลัดขิก\nปลา\nปลาต\nปลาบ\nปลาย\nปลาสเตอร์\nปลาสนาการ\nปล้ำ\nปลิง\nปลิด\nปลิ้น\nปลิโพธ\nปลิม\nปลิ่ม\nปลิว\nปลี\nปลีก\nปลื้ม\nปลุก\nปลูก\nปวกเปียก\nปวง\nป่วง\nปวด\nป่วน\nป้วน\nป้วนเปี้ยน\nป่วย\nปวัตน์\nปวารณา\nปวาล\nปวาส\nปวาฬ\nปวิช\nปวิตร\nปวิธ\nปวิเวก\nปวีณ\nปวุติ\nปเวณี\nปเวส\nปเวสน์\nปศุ\nปสันนะ\nปสันนาการ\nปสาท\nปสาน\nปสาสน์\nปสุ\nปสุต\nปสูติ\nปหังสนะ\nปหาน\nปหาร\nปหาส\nปอ\nป้อ\nป๋อ\nปอก\nปอง\nป่อง\nป้อง\nปอด\nปอน\nป้อน\nปอนด์\nปอเนาะ\nปอบ\nป้อแป้\nปอม\nป้อม\nป๋อม\nปอย\nป้อย\nป้อยอ\nปะ\nปะกน\nปะกัง\nปะการัง\nปะกำ\nปะขาว\nปะงาบ\nปะตาปา\nปะตาระกาหลา\nปะติดปะต่อ\nปะติยาน\nปะทะ\nปะทะปะทัง\nปะทุ\nปะทุน\nปะปน\nปะมง\nปะราลี\nปะรำ\nปะไร\nปะลอม\nปะเลง\nปะแล่ม\nปะโลง\nปะวะหล่ำ\nปะหงับ\nปะหนัน\nปะหัง\nปะเหลาะ\nปัก\nปักข์\nปักเป้า\nปักษ์\nปักษา\nปักษิน\nปักษี\nปัง\nปั๋ง\nปังสุ์\nปังสุกุล\nปัจจัตตะ\nปัจจันต์\nปัจจันตคาม\nปัจจันตชนบท\nปัจจันตประเทศ\nปัจจัย\nปัจจามิตร\nปัจจุคมน์\nปัจจุทธรณ์\nปัจจุบัน\nปัจจุสมัย\nปัจเจก\nปัจโจปการกิจ\nปัจฉา\nปัจฉิม\nปัจถรณ์\nปัจนึก\nปัจยาการ\nปัจเวกขณ์\nปัชชุน\nปัญจนที\nปัญจวัคคีย์\nปัญจก\nปัญจกะ\nปัญจมี\nปัญจวีสติ\nปัญญัติ\nปัญญา\nปัญหา\nปัฏ\nปัฏนะ\nปัฐยาวัต\nปัณฑรหัตถี\nปัณณะ\nปัณณาส\nปัณณาสก์\nปัณรสี\nปัณหิ\nปัด\nปัตคาด\nปัตตะ\nปัตตานึก\nปัตตานุโมทนา\nปัตตาเวีย\nปัตติ\nปัตติก\nปัตถร\nปัตถะ\nปัตนิ\nปัตนี\nปัตหล่า\nปัถพี\nปัถวี\nปัทม์\nปัทมะ\nปัทมาสน์\nปัน\nปั่น\nปั้น\nปั้นจั่น\nปันจุเหร็จ\nปั้นลม\nปั้นหยา\nปั้นเหน่ง\nปับ\nปั๊บ\nปัปผาสะ\nปัพพาชนียกรรม\nปัพภาระ\nปั๊ม\nปัยกา\nปัยยิกา\nปัวเปีย\nปัศจิม\nปัศตัน\nปัสสาวะ\nปัสสาสะ\nปา\nป่า\nป้า\nปาก\nปาง\nป้าง\nปาจรีย์\nปาจิตตีย์\nปาจีน\nปาฏลิ\nปาฏิบท\nปาฏิบุคลิก\nปาฏิโภค\nปาฏิหาริย์\nปาฐก\nปาฐกถา\nปาฐะ\nปาณกชาติ\nปาณะ\nปาณาติบาต\nปาณิ\nปาณี\nปาด\nปาติโมกข์\nปาตี\nปาเต๊ะ\nปาท่องโก๋\nปาทังกา\nปาทาน\nปาทุกา\nปาน\nป่าน\nป้าน\nปานะ\nปานียะ\nป้าบ\nป๊าบ\nปาพจน์\nปาม\nปาโมกข์\nป่าย\nป้าย\nปายาส\nปาร์เกต์\nปารมี\nปารเมศ\nปาราชิก\nปาริฉัตร\nปาริชาต\nปารุสกวัน\nปาล\nปาล์ม\nปาลิไลยก์\nปาลี\nปาว\nป่าว\nป๊าว\nปาวาร\nปาษาณ\nปาส\nปาสาณ\nปาสาทิกะ\nปาหนัน\nปาหี่\nปำ\nป้ำ\nป้ำเป๋อ\nปิกนิก\nปิ้ง\nปิงคละ\nปิงปอง\nปิฎก\nปิฏฐะ\nปิฐิ\nปิณฑะ\nปิด\nปิตตะ\nปิตา\nปิตามหัยกา\nปิตามหัยยิกา\nปิตุ\nปิตุจฉา\nปิตุภูมิ\nปิตุลา\nปิโตรเลียม\nปิ่น\nปิ่นแก้ว\nปิ่นโต\nปิปผลี\nปิ่ม\nปิ้ม\nปิยะ\nปิยังคุ\nปิโยรส\nปิลันธน์\nปิ๋ว\nปิศาจ\nปิหกะ\nปี\nปี่\nปี้\nปี๋\nปีก\nปีฐะ\nปี๊ด\nปีติ\nปีน\nปีบ\nปี๊บ\nปีศาจ\nปีฬกะ\nปึก\nปึง\nปึ่ง\nปึ๋ง\nปึ้ด\nปึมปื้อ\nปืน\nปื้น\nปือ\nปื้อ\nปื๋อ\nปุ\nปุ๊\nปุก\nปุกปุย\nปุคละ\nปุ้งกี๋\nปุงควะ\nปุงลิงค์\nปุงลึงค์\nปุจฉา\nปุฏะ\nปุณฑริก\nปุด\nปุตตะ\nปุถุชน\nปุนนาค\nปุนภพ\nปุนัพสุ\nปุบ\nปุ๊บ\nปุปผะ\nปุปะ\nปุพพะ\nปุ่ม\nปุ่มป่ำ\nปุ้ม\nปุ๋ม\nปุย\nปุ้ย\nปุ๋ย\nปุรณะ\nปุระ\nปุราณ\nปุราณะ\nปุริมพรรษา\nปุเรจาริก\nปุโรหิต\nปุลลิงค์\nปุลลึงค์\nปุลินท์\nปุโลปุเล\nปุษยะ\nปุสสะ\nปู\nปู่\nปูชกะ\nปูชนียบุคคล\nปูชนียวัตถุ\nปูชนียะ\nปูชา\nปูชิต\nปูด\nปูน\nปูม\nปู้ยี่ปู้ยำ\nปูระ\nปูลู\nเป้\nเป๋\nเปก\nเป๊ก\nเป่ง\nเป้ง\nเป๋ง\nเป็ด\nเปตพลี\nเปตอง\nเป็น\nเปยยาล\nเปร็ง\nเปรต\nเปรม\nเปรย\nเปรอ\nเปรอะ\nเปราะ\nเปรียง\nเปรี้ยง\nเปรี้ยงปร้าง\nเปรียญ\nเปรียบ\nเปรี่ยม\nเปรียว\nเปรี้ยว\nเปรียะ\nเปรี๊ยะ\nเปรื่อง\nเปรื้อย\nเปล\nเปล่ง\nเปลว\nเปลา\nเปล่า\nเปล้า\nเปลาะ\nเปลี้ย\nเปลี่ยน\nเปลี่ยม\nเปลี่ยว\nเปลือก\nเปลือง\nเปลื้อง\nเปลือย\nเปศะ\nเปศัส\nเปสการ\nเปสละ\nเปสุญวาท\nเป๋อ\nเป้อเย้อ\nเปอร์\nเปอร์เซ็นต์\nเปะ\nเปา\nเป่า\nเป้า\nเป๊า\nเป๋า\nเป๋าฮื้อ\nเปาะ\nเป๊าะ\nเปาะเปี๊ยะ\nเปาะแปะ\nเปิก\nเปิง\nเปิงมาง\nเปิด\nเปิ่น\nเปิบ\nเปิ๊บ\nเปีย\nเปียก\nเปี๊ยก\nเปี๊ยบ\nเปี่ยม\nเปี้ยว\nเปี๊ยว\nเปียะ\nเปี๊ยะ\nเปือก\nเปื้อน\nเปื่อย\nแป\nแป้ง\nแป๋ง\nแปด\nแป๊ด\nแปทู\nแป้น\nแป๊น\nแปบ\nแป๊บ\nแปม\nแปร\nแปร๋\nแปรก\nแปรง\nแปร่ง\nแปร๊ด\nแปร้น\nแปร๋น\nแปรปรวน\nแประ\nแปล\nแปล้\nแปลก\nแปลง\nแปลน\nแปลบ\nแปล๊บ\nแป้ว\nแป๊ว\nแปะ\nแป๊ะ\nแป๊ะซะ\nโป\nโป่\nโป้\nโป๊\nโปก\nโป๊ก\nโป๊กเกอร์\nโปกขรณี\nโปกขรพรรษ\nโปเก\nโปง\nโป่ง\nโป้ง\nโป่งข่าม\nโปงลาง\nโป่งวิด\nโปฐบท\nโปฐปทมาส\nโปดก\nโปตถกะ\nโปน\nโป๊ป\nโป๊ยเซียน\nโปรแกรม\nโปรง\nโปร่ง\nโปรด\nโปรตอน\nโปรตีน\nโปรเตสแตนต์\nโปรแทรกเตอร์\nโปรย\nโปล่ง\nโปลิโอ\nโปโล\nโปสก\nโปสต์การ์ด\nโปะ\nโป๊ะ\nโป๊ะจ้าย\nไป\nไป่\nไป๋\nไปยาล\nไปรษณีย์\nไปรษณียบัตร\nไปรษณียภัณฑ์\nไปรษณียากร\nไปล่\nไปศาจ\nผก\nผกา\nผกาย\nผคม\nผง\nผงก\nผงม\nผงะ\nผงาด\nผง่าน\nผจง\nผจญ\nผจัญ\nผจาน\nผชุม\nผณิน\nผณินทร\nผณิศวร\nผด\nผดุง\nผเดิน\nผทม\nผนวก\nผนวช\nผนัง\nผนิด\nผนึก\nผม\nผยอง\nผรณาปีติ\nผรสุ\nผริต\nผรุสวาท\nผล\nผลคุน\nผลคุนี\nผล็อย\nผละ\nผลัก\nผลัด\nผลับ\nผลัวะ\nผลา\nผลาญ\nผลานิสงส์\nผลาผล\nผลาหาร\nผลิ\nผลิกะ\nผลิต\nผลิน\nผลี\nผลีผลาม\nผลึก\nผลึ่ง\nผลือ\nผลุ\nผลุง\nผลุด\nผลุน\nผลุนผลัน\nผลุบ\nผลุบผลับ\nผลุย\nผลู\nผวน\nผวย\nผวา\nผสม\nผสาน\nผอง\nผ่อง\nผ่อน\nผอบ\nผอม\nผ็อย\nผอูน\nผะ\nผะดา\nผะสา\nผัก\nผัคคุณ\nผัคคุณี\nผัง\nผัด\nผัน\nผับ\nผัว\nผัวะ\nผัสสะ\nผัสสาหาร\nผา\nผ่า\nผ้า\nผาก\nผาง\nผ่าง\nผาณิต\nผาด\nผาติ\nผ่าน\nผาม\nผาย\nผ่ายผอม\nผาล\nผาลคุน\nผาลา\nผ่าว\nผาสุก\nผ้าฮาด\nผำ\nผ้ำ\nผิ\nผิง\nผิด\nผิตะ\nผิน\nผิว\nผี\nผี้ว์\nผึง\nผึ่ง\nผึ้ง\nผึ้งรวง\nผืน\nผื่น\nผุ\nผุด\nผุยผง\nผุสราคา\nผู้\nผูก\nเผ\nเผง\nเผชิญ\nเผ็ด\nเผด็จ\nเผดิม\nเผดียง\nเผ่น\nเผนิก\nเผย\nเผยอ\nเผยิบ\nเผยิบผยาบ\nเผล\nเผล่\nเผล็ด\nเผลอ\nเผลอไผล\nเผละ\nเผลาะ\nเผลาะแผละ\nเผลียง\nเผอเรอ\nเผอิญ\nเผอิล\nเผะ\nเผา\nเผ่า\nเผ้า\nเผาะ\nเผิ้ง\nเผิน\nเผียน\nเผือ\nเผื่อ\nเผือก\nเผือด\nเผือน\nเผื่อน\nแผ่\nแผก\nแผง\nแผด\nแผน\nแผ่น\nแผนก\nแผล\nแผลง\nแผล็บ\nแผล็ว\nแผละ\nแผ่ว\nแผ้ว\nโผ\nโผง\nโผฏฐัพพะ\nโผน\nโผเผ\nโผย\nโผล่\nโผลกเผลก\nโผละ\nโผอน\nโผะ\nไผ\nไผ่\nไผท\nฝน\nฝรั่ง\nฝรั่งเศส\nฝ่อ\nฝอย\nฝัก\nฝัง\nฝั่ง\nฝัด\nฝัน\nฝา\nฝ่า\nฝ้า\nฝาก\nฝาง\nฝาด\nฝาน\nฝาย\nฝ่าย\nฝ้าย\nฝิ่น\nฝี\nฝี่\nฝีก\nฝึก\nฝืด\nฝืน\nฝุ่น\nฝูง\nเฝ้า\nเฝือ\nเฝือก\nเฝือง\nเฝื่อน\nแฝก\nแฝง\nแฝด\nใฝ่\nไฝ\nพก\nพกุล\nพง\nพงศ์\nพงศกร\nพงศธร\nพงศา\nพงศาวดาร\nพจน์\nพจนา\nพจนานุกรม\nพจนารถ\nพจนีย์\nพจมาน\nพจี\nพชระ\nพญา\nพญาลอ\nพณิช\nพณิชย์\nพดด้วง\nพธู\nพนันดร\nพนาดร\nพนาดอน\nพนาราม\nพนาลัย\nพนาลี\nพนาวาส\nพนาเวศ\nพนาศรม\nพนาสณฑ์\nพนาสัณฑ์\nพเนจร\nพ่น\nพ้น\nพนม\nพนอง\nพนอม\nพนัก\nพนักงาน\nพนัง\nพนัน\nพนัส\nพนา\nพนาย\nพนิดา\nพนิต\nพบ\nพม่า\nพยนต์\nพยศ\nพยัก\nพยักพเยิด\nพยัคฆ์\nพยัคฆา\nพยัคฆิน\nพยัคฆี\nพยัชน์\nพยัญชนะ\nพยัต\nพยับ\nพยากรณ์\nพยาฆร์\nพยางค์\nพยาธิ\nพยาน\nพยาบาท\nพยาบาล\nพยาม\nพยามะ\nพยายาม\nพยุ\nพยุง\nพยุหยาตรา\nพยุหโยธา\nพยุหเสนา\nพยุหะ\nพยู่ห์\nพเยีย\nพร\nพรต\nพรม\nพรรค\nพรรค์\nพรรคานต์\nพรรณ\nพรรณนา\nพรรดึก\nพรรลาย\nพรรษ\nพรรษา\nพรรเอิญ\nพรวด\nพรวน\nพรหม\nพรหมจรรย์\nพรหมจาริณี\nพรหมจารี\nพรหมา\nพรหมาสตร์\nพรหมินทร์\nพรอก\nพร่อง\nพร้อง\nพรอด\nพร้อม\nพร้อมพรัก\nพร่อย\nพร้อย\nพระ\nพระนอม\nพระนาด\nพระฮาม\nพรักพร้อม\nพรั่ง\nพรัด\nพรั่น\nพรับ\nพร่า\nพร้า\nพราก\nพราง\nพร่าง\nพราด\nพราน\nพราย\nพราว\nพราหมณ์\nพราหมณะ\nพราหมณี\nพราหมี\nพรำ\nพร่ำ\nพริก\nพริ้ง\nพริบ\nพริ้ม\nพรึง\nพรึน\nพรึบ\nพรึ่บ\nพรืด\nพรุ\nพรุ่ง\nพรุน\nพรู\nพรูด\nพฤกษ์\nพฤกษชาติ\nพฤกษเทวดา\nพฤกษราช\nพฤกษศาสตร์\nพฤกษา\nพฤฒ\nพฤฒา\nพฤฒาจารย์\nพฤฒิ\nพฤต\nพฤติ\nพฤทธ์\nพฤทธิ์\nพฤนต์\nพฤนท์\nพฤศจิก\nพฤศจิกายน\nพฤษภ\nพฤษภาคม\nพฤหัสบดี\nพล\nพละ\nพลากร\nพลาดิศัย\nพลาธิการ\nพลานามัย\nพลบ\nพลวก\nพลวง\nพลวัต\nพลศาสตร์\nพลอ\nพล้อ\nพลอง\nพลอด\nพลอน\nพลอมแพลม\nพลอย\nพล่อย\nพลั่ก\nพลัง\nพลั่ง\nพลั้ง\nพลัด\nพลัน\nพลับ\nพลับพลา\nพลับพลึง\nพลั่ว\nพล่า\nพลาง\nพลาญ\nพลาด\nพล่าน\nพลาม\nพล่าม\nพลาย\nพลาสติก\nพลาสมา\nพลาหก\nพลำ\nพล้ำ\nพลำภัง\nพลิก\nพลิพัท\nพลิ้ว\nพลี\nพลุ\nพลุก\nพลุ่ก\nพลุกพล่าน\nพลุ่ง\nพลุ้ย\nพลู\nพลูโต\nพลูโทเนียม\nพวก\nพวง\nพ่วง\nพวน\nพวย\nพสก\nพสุ\nพสุธา\nพสุสงกรานต์\nพหล\nพหุ\nพหุล\nพหู\nพอ\nพ่อ\nพ้อ\nพอก\nพอง\nพ้อง\nพอน\nพ้อม\nพอโลเนียม\nพะ\nพะงา\nพะงาบ\nพะจง\nพะทำมะรง\nพะนอ\nพะเน้าพะนอ\nพะเนิน\nพะเนียง\nพะแนง\nพะพาน\nพะพิง\nพะเพิง\nพะยอม\nพ่ะย่ะค่ะ\nพะยูง\nพะยูน\nพะเยิบ\nพะเยิบพะยาบ\nพะรุงพะรัง\nพะโล้\nพะไล\nพะวง\nพะวักพะวน\nพะวา\nพะว้าพะวัง\nพะอง\nพะอากพะอำ\nพะอืดพะอม\nพัก\nพักตร์\nพักตรา\nพักร\nพัง\nพังกา\nพังงา\nพังผืด\nพังพวย\nพังพอน\nพังพาน\nพังพาบ\nพังเพย\nพัช\nพัชนี\nพัชระ\nพัญจน์\nพัฒนะ\nพัฒนา\nพัฒนากร\nพัฒนาการ\nพัด\nพัดชา\nพัดดึงส์\nพัตร\nพัทธ์\nพัทธยา\nพัทธสีมา\nพัทร\nพัน\nพันตู\nพันทาง\nพันธ์\nพันธะ\nพันธกรณี\nพันธบัตร\nพันธมิตร\nพันธนะ\nพันธนาคาร\nพันธนาการ\nพันธุ์\nพันธุกรรม\nพันลึก\nพันลือ\nพันเลิศ\nพันเอิญ\nพับ\nพัลลภ\nพัลวัน\nพัว\nพัวะ\nพัศดี\nพัสดุ\nพัสตร์\nพัสถาน\nพา\nพาก\nพากเพียร\nพากย์\nพาง\nพ่าง\nพาชี\nพาณิช\nพาณิชย์\nพาณิชยกรรม\nพาณิชยการ\nพาณิชยศาสตร์\nพาณิชยศิลป์\nพาณินี\nพาณี\nพาณีนี\nพาด\nพาท\nพาทย์\nพาธ\nพาธา\nพาน\nพ่าน\nพานร\nพานรินทร์\nพาม\nพาย\nพ่าย\nพายม้า\nพายัพ\nพายุ\nพาร์เซก\nพารณ\nพารา\nพาราฟิน\nพาล\nพาลา\nพาลี\nพาลุก\nพาโล\nพาไล\nพาส\nพาสน์\nพาสนา\nพาสุกรี\nพ่าห์\nพาหนะ\nพาหะ\nพาหา\nพาหิรกะ\nพาหิระ\nพาหุ\nพาหุรัด\nพาหุสัจจะ\nพาเหียร\nพาฬ\nพำ\nพำนัก\nพำพึม\nพำลา\nพิกล\nพิกสิต\nพิกัด\nพิกัติ\nพิกัน\nพิการ\nพิกุล\nพิเคราะห์\nพิฆน์\nพิฆเนศ\nพิฆเนศวร\nพิฆาต\nพิง\nพิจัย\nพิจาร\nพิจารณ์\nพิจารณา\nพิจิก\nพิจิต\nพิจิตร\nพิชญ์\nพิชัย\nพิชาน\nพิชิต\nพิเชฐ\nพิเชียร\nพิฑูรย์\nพิณ\nพิดทูล\nพิดาน\nพิโดร\nพิตร\nพิถี\nพิถีพิถัน\nพิทย\nพิทย์\nพิทยา\nพิทยาคม\nพิทยาคาร\nพิทยาธร\nพิทยาลัย\nพิทักษ์\nพิทูร\nพิเทศ\nพิธาน\nพิธี\nพิธุ\nพินทุ\nพินอบพิเทา\nพินัย\nพินาศ\nพินิจ\nพินิต\nพินิศ\nพินิศจัย\nพิเนต\nพิบัติ\nพิบุล\nพิบูล\nพิปริต\nพิปลาส\nพิพรรธ\nพิพรรธน์\nพิพักพิพ่วน\nพิพัฒ\nพิพัฒน์\nพิพากษ์\nพิพากษา\nพิพาท\nพิพิธ\nพิพิธภัณฑ์\nพิพิธภัณฑสถาน\nพิภพ\nพิภัช\nพิภาค\nพิภูษณะ\nพิเภก\nพิมปะการัง\nพิมพ์\nพิมพการัง\nพิมพา\nพิมพาภรณ์\nพิมล\nพิมเสน\nพิมาน\nพิมุข\nพิโมกข์\nพิโมกษ์\nพิโยกพิเกน\nพิโยค\nพิรอด\nพิระ\nพิรากล\nพิราบ\nพิราม\nพิราลัย\nพิริยะ\nพิรี้พิไร\nพิรุณ\nพิรุธ\nพิรุฬห์\nพิเรนทร์\nพิเราะ\nพิโรธ\nพิไร\nพิลังกาสา\nพิลาป\nพิลาส\nพิลิปดา\nพิลึก\nพิลึกกึกกือ\nพิลึกพิลั่น\nพิโลน\nพิไล\nพิศ\nพิศวง\nพิศวาส\nพิศาล\nพิศุทธ์\nพิศุทธิ์\nพิเศษ\nพิษ\nพิษฐาน\nพิษนาศน์\nพิสดาร\nพิสมร\nพิสมัย\nพิสัง\nพิสัช\nพิสัย\nพิสิฐ\nพิสุทธิ์\nพิสูจน์\nพิหค\nพิหาร\nพิฬาร\nพี\nพี่\nพี้\nพีชคณิต\nพีระมิด\nพึง\nพึ่ง\nพึ่บ\nพึ่บพั่บ\nพึม\nพึมพำ\nพืช\nพืด\nพื้น\nพุ\nพุก\nพุกาม\nพุง\nพุ่ง\nพุงดอ\nพุฒ\nพุฒิ\nพุด\nพุดตาน\nพุทธ\nพุทธะ\nพุทธังกูร\nพุทธางกูร\nพุทธันดร\nพุทธาภิเษก\nพุทธาวาส\nพุทธิ\nพุทโธ่\nพุทรา\nพุธ\nพุ่ม\nพุมเรียง\nพุ้ย\nพู\nพูพอน\nพู่\nพูด\nพูน\nพู้น\nพู่ระหง\nเพ\nเพ็ก\nเพกา\nเพคะ\nเพ็ง\nเพ่ง\nเพ็จ\nเพชฉลูกรรม\nเพชฌฆาต\nเพชร\nเพชรดา\nเพชรปาณี\nเพชรฤกษ์\nเพชรายุธ\nเพชรกลับ\nเพชรสังฆาต\nเพชรหลีก\nเพชรหึง\nเพ็ญ\nเพฑูริย์\nเพณี\nเพ็ดทูล\nเพดาน\nเพท\nเพทนา\nเพทาย\nเพทุบาย\nเพโทบาย\nเพ่นพ่าน\nเพนียด\nเพไนย\nเพ้ย\nเพรง\nเพรซีโอดิเมียม\nเพรา\nเพราะ\nเพริด\nเพริศ\nเพรียก\nเพรียง\nเพรียบ\nเพรี้ยม\nเพรียว\nเพรื่อ\nเพรือง\nเพล\nเพลง\nเพล็ด\nเพล้โพล้\nเพลา\nเพลาะ\nเพลิง\nเพลิดเพลิน\nเพลิน\nเพลีย\nเพลี้ย\nเพลี่ยง\nเพศ\nเพส\nเพสลาด\nเพ่อ\nเพ้อ\nเพ้อเจ้อ\nเพอิญ\nเพะ\nเพา\nเพาะ\nเพิก\nเพิง\nเพิ่ง\nเพิดเพ้ย\nเพิ่ม\nเพี้ย\nเพียง\nเพี้ยง\nเพียงออ\nเพี้ยน\nเพียบ\nเพียร\nเพื่อ\nเพื่อน\nแพ\nแพ้\nแพง\nแพ่ง\nแพงพวย\nแพทย์\nแพทยศาสตร์\nแพน\nแพ่น\nแพนก\nแพนงเชิง\nแพร\nแพร่\nแพรก\nแพร่ง\nแพรว\nแพร้ว\nแพลง\nแพลทินัม\nแพล็บ\nแพลม\nแพลเลเดียม\nแพละ\nแพละโลม\nแพว\nแพ้ว\nแพศย์\nแพศยา\nแพะ\nโพ\nโพก\nโพกพาย\nโพง\nโพงพาง\nโพชฌงค์\nโพซิตรอน\nโพด\nโพทะเล\nโพแทสเซียม\nโพธ\nโพธิ\nโพธิ์\nโพน\nโพ้น\nโพนทะนา\nโพบาย\nโพย\nโพยก๊วน\nโพยม\nโพรก\nโพรง\nโพรโทแอกทิเนียม\nโพรมีเทียม\nโพระดก\nโพล่\nโพลง\nโพล่ง\nโพล้ง\nโพลน\nโพล้เพล้\nโพละ\nโพสพ\nไพ\nไพ่\nไพจิตร\nไพชน\nไพชยนต์\nไพฑูรย์\nไพที\nไพบูลย์\nไพพรรณ\nไพร\nไพร่\nไพรจิตร\nไพรชน\nไพรชยนต์\nไพรฑูรย์\nไพรที\nไพรบูลย์\nไพรเราะ\nไพรัช\nไพรำ\nไพริน\nไพรินทร์\nไพรี\nไพเราะ\nไพโรจน์\nไพล\nไพล่\nไพศาขะ\nไพศาล\nไพเศษ\nไพสพ\nไพสิฐ\nไพหาร\nฟก\nฟ้ง\nฟรักโทส\nฟรี\nฟลูออรีน\nฟ่อ\nฟ้อ\nฟอก\nฟอง\nฟ่อง\nฟ้อง\nฟอด\nฟอน\nฟ่อน\nฟ้อน\nฟ้อแฟ้\nฟอร์มาลดีไฮด์\nฟอร์มาลิน\nฟอสฟอรัส\nฟอสเฟต\nฟัก\nฟักฟุ้น\nฟัง\nฟังก์ชัน\nฟัด\nฟัน\nฟั่น\nฟั้น\nฟ้า\nฟาก\nฟาง\nฟ่าง\nฟาด\nฟาทอม\nฟาน\nฟ่าม\nฟาย\nฟาร์ม\nฟาสซิสต์\nฟิด\nฟิต\nฟิบ\nฟิล์ม\nฟิวส์\nฟิสิกส์\nฟี่\nฟี้\nฟืดฟาด\nฟืน\nฟื้น\nฟืม\nฟุ\nฟุ้ง\nฟุต\nฟุน\nฟุบ\nฟุ่บ\nฟุ่มเฟือย\nฟุลสแก๊ป\nฟู\nฟู่\nฟูก\nฟูด\nฟูม\nเฟ็ด\nเฟ้น\nเฟลด์สปาร์\nเฟ้อ\nเฟอร์เมียม\nเฟอะ\nเฟอะฟะ\nเฟะ\nเฟะฟะ\nเฟิน\nเฟี้ยม\nเฟี้ยว\nเฟือ\nเฟื้อ\nเฟือง\nเฟื่อง\nเฟื้อง\nเฟือน\nเฟือย\nเฟื้อย\nแฟ่\nแฟง\nแฟชั่น\nแฟน\nแฟบ\nแฟ้ม\nแฟรนเซียม\nแฟลกซ์\nแฟลต\nแฟะ\nโฟกัส\nไฟ\nภควดี\nภควัต\nภควันต์\nภควัม\nภควา\nภควาน\nภคะ\nภคันทลา\nภคินี\nภณะ\nภณิดา\nภพ\nภมร\nภมริน\nภมรี\nภมุกา\nภยันตราย\nภยาคติ\nภระ\nภรณี\nภรต\nภรรดร\nภรรดา\nภรรยา\nภระมร\nภระมรี\nภราดร\nภราดรภาพ\nภราดา\nภริยา\nภฤศ\nภวะ\nภวตัณหา\nภวนะ\nภวังค์\nภวังคจิต\nภักดี\nภักตะ\nภักติ\nภักษ์\nภักษา\nภักษาหาร\nภัค\nภัคน์\nภังคะ\nภังคี\nภัจ\nภัณฑ์\nภัณฑาคาร\nภัณฑาคาริก\nภัณฑารักษ์\nภัณฑนะ\nภัณฑู\nภัต\nภัตตาคาร\nภัตตาหาร\nภัตร\nภัทระ\nภัทรกัป\nภัพ\nภัย\nภัสดา\nภัสตรา\nภัสมะ\nภัสสร\nภา\nภาค\nภาคย์\nภาคยานุวัติ\nภาคินี\nภาคิไนย\nภาคี\nภาคียะ\nภาชนะ\nภาชี\nภาณ\nภาณวาร\nภาณกะ\nภาณี\nภาณุ\nภาดร\nภาดา\nภาตระ\nภาตา\nภาตุ\nภาติกะ\nภาติยะ\nภาพ\nภาพย์\nภาม\nภาย\nภาร\nภาระ\nภารดี\nภารต\nภารตี\nภารยทรัพย์\nภารยา\nภารา\nภาวนา\nภาวะ\nภาษ\nภาษณ์\nภาษา\nภาษิต\nภาษี\nภาส\nภาสน์\nภาสวร\nภาสา\nภาสุระ\nภิกขา\nภิกขาจาร\nภิกขุ\nภิกขุนี\nภิกษา\nภิกษาจาร\nภิกษาหาร\nภิกษุ\nภิกษุณี\nภิงคาร\nภิญโญ\nภิตติ\nภินท์\nภินทนาการ\nภิยโย\nภิรมย์\nภิรมย์สุรางค์\nภิษัช\nภิสัก\nภีตะ\nภีมะ\nภีรุ\nภุกต์\nภุขัน\nภุช\nภุชงค์\nภุต\nภุมมะ\nภุมรัตน์\nภุมวาร\nภุมรา\nภุมริน\nภุมรี\nภุมเรศ\nภู\nภู่\nภูต\nภูติ\nภูม\nภูมิ\nภูมี\nภูริ\nภูรี\nภูวดล\nภูวนาถ\nภูวเนตร\nภูวไนย\nภูษา\nภูษิต\nเภกะ\nเภตรา\nเภท\nเภทุบาย\nเภรี\nเภสัช\nโภค\nโภคะ\nโภคิน\nโภคี\nโภไคย\nโภไคศวรรย์\nโภช\nโภชย์\nโภชก\nโภชนะ\nโภชนา\nโภชนาหาร\nโภชนียะ\nไภริน\nไภรี\nไภษัชคุรุ\nไภษัชย์\nมกร\nมกราคม\nมกุฎ\nมคธ\nมฆวัน\nมฆะ\nมฆา\nม่ง\nมงกุฎ\nมงโกรย\nมงคล\nมงคลวาร\nมณฑ์\nมณฑก\nมณฑนะ\nมณฑป\nมณฑล\nมณฑา\nมณฑารพ\nมณฑิระ\nมณเฑียร\nมณี\nมด\nมตะ\nมตกภัต\nมติ\nมทนะ\nมทะ\nมธุ\nมธุกร\nมธุการี\nมธุลีห์\nมธุระ\nมธุรพจน์\nมน\nมนินทรีย์\nม่น\nมนต์\nมนตร์\nมนตรี\nมนท์\nมนทิราลัย\nมนเทียร\nมนสิการ\nมนัส\nมนัสวี\nมนินทรีย์\nมนิมนา\nมนิลา\nมนุญ\nมนุษย์\nมนุษยชาติ\nมนุษยธรรม\nมนุษย์มนา\nมนุษยโลก\nมนุษยศาสตร์\nมนุษยสัมพันธ์\nมนุสาร\nมนู\nมนูสาร\nมโน\nมโนช\nมโนชญ์\nมโนราห์\nมโนสาเร่\nมโนห์รา\nมมังการ\nมยุรฉัตร\nมยุระ\nมยุรา\nมยุรี\nมยุเรศ\nมยูร\nมรกต\nมรคา\nมรฑป\nมรณ์\nมรณะ\nมรณกรรม\nมรณบัตร\nมรณภัย\nมรณภาพ\nมรดก\nมรรค\nมรรคา\nมรรตัย\nมรรยาท\nมรรษ\nมรสุม\nมริจ\nมริยาท\nมรีจิ\nมรุต\nมฤค\nมฤคย์\nมฤคศิระ\nมฤคศิรมาส\nมฤคเศียร\nมฤคินทร์\nมฤเคนทร์\nมฤดก\nมฤต\nมฤตยู\nมฤทุ\nมล\nมละ\nมลัก\nมลังเมลือง\nมล้าง\nมลาย\nมลายู\nมวก\nม่วง\nมวน\nม่วน\nม้วน\nม้วนต้วน\nมวย\nม้วย\nมวล\nมหกรรม\nมหรณพ\nมหรรณพ\nมหรสพ\nมหัจฉริยะ\nมหัต\nมหัทธนะ\nมหันต์\nมหันตโทษ\nมหัพภาค\nมหัศจรรย์\nมหา\nมหากฐิน\nมหากาฬ\nมหาขันธกะ\nมหาจักร\nมหาชน\nมหาชัย\nมหาชาติ\nมหาโชตรัต\nมหาดไทย\nมหาดเล็ก\nมหาตมะ\nมหาไถ่\nมหาเทพ\nมหาเทพี\nมหาเทวี\nมหาธาตุ\nมหานิกาย\nมหานิล\nมหาบพิตร\nมหาบัณฑิต\nมหาพน\nมหาพรหม\nมหาภารตะ\nมหาภิเนษกรมณ์\nมหาภูต\nมหาเมฆ\nมหายาน\nมหายุค\nมหาราช\nมหาฤกษ์\nมหาละลวย\nมหาละลาย\nมหาวงศ์\nมหาวรรค\nมหาวิทยาลัย\nมหาศักราช\nมหาศาล\nมหาสงกรานต์\nมหาสดมภ์\nมหาสดำ\nมหาสมุทร\nมหาสาวก\nมหาหงส์\nมหาหิงคุ์\nมหาอำนาจ\nมหาอุจ\nมหาอุด\nมหาอุปรากร\nมหาอุปราช\nมหิ\nมหิดล\nมหิธร\nมหิป\nมหิงส์\nมหิทธิ\nมหินท์\nมหิมา\nมหิศร\nมหิศวร\nมหิษ\nมหิษี\nมหึมา\nมเหยงค์\nมเหศ\nมเหศวร\nมเหศักดิ์\nมเหสักข์\nมเหสิ\nมเหสี\nมเหาฬาร\nมโหรสพ\nมโหระทึก\nมโหรี\nมโหฬาร\nมไหศวรรย์\nมอ\nมอง\nมองโกลอยด์\nมองโกเลีย\nมองคร่อ\nมอญ\nมอด\nม่อต้อ\nมอเตอร์\nมอเตอร์ไซค์\nมอน\nม่อน\nมอบ\nมอม\nมอมแมม\nม่อย\nมอร์ฟีน\nมอระกู่\nมอลโทส\nม่อลอกม่อแลก\nม่อห้อม\nม่อฮ่อม\nมะ\nมะกรูด\nมะกล่ำ\nมะกอก\nมะก่อง\nมะกะโรนี\nมะกา\nมะเกลือ\nมะเกี๋ยง\nมะข่วง\nมะขวิด\nมะขาม\nมะเขือ\nมะแข่น\nมะคังแดง\nมะค่า\nมะคำไก่\nมะคำดีควาย\nมะงั่ว\nมะงุมมะงาหรา\nมะซัก\nมะซาง\nมะดัน\nมะดีหวี\nมะดูก\nมะเดหวี\nมะเดื่อ\nมะต้อง\nมะตะบะ\nมะตาด\nมะตาหะรี\nมะตึ่ง\nมะตื๋น\nมะตูม\nมะแตก\nมะโต\nมะนาว\nมะปราง\nมะปริง\nมะฝ่อ\nมะพร้าว\nมะพลับ\nมะพูด\nมะแพน\nมะแพร้ว\nมะเฟือง\nมะแฟน\nมะไฟ\nมะม่วง\nมะม่าว\nมะมี่\nมะมื่น\nมะมุด\nมะเมอ\nมะเมีย\nมะเมื่อย\nมะแม\nมะยง\nมะยม\nมะระ\nมะริด\nมะรืน\nมะรุม\nมะรุมมะตุ้ม\nมะเร็ง\nมะเรื่อง\nมะโรง\nมะลอกมะแลก\nมะละกอ\nมะลิ\nมะลื่น\nมะลืมดำ\nมะลุลี\nมะแว้ง\nมะสัง\nมะเส็ง\nมะหวด\nมะหะหมัด\nมะหาด\nมะหิ่ง\nมะเหงก\nมะอึก\nมะฮอกกานี\nมัก\nมักกะโรนี\nมักกะลีผล\nมักกะสัน\nมักขะ\nมั่กขั้ก\nมักขิกา\nมัค\nมัคคะ\nมัคคุเทศก์\nมัคนายก\nมัฆวาน\nมั่ง\nมังกง\nมังกร\nมังกุ\nมังคละ\nมังค่า\nมังคุด\nมังตาน\nมังสวิรัติ\nมังสะ\nมังสี\nมัจจะ\nมัจจุ\nมัจฉริยะ\nมัจฉรี\nมัจฉะ\nมัจฉา\nมัชชะ\nมัชวิรัติ\nมัชชาระ\nมัชฌันติกสมัย\nมัชฌิม\nมัชฌิมา\nมัญจา\nมัญชิษฐา\nมัญชุ\nมัญชุสา\nมัญชูสา\nมัญเชฏฐะ\nมัฏฐะ\nมัณฑนศิลป์\nมัณฑนา\nมัด\nมัตตะ\nมัตตัญญู\nมัตตา\nมัตติกา\nมัตถกะ\nมัตถลุงค์\nมัตสยะ\nมัตสยา\nมัตสระ\nมัตสริน\nมัททวะ\nมัทนะ\nมัทยะ\nมัธยฐาน\nมัธยม\nมัธยันห์\nมัธยัสถ์\nมัน\nมั่น\nมันตา\nมันถะ\nมันทิระ\nมันทิราลัย\nมับ\nมั้ม\nมัมมี่\nมัย\nมัลละ\nมัลลิกา\nมัว\nมัวซัว\nมั่ว\nมัศยา\nมัสตุ\nมัสตาร์ด\nมัสมั่น\nมัสยิด\nมัสรู่\nมัสลิน\nมัสสุ\nมา\nม้า\nมาก\nมาคสิระ\nมาฆบูชา\nมาฆะ\nม้าง\nมางสะ\nมาณพ\nมาณวิกา\nมาด\nมาดา\nมาตงค์\nมาตร\nมาตรา\nมาตฤ\nมาตังคะ\nมาตา\nมาตามหัยกะ\nมาตามหัยกา\nมาตามหัยยิกา\nมาติกะ\nมาติกา\nมาตุ\nมาตุจฉา\nมาตุรงค์\nมาตุเรศ\nมาตุละ\nมาตุลา\nมาตุลานี\nมาทะ\nมาธยมิก\nมาธยมิกะ\nมาธุระ\nมาธุสร\nมาธูระ\nมาน\nม่าน\nม้าน\nมานพ\nมานะ\nมานัต\nมานัส\nมานิต\nมานี\nมานุษ\nมานุษยวิทยา\nมาโนชญ์\nมาบ\nมาภา\nม้าม\nม่าย\nมายา\nมาร\nมาราธิราช\nมารค\nมารดร\nมารดา\nมารยา\nมารยาท\nมารศรี\nมารษา\nมาริต\nมารุต\nมาลย์\nมาลัย\nมาลา\nมาลาตี\nมาลาเรีย\nมาลินี\nมาลี\nมาลุต\nมาศ\nมาส\nมาสก\nมาห์\nม่าห์\nมาหิส\nม่าเหมี่ยว\nมาฬก\nมิ\nมิค\nมิคสัญญี\nมิ่ง\nมิจฉา\nมิด\nมิตร\nมิติ\nมิเตอร์\nมิถยา\nมิถุน\nมิถุนายน\nมิทธะ\nมินตรา\nมินตา\nมินหม้อ\nมิ่ม\nมิ้ม\nมิไย\nมิรันตี\nมิลลิกรัม\nมิลลิบาร์\nมิลลิเมตร\nมิลลิลิตร\nมิลักขะ\nมิลักขู\nมิส\nมิสกรี\nมิสกวัน\nมิสซา\nมี\nมี่\nมีด\nมีเทน\nมีน\nมีนาคม\nมี่สั้ว\nมึง\nมึน\nมืด\nมืน\nมื่น\nมือ\nมื้อ\nมุ\nมุก\nมุกดา\nมุกดาหาร\nมุกุระ\nมุข\nมุขเด็จ\nมุขยประโยค\nมุโขโลกนะ\nมุคคะ\nมุง\nมุ่ง\nมุ้ง\nมุจฉา\nมุจนะ\nมุจลินท์\nมุญจนะ\nมุญชะ\nมุฐิ\nมุณฑกะ\nมุณฑะ\nมุด\nมุตกิด\nมุตฆาต\nมุตตะ\nมุตตา\nมุตติ\nมุตะ\nมุติ\nมุททา\nมุทธชะ\nมุทธา\nมุทธาภิเษก\nมุทรา\nมุทริกา\nมุทะลุ\nมุทา\nมุทิกา\nมุทิงค์\nมุทิตา\nมุทุ\nมุทุตา\nมุ่น\nมุนิ\nมุนินทร์\nมุนี\nมุบ\nมุบมิบ\nมุม\nมุ้ม\nมุ่ย\nมุรธา\nมุรธาภิเษก\nมุสละ\nมุสลิม\nมุสา\nมุสิก\nมุหงิด\nมุหน่าย\nมุหุต\nมุฮัมมัด\nมูก\nมูเซอ\nมูตร\nมู่ทู่\nมูน\nมูมมาม\nมูรติ\nมูรธา\nมูรธาภิเษก\nมูล\nมูละ\nมูลา\nมูลิกากร\nมู่ลี่\nมู่เล่\nมูสัง\nมูสิก\nมูสิกะ\nมูสิกทันต์\nเม\nเม็ก\nเมกะเฮิรตซ์\nเมขลา\nเมฆ\nเมฆา\nเมฆินทร์\nเมฆี\nเม็ง\nเม็ด\nเมตตา\nเมตไตรย\nเมตร\nเมตริก\nเมตริกตัน\nเมถุน\nเมท\nเมโท\nเมทนี\nเมทินี\nเมทนีดล\nเมทานอล\nเมทิลแอลกอฮอล์\nเมธ\nเมธา\nเมธาวี\nเมธี\nเมน\nเม่น\nเม้น\nเมนเดลีเวียม\nเมนทอล\nเม้ม\nเมรัย\nเมริเดียน\nเมรุ\nเมล์\nเมล็ด\nเมลือง\nเมษ\nเมษายน\nเมห์\nเมหนะ\nเมหะ\nเมะ\nเมา\nเม่า\nเม้า\nเมารี\nเมาลี\nเมาฬี\nเมาะ\nเมิง\nเมิน\nเมิล\nเมีย\nเมียง\nเมี่ยง\nเมี้ยน\nเมือ\nเมื้อ\nเมื่อ\nเมือก\nเมือง\nเมือบ\nเมื่อย\nแม่\nแม้\nแมก\nแมกนีเซียม\nแมง\nแมงกะพรุน\nแมงกานิน\nแมงกานีส\nแมงคา\nแมงคาเรือง\nแมงช้าง\nแมงดา\nแมงลัก\nแม่ตะงาว\nแมน\nแม่น\nแม้น\nแมลง\nแมลบ\nแมว\nแม้ว\nแมะ\nโม\nโม่\nโม้\nโมก\nโมกข์\nโมกษะ\nโมฆกรรม\nโมฆสัญญา\nโมฆะ\nโมฆียกรรม\nโมฆียะ\nโมง\nโม่ง\nโมงครุ่ม\nโมทนา\nโมโนแซ็กคาไรด์\nโมไนย\nโมเม\nโมเมนต์\nโมเย\nโมรา\nโมรี\nโมเรส\nโมลิบดีนัม\nโมลี\nโมเลกุล\nโมเสก\nโมเสส\nโม่ห์\nโมหะ\nโมหันธ์\nโมหาคติ\nโมโห\nไม่\nไม้\nไมกา\nไมครอน\nไมโครกรัม\nไมโครฟิล์ม\nไมโครโฟน\nไมโครมิเตอร์\nไมโครเมตร\nไมโครลิตร\nไมโครเวฟ\nไมตรี\nไมยราบ\nไมล์\nยก\nยกกระบัตร\nยกนะ\nยง\nยงโย่\nยชุรเวท\nยติ\nยติภังค์\nยถากรรม\nยถาภูตญาณ\nย่น\nยนต์\nยนตร์\nยม\nยมก\nยมโดย\nยมนา\nยมล\nยมะ\nยรรยง\nยล\nยวง\nยวด\nยวน\nยวบ\nย้วย\nยวรยาตร\nยศ\nยโส\nยอ\nย่อ\nยอก\nย็อกแย็ก\nยอง\nย่อง\nย้อง\nยอด\nยอน\nย้อน\nยอบ\nยอม\nย่อม\nย้อม\nย่อย\nย้อย\nย้อแย้\nยะ\nย่ะ\nยะยอบ\nยะยับ\nยัก\nยักข์\nยักขินี\nยักษ์\nยักษา\nยักษิณี\nยักษี\nยัง\nยั้ง\nยั่งยืน\nยัชโญปวีต\nยัญ\nยัญญะ\nยัด\nยัติภังค์\nยัน\nยั่น\nยันต์\nยันตร\nยันตร์\nยันตรกรรม\nยั่นตะนี\nยับ\nยั่ว\nยั้ว\nยั้วเยี้ย\nยัวรยาตร\nยัวะ\nยัษฏิ\nยา\nย่า\nยาก\nยาคุ\nยาคู\nยาง\nย่าง\nยางพารา\nยาจก\nยาจนา\nยาไฉน\nยาด\nยาดา\nยาตร\nยาตรา\nยาน\nย่าน\nย่านพาโหม\nยานมาศ\nยานุมาศ\nยานี\nยาม\nย่าม\nยามะ\nยามักการ\nยามา\nยาย\nย้าย\nยายี\nยาว\nย้าว\nยาวกาลิก\nยาวชีวิก\nยาสูบ\nย่าหยา\nยาหยี\nยำ\nย่ำ\nย้ำ\nยำเยีย\nยิก\nยิง\nยิ่ง\nยิฏฐะ\nยิน\nยิบ\nยิบหยี\nยิปซัม\nยิปซี\nยิ้ม\nยิมนาสติก\nยิหวา\nยี\nยี่\nยี้\nยี่ก่า\nยี่เก\nยี่เข่ง\nยี่โถ\nยีน\nยี่โป้\nยี่ภู่\nยีราฟ\nยี่สก\nยี่สง\nยี่สน\nยี่สาน\nยี่สุ่น\nยี่หระ\nยี่หร่า\nยี่ห้อ\nยี่หุบ\nยึกยัก\nยึกยือ\nยึด\nยืด\nยืน\nยื่น\nยืม\nยื้อ\nยุ\nยุกกระบัตร\nยุกดิ\nยุกติ\nยุกติธรรม\nยุกต์\nยุค\nยุคนธร\nยุคล\nยุคันต์\nยุคันธร\nยุคุนธร\nยุง\nยุ่ง\nยุ้ง\nยุด\nยุต\nยุติ\nยุทธ\nยุทธ์\nยุทธนา\nยุทโธปกรณ์\nยุบ\nยุ่บ\nยุ่บยั่บ\nยุบล\nยุพดี\nยุพเรศ\nยุพา\nยุพาน\nยุพาพาล\nยุพาพิน\nยุ่มย่าม\nยุ่ย\nยุ้ย\nยุรยาตร\nยูรยาตร\nยุวชน\nยุวดี\nยุวราช\nยุวา\nยุวาน\nยู\nยู่\nยูง\nยูโด\nยูถะ\nยูถิกา\nยูริก\nยูเรนัส\nยูเรเนียม\nยูโรเพียม\nเย\nเย้\nเยง\nเยซู\nเย็ด\nเย็น\nเย็นตาโฟ\nเย็นเตาโฟ\nเย็บ\nเย้ย\nเยอ\nเย่อ\nเยอรมัน\nเยอว\nเย่อหยิ่ง\nเยอะ\nเยอะแยะ\nเยา\nเย้า\nเยาว์\nเยาวชน\nเยาวมาลย์\nเยาวยอด\nเยาวราช\nเยาวเรศ\nเยาวลักษณ์\nเยาวพา\nเยาวพาณี\nเยาวพาน\nเยาะ\nเยิง\nเยิน\nเยิ่น\nเยิ่นเย้อ\nเยินยอ\nเยิบ\nเยิบยาบ\nเยิ้ม\nเยีย\nเยี่ยง\nเยี่ยงอย่าง\nเยียงผา\nเยียดยัด\nเยียน\nเยียบ\nเยี่ยม\nเยียรบับ\nเยียรยง\nเยียว\nเยี่ยว\nเยียวยา\nเยือ\nเยื่อ\nเยื้อ\nเยือก\nเยือง\nเยื่อง\nเยื้อง\nเยือน\nเยื้อน\nแย่\nแย้\nแยก\nแยง\nแย่ง\nแย้ง\nแยงแย่\nแยงแย้\nแยบ\nแย็บ\nแยม\nแย้ม\nแยแส\nแยะ\nโย\nโย้\nโยก\nโยกเยก\nโยคาพจร\nโยคาวจร\nโยคเกณฑ์\nโยคยะ\nโยคะ\nโยคิน\nโยคี\nโยง\nโย่ง\nโย่งเย่ง\nโยงโย่\nโยชน์\nโยชนา\nโยถิกะ\nโยทะกา\nโยธวาทิต\nโยธา\nโยธิน\nโยน\nโยนก\nโยนิโส\nโยนี\nโยม\nโยโส\nใย\nไย\nไย่\nไยดี\nไยไพ\nรก\nรง\nรงค์\nรงควัตถุ\nรงรอง\nรจนา\nรจเรข\nรจเลข\nรจิต\nรชตะ\nรชนิ\nรชนี\nรชะ\nรณรงค์\nรด\nรดี\nรตนะ\nรตะ\nรติ\nรถ\nรน\nร่น\nรบ\nรบาญ\nรพี\nรม\nร่ม\nรมณี\nรมณีย์\nรมณียสถาน\nรมย์\nรมเยศ\nรยางค์\nรวก\nรวง\nร่วง\nรวด\nรวน\nรวนเร\nร่วน\nรวบ\nรวม\nร่วม\nรวย\nรวิ\nรวิวาร\nรวี\nรศนา\nรส\nรสนา\nรสสุคนธ์\nรสายนเวท\nรสิก\nรหัท\nรหัส\nรโห\nรโหฐาน\nรอ\nร่อ\nรอก\nรอง\nร่อง\nร้อง\nรองเง็ง\nร่องแร่ง\nรอด\nรอน\nร่อน\nร้อน\nรอบ\nรอบคอบ\nรอม\nรอมชอม\nรอมร่อ\nรอย\nร่อย\nร้อย\nร่อแร่\nระ\nระกะ\nระกา\nระกำ\nระเกะระกะ\nระคน\nระคาง\nระคาย\nระแคะ\nระฆัง\nระงม\nระงับ\nระแง้\nระโงกหิน\nระชวย\nระดม\nระดะ\nระดับ\nระดา\nระด่าว\nระดู\nระเด่น\nระเดียง\nระแด\nระตู\nระทก\nระทด\nระทม\nระทวย\nระทา\nระทึก\nระแทะ\nระนาด\nระนาบ\nระนาม\nระนาว\nระเนน\nระเนระนาด\nระเนียด\nระแนง\nระแนะ\nระบบ\nระบม\nระบอบ\nระบัด\nระบับ\nระบาด\nระบาย\nระบำ\nระบิล\nระบือ\nระบุ\nระเบง\nระเบ็ง\nระเบิด\nระเบียง\nระเบียน\nระเบียบ\nระแบบ\nระมัดระวัง\nระมาด\nระเมียร\nระย่อ\nระย่อม\nระยะ\nระยั้ง\nระยับ\nระย้า\nระยาบ\nระยำ\nระยิบระยับ\nระโยง\nระโยงระยาง\nระรวย\nระรอง\nระร่อน\nระรัว\nระราน\nระร่าย\nระริก\nระรี่\nระรึง\nระรื่น\nระรื้น\nระเร้ง\nระเริง\nระเรียง\nระเรื่อย\nระแรง\nระลวง\nระลอก\nระลึก\nระวัง\nระวาง\nระวาย\nระวิง\nระแวง\nระแวดระวัง\nระไว\nระส่ำระสาย\nระหกระเหิน\nระหง\nระหวย\nระหว่าง\nระหองระแหง\nระหัด\nระหาย\nระเห็จ\nระเหย\nระเหระหน\nระเหหน\nระเหิด\nระเหินระหก\nระแหง\nระโหย\nระอา\nระอิดระอา\nระอุ\nรัก\nรักข์\nรักขิต\nรักตะ\nรักบี้\nรักเร่\nรักแร้\nรักษ์\nรักษา\nรัง\nรั้ง\nรังเกียจ\nรังแก\nรังค์\nรังควาน\nรังแค\nรังรอง\nรังวัด\nรังสิ\nรังสี\nรังสิมันตุ์\nรังสิมา\nรัจฉา\nรัช\nรัชชูปการ\nรัชมังคลาภิเษก\nรัชชุ\nรัชฎาภิเษก\nรัชดาภิเษก\nรัชนะ\nรัชนี\nรัญจวน\nรัฏฐาภิปาลโนบาย\nรัฐ\nรัฐประศาสโนบาย\nรัฐประศาสนศาสตร์\nรัด\nรัต\nรัตกัมพล\nรัตมณี\nรัตคน\nรัตจันทน์\nรัตตัญญู\nรัตติ\nรัตน์\nรัตนะ\nรัตนโกสินทร์\nรัตนโกสินทรศก\nรัตนชาติ\nรัตนตรัย\nรัตนบัลลังก์\nรัตนวราภรณ์\nรัตนสิงหาสน์\nรัตนา\nรัตนากร\nรัตนาภรณ์\nรัตนาวลี\nรัตมา\nรัถ\nรัถยา\nรัทเทอร์ฟอร์เดียม\nรัน\nรั้น\nรันทด\nรันทวย\nรับ\nรัมณียสถาน\nรัมภา\nรัมมี่\nรัมย์\nรัย\nรัว\nรั่ว\nรั้ว\nรัศมิมัต\nรัศมิมาน\nรัศมี\nรัษฎากร\nรัสเซีย\nรัสสะ\nรัสสระ\nรา\nร่า\nร้า\nราก\nรากษส\nรากสาด\nราคะ\nราคจริต\nราคา\nราคิน\nราคี\nราง\nร่าง\nร้าง\nรางจืด\nรางชาง\nรางวัล\nราช\nราชกิจจานุเบกษา\nราชนิกุล\nราชวโรงการ\nราชญี\nราชดัด\nราชพฤกษ์\nราชมาณพ\nราชมาษ\nราชมาส\nราชย์\nราชสีห์\nราชะ\nราชัน\nราชันย์\nราชัย\nราชา\nราชาธิปไตย\nราชาธิราช\nราชาภิเษก\nราชายตนะ\nราชาวดี\nราชี\nราชินิกุล\nราชินีกุล\nราชินี\nราชินูปถัมภ์\nราชูปถัมภ์\nราชูปโภค\nราเชน\nราเชนทร์\nราเชนทรยาน\nราโชวาท\nราไชศวรรย์\nราญ\nราญรอน\nราด\nราต\nราตร\nราตรี\nราน\nร่าน\nร้าน\nราบ\nราพณ์\nราพณาสูร\nราม\nรามเกียรติ์\nรามสูร\nรามัญ\nรามา\nราย\nร่าย\nร้าย\nราว\nร้าว\nราวี\nราศี\nราษฎร\nราษฎร์\nราษตรี\nราษราตรี\nราหุ\nราหู\nรำ\nร่ำ\nรำคาญ\nรำงับ\nรำจวน\nรำบาญ\nรำพัน\nรำพาย\nรำพึง\nรำเพย\nรำไพ\nรำมะนา\nรำมะนาด\nรำมะร่อ\nร่ำรวย\nร่ำร่ำ\nรำไร\nรำลึก\nรำหัด\nรำหัส\nริ\nริก\nริดสีดวง\nริน\nริ้น\nริบ\nริบบิ้น\nริบรี่\nริบหรี่\nริปุ\nริปู\nริม\nริ้ว\nริษยา\nรี\nรี่\nรี้พล\nรีด\nรีดักชัน\nรีต\nรีเนียม\nรีบ\nรีม\nรีรอ\nรี้ริก\nรึง\nรึ้ง\nรื่น\nรื้น\nรื้อ\nรุ\nรุก\nรุกข์\nรุกขชาติ\nรุกขเทวดา\nรุกขมูล\nรุกขา\nรุกรุย\nรุ่ง\nรุ้ง\nรุงรัง\nรุ่งริ่ง\nรุจ\nรุจา\nรุจนะ\nรุจิ\nรุจี\nรุจิระ\nรุจิรา\nรุด\nรุต\nรุทธ์\nรุทระ\nรุธิร\nรุธิระ\nรุเธียร\nรุน\nรุ่น\nรุบรู่\nรุม\nรุ่ม\nรุ่มร่าม\nรุย\nรุ่ย\nรุรุ\nรุหะ\nรู\nรู่\nรู้\nรูจี\nรูด\nรูทีเนียม\nรูบิเดียม\nรูป\nรูปิยะ\nรูปี\nรูเล็ตต์\nเร่\nเรข\nเรขา\nเรขาคณิต\nเร็ง\nเร่ง\nเร้ง\nเรณุ\nเรณู\nเรดอน\nเรดาร์\nเรเดียม\nเร้น\nเรรวน\nเรไร\nเร็ว\nเร่ว\nเรวดี\nเรอ\nเร่อ\nเรา\nเร่า\nเร้า\nเราะ\nเริง\nเริด\nเริม\nเริ่ม\nเริ้ม\nเริศร้าง\nเรี่ย\nเรี้ย\nเรียก\nเรียง\nเรียด\nเรียน\nเรียบ\nเรียม\nเรี่ยม\nเรียว\nเรี่ยว\nเรี้ยวรก\nเรือ\nเรื่อ\nเรื้อ\nเรือก\nเรือง\nเรื่อง\nเรื้อง\nเรืองรอง\nเรือด\nเรือน\nเรื้อน\nเรื่อย\nแร\nแร่\nแรก\nแร็กเกต\nแรง\nแร่ง\nแร้ง\nแรด\nแร้นแค้น\nแรม\nแร้ว\nแระ\nโร\nโร่\nโรค\nโรคา\nโรคาพาธ\nโรง\nโรจ\nโรจน์\nโรเดียม\nโรตี\nโรท\nโรธ\nโรม\nโรมัน\nโรเมอร์\nโรย\nโรเร\nโรหิณี\nโรหิต\nไร\nไร่\nไร้\nไรย์\nฤกษ์\nฤกษณะ\nฤคเวท\nฤชา\nฤชุ\nฤณ\nฤดี\nฤดียา\nฤดู\nฤต\nฤติยา\nฤตุ\nฤทธา\nฤทธิ์\nฤทัย\nฤษภ\nฤษยา\nฤษี\nฤๅ\nฤๅดี\nฤๅทัย\nฤๅษี\nฤๅสาย\nลก\nล่ก\nลฆุ\nลง\nล่ง\nลงกา\nล้งเล้ง\nลด\nลดา\nลดาวัลย์\nลน\nล้น\nลบ\nลบอง\nลพ\nลพุช\nลม\nล่ม\nล้ม\nลมาด\nลรรลุง\nลลนา\nลลิต\nลวก\nลวง\nล่วง\nล้วง\nลวณะ\nลวด\nล้วน\nลวนลาม\nลวนะ\nล่วม\nลวะ\nลวิตร\nลหุ\nลหุกาบัติ\nล่อ\nล้อ\nลอก\nล็อก\nล็อกเกต\nลอกแลก\nลอการิทึม\nลอง\nล่อง\nลองกอง\nลองจิจูด\nลองไน\nลอด\nลอตเตอรี่\nลอน\nล่อน\nลอบ\nลอม\nล้อม\nลอมชอม\nลอมพอก\nลอย\nล่อย\nล่อแล่\nลอว์เรนเซียม\nลออ\nละ\nล่ะ\nละคร\nละติจูด\nละบม\nละบอง\nละบือ\nละเบ็ง\nละโบม\nละม่อม\nละมั่ง\nละมาน\nละม้าย\nละมุ\nละมุด\nละมุน\nละเมอ\nละเมาะ\nละเมิด\nละเมียด\nละแมะ\nละโมก\nละโมบ\nละไม\nละลวย\nละลอก\nละล้า\nละล้าละลัง\nละลาน\nละลาบละล้วง\nละลาย\nละล้าว\nละล่ำละลัก\nละลิบ\nละลุม\nละเลง\nละเล้า\nละเลาะ\nละเลิง\nละเลียด\nละเลียบ\nละไล้\nละว้า\nละวาด\nละเวง\nละแวก\nละโว้\nละหมาด\nละห้อย\nละหาน\nละหาร\nละหุ่ง\nละเหย\nละเหี่ย\nละอง\nละออง\nละอาย\nละเอียด\nละแอน\nลัก\nลักขณะ\nลักขณา\nลักขะ\nลักขี\nลักจั่น\nลักปิดลักเปิด\nลักษณ์\nลักษณนาม\nลักษณะ\nลักษณาการ\nลักษมณ์\nลักษมาณา\nลักษมี\nลักษะ\nลัคคะ\nลัคน์\nลัคนา\nลัง\nลั่ง\nลังกา\nลังคี\nลังถึง\nลังลอง\nลังเล\nลังสาด\nลัชชา\nลัชชี\nลัญจ์\nลัญจกร\nลัญฉกร\nลัญฉน์\nลัฐิ\nลัฐิกา\nลัด\nลัดา\nลัทธ์\nลัทธิ\nลัน\nลั่น\nลันเต\nลันเตา\nลันไต\nลั่นทม\nลันโทม\nลับ\nลัพธ์\nลัพธิ\nลัภ\nลัภนะ\nลัภย์\nลัมพ์\nลัย\nลา\nล่า\nล้า\nลาก\nลาง\nล่าง\nล้าง\nลางลิง\nลางสาด\nลาช\nลาชะ\nลาชา\nลาญ\nลาด\nลาดเลา\nล้าต้า\nล่าเตียง\nลาน\nล่าน\nล้าน\nลาบ\nลาพอน\nลาภ\nลาม\nล่าม\nลามก\nลาย\nล้าย\nลายสือ\nลาลา\nลาว\nลาวัณย์\nลาวา\nลำ\nล่ำ\nล้ำ\nลำเข็ญ\nลำแข\nลำเค็ญ\nลำเจียก\nลำดวน\nลำดับ\nลำเนา\nลำบอง\nลำบาก\nลำปำ\nลำพวน\nลำพอง\nลำพัง\nลำพู\nลำเพ็ญ\nลำเพา\nลำแพน\nลำโพง\nลำไพ่\nลำภุขัน\nลำมะลอก\nลำยอง\nลำไย\nลำลอง\nล่ำลา\nลำลาบ\nลำลึก\nลำเลาะ\nลำเลิก\nลำเลียง\nลำเวียง\nลำเอียก\nลำเอียง\nลิ\nลิกขา\nลิกไนต์\nลิกู\nลิเก\nลิขนะ\nลิขสิทธิ์\nลิขิต\nลิง\nลิงค์\nลิด\nลิต\nลิตมัส\nลิตร\nลิเทียม\nลิ่น\nลิ้น\nลินจง\nลิ้นจี่\nลินลา\nลินสีด\nลิ่นฮื้อ\nลินิน\nลิบ\nลิปดา\nลิปสติก\nลิปิ\nลิฟต์\nลิเภา\nลิ่ม\nลิ้ม\nลิมป์\nลิมปนะ\nลิลิต\nลิว\nลิ่ว\nลิสง\nลี\nลี่\nลี้\nลีซอ\nลีบ\nลีลา\nลีลาศ\nลีฬหา\nลึก\nลึงค์\nลืด\nลื่น\nลื้น\nลืบ\nลืม\nลือ\nลื่อ\nลื้อ\nลุ\nลุก\nลุง\nลุ้ง\nลุ่น\nลุ้น\nลุพธ์\nลุ่ม\nลุมพี\nลุมพู\nลุย\nลุ่ย\nลุ้ย\nลู่\nลูก\nลูกระมาศ\nลูกเอ็น\nลูขะ\nลูทีเชียม\nลูบ\nเลก\nเล็ก\nเลข\nเลขา\nเลขาธิการ\nเลขานุการ\nเล็ง\nเล้ง\nเล่งฮื้อ\nเลเซอร์\nเลฑฑุ\nเลณฑุ\nเลณะ\nเล็ด\nเลน\nเล็น\nเล่น\nเลนส์\nเล็บ\nเลบง\nเลปกร\nเลปน์\nเลเป\nเลเพ\nเล็ม\nเล่ม\nเลย\nเลว\nเลวง\nเลวูโลส\nเลศ\nเลษฏุ\nเล่ห์\nเล่ห์กระเท่ห์\nเลหลัง\nเลหะ\nเลอ\nเล่อ\nเลอะ\nเลอะเทอะ\nเละ\nเละเทะ\nเลา\nเล่า\nเล้า\nเลากัย\nเล้าโลม\nเลาะ\nเลิก\nเลิ่กลั่ก\nเลิง\nเลิ้ง\nเลินเล่อ\nเลิศ\nเลีย\nเลียง\nเลี่ยง\nเลี้ยง\nเลียงผา\nเลียงฝ้าย\nเลียงมัน\nเลียน\nเลี่ยน\nเลียนไฟ\nเลียบ\nเลี่ยม\nเลียว\nเลี้ยว\nเลือก\nเลือง\nเลื่อง\nเลือด\nเลือน\nเลื่อน\nเลื่อม\nเลื่อย\nเลื้อย\nเลื่อยล้า\nแล\nแล่\nแล้\nแลก\nแล็กเกอร์\nแล็กโทส\nแลง\nแล่ง\nแล้ง\nแลน\nแล่น\nแลนทานัม\nแลบ\nแล้ว\nและ\nโล่\nโล้\nโลก\nโลกเชษฐ์\nโลกธรรม\nโลกธาตุ\nโลกนาถ\nโลกบาล\nโลกย์\nโลกัย\nโลกวัชชะ\nโลกวิทู\nโลกัตถจริยา\nโลกันตร์\nโลกา\nโลกาธิบดี\nโลกาธิปไตย\nโลกานุวัตร\nโลกาภิวัตน์\nโลกามิส\nโลกายัต\nโลกาวินาศ\nโลกิยะ\nโลกีย์\nโลกียวัตร\nโลกียวิสัย\nโลกียสุข\nโลกุตระ\nโลกุตรธรรม\nโลกุตรภูมิ\nโลง\nโล่ง\nโล้ง\nโล่งโจ้ง\nโล่งโต้ง\nโล้งโต้ง\nโลจนะ\nโลณะ\nโลด\nโล่ติ๊น\nโลโต\nโลท\nโลน\nโล้น\nโลภ\nโลม\nโลมเล้า\nโลมะ\nโลมา\nโลลุป\nโลเล\nโลโล\nโลโล้\nโลหะ\nโลหกุมภี\nโลหัช\nโลหิต\nไล่\nไล้\nไลย\nไลลา\nไล่เลี่ย\nฦๅ\nฦๅชา\nฦๅสาย\nวก\nวง\nวงก์\nวงกต\nวงศ์\nวงศกร\nวงศา\nวงษ์\nวจนะ\nวจี\nวชิระ\nวชิรปาณี\nวชิรหัตถ์\nวชิราวุธ\nวฏะ\nวฏาการ\nวณิช\nวณิชชา\nวณิชย์\nวณิชยา\nวณิพก\nวดี\nวทนะ\nวทัญญุตา\nวทัญญู\nวธุกา\nวธู\nวน\nวนศาสตร์\nวนสณฑ์\nวนสัณฑ์\nวนอุทยาน\nวนัส\nวนัสบดี\nวนา\nวนาดร\nวนาดอน\nวนานต์\nวนาลัย\nวนาลี\nวนาวาส\nวนาศรม\nวนาสณฑ์\nวนาสัณฑ์\nวนิดา\nวนิพก\nวเนจร\nวโนทยาน\nวยัคฆ์\nวยากรณ์\nวรดนู\nวรทาน\nวรมหาวิหาร\nวรงค์\nวรณะ\nวรรค\nวรรคย์\nวรรช\nวรรชย์\nวรรณะ\nวรรณกรรม\nวรรณคดี\nวรรณยุกต์\nวรรณยุต\nวรรณศิลป์\nวรรณนา\nวรรณพฤติ\nวรรณึก\nวรรธกะ\nวรรธนะ\nวรรษ\nวรรษา\nวรวิหาร\nวรัญญู\nวรางคณา\nวรางคนา\nวราห์\nวราหะ\nวรุณ\nวโรดม\nวฤก\nวลัช\nวลัญช์\nวลัญชน์\nวลัย\nวลาหก\nวลี\nวศค\nวศะ\nวศิน\nวสนะ\nวสภะ\nวสละ\nวสวัดดี\nวสวัตตี\nวสะ\nวสันต์\nวสันตดิลก\nวสันตฤดู\nวสันตวิษุวัต\nวสา\nวสี\nวสุ\nวสุธา\nวสุนธรา\nวสุมดี\nวหะ\nวอ\nวอก\nวอกแวก\nว่องไว\nวอด\nวอน\nว่อน\nว็อบ\nวอมแวม\nวอลเลย์บอล\nวอแว\nวะ\nวัก\nวักกะ\nวัคคีย์\nวัคคุ\nวัคซีน\nวัง\nวังก์\nวังชา\nวังเวง\nวังศะ\nวังสะ\nวัจจะ\nวัจกุฎี\nวัจฉละ\nวัจน์\nวัช\nวัชชะ\nวัชพืช\nวัชฌ์\nวัชระ\nวัชรปาณี\nวัชรยาน\nวัชรอาสน์\nวัชราสน์\nวัชรินทร์\nวัชรี\nวัชเรนทร์\nวัฏ\nวัฏฏะ\nวัฏจักร\nวัฏทุกข์\nวัฏสงสาร\nวัฏกะ\nวัฏฏิ\nวัฒกะ\nวัฒกี\nวัฒนธรรม\nวัฒนะ\nวัฒนา\nวัณ\nวัณโรค\nวัณฏ์\nวัณณะ\nวัณนา\nวัด\nวัต\nวัตต์\nวัตตา\nวัตถ์\nวัตถาภรณ์\nวัตถาลังการ\nวัตถุ\nวัตนะ\nวัตร\nวัตสดร\nวัตสะ\nวัติ\nวัทน์\nวัน\nวันต์\nวันทนา\nวันทนาการ\nวันทนีย์\nวันทยหัตถ์\nวันทยาวุธ\nวันทา\nวันทิ\nวับ\nวับวาบ\nวับวาม\nวับแวบ\nวับแวม\nวัปปะ\nวัมมิกะ\nวัย\nวัลก์\nวัลคุ\nวัลย์\nวัลลภ\nวัลลี\nวัว\nวัสสะ\nวัสโสทก\nวัสดุ\nวัสตร์\nวัสน์\nวัสนะ\nวัสสานะ\nวัสสานฤดู\nวา\nว่า\nว้า\nว้าเหว่\nวาก\nว้าก\nวากยสัมพันธ์\nวากยะ\nวาง\nว่าง\nว้าง\nวาจก\nวาจา\nวาจาไปยะ\nวาจาล\nวาชเปยะ\nวาณิช\nวาณิชกะ\nวาณิชย์\nวาณี\nวาด\nวาต\nวาตะ\nวาตภัย\nวาท\nวาทศาสตร์\nวาทศิลป์\nวาทกะ\nวาทนะ\nวาทย์\nวาทยกร\nวาทิต\nวาทิน\nวาที\nวาน\nวานซืน\nว่าน\nวานร\nวานรินทร์\nวาเนเดียม\nวาบ\nวาปี\nวาม\nวามน\nวามนาวตาร\nวามะ\nวาย\nว่าย\nว้าย\nวายะ\nวาโย\nวายามะ\nวายุ\nวายุกูล\nวาร\nวาระ\nวารสาร\nวารสารศาสตร์\nวาริ\nวารี\nวาริช\nวารีช\nวาริท\nวาริธร\nวารุณ\nวารุณี\nวาล\nวาลวีชนี\nวาล์ว\nวาลิกา\nวาลุกา\nวาว\nว่าว\nว้าว่อน\nว้าวุ่น\nวาสนะ\nวาสนา\nวาสพ\nวาสะ\nวาสิน\nวาสี\nวาสุกรี\nวาสุกี\nวาสุเทพ\nวาหนะ\nวาหะ\nวาหินี\nวาฬ\nวิกขัมภ์\nวิกขัมภนะ\nวิกเขป\nวิกรม\nวิกรัย\nวิกรานต์\nวิกฤต\nวิกฤติ\nวิกล\nวิกสิต\nวิกัต\nวิกัติ\nวิกัติการก\nวิกัป\nวิกัย\nวิการ\nวิกาล\nวิกาลโภชน์\nวิคหะ\nวิเคราะห์\nวิฆเนศ\nวิฆเนศวร\nวิฆาต\nวิง\nวิ่ง\nวิ่งเปี้ยว\nวิงวอน\nวิจฉิกะ\nวิจล\nวิจักขณ์\nวิจักษ์\nวิจักษณ์\nวิจัย\nวิจาร\nวิจารณ์\nวิจารณญาณ\nวิจิ\nวิจิกิจฉา\nวิจิต\nวิจิตร\nวิจิน\nวิจุณ\nวิจุรณ\nวิชชา\nวิชชุ\nวิชชุดา\nวิชชุตา\nวิชชุลดา\nวิชญะ\nวิชน\nวิชนี\nวิชย\nวิชัย\nวิชา\nวิชานนะ\nวิชิต\nวิเชียร\nวิญญัตติ\nวิญญาณ\nวิญญาณกทรัพย์\nวิญญู\nวิฑูรย์\nวิด\nวิตก\nวิตถาร\nวิตามิน\nวิถี\nวิทธะ\nวิทยฐานะ\nวิทยา\nวิทยาคม\nวิทยาคาร\nวิทยาลัย\nวิทยุ\nวิทยุต\nวิทวัส\nวิทัตถิ\nวิทัศน์\nวิทารณ์\nวิทิต\nวิทู\nวิทูร\nวิเทศ\nวิเทโศบาย\nวิธ\nวิธวา\nวิธาน\nวิธี\nวิธุระ\nวิธู\nวิธูปนะ\nวิ่น\nวินตกะ\nวินัย\nวินาที\nวินายก\nวินาศ\nวินิจ\nวินิจฉัย\nวินิต\nวินิบาต\nวินิปาติก\nวิเนต\nวิบัติ\nวิบาก\nวิบุล\nวิบุลย์\nวิบูล\nวิบูลย์\nวิปการ\nวิปฏิสาร\nวิปโยค\nวิประโยค\nวิปริต\nวิปลาส\nวิปวาส\nวิปักษ์\nวิปัสสก\nวิปัสสนา\nวิปัสสนายานิก\nวิพากษ์\nวิพิธทัศนา\nวิพุธ\nวิภว\nวิภวตัณหา\nวิภังค์\nวิภัช\nวิภัตติ\nวิภา\nวิภาค\nวิภาช\nวิภาดา\nวิภาวี\nวิภาษ\nวิภาส\nวิภู\nวิภูษณะ\nวิภูษา\nวิภูษิต\nวิมน\nวิมล\nวิมลัก\nวิมังสา\nวิมัติ\nวิมาน\nวิมุข\nวิมุต\nวิมุตติ\nวิเมลือง\nวิโมกข์\nวิโยค\nวิระ\nวิรงรอง\nวิรังรอง\nวิรัช\nวิรัต\nวิรัติ\nวิราคะ\nวิราม\nวิริยภาพ\nวิริยะ\nวิรุธ\nวิรุฬห์\nวิรุฬหก\nวิรูป\nวิรูปักษ์\nวิเรนทร์\nวิโรจ\nวิโรจน์\nวิโรฒ\nวิโรธ\nวิลันดา\nวิลัย\nวิลาด\nวิลาศ\nวิลาป\nวิลาวัณย์\nวิลาส\nวิลาสินี\nวิลิปดา\nวิลิศมาหรา\nวิเลป\nวิเลปนะ\nวิโลกนะ\nวิโลม\nวิไล\nวิไลวรรณ\nวิวรณ์\nวิวรรธน์\nวิวัฏ\nวิวัฒน์\nวิวัฒนาการ\nวิวัน\nวิวาท\nวิวาห์\nวิวาหมงคล\nวิวาหะ\nวิวิต\nวิวิธ\nวิเวก\nวิศรุต\nวิศว\nวิศวกร\nวิศวกรรม\nวิศวกรรมศาสตร์\nวิศัลย์\nวิศาขบูชา\nวิศาขา\nวิศาล\nวิศิษฏ์\nวิศุทธ์\nวิศุทธิ์\nวิเศษ\nวิเศษณ์\nวิษณุ\nวิษณุกรรม\nวิษธร\nวิษัย\nวิษาณ\nวิษุวัต\nวิสกี้\nวิสรรชนีย์\nวิสฤต\nวิสสุกรรม\nวิสัชนา\nวิสัญญี\nวิสัย\nวิสัยทัศน์\nวิสาขบูชา\nวิสาขะ\nวิสาขา\nวิสามัญ\nวิสามานยนาม\nวิสาร\nวิสารทะ\nวิสาล\nวิสาสะ\nวิสาหกิจ\nวิสิฐ\nวิสุงคามสีมา\nวิสุทธ์\nวิสุทธิ์\nวิสูตร\nวิเสท\nวิหค\nวิหลั่น\nวิหาร\nวิหิงสา\nวิเหสา\nวิฬาร\nวิฬาร์\nวี\nวีจิ\nวีชนี\nวีณา\nวี้ด\nวีรกรรม\nวีรชน\nวีรบุรุษ\nวีรสตรี\nวี่วัน\nวี่แวว\nวีสะ\nวุ้ง\nวุฐิ\nวุฒ\nวุฒิ\nวุด\nวุ่น\nวุ้น\nวุบ\nวุ้ย\nวุลแฟรม\nวู้\nวูดวาด\nวูบ\nวู่วาม\nเว้\nเวค\nเวคิน\nเวคี\nเวจ\nเวช\nเวชยันต์\nเวฐน์\nเวณิ\nเวณิก\nเวณุ\nเวตน์\nเวตร\nเวตาล\nเวท\nเวทคู\nเวทนา\nเวทย์\nเวทัลละ\nเวทางค์\nเวทางคศาสตร์\nเวทานต์\nเวทานตะ\nเวทิ\nเวที\nเวธะ\nเวน\nเว้น\nเวนไตย\nเวไนย\nเวมัต\nเว้ย\nเวยยากรณะ\nเวร\nเวรมณี\nเวรี\nเวโรจน์\nเวลา\nเวเลนซี\nเวศม์\nเวศย์\nเวศยา\nเวสน์\nเวสภู\nเวสม์\nเวสวัณ\nเวสสะ\nเวสสันดร\nเวสสุกรรม\nเวสสุวัณ\nเวสารัช\nเวสิยา\nเวหน\nเวหะ\nเวหา\nเวหาส\nเวฬุ\nเวฬุริยะ\nเว่อ\nเว้า\nเวิก\nเวิ้ง\nเวี่ย\nเวียง\nเวียด\nเวียดนาม\nเวียน\nเวียร\nเวี่ยว\nแว้\nแวง\nแว้ง\nแวด\nแว้ด\nแวน\nแว่น\nแวนดา\nแวบ\nแว็บ\nแวม\nแว็ม\nแวว\nแว่ว\nแวะ\nโว\nโว่\nโวการ\nโว่ง\nโวทาน\nโวย\nโว้ย\nโว้เว้\nโวหาร\nไว\nไว้\nไวกูณฐ์\nไวฑูรย์\nไวทย์\nไวน์\nไวพจน์\nไวยากรณ์\nไวยาวัจกร\nไวยาวัจมัย\nไวรัส\nไววรรณ\nไวษณพ\nไวโอลิน\nศก\nศกุน\nศกุนต์\nศกุนิ\nศกุนี\nศจี\nศตะ\nศตภิษัช\nศตวรรษ\nศตพรรษ\nศตกะ\nศนิ\nศพ\nศมนะ\nศมะ\nศยาม\nศยามล\nศร\nศรายุธ\nศราวรณ์\nศรรกรา\nศรวณะ\nศรวณีย์\nศรวิษฐา\nศรัณย์\nศรัณยู\nศรัท\nศรัทธา\nศรัย\nศราทธ์\nศราทธพรต\nศราพก\nศราวก\nศราวณะ\nศรี\nศรีตรัง\nศรุติ\nศฤคาล\nศฤงค์\nศฤงคาร\nศฤงคาริน\nศฤงคารี\nศลิษฏ์\nศลิษา\nศวะ\nศวัส\nศวา\nศวาน\nศศะ\nศศธร\nศศพินทุ์\nศศลักษณ์\nศศิ\nศศิน\nศศี\nศศิขัณฑ์\nศศิธร\nศศิมณฑล\nศศิวิมล\nศอ\nศอก\nศักดา\nศักดิ\nศักดิ์\nศักดินา\nศักติ\nศักย\nศักยภาพ\nศักย์\nศักยะ\nศักร\nศักรินทร์\nศักเรนทร์\nศักราช\nศังกร\nศัตรู\nศันสนะ\nศันสนีย์\nศัพท์\nศัยยา\nศัล\nศัลย์\nศัลยกรรม\nศัลยแพทย์\nศัลยศาสตร์\nศัสดร\nศัสตร\nศัสตรศาสตร์\nศัสตรา\nศัสตราวุธ\nศากตะ\nศากย\nศากยะ\nศากยพุทธ\nศากยมุนี\nศาฎก\nศาณ\nศานต์\nศานติ\nศาป\nศารท\nศารทูล\nศาริกา\nศาล\nศาลา\nศาศวัต\nศาสดา\nศาสตร์\nศาสตรา\nศาสตราจารย์\nศาสนา\nศาสนกิจ\nศาสนจักร\nศาสนธรรม\nศาสนบุคคล\nศาสนพิธี\nศาสนวัตถุ\nศาสนศาสตร์\nศาสนสถาน\nศาสนสมบัติ\nศาสนิกชน\nศาสนีย์\nศาสนูปถัมภก\nศาสน์\nศิกษก\nศิการ\nศิขร\nศิขริน\nศิขรี\nศิขัณฑ์\nศิคาล\nศิงขร\nศิงขริน\nศิตะ\nศิถี\nศิพิระ\nศิระ\nศิรประภา\nศิราภรณ์\nศิโรรัตน์\nศิโรเวฐน์\nศิรา\nศิรามพุช\nศิโรราบ\nศิลป\nศิลป์\nศิลปะ\nศิลปกร\nศิลปกรรม\nศิลปกิจ\nศิลปวัตถุ\nศิลปวิทยา\nศิลปศาสตร์\nศิลปศึกษา\nศิลปหัตถกรรม\nศิลปิน\nศิลปี\nศิลา\nศิวะ\nศิวโมกข์\nศิวลึงค์\nศิวเวท\nศิวาลัย\nศิศีระ\nศิษฎิ\nศิษฏ์\nศิษย์\nศิษยานุศิษย์\nศีขร\nศีต\nศีตกาล\nศีรษะ\nศีล\nศึก\nศึกษา\nศึกษาธิการ\nศึกษานิเทศก์\nศุกร์\nศุกรวรรณ\nศุกรวาร\nศุกระ\nศุกล\nศุกลปักษ์\nศุจิ\nศุทธะ\nศุทธิ\nศุนะ\nศุนิ\nศุภกร\nศุภเคราะห์\nศุภนิมิต\nศุภมัสดุ\nศุภมาตรา\nศุภมาส\nศุภอักษร\nศุภางค์\nศูกร\nศุลกากร\nศุลการักษ์\nศุลี\nศุษิร\nศูทร\nศูนย์\nศูนยวาท\nศูละ\nศูลิน\nเศรณี\nเศรษฐ\nเศรษฐ์\nเศรษฐกิจ\nเศรษฐศาสตร์\nเศรษฐี\nเศร้า\nเศลษ\nเศวต\nเศวตร\nเศวตัมพร\nเศษ\nเศาจ\nเศาร์\nเศารยะ\nเศิก\nเศียร\nโศก\nโศกา\nโศกาดูร\nโศกาลัย\nโศกี\nโศจิ\nโศธนะ\nโศภน\nโศภะ\nโศภา\nโศภิต\nโศภิน\nโศภิษฐ์\nโศภี\nโศรดา\nโศรตร\nโศลก\nไศล\nไศวะ\nษมา\nษัฏ\nษัฑ\nษัณ\nษัษ\nษัษฐะ\nษัษฐี\nโษฑศัน\nสก\nสกวาที\nสกฏะ\nสกทาคามิผล\nสกิทาคามิผล\nสกทาคามิมรรค\nสกิทาคามิมรรค\nสกทาคามี\nสกิทาคามี\nสกนธ์\nสกปรก\nสกรณีย์\nสกรรจ์\nสกรรมกริยา\nสกล\nสกลมหาสังฆปริณายก\nสกัด\nสกา\nสกาว\nสกี\nสกุณ\nสกุณา\nสกุณี\nสกุน\nสกุนต์\nสกุล\nสเกต\nสแกนเดียม\nสขะ\nสง\nส่ง\nสงกร\nสงกรานต์\nสงกา\nสงค์\nสงคร\nสงคราม\nสงเคราะห์\nสงฆ์\nสงบ\nสงวน\nส่งสการ\nสงสัย\nสงสาร\nสงสารวัฏ\nสงัด\nสง่า\nสฐะ\nสณฑ์\nสด\nสดมภ์\nสดับ\nสดับปกรณ์\nสดำ\nสดุดี\nสตะ\nสตน\nสตภิสชะ\nสตรอนเชียม\nสตริกนิน\nสตรี\nสตัฟฟ์\nสตัมภ์\nสตางค์\nสติ\nสติปัฏฐาน\nสตี\nสตู\nสตูป\nสเต๊ก\nสถบดี\nสถล\nสถวีระ\nสถาน\nสถานะ\nสถานี\nสถาบัน\nสถาปนา\nสถาปนิก\nสถาปัตยกรรม\nสถาปัตยกรรมศาสตร์\nสถาปัตยเรขา\nสถาปัตยเวท\nสถาพร\nสถาวร\nสถิต\nสถิตยศาสตร์\nสถิติ\nสถิร\nสถีรวาท\nสถุล\nสถูป\nสทิง\nสทึง\nสทุม\nสธนะ\nสาธุสะ\nสน\nส้น\nสนทนา\nสนทรรศ\nสนทรรศน์\nสนเทศ\nสนเท่ห์\nสนธยา\nสนธิ\nสนน\nสนม\nสนวน\nสนอง\nสนอบ\nสนอม\nสนะ\nสนัด\nสนั่น\nสนับ\nสนับทึบ\nสนับสนุน\nสนาน\nสนาม\nสนายุ\nสนิกะ\nสนิท\nสนิธ\nสนิม\nสนุก\nสนุกเกอร์\nสนุข\nสนุต\nสนุ่น\nสบ\nสบง\nสบถ\nสบัน\nสบาย\nสบู่\nสไบ\nสปริง\nสปอร์\nสปาเกตตี\nสเปกตรัม\nสเปกโทรสโกป\nสไปริลลัม\nสพาบ\nสภา\nสภาพ\nสภาวการณ์\nสภาวะ\nสม\nสมการ\nสมจารี\nสมดุล\nสมมูล\nส้ม\nสมญา\nสมณะ\nสมณบริขาร\nสมณศักดิ์\nสมณสารูป\nสมเด็จ\nสมถะ\nสมถยานิก\nสมถวิปัสสนา\nสมนาคุณ\nสมบัติ\nสมบุกสมบัน\nสมบูรณ์\nสมบูรณาญาสิทธิราชย์\nสมประดี\nสมปฤดี\nสมปฤๅดี\nส้มป่อย\nสมปัก\nสมผุส\nสมพง\nสมพงศ์\nสมพล\nสมพัตสร\nสมพาส\nสมเพช\nสมโพธน์\nสมโพธิ\nสมภพ\nสมภาร\nสมโภค\nสมโภช\nสมมต\nสมมติ\nสมมุติ\nสมมาตร\nส้มมือ\nสมโมท\nสมโยค\nสมร\nสมรด\nสมรรถ\nสมรรถนะ\nสมรรถภาพ\nสมรส\nสมฤดี\nสมฤติ\nสมวายะ\nสมเสร็จ\nสมอ\nสมอง\nสมะ\nสมัคร\nสมังคี\nสมัช\nสมัชชา\nสมัญญา\nสมัต\nสมัน\nสมันต์\nสมัย\nสมา\nสมาคม\nสมาจาร\nสมาชิก\nสมาทาน\nสมาธิ\nสมาน\nสมานฉันท์\nสมาบัติ\nสมาพันธรัฐ\nสมาส\nสม่ำเสมอ\nสมิง\nสมิต\nสมิติ\nสมิทธ์\nสมิทธิ\nสมี\nสมุก\nสมุจจัย\nสมุจเฉท\nสมุฏฐาน\nสมุด\nสมุทร\nสมุทรโคดม\nสมุทัย\nสมุน\nสมุนไพร\nสมุลแว้ง\nสมุห\nสมุห์\nสมุหกลาโหม\nสมุหเทศาภิบาล\nสมุหนาม\nสมุหนายก\nสโมธาน\nสโมสร\nสยด\nสยนะ\nสยบ\nสยมพร\nสยมภู\nสยอง\nสยอน\nสยัมวรา\nสยาม\nสยามานุสติ\nสยามินทร์\nสยาย\nสยิว\nสยิ้ว\nสยุมพร\nสยุมภู\nสร\nสรง\nสร่ง\nสรณะ\nสรณคมน์\nสรณาคมน์\nสรณตรัย\nสรตะ\nสรทะ\nสรนุก\nสรเนาะ\nสรไน\nสรเพชญ\nสรภะ\nสรภัญญะ\nสรภู\nสรม\nสรร\nสรรค์\nสรรพ\nสรรพคุณ\nสรรพนาม\nสรรพสามิต\nสรรพัชญ\nสรรพากร\nสรรพางค์\nสรรเพชญ\nสรรเพชุดา\nสรรเสริญ\nสรลอน\nสรเลข\nสรวง\nสรวม\nสรวล\nสรเสริญ\nสร้อย\nสระ\nสระกอ\nสระท้อน\nสระพรั่ง\nสระอาด\nสรั่ง\nสรัสวดี\nสร่าง\nสร้าง\nสราญ\nสรี้\nสรีระ\nสรีรกิจ\nสรีรธาตุ\nสรีรวิทยา\nสรีรศาสตร์\nสรีรังคาร\nสรีรางคาร\nสรุป\nสโรช\nสโรชะ\nสฤก\nสฤต\nสฤษฎิ\nสฤษฎี\nสฤษฏ์\nสฤษดิ์\nสลด\nสลบ\nสลวน\nสลวย\nสลอด\nสลอน\nสลอย\nสละ\nสลัก\nสลัด\nสลัดได\nสลับ\nสลัว\nสลา\nสลาก\nสลาง\nสล้าง\nสลาด\nสลาตัน\nสลาบ\nสลาย\nสลิด\nสลิล\nสลึก\nสลึง\nสลุต\nสลุบ\nสลุมพร\nสแลง\nสวการย์\nสวภาพ\nสวราชย์\nสวก\nส้วง\nสวด\nสวน\nสวนะ\nสวนาการ\nส่วน\nสวนิต\nสวบ\nสวม\nส้วม\nสวย\nส่วย\nส้วย\nสวยม\nสวรรค\nสวรรค์\nสวรรคต\nสวรรคาลัย\nสวรรยา\nสวระ\nสวะ\nสวัสดิ\nสวัสดิ์\nสวัสดิการ\nสวัสดิภาพ\nสวัสดิมงคล\nสวัสดี\nสวัสติ\nสวาตี\nสวัสติกะ\nสวา\nสวาปาม\nสวาคตะ\nสวาง\nสว่าง\nสวาด\nสวาดิ\nสวาท\nสว่าน\nสว้าน\nสวาบ\nสวามิ\nสวามี\nสวามินี\nสวาย\nสวาสดิ์\nสวาหะ\nสวิง\nสวิญญาณกทรัพย์\nสวิตช์\nสสาร\nสสุระ\nสสุรี\nสหกรณ์\nสหการ\nสหจร\nสหชาต\nสหชาติ\nสหธรรม\nสหธรรมิก\nสหประชาชาติ\nสหพันธ์\nสหพันธรัฐ\nสหภาพ\nสหศึกษา\nสหัช\nสหัมบดี\nสหัส\nสหัสสะ\nสหัสธารา\nสหัสนัยน์\nสหัสเนตร\nสหัสรังสี\nสหัสา\nสหาย\nสอ\nส่อ\nสอง\nส่อง\nส้อง\nสอด\nสอน\nส่อน\nสอบ\nสอพลอ\nส้อม\nสอย\nสะ\nสะกด\nสะกอ\nสะกาง\nสะการะ\nสะกิด\nสะกิดสะเกา\nสะเก็ด\nสะแก\nสะคร้อ\nสะคราญ\nสะค้าน\nสะเงาะสะแงะ\nสะดม\nสะดวก\nสะดิ้ง\nสะดึง\nสะดือ\nสะดุ้ง\nสะดุด\nสะเด็ด\nสะเดา\nสะเดาะ\nสะตอ\nสะตาหมัน\nสะตึ\nสะตือ\nสะตุ\nสะเต๊ะ\nสะโตก\nสะทก\nสะท้อน\nสะท้าน\nสะทึก\nสะเทิน\nสะเทิ้น\nสะเทือน\nสะเทื้อน\nสะบะ\nสะบัก\nสะบักสะบอม\nสะบัด\nสะบัดสะบิ้ง\nสะบั้น\nสะบันงา\nสะบ้า\nสะบู\nสะแบง\nสะเปะสะปะ\nสะพรั่ง\nสะพรึงกลัว\nสะพรึบ\nสะพรึ่บ\nสะพัก\nสะพัง\nสะพัด\nสะพั้น\nสะพาน\nสะพาย\nสะเพร่า\nสะโพก\nสะเภา\nสะใภ้\nสะโมง\nสะระตะ\nสะระแหน่\nสะลาง\nสะลาบ\nสะลึมสะลือ\nสะวี้ดสะว้าด\nสะสม\nสะสวย\nสะสาง\nสะเหล่อ\nสะอาง\nสะอาด\nสะอ้าน\nสะอิ้ง\nสะอิดสะเอียน\nสะอึก\nสะอื้น\nสะเอ้ง\nสะเอว\nสะเออะ\nสะโอดสะอง\nสะไอ\nสัก\nสักกะ\nสักยะ\nสักกัจจะ\nสักกายทิฐิ\nสักการ\nสักการะ\nสักขี\nสักวา\nสักหลาด\nสัค\nสัคคะ\nสั่ง\nสังกร\nสังกรณี\nสังกรประโยค\nสังกะตัง\nสังกะวัง\nสังกะวาด\nสังกะสี\nสังกัด\nสังกัปปะ\nสังกา\nสังการ\nสังกาศ\nสังกิเลส\nสังเกต\nสังข์\nสังขกร\nสังขตธรรม\nสังขตะ\nสังขยา\nสังขลิก\nสังขลิกา\nสังขาร\nสังขารา\nสังเขป\nสังค์\nสังคญาติ\nสังคม\nสังคหะ\nสังคัง\nสังคายนา\nสังคายนาย\nสังคีต\nสังคีติ\nสังเค็ด\nสังเคราะห์\nสังฆกรรม\nสังฆการี\nสังฆเถระ\nสังฆทาน\nสังฆนายก\nสังฆปาโมกข์\nสังฆภัต\nสังฆเภท\nสังฆมณฑล\nสังฆมนตรี\nสังฆราช\nสังฆสภา\nสังฆาณัติ\nสังฆาฏิ\nสังฆาทิเสส\nสังฆาธิการ\nสังฆานุสติ\nสังฆาวาส\nสังยุตนิกาย\nสังโยค\nสังโยชน์\nสังวร\nสังวัจฉระ\nสังวัธยาย\nสังวาล\nสังวาส\nสังเวคะ\nสังเวช\nสังเวชนียสถาน\nสังเวย\nสังเวียน\nสังสกฤต\nสังสการ\nสังสนทนา\nสั่งสนทนา\nสังสรรค์\nสังสารวัฏ\nสังสิทธิ\nสังสุทธ์\nสังสุทธิ\nสังหร\nสังหรณ์\nสังหาร\nสังหาริมทรัพย์\nสังหาริมะ\nสังหิต\nสัจ\nสัจกิริยา\nสัจจะ\nสัจญาณ\nสัจธรรม\nสัจนิยม\nสัจพจน์\nสัชฌะ\nสัชฌุ\nสัญจร\nสัญเจตนา\nสัญชาตญาณ\nสัญชาติ\nสัญฌา\nสัญญา\nสัญญาณ\nสัญญี\nสัญโญชน์\nสัญนิยม\nสัญประกาศ\nสัญลักษณ์\nสัฐิ\nสัณฐาน\nสัณฐิติ\nสัณฑ์\nสัณห์\nสัด\nสัดจอง\nสัต\nสัตตะ\nสัตตาหกรณียะ\nสัตตาหกาลิก\nสัตมวาร\nสัตสดก\nสัตตบงกช\nสัตตบรรณ\nสัตตบุษย์\nสัตตู\nสัตถันดร\nสัตถา\nสัตถิ\nสัตถุ\nสัตถุศาสนา\nสัตบรรณ\nสัตย์\nสัตยพรต\nสัตยวาที\nสัตยาเคราะห์\nสัตยาธิษฐาน\nสัตยาบัน\nสัตว์\nสัตวชาติ\nสัตวบาล\nสัตวแพทย์\nสัตววิทยา\nสัตวา\nสัทธรรม\nสัทธา\nสัทธาจริต\nสัทธาธิกะ\nสัทธินทรีย์\nสัทธิงวิหาริก\nสัทธิวิหาริก\nสัทวิทยา\nสัทศาสตร์\nสัทอักษร\nสัน\nสั่น\nสั้น\nสันดาน\nสันดาป\nสันโดษ\nสันต์\nสันตติ\nสันตะปาปา\nสันตะวา\nสันติ\nสันตุฏฐี\nสันถวไมตรี\nสันถวะ\nสันถัต\nสันถาร\nสันทนะ\nสันทะ\nสันทัด\nสันทัสนะ\nสันทาน\nสันทิฐิก\nสันทิส\nสันเทหะ\nสันธาน\nสันนิธิ\nสันนิบาต\nสันนิวาส\nสันนิษฐาน\nสันสกฤต\nสับ\nสับปลับ\nสับปลี้\nสับปะรด\nสัปคับ\nสัปดาห์\nสัปดาหะ\nสัปดน\nสัปตศก\nสัปทน\nสัปปะ\nสัปปิ\nสัปปุริส\nสัปปุรุษ\nสัประยุทธ์\nสัปหงก\nสัปเหร่อ\nสัพ\nสัพพะ\nสัพพัญญู\nสัพเพเหระ\nสัพยอก\nสัมบูรณ์\nสัมปชัญญะ\nสัมปทา\nสัมปทาน\nสัมปยุต\nสัมปโยค\nสัมประสิทธิ์\nสัมประหาร\nสัมปรายภพ\nสัมปรายิกภพ\nสัมปัตติ\nสัมผัปลาป\nสัมผัปลาปะ\nสัมผัส\nสัมพล\nสัมพหุลา\nสัมพัจฉรฉินท์\nสัมพัตสร\nสัมพัทธ์\nสัมพันธ์\nสัมพันธน์\nสัมพันธภาพ\nสัมพันธมิตร\nสัมพันธไมตรี\nสัมพาหะ\nสัมพุทธ\nสัมพุทธะ\nสัมโพธิ\nสัมภวะ\nสัมภเวสี\nสัมภัต\nสัมภัตตะ\nสัมภาระ\nสัมภาษณ์\nสัมโภคกาย\nสัมมนา\nสัมมัปธาน\nสัมมา\nสัมโมทนียกถา\nสัมฤทธิ\nสัมฤทธิ์\nสัมฤทธิศก\nสัยน์\nสัลเลข\nสัสดี\nสัสตทิฐิ\nสัสสะ\nสัสสุ\nสัสสู\nสา\nส่า\nสาก\nสากรรจ์\nสากล\nสากัจฉา\nสากัลย์\nสากิยะ\nสาเก\nสาขา\nสาคร\nสาคเรศ\nสาคู\nสาง\nส้าง\nสาชล\nสาฎก\nสาฏิก\nสาณี\nสาด\nสาไถย\nสาทร\nสาทิส\nสาทุ\nสาโท\nสาธก\nสาธยะ\nสาธยาย\nสาธารณะ\nสาธารณชน\nสาธารณประโยชน์\nสาธารณภัย\nสาธารณรัฐ\nสาธารณสถาน\nสาธารณสมบัติ\nสาธารณสุข\nสาธารณูปการ\nสาธารณูปโภค\nสาธารณ์\nสาธิต\nสาธุ\nสาน\nส่าน\nสานุ\nสานู\nสานุศิษย์\nสาบ\nสาบสูญ\nสาบาน\nสาป\nสาปไตย\nสาม\nสามชุก\nสามเณร\nสามเณรี\nสามนต์\nสามนตราช\nสามยทรัพย์\nสามล\nสามหาว\nสามะ\nสามัคคี\nสามัญ\nสามัตถิยะ\nสามานย์\nสามานยนาม\nสามารถ\nสามิต\nสามินี\nสามิภักดิ์\nสามี\nสามีจิกรรม\nสาย\nส่าย\nส้าย\nสายชู\nสายัณห์\nสายาห์\nสาร\nสารคดี\nสารธรรม\nสารนิเทศ\nสารบบ\nสารบรรณ\nสารบัญ\nสารบาญ\nสารบาญชี\nสารประโยชน์\nสารสนเทศ\nสารทุกข์\nสารถี\nสารท\nสารพัด\nสารพัน\nสารพางค์\nสารภาพ\nสารภี\nสารวัตร\nสาระ\nสาระแน\nสาระพา\nสาระยำ\nสาระวารี\nสาระสะมา\nสารัตถประโยชน์\nสารัตถศึกษา\nสารัตถะ\nสารัทธ์\nสารัมภ์\nสาราณียกร\nสาราณียธรรม\nสาราณียะ\nสารานุกรม\nสารีริกธาตุ\nสารูป\nสาโรช\nสาละ\nสาละวน\nสาลิ\nสาลิกา\nสาลินี\nสาลี\nสาลี่\nสาลู\nสาโลหิต\nสาว\nสาวก\nสาวิกา\nสาวิตร\nสาวิตรี\nสาสน\nสาสน์\nสาส์น\nสาสนา\nสาสม\nสาหร่าย\nสาหรี\nส่าหรี\nสาหัส\nสาเหตุ\nสาแหรก\nสำ\nสำส่อน\nส่ำ\nสำคัญ\nสำซ่าง\nสำแดง\nสำทับ\nสำนวน\nสำนอง\nสำนัก\nสำนาน\nสำนึก\nสำนึง\nสำเนา\nสำเนียง\nสำบัด\nสำปะลอ\nสำปะหลัง\nสำปั้น\nสำปันนี\nสำเภา\nสำมะงา\nสำมะโน\nสำมะลอ\nสำมะเลเทเมา\nสำมะหา\nสำรด\nสำรวจ\nสำรวม\nสำรวย\nสำรวล\nสำรอก\nสำรอง\nสำรับ\nสำราก\nสำราญ\nสำริด\nสำเร็จ\nสำเรา\nสำเริง\nสำโรง\nสำลัก\nสำลาน\nสำลี\nสำแลง\nสำหรวด\nสำหรับ\nสำหา\nสำเหนียก\nสำเหร่\nสำออย\nสำอาง\nสิ\nสิกข์\nสิข\nสิกขมานา\nสิกขา\nสิขร\nสิขรี\nสิขเรศ\nสิขา\nสิขานล\nสิขี\nสิคาล\nสิง\nสิ่ง\nสิงขร\nสิงค์\nสิงคลิ้ง\nสิงคลี\nสิงคาร\nสิงคาล\nสิงคี\nสิงโต\nสิงห์\nสิงหนาท\nสิงหบัญชร\nสิงหรา\nสิงหราช\nสิงหาคม\nสิงหาสน์\nสิงหล\nสิญจน์\nสิตะ\nสิตางศุ์\nสิถิล\nสิทธ์\nสิทธัตถะ\nสิทธา\nสิทธาจารย์\nสิทธารถ\nสิทธิ\nสิทธิ์\nสิทธิการิยะ\nสิธยะ\nสิน\nสิ้น\nสินเทา\nสินธพ\nสินธุ\nสินธุ์\nสินธุระ\nสินธู\nสินเธาว์\nสินาด\nสินิทธ์\nสินี\nสิเนรุ\nสิเนหก\nสิเนหะ\nสิเนหา\nสิเน่หา\nสิบ\nสิปปะ\nสิมพลี\nสิระ\nสิโรดม\nสิโรตม์\nสิริ\nสิรี\nสิลา\nสิว\nสิ่ว\nสิวะ\nสิวาลัย\nสิวิกา\nสี\nสี่\nสี้\nสีกา\nสีกุน\nสีข้าง\nสีด\nสีดอ\nสีดา\nสีตลรัศมี\nสีตโลทก\nสีโตทก\nสีทันดร\nสีมันต์\nสีมา\nสีละมัน\nสีวิกา\nสีสอ\nสีสะ\nสีสา\nสีสุก\nสีเสียด\nสีห์\nสีหนาท\nสีหบัญชร\nสีหราช\nสีหไสยา\nสีหไสยาสน์\nสีหะ\nสึก\nสึง\nสืบ\nสื่อ\nสุ\nสุก\nสุกข์\nสุกร\nสุกรม\nสุกำศพ\nสุกียากี้\nสุข\nสุขา\nสุขาภิบาล\nสุขารมณ์\nสุขาวดี\nสุขิน\nสุขี\nสุขุม\nสุขุมาล\nสุโข\nสุคต\nสุคติ\nสุคนธ\nสุคนธ์\nสุคนธชาติ\nสุคนธรส\nสุคันธ์\nสุคันธรส\nสุงกะ\nสุงกากร\nสุงสิง\nสุงสุมาร\nสุจริต\nสุจหนี่\nสุจิ\nสุจิต\nสุจิตร\nสุชน\nสุชัมบดี\nสุชา\nสุชาดา\nสุญ\nสุญญากาศ\nสุญตา\nสุญนิยม\nสุณ\nสุณิสา\nสุด\nสุดา\nสุต\nสุตตนิบาต\nสุตตะ\nสุตตันตปิฎก\nสุตตันตะ\nสุติ\nสุทธ\nสุทธ์\nสุทธาวาส\nสุทธิ\nสุทรรศน์\nสุทัศน์\nสุธา\nสุธาโภชน์\nสุธารส\nสุธาสินี\nสุธาสี\nสุธี\nสุนทร\nสุนทรี\nสุนทรียภาพ\nสุนทรียศาสตร์\nสุนทรียะ\nสุนัข\nสุนันท์\nสุโนก\nสุบดี\nสุบรรณ\nสุบิน\nสุปรีดิ์\nสุปรีย์\nสุปาณี\nสุพพัต\nสุพรรณ\nสุพรรณบัฏ\nสุพรรณภาชน์\nสุพรรณราช\nสุพรรณศรี\nสุพรรณถัน\nสุพรรณิการ์\nสุภร\nสุภัค\nสุภา\nสุภาพ\nสุภาษิต\nสุม\nสุ่ม\nสุมทุม\nสุมน\nสุมนะ\nสุมนัส\nสุมนา\nสุ้มเสียง\nสุมะ\nสุมาลี\nสุเมธ\nสุเมรุ\nสุรคต\nสุรเชษฐ์\nสุรบดี\nสุรภาพ\nสุรโลก\nสุรสีหนาท\nสุรเสียง\nสุรงค์\nสุรังค์\nสุรภี\nสุรัติ\nสุรัสวดี\nสุรา\nสุรางค์จำเรียง\nสุรางคนา\nสุรางคนางค์\nสุรารักษ์\nสุราลัย\nสุรินทร์\nสุรินทราหู\nสุริยะ\nสุริยกันต์\nสุริยกานต์\nสุริยการ\nสุริยกาล\nสุริยคติ\nสุริยคราส\nสุริยมณฑล\nสุริยวงศ์\nสุริยง\nสุริยา\nสุริเยนทร์\nสุริเยศ\nสุริโย\nสุริยน\nสุริยัน\nสุริยุปราคา\nสุรีย์\nสุรุ่ยสุร่าย\nสุลต่าน\nสุวคนธ์\nสุวภาพ\nสุวรรณ\nสุวรรณภูมิ\nสุวะ\nสุวาน\nสุวินัย\nสุวิมล\nสุษิระ\nสุสาน\nสุหนัต\nสุหร่ง\nสุหร่าย\nสุหฤท\nสุหัท\nสุเหร่า\nสู\nสู่\nสู้\nสูง\nสูจิ\nสูจิบัตร\nสูญ\nสูด\nสูต\nสูตร\nสูติ\nสูติกรรม\nสูตินรีเวช\nสูติบัตร\nสูติแพทย์\nสูติศาสตร์\nสูท\nสูทกรรม\nสูทศาสตร์\nสูบ\nสูปะ\nสูร\nสูรย์\nสูรยกานต์\nสูริ\nสูสี\nเส\nเสก\nเสกขบุคคล\nเสกขะ\nเสขบุคคล\nเสขะ\nเส็ง\nเส้ง\nเส็งเคร็ง\nเสงี่ยม\nเสฏฐี\nเสณี\nเสด\nเสด็จ\nเสตุ\nเสถียร\nเสทะ\nเสโท\nเสน\nเส้น\nเสนง\nเสน่ง\nเสน่ห์\nเสนหา\nเสน่หา\nเสนอ\nเสนะ\nเสนา\nเสนาธิการ\nเสนาบดี\nเสน่า\nเสนากุฎ\nเสนางค์\nเสนางคนิกร\nเสนานี\nเสนาสนะ\nเสนาะ\nเสนี\nเสนีย์\nเสนียะ\nเสนียด\nเสบย\nเสบียง\nเสพ\nเสพย์\nเสเพล\nเสภา\nเสม็ด\nเสมหะ\nเสมอ\nเสมา\nเสมียน\nเสมือน\nเสย\nเสร็จ\nเสริด\nเสริม\nเสรี\nเสลด\nเสลบรรพต\nเสลา\nเสลี่ยง\nเสลือกสลน\nเสโล\nเสวก\nเสวกามาตย์\nเสวนะ\nเสวนา\nเสวย\nเสวียน\nเสสรวง\nเสสรวล\nเสา\nเส้า\nเสาร์\nเสารภย์\nเสารี\nเสาวคนธ์\nเสาวธาร\nเสาวภา\nเสาวภาคย์\nเสาวภาพ\nเสาวรภย์\nเสาวรส\nเสาวลักษณ์\nเสาวณิต\nเสาวนะ\nเสาวนา\nเสาวนีย์\nเสาหฤท\nเสาะ\nเสาะแสะ\nเสิร์จ\nเสิร์ฟ\nเสีย\nเสียง\nเสี่ยง\nเสียด\nเสี้ยน\nเสียบ\nเสียม\nเสี่ยม\nเสี้ยม\nเสียว\nเสี่ยว\nเสี้ยว\nเสือ\nเสื่อ\nเสื้อ\nเสือก\nเสื่อม\nแส\nแส่\nแส้\nแสก\nแสง\nแสด\nแสดง\nแสตมป์\nแสน\nแสนย์\nแสนยากร\nแสนยานุภาพ\nแสบ\nแสม\nแสยก\nแสยง\nแสยะ\nแสรก\nแสร้ง\nแสลง\nแสล้ม\nแสวง\nแสะ\nโสก\nโสกโดก\nโสกันต์\nโสโครก\nโสณฑ์\nโสณิ\nโสณี\nโสด\nโสดก\nโสดม\nโสดา\nโสดาบัน\nโสดาปัตติผล\nโสดาปัตติมรรค\nโสต\nโสตทัศนวัสดุ\nโสตทัศนอุปกรณ์\nโสตทัศนูปกรณ์\nโสตินทรีย์\nโสตถิ\nโสทก\nโสทร\nโสธก\nโสธนะ\nโสน\nโสภณ\nโสภา\nโสภี\nโสภิณี\nโสเภณี\nโสม\nโสมนัส\nโสมม\nโสมย์\nโสร่ง\nโสรจ\nโสรวาร\nโสโร\nโสวรรณ\nโสหุ้ย\nโสฬส\nใส\nใส่\nไส\nไส้\nไสย\nไสยา\nไสยาสน์\nไสร้\nไสว\nหก\nหกคะเมน\nหง\nหงก\nหงส์\nหงสบาท\nหงสรถ\nหงอ\nหงอก\nหง่อง\nหงองแหงง\nหงอด\nหงอน\nหง่อม\nหงอย\nหง่อย\nหงัก\nหงับ\nหง่าง\nหงาย\nหง่าว\nหงำ\nหงิก\nหงิง\nหงิม\nหงึก\nหงุงหงิง\nหงุดหงิด\nหงุบ\nหงุ่ย\nหญ้า\nหญ้าฝรั่น\nหญ้ายายเภา\nหญิง\nหญิบ\nหด\nหตะ\nหทัย\nหน\nหนวก\nหน่วง\nหนวด\nหน่วย\nหน่วยกิต\nหนอ\nหน่อ\nหนอก\nหนอง\nหนอน\nหนอนตายหยาก\nหน่อย\nหน็อยแน่\nหนัก\nหนัง\nหนังสติ๊ก\nหนังสือ\nหนั่น\nหนับ\nหนา\nหน้า\nหน่าง\nหนาด\nหนาน\nหนาม\nหน่าย\nหนาว\nหนำ\nหนำเลี้ยบ\nหนี\nหนี้\nหนีบ\nหนึก\nหนึ่ง\nหนึบ\nหนืด\nหนุ\nหนุน\nหนุบ\nหนุ่ม\nหนุ่ย\nหนู\nห่ม\nหมก\nหมด\nหม่น\nหมวก\nหมวด\nหมวน\nหมอ\nหม่อ\nหม้อ\nหมอก\nหมอง\nหม่อง\nหมอน\nหม่อน\nหมอบ\nหม่อม\nหมอย\nหม้อห้อม\nหมัก\nหมักหมม\nหมัด\nหมัน\nหมั่น\nหมั้น\nหมับ\nหมา\nหม่า\nหมาก\nหมากฮอส\nหมาง\nหมาด\nหมามุ่ย\nหมามุ้ย\nหมาย\nหม้าย\nหมาร่า\nหม่ำ\nหม้ำ\nหมิ่น\nหมี\nหมี่\nหมึก\nหมืน\nหมื่น\nหมุด\nหมุน\nหมุบ\nหมุบหมับ\nหมุบหมิบ\nหมุ่ย\nหมุยขาว\nหมู\nหมู่\nหมูหริ่ง\nหยก\nหย่ง\nหยด\nหยวก\nหยวบ\nหยอก\nหยอกเอิน\nหย็อกหย็อย\nหยอง\nหย็อง\nหย่อง\nหย็องกรอด\nหย็องแหย็ง\nหยอด\nหยอน\nหย่อน\nหย่อม\nหย็อมแหย็ม\nหย็อย\nหย่อย\nหยัก\nหยักไย่\nหยักเหยา\nหยัง\nหยั่ง\nหยังหยัง\nหยัด\nหยัน\nหยับ\nหยั่วเมือง\nหย่า\nหยากเยื่อ\nหยากไย่\nหยาด\nหยาบ\nหยาม\nหยาว\nหย้าว\nหยำเป\nหยำเหยอะ\nหยำแหยะ\nหยิก\nหยิ่ง\nหยิบ\nหยิม\nหยี\nหยี่\nหยุกหยิก\nหยุด\nหยุ่น\nหยุบ\nหยุมหยิม\nหยูกยา\nหโยดม\nหรคุณ\nหรณะ\nหรดาล\nหรดี\nหรรษ์\nหรรษา\nหรอ\nหรอก\nหร็อมแหร็ม\nหรอย\nหระ\nหรับ\nหรา\nหริ\nหริ่ง\nหริณะ\nหริต\nหริตกี\nหรีตกี\nหรี่\nหรีด\nหรือ\nหรุบ\nหรุบรู่\nหรุบหรู่\nหรุ่ม\nหรู\nหรูหรา\nหฤทัย\nหฤทย์\nหฤษฎ์\nหฤษฎี\nหฤหรรษ์\nหฤโหด\nหลง\nหลงใหล\nหลงจู๊\nหลด\nหลน\nหล่น\nหลบ\nหล่ม\nหลวง\nหลวม\nหลอ\nหล่อ\nหลอก\nหลอด\nหลอน\nหล็อน\nหล่อน\nหลอม\nหละ\nหละหลวม\nหลัก\nหลัง\nหลั่ง\nหลัด\nหลั่น\nหลับ\nหลัว\nหลา\nหล้า\nหลาก\nหลาน\nหลาบ\nหลาม\nหลาย\nหลาว\nหลิ่ง\nหลิท\nหลิน\nหลิม\nหลิว\nหลิ่ว\nหลี\nหลีก\nหลีโก\nหลีบ\nหลีฮื้อ\nหลืบ\nหลุกหลิก\nหลุด\nหลุน\nหลุบ\nหลุม\nหลุมพอ\nหลุมพี\nหลู่\nหวง\nห่วง\nห้วง\nหวด\nหวน\nห้วน\nหวย\nห้วย\nหวอ\nหวอด\nหวะ\nหวัง\nหวัด\nหวั่น\nหวันยิหวา\nหวัว\nหวัวร่อ\nหวัวเราะ\nหวา\nหว่า\nหว้า\nหวาก\nหว่าง\nหวาด\nหวาน\nหว่าน\nหวาม\nหวาย\nหวำ\nหวิด\nหวิว\nหวี\nหวี่\nหวีด\nหวือ\nหวุดหวิด\nหวูด\nหอ\nห่อ\nห้อ\nหอก\nหอง\nห้อง\nหอน\nห่อน\nหอบ\nหอม\nห้อม\nหอย\nห้อย\nหะ\nหะยี\nหะหาย\nหัก\nหัจญ์\nหัจญี\nหัช\nหัฏฐะ\nหัด\nหัต\nหัตถ์\nหัตถกรรม\nหัตถการ\nหัตถกิจ\nหัตถบาส\nหัตถพันธ์\nหัตถาภรณ์\nหัตถศาสตร์\nหัตถศิลป์\nหัตถศึกษา\nหัตถาจารย์\nหัตถินี\nหัตถี\nหัน\nหั่น\nหั้น\nหันตรา\nหับ\nหัย\nหัว\nหัวร่อ\nหัวเราะ\nหัส\nหัสดิน\nหัสดี\nหัสต์\nหัสตะ\nหา\nห่า\nห้า\nหาก\nหาง\nห่าง\nห้าง\nหาญ\nหาด\nห่าน\nหาบ\nหาม\nห่าม\nห้าม\nหาย\nหายใจ\nหายนะ\nหาร\nหารือ\nหาว\nห้าว\nหาสะ\nหำ\nห้ำ\nหิ้ง\nหิงคุ\nหิงสา\nหิงห้อย\nหิ่งห้อย\nหิ่งหาย\nหิด\nหิต\nหิตานุหิตประโยชน์\nหิน\nหิมพาน\nหิมพานต์\nหิมวัต\nหิมวันต์\nหิมวา\nหิมะ\nหิมาลัย\nหิรัญ\nหิรัญญิการ์\nหิรัญบัฏ\nหิรัณย์\nหิรัณยรัศมี\nหิริ\nหิว\nหิ้ว\nหี\nหีด\nหีนยาน\nหีบ\nหึ\nหึง\nหึ่ง\nหึงสา\nหืด\nหืน\nหื่น\nหือ\nหื้อ\nหุง\nหุน\nหุ่น\nหุ้น\nหุนหัน\nหุบ\nหุ้ม\nหุยฮา\nหู\nหู่\nหูก\nหูด\nเห\nเห่\nเหง\nเหง่ง\nเหงา\nเหง้า\nเหงื่อ\nเหงือก\nเห็จ\nเห็ด\nเหติ\nเหตุ\nเห็น\nเหน่ง\nเหนงนายพราน\nเหน็ดเหนื่อย\nเหน็บ\nเหน่อ\nเห็นอ้ม\nเหนอะ\nเหนอะหนะ\nเหน้า\nเหนาะ\nเหนียง\nเหนี่ยง\nเหนี่ยน\nเหนียม\nเหนียว\nเหนี่ยว\nเหนือ\nเหนื่อย\nเห็บ\nเหม\nเหม่\nเหม็ง\nเหม่ง\nเหม็น\nเหมวดี\nเหม่อ\nเหมันต์\nเหมันตฤดู\nเหมา\nเหมายัน\nเหมาะ\nเหมียว\nเหมี่ยว\nเหมือง\nเหมือด\nเหมือน\nเหมื่อย\nเหย\nเหยง\nเหย่อย\nเหยา\nเหย่า\nเหย้า\nเหยาะ\nเหยาะแหยะ\nเหยิง\nเหยิบ\nเหยียด\nเหยียบ\nเหยี่ยว\nเหยื่อ\nเหยือก\nเหรอ\nเหรอะ\nเหรัญญิก\nเหรา\nเหราะ\nเหรียญ\nเหล่\nเหล็ก\nเหลน\nเหลว\nเหลอ\nเหลา\nเหล่า\nเหล้า\nเหลาะแหละ\nเหลิง\nเหลิงเจิ้ง\nเหลียน\nเหลี่ยม\nเหลียว\nเหลือ\nเหลือก\nเหลือง\nเหลือบ\nเหลือม\nเหลื่อม\nเหว\nเหว่\nเหวง\nเหวย\nเหวอะ\nเหวอะหวะ\nเหวี่ยง\nเห่อ\nเหอะ\nเหะ\nเหะหะ\nเหา\nเห่า\nเหาะ\nเหิน\nเหิม\nเหี้ย\nเหียง\nเหียน\nเหี้ยน\nเหี้ยม\nเหี่ยว\nเหื่อ\nเหือด\nแห\nแห่\nแห้\nแหก\nแหง\nแหง่\nแห่ง\nแห้ง\nแหงแก๋\nแหง่ง\nแหงน\nแหน\nแห้น\nแหนง\nแหนบ\nแหนม\nแหบ\nแหม\nแหม่\nแหม่ม\nแหมะ\nแหย\nแหย่\nแหยง\nแหย่ง\nแหยม\nแหย็ม\nแหยะ\nแหล่\nแหลก\nแหล่ง\nแหลน\nแหลม\nแหละ\nแหว\nแห้ว\nแหวก\nแหว่ง\nแหวด\nแหวน\nแหวะ\nแหะ\nโห่\nโหง\nโหด\nโหน\nโหนก\nโหน่ง\nโหม\nโหม่ง\nโหมด\nโหย\nโหยกเหยก\nโหยง\nโหย่ง\nโหร\nโหรง\nโหรงเหรง\nโหรดาจารย์\nโหระพา\nโหรา\nโหราจารย์\nโหราศาสตร์\nโหล\nโหล่\nโหลงโจ้ง\nโหว\nโหว่\nโหว้\nโหวกเหวก\nโหวง\nโหวด\nโหวต\nให้\nใหญ่\nใหม่\nไห\nไห่\nไห้\nไหน\nไหม\nไหม้\nไหรณย์\nไหล\nไหล่\nไหว\nไหว้\nไหหลำ\nอก\nอกตเวทิตา\nอกตเวที\nอกตัญญุตา\nอกตัญญู\nอกนิษฐ์\nอกรณีย์\nอกรรมกริยา\nอกัปปิยวัตถุ\nอกัปปิยะ\nอกุศล\nอคติ\nอคาธ\nอโฆษะ\nองก์\nองค์\nองคชาต\nองคมนตรี\nองครักษ์\nองคาพยพ\nองคุลี\nองศ์\nองศา\nองอาจ\nองุ่น\nอจลา\nอจินตา\nอจินไตย\nอจิระ\nอเจลก\nอเจละ\nอชะ\nอชิน\nอชินี\nอชิระ\nอฏวี\nอณิ\nอณู\nอโณทัย\nอด\nอดิถี\nอดิเทพ\nอดิเรก\nอดิศร\nอดิศวร\nอดิศัย\nอดีต\nอดุล\nอดุลย์\nอติ\nอติชาต\nอติมานะ\nอติราช\nอติเรก\nอติสาร\nอถรรพเวท\nอาถรรพเวท\nอทระ\nอทินนาทาน\nอธรรม\nอธิ\nอธิกมาส\nอธิกรณ์\nอธิกวาร\nอธิกสุรทิน\nอธิการ\nอธิคม\nอธิฏฐาน\nอธิบดี\nอธิบาย\nอธิป\nอธิปไตย\nอธิมาตร\nอธิมุตติ\nอธิโมกข์\nอธิราช\nอธิวาส\nอธิวาสนะ\nอธิศีล\nอธิษฐาน\nอธึก\nอ้น\nอนงค์\nอนงคณะ\nอนงคเลขา\nอนธการ\nอนนต์\nอนยะ\nอนรรฆ\nอนรรถ\nอนล\nอนวัช\nอนัญ\nอนัตตา\nอนันต์\nอนันตริยกรรม\nอนัม\nอนาคต\nอนาคามิผล\nอนาคามิมรรค\nอนาคามี\nอนาจาร\nอนาถ\nอนาถา\nอนาทร\nอนาธิปไตย\nอนามัย\nอนามิกา\nอนารยชน\nอนารยธรรม\nอนารยะ\nอนาลัย\nอนำ\nอนิจ\nอนิจจัง\nอนิจจา\nอนิฏฐารมณ์\nอนิยต\nอนิยม\nอนิล\nอนิวรรต\nอนิวรรตน์\nอนีกะ\nอนีจะ\nอนึก\nอนึ่ง\nอนุ\nอนุกร\nอนุกรม\nอนุกรรมการ\nอนุกระเบียด\nอนุกาชาด\nอนุการ\nอนุกูล\nอนุคามิก\nอนุเคราะห์\nอนุจร\nอนุช\nอนุชน\nอนุชา\nอนุชาต\nอนุชิต\nอนุญาต\nอนุญาโตตุลาการ\nอนุตร\nอนุเถระ\nอนุทิน\nอนุบท\nอนุบาล\nอนุประโยค\nอนุปริญญา\nอนุปสัมบัน\nอนุปัสนา\nอนุพงศ์\nอนุพัทธ์\nอนุพันธ์\nอนุโพธ\nอนุภรรยา\nอนุภริยา\nอนุภาค\nอนุภาษ\nอนุมัติ\nอนุมาตรา\nอนุมาน\nอนุมูล\nอนุโมทนา\nอนุโยค\nอนุรักษ์\nอนุรักษนิยม\nอนุราช\nอนุราธ\nอนุราธะ\nอนุราธา\nอนุรูป\nอนุโลม\nอนุวงศ์\nอนุวรรตน์\nอนุวัต\nอนุวัตน์\nอนุวัตร\nอนุวัติ\nอนุวาต\nอนุศาสก\nอนุศาสน์\nอนุศาสนาจารย์\nอนุศิษฏ์\nอนุสติ\nอนุสนธิ\nอนุสร\nอนุสรณ์\nอนุสัญญา\nอนุสัย\nอนุสาวรีย์\nอนุสาสนี\nอเนก\nอเนกคุณ\nอเนกรรถประโยค\nอเนจอนาถ\nอโนชา\nอโนดาต\nอบ\nอบเชย\nอบาย\nอปจายนธรรม\nอปจายนมัย\nอปมงคล\nอปยศ\nอประไมย\nอปรัณณชาติ\nอปรา\nอปราชัย\nอปราชิต\nอปริมาณ\nอปลักษณ์\nอปโลกน์\nอปวาท\nอเปหิ\nอพพะ\nอพยพ\nอภัพ\nอภัย\nอภิ\nอภิฆาต\nอภิชฌา\nอภิชน\nอภิชนาธิปไตย\nอภิชัย\nอภิชาต\nอภิชิต\nอภิญญา\nอภิญญาณ\nอภิธรรม\nอภิธาน\nอภิไธย\nอภินันท์\nอภินันทนาการ\nอภินัย\nอภินิหาร\nอภิเนษกรมณ์\nอภิบาล\nอภิปรัชญา\nอภิปราย\nอภิมหาอำนาจ\nอภิมานะ\nอภิมุข\nอภิรดี\nอภิรติ\nอภิรมย์\nอภิรักษ์\nอภิราม\nอภิรุต\nอภิรุม\nอภิรูป\nอภิลักขิต\nอภิลักขิตสมัย\nอภิเลปน์\nอภิวันท์\nอภิวาท\nอภิวาทน์\nอภิเษก\nอภิสมโพธิ\nอภิสมัย\nอภิสมาจาร\nอภิสัมโพธิ\nอภิสัมโพธิญาณ\nอภิสิต\nอภิสิทธิ์\nอภูตะ\nอม\nอมพะนำ\nอ้ม\nอมตธรรม\nอมตบท\nอมตะ\nอมนุษย์\nอมร\nอมรา\nอมราวดี\nอมรินทร์\nอมเรนทร์\nอมเรศ\nอมฤต\nอมัตร\nอมาตย์\nอมาวสี\nอมาวสุ\nอมาวาสี\nอมิตร\nอเมริกัน\nอย่า\nอยาก\nอย่าง\nอยุทธ์\nอยู่\nอร\nอรชร\nอรชุน\nอรดี\nอรติ\nอรทัย\nอรไท\nอรนุช\nอรพินท์\nอรพิม\nอรรค\nอรรฆ\nอรรฆย์\nอรรจน์\nอรรณพ\nอรรถ\nอรรถกถา\nอรรถกถาจารย์\nอรรถาธิบาย\nอรรธ\nอรสุม\nอรหะ\nอรหัง\nอรหัต\nอรหัตผล\nอรหัตมรรค\nอรหัน\nอรหันต์\nอรหันตฆาต\nอร่อย\nอรัญ\nอรัญญิก\nอรัญวาส\nอรัญวาสี\nอรัณย์\nอราดี\nอร่าม\nอริ\nอรินทร์\nอริน\nอริยกะ\nอริยทรัพย์\nอริยบุคคล\nอริยผล\nอริยมรรค\nอริยสั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nอำพล\nอำพะนำ\nอำพัน\nอำไพ\nอำเภอ\nอำมร\nอำมฤคโชค\nอำมฤต\nอำมหิต\nอำมาตย์\nอำมาตยาธิปไตย\nอำยวน\nอำรุง\nอำลา\nอำอวม\nอ้ำอึ้ง\nอิก\nอิง\nอิงค์\nอิงอร\nอิจฉา\nอิฉัน\nอิชยา\nอิฏฐารมณ์\nอิฐ\nอิฐผล\nอิด\nอิตถี\nอิตเทรียม\nอิตเทอร์เบียม\nอิติวุตตกะ\nอิทธิ\nอิน\nอินซูลิน\nอินเดีย\nอินเดียนแดง\nอินเดียม\nอินท์\nอินทขีล\nอินทนิล\nอินทผลัม\nอินทร์\nอินทรธนู\nอินทรวงศ์\nอินทรวิเชียร\nอินทรศักดิ์\nอินทราณี\nอินทราภิเษก\nอินทรายุธ\nอินทรี\nอินทรีย์\nอินทรียสังวร\nอินทีวร\nอินทุ\nอินฟราเรด\nอินัง\nอิ่ม\nอิมัลชัน\nอิริเดียม\nอิริยา\nอิริยาบถ\nอิรุพเพท\nอิเล็กตรอน\nอิเล็กทรอนิกส์\nอิเล็กโทน\nอิศร\nอิศวร\nอิษฏ์\nอิษฏี\nอิส\nอิสตรี\nอิสัตรี\nอิสรภาพ\nอิสระ\nอิสริยยศ\nอิสริยะ\nอิสริยาภรณ์\nอิสลาม\nอิสสา\nอิสิ\nอิสี\nอิหม่าม\nอิหลักอิเหลื่อ\nอี\nอี่\nอี้\nอี๊\nอี๋\nอี๋อ๋อ\nอีก\nอีก้อ\nอีก๋อย\nอีโก้ง\nอีจู้\nอี๊ด\nอีเต้อ\nอีโต้\nอีทุบ\nอีเทอร์\nอีนุงตุงนัง\nอีนูน\nอีโน\nอีแปะ\nอีโปง\nอีเพา\nอีมู\nอีรม\nอีลุ้ม\nอีลุ่ยฉุยแฉก\nอีเลิ้ง\nอีศ\nอีศวร\nอีส\nอีสาน\nอีสุกอีใส\nอีหรอบ\nอีหลักอีเหลื่อ\nอีหลี\nอีหลุกขลุกขลัก\nอีหลุกขลุกขลุ่ย\nอีเห็น\nอีเหน็บ\nอีเหนียว\nอีเหละเขละขละ\nอีเหละเขะขะ\nอีโหน่อีเหน่\nอีโหลกโขลกเขลก\nอีแอ่น\nอึ\nอึก\nอึ้ก\nอึ๊ก\nอึกทึก\nอึกอัก\nอึง\nอึ่ง\nอึ้ง\nอึด\nอึดตะปือ\nอึ้ดทึ่ด\nอึน\nอืด\nอื่น\nอื้น\nอือ\nอื้อ\nอื้อฮือ\nอุ\nอุก\nอุกกา\nอุกกาบาต\nอุกฤษฏ์\nอุกลาบาต\nอุค\nอุคระ\nอุคหนิมิต\nอุโฆษ\nอุ้ง\nอุจ\nอุจจาระ\nอุจฉุ\nอุจเฉท\nอุจเฉททิฐิ\nอุจาด\nอุชุ\nอุฏฐาการ\nอุณหภูมิ\nอุณหะ\nอุณหาหาร\nอุณหิส\nอุณา\nอุณาโลม\nอุด\nอุดเตา\nอุดม\nอุดมการณ์\nอุดมคติ\nอุดมศึกษา\nอุดร\nอุดหนุน\nอุตดม\nอุตตมะ\nอุตมภาพ\nอุตมางค์\nอุตดร\nอุตรกุรุทวีป\nอุตตรายัน\nอุตรนิกาย\nอุตรผลคุนี\nอุตตรผลคุนี\nอุตรภัทรบท\nอุตตรภัทรบท\nอุตตรภัททะ\nอุตราภิมุข\nอุตราวรรต\nอุตราวัฏ\nอุตราษาฒ\nอุตตราสาฬหะ\nอุตราสงค์\nอุตตานภาพ\nอุตพิด\nอุตรา\nอุตริ\nอุตริมนุสธรรม\nอุตลุด\nอุตส่าห์\nอุตสาหกรรม\nอุตสาหะ\nอุตุ\nอุตุนิยม\nอุตุนิยมวิทยา\nอุทก\nอุทกธาร\nอุทกธารา\nอุทกภัย\nอุทกวิทยา\nอุทกศาสตร์\nอุทธรณ์\nอุทธัจ\nอุทยาน\nอุทร\nอุทริยะ\nอุทลุม\nอุทัช\nอุทัย\nอุทาน\nอุทาร\nอุทาหรณ์\nอุทิศ\nอุทุมพร\nอุเทศ\nอุเทสิกเจดีย์\nอุธัจ\nอุ่น\nอุบ\nอุบล\nอุบะ\nอุบ๊ะ\nอุบัติ\nอุบาท\nอุบาทว์\nอุบาย\nอุบาสก\nอุบาสิกา\nอุเบกขา\nอุโบสถ\nอุปกรณ์\nอุปกรม\nอุปการ\nอุปการะ\nอุปการี\nอุปกิเลส\nอุปจาร\nอุปถัมภ์\nอุปถัมภก\nอุปทม\nอุปทูต\nอุปเทศ\nอุปเท่ห์\nอุปธิ\nอุปนัย\nอุปนิกขิต\nอุปนิษัท\nอุปนิสัย\nอุปบัติ\nอุปปาติกะ\nอุปพัทธ์\nอุปพันธ์\nอุปโภค\nอุปมา\nอุปมาน\nอุปไมย\nอุปยุวราช\nอุปรากร\nอุปราคา\nอุปราช\nอุปริ\nอุปริมปริยาย\nอุปโลกน์\nอุปเวท\nอุปสมบท\nอุปสมบัน\nอุปสัมบัน\nอุปสรรค\nอุปสัมปทา\nอุปฮาด\nอุปัชฌาย์\nอุปัชฌายวัตร\nอุปัชฌายะ\nอุปัฏฐาก\nอุปัฏฐานะ\nอุปัทวะ\nอุปัทวันตราย\nอุปาทาน\nอุปาหนา\nอุภัย\nอุ้ม\nอุมงค์\nอุโมงค์\nอุย\nอุ่ย\nอุ้ย\nอุ๊ย\nอุยยาน\nอุยยาม\nอุรณะ\nอุรพี\nอุระ\nอุรังอุตัง\nอุรัจฉัท\nอุรัจฉทะ\nอุรา\nอุรุ\nอุไร\nอุลกมณี\nอุลโลจ\nอุลามก\nอุลิด\nอุโลก\nอุแว้\nอุษณกร\nอุษณกาล\nอุษณรัศมี\nอุษณรุจี\nอุษณาการ\nอุษณีษ์\nอุษมะ\nอุษมัน\nอุษา\nอุษาโยค\nอุสภ\nอุสส่าห์\nอุสสาหะ\nอุสา\nอุสุ\nอุสุภ\nอุสุภราช\nอุสุม\nอุหรับ\nอุหลบ\nอุเหม่\nอุฬาร\nอู\nอู่\nอู้\nอูฐ\nอูด\nอูม\nอูย\nอูรุ\nอู๋อี๋\nเอ\nเอ้\nเอ๊\nเอก\nเอกเขนก\nเอกซเรย์\nเอกรรถประโยค\nเอกัคตา\nเอกังสพยากรณ์\nเอกังสวาที\nเอกา\nเอ้กา\nเอกาธิปไตย\nเอเคอร์\nเอง\nเอ็ง\nเอ๋ง\nเอ็ด\nเอ็ดตะโร\nเอดส์\nเอตทัคคะ\nเอ้เต\nเอทิล\nเอน\nเอ็น\nเอนไซม์\nเอ็นดู\nเอ็นอ่อน\nเอม\nเอ็มบริโอ\nเอย\nเอ่ย\nเอ๊ย\nเอ๋ย\nเอร็ดอร่อย\nเอราวัณ\nเอว\nเอ๊ว\nเอวัง\nเอฬกะ\nเอฬา\nเออ\nเอ่อ\nเออร์เบียม\nเอ้อระเหย\nเอ้อเร้อ\nเอ้อเฮอ\nเอ๊ะ\nเอะใจ\nเอะอะ\nเอะอะมะเทิ่ง\nเอา\nเอาทาร\nเอาทารย์\nเอารส\nเอาฬาร\nเอาะลาย\nเอิก\nเอิกเกริก\nเอิ้น\nเอิบ\nเอียง\nเอี้ยง\nเอียด\nเอี๊ยด\nเอียน\nเอี่ยน\nเอี่ยม\nเอี๊ยม\nเอี้ยมจุ๊น\nเอี้ยมเฟี้ยม\nเอี่ยว\nเอี้ยว\nเอื้อ\nเอื๊อก\nเอื้อง\nเอือด\nเอือน\nเอื้อน\nเอือม\nเอื้อม\nเอื่อย\nเอื้อย\nแอ\nแอ้\nแอ๋\nแอก\nแอกทิเนียม\nแอ่ง\nแอ้งแม้ง\nแอด\nแอ้ด\nแอ๊ด\nแอ่น\nแอนติเจน\nแอนติบอดี\nแอนติอิเล็กตรอน\nแอโนด\nแอบ\nแอม\nแอ้ม\nแอมแปร์\nแอมมิเตอร์\nแอมโมเนีย\nแอร่ม\nแอลกอฮอล์\nแอลฟา\nแอว\nแอ่ว\nแอ้วแซ่ว\nแอสทาทีน\nแอสไพริน\nแอสฟัลต์\nแอหนัง\nแออัด\nโอ\nโอ่\nโอ้\nโอ๋\nโอก\nโอ้ก\nโอ้กอ้าก\nโอ๊ก\nโอกาส\nโอฆชล\nโอฆสงสาร\nโอฆะ\nโอ่ง\nโองการ\nโองโขดง\nโอชะ\nโอชา\nโอโซน\nโอฐ\nโอด\nโอ๊ต\nโอตตัปปะ\nโอทนะ\nโอน\nโอบ\nโอปปาติกะ\nโอภา\nโอภาส\nโอม\nโอย\nโอ๊ย\nโอรส\nโอละพ่อ\nโอลิมปิก\nโอวาท\nโอษฐ์\nโอษฐชะ\nโอษฐภัย\nโอสถ\nโอห์ม\nโอหัง\nโอฬาร\nโอฬาริก\nโอฬารึก\nโอ้เอ้\nโอเอซิส\nโอ้โฮ\nไอ\nไอ้\nไอโซโทป\nไอน์สไตเนียม\nไอยรา\nไอยเรศ\nไอราพต\nไอราวัณ\nไอราวัต\nไอศกรีม\nไอศวรรย์\nไอศุริยสมบัติ\nไอศูรย์\nไอออน\nไอโอดีน\nฮกเกี้ยน\nฮด\nฮวงซุ้ย\nฮวน\nฮ้วนหมู\nฮวบ\nฮ่อ\nฮ้อ\nฮอกกี้\nฮอด\nฮ่อม\nฮ่อยจ๊อ\nฮอร์โมน\nฮอลแลนด์\nฮอลันดา\nฮะ\nฮะเบส\nฮะเรีย\nฮัก\nฮังเล\nฮัจญ์\nฮัจญะฮ์\nฮัจญี\nฮั่น\nฮั้ว\nฮา\nฮ้า\nฮ่างหลวง\nฮาจญ์\nฮาม\nฮาเร็ม\nฮาห์เนียม\nฮิจเราะห์\nฮินดู\nฮิปโปโปเตมัส\nฮิสทีเรีย\nฮีเลียม\nฮึ\nฮึก\nฮึด\nฮึดฮัด\nฮึ่ม\nฮึย\nฮึ่ย\nฮืดฮาด\nฮือ\nฮื่อ\nฮื้อ\nฮื้อฉี่\nฮุด\nฮุบ\nฮุยเลฮุย\nฮู้\nฮูก\nฮูม\nเฮ\nเฮฮา\nเฮกตาร์\nเฮกโตกรัม\nเฮกโตเมตร\nเฮกโตลิตร\nเฮง\nเฮ็ด\nเฮโมโกลบิน\nเฮย\nเฮ่ย\nเฮ้ย\nเฮโรอีน\nเฮลิคอปเตอร์\nเฮโล\nเฮละโล\nเฮ้ว\nเฮอ\nเฮ่อ\nเฮ้อ\nเฮอริเคน\nเฮิรตซ์\nเฮี้ยน\nเฮี้ยบ\nเฮี้ยว\nเฮือก\nเฮือน\nแฮ\nแฮ่\nแฮก\nแฮ่กึ๊น\nแฮนด์บอล\nแฮฟเนียม\nแฮม\nแฮะ\nโฮ\nโฮก\nโฮ่ง\nโฮ้ง\nโฮเต็ล\nโฮลเมียม\nโฮะ\nไฮ้\nไฮโกรมิเตอร์\nไฮดรา\nไฮโดร\nไฮโดรคาร์บอน\nไฮโดรเจน\nไฮโดรมิเตอร์\nไฮไฟ\nไฮโล\nไฮฮี\n"
+              .split(/[\r\n]+/)
+              .filter(function (w) {
+                return w.length > 1;
+              })
+      this.addWords(words, false)
+    }
+    if(finalize){
+      this.finalizeDict();
+    }
+  },
+
+  dictSeek: function (l, r, ch, strOffset, pos) {
+    var ans = null;
+    while (l <= r) {
+      var m = Math.floor((l + r) / 2),
+        dict_item = this.dict[m],
+        len = dict_item.length;
+      if (len <= strOffset) {
+        l = m + 1;
+      } else {
+        var ch_ = dict_item[strOffset];
+        if (ch_ < ch) {
+          l = m + 1;
+        } else if (ch_ > ch) {
+          r = m - 1;
+        } else {
+          ans = m;
+          if (pos == LEFT) {
+            r = m - 1;
+          } else {
+            l = m + 1;
+          }
+        }
+      }
+    }
+    return ans;
+  },
+
+  isFinal: function (acceptor) {
+    return this.dict[acceptor.l].length == acceptor.strOffset;
+  },
+
+  createAcceptor: function () {
+    return {
+      l: 0,
+      r: this.dict.length - 1,
+      strOffset: 0,
+      isFinal: false,
+      dict: this,
+      transit: function (ch) {
+        return this.dict.transit(this, ch);
+      },
+      isError: false,
+      tag: "DICT",
+      w: 1,
+      type: "DICT"
+    };
+  },
+
+  transit: function (acceptor, ch) {
+    var l = this.dictSeek(acceptor.l,
+      acceptor.r,
+      ch,
+      acceptor.strOffset,
+      LEFT);
+    if (l !== null) {
+      var r = this.dictSeek(l,
+        acceptor.r,
+        ch,
+        acceptor.strOffset,
+        RIGHT);
+      acceptor.l = l;
+      acceptor.r = r;
+      acceptor.strOffset++;
+      acceptor.isFinal = this.isFinal(acceptor);
+    } else {
+      acceptor.isError = true;
+    }
+    return acceptor;
+  },
+
+  sortuniq: function(a){
+    return a.sort().filter(function(item, pos, arr){
+      return !pos || item != arr[pos - 1];
+    })
+  },
+
+  flatten: function(a){
+    //[[1,2],[3]] -> [1,2,3]
+    return [].concat.apply([], a);
+  }
+};
+module.exports = WordcutDict;
+
+}).call(this,"/dist/tmp")
+},{"glob":16,"path":22}],3:[function(require,module,exports){
+var WordRule = {
+  createAcceptor: function(tag) {
+    if (tag["WORD_RULE"])
+      return null;
+
+    return {strOffset: 0,
+            isFinal: false,
+            transit: function(ch) {
+              var lch = ch.toLowerCase();
+              if (lch >= "a" && lch <= "z") {
+                this.isFinal = true;
+                this.strOffset++;
+              } else {
+                this.isError = true;
+              }
+              return this;
+            },
+            isError: false,
+            tag: "WORD_RULE",
+            type: "WORD_RULE",
+            w: 1};
+  }
+};
+
+var NumberRule = {
+  createAcceptor: function(tag) {
+    if (tag["NUMBER_RULE"])
+      return null;
+
+    return {strOffset: 0,
+            isFinal: false,
+            transit: function(ch) {
+              if (ch >= "0" && ch <= "9") {
+                this.isFinal = true;
+                this.strOffset++;
+              } else {
+                this.isError = true;
+              }
+              return this;
+            },
+            isError: false,
+            tag: "NUMBER_RULE",
+            type: "NUMBER_RULE",
+            w: 1};
+  }
+};
+
+var SpaceRule = {
+  tag: "SPACE_RULE",
+  createAcceptor: function(tag) {
+
+    if (tag["SPACE_RULE"])
+      return null;
+
+    return {strOffset: 0,
+            isFinal: false,
+            transit: function(ch) {
+              if (ch == " " || ch == "\t" || ch == "\r" || ch == "\n" ||
+                  ch == "\u00A0" || ch=="\u2003"//nbsp and emsp
+                 ) {
+                this.isFinal = true;
+                this.strOffset++;
+              } else {
+                this.isError = true;
+              }
+              return this;
+            },
+            isError: false,
+            tag: SpaceRule.tag,
+            w: 1,
+            type: "SPACE_RULE"};
+  }
+}
+
+var SingleSymbolRule = {
+  tag: "SINSYM",
+  createAcceptor: function(tag) {
+    return {strOffset: 0,
+            isFinal: false,
+            transit: function(ch) {
+              if (this.strOffset == 0 && ch.match(/^[\@\(\)\/\,\-\."`]$/)) {
+                this.isFinal = true;
+                this.strOffset++;
+              } else {
+                this.isError = true;
+              }
+              return this;
+            },
+            isError: false,
+            tag: "SINSYM",
+            w: 1,
+            type: "SINSYM"};
+  }
+}
+
+
+var LatinRules = [WordRule, SpaceRule, SingleSymbolRule, NumberRule];
+
+module.exports = LatinRules;
+
+},{}],4:[function(require,module,exports){
+var _ = require("underscore")
+  , WordcutCore = require("./wordcut_core");
+var PathInfoBuilder = {
+
+  /*
+    buildByPartAcceptors: function(path, acceptors, i) {
+    var 
+    var genInfos = partAcceptors.reduce(function(genInfos, acceptor) {
+      
+    }, []);
+    
+    return genInfos;
+  } 
+  */
+
+  buildByAcceptors: function(path, finalAcceptors, i) {
+    var self = this;
+    var infos = finalAcceptors.map(function(acceptor) {
+      var p = i - acceptor.strOffset + 1
+        , _info = path[p];            
+      
+      var info = {p: p, 
+                  mw: _info.mw + (acceptor.mw === undefined ? 0 : acceptor.mw),
+                  w: acceptor.w + _info.w,
+                  unk: (acceptor.unk ? acceptor.unk : 0) + _info.unk, 
+                  type: acceptor.type};
+
+      if (acceptor.type == "PART") {
+        for(var j = p + 1; j <= i; j++) {
+          path[j].merge = p;
+        }
+        info.merge = p;
+      }
+
+      return info;
+    });
+    return infos.filter(function(info) { return info; });
+  },
+  
+  fallback: function(path, leftBoundary, text, i) {
+    var _info = path[leftBoundary];
+    if (text[i].match(/[\u0E48-\u0E4E]/)) {
+      if (leftBoundary != 0) 
+        leftBoundary = path[leftBoundary].p;
+      return {p: leftBoundary,
+              mw: 0,
+              w: 1 + _info.w,
+              unk: 1 + _info.unk,
+              type: "UNK"};      
+/*    } else if(leftBoundary > 0 && path[leftBoundary].type !== "UNK") {
+      leftBoundary = path[leftBoundary].p;
+      return {p: leftBoundary,
+              w: 1 + _info.w,
+              unk: 1 + _info.unk,
+              type: "UNK"};            */
+    } else {      
+      return {p: leftBoundary,
+              mw: _info.mw,
+              w: 1 + _info.w,
+              unk: 1 + _info.unk,
+              type: "UNK"};
+    }
+  },
+  
+  build: function(path, finalAcceptors, i, leftBoundary, text) {
+    var basicPathInfos = this.buildByAcceptors(path, finalAcceptors, i);
+    if (basicPathInfos.length > 0) {
+      return basicPathInfos;
+    } else {
+      return [this.fallback(path, leftBoundary, text, i)];
+    }
+  }
+};
+
+module.exports = function() {
+  return _.clone(PathInfoBuilder);
+}
+
+},{"./wordcut_core":8,"underscore":25}],5:[function(require,module,exports){
+var _ = require("underscore");
+
+
+var PathSelector = {
+  selectPath: function(paths) {
+    var path = paths.reduce(function(selectedPath, path) {
+      if (selectedPath == null) {        
+        return path;
+      } else {
+        if (path.unk < selectedPath.unk) 
+          return path;        
+        if (path.unk == selectedPath.unk) {
+          if (path.mw < selectedPath.mw)
+            return path
+          if (path.mw == selectedPath.mw) {
+            if (path.w < selectedPath.w) 
+              return path;
+          }
+        }
+        return selectedPath;
+      }
+    }, null);
+    return path;
+  },
+  
+  createPath: function() {
+    return [{p:null, w:0, unk:0, type: "INIT", mw:0}];
+  }
+};
+
+module.exports = function() {
+  return _.clone(PathSelector);
+};
+
+},{"underscore":25}],6:[function(require,module,exports){
+function isMatch(pat, offset, ch) {
+  if (pat.length <= offset)
+    return false;
+  var _ch = pat[offset];
+  return _ch == ch ||
+         (_ch.match(/[กข]/) && ch.match(/[ก-ฮ]/)) ||
+         (_ch.match(/[มบ]/) && ch.match(/[ก-ฮ]/)) ||
+         (_ch.match(/\u0E49/) && ch.match(/[\u0E48-\u0E4B]/));
+}
+
+var Rule0 = {
+  pat: "เหก็ม",
+  createAcceptor: function(tag) {
+    return {strOffset: 0,
+            isFinal: false,
+            transit: function(ch) {
+              if (isMatch(Rule0.pat, this.strOffset,ch)) {                 
+                this.isFinal = (this.strOffset + 1 == Rule0.pat.length);                
+                this.strOffset++;
+              } else {              
+                this.isError = true;             
+              }
+              return this;
+            },
+            isError: false,
+            tag: "THAI_RULE",
+            type: "THAI_RULE", 
+            w: 1};                        
+  }
+};
+
+var PartRule = {
+  createAcceptor: function(tag) {
+    return {strOffset: 0,
+            patterns: [
+              "แก", "เก", "ก้", "กก์", "กา", "กี", "กิ", "กืก"  
+            ],
+            isFinal: false,
+            transit: function(ch) {
+              var offset = this.strOffset;
+              this.patterns = this.patterns.filter(function(pat) {
+                return isMatch(pat, offset, ch);
+              });
+              
+              if (this.patterns.length > 0) {
+                var len = 1 + offset;
+                this.isFinal = this.patterns.some(function(pat) {
+                  return pat.length == len; 
+                });
+                this.strOffset++;
+              } else {              
+                this.isError = true;             
+              }
+              return this;
+            },
+            isError: false,
+            tag: "PART",
+            type: "PART", 
+            unk: 1,
+            w: 1};                        
+  }
+};
+
+var ThaiRules = [Rule0, PartRule];
+
+module.exports = ThaiRules;
+
+},{}],7:[function(require,module,exports){
+var sys = require("sys")
+  , WordcutDict = require("./dict")
+  , WordcutCore = require("./wordcut_core")
+  , PathInfoBuilder = require("./path_info_builder")
+  , PathSelector = require("./path_selector")
+  , Acceptors = require("./acceptors")
+  , latinRules = require("./latin_rules")
+  , thaiRules = require("./thai_rules")
+  , _ = require("underscore");
+
+
+var Wordcut = Object.create(WordcutCore);
+Wordcut.defaultPathInfoBuilder = PathInfoBuilder;
+Wordcut.defaultPathSelector = PathSelector;
+Wordcut.defaultAcceptors = Acceptors;
+Wordcut.defaultLatinRules = latinRules;
+Wordcut.defaultThaiRules = thaiRules;
+Wordcut.defaultDict = WordcutDict;
+
+
+Wordcut.initNoDict = function(dict_path) {
+  var self = this;
+  self.pathInfoBuilder = new self.defaultPathInfoBuilder;
+  self.pathSelector = new self.defaultPathSelector;
+  self.acceptors = new self.defaultAcceptors;
+  self.defaultLatinRules.forEach(function(rule) {
+    self.acceptors.creators.push(rule);
+  });
+  self.defaultThaiRules.forEach(function(rule) {
+    self.acceptors.creators.push(rule);
+  });
+};
+
+Wordcut.init = function(dict_path, withDefault, additionalWords) {
+  withDefault = withDefault || false;
+  this.initNoDict();
+  var dict = _.clone(this.defaultDict);
+  dict.init(dict_path, withDefault, additionalWords);
+  this.acceptors.creators.push(dict);
+};
+
+module.exports = Wordcut;
+
+},{"./acceptors":1,"./dict":2,"./latin_rules":3,"./path_info_builder":4,"./path_selector":5,"./thai_rules":6,"./wordcut_core":8,"sys":28,"underscore":25}],8:[function(require,module,exports){
+var WordcutCore = {
+
+  buildPath: function(text) {
+    var self = this
+      , path = self.pathSelector.createPath()
+      , leftBoundary = 0;
+    self.acceptors.reset();
+    for (var i = 0; i < text.length; i++) {
+      var ch = text[i];
+      self.acceptors.transit(ch);
+
+      var possiblePathInfos = self
+        .pathInfoBuilder
+        .build(path,
+               self.acceptors.getFinalAcceptors(),
+               i,
+               leftBoundary,
+               text);
+      var selectedPath = self.pathSelector.selectPath(possiblePathInfos)
+
+      path.push(selectedPath);
+      if (selectedPath.type !== "UNK") {
+        leftBoundary = i;
+      }
+    }
+    return path;
+  },
+
+  pathToRanges: function(path) {
+    var e = path.length - 1
+     , ranges = [];
+
+    while (e > 0) {
+      var info = path[e]
+       , s = info.p;
+
+      if (info.merge !== undefined && ranges.length > 0) {
+        var r = ranges[ranges.length - 1];
+        r.s = info.merge;
+        s = r.s;
+      } else {
+        ranges.push({s:s, e:e});
+      }
+      e = s;
+    }
+    return ranges.reverse();
+  },
+
+  rangesToText: function(text, ranges, delimiter) {
+    return ranges.map(function(r) {
+      return text.substring(r.s, r.e);
+    }).join(delimiter);
+  },
+
+  cut: function(text, delimiter) {
+    var path = this.buildPath(text)
+      , ranges = this.pathToRanges(path);
+    return this
+      .rangesToText(text, ranges,
+                    (delimiter === undefined ? "|" : delimiter));
+  },
+
+  cutIntoRanges: function(text, noText) {
+    var path = this.buildPath(text)
+      , ranges = this.pathToRanges(path);
+
+    if (!noText) {
+      ranges.forEach(function(r) {
+        r.text = text.substring(r.s, r.e);
+      });
+    }
+    return ranges;
+  },
+
+  cutIntoArray: function(text) {
+    var path = this.buildPath(text)
+      , ranges = this.pathToRanges(path);
+    
+    return ranges.map(function(r) {
+      return text.substring(r.s, r.e)
+    });
+  }
+};
+
+module.exports = WordcutCore;
+
+},{}],9:[function(require,module,exports){
+// http://wiki.commonjs.org/wiki/Unit_Testing/1.0
+//
+// THIS IS NOT TESTED NOR LIKELY TO WORK OUTSIDE V8!
+//
+// Originally from narwhal.js (http://narwhaljs.org)
+// Copyright (c) 2009 Thomas Robinson <280north.com>
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the 'Software'), to
+// deal in the Software without restriction, including without limitation the
+// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+// sell copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+// ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+// WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+// when used in node, this will actually load the util module we depend on
+// versus loading the builtin util module as happens otherwise
+// this is a bug in node module loading as far as I am concerned
+var util = require('util/');
+
+var pSlice = Array.prototype.slice;
+var hasOwn = Object.prototype.hasOwnProperty;
+
+// 1. The assert module provides functions that throw
+// AssertionError's when particular conditions are not met. The
+// assert module must conform to the following interface.
+
+var assert = module.exports = ok;
+
+// 2. The AssertionError is defined in assert.
+// new assert.AssertionError({ message: message,
+//                             actual: actual,
+//                             expected: expected })
+
+assert.AssertionError = function AssertionError(options) {
+  this.name = 'AssertionError';
+  this.actual = options.actual;
+  this.expected = options.expected;
+  this.operator = options.operator;
+  if (options.message) {
+    this.message = options.message;
+    this.generatedMessage = false;
+  } else {
+    this.message = getMessage(this);
+    this.generatedMessage = true;
+  }
+  var stackStartFunction = options.stackStartFunction || fail;
+
+  if (Error.captureStackTrace) {
+    Error.captureStackTrace(this, stackStartFunction);
+  }
+  else {
+    // non v8 browsers so we can have a stacktrace
+    var err = new Error();
+    if (err.stack) {
+      var out = err.stack;
+
+      // try to strip useless frames
+      var fn_name = stackStartFunction.name;
+      var idx = out.indexOf('\n' + fn_name);
+      if (idx >= 0) {
+        // once we have located the function frame
+        // we need to strip out everything before it (and its line)
+        var next_line = out.indexOf('\n', idx + 1);
+        out = out.substring(next_line + 1);
+      }
+
+      this.stack = out;
+    }
+  }
+};
+
+// assert.AssertionError instanceof Error
+util.inherits(assert.AssertionError, Error);
+
+function replacer(key, value) {
+  if (util.isUndefined(value)) {
+    return '' + value;
+  }
+  if (util.isNumber(value) && !isFinite(value)) {
+    return value.toString();
+  }
+  if (util.isFunction(value) || util.isRegExp(value)) {
+    return value.toString();
+  }
+  return value;
+}
+
+function truncate(s, n) {
+  if (util.isString(s)) {
+    return s.length < n ? s : s.slice(0, n);
+  } else {
+    return s;
+  }
+}
+
+function getMessage(self) {
+  return truncate(JSON.stringify(self.actual, replacer), 128) + ' ' +
+         self.operator + ' ' +
+         truncate(JSON.stringify(self.expected, replacer), 128);
+}
+
+// At present only the three keys mentioned above are used and
+// understood by the spec. Implementations or sub modules can pass
+// other keys to the AssertionError's constructor - they will be
+// ignored.
+
+// 3. All of the following functions must throw an AssertionError
+// when a corresponding condition is not met, with a message that
+// may be undefined if not provided.  All assertion methods provide
+// both the actual and expected values to the assertion error for
+// display purposes.
+
+function fail(actual, expected, message, operator, stackStartFunction) {
+  throw new assert.AssertionError({
+    message: message,
+    actual: actual,
+    expected: expected,
+    operator: operator,
+    stackStartFunction: stackStartFunction
+  });
+}
+
+// EXTENSION! allows for well behaved errors defined elsewhere.
+assert.fail = fail;
+
+// 4. Pure assertion tests whether a value is truthy, as determined
+// by !!guard.
+// assert.ok(guard, message_opt);
+// This statement is equivalent to assert.equal(true, !!guard,
+// message_opt);. To test strictly for the value true, use
+// assert.strictEqual(true, guard, message_opt);.
+
+function ok(value, message) {
+  if (!value) fail(value, true, message, '==', assert.ok);
+}
+assert.ok = ok;
+
+// 5. The equality assertion tests shallow, coercive equality with
+// ==.
+// assert.equal(actual, expected, message_opt);
+
+assert.equal = function equal(actual, expected, message) {
+  if (actual != expected) fail(actual, expected, message, '==', assert.equal);
+};
+
+// 6. The non-equality assertion tests for whether two objects are not equal
+// with != assert.notEqual(actual, expected, message_opt);
+
+assert.notEqual = function notEqual(actual, expected, message) {
+  if (actual == expected) {
+    fail(actual, expected, message, '!=', assert.notEqual);
+  }
+};
+
+// 7. The equivalence assertion tests a deep equality relation.
+// assert.deepEqual(actual, expected, message_opt);
+
+assert.deepEqual = function deepEqual(actual, expected, message) {
+  if (!_deepEqual(actual, expected)) {
+    fail(actual, expected, message, 'deepEqual', assert.deepEqual);
+  }
+};
+
+function _deepEqual(actual, expected) {
+  // 7.1. All identical values are equivalent, as determined by ===.
+  if (actual === expected) {
+    return true;
+
+  } else if (util.isBuffer(actual) && util.isBuffer(expected)) {
+    if (actual.length != expected.length) return false;
+
+    for (var i = 0; i < actual.length; i++) {
+      if (actual[i] !== expected[i]) return false;
+    }
+
+    return true;
+
+  // 7.2. If the expected value is a Date object, the actual value is
+  // equivalent if it is also a Date object that refers to the same time.
+  } else if (util.isDate(actual) && util.isDate(expected)) {
+    return actual.getTime() === expected.getTime();
+
+  // 7.3 If the expected value is a RegExp object, the actual value is
+  // equivalent if it is also a RegExp object with the same source and
+  // properties (`global`, `multiline`, `lastIndex`, `ignoreCase`).
+  } else if (util.isRegExp(actual) && util.isRegExp(expected)) {
+    return actual.source === expected.source &&
+           actual.global === expected.global &&
+           actual.multiline === expected.multiline &&
+           actual.lastIndex === expected.lastIndex &&
+           actual.ignoreCase === expected.ignoreCase;
+
+  // 7.4. Other pairs that do not both pass typeof value == 'object',
+  // equivalence is determined by ==.
+  } else if (!util.isObject(actual) && !util.isObject(expected)) {
+    return actual == expected;
+
+  // 7.5 For all other Object pairs, including Array objects, equivalence is
+  // determined by having the same number of owned properties (as verified
+  // with Object.prototype.hasOwnProperty.call), the same set of keys
+  // (although not necessarily the same order), equivalent values for every
+  // corresponding key, and an identical 'prototype' property. Note: this
+  // accounts for both named and indexed properties on Arrays.
+  } else {
+    return objEquiv(actual, expected);
+  }
+}
+
+function isArguments(object) {
+  return Object.prototype.toString.call(object) == '[object Arguments]';
+}
+
+function objEquiv(a, b) {
+  if (util.isNullOrUndefined(a) || util.isNullOrUndefined(b))
+    return false;
+  // an identical 'prototype' property.
+  if (a.prototype !== b.prototype) return false;
+  // if one is a primitive, the other must be same
+  if (util.isPrimitive(a) || util.isPrimitive(b)) {
+    return a === b;
+  }
+  var aIsArgs = isArguments(a),
+      bIsArgs = isArguments(b);
+  if ((aIsArgs && !bIsArgs) || (!aIsArgs && bIsArgs))
+    return false;
+  if (aIsArgs) {
+    a = pSlice.call(a);
+    b = pSlice.call(b);
+    return _deepEqual(a, b);
+  }
+  var ka = objectKeys(a),
+      kb = objectKeys(b),
+      key, i;
+  // having the same number of owned properties (keys incorporates
+  // hasOwnProperty)
+  if (ka.length != kb.length)
+    return false;
+  //the same set of keys (although not necessarily the same order),
+  ka.sort();
+  kb.sort();
+  //~~~cheap key test
+  for (i = ka.length - 1; i >= 0; i--) {
+    if (ka[i] != kb[i])
+      return false;
+  }
+  //equivalent values for every corresponding key, and
+  //~~~possibly expensive deep test
+  for (i = ka.length - 1; i >= 0; i--) {
+    key = ka[i];
+    if (!_deepEqual(a[key], b[key])) return false;
+  }
+  return true;
+}
+
+// 8. The non-equivalence assertion tests for any deep inequality.
+// assert.notDeepEqual(actual, expected, message_opt);
+
+assert.notDeepEqual = function notDeepEqual(actual, expected, message) {
+  if (_deepEqual(actual, expected)) {
+    fail(actual, expected, message, 'notDeepEqual', assert.notDeepEqual);
+  }
+};
+
+// 9. The strict equality assertion tests strict equality, as determined by ===.
+// assert.strictEqual(actual, expected, message_opt);
+
+assert.strictEqual = function strictEqual(actual, expected, message) {
+  if (actual !== expected) {
+    fail(actual, expected, message, '===', assert.strictEqual);
+  }
+};
+
+// 10. The strict non-equality assertion tests for strict inequality, as
+// determined by !==.  assert.notStrictEqual(actual, expected, message_opt);
+
+assert.notStrictEqual = function notStrictEqual(actual, expected, message) {
+  if (actual === expected) {
+    fail(actual, expected, message, '!==', assert.notStrictEqual);
+  }
+};
+
+function expectedException(actual, expected) {
+  if (!actual || !expected) {
+    return false;
+  }
+
+  if (Object.prototype.toString.call(expected) == '[object RegExp]') {
+    return expected.test(actual);
+  } else if (actual instanceof expected) {
+    return true;
+  } else if (expected.call({}, actual) === true) {
+    return true;
+  }
+
+  return false;
+}
+
+function _throws(shouldThrow, block, expected, message) {
+  var actual;
+
+  if (util.isString(expected)) {
+    message = expected;
+    expected = null;
+  }
+
+  try {
+    block();
+  } catch (e) {
+    actual = e;
+  }
+
+  message = (expected && expected.name ? ' (' + expected.name + ').' : '.') +
+            (message ? ' ' + message : '.');
+
+  if (shouldThrow && !actual) {
+    fail(actual, expected, 'Missing expected exception' + message);
+  }
+
+  if (!shouldThrow && expectedException(actual, expected)) {
+    fail(actual, expected, 'Got unwanted exception' + message);
+  }
+
+  if ((shouldThrow && actual && expected &&
+      !expectedException(actual, expected)) || (!shouldThrow && actual)) {
+    throw actual;
+  }
+}
+
+// 11. Expected to throw an error:
+// assert.throws(block, Error_opt, message_opt);
+
+assert.throws = function(block, /*optional*/error, /*optional*/message) {
+  _throws.apply(this, [true].concat(pSlice.call(arguments)));
+};
+
+// EXTENSION! This is annoying to write outside this module.
+assert.doesNotThrow = function(block, /*optional*/message) {
+  _throws.apply(this, [false].concat(pSlice.call(arguments)));
+};
+
+assert.ifError = function(err) { if (err) {throw err;}};
+
+var objectKeys = Object.keys || function (obj) {
+  var keys = [];
+  for (var key in obj) {
+    if (hasOwn.call(obj, key)) keys.push(key);
+  }
+  return keys;
+};
+
+},{"util/":28}],10:[function(require,module,exports){
+'use strict';
+module.exports = balanced;
+function balanced(a, b, str) {
+  if (a instanceof RegExp) a = maybeMatch(a, str);
+  if (b instanceof RegExp) b = maybeMatch(b, str);
+
+  var r = range(a, b, str);
+
+  return r && {
+    start: r[0],
+    end: r[1],
+    pre: str.slice(0, r[0]),
+    body: str.slice(r[0] + a.length, r[1]),
+    post: str.slice(r[1] + b.length)
+  };
+}
+
+function maybeMatch(reg, str) {
+  var m = str.match(reg);
+  return m ? m[0] : null;
+}
+
+balanced.range = range;
+function range(a, b, str) {
+  var begs, beg, left, right, result;
+  var ai = str.indexOf(a);
+  var bi = str.indexOf(b, ai + 1);
+  var i = ai;
+
+  if (ai >= 0 && bi > 0) {
+    begs = [];
+    left = str.length;
+
+    while (i >= 0 && !result) {
+      if (i == ai) {
+        begs.push(i);
+        ai = str.indexOf(a, i + 1);
+      } else if (begs.length == 1) {
+        result = [ begs.pop(), bi ];
+      } else {
+        beg = begs.pop();
+        if (beg < left) {
+          left = beg;
+          right = bi;
+        }
+
+        bi = str.indexOf(b, i + 1);
+      }
+
+      i = ai < bi && ai >= 0 ? ai : bi;
+    }
+
+    if (begs.length) {
+      result = [ left, right ];
+    }
+  }
+
+  return result;
+}
+
+},{}],11:[function(require,module,exports){
+var concatMap = require('concat-map');
+var balanced = require('balanced-match');
+
+module.exports = expandTop;
+
+var escSlash = '\0SLASH'+Math.random()+'\0';
+var escOpen = '\0OPEN'+Math.random()+'\0';
+var escClose = '\0CLOSE'+Math.random()+'\0';
+var escComma = '\0COMMA'+Math.random()+'\0';
+var escPeriod = '\0PERIOD'+Math.random()+'\0';
+
+function numeric(str) {
+  return parseInt(str, 10) == str
+    ? parseInt(str, 10)
+    : str.charCodeAt(0);
+}
+
+function escapeBraces(str) {
+  return str.split('\\\\').join(escSlash)
+            .split('\\{').join(escOpen)
+            .split('\\}').join(escClose)
+            .split('\\,').join(escComma)
+            .split('\\.').join(escPeriod);
+}
+
+function unescapeBraces(str) {
+  return str.split(escSlash).join('\\')
+            .split(escOpen).join('{')
+            .split(escClose).join('}')
+            .split(escComma).join(',')
+            .split(escPeriod).join('.');
+}
+
+
+// Basically just str.split(","), but handling cases
+// where we have nested braced sections, which should be
+// treated as individual members, like {a,{b,c},d}
+function parseCommaParts(str) {
+  if (!str)
+    return [''];
+
+  var parts = [];
+  var m = balanced('{', '}', str);
+
+  if (!m)
+    return str.split(',');
+
+  var pre = m.pre;
+  var body = m.body;
+  var post = m.post;
+  var p = pre.split(',');
+
+  p[p.length-1] += '{' + body + '}';
+  var postParts = parseCommaParts(post);
+  if (post.length) {
+    p[p.length-1] += postParts.shift();
+    p.push.apply(p, postParts);
+  }
+
+  parts.push.apply(parts, p);
+
+  return parts;
+}
+
+function expandTop(str) {
+  if (!str)
+    return [];
+
+  // I don't know why Bash 4.3 does this, but it does.
+  // Anything starting with {} will have the first two bytes preserved
+  // but *only* at the top level, so {},a}b will not expand to anything,
+  // but a{},b}c will be expanded to [a}c,abc].
+  // One could argue that this is a bug in Bash, but since the goal of
+  // this module is to match Bash's rules, we escape a leading {}
+  if (str.substr(0, 2) === '{}') {
+    str = '\\{\\}' + str.substr(2);
+  }
+
+  return expand(escapeBraces(str), true).map(unescapeBraces);
+}
+
+function identity(e) {
+  return e;
+}
+
+function embrace(str) {
+  return '{' + str + '}';
+}
+function isPadded(el) {
+  return /^-?0\d/.test(el);
+}
+
+function lte(i, y) {
+  return i <= y;
+}
+function gte(i, y) {
+  return i >= y;
+}
+
+function expand(str, isTop) {
+  var expansions = [];
+
+  var m = balanced('{', '}', str);
+  if (!m || /\$$/.test(m.pre)) return [str];
+
+  var isNumericSequence = /^-?\d+\.\.-?\d+(?:\.\.-?\d+)?$/.test(m.body);
+  var isAlphaSequence = /^[a-zA-Z]\.\.[a-zA-Z](?:\.\.-?\d+)?$/.test(m.body);
+  var isSequence = isNumericSequence || isAlphaSequence;
+  var isOptions = m.body.indexOf(',') >= 0;
+  if (!isSequence && !isOptions) {
+    // {a},b}
+    if (m.post.match(/,.*\}/)) {
+      str = m.pre + '{' + m.body + escClose + m.post;
+      return expand(str);
+    }
+    return [str];
+  }
+
+  var n;
+  if (isSequence) {
+    n = m.body.split(/\.\./);
+  } else {
+    n = parseCommaParts(m.body);
+    if (n.length === 1) {
+      // x{{a,b}}y ==> x{a}y x{b}y
+      n = expand(n[0], false).map(embrace);
+      if (n.length === 1) {
+        var post = m.post.length
+          ? expand(m.post, false)
+          : [''];
+        return post.map(function(p) {
+          return m.pre + n[0] + p;
+        });
+      }
+    }
+  }
+
+  // at this point, n is the parts, and we know it's not a comma set
+  // with a single entry.
+
+  // no need to expand pre, since it is guaranteed to be free of brace-sets
+  var pre = m.pre;
+  var post = m.post.length
+    ? expand(m.post, false)
+    : [''];
+
+  var N;
+
+  if (isSequence) {
+    var x = numeric(n[0]);
+    var y = numeric(n[1]);
+    var width = Math.max(n[0].length, n[1].length)
+    var incr = n.length == 3
+      ? Math.abs(numeric(n[2]))
+      : 1;
+    var test = lte;
+    var reverse = y < x;
+    if (reverse) {
+      incr *= -1;
+      test = gte;
+    }
+    var pad = n.some(isPadded);
+
+    N = [];
+
+    for (var i = x; test(i, y); i += incr) {
+      var c;
+      if (isAlphaSequence) {
+        c = String.fromCharCode(i);
+        if (c === '\\')
+          c = '';
+      } else {
+        c = String(i);
+        if (pad) {
+          var need = width - c.length;
+          if (need > 0) {
+            var z = new Array(need + 1).join('0');
+            if (i < 0)
+              c = '-' + z + c.slice(1);
+            else
+              c = z + c;
+          }
+        }
+      }
+      N.push(c);
+    }
+  } else {
+    N = concatMap(n, function(el) { return expand(el, false) });
+  }
+
+  for (var j = 0; j < N.length; j++) {
+    for (var k = 0; k < post.length; k++) {
+      var expansion = pre + N[j] + post[k];
+      if (!isTop || isSequence || expansion)
+        expansions.push(expansion);
+    }
+  }
+
+  return expansions;
+}
+
+
+},{"balanced-match":10,"concat-map":13}],12:[function(require,module,exports){
+
+},{}],13:[function(require,module,exports){
+module.exports = function (xs, fn) {
+    var res = [];
+    for (var i = 0; i < xs.length; i++) {
+        var x = fn(xs[i], i);
+        if (isArray(x)) res.push.apply(res, x);
+        else res.push(x);
+    }
+    return res;
+};
+
+var isArray = Array.isArray || function (xs) {
+    return Object.prototype.toString.call(xs) === '[object Array]';
+};
+
+},{}],14:[function(require,module,exports){
+// Copyright Joyent, Inc. and other Node contributors.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a
+// copy of this software and associated documentation files (the
+// "Software"), to deal in the Software without restriction, including
+// without limitation the rights to use, copy, modify, merge, publish,
+// distribute, sublicense, and/or sell copies of the Software, and to permit
+// persons to whom the Software is furnished to do so, subject to the
+// following conditions:
+//
+// The above copyright notice and this permission notice shall be included
+// in all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+// USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+function EventEmitter() {
+  this._events = this._events || {};
+  this._maxListeners = this._maxListeners || undefined;
+}
+module.exports = EventEmitter;
+
+// Backwards-compat with node 0.10.x
+EventEmitter.EventEmitter = EventEmitter;
+
+EventEmitter.prototype._events = undefined;
+EventEmitter.prototype._maxListeners = undefined;
+
+// By default EventEmitters will print a warning if more than 10 listeners are
+// added to it. This is a useful default which helps finding memory leaks.
+EventEmitter.defaultMaxListeners = 10;
+
+// Obviously not all Emitters should be limited to 10. This function allows
+// that to be increased. Set to zero for unlimited.
+EventEmitter.prototype.setMaxListeners = function(n) {
+  if (!isNumber(n) || n < 0 || isNaN(n))
+    throw TypeError('n must be a positive number');
+  this._maxListeners = n;
+  return this;
+};
+
+EventEmitter.prototype.emit = function(type) {
+  var er, handler, len, args, i, listeners;
+
+  if (!this._events)
+    this._events = {};
+
+  // If there is no 'error' event listener then throw.
+  if (type === 'error') {
+    if (!this._events.error ||
+        (isObject(this._events.error) && !this._events.error.length)) {
+      er = arguments[1];
+      if (er instanceof Error) {
+        throw er; // Unhandled 'error' event
+      }
+      throw TypeError('Uncaught, unspecified "error" event.');
+    }
+  }
+
+  handler = this._events[type];
+
+  if (isUndefined(handler))
+    return false;
+
+  if (isFunction(handler)) {
+    switch (arguments.length) {
+      // fast cases
+      case 1:
+        handler.call(this);
+        break;
+      case 2:
+        handler.call(this, arguments[1]);
+        break;
+      case 3:
+        handler.call(this, arguments[1], arguments[2]);
+        break;
+      // slower
+      default:
+        len = arguments.length;
+        args = new Array(len - 1);
+        for (i = 1; i < len; i++)
+          args[i - 1] = arguments[i];
+        handler.apply(this, args);
+    }
+  } else if (isObject(handler)) {
+    len = arguments.length;
+    args = new Array(len - 1);
+    for (i = 1; i < len; i++)
+      args[i - 1] = arguments[i];
+
+    listeners = handler.slice();
+    len = listeners.length;
+    for (i = 0; i < len; i++)
+      listeners[i].apply(this, args);
+  }
+
+  return true;
+};
+
+EventEmitter.prototype.addListener = function(type, listener) {
+  var m;
+
+  if (!isFunction(listener))
+    throw TypeError('listener must be a function');
+
+  if (!this._events)
+    this._events = {};
+
+  // To avoid recursion in the case that type === "newListener"! Before
+  // adding it to the listeners, first emit "newListener".
+  if (this._events.newListener)
+    this.emit('newListener', type,
+              isFunction(listener.listener) ?
+              listener.listener : listener);
+
+  if (!this._events[type])
+    // Optimize the case of one listener. Don't need the extra array object.
+    this._events[type] = listener;
+  else if (isObject(this._events[type]))
+    // If we've already got an array, just append.
+    this._events[type].push(listener);
+  else
+    // Adding the second element, need to change to array.
+    this._events[type] = [this._events[type], listener];
+
+  // Check for listener leak
+  if (isObject(this._events[type]) && !this._events[type].warned) {
+    var m;
+    if (!isUndefined(this._maxListeners)) {
+      m = this._maxListeners;
+    } else {
+      m = EventEmitter.defaultMaxListeners;
+    }
+
+    if (m && m > 0 && this._events[type].length > m) {
+      this._events[type].warned = true;
+      console.error('(node) warning: possible EventEmitter memory ' +
+                    'leak detected. %d listeners added. ' +
+                    'Use emitter.setMaxListeners() to increase limit.',
+                    this._events[type].length);
+      if (typeof console.trace === 'function') {
+        // not supported in IE 10
+        console.trace();
+      }
+    }
+  }
+
+  return this;
+};
+
+EventEmitter.prototype.on = EventEmitter.prototype.addListener;
+
+EventEmitter.prototype.once = function(type, listener) {
+  if (!isFunction(listener))
+    throw TypeError('listener must be a function');
+
+  var fired = false;
+
+  function g() {
+    this.removeListener(type, g);
+
+    if (!fired) {
+      fired = true;
+      listener.apply(this, arguments);
+    }
+  }
+
+  g.listener = listener;
+  this.on(type, g);
+
+  return this;
+};
+
+// emits a 'removeListener' event iff the listener was removed
+EventEmitter.prototype.removeListener = function(type, listener) {
+  var list, position, length, i;
+
+  if (!isFunction(listener))
+    throw TypeError('listener must be a function');
+
+  if (!this._events || !this._events[type])
+    return this;
+
+  list = this._events[type];
+  length = list.length;
+  position = -1;
+
+  if (list === listener ||
+      (isFunction(list.listener) && list.listener === listener)) {
+    delete this._events[type];
+    if (this._events.removeListener)
+      this.emit('removeListener', type, listener);
+
+  } else if (isObject(list)) {
+    for (i = length; i-- > 0;) {
+      if (list[i] === listener ||
+          (list[i].listener && list[i].listener === listener)) {
+        position = i;
+        break;
+      }
+    }
+
+    if (position < 0)
+      return this;
+
+    if (list.length === 1) {
+      list.length = 0;
+      delete this._events[type];
+    } else {
+      list.splice(position, 1);
+    }
+
+    if (this._events.removeListener)
+      this.emit('removeListener', type, listener);
+  }
+
+  return this;
+};
+
+EventEmitter.prototype.removeAllListeners = function(type) {
+  var key, listeners;
+
+  if (!this._events)
+    return this;
+
+  // not listening for removeListener, no need to emit
+  if (!this._events.removeListener) {
+    if (arguments.length === 0)
+      this._events = {};
+    else if (this._events[type])
+      delete this._events[type];
+    return this;
+  }
+
+  // emit removeListener for all listeners on all events
+  if (arguments.length === 0) {
+    for (key in this._events) {
+      if (key === 'removeListener') continue;
+      this.removeAllListeners(key);
+    }
+    this.removeAllListeners('removeListener');
+    this._events = {};
+    return this;
+  }
+
+  listeners = this._events[type];
+
+  if (isFunction(listeners)) {
+    this.removeListener(type, listeners);
+  } else {
+    // LIFO order
+    while (listeners.length)
+      this.removeListener(type, listeners[listeners.length - 1]);
+  }
+  delete this._events[type];
+
+  return this;
+};
+
+EventEmitter.prototype.listeners = function(type) {
+  var ret;
+  if (!this._events || !this._events[type])
+    ret = [];
+  else if (isFunction(this._events[type]))
+    ret = [this._events[type]];
+  else
+    ret = this._events[type].slice();
+  return ret;
+};
+
+EventEmitter.listenerCount = function(emitter, type) {
+  var ret;
+  if (!emitter._events || !emitter._events[type])
+    ret = 0;
+  else if (isFunction(emitter._events[type]))
+    ret = 1;
+  else
+    ret = emitter._events[type].length;
+  return ret;
+};
+
+function isFunction(arg) {
+  return typeof arg === 'function';
+}
+
+function isNumber(arg) {
+  return typeof arg === 'number';
+}
+
+function isObject(arg) {
+  return typeof arg === 'object' && arg !== null;
+}
+
+function isUndefined(arg) {
+  return arg === void 0;
+}
+
+},{}],15:[function(require,module,exports){
+(function (process){
+exports.alphasort = alphasort
+exports.alphasorti = alphasorti
+exports.setopts = setopts
+exports.ownProp = ownProp
+exports.makeAbs = makeAbs
+exports.finish = finish
+exports.mark = mark
+exports.isIgnored = isIgnored
+exports.childrenIgnored = childrenIgnored
+
+function ownProp (obj, field) {
+  return Object.prototype.hasOwnProperty.call(obj, field)
+}
+
+var path = require("path")
+var minimatch = require("minimatch")
+var isAbsolute = require("path-is-absolute")
+var Minimatch = minimatch.Minimatch
+
+function alphasorti (a, b) {
+  return a.toLowerCase().localeCompare(b.toLowerCase())
+}
+
+function alphasort (a, b) {
+  return a.localeCompare(b)
+}
+
+function setupIgnores (self, options) {
+  self.ignore = options.ignore || []
+
+  if (!Array.isArray(self.ignore))
+    self.ignore = [self.ignore]
+
+  if (self.ignore.length) {
+    self.ignore = self.ignore.map(ignoreMap)
+  }
+}
+
+function ignoreMap (pattern) {
+  var gmatcher = null
+  if (pattern.slice(-3) === '/**') {
+    var gpattern = pattern.replace(/(\/\*\*)+$/, '')
+    gmatcher = new Minimatch(gpattern)
+  }
+
+  return {
+    matcher: new Minimatch(pattern),
+    gmatcher: gmatcher
+  }
+}
+
+function setopts (self, pattern, options) {
+  if (!options)
+    options = {}
+
+  // base-matching: just use globstar for that.
+  if (options.matchBase && -1 === pattern.indexOf("/")) {
+    if (options.noglobstar) {
+      throw new Error("base matching requires globstar")
+    }
+    pattern = "**/" + pattern
+  }
+
+  self.silent = !!options.silent
+  self.pattern = pattern
+  self.strict = options.strict !== false
+  self.realpath = !!options.realpath
+  self.realpathCache = options.realpathCache || Object.create(null)
+  self.follow = !!options.follow
+  self.dot = !!options.dot
+  self.mark = !!options.mark
+  self.nodir = !!options.nodir
+  if (self.nodir)
+    self.mark = true
+  self.sync = !!options.sync
+  self.nounique = !!options.nounique
+  self.nonull = !!options.nonull
+  self.nosort = !!options.nosort
+  self.nocase = !!options.nocase
+  self.stat = !!options.stat
+  self.noprocess = !!options.noprocess
+
+  self.maxLength = options.maxLength || Infinity
+  self.cache = options.cache || Object.create(null)
+  self.statCache = options.statCache || Object.create(null)
+  self.symlinks = options.symlinks || Object.create(null)
+
+  setupIgnores(self, options)
+
+  self.changedCwd = false
+  var cwd = process.cwd()
+  if (!ownProp(options, "cwd"))
+    self.cwd = cwd
+  else {
+    self.cwd = options.cwd
+    self.changedCwd = path.resolve(options.cwd) !== cwd
+  }
+
+  self.root = options.root || path.resolve(self.cwd, "/")
+  self.root = path.resolve(self.root)
+  if (process.platform === "win32")
+    self.root = self.root.replace(/\\/g, "/")
+
+  self.nomount = !!options.nomount
+
+  // disable comments and negation unless the user explicitly
+  // passes in false as the option.
+  options.nonegate = options.nonegate === false ? false : true
+  options.nocomment = options.nocomment === false ? false : true
+  deprecationWarning(options)
+
+  self.minimatch = new Minimatch(pattern, options)
+  self.options = self.minimatch.options
+}
+
+// TODO(isaacs): remove entirely in v6
+// exported to reset in tests
+exports.deprecationWarned
+function deprecationWarning(options) {
+  if (!options.nonegate || !options.nocomment) {
+    if (process.noDeprecation !== true && !exports.deprecationWarned) {
+      var msg = 'glob WARNING: comments and negation will be disabled in v6'
+      if (process.throwDeprecation)
+        throw new Error(msg)
+      else if (process.traceDeprecation)
+        console.trace(msg)
+      else
+        console.error(msg)
+
+      exports.deprecationWarned = true
+    }
+  }
+}
+
+function finish (self) {
+  var nou = self.nounique
+  var all = nou ? [] : Object.create(null)
+
+  for (var i = 0, l = self.matches.length; i < l; i ++) {
+    var matches = self.matches[i]
+    if (!matches || Object.keys(matches).length === 0) {
+      if (self.nonull) {
+        // do like the shell, and spit out the literal glob
+        var literal = self.minimatch.globSet[i]
+        if (nou)
+          all.push(literal)
+        else
+          all[literal] = true
+      }
+    } else {
+      // had matches
+      var m = Object.keys(matches)
+      if (nou)
+        all.push.apply(all, m)
+      else
+        m.forEach(function (m) {
+          all[m] = true
+        })
+    }
+  }
+
+  if (!nou)
+    all = Object.keys(all)
+
+  if (!self.nosort)
+    all = all.sort(self.nocase ? alphasorti : alphasort)
+
+  // at *some* point we statted all of these
+  if (self.mark) {
+    for (var i = 0; i < all.length; i++) {
+      all[i] = self._mark(all[i])
+    }
+    if (self.nodir) {
+      all = all.filter(function (e) {
+        return !(/\/$/.test(e))
+      })
+    }
+  }
+
+  if (self.ignore.length)
+    all = all.filter(function(m) {
+      return !isIgnored(self, m)
+    })
+
+  self.found = all
+}
+
+function mark (self, p) {
+  var abs = makeAbs(self, p)
+  var c = self.cache[abs]
+  var m = p
+  if (c) {
+    var isDir = c === 'DIR' || Array.isArray(c)
+    var slash = p.slice(-1) === '/'
+
+    if (isDir && !slash)
+      m += '/'
+    else if (!isDir && slash)
+      m = m.slice(0, -1)
+
+    if (m !== p) {
+      var mabs = makeAbs(self, m)
+      self.statCache[mabs] = self.statCache[abs]
+      self.cache[mabs] = self.cache[abs]
+    }
+  }
+
+  return m
+}
+
+// lotta situps...
+function makeAbs (self, f) {
+  var abs = f
+  if (f.charAt(0) === '/') {
+    abs = path.join(self.root, f)
+  } else if (isAbsolute(f) || f === '') {
+    abs = f
+  } else if (self.changedCwd) {
+    abs = path.resolve(self.cwd, f)
+  } else {
+    abs = path.resolve(f)
+  }
+  return abs
+}
+
+
+// Return true, if pattern ends with globstar '**', for the accompanying parent directory.
+// Ex:- If node_modules/** is the pattern, add 'node_modules' to ignore list along with it's contents
+function isIgnored (self, path) {
+  if (!self.ignore.length)
+    return false
+
+  return self.ignore.some(function(item) {
+    return item.matcher.match(path) || !!(item.gmatcher && item.gmatcher.match(path))
+  })
+}
+
+function childrenIgnored (self, path) {
+  if (!self.ignore.length)
+    return false
+
+  return self.ignore.some(function(item) {
+    return !!(item.gmatcher && item.gmatcher.match(path))
+  })
+}
+
+}).call(this,require('_process'))
+},{"_process":24,"minimatch":20,"path":22,"path-is-absolute":23}],16:[function(require,module,exports){
+(function (process){
+// Approach:
+//
+// 1. Get the minimatch set
+// 2. For each pattern in the set, PROCESS(pattern, false)
+// 3. Store matches per-set, then uniq them
+//
+// PROCESS(pattern, inGlobStar)
+// Get the first [n] items from pattern that are all strings
+// Join these together.  This is PREFIX.
+//   If there is no more remaining, then stat(PREFIX) and
+//   add to matches if it succeeds.  END.
+//
+// If inGlobStar and PREFIX is symlink and points to dir
+//   set ENTRIES = []
+// else readdir(PREFIX) as ENTRIES
+//   If fail, END
+//
+// with ENTRIES
+//   If pattern[n] is GLOBSTAR
+//     // handle the case where the globstar match is empty
+//     // by pruning it out, and testing the resulting pattern
+//     PROCESS(pattern[0..n] + pattern[n+1 .. $], false)
+//     // handle other cases.
+//     for ENTRY in ENTRIES (not dotfiles)
+//       // attach globstar + tail onto the entry
+//       // Mark that this entry is a globstar match
+//       PROCESS(pattern[0..n] + ENTRY + pattern[n .. $], true)
+//
+//   else // not globstar
+//     for ENTRY in ENTRIES (not dotfiles, unless pattern[n] is dot)
+//       Test ENTRY against pattern[n]
+//       If fails, continue
+//       If passes, PROCESS(pattern[0..n] + item + pattern[n+1 .. $])
+//
+// Caveat:
+//   Cache all stats and readdirs results to minimize syscall.  Since all
+//   we ever care about is existence and directory-ness, we can just keep
+//   `true` for files, and [children,...] for directories, or `false` for
+//   things that don't exist.
+
+module.exports = glob
+
+var fs = require('fs')
+var minimatch = require('minimatch')
+var Minimatch = minimatch.Minimatch
+var inherits = require('inherits')
+var EE = require('events').EventEmitter
+var path = require('path')
+var assert = require('assert')
+var isAbsolute = require('path-is-absolute')
+var globSync = require('./sync.js')
+var common = require('./common.js')
+var alphasort = common.alphasort
+var alphasorti = common.alphasorti
+var setopts = common.setopts
+var ownProp = common.ownProp
+var inflight = require('inflight')
+var util = require('util')
+var childrenIgnored = common.childrenIgnored
+var isIgnored = common.isIgnored
+
+var once = require('once')
+
+function glob (pattern, options, cb) {
+  if (typeof options === 'function') cb = options, options = {}
+  if (!options) options = {}
+
+  if (options.sync) {
+    if (cb)
+      throw new TypeError('callback provided to sync glob')
+    return globSync(pattern, options)
+  }
+
+  return new Glob(pattern, options, cb)
+}
+
+glob.sync = globSync
+var GlobSync = glob.GlobSync = globSync.GlobSync
+
+// old api surface
+glob.glob = glob
+
+glob.hasMagic = function (pattern, options_) {
+  var options = util._extend({}, options_)
+  options.noprocess = true
+
+  var g = new Glob(pattern, options)
+  var set = g.minimatch.set
+  if (set.length > 1)
+    return true
+
+  for (var j = 0; j < set[0].length; j++) {
+    if (typeof set[0][j] !== 'string')
+      return true
+  }
+
+  return false
+}
+
+glob.Glob = Glob
+inherits(Glob, EE)
+function Glob (pattern, options, cb) {
+  if (typeof options === 'function') {
+    cb = options
+    options = null
+  }
+
+  if (options && options.sync) {
+    if (cb)
+      throw new TypeError('callback provided to sync glob')
+    return new GlobSync(pattern, options)
+  }
+
+  if (!(this instanceof Glob))
+    return new Glob(pattern, options, cb)
+
+  setopts(this, pattern, options)
+  this._didRealPath = false
+
+  // process each pattern in the minimatch set
+  var n = this.minimatch.set.length
+
+  // The matches are stored as {<filename>: true,...} so that
+  // duplicates are automagically pruned.
+  // Later, we do an Object.keys() on these.
+  // Keep them as a list so we can fill in when nonull is set.
+  this.matches = new Array(n)
+
+  if (typeof cb === 'function') {
+    cb = once(cb)
+    this.on('error', cb)
+    this.on('end', function (matches) {
+      cb(null, matches)
+    })
+  }
+
+  var self = this
+  var n = this.minimatch.set.length
+  this._processing = 0
+  this.matches = new Array(n)
+
+  this._emitQueue = []
+  this._processQueue = []
+  this.paused = false
+
+  if (this.noprocess)
+    return this
+
+  if (n === 0)
+    return done()
+
+  for (var i = 0; i < n; i ++) {
+    this._process(this.minimatch.set[i], i, false, done)
+  }
+
+  function done () {
+    --self._processing
+    if (self._processing <= 0)
+      self._finish()
+  }
+}
+
+Glob.prototype._finish = function () {
+  assert(this instanceof Glob)
+  if (this.aborted)
+    return
+
+  if (this.realpath && !this._didRealpath)
+    return this._realpath()
+
+  common.finish(this)
+  this.emit('end', this.found)
+}
+
+Glob.prototype._realpath = function () {
+  if (this._didRealpath)
+    return
+
+  this._didRealpath = true
+
+  var n = this.matches.length
+  if (n === 0)
+    return this._finish()
+
+  var self = this
+  for (var i = 0; i < this.matches.length; i++)
+    this._realpathSet(i, next)
+
+  function next () {
+    if (--n === 0)
+      self._finish()
+  }
+}
+
+Glob.prototype._realpathSet = function (index, cb) {
+  var matchset = this.matches[index]
+  if (!matchset)
+    return cb()
+
+  var found = Object.keys(matchset)
+  var self = this
+  var n = found.length
+
+  if (n === 0)
+    return cb()
+
+  var set = this.matches[index] = Object.create(null)
+  found.forEach(function (p, i) {
+    // If there's a problem with the stat, then it means that
+    // one or more of the links in the realpath couldn't be
+    // resolved.  just return the abs value in that case.
+    p = self._makeAbs(p)
+    fs.realpath(p, self.realpathCache, function (er, real) {
+      if (!er)
+        set[real] = true
+      else if (er.syscall === 'stat')
+        set[p] = true
+      else
+        self.emit('error', er) // srsly wtf right here
+
+      if (--n === 0) {
+        self.matches[index] = set
+        cb()
+      }
+    })
+  })
+}
+
+Glob.prototype._mark = function (p) {
+  return common.mark(this, p)
+}
+
+Glob.prototype._makeAbs = function (f) {
+  return common.makeAbs(this, f)
+}
+
+Glob.prototype.abort = function () {
+  this.aborted = true
+  this.emit('abort')
+}
+
+Glob.prototype.pause = function () {
+  if (!this.paused) {
+    this.paused = true
+    this.emit('pause')
+  }
+}
+
+Glob.prototype.resume = function () {
+  if (this.paused) {
+    this.emit('resume')
+    this.paused = false
+    if (this._emitQueue.length) {
+      var eq = this._emitQueue.slice(0)
+      this._emitQueue.length = 0
+      for (var i = 0; i < eq.length; i ++) {
+        var e = eq[i]
+        this._emitMatch(e[0], e[1])
+      }
+    }
+    if (this._processQueue.length) {
+      var pq = this._processQueue.slice(0)
+      this._processQueue.length = 0
+      for (var i = 0; i < pq.length; i ++) {
+        var p = pq[i]
+        this._processing--
+        this._process(p[0], p[1], p[2], p[3])
+      }
+    }
+  }
+}
+
+Glob.prototype._process = function (pattern, index, inGlobStar, cb) {
+  assert(this instanceof Glob)
+  assert(typeof cb === 'function')
+
+  if (this.aborted)
+    return
+
+  this._processing++
+  if (this.paused) {
+    this._processQueue.push([pattern, index, inGlobStar, cb])
+    return
+  }
+
+  //console.error('PROCESS %d', this._processing, pattern)
+
+  // Get the first [n] parts of pattern that are all strings.
+  var n = 0
+  while (typeof pattern[n] === 'string') {
+    n ++
+  }
+  // now n is the index of the first one that is *not* a string.
+
+  // see if there's anything else
+  var prefix
+  switch (n) {
+    // if not, then this is rather simple
+    case pattern.length:
+      this._processSimple(pattern.join('/'), index, cb)
+      return
+
+    case 0:
+      // pattern *starts* with some non-trivial item.
+      // going to readdir(cwd), but not include the prefix in matches.
+      prefix = null
+      break
+
+    default:
+      // pattern has some string bits in the front.
+      // whatever it starts with, whether that's 'absolute' like /foo/bar,
+      // or 'relative' like '../baz'
+      prefix = pattern.slice(0, n).join('/')
+      break
+  }
+
+  var remain = pattern.slice(n)
+
+  // get the list of entries.
+  var read
+  if (prefix === null)
+    read = '.'
+  else if (isAbsolute(prefix) || isAbsolute(pattern.join('/'))) {
+    if (!prefix || !isAbsolute(prefix))
+      prefix = '/' + prefix
+    read = prefix
+  } else
+    read = prefix
+
+  var abs = this._makeAbs(read)
+
+  //if ignored, skip _processing
+  if (childrenIgnored(this, read))
+    return cb()
+
+  var isGlobStar = remain[0] === minimatch.GLOBSTAR
+  if (isGlobStar)
+    this._processGlobStar(prefix, read, abs, remain, index, inGlobStar, cb)
+  else
+    this._processReaddir(prefix, read, abs, remain, index, inGlobStar, cb)
+}
+
+Glob.prototype._processReaddir = function (prefix, read, abs, remain, index, inGlobStar, cb) {
+  var self = this
+  this._readdir(abs, inGlobStar, function (er, entries) {
+    return self._processReaddir2(prefix, read, abs, remain, index, inGlobStar, entries, cb)
+  })
+}
+
+Glob.prototype._processReaddir2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) {
+
+  // if the abs isn't a dir, then nothing can match!
+  if (!entries)
+    return cb()
+
+  // It will only match dot entries if it starts with a dot, or if
+  // dot is set.  Stuff like @(.foo|.bar) isn't allowed.
+  var pn = remain[0]
+  var negate = !!this.minimatch.negate
+  var rawGlob = pn._glob
+  var dotOk = this.dot || rawGlob.charAt(0) === '.'
+
+  var matchedEntries = []
+  for (var i = 0; i < entries.length; i++) {
+    var e = entries[i]
+    if (e.charAt(0) !== '.' || dotOk) {
+      var m
+      if (negate && !prefix) {
+        m = !e.match(pn)
+      } else {
+        m = e.match(pn)
+      }
+      if (m)
+        matchedEntries.push(e)
+    }
+  }
+
+  //console.error('prd2', prefix, entries, remain[0]._glob, matchedEntries)
+
+  var len = matchedEntries.length
+  // If there are no matched entries, then nothing matches.
+  if (len === 0)
+    return cb()
+
+  // if this is the last remaining pattern bit, then no need for
+  // an additional stat *unless* the user has specified mark or
+  // stat explicitly.  We know they exist, since readdir returned
+  // them.
+
+  if (remain.length === 1 && !this.mark && !this.stat) {
+    if (!this.matches[index])
+      this.matches[index] = Object.create(null)
+
+    for (var i = 0; i < len; i ++) {
+      var e = matchedEntries[i]
+      if (prefix) {
+        if (prefix !== '/')
+          e = prefix + '/' + e
+        else
+          e = prefix + e
+      }
+
+      if (e.charAt(0) === '/' && !this.nomount) {
+        e = path.join(this.root, e)
+      }
+      this._emitMatch(index, e)
+    }
+    // This was the last one, and no stats were needed
+    return cb()
+  }
+
+  // now test all matched entries as stand-ins for that part
+  // of the pattern.
+  remain.shift()
+  for (var i = 0; i < len; i ++) {
+    var e = matchedEntries[i]
+    var newPattern
+    if (prefix) {
+      if (prefix !== '/')
+        e = prefix + '/' + e
+      else
+        e = prefix + e
+    }
+    this._process([e].concat(remain), index, inGlobStar, cb)
+  }
+  cb()
+}
+
+Glob.prototype._emitMatch = function (index, e) {
+  if (this.aborted)
+    return
+
+  if (this.matches[index][e])
+    return
+
+  if (isIgnored(this, e))
+    return
+
+  if (this.paused) {
+    this._emitQueue.push([index, e])
+    return
+  }
+
+  var abs = this._makeAbs(e)
+
+  if (this.nodir) {
+    var c = this.cache[abs]
+    if (c === 'DIR' || Array.isArray(c))
+      return
+  }
+
+  if (this.mark)
+    e = this._mark(e)
+
+  this.matches[index][e] = true
+
+  var st = this.statCache[abs]
+  if (st)
+    this.emit('stat', e, st)
+
+  this.emit('match', e)
+}
+
+Glob.prototype._readdirInGlobStar = function (abs, cb) {
+  if (this.aborted)
+    return
+
+  // follow all symlinked directories forever
+  // just proceed as if this is a non-globstar situation
+  if (this.follow)
+    return this._readdir(abs, false, cb)
+
+  var lstatkey = 'lstat\0' + abs
+  var self = this
+  var lstatcb = inflight(lstatkey, lstatcb_)
+
+  if (lstatcb)
+    fs.lstat(abs, lstatcb)
+
+  function lstatcb_ (er, lstat) {
+    if (er)
+      return cb()
+
+    var isSym = lstat.isSymbolicLink()
+    self.symlinks[abs] = isSym
+
+    // If it's not a symlink or a dir, then it's definitely a regular file.
+    // don't bother doing a readdir in that case.
+    if (!isSym && !lstat.isDirectory()) {
+      self.cache[abs] = 'FILE'
+      cb()
+    } else
+      self._readdir(abs, false, cb)
+  }
+}
+
+Glob.prototype._readdir = function (abs, inGlobStar, cb) {
+  if (this.aborted)
+    return
+
+  cb = inflight('readdir\0'+abs+'\0'+inGlobStar, cb)
+  if (!cb)
+    return
+
+  //console.error('RD %j %j', +inGlobStar, abs)
+  if (inGlobStar && !ownProp(this.symlinks, abs))
+    return this._readdirInGlobStar(abs, cb)
+
+  if (ownProp(this.cache, abs)) {
+    var c = this.cache[abs]
+    if (!c || c === 'FILE')
+      return cb()
+
+    if (Array.isArray(c))
+      return cb(null, c)
+  }
+
+  var self = this
+  fs.readdir(abs, readdirCb(this, abs, cb))
+}
+
+function readdirCb (self, abs, cb) {
+  return function (er, entries) {
+    if (er)
+      self._readdirError(abs, er, cb)
+    else
+      self._readdirEntries(abs, entries, cb)
+  }
+}
+
+Glob.prototype._readdirEntries = function (abs, entries, cb) {
+  if (this.aborted)
+    return
+
+  // if we haven't asked to stat everything, then just
+  // assume that everything in there exists, so we can avoid
+  // having to stat it a second time.
+  if (!this.mark && !this.stat) {
+    for (var i = 0; i < entries.length; i ++) {
+      var e = entries[i]
+      if (abs === '/')
+        e = abs + e
+      else
+        e = abs + '/' + e
+      this.cache[e] = true
+    }
+  }
+
+  this.cache[abs] = entries
+  return cb(null, entries)
+}
+
+Glob.prototype._readdirError = function (f, er, cb) {
+  if (this.aborted)
+    return
+
+  // handle errors, and cache the information
+  switch (er.code) {
+    case 'ENOTSUP': // https://github.com/isaacs/node-glob/issues/205
+    case 'ENOTDIR': // totally normal. means it *does* exist.
+      this.cache[this._makeAbs(f)] = 'FILE'
+      break
+
+    case 'ENOENT': // not terribly unusual
+    case 'ELOOP':
+    case 'ENAMETOOLONG':
+    case 'UNKNOWN':
+      this.cache[this._makeAbs(f)] = false
+      break
+
+    default: // some unusual error.  Treat as failure.
+      this.cache[this._makeAbs(f)] = false
+      if (this.strict) {
+        this.emit('error', er)
+        // If the error is handled, then we abort
+        // if not, we threw out of here
+        this.abort()
+      }
+      if (!this.silent)
+        console.error('glob error', er)
+      break
+  }
+
+  return cb()
+}
+
+Glob.prototype._processGlobStar = function (prefix, read, abs, remain, index, inGlobStar, cb) {
+  var self = this
+  this._readdir(abs, inGlobStar, function (er, entries) {
+    self._processGlobStar2(prefix, read, abs, remain, index, inGlobStar, entries, cb)
+  })
+}
+
+
+Glob.prototype._processGlobStar2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) {
+  //console.error('pgs2', prefix, remain[0], entries)
+
+  // no entries means not a dir, so it can never have matches
+  // foo.txt/** doesn't match foo.txt
+  if (!entries)
+    return cb()
+
+  // test without the globstar, and with every child both below
+  // and replacing the globstar.
+  var remainWithoutGlobStar = remain.slice(1)
+  var gspref = prefix ? [ prefix ] : []
+  var noGlobStar = gspref.concat(remainWithoutGlobStar)
+
+  // the noGlobStar pattern exits the inGlobStar state
+  this._process(noGlobStar, index, false, cb)
+
+  var isSym = this.symlinks[abs]
+  var len = entries.length
+
+  // If it's a symlink, and we're in a globstar, then stop
+  if (isSym && inGlobStar)
+    return cb()
+
+  for (var i = 0; i < len; i++) {
+    var e = entries[i]
+    if (e.charAt(0) === '.' && !this.dot)
+      continue
+
+    // these two cases enter the inGlobStar state
+    var instead = gspref.concat(entries[i], remainWithoutGlobStar)
+    this._process(instead, index, true, cb)
+
+    var below = gspref.concat(entries[i], remain)
+    this._process(below, index, true, cb)
+  }
+
+  cb()
+}
+
+Glob.prototype._processSimple = function (prefix, index, cb) {
+  // XXX review this.  Shouldn't it be doing the mounting etc
+  // before doing stat?  kinda weird?
+  var self = this
+  this._stat(prefix, function (er, exists) {
+    self._processSimple2(prefix, index, er, exists, cb)
+  })
+}
+Glob.prototype._processSimple2 = function (prefix, index, er, exists, cb) {
+
+  //console.error('ps2', prefix, exists)
+
+  if (!this.matches[index])
+    this.matches[index] = Object.create(null)
+
+  // If it doesn't exist, then just mark the lack of results
+  if (!exists)
+    return cb()
+
+  if (prefix && isAbsolute(prefix) && !this.nomount) {
+    var trail = /[\/\\]$/.test(prefix)
+    if (prefix.charAt(0) === '/') {
+      prefix = path.join(this.root, prefix)
+    } else {
+      prefix = path.resolve(this.root, prefix)
+      if (trail)
+        prefix += '/'
+    }
+  }
+
+  if (process.platform === 'win32')
+    prefix = prefix.replace(/\\/g, '/')
+
+  // Mark this as a match
+  this._emitMatch(index, prefix)
+  cb()
+}
+
+// Returns either 'DIR', 'FILE', or false
+Glob.prototype._stat = function (f, cb) {
+  var abs = this._makeAbs(f)
+  var needDir = f.slice(-1) === '/'
+
+  if (f.length > this.maxLength)
+    return cb()
+
+  if (!this.stat && ownProp(this.cache, abs)) {
+    var c = this.cache[abs]
+
+    if (Array.isArray(c))
+      c = 'DIR'
+
+    // It exists, but maybe not how we need it
+    if (!needDir || c === 'DIR')
+      return cb(null, c)
+
+    if (needDir && c === 'FILE')
+      return cb()
+
+    // otherwise we have to stat, because maybe c=true
+    // if we know it exists, but not what it is.
+  }
+
+  var exists
+  var stat = this.statCache[abs]
+  if (stat !== undefined) {
+    if (stat === false)
+      return cb(null, stat)
+    else {
+      var type = stat.isDirectory() ? 'DIR' : 'FILE'
+      if (needDir && type === 'FILE')
+        return cb()
+      else
+        return cb(null, type, stat)
+    }
+  }
+
+  var self = this
+  var statcb = inflight('stat\0' + abs, lstatcb_)
+  if (statcb)
+    fs.lstat(abs, statcb)
+
+  function lstatcb_ (er, lstat) {
+    if (lstat && lstat.isSymbolicLink()) {
+      // If it's a symlink, then treat it as the target, unless
+      // the target does not exist, then treat it as a file.
+      return fs.stat(abs, function (er, stat) {
+        if (er)
+          self._stat2(f, abs, null, lstat, cb)
+        else
+          self._stat2(f, abs, er, stat, cb)
+      })
+    } else {
+      self._stat2(f, abs, er, lstat, cb)
+    }
+  }
+}
+
+Glob.prototype._stat2 = function (f, abs, er, stat, cb) {
+  if (er) {
+    this.statCache[abs] = false
+    return cb()
+  }
+
+  var needDir = f.slice(-1) === '/'
+  this.statCache[abs] = stat
+
+  if (abs.slice(-1) === '/' && !stat.isDirectory())
+    return cb(null, false, stat)
+
+  var c = stat.isDirectory() ? 'DIR' : 'FILE'
+  this.cache[abs] = this.cache[abs] || c
+
+  if (needDir && c !== 'DIR')
+    return cb()
+
+  return cb(null, c, stat)
+}
+
+}).call(this,require('_process'))
+},{"./common.js":15,"./sync.js":17,"_process":24,"assert":9,"events":14,"fs":12,"inflight":18,"inherits":19,"minimatch":20,"once":21,"path":22,"path-is-absolute":23,"util":28}],17:[function(require,module,exports){
+(function (process){
+module.exports = globSync
+globSync.GlobSync = GlobSync
+
+var fs = require('fs')
+var minimatch = require('minimatch')
+var Minimatch = minimatch.Minimatch
+var Glob = require('./glob.js').Glob
+var util = require('util')
+var path = require('path')
+var assert = require('assert')
+var isAbsolute = require('path-is-absolute')
+var common = require('./common.js')
+var alphasort = common.alphasort
+var alphasorti = common.alphasorti
+var setopts = common.setopts
+var ownProp = common.ownProp
+var childrenIgnored = common.childrenIgnored
+
+function globSync (pattern, options) {
+  if (typeof options === 'function' || arguments.length === 3)
+    throw new TypeError('callback provided to sync glob\n'+
+                        'See: https://github.com/isaacs/node-glob/issues/167')
+
+  return new GlobSync(pattern, options).found
+}
+
+function GlobSync (pattern, options) {
+  if (!pattern)
+    throw new Error('must provide pattern')
+
+  if (typeof options === 'function' || arguments.length === 3)
+    throw new TypeError('callback provided to sync glob\n'+
+                        'See: https://github.com/isaacs/node-glob/issues/167')
+
+  if (!(this instanceof GlobSync))
+    return new GlobSync(pattern, options)
+
+  setopts(this, pattern, options)
+
+  if (this.noprocess)
+    return this
+
+  var n = this.minimatch.set.length
+  this.matches = new Array(n)
+  for (var i = 0; i < n; i ++) {
+    this._process(this.minimatch.set[i], i, false)
+  }
+  this._finish()
+}
+
+GlobSync.prototype._finish = function () {
+  assert(this instanceof GlobSync)
+  if (this.realpath) {
+    var self = this
+    this.matches.forEach(function (matchset, index) {
+      var set = self.matches[index] = Object.create(null)
+      for (var p in matchset) {
+        try {
+          p = self._makeAbs(p)
+          var real = fs.realpathSync(p, self.realpathCache)
+          set[real] = true
+        } catch (er) {
+          if (er.syscall === 'stat')
+            set[self._makeAbs(p)] = true
+          else
+            throw er
+        }
+      }
+    })
+  }
+  common.finish(this)
+}
+
+
+GlobSync.prototype._process = function (pattern, index, inGlobStar) {
+  assert(this instanceof GlobSync)
+
+  // Get the first [n] parts of pattern that are all strings.
+  var n = 0
+  while (typeof pattern[n] === 'string') {
+    n ++
+  }
+  // now n is the index of the first one that is *not* a string.
+
+  // See if there's anything else
+  var prefix
+  switch (n) {
+    // if not, then this is rather simple
+    case pattern.length:
+      this._processSimple(pattern.join('/'), index)
+      return
+
+    case 0:
+      // pattern *starts* with some non-trivial item.
+      // going to readdir(cwd), but not include the prefix in matches.
+      prefix = null
+      break
+
+    default:
+      // pattern has some string bits in the front.
+      // whatever it starts with, whether that's 'absolute' like /foo/bar,
+      // or 'relative' like '../baz'
+      prefix = pattern.slice(0, n).join('/')
+      break
+  }
+
+  var remain = pattern.slice(n)
+
+  // get the list of entries.
+  var read
+  if (prefix === null)
+    read = '.'
+  else if (isAbsolute(prefix) || isAbsolute(pattern.join('/'))) {
+    if (!prefix || !isAbsolute(prefix))
+      prefix = '/' + prefix
+    read = prefix
+  } else
+    read = prefix
+
+  var abs = this._makeAbs(read)
+
+  //if ignored, skip processing
+  if (childrenIgnored(this, read))
+    return
+
+  var isGlobStar = remain[0] === minimatch.GLOBSTAR
+  if (isGlobStar)
+    this._processGlobStar(prefix, read, abs, remain, index, inGlobStar)
+  else
+    this._processReaddir(prefix, read, abs, remain, index, inGlobStar)
+}
+
+
+GlobSync.prototype._processReaddir = function (prefix, read, abs, remain, index, inGlobStar) {
+  var entries = this._readdir(abs, inGlobStar)
+
+  // if the abs isn't a dir, then nothing can match!
+  if (!entries)
+    return
+
+  // It will only match dot entries if it starts with a dot, or if
+  // dot is set.  Stuff like @(.foo|.bar) isn't allowed.
+  var pn = remain[0]
+  var negate = !!this.minimatch.negate
+  var rawGlob = pn._glob
+  var dotOk = this.dot || rawGlob.charAt(0) === '.'
+
+  var matchedEntries = []
+  for (var i = 0; i < entries.length; i++) {
+    var e = entries[i]
+    if (e.charAt(0) !== '.' || dotOk) {
+      var m
+      if (negate && !prefix) {
+        m = !e.match(pn)
+      } else {
+        m = e.match(pn)
+      }
+      if (m)
+        matchedEntries.push(e)
+    }
+  }
+
+  var len = matchedEntries.length
+  // If there are no matched entries, then nothing matches.
+  if (len === 0)
+    return
+
+  // if this is the last remaining pattern bit, then no need for
+  // an additional stat *unless* the user has specified mark or
+  // stat explicitly.  We know they exist, since readdir returned
+  // them.
+
+  if (remain.length === 1 && !this.mark && !this.stat) {
+    if (!this.matches[index])
+      this.matches[index] = Object.create(null)
+
+    for (var i = 0; i < len; i ++) {
+      var e = matchedEntries[i]
+      if (prefix) {
+        if (prefix.slice(-1) !== '/')
+          e = prefix + '/' + e
+        else
+          e = prefix + e
+      }
+
+      if (e.charAt(0) === '/' && !this.nomount) {
+        e = path.join(this.root, e)
+      }
+      this.matches[index][e] = true
+    }
+    // This was the last one, and no stats were needed
+    return
+  }
+
+  // now test all matched entries as stand-ins for that part
+  // of the pattern.
+  remain.shift()
+  for (var i = 0; i < len; i ++) {
+    var e = matchedEntries[i]
+    var newPattern
+    if (prefix)
+      newPattern = [prefix, e]
+    else
+      newPattern = [e]
+    this._process(newPattern.concat(remain), index, inGlobStar)
+  }
+}
+
+
+GlobSync.prototype._emitMatch = function (index, e) {
+  var abs = this._makeAbs(e)
+  if (this.mark)
+    e = this._mark(e)
+
+  if (this.matches[index][e])
+    return
+
+  if (this.nodir) {
+    var c = this.cache[this._makeAbs(e)]
+    if (c === 'DIR' || Array.isArray(c))
+      return
+  }
+
+  this.matches[index][e] = true
+  if (this.stat)
+    this._stat(e)
+}
+
+
+GlobSync.prototype._readdirInGlobStar = function (abs) {
+  // follow all symlinked directories forever
+  // just proceed as if this is a non-globstar situation
+  if (this.follow)
+    return this._readdir(abs, false)
+
+  var entries
+  var lstat
+  var stat
+  try {
+    lstat = fs.lstatSync(abs)
+  } catch (er) {
+    // lstat failed, doesn't exist
+    return null
+  }
+
+  var isSym = lstat.isSymbolicLink()
+  this.symlinks[abs] = isSym
+
+  // If it's not a symlink or a dir, then it's definitely a regular file.
+  // don't bother doing a readdir in that case.
+  if (!isSym && !lstat.isDirectory())
+    this.cache[abs] = 'FILE'
+  else
+    entries = this._readdir(abs, false)
+
+  return entries
+}
+
+GlobSync.prototype._readdir = function (abs, inGlobStar) {
+  var entries
+
+  if (inGlobStar && !ownProp(this.symlinks, abs))
+    return this._readdirInGlobStar(abs)
+
+  if (ownProp(this.cache, abs)) {
+    var c = this.cache[abs]
+    if (!c || c === 'FILE')
+      return null
+
+    if (Array.isArray(c))
+      return c
+  }
+
+  try {
+    return this._readdirEntries(abs, fs.readdirSync(abs))
+  } catch (er) {
+    this._readdirError(abs, er)
+    return null
+  }
+}
+
+GlobSync.prototype._readdirEntries = function (abs, entries) {
+  // if we haven't asked to stat everything, then just
+  // assume that everything in there exists, so we can avoid
+  // having to stat it a second time.
+  if (!this.mark && !this.stat) {
+    for (var i = 0; i < entries.length; i ++) {
+      var e = entries[i]
+      if (abs === '/')
+        e = abs + e
+      else
+        e = abs + '/' + e
+      this.cache[e] = true
+    }
+  }
+
+  this.cache[abs] = entries
+
+  // mark and cache dir-ness
+  return entries
+}
+
+GlobSync.prototype._readdirError = function (f, er) {
+  // handle errors, and cache the information
+  switch (er.code) {
+    case 'ENOTSUP': // https://github.com/isaacs/node-glob/issues/205
+    case 'ENOTDIR': // totally normal. means it *does* exist.
+      this.cache[this._makeAbs(f)] = 'FILE'
+      break
+
+    case 'ENOENT': // not terribly unusual
+    case 'ELOOP':
+    case 'ENAMETOOLONG':
+    case 'UNKNOWN':
+      this.cache[this._makeAbs(f)] = false
+      break
+
+    default: // some unusual error.  Treat as failure.
+      this.cache[this._makeAbs(f)] = false
+      if (this.strict)
+        throw er
+      if (!this.silent)
+        console.error('glob error', er)
+      break
+  }
+}
+
+GlobSync.prototype._processGlobStar = function (prefix, read, abs, remain, index, inGlobStar) {
+
+  var entries = this._readdir(abs, inGlobStar)
+
+  // no entries means not a dir, so it can never have matches
+  // foo.txt/** doesn't match foo.txt
+  if (!entries)
+    return
+
+  // test without the globstar, and with every child both below
+  // and replacing the globstar.
+  var remainWithoutGlobStar = remain.slice(1)
+  var gspref = prefix ? [ prefix ] : []
+  var noGlobStar = gspref.concat(remainWithoutGlobStar)
+
+  // the noGlobStar pattern exits the inGlobStar state
+  this._process(noGlobStar, index, false)
+
+  var len = entries.length
+  var isSym = this.symlinks[abs]
+
+  // If it's a symlink, and we're in a globstar, then stop
+  if (isSym && inGlobStar)
+    return
+
+  for (var i = 0; i < len; i++) {
+    var e = entries[i]
+    if (e.charAt(0) === '.' && !this.dot)
+      continue
+
+    // these two cases enter the inGlobStar state
+    var instead = gspref.concat(entries[i], remainWithoutGlobStar)
+    this._process(instead, index, true)
+
+    var below = gspref.concat(entries[i], remain)
+    this._process(below, index, true)
+  }
+}
+
+GlobSync.prototype._processSimple = function (prefix, index) {
+  // XXX review this.  Shouldn't it be doing the mounting etc
+  // before doing stat?  kinda weird?
+  var exists = this._stat(prefix)
+
+  if (!this.matches[index])
+    this.matches[index] = Object.create(null)
+
+  // If it doesn't exist, then just mark the lack of results
+  if (!exists)
+    return
+
+  if (prefix && isAbsolute(prefix) && !this.nomount) {
+    var trail = /[\/\\]$/.test(prefix)
+    if (prefix.charAt(0) === '/') {
+      prefix = path.join(this.root, prefix)
+    } else {
+      prefix = path.resolve(this.root, prefix)
+      if (trail)
+        prefix += '/'
+    }
+  }
+
+  if (process.platform === 'win32')
+    prefix = prefix.replace(/\\/g, '/')
+
+  // Mark this as a match
+  this.matches[index][prefix] = true
+}
+
+// Returns either 'DIR', 'FILE', or false
+GlobSync.prototype._stat = function (f) {
+  var abs = this._makeAbs(f)
+  var needDir = f.slice(-1) === '/'
+
+  if (f.length > this.maxLength)
+    return false
+
+  if (!this.stat && ownProp(this.cache, abs)) {
+    var c = this.cache[abs]
+
+    if (Array.isArray(c))
+      c = 'DIR'
+
+    // It exists, but maybe not how we need it
+    if (!needDir || c === 'DIR')
+      return c
+
+    if (needDir && c === 'FILE')
+      return false
+
+    // otherwise we have to stat, because maybe c=true
+    // if we know it exists, but not what it is.
+  }
+
+  var exists
+  var stat = this.statCache[abs]
+  if (!stat) {
+    var lstat
+    try {
+      lstat = fs.lstatSync(abs)
+    } catch (er) {
+      return false
+    }
+
+    if (lstat.isSymbolicLink()) {
+      try {
+        stat = fs.statSync(abs)
+      } catch (er) {
+        stat = lstat
+      }
+    } else {
+      stat = lstat
+    }
+  }
+
+  this.statCache[abs] = stat
+
+  var c = stat.isDirectory() ? 'DIR' : 'FILE'
+  this.cache[abs] = this.cache[abs] || c
+
+  if (needDir && c !== 'DIR')
+    return false
+
+  return c
+}
+
+GlobSync.prototype._mark = function (p) {
+  return common.mark(this, p)
+}
+
+GlobSync.prototype._makeAbs = function (f) {
+  return common.makeAbs(this, f)
+}
+
+}).call(this,require('_process'))
+},{"./common.js":15,"./glob.js":16,"_process":24,"assert":9,"fs":12,"minimatch":20,"path":22,"path-is-absolute":23,"util":28}],18:[function(require,module,exports){
+(function (process){
+var wrappy = require('wrappy')
+var reqs = Object.create(null)
+var once = require('once')
+
+module.exports = wrappy(inflight)
+
+function inflight (key, cb) {
+  if (reqs[key]) {
+    reqs[key].push(cb)
+    return null
+  } else {
+    reqs[key] = [cb]
+    return makeres(key)
+  }
+}
+
+function makeres (key) {
+  return once(function RES () {
+    var cbs = reqs[key]
+    var len = cbs.length
+    var args = slice(arguments)
+
+    // XXX It's somewhat ambiguous whether a new callback added in this
+    // pass should be queued for later execution if something in the
+    // list of callbacks throws, or if it should just be discarded.
+    // However, it's such an edge case that it hardly matters, and either
+    // choice is likely as surprising as the other.
+    // As it happens, we do go ahead and schedule it for later execution.
+    try {
+      for (var i = 0; i < len; i++) {
+        cbs[i].apply(null, args)
+      }
+    } finally {
+      if (cbs.length > len) {
+        // added more in the interim.
+        // de-zalgo, just in case, but don't call again.
+        cbs.splice(0, len)
+        process.nextTick(function () {
+          RES.apply(null, args)
+        })
+      } else {
+        delete reqs[key]
+      }
+    }
+  })
+}
+
+function slice (args) {
+  var length = args.length
+  var array = []
+
+  for (var i = 0; i < length; i++) array[i] = args[i]
+  return array
+}
+
+}).call(this,require('_process'))
+},{"_process":24,"once":21,"wrappy":29}],19:[function(require,module,exports){
+if (typeof Object.create === 'function') {
+  // implementation from standard node.js 'util' module
+  module.exports = function inherits(ctor, superCtor) {
+    ctor.super_ = superCtor
+    ctor.prototype = Object.create(superCtor.prototype, {
+      constructor: {
+        value: ctor,
+        enumerable: false,
+        writable: true,
+        configurable: true
+      }
+    });
+  };
+} else {
+  // old school shim for old browsers
+  module.exports = function inherits(ctor, superCtor) {
+    ctor.super_ = superCtor
+    var TempCtor = function () {}
+    TempCtor.prototype = superCtor.prototype
+    ctor.prototype = new TempCtor()
+    ctor.prototype.constructor = ctor
+  }
+}
+
+},{}],20:[function(require,module,exports){
+module.exports = minimatch
+minimatch.Minimatch = Minimatch
+
+var path = { sep: '/' }
+try {
+  path = require('path')
+} catch (er) {}
+
+var GLOBSTAR = minimatch.GLOBSTAR = Minimatch.GLOBSTAR = {}
+var expand = require('brace-expansion')
+
+var plTypes = {
+  '!': { open: '(?:(?!(?:', close: '))[^/]*?)'},
+  '?': { open: '(?:', close: ')?' },
+  '+': { open: '(?:', close: ')+' },
+  '*': { open: '(?:', close: ')*' },
+  '@': { open: '(?:', close: ')' }
+}
+
+// any single thing other than /
+// don't need to escape / when using new RegExp()
+var qmark = '[^/]'
+
+// * => any number of characters
+var star = qmark + '*?'
+
+// ** when dots are allowed.  Anything goes, except .. and .
+// not (^ or / followed by one or two dots followed by $ or /),
+// followed by anything, any number of times.
+var twoStarDot = '(?:(?!(?:\\\/|^)(?:\\.{1,2})($|\\\/)).)*?'
+
+// not a ^ or / followed by a dot,
+// followed by anything, any number of times.
+var twoStarNoDot = '(?:(?!(?:\\\/|^)\\.).)*?'
+
+// characters that need to be escaped in RegExp.
+var reSpecials = charSet('().*{}+?[]^$\\!')
+
+// "abc" -> { a:true, b:true, c:true }
+function charSet (s) {
+  return s.split('').reduce(function (set, c) {
+    set[c] = true
+    return set
+  }, {})
+}
+
+// normalizes slashes.
+var slashSplit = /\/+/
+
+minimatch.filter = filter
+function filter (pattern, options) {
+  options = options || {}
+  return function (p, i, list) {
+    return minimatch(p, pattern, options)
+  }
+}
+
+function ext (a, b) {
+  a = a || {}
+  b = b || {}
+  var t = {}
+  Object.keys(b).forEach(function (k) {
+    t[k] = b[k]
+  })
+  Object.keys(a).forEach(function (k) {
+    t[k] = a[k]
+  })
+  return t
+}
+
+minimatch.defaults = function (def) {
+  if (!def || !Object.keys(def).length) return minimatch
+
+  var orig = minimatch
+
+  var m = function minimatch (p, pattern, options) {
+    return orig.minimatch(p, pattern, ext(def, options))
+  }
+
+  m.Minimatch = function Minimatch (pattern, options) {
+    return new orig.Minimatch(pattern, ext(def, options))
+  }
+
+  return m
+}
+
+Minimatch.defaults = function (def) {
+  if (!def || !Object.keys(def).length) return Minimatch
+  return minimatch.defaults(def).Minimatch
+}
+
+function minimatch (p, pattern, options) {
+  if (typeof pattern !== 'string') {
+    throw new TypeError('glob pattern string required')
+  }
+
+  if (!options) options = {}
+
+  // shortcut: comments match nothing.
+  if (!options.nocomment && pattern.charAt(0) === '#') {
+    return false
+  }
+
+  // "" only matches ""
+  if (pattern.trim() === '') return p === ''
+
+  return new Minimatch(pattern, options).match(p)
+}
+
+function Minimatch (pattern, options) {
+  if (!(this instanceof Minimatch)) {
+    return new Minimatch(pattern, options)
+  }
+
+  if (typeof pattern !== 'string') {
+    throw new TypeError('glob pattern string required')
+  }
+
+  if (!options) options = {}
+  pattern = pattern.trim()
+
+  // windows support: need to use /, not \
+  if (path.sep !== '/') {
+    pattern = pattern.split(path.sep).join('/')
+  }
+
+  this.options = options
+  this.set = []
+  this.pattern = pattern
+  this.regexp = null
+  this.negate = false
+  this.comment = false
+  this.empty = false
+
+  // make the set of regexps etc.
+  this.make()
+}
+
+Minimatch.prototype.debug = function () {}
+
+Minimatch.prototype.make = make
+function make () {
+  // don't do it more than once.
+  if (this._made) return
+
+  var pattern = this.pattern
+  var options = this.options
+
+  // empty patterns and comments match nothing.
+  if (!options.nocomment && pattern.charAt(0) === '#') {
+    this.comment = true
+    return
+  }
+  if (!pattern) {
+    this.empty = true
+    return
+  }
+
+  // step 1: figure out negation, etc.
+  this.parseNegate()
+
+  // step 2: expand braces
+  var set = this.globSet = this.braceExpand()
+
+  if (options.debug) this.debug = console.error
+
+  this.debug(this.pattern, set)
+
+  // step 3: now we have a set, so turn each one into a series of path-portion
+  // matching patterns.
+  // These will be regexps, except in the case of "**", which is
+  // set to the GLOBSTAR object for globstar behavior,
+  // and will not contain any / characters
+  set = this.globParts = set.map(function (s) {
+    return s.split(slashSplit)
+  })
+
+  this.debug(this.pattern, set)
+
+  // glob --> regexps
+  set = set.map(function (s, si, set) {
+    return s.map(this.parse, this)
+  }, this)
+
+  this.debug(this.pattern, set)
+
+  // filter out everything that didn't compile properly.
+  set = set.filter(function (s) {
+    return s.indexOf(false) === -1
+  })
+
+  this.debug(this.pattern, set)
+
+  this.set = set
+}
+
+Minimatch.prototype.parseNegate = parseNegate
+function parseNegate () {
+  var pattern = this.pattern
+  var negate = false
+  var options = this.options
+  var negateOffset = 0
+
+  if (options.nonegate) return
+
+  for (var i = 0, l = pattern.length
+    ; i < l && pattern.charAt(i) === '!'
+    ; i++) {
+    negate = !negate
+    negateOffset++
+  }
+
+  if (negateOffset) this.pattern = pattern.substr(negateOffset)
+  this.negate = negate
+}
+
+// Brace expansion:
+// a{b,c}d -> abd acd
+// a{b,}c -> abc ac
+// a{0..3}d -> a0d a1d a2d a3d
+// a{b,c{d,e}f}g -> abg acdfg acefg
+// a{b,c}d{e,f}g -> abdeg acdeg abdeg abdfg
+//
+// Invalid sets are not expanded.
+// a{2..}b -> a{2..}b
+// a{b}c -> a{b}c
+minimatch.braceExpand = function (pattern, options) {
+  return braceExpand(pattern, options)
+}
+
+Minimatch.prototype.braceExpand = braceExpand
+
+function braceExpand (pattern, options) {
+  if (!options) {
+    if (this instanceof Minimatch) {
+      options = this.options
+    } else {
+      options = {}
+    }
+  }
+
+  pattern = typeof pattern === 'undefined'
+    ? this.pattern : pattern
+
+  if (typeof pattern === 'undefined') {
+    throw new TypeError('undefined pattern')
+  }
+
+  if (options.nobrace ||
+    !pattern.match(/\{.*\}/)) {
+    // shortcut. no need to expand.
+    return [pattern]
+  }
+
+  return expand(pattern)
+}
+
+// parse a component of the expanded set.
+// At this point, no pattern may contain "/" in it
+// so we're going to return a 2d array, where each entry is the full
+// pattern, split on '/', and then turned into a regular expression.
+// A regexp is made at the end which joins each array with an
+// escaped /, and another full one which joins each regexp with |.
+//
+// Following the lead of Bash 4.1, note that "**" only has special meaning
+// when it is the *only* thing in a path portion.  Otherwise, any series
+// of * is equivalent to a single *.  Globstar behavior is enabled by
+// default, and can be disabled by setting options.noglobstar.
+Minimatch.prototype.parse = parse
+var SUBPARSE = {}
+function parse (pattern, isSub) {
+  if (pattern.length > 1024 * 64) {
+    throw new TypeError('pattern is too long')
+  }
+
+  var options = this.options
+
+  // shortcuts
+  if (!options.noglobstar && pattern === '**') return GLOBSTAR
+  if (pattern === '') return ''
+
+  var re = ''
+  var hasMagic = !!options.nocase
+  var escaping = false
+  // ? => one single character
+  var patternListStack = []
+  var negativeLists = []
+  var stateChar
+  var inClass = false
+  var reClassStart = -1
+  var classStart = -1
+  // . and .. never match anything that doesn't start with .,
+  // even when options.dot is set.
+  var patternStart = pattern.charAt(0) === '.' ? '' // anything
+  // not (start or / followed by . or .. followed by / or end)
+  : options.dot ? '(?!(?:^|\\\/)\\.{1,2}(?:$|\\\/))'
+  : '(?!\\.)'
+  var self = this
+
+  function clearStateChar () {
+    if (stateChar) {
+      // we had some state-tracking character
+      // that wasn't consumed by this pass.
+      switch (stateChar) {
+        case '*':
+          re += star
+          hasMagic = true
+        break
+        case '?':
+          re += qmark
+          hasMagic = true
+        break
+        default:
+          re += '\\' + stateChar
+        break
+      }
+      self.debug('clearStateChar %j %j', stateChar, re)
+      stateChar = false
+    }
+  }
+
+  for (var i = 0, len = pattern.length, c
+    ; (i < len) && (c = pattern.charAt(i))
+    ; i++) {
+    this.debug('%s\t%s %s %j', pattern, i, re, c)
+
+    // skip over any that are escaped.
+    if (escaping && reSpecials[c]) {
+      re += '\\' + c
+      escaping = false
+      continue
+    }
+
+    switch (c) {
+      case '/':
+        // completely not allowed, even escaped.
+        // Should already be path-split by now.
+        return false
+
+      case '\\':
+        clearStateChar()
+        escaping = true
+      continue
+
+      // the various stateChar values
+      // for the "extglob" stuff.
+      case '?':
+      case '*':
+      case '+':
+      case '@':
+      case '!':
+        this.debug('%s\t%s %s %j <-- stateChar', pattern, i, re, c)
+
+        // all of those are literals inside a class, except that
+        // the glob [!a] means [^a] in regexp
+        if (inClass) {
+          this.debug('  in class')
+          if (c === '!' && i === classStart + 1) c = '^'
+          re += c
+          continue
+        }
+
+        // if we already have a stateChar, then it means
+        // that there was something like ** or +? in there.
+        // Handle the stateChar, then proceed with this one.
+        self.debug('call clearStateChar %j', stateChar)
+        clearStateChar()
+        stateChar = c
+        // if extglob is disabled, then +(asdf|foo) isn't a thing.
+        // just clear the statechar *now*, rather than even diving into
+        // the patternList stuff.
+        if (options.noext) clearStateChar()
+      continue
+
+      case '(':
+        if (inClass) {
+          re += '('
+          continue
+        }
+
+        if (!stateChar) {
+          re += '\\('
+          continue
+        }
+
+        patternListStack.push({
+          type: stateChar,
+          start: i - 1,
+          reStart: re.length,
+          open: plTypes[stateChar].open,
+          close: plTypes[stateChar].close
+        })
+        // negation is (?:(?!js)[^/]*)
+        re += stateChar === '!' ? '(?:(?!(?:' : '(?:'
+        this.debug('plType %j %j', stateChar, re)
+        stateChar = false
+      continue
+
+      case ')':
+        if (inClass || !patternListStack.length) {
+          re += '\\)'
+          continue
+        }
+
+        clearStateChar()
+        hasMagic = true
+        var pl = patternListStack.pop()
+        // negation is (?:(?!js)[^/]*)
+        // The others are (?:<pattern>)<type>
+        re += pl.close
+        if (pl.type === '!') {
+          negativeLists.push(pl)
+        }
+        pl.reEnd = re.length
+      continue
+
+      case '|':
+        if (inClass || !patternListStack.length || escaping) {
+          re += '\\|'
+          escaping = false
+          continue
+        }
+
+        clearStateChar()
+        re += '|'
+      continue
+
+      // these are mostly the same in regexp and glob
+      case '[':
+        // swallow any state-tracking char before the [
+        clearStateChar()
+
+        if (inClass) {
+          re += '\\' + c
+          continue
+        }
+
+        inClass = true
+        classStart = i
+        reClassStart = re.length
+        re += c
+      continue
+
+      case ']':
+        //  a right bracket shall lose its special
+        //  meaning and represent itself in
+        //  a bracket expression if it occurs
+        //  first in the list.  -- POSIX.2 2.8.3.2
+        if (i === classStart + 1 || !inClass) {
+          re += '\\' + c
+          escaping = false
+          continue
+        }
+
+        // handle the case where we left a class open.
+        // "[z-a]" is valid, equivalent to "\[z-a\]"
+        if (inClass) {
+          // split where the last [ was, make sure we don't have
+          // an invalid re. if so, re-walk the contents of the
+          // would-be class to re-translate any characters that
+          // were passed through as-is
+          // TODO: It would probably be faster to determine this
+          // without a try/catch and a new RegExp, but it's tricky
+          // to do safely.  For now, this is safe and works.
+          var cs = pattern.substring(classStart + 1, i)
+          try {
+            RegExp('[' + cs + ']')
+          } catch (er) {
+            // not a valid class!
+            var sp = this.parse(cs, SUBPARSE)
+            re = re.substr(0, reClassStart) + '\\[' + sp[0] + '\\]'
+            hasMagic = hasMagic || sp[1]
+            inClass = false
+            continue
+          }
+        }
+
+        // finish up the class.
+        hasMagic = true
+        inClass = false
+        re += c
+      continue
+
+      default:
+        // swallow any state char that wasn't consumed
+        clearStateChar()
+
+        if (escaping) {
+          // no need
+          escaping = false
+        } else if (reSpecials[c]
+          && !(c === '^' && inClass)) {
+          re += '\\'
+        }
+
+        re += c
+
+    } // switch
+  } // for
+
+  // handle the case where we left a class open.
+  // "[abc" is valid, equivalent to "\[abc"
+  if (inClass) {
+    // split where the last [ was, and escape it
+    // this is a huge pita.  We now have to re-walk
+    // the contents of the would-be class to re-translate
+    // any characters that were passed through as-is
+    cs = pattern.substr(classStart + 1)
+    sp = this.parse(cs, SUBPARSE)
+    re = re.substr(0, reClassStart) + '\\[' + sp[0]
+    hasMagic = hasMagic || sp[1]
+  }
+
+  // handle the case where we had a +( thing at the *end*
+  // of the pattern.
+  // each pattern list stack adds 3 chars, and we need to go through
+  // and escape any | chars that were passed through as-is for the regexp.
+  // Go through and escape them, taking care not to double-escape any
+  // | chars that were already escaped.
+  for (pl = patternListStack.pop(); pl; pl = patternListStack.pop()) {
+    var tail = re.slice(pl.reStart + pl.open.length)
+    this.debug('setting tail', re, pl)
+    // maybe some even number of \, then maybe 1 \, followed by a |
+    tail = tail.replace(/((?:\\{2}){0,64})(\\?)\|/g, function (_, $1, $2) {
+      if (!$2) {
+        // the | isn't already escaped, so escape it.
+        $2 = '\\'
+      }
+
+      // need to escape all those slashes *again*, without escaping the
+      // one that we need for escaping the | character.  As it works out,
+      // escaping an even number of slashes can be done by simply repeating
+      // it exactly after itself.  That's why this trick works.
+      //
+      // I am sorry that you have to see this.
+      return $1 + $1 + $2 + '|'
+    })
+
+    this.debug('tail=%j\n   %s', tail, tail, pl, re)
+    var t = pl.type === '*' ? star
+      : pl.type === '?' ? qmark
+      : '\\' + pl.type
+
+    hasMagic = true
+    re = re.slice(0, pl.reStart) + t + '\\(' + tail
+  }
+
+  // handle trailing things that only matter at the very end.
+  clearStateChar()
+  if (escaping) {
+    // trailing \\
+    re += '\\\\'
+  }
+
+  // only need to apply the nodot start if the re starts with
+  // something that could conceivably capture a dot
+  var addPatternStart = false
+  switch (re.charAt(0)) {
+    case '.':
+    case '[':
+    case '(': addPatternStart = true
+  }
+
+  // Hack to work around lack of negative lookbehind in JS
+  // A pattern like: *.!(x).!(y|z) needs to ensure that a name
+  // like 'a.xyz.yz' doesn't match.  So, the first negative
+  // lookahead, has to look ALL the way ahead, to the end of
+  // the pattern.
+  for (var n = negativeLists.length - 1; n > -1; n--) {
+    var nl = negativeLists[n]
+
+    var nlBefore = re.slice(0, nl.reStart)
+    var nlFirst = re.slice(nl.reStart, nl.reEnd - 8)
+    var nlLast = re.slice(nl.reEnd - 8, nl.reEnd)
+    var nlAfter = re.slice(nl.reEnd)
+
+    nlLast += nlAfter
+
+    // Handle nested stuff like *(*.js|!(*.json)), where open parens
+    // mean that we should *not* include the ) in the bit that is considered
+    // "after" the negated section.
+    var openParensBefore = nlBefore.split('(').length - 1
+    var cleanAfter = nlAfter
+    for (i = 0; i < openParensBefore; i++) {
+      cleanAfter = cleanAfter.replace(/\)[+*?]?/, '')
+    }
+    nlAfter = cleanAfter
+
+    var dollar = ''
+    if (nlAfter === '' && isSub !== SUBPARSE) {
+      dollar = '$'
+    }
+    var newRe = nlBefore + nlFirst + nlAfter + dollar + nlLast
+    re = newRe
+  }
+
+  // if the re is not "" at this point, then we need to make sure
+  // it doesn't match against an empty path part.
+  // Otherwise a/* will match a/, which it should not.
+  if (re !== '' && hasMagic) {
+    re = '(?=.)' + re
+  }
+
+  if (addPatternStart) {
+    re = patternStart + re
+  }
+
+  // parsing just a piece of a larger pattern.
+  if (isSub === SUBPARSE) {
+    return [re, hasMagic]
+  }
+
+  // skip the regexp for non-magical patterns
+  // unescape anything in it, though, so that it'll be
+  // an exact match against a file etc.
+  if (!hasMagic) {
+    return globUnescape(pattern)
+  }
+
+  var flags = options.nocase ? 'i' : ''
+  try {
+    var regExp = new RegExp('^' + re + '$', flags)
+  } catch (er) {
+    // If it was an invalid regular expression, then it can't match
+    // anything.  This trick looks for a character after the end of
+    // the string, which is of course impossible, except in multi-line
+    // mode, but it's not a /m regex.
+    return new RegExp('$.')
+  }
+
+  regExp._glob = pattern
+  regExp._src = re
+
+  return regExp
+}
+
+minimatch.makeRe = function (pattern, options) {
+  return new Minimatch(pattern, options || {}).makeRe()
+}
+
+Minimatch.prototype.makeRe = makeRe
+function makeRe () {
+  if (this.regexp || this.regexp === false) return this.regexp
+
+  // at this point, this.set is a 2d array of partial
+  // pattern strings, or "**".
+  //
+  // It's better to use .match().  This function shouldn't
+  // be used, really, but it's pretty convenient sometimes,
+  // when you just want to work with a regex.
+  var set = this.set
+
+  if (!set.length) {
+    this.regexp = false
+    return this.regexp
+  }
+  var options = this.options
+
+  var twoStar = options.noglobstar ? star
+    : options.dot ? twoStarDot
+    : twoStarNoDot
+  var flags = options.nocase ? 'i' : ''
+
+  var re = set.map(function (pattern) {
+    return pattern.map(function (p) {
+      return (p === GLOBSTAR) ? twoStar
+      : (typeof p === 'string') ? regExpEscape(p)
+      : p._src
+    }).join('\\\/')
+  }).join('|')
+
+  // must match entire pattern
+  // ending in a * or ** will make it less strict.
+  re = '^(?:' + re + ')$'
+
+  // can match anything, as long as it's not this.
+  if (this.negate) re = '^(?!' + re + ').*$'
+
+  try {
+    this.regexp = new RegExp(re, flags)
+  } catch (ex) {
+    this.regexp = false
+  }
+  return this.regexp
+}
+
+minimatch.match = function (list, pattern, options) {
+  options = options || {}
+  var mm = new Minimatch(pattern, options)
+  list = list.filter(function (f) {
+    return mm.match(f)
+  })
+  if (mm.options.nonull && !list.length) {
+    list.push(pattern)
+  }
+  return list
+}
+
+Minimatch.prototype.match = match
+function match (f, partial) {
+  this.debug('match', f, this.pattern)
+  // short-circuit in the case of busted things.
+  // comments, etc.
+  if (this.comment) return false
+  if (this.empty) return f === ''
+
+  if (f === '/' && partial) return true
+
+  var options = this.options
+
+  // windows: need to use /, not \
+  if (path.sep !== '/') {
+    f = f.split(path.sep).join('/')
+  }
+
+  // treat the test path as a set of pathparts.
+  f = f.split(slashSplit)
+  this.debug(this.pattern, 'split', f)
+
+  // just ONE of the pattern sets in this.set needs to match
+  // in order for it to be valid.  If negating, then just one
+  // match means that we have failed.
+  // Either way, return on the first hit.
+
+  var set = this.set
+  this.debug(this.pattern, 'set', set)
+
+  // Find the basename of the path by looking for the last non-empty segment
+  var filename
+  var i
+  for (i = f.length - 1; i >= 0; i--) {
+    filename = f[i]
+    if (filename) break
+  }
+
+  for (i = 0; i < set.length; i++) {
+    var pattern = set[i]
+    var file = f
+    if (options.matchBase && pattern.length === 1) {
+      file = [filename]
+    }
+    var hit = this.matchOne(file, pattern, partial)
+    if (hit) {
+      if (options.flipNegate) return true
+      return !this.negate
+    }
+  }
+
+  // didn't get any hits.  this is success if it's a negative
+  // pattern, failure otherwise.
+  if (options.flipNegate) return false
+  return this.negate
+}
+
+// set partial to true to test if, for example,
+// "/a/b" matches the start of "/*/b/*/d"
+// Partial means, if you run out of file before you run
+// out of pattern, then that's fine, as long as all
+// the parts match.
+Minimatch.prototype.matchOne = function (file, pattern, partial) {
+  var options = this.options
+
+  this.debug('matchOne',
+    { 'this': this, file: file, pattern: pattern })
+
+  this.debug('matchOne', file.length, pattern.length)
+
+  for (var fi = 0,
+      pi = 0,
+      fl = file.length,
+      pl = pattern.length
+      ; (fi < fl) && (pi < pl)
+      ; fi++, pi++) {
+    this.debug('matchOne loop')
+    var p = pattern[pi]
+    var f = file[fi]
+
+    this.debug(pattern, p, f)
+
+    // should be impossible.
+    // some invalid regexp stuff in the set.
+    if (p === false) return false
+
+    if (p === GLOBSTAR) {
+      this.debug('GLOBSTAR', [pattern, p, f])
+
+      // "**"
+      // a/**/b/**/c would match the following:
+      // a/b/x/y/z/c
+      // a/x/y/z/b/c
+      // a/b/x/b/x/c
+      // a/b/c
+      // To do this, take the rest of the pattern after
+      // the **, and see if it would match the file remainder.
+      // If so, return success.
+      // If not, the ** "swallows" a segment, and try again.
+      // This is recursively awful.
+      //
+      // a/**/b/**/c matching a/b/x/y/z/c
+      // - a matches a
+      // - doublestar
+      //   - matchOne(b/x/y/z/c, b/**/c)
+      //     - b matches b
+      //     - doublestar
+      //       - matchOne(x/y/z/c, c) -> no
+      //       - matchOne(y/z/c, c) -> no
+      //       - matchOne(z/c, c) -> no
+      //       - matchOne(c, c) yes, hit
+      var fr = fi
+      var pr = pi + 1
+      if (pr === pl) {
+        this.debug('** at the end')
+        // a ** at the end will just swallow the rest.
+        // We have found a match.
+        // however, it will not swallow /.x, unless
+        // options.dot is set.
+        // . and .. are *never* matched by **, for explosively
+        // exponential reasons.
+        for (; fi < fl; fi++) {
+          if (file[fi] === '.' || file[fi] === '..' ||
+            (!options.dot && file[fi].charAt(0) === '.')) return false
+        }
+        return true
+      }
+
+      // ok, let's see if we can swallow whatever we can.
+      while (fr < fl) {
+        var swallowee = file[fr]
+
+        this.debug('\nglobstar while', file, fr, pattern, pr, swallowee)
+
+        // XXX remove this slice.  Just pass the start index.
+        if (this.matchOne(file.slice(fr), pattern.slice(pr), partial)) {
+          this.debug('globstar found match!', fr, fl, swallowee)
+          // found a match.
+          return true
+        } else {
+          // can't swallow "." or ".." ever.
+          // can only swallow ".foo" when explicitly asked.
+          if (swallowee === '.' || swallowee === '..' ||
+            (!options.dot && swallowee.charAt(0) === '.')) {
+            this.debug('dot detected!', file, fr, pattern, pr)
+            break
+          }
+
+          // ** swallows a segment, and continue.
+          this.debug('globstar swallow a segment, and continue')
+          fr++
+        }
+      }
+
+      // no match was found.
+      // However, in partial mode, we can't say this is necessarily over.
+      // If there's more *pattern* left, then
+      if (partial) {
+        // ran out of file
+        this.debug('\n>>> no match, partial?', file, fr, pattern, pr)
+        if (fr === fl) return true
+      }
+      return false
+    }
+
+    // something other than **
+    // non-magic patterns just have to match exactly
+    // patterns with magic have been turned into regexps.
+    var hit
+    if (typeof p === 'string') {
+      if (options.nocase) {
+        hit = f.toLowerCase() === p.toLowerCase()
+      } else {
+        hit = f === p
+      }
+      this.debug('string match', p, f, hit)
+    } else {
+      hit = f.match(p)
+      this.debug('pattern match', p, f, hit)
+    }
+
+    if (!hit) return false
+  }
+
+  // Note: ending in / means that we'll get a final ""
+  // at the end of the pattern.  This can only match a
+  // corresponding "" at the end of the file.
+  // If the file ends in /, then it can only match a
+  // a pattern that ends in /, unless the pattern just
+  // doesn't have any more for it. But, a/b/ should *not*
+  // match "a/b/*", even though "" matches against the
+  // [^/]*? pattern, except in partial mode, where it might
+  // simply not be reached yet.
+  // However, a/b/ should still satisfy a/*
+
+  // now either we fell off the end of the pattern, or we're done.
+  if (fi === fl && pi === pl) {
+    // ran out of pattern and filename at the same time.
+    // an exact hit!
+    return true
+  } else if (fi === fl) {
+    // ran out of file, but still had pattern left.
+    // this is ok if we're doing the match as part of
+    // a glob fs traversal.
+    return partial
+  } else if (pi === pl) {
+    // ran out of pattern, still have file left.
+    // this is only acceptable if we're on the very last
+    // empty segment of a file with a trailing slash.
+    // a/* should match a/b/
+    var emptyFileEnd = (fi === fl - 1) && (file[fi] === '')
+    return emptyFileEnd
+  }
+
+  // should be unreachable.
+  throw new Error('wtf?')
+}
+
+// replace stuff like \* with *
+function globUnescape (s) {
+  return s.replace(/\\(.)/g, '$1')
+}
+
+function regExpEscape (s) {
+  return s.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, '\\$&')
+}
+
+},{"brace-expansion":11,"path":22}],21:[function(require,module,exports){
+var wrappy = require('wrappy')
+module.exports = wrappy(once)
+module.exports.strict = wrappy(onceStrict)
+
+once.proto = once(function () {
+  Object.defineProperty(Function.prototype, 'once', {
+    value: function () {
+      return once(this)
+    },
+    configurable: true
+  })
+
+  Object.defineProperty(Function.prototype, 'onceStrict', {
+    value: function () {
+      return onceStrict(this)
+    },
+    configurable: true
+  })
+})
+
+function once (fn) {
+  var f = function () {
+    if (f.called) return f.value
+    f.called = true
+    return f.value = fn.apply(this, arguments)
+  }
+  f.called = false
+  return f
+}
+
+function onceStrict (fn) {
+  var f = function () {
+    if (f.called)
+      throw new Error(f.onceError)
+    f.called = true
+    return f.value = fn.apply(this, arguments)
+  }
+  var name = fn.name || 'Function wrapped with `once`'
+  f.onceError = name + " shouldn't be called more than once"
+  f.called = false
+  return f
+}
+
+},{"wrappy":29}],22:[function(require,module,exports){
+(function (process){
+// Copyright Joyent, Inc. and other Node contributors.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a
+// copy of this software and associated documentation files (the
+// "Software"), to deal in the Software without restriction, including
+// without limitation the rights to use, copy, modify, merge, publish,
+// distribute, sublicense, and/or sell copies of the Software, and to permit
+// persons to whom the Software is furnished to do so, subject to the
+// following conditions:
+//
+// The above copyright notice and this permission notice shall be included
+// in all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+// USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+// resolves . and .. elements in a path array with directory names there
+// must be no slashes, empty elements, or device names (c:\) in the array
+// (so also no leading and trailing slashes - it does not distinguish
+// relative and absolute paths)
+function normalizeArray(parts, allowAboveRoot) {
+  // if the path tries to go above the root, `up` ends up > 0
+  var up = 0;
+  for (var i = parts.length - 1; i >= 0; i--) {
+    var last = parts[i];
+    if (last === '.') {
+      parts.splice(i, 1);
+    } else if (last === '..') {
+      parts.splice(i, 1);
+      up++;
+    } else if (up) {
+      parts.splice(i, 1);
+      up--;
+    }
+  }
+
+  // if the path is allowed to go above the root, restore leading ..s
+  if (allowAboveRoot) {
+    for (; up--; up) {
+      parts.unshift('..');
+    }
+  }
+
+  return parts;
+}
+
+// Split a filename into [root, dir, basename, ext], unix version
+// 'root' is just a slash, or nothing.
+var splitPathRe =
+    /^(\/?|)([\s\S]*?)((?:\.{1,2}|[^\/]+?|)(\.[^.\/]*|))(?:[\/]*)$/;
+var splitPath = function(filename) {
+  return splitPathRe.exec(filename).slice(1);
+};
+
+// path.resolve([from ...], to)
+// posix version
+exports.resolve = function() {
+  var resolvedPath = '',
+      resolvedAbsolute = false;
+
+  for (var i = arguments.length - 1; i >= -1 && !resolvedAbsolute; i--) {
+    var path = (i >= 0) ? arguments[i] : process.cwd();
+
+    // Skip empty and invalid entries
+    if (typeof path !== 'string') {
+      throw new TypeError('Arguments to path.resolve must be strings');
+    } else if (!path) {
+      continue;
+    }
+
+    resolvedPath = path + '/' + resolvedPath;
+    resolvedAbsolute = path.charAt(0) === '/';
+  }
+
+  // At this point the path should be resolved to a full absolute path, but
+  // handle relative paths to be safe (might happen when process.cwd() fails)
+
+  // Normalize the path
+  resolvedPath = normalizeArray(filter(resolvedPath.split('/'), function(p) {
+    return !!p;
+  }), !resolvedAbsolute).join('/');
+
+  return ((resolvedAbsolute ? '/' : '') + resolvedPath) || '.';
+};
+
+// path.normalize(path)
+// posix version
+exports.normalize = function(path) {
+  var isAbsolute = exports.isAbsolute(path),
+      trailingSlash = substr(path, -1) === '/';
+
+  // Normalize the path
+  path = normalizeArray(filter(path.split('/'), function(p) {
+    return !!p;
+  }), !isAbsolute).join('/');
+
+  if (!path && !isAbsolute) {
+    path = '.';
+  }
+  if (path && trailingSlash) {
+    path += '/';
+  }
+
+  return (isAbsolute ? '/' : '') + path;
+};
+
+// posix version
+exports.isAbsolute = function(path) {
+  return path.charAt(0) === '/';
+};
+
+// posix version
+exports.join = function() {
+  var paths = Array.prototype.slice.call(arguments, 0);
+  return exports.normalize(filter(paths, function(p, index) {
+    if (typeof p !== 'string') {
+      throw new TypeError('Arguments to path.join must be strings');
+    }
+    return p;
+  }).join('/'));
+};
+
+
+// path.relative(from, to)
+// posix version
+exports.relative = function(from, to) {
+  from = exports.resolve(from).substr(1);
+  to = exports.resolve(to).substr(1);
+
+  function trim(arr) {
+    var start = 0;
+    for (; start < arr.length; start++) {
+      if (arr[start] !== '') break;
+    }
+
+    var end = arr.length - 1;
+    for (; end >= 0; end--) {
+      if (arr[end] !== '') break;
+    }
+
+    if (start > end) return [];
+    return arr.slice(start, end - start + 1);
+  }
+
+  var fromParts = trim(from.split('/'));
+  var toParts = trim(to.split('/'));
+
+  var length = Math.min(fromParts.length, toParts.length);
+  var samePartsLength = length;
+  for (var i = 0; i < length; i++) {
+    if (fromParts[i] !== toParts[i]) {
+      samePartsLength = i;
+      break;
+    }
+  }
+
+  var outputParts = [];
+  for (var i = samePartsLength; i < fromParts.length; i++) {
+    outputParts.push('..');
+  }
+
+  outputParts = outputParts.concat(toParts.slice(samePartsLength));
+
+  return outputParts.join('/');
+};
+
+exports.sep = '/';
+exports.delimiter = ':';
+
+exports.dirname = function(path) {
+  var result = splitPath(path),
+      root = result[0],
+      dir = result[1];
+
+  if (!root && !dir) {
+    // No dirname whatsoever
+    return '.';
+  }
+
+  if (dir) {
+    // It has a dirname, strip trailing slash
+    dir = dir.substr(0, dir.length - 1);
+  }
+
+  return root + dir;
+};
+
+
+exports.basename = function(path, ext) {
+  var f = splitPath(path)[2];
+  // TODO: make this comparison case-insensitive on windows?
+  if (ext && f.substr(-1 * ext.length) === ext) {
+    f = f.substr(0, f.length - ext.length);
+  }
+  return f;
+};
+
+
+exports.extname = function(path) {
+  return splitPath(path)[3];
+};
+
+function filter (xs, f) {
+    if (xs.filter) return xs.filter(f);
+    var res = [];
+    for (var i = 0; i < xs.length; i++) {
+        if (f(xs[i], i, xs)) res.push(xs[i]);
+    }
+    return res;
+}
+
+// String.prototype.substr - negative index don't work in IE8
+var substr = 'ab'.substr(-1) === 'b'
+    ? function (str, start, len) { return str.substr(start, len) }
+    : function (str, start, len) {
+        if (start < 0) start = str.length + start;
+        return str.substr(start, len);
+    }
+;
+
+}).call(this,require('_process'))
+},{"_process":24}],23:[function(require,module,exports){
+(function (process){
+'use strict';
+
+function posix(path) {
+	return path.charAt(0) === '/';
+}
+
+function win32(path) {
+	// https://github.com/nodejs/node/blob/b3fcc245fb25539909ef1d5eaa01dbf92e168633/lib/path.js#L56
+	var splitDeviceRe = /^([a-zA-Z]:|[\\\/]{2}[^\\\/]+[\\\/]+[^\\\/]+)?([\\\/])?([\s\S]*?)$/;
+	var result = splitDeviceRe.exec(path);
+	var device = result[1] || '';
+	var isUnc = Boolean(device && device.charAt(1) !== ':');
+
+	// UNC paths are always absolute
+	return Boolean(result[2] || isUnc);
+}
+
+module.exports = process.platform === 'win32' ? win32 : posix;
+module.exports.posix = posix;
+module.exports.win32 = win32;
+
+}).call(this,require('_process'))
+},{"_process":24}],24:[function(require,module,exports){
+// shim for using process in browser
+var process = module.exports = {};
+
+// cached from whatever global is present so that test runners that stub it
+// don't break things.  But we need to wrap it in a try catch in case it is
+// wrapped in strict mode code which doesn't define any globals.  It's inside a
+// function because try/catches deoptimize in certain engines.
+
+var cachedSetTimeout;
+var cachedClearTimeout;
+
+function defaultSetTimout() {
+    throw new Error('setTimeout has not been defined');
+}
+function defaultClearTimeout () {
+    throw new Error('clearTimeout has not been defined');
+}
+(function () {
+    try {
+        if (typeof setTimeout === 'function') {
+            cachedSetTimeout = setTimeout;
+        } else {
+            cachedSetTimeout = defaultSetTimout;
+        }
+    } catch (e) {
+        cachedSetTimeout = defaultSetTimout;
+    }
+    try {
+        if (typeof clearTimeout === 'function') {
+            cachedClearTimeout = clearTimeout;
+        } else {
+            cachedClearTimeout = defaultClearTimeout;
+        }
+    } catch (e) {
+        cachedClearTimeout = defaultClearTimeout;
+    }
+} ())
+function runTimeout(fun) {
+    if (cachedSetTimeout === setTimeout) {
+        //normal enviroments in sane situations
+        return setTimeout(fun, 0);
+    }
+    // if setTimeout wasn't available but was latter defined
+    if ((cachedSetTimeout === defaultSetTimout || !cachedSetTimeout) && setTimeout) {
+        cachedSetTimeout = setTimeout;
+        return setTimeout(fun, 0);
+    }
+    try {
+        // when when somebody has screwed with setTimeout but no I.E. maddness
+        return cachedSetTimeout(fun, 0);
+    } catch(e){
+        try {
+            // When we are in I.E. but the script has been evaled so I.E. doesn't trust the global object when called normally
+            return cachedSetTimeout.call(null, fun, 0);
+        } catch(e){
+            // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error
+            return cachedSetTimeout.call(this, fun, 0);
+        }
+    }
+
+
+}
+function runClearTimeout(marker) {
+    if (cachedClearTimeout === clearTimeout) {
+        //normal enviroments in sane situations
+        return clearTimeout(marker);
+    }
+    // if clearTimeout wasn't available but was latter defined
+    if ((cachedClearTimeout === defaultClearTimeout || !cachedClearTimeout) && clearTimeout) {
+        cachedClearTimeout = clearTimeout;
+        return clearTimeout(marker);
+    }
+    try {
+        // when when somebody has screwed with setTimeout but no I.E. maddness
+        return cachedClearTimeout(marker);
+    } catch (e){
+        try {
+            // When we are in I.E. but the script has been evaled so I.E. doesn't  trust the global object when called normally
+            return cachedClearTimeout.call(null, marker);
+        } catch (e){
+            // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error.
+            // Some versions of I.E. have different rules for clearTimeout vs setTimeout
+            return cachedClearTimeout.call(this, marker);
+        }
+    }
+
+
+
+}
+var queue = [];
+var draining = false;
+var currentQueue;
+var queueIndex = -1;
+
+function cleanUpNextTick() {
+    if (!draining || !currentQueue) {
+        return;
+    }
+    draining = false;
+    if (currentQueue.length) {
+        queue = currentQueue.concat(queue);
+    } else {
+        queueIndex = -1;
+    }
+    if (queue.length) {
+        drainQueue();
+    }
+}
+
+function drainQueue() {
+    if (draining) {
+        return;
+    }
+    var timeout = runTimeout(cleanUpNextTick);
+    draining = true;
+
+    var len = queue.length;
+    while(len) {
+        currentQueue = queue;
+        queue = [];
+        while (++queueIndex < len) {
+            if (currentQueue) {
+                currentQueue[queueIndex].run();
+            }
+        }
+        queueIndex = -1;
+        len = queue.length;
+    }
+    currentQueue = null;
+    draining = false;
+    runClearTimeout(timeout);
+}
+
+process.nextTick = function (fun) {
+    var args = new Array(arguments.length - 1);
+    if (arguments.length > 1) {
+        for (var i = 1; i < arguments.length; i++) {
+            args[i - 1] = arguments[i];
+        }
+    }
+    queue.push(new Item(fun, args));
+    if (queue.length === 1 && !draining) {
+        runTimeout(drainQueue);
+    }
+};
+
+// v8 likes predictible objects
+function Item(fun, array) {
+    this.fun = fun;
+    this.array = array;
+}
+Item.prototype.run = function () {
+    this.fun.apply(null, this.array);
+};
+process.title = 'browser';
+process.browser = true;
+process.env = {};
+process.argv = [];
+process.version = ''; // empty string to avoid regexp issues
+process.versions = {};
+
+function noop() {}
+
+process.on = noop;
+process.addListener = noop;
+process.once = noop;
+process.off = noop;
+process.removeListener = noop;
+process.removeAllListeners = noop;
+process.emit = noop;
+process.prependListener = noop;
+process.prependOnceListener = noop;
+
+process.listeners = function (name) { return [] }
+
+process.binding = function (name) {
+    throw new Error('process.binding is not supported');
+};
+
+process.cwd = function () { return '/' };
+process.chdir = function (dir) {
+    throw new Error('process.chdir is not supported');
+};
+process.umask = function() { return 0; };
+
+},{}],25:[function(require,module,exports){
+//     Underscore.js 1.8.3
+//     http://underscorejs.org
+//     (c) 2009-2015 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors
+//     Underscore may be freely distributed under the MIT license.
+
+(function() {
+
+  // Baseline setup
+  // --------------
+
+  // Establish the root object, `window` in the browser, or `exports` on the server.
+  var root = this;
+
+  // Save the previous value of the `_` variable.
+  var previousUnderscore = root._;
+
+  // Save bytes in the minified (but not gzipped) version:
+  var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
+
+  // Create quick reference variables for speed access to core prototypes.
+  var
+    push             = ArrayProto.push,
+    slice            = ArrayProto.slice,
+    toString         = ObjProto.toString,
+    hasOwnProperty   = ObjProto.hasOwnProperty;
+
+  // All **ECMAScript 5** native function implementations that we hope to use
+  // are declared here.
+  var
+    nativeIsArray      = Array.isArray,
+    nativeKeys         = Object.keys,
+    nativeBind         = FuncProto.bind,
+    nativeCreate       = Object.create;
+
+  // Naked function reference for surrogate-prototype-swapping.
+  var Ctor = function(){};
+
+  // Create a safe reference to the Underscore object for use below.
+  var _ = function(obj) {
+    if (obj instanceof _) return obj;
+    if (!(this instanceof _)) return new _(obj);
+    this._wrapped = obj;
+  };
+
+  // Export the Underscore object for **Node.js**, with
+  // backwards-compatibility for the old `require()` API. If we're in
+  // the browser, add `_` as a global object.
+  if (typeof exports !== 'undefined') {
+    if (typeof module !== 'undefined' && module.exports) {
+      exports = module.exports = _;
+    }
+    exports._ = _;
+  } else {
+    root._ = _;
+  }
+
+  // Current version.
+  _.VERSION = '1.8.3';
+
+  // Internal function that returns an efficient (for current engines) version
+  // of the passed-in callback, to be repeatedly applied in other Underscore
+  // functions.
+  var optimizeCb = function(func, context, argCount) {
+    if (context === void 0) return func;
+    switch (argCount == null ? 3 : argCount) {
+      case 1: return function(value) {
+        return func.call(context, value);
+      };
+      case 2: return function(value, other) {
+        return func.call(context, value, other);
+      };
+      case 3: return function(value, index, collection) {
+        return func.call(context, value, index, collection);
+      };
+      case 4: return function(accumulator, value, index, collection) {
+        return func.call(context, accumulator, value, index, collection);
+      };
+    }
+    return function() {
+      return func.apply(context, arguments);
+    };
+  };
+
+  // A mostly-internal function to generate callbacks that can be applied
+  // to each element in a collection, returning the desired result — either
+  // identity, an arbitrary callback, a property matcher, or a property accessor.
+  var cb = function(value, context, argCount) {
+    if (value == null) return _.identity;
+    if (_.isFunction(value)) return optimizeCb(value, context, argCount);
+    if (_.isObject(value)) return _.matcher(value);
+    return _.property(value);
+  };
+  _.iteratee = function(value, context) {
+    return cb(value, context, Infinity);
+  };
+
+  // An internal function for creating assigner functions.
+  var createAssigner = function(keysFunc, undefinedOnly) {
+    return function(obj) {
+      var length = arguments.length;
+      if (length < 2 || obj == null) return obj;
+      for (var index = 1; index < length; index++) {
+        var source = arguments[index],
+            keys = keysFunc(source),
+            l = keys.length;
+        for (var i = 0; i < l; i++) {
+          var key = keys[i];
+          if (!undefinedOnly || obj[key] === void 0) obj[key] = source[key];
+        }
+      }
+      return obj;
+    };
+  };
+
+  // An internal function for creating a new object that inherits from another.
+  var baseCreate = function(prototype) {
+    if (!_.isObject(prototype)) return {};
+    if (nativeCreate) return nativeCreate(prototype);
+    Ctor.prototype = prototype;
+    var result = new Ctor;
+    Ctor.prototype = null;
+    return result;
+  };
+
+  var property = function(key) {
+    return function(obj) {
+      return obj == null ? void 0 : obj[key];
+    };
+  };
+
+  // Helper for collection methods to determine whether a collection
+  // should be iterated as an array or as an object
+  // Related: http://people.mozilla.org/~jorendorff/es6-draft.html#sec-tolength
+  // Avoids a very nasty iOS 8 JIT bug on ARM-64. #2094
+  var MAX_ARRAY_INDEX = Math.pow(2, 53) - 1;
+  var getLength = property('length');
+  var isArrayLike = function(collection) {
+    var length = getLength(collection);
+    return typeof length == 'number' && length >= 0 && length <= MAX_ARRAY_INDEX;
+  };
+
+  // Collection Functions
+  // --------------------
+
+  // The cornerstone, an `each` implementation, aka `forEach`.
+  // Handles raw objects in addition to array-likes. Treats all
+  // sparse array-likes as if they were dense.
+  _.each = _.forEach = function(obj, iteratee, context) {
+    iteratee = optimizeCb(iteratee, context);
+    var i, length;
+    if (isArrayLike(obj)) {
+      for (i = 0, length = obj.length; i < length; i++) {
+        iteratee(obj[i], i, obj);
+      }
+    } else {
+      var keys = _.keys(obj);
+      for (i = 0, length = keys.length; i < length; i++) {
+        iteratee(obj[keys[i]], keys[i], obj);
+      }
+    }
+    return obj;
+  };
+
+  // Return the results of applying the iteratee to each element.
+  _.map = _.collect = function(obj, iteratee, context) {
+    iteratee = cb(iteratee, context);
+    var keys = !isArrayLike(obj) && _.keys(obj),
+        length = (keys || obj).length,
+        results = Array(length);
+    for (var index = 0; index < length; index++) {
+      var currentKey = keys ? keys[index] : index;
+      results[index] = iteratee(obj[currentKey], currentKey, obj);
+    }
+    return results;
+  };
+
+  // Create a reducing function iterating left or right.
+  function createReduce(dir) {
+    // Optimized iterator function as using arguments.length
+    // in the main function will deoptimize the, see #1991.
+    function iterator(obj, iteratee, memo, keys, index, length) {
+      for (; index >= 0 && index < length; index += dir) {
+        var currentKey = keys ? keys[index] : index;
+        memo = iteratee(memo, obj[currentKey], currentKey, obj);
+      }
+      return memo;
+    }
+
+    return function(obj, iteratee, memo, context) {
+      iteratee = optimizeCb(iteratee, context, 4);
+      var keys = !isArrayLike(obj) && _.keys(obj),
+          length = (keys || obj).length,
+          index = dir > 0 ? 0 : length - 1;
+      // Determine the initial value if none is provided.
+      if (arguments.length < 3) {
+        memo = obj[keys ? keys[index] : index];
+        index += dir;
+      }
+      return iterator(obj, iteratee, memo, keys, index, length);
+    };
+  }
+
+  // **Reduce** builds up a single result from a list of values, aka `inject`,
+  // or `foldl`.
+  _.reduce = _.foldl = _.inject = createReduce(1);
+
+  // The right-associative version of reduce, also known as `foldr`.
+  _.reduceRight = _.foldr = createReduce(-1);
+
+  // Return the first value which passes a truth test. Aliased as `detect`.
+  _.find = _.detect = function(obj, predicate, context) {
+    var key;
+    if (isArrayLike(obj)) {
+      key = _.findIndex(obj, predicate, context);
+    } else {
+      key = _.findKey(obj, predicate, context);
+    }
+    if (key !== void 0 && key !== -1) return obj[key];
+  };
+
+  // Return all the elements that pass a truth test.
+  // Aliased as `select`.
+  _.filter = _.select = function(obj, predicate, context) {
+    var results = [];
+    predicate = cb(predicate, context);
+    _.each(obj, function(value, index, list) {
+      if (predicate(value, index, list)) results.push(value);
+    });
+    return results;
+  };
+
+  // Return all the elements for which a truth test fails.
+  _.reject = function(obj, predicate, context) {
+    return _.filter(obj, _.negate(cb(predicate)), context);
+  };
+
+  // Determine whether all of the elements match a truth test.
+  // Aliased as `all`.
+  _.every = _.all = function(obj, predicate, context) {
+    predicate = cb(predicate, context);
+    var keys = !isArrayLike(obj) && _.keys(obj),
+        length = (keys || obj).length;
+    for (var index = 0; index < length; index++) {
+      var currentKey = keys ? keys[index] : index;
+      if (!predicate(obj[currentKey], currentKey, obj)) return false;
+    }
+    return true;
+  };
+
+  // Determine if at least one element in the object matches a truth test.
+  // Aliased as `any`.
+  _.some = _.any = function(obj, predicate, context) {
+    predicate = cb(predicate, context);
+    var keys = !isArrayLike(obj) && _.keys(obj),
+        length = (keys || obj).length;
+    for (var index = 0; index < length; index++) {
+      var currentKey = keys ? keys[index] : index;
+      if (predicate(obj[currentKey], currentKey, obj)) return true;
+    }
+    return false;
+  };
+
+  // Determine if the array or object contains a given item (using `===`).
+  // Aliased as `includes` and `include`.
+  _.contains = _.includes = _.include = function(obj, item, fromIndex, guard) {
+    if (!isArrayLike(obj)) obj = _.values(obj);
+    if (typeof fromIndex != 'number' || guard) fromIndex = 0;
+    return _.indexOf(obj, item, fromIndex) >= 0;
+  };
+
+  // Invoke a method (with arguments) on every item in a collection.
+  _.invoke = function(obj, method) {
+    var args = slice.call(arguments, 2);
+    var isFunc = _.isFunction(method);
+    return _.map(obj, function(value) {
+      var func = isFunc ? method : value[method];
+      return func == null ? func : func.apply(value, args);
+    });
+  };
+
+  // Convenience version of a common use case of `map`: fetching a property.
+  _.pluck = function(obj, key) {
+    return _.map(obj, _.property(key));
+  };
+
+  // Convenience version of a common use case of `filter`: selecting only objects
+  // containing specific `key:value` pairs.
+  _.where = function(obj, attrs) {
+    return _.filter(obj, _.matcher(attrs));
+  };
+
+  // Convenience version of a common use case of `find`: getting the first object
+  // containing specific `key:value` pairs.
+  _.findWhere = function(obj, attrs) {
+    return _.find(obj, _.matcher(attrs));
+  };
+
+  // Return the maximum element (or element-based computation).
+  _.max = function(obj, iteratee, context) {
+    var result = -Infinity, lastComputed = -Infinity,
+        value, computed;
+    if (iteratee == null && obj != null) {
+      obj = isArrayLike(obj) ? obj : _.values(obj);
+      for (var i = 0, length = obj.length; i < length; i++) {
+        value = obj[i];
+        if (value > result) {
+          result = value;
+        }
+      }
+    } else {
+      iteratee = cb(iteratee, context);
+      _.each(obj, function(value, index, list) {
+        computed = iteratee(value, index, list);
+        if (computed > lastComputed || computed === -Infinity && result === -Infinity) {
+          result = value;
+          lastComputed = computed;
+        }
+      });
+    }
+    return result;
+  };
+
+  // Return the minimum element (or element-based computation).
+  _.min = function(obj, iteratee, context) {
+    var result = Infinity, lastComputed = Infinity,
+        value, computed;
+    if (iteratee == null && obj != null) {
+      obj = isArrayLike(obj) ? obj : _.values(obj);
+      for (var i = 0, length = obj.length; i < length; i++) {
+        value = obj[i];
+        if (value < result) {
+          result = value;
+        }
+      }
+    } else {
+      iteratee = cb(iteratee, context);
+      _.each(obj, function(value, index, list) {
+        computed = iteratee(value, index, list);
+        if (computed < lastComputed || computed === Infinity && result === Infinity) {
+          result = value;
+          lastComputed = computed;
+        }
+      });
+    }
+    return result;
+  };
+
+  // Shuffle a collection, using the modern version of the
+  // [Fisher-Yates shuffle](http://en.wikipedia.org/wiki/Fisher–Yates_shuffle).
+  _.shuffle = function(obj) {
+    var set = isArrayLike(obj) ? obj : _.values(obj);
+    var length = set.length;
+    var shuffled = Array(length);
+    for (var index = 0, rand; index < length; index++) {
+      rand = _.random(0, index);
+      if (rand !== index) shuffled[index] = shuffled[rand];
+      shuffled[rand] = set[index];
+    }
+    return shuffled;
+  };
+
+  // Sample **n** random values from a collection.
+  // If **n** is not specified, returns a single random element.
+  // The internal `guard` argument allows it to work with `map`.
+  _.sample = function(obj, n, guard) {
+    if (n == null || guard) {
+      if (!isArrayLike(obj)) obj = _.values(obj);
+      return obj[_.random(obj.length - 1)];
+    }
+    return _.shuffle(obj).slice(0, Math.max(0, n));
+  };
+
+  // Sort the object's values by a criterion produced by an iteratee.
+  _.sortBy = function(obj, iteratee, context) {
+    iteratee = cb(iteratee, context);
+    return _.pluck(_.map(obj, function(value, index, list) {
+      return {
+        value: value,
+        index: index,
+        criteria: iteratee(value, index, list)
+      };
+    }).sort(function(left, right) {
+      var a = left.criteria;
+      var b = right.criteria;
+      if (a !== b) {
+        if (a > b || a === void 0) return 1;
+        if (a < b || b === void 0) return -1;
+      }
+      return left.index - right.index;
+    }), 'value');
+  };
+
+  // An internal function used for aggregate "group by" operations.
+  var group = function(behavior) {
+    return function(obj, iteratee, context) {
+      var result = {};
+      iteratee = cb(iteratee, context);
+      _.each(obj, function(value, index) {
+        var key = iteratee(value, index, obj);
+        behavior(result, value, key);
+      });
+      return result;
+    };
+  };
+
+  // Groups the object's values by a criterion. Pass either a string attribute
+  // to group by, or a function that returns the criterion.
+  _.groupBy = group(function(result, value, key) {
+    if (_.has(result, key)) result[key].push(value); else result[key] = [value];
+  });
+
+  // Indexes the object's values by a criterion, similar to `groupBy`, but for
+  // when you know that your index values will be unique.
+  _.indexBy = group(function(result, value, key) {
+    result[key] = value;
+  });
+
+  // Counts instances of an object that group by a certain criterion. Pass
+  // either a string attribute to count by, or a function that returns the
+  // criterion.
+  _.countBy = group(function(result, value, key) {
+    if (_.has(result, key)) result[key]++; else result[key] = 1;
+  });
+
+  // Safely create a real, live array from anything iterable.
+  _.toArray = function(obj) {
+    if (!obj) return [];
+    if (_.isArray(obj)) return slice.call(obj);
+    if (isArrayLike(obj)) return _.map(obj, _.identity);
+    return _.values(obj);
+  };
+
+  // Return the number of elements in an object.
+  _.size = function(obj) {
+    if (obj == null) return 0;
+    return isArrayLike(obj) ? obj.length : _.keys(obj).length;
+  };
+
+  // Split a collection into two arrays: one whose elements all satisfy the given
+  // predicate, and one whose elements all do not satisfy the predicate.
+  _.partition = function(obj, predicate, context) {
+    predicate = cb(predicate, context);
+    var pass = [], fail = [];
+    _.each(obj, function(value, key, obj) {
+      (predicate(value, key, obj) ? pass : fail).push(value);
+    });
+    return [pass, fail];
+  };
+
+  // Array Functions
+  // ---------------
+
+  // Get the first element of an array. Passing **n** will return the first N
+  // values in the array. Aliased as `head` and `take`. The **guard** check
+  // allows it to work with `_.map`.
+  _.first = _.head = _.take = function(array, n, guard) {
+    if (array == null) return void 0;
+    if (n == null || guard) return array[0];
+    return _.initial(array, array.length - n);
+  };
+
+  // Returns everything but the last entry of the array. Especially useful on
+  // the arguments object. Passing **n** will return all the values in
+  // the array, excluding the last N.
+  _.initial = function(array, n, guard) {
+    return slice.call(array, 0, Math.max(0, array.length - (n == null || guard ? 1 : n)));
+  };
+
+  // Get the last element of an array. Passing **n** will return the last N
+  // values in the array.
+  _.last = function(array, n, guard) {
+    if (array == null) return void 0;
+    if (n == null || guard) return array[array.length - 1];
+    return _.rest(array, Math.max(0, array.length - n));
+  };
+
+  // Returns everything but the first entry of the array. Aliased as `tail` and `drop`.
+  // Especially useful on the arguments object. Passing an **n** will return
+  // the rest N values in the array.
+  _.rest = _.tail = _.drop = function(array, n, guard) {
+    return slice.call(array, n == null || guard ? 1 : n);
+  };
+
+  // Trim out all falsy values from an array.
+  _.compact = function(array) {
+    return _.filter(array, _.identity);
+  };
+
+  // Internal implementation of a recursive `flatten` function.
+  var flatten = function(input, shallow, strict, startIndex) {
+    var output = [], idx = 0;
+    for (var i = startIndex || 0, length = getLength(input); i < length; i++) {
+      var value = input[i];
+      if (isArrayLike(value) && (_.isArray(value) || _.isArguments(value))) {
+        //flatten current level of array or arguments object
+        if (!shallow) value = flatten(value, shallow, strict);
+        var j = 0, len = value.length;
+        output.length += len;
+        while (j < len) {
+          output[idx++] = value[j++];
+        }
+      } else if (!strict) {
+        output[idx++] = value;
+      }
+    }
+    return output;
+  };
+
+  // Flatten out an array, either recursively (by default), or just one level.
+  _.flatten = function(array, shallow) {
+    return flatten(array, shallow, false);
+  };
+
+  // Return a version of the array that does not contain the specified value(s).
+  _.without = function(array) {
+    return _.difference(array, slice.call(arguments, 1));
+  };
+
+  // Produce a duplicate-free version of the array. If the array has already
+  // been sorted, you have the option of using a faster algorithm.
+  // Aliased as `unique`.
+  _.uniq = _.unique = function(array, isSorted, iteratee, context) {
+    if (!_.isBoolean(isSorted)) {
+      context = iteratee;
+      iteratee = isSorted;
+      isSorted = false;
+    }
+    if (iteratee != null) iteratee = cb(iteratee, context);
+    var result = [];
+    var seen = [];
+    for (var i = 0, length = getLength(array); i < length; i++) {
+      var value = array[i],
+          computed = iteratee ? iteratee(value, i, array) : value;
+      if (isSorted) {
+        if (!i || seen !== computed) result.push(value);
+        seen = computed;
+      } else if (iteratee) {
+        if (!_.contains(seen, computed)) {
+          seen.push(computed);
+          result.push(value);
+        }
+      } else if (!_.contains(result, value)) {
+        result.push(value);
+      }
+    }
+    return result;
+  };
+
+  // Produce an array that contains the union: each distinct element from all of
+  // the passed-in arrays.
+  _.union = function() {
+    return _.uniq(flatten(arguments, true, true));
+  };
+
+  // Produce an array that contains every item shared between all the
+  // passed-in arrays.
+  _.intersection = function(array) {
+    var result = [];
+    var argsLength = arguments.length;
+    for (var i = 0, length = getLength(array); i < length; i++) {
+      var item = array[i];
+      if (_.contains(result, item)) continue;
+      for (var j = 1; j < argsLength; j++) {
+        if (!_.contains(arguments[j], item)) break;
+      }
+      if (j === argsLength) result.push(item);
+    }
+    return result;
+  };
+
+  // Take the difference between one array and a number of other arrays.
+  // Only the elements present in just the first array will remain.
+  _.difference = function(array) {
+    var rest = flatten(arguments, true, true, 1);
+    return _.filter(array, function(value){
+      return !_.contains(rest, value);
+    });
+  };
+
+  // Zip together multiple lists into a single array -- elements that share
+  // an index go together.
+  _.zip = function() {
+    return _.unzip(arguments);
+  };
+
+  // Complement of _.zip. Unzip accepts an array of arrays and groups
+  // each array's elements on shared indices
+  _.unzip = function(array) {
+    var length = array && _.max(array, getLength).length || 0;
+    var result = Array(length);
+
+    for (var index = 0; index < length; index++) {
+      result[index] = _.pluck(array, index);
+    }
+    return result;
+  };
+
+  // Converts lists into objects. Pass either a single array of `[key, value]`
+  // pairs, or two parallel arrays of the same length -- one of keys, and one of
+  // the corresponding values.
+  _.object = function(list, values) {
+    var result = {};
+    for (var i = 0, length = getLength(list); i < length; i++) {
+      if (values) {
+        result[list[i]] = values[i];
+      } else {
+        result[list[i][0]] = list[i][1];
+      }
+    }
+    return result;
+  };
+
+  // Generator function to create the findIndex and findLastIndex functions
+  function createPredicateIndexFinder(dir) {
+    return function(array, predicate, context) {
+      predicate = cb(predicate, context);
+      var length = getLength(array);
+      var index = dir > 0 ? 0 : length - 1;
+      for (; index >= 0 && index < length; index += dir) {
+        if (predicate(array[index], index, array)) return index;
+      }
+      return -1;
+    };
+  }
+
+  // Returns the first index on an array-like that passes a predicate test
+  _.findIndex = createPredicateIndexFinder(1);
+  _.findLastIndex = createPredicateIndexFinder(-1);
+
+  // Use a comparator function to figure out the smallest index at which
+  // an object should be inserted so as to maintain order. Uses binary search.
+  _.sortedIndex = function(array, obj, iteratee, context) {
+    iteratee = cb(iteratee, context, 1);
+    var value = iteratee(obj);
+    var low = 0, high = getLength(array);
+    while (low < high) {
+      var mid = Math.floor((low + high) / 2);
+      if (iteratee(array[mid]) < value) low = mid + 1; else high = mid;
+    }
+    return low;
+  };
+
+  // Generator function to create the indexOf and lastIndexOf functions
+  function createIndexFinder(dir, predicateFind, sortedIndex) {
+    return function(array, item, idx) {
+      var i = 0, length = getLength(array);
+      if (typeof idx == 'number') {
+        if (dir > 0) {
+            i = idx >= 0 ? idx : Math.max(idx + length, i);
+        } else {
+            length = idx >= 0 ? Math.min(idx + 1, length) : idx + length + 1;
+        }
+      } else if (sortedIndex && idx && length) {
+        idx = sortedIndex(array, item);
+        return array[idx] === item ? idx : -1;
+      }
+      if (item !== item) {
+        idx = predicateFind(slice.call(array, i, length), _.isNaN);
+        return idx >= 0 ? idx + i : -1;
+      }
+      for (idx = dir > 0 ? i : length - 1; idx >= 0 && idx < length; idx += dir) {
+        if (array[idx] === item) return idx;
+      }
+      return -1;
+    };
+  }
+
+  // Return the position of the first occurrence of an item in an array,
+  // or -1 if the item is not included in the array.
+  // If the array is large and already in sort order, pass `true`
+  // for **isSorted** to use binary search.
+  _.indexOf = createIndexFinder(1, _.findIndex, _.sortedIndex);
+  _.lastIndexOf = createIndexFinder(-1, _.findLastIndex);
+
+  // Generate an integer Array containing an arithmetic progression. A port of
+  // the native Python `range()` function. See
+  // [the Python documentation](http://docs.python.org/library/functions.html#range).
+  _.range = function(start, stop, step) {
+    if (stop == null) {
+      stop = start || 0;
+      start = 0;
+    }
+    step = step || 1;
+
+    var length = Math.max(Math.ceil((stop - start) / step), 0);
+    var range = Array(length);
+
+    for (var idx = 0; idx < length; idx++, start += step) {
+      range[idx] = start;
+    }
+
+    return range;
+  };
+
+  // Function (ahem) Functions
+  // ------------------
+
+  // Determines whether to execute a function as a constructor
+  // or a normal function with the provided arguments
+  var executeBound = function(sourceFunc, boundFunc, context, callingContext, args) {
+    if (!(callingContext instanceof boundFunc)) return sourceFunc.apply(context, args);
+    var self = baseCreate(sourceFunc.prototype);
+    var result = sourceFunc.apply(self, args);
+    if (_.isObject(result)) return result;
+    return self;
+  };
+
+  // Create a function bound to a given object (assigning `this`, and arguments,
+  // optionally). Delegates to **ECMAScript 5**'s native `Function.bind` if
+  // available.
+  _.bind = function(func, context) {
+    if (nativeBind && func.bind === nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
+    if (!_.isFunction(func)) throw new TypeError('Bind must be called on a function');
+    var args = slice.call(arguments, 2);
+    var bound = function() {
+      return executeBound(func, bound, context, this, args.concat(slice.call(arguments)));
+    };
+    return bound;
+  };
+
+  // Partially apply a function by creating a version that has had some of its
+  // arguments pre-filled, without changing its dynamic `this` context. _ acts
+  // as a placeholder, allowing any combination of arguments to be pre-filled.
+  _.partial = function(func) {
+    var boundArgs = slice.call(arguments, 1);
+    var bound = function() {
+      var position = 0, length = boundArgs.length;
+      var args = Array(length);
+      for (var i = 0; i < length; i++) {
+        args[i] = boundArgs[i] === _ ? arguments[position++] : boundArgs[i];
+      }
+      while (position < arguments.length) args.push(arguments[position++]);
+      return executeBound(func, bound, this, this, args);
+    };
+    return bound;
+  };
+
+  // Bind a number of an object's methods to that object. Remaining arguments
+  // are the method names to be bound. Useful for ensuring that all callbacks
+  // defined on an object belong to it.
+  _.bindAll = function(obj) {
+    var i, length = arguments.length, key;
+    if (length <= 1) throw new Error('bindAll must be passed function names');
+    for (i = 1; i < length; i++) {
+      key = arguments[i];
+      obj[key] = _.bind(obj[key], obj);
+    }
+    return obj;
+  };
+
+  // Memoize an expensive function by storing its results.
+  _.memoize = function(func, hasher) {
+    var memoize = function(key) {
+      var cache = memoize.cache;
+      var address = '' + (hasher ? hasher.apply(this, arguments) : key);
+      if (!_.has(cache, address)) cache[address] = func.apply(this, arguments);
+      return cache[address];
+    };
+    memoize.cache = {};
+    return memoize;
+  };
+
+  // Delays a function for the given number of milliseconds, and then calls
+  // it with the arguments supplied.
+  _.delay = function(func, wait) {
+    var args = slice.call(arguments, 2);
+    return setTimeout(function(){
+      return func.apply(null, args);
+    }, wait);
+  };
+
+  // Defers a function, scheduling it to run after the current call stack has
+  // cleared.
+  _.defer = _.partial(_.delay, _, 1);
+
+  // Returns a function, that, when invoked, will only be triggered at most once
+  // during a given window of time. Normally, the throttled function will run
+  // as much as it can, without ever going more than once per `wait` duration;
+  // but if you'd like to disable the execution on the leading edge, pass
+  // `{leading: false}`. To disable execution on the trailing edge, ditto.
+  _.throttle = function(func, wait, options) {
+    var context, args, result;
+    var timeout = null;
+    var previous = 0;
+    if (!options) options = {};
+    var later = function() {
+      previous = options.leading === false ? 0 : _.now();
+      timeout = null;
+      result = func.apply(context, args);
+      if (!timeout) context = args = null;
+    };
+    return function() {
+      var now = _.now();
+      if (!previous && options.leading === false) previous = now;
+      var remaining = wait - (now - previous);
+      context = this;
+      args = arguments;
+      if (remaining <= 0 || remaining > wait) {
+        if (timeout) {
+          clearTimeout(timeout);
+          timeout = null;
+        }
+        previous = now;
+        result = func.apply(context, args);
+        if (!timeout) context = args = null;
+      } else if (!timeout && options.trailing !== false) {
+        timeout = setTimeout(later, remaining);
+      }
+      return result;
+    };
+  };
+
+  // Returns a function, that, as long as it continues to be invoked, will not
+  // be triggered. The function will be called after it stops being called for
+  // N milliseconds. If `immediate` is passed, trigger the function on the
+  // leading edge, instead of the trailing.
+  _.debounce = function(func, wait, immediate) {
+    var timeout, args, context, timestamp, result;
+
+    var later = function() {
+      var last = _.now() - timestamp;
+
+      if (last < wait && last >= 0) {
+        timeout = setTimeout(later, wait - last);
+      } else {
+        timeout = null;
+        if (!immediate) {
+          result = func.apply(context, args);
+          if (!timeout) context = args = null;
+        }
+      }
+    };
+
+    return function() {
+      context = this;
+      args = arguments;
+      timestamp = _.now();
+      var callNow = immediate && !timeout;
+      if (!timeout) timeout = setTimeout(later, wait);
+      if (callNow) {
+        result = func.apply(context, args);
+        context = args = null;
+      }
+
+      return result;
+    };
+  };
+
+  // Returns the first function passed as an argument to the second,
+  // allowing you to adjust arguments, run code before and after, and
+  // conditionally execute the original function.
+  _.wrap = function(func, wrapper) {
+    return _.partial(wrapper, func);
+  };
+
+  // Returns a negated version of the passed-in predicate.
+  _.negate = function(predicate) {
+    return function() {
+      return !predicate.apply(this, arguments);
+    };
+  };
+
+  // Returns a function that is the composition of a list of functions, each
+  // consuming the return value of the function that follows.
+  _.compose = function() {
+    var args = arguments;
+    var start = args.length - 1;
+    return function() {
+      var i = start;
+      var result = args[start].apply(this, arguments);
+      while (i--) result = args[i].call(this, result);
+      return result;
+    };
+  };
+
+  // Returns a function that will only be executed on and after the Nth call.
+  _.after = function(times, func) {
+    return function() {
+      if (--times < 1) {
+        return func.apply(this, arguments);
+      }
+    };
+  };
+
+  // Returns a function that will only be executed up to (but not including) the Nth call.
+  _.before = function(times, func) {
+    var memo;
+    return function() {
+      if (--times > 0) {
+        memo = func.apply(this, arguments);
+      }
+      if (times <= 1) func = null;
+      return memo;
+    };
+  };
+
+  // Returns a function that will be executed at most one time, no matter how
+  // often you call it. Useful for lazy initialization.
+  _.once = _.partial(_.before, 2);
+
+  // Object Functions
+  // ----------------
+
+  // Keys in IE < 9 that won't be iterated by `for key in ...` and thus missed.
+  var hasEnumBug = !{toString: null}.propertyIsEnumerable('toString');
+  var nonEnumerableProps = ['valueOf', 'isPrototypeOf', 'toString',
+                      'propertyIsEnumerable', 'hasOwnProperty', 'toLocaleString'];
+
+  function collectNonEnumProps(obj, keys) {
+    var nonEnumIdx = nonEnumerableProps.length;
+    var constructor = obj.constructor;
+    var proto = (_.isFunction(constructor) && constructor.prototype) || ObjProto;
+
+    // Constructor is a special case.
+    var prop = 'constructor';
+    if (_.has(obj, prop) && !_.contains(keys, prop)) keys.push(prop);
+
+    while (nonEnumIdx--) {
+      prop = nonEnumerableProps[nonEnumIdx];
+      if (prop in obj && obj[prop] !== proto[prop] && !_.contains(keys, prop)) {
+        keys.push(prop);
+      }
+    }
+  }
+
+  // Retrieve the names of an object's own properties.
+  // Delegates to **ECMAScript 5**'s native `Object.keys`
+  _.keys = function(obj) {
+    if (!_.isObject(obj)) return [];
+    if (nativeKeys) return nativeKeys(obj);
+    var keys = [];
+    for (var key in obj) if (_.has(obj, key)) keys.push(key);
+    // Ahem, IE < 9.
+    if (hasEnumBug) collectNonEnumProps(obj, keys);
+    return keys;
+  };
+
+  // Retrieve all the property names of an object.
+  _.allKeys = function(obj) {
+    if (!_.isObject(obj)) return [];
+    var keys = [];
+    for (var key in obj) keys.push(key);
+    // Ahem, IE < 9.
+    if (hasEnumBug) collectNonEnumProps(obj, keys);
+    return keys;
+  };
+
+  // Retrieve the values of an object's properties.
+  _.values = function(obj) {
+    var keys = _.keys(obj);
+    var length = keys.length;
+    var values = Array(length);
+    for (var i = 0; i < length; i++) {
+      values[i] = obj[keys[i]];
+    }
+    return values;
+  };
+
+  // Returns the results of applying the iteratee to each element of the object
+  // In contrast to _.map it returns an object
+  _.mapObject = function(obj, iteratee, context) {
+    iteratee = cb(iteratee, context);
+    var keys =  _.keys(obj),
+          length = keys.length,
+          results = {},
+          currentKey;
+      for (var index = 0; index < length; index++) {
+        currentKey = keys[index];
+        results[currentKey] = iteratee(obj[currentKey], currentKey, obj);
+      }
+      return results;
+  };
+
+  // Convert an object into a list of `[key, value]` pairs.
+  _.pairs = function(obj) {
+    var keys = _.keys(obj);
+    var length = keys.length;
+    var pairs = Array(length);
+    for (var i = 0; i < length; i++) {
+      pairs[i] = [keys[i], obj[keys[i]]];
+    }
+    return pairs;
+  };
+
+  // Invert the keys and values of an object. The values must be serializable.
+  _.invert = function(obj) {
+    var result = {};
+    var keys = _.keys(obj);
+    for (var i = 0, length = keys.length; i < length; i++) {
+      result[obj[keys[i]]] = keys[i];
+    }
+    return result;
+  };
+
+  // Return a sorted list of the function names available on the object.
+  // Aliased as `methods`
+  _.functions = _.methods = function(obj) {
+    var names = [];
+    for (var key in obj) {
+      if (_.isFunction(obj[key])) names.push(key);
+    }
+    return names.sort();
+  };
+
+  // Extend a given object with all the properties in passed-in object(s).
+  _.extend = createAssigner(_.allKeys);
+
+  // Assigns a given object with all the own properties in the passed-in object(s)
+  // (https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object/assign)
+  _.extendOwn = _.assign = createAssigner(_.keys);
+
+  // Returns the first key on an object that passes a predicate test
+  _.findKey = function(obj, predicate, context) {
+    predicate = cb(predicate, context);
+    var keys = _.keys(obj), key;
+    for (var i = 0, length = keys.length; i < length; i++) {
+      key = keys[i];
+      if (predicate(obj[key], key, obj)) return key;
+    }
+  };
+
+  // Return a copy of the object only containing the whitelisted properties.
+  _.pick = function(object, oiteratee, context) {
+    var result = {}, obj = object, iteratee, keys;
+    if (obj == null) return result;
+    if (_.isFunction(oiteratee)) {
+      keys = _.allKeys(obj);
+      iteratee = optimizeCb(oiteratee, context);
+    } else {
+      keys = flatten(arguments, false, false, 1);
+      iteratee = function(value, key, obj) { return key in obj; };
+      obj = Object(obj);
+    }
+    for (var i = 0, length = keys.length; i < length; i++) {
+      var key = keys[i];
+      var value = obj[key];
+      if (iteratee(value, key, obj)) result[key] = value;
+    }
+    return result;
+  };
+
+   // Return a copy of the object without the blacklisted properties.
+  _.omit = function(obj, iteratee, context) {
+    if (_.isFunction(iteratee)) {
+      iteratee = _.negate(iteratee);
+    } else {
+      var keys = _.map(flatten(arguments, false, false, 1), String);
+      iteratee = function(value, key) {
+        return !_.contains(keys, key);
+      };
+    }
+    return _.pick(obj, iteratee, context);
+  };
+
+  // Fill in a given object with default properties.
+  _.defaults = createAssigner(_.allKeys, true);
+
+  // Creates an object that inherits from the given prototype object.
+  // If additional properties are provided then they will be added to the
+  // created object.
+  _.create = function(prototype, props) {
+    var result = baseCreate(prototype);
+    if (props) _.extendOwn(result, props);
+    return result;
+  };
+
+  // Create a (shallow-cloned) duplicate of an object.
+  _.clone = function(obj) {
+    if (!_.isObject(obj)) return obj;
+    return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
+  };
+
+  // Invokes interceptor with the obj, and then returns obj.
+  // The primary purpose of this method is to "tap into" a method chain, in
+  // order to perform operations on intermediate results within the chain.
+  _.tap = function(obj, interceptor) {
+    interceptor(obj);
+    return obj;
+  };
+
+  // Returns whether an object has a given set of `key:value` pairs.
+  _.isMatch = function(object, attrs) {
+    var keys = _.keys(attrs), length = keys.length;
+    if (object == null) return !length;
+    var obj = Object(object);
+    for (var i = 0; i < length; i++) {
+      var key = keys[i];
+      if (attrs[key] !== obj[key] || !(key in obj)) return false;
+    }
+    return true;
+  };
+
+
+  // Internal recursive comparison function for `isEqual`.
+  var eq = function(a, b, aStack, bStack) {
+    // Identical objects are equal. `0 === -0`, but they aren't identical.
+    // See the [Harmony `egal` proposal](http://wiki.ecmascript.org/doku.php?id=harmony:egal).
+    if (a === b) return a !== 0 || 1 / a === 1 / b;
+    // A strict comparison is necessary because `null == undefined`.
+    if (a == null || b == null) return a === b;
+    // Unwrap any wrapped objects.
+    if (a instanceof _) a = a._wrapped;
+    if (b instanceof _) b = b._wrapped;
+    // Compare `[[Class]]` names.
+    var className = toString.call(a);
+    if (className !== toString.call(b)) return false;
+    switch (className) {
+      // Strings, numbers, regular expressions, dates, and booleans are compared by value.
+      case '[object RegExp]':
+      // RegExps are coerced to strings for comparison (Note: '' + /a/i === '/a/i')
+      case '[object String]':
+        // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
+        // equivalent to `new String("5")`.
+        return '' + a === '' + b;
+      case '[object Number]':
+        // `NaN`s are equivalent, but non-reflexive.
+        // Object(NaN) is equivalent to NaN
+        if (+a !== +a) return +b !== +b;
+        // An `egal` comparison is performed for other numeric values.
+        return +a === 0 ? 1 / +a === 1 / b : +a === +b;
+      case '[object Date]':
+      case '[object Boolean]':
+        // Coerce dates and booleans to numeric primitive values. Dates are compared by their
+        // millisecond representations. Note that invalid dates with millisecond representations
+        // of `NaN` are not equivalent.
+        return +a === +b;
+    }
+
+    var areArrays = className === '[object Array]';
+    if (!areArrays) {
+      if (typeof a != 'object' || typeof b != 'object') return false;
+
+      // Objects with different constructors are not equivalent, but `Object`s or `Array`s
+      // from different frames are.
+      var aCtor = a.constructor, bCtor = b.constructor;
+      if (aCtor !== bCtor && !(_.isFunction(aCtor) && aCtor instanceof aCtor &&
+                               _.isFunction(bCtor) && bCtor instanceof bCtor)
+                          && ('constructor' in a && 'constructor' in b)) {
+        return false;
+      }
+    }
+    // Assume equality for cyclic structures. The algorithm for detecting cyclic
+    // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
+
+    // Initializing stack of traversed objects.
+    // It's done here since we only need them for objects and arrays comparison.
+    aStack = aStack || [];
+    bStack = bStack || [];
+    var length = aStack.length;
+    while (length--) {
+      // Linear search. Performance is inversely proportional to the number of
+      // unique nested structures.
+      if (aStack[length] === a) return bStack[length] === b;
+    }
+
+    // Add the first object to the stack of traversed objects.
+    aStack.push(a);
+    bStack.push(b);
+
+    // Recursively compare objects and arrays.
+    if (areArrays) {
+      // Compare array lengths to determine if a deep comparison is necessary.
+      length = a.length;
+      if (length !== b.length) return false;
+      // Deep compare the contents, ignoring non-numeric properties.
+      while (length--) {
+        if (!eq(a[length], b[length], aStack, bStack)) return false;
+      }
+    } else {
+      // Deep compare objects.
+      var keys = _.keys(a), key;
+      length = keys.length;
+      // Ensure that both objects contain the same number of properties before comparing deep equality.
+      if (_.keys(b).length !== length) return false;
+      while (length--) {
+        // Deep compare each member
+        key = keys[length];
+        if (!(_.has(b, key) && eq(a[key], b[key], aStack, bStack))) return false;
+      }
+    }
+    // Remove the first object from the stack of traversed objects.
+    aStack.pop();
+    bStack.pop();
+    return true;
+  };
+
+  // Perform a deep comparison to check if two objects are equal.
+  _.isEqual = function(a, b) {
+    return eq(a, b);
+  };
+
+  // Is a given array, string, or object empty?
+  // An "empty" object has no enumerable own-properties.
+  _.isEmpty = function(obj) {
+    if (obj == null) return true;
+    if (isArrayLike(obj) && (_.isArray(obj) || _.isString(obj) || _.isArguments(obj))) return obj.length === 0;
+    return _.keys(obj).length === 0;
+  };
+
+  // Is a given value a DOM element?
+  _.isElement = function(obj) {
+    return !!(obj && obj.nodeType === 1);
+  };
+
+  // Is a given value an array?
+  // Delegates to ECMA5's native Array.isArray
+  _.isArray = nativeIsArray || function(obj) {
+    return toString.call(obj) === '[object Array]';
+  };
+
+  // Is a given variable an object?
+  _.isObject = function(obj) {
+    var type = typeof obj;
+    return type === 'function' || type === 'object' && !!obj;
+  };
+
+  // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp, isError.
+  _.each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp', 'Error'], function(name) {
+    _['is' + name] = function(obj) {
+      return toString.call(obj) === '[object ' + name + ']';
+    };
+  });
+
+  // Define a fallback version of the method in browsers (ahem, IE < 9), where
+  // there isn't any inspectable "Arguments" type.
+  if (!_.isArguments(arguments)) {
+    _.isArguments = function(obj) {
+      return _.has(obj, 'callee');
+    };
+  }
+
+  // Optimize `isFunction` if appropriate. Work around some typeof bugs in old v8,
+  // IE 11 (#1621), and in Safari 8 (#1929).
+  if (typeof /./ != 'function' && typeof Int8Array != 'object') {
+    _.isFunction = function(obj) {
+      return typeof obj == 'function' || false;
+    };
+  }
+
+  // Is a given object a finite number?
+  _.isFinite = function(obj) {
+    return isFinite(obj) && !isNaN(parseFloat(obj));
+  };
+
+  // Is the given value `NaN`? (NaN is the only number which does not equal itself).
+  _.isNaN = function(obj) {
+    return _.isNumber(obj) && obj !== +obj;
+  };
+
+  // Is a given value a boolean?
+  _.isBoolean = function(obj) {
+    return obj === true || obj === false || toString.call(obj) === '[object Boolean]';
+  };
+
+  // Is a given value equal to null?
+  _.isNull = function(obj) {
+    return obj === null;
+  };
+
+  // Is a given variable undefined?
+  _.isUndefined = function(obj) {
+    return obj === void 0;
+  };
+
+  // Shortcut function for checking if an object has a given property directly
+  // on itself (in other words, not on a prototype).
+  _.has = function(obj, key) {
+    return obj != null && hasOwnProperty.call(obj, key);
+  };
+
+  // Utility Functions
+  // -----------------
+
+  // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
+  // previous owner. Returns a reference to the Underscore object.
+  _.noConflict = function() {
+    root._ = previousUnderscore;
+    return this;
+  };
+
+  // Keep the identity function around for default iteratees.
+  _.identity = function(value) {
+    return value;
+  };
+
+  // Predicate-generating functions. Often useful outside of Underscore.
+  _.constant = function(value) {
+    return function() {
+      return value;
+    };
+  };
+
+  _.noop = function(){};
+
+  _.property = property;
+
+  // Generates a function for a given object that returns a given property.
+  _.propertyOf = function(obj) {
+    return obj == null ? function(){} : function(key) {
+      return obj[key];
+    };
+  };
+
+  // Returns a predicate for checking whether an object has a given set of
+  // `key:value` pairs.
+  _.matcher = _.matches = function(attrs) {
+    attrs = _.extendOwn({}, attrs);
+    return function(obj) {
+      return _.isMatch(obj, attrs);
+    };
+  };
+
+  // Run a function **n** times.
+  _.times = function(n, iteratee, context) {
+    var accum = Array(Math.max(0, n));
+    iteratee = optimizeCb(iteratee, context, 1);
+    for (var i = 0; i < n; i++) accum[i] = iteratee(i);
+    return accum;
+  };
+
+  // Return a random integer between min and max (inclusive).
+  _.random = function(min, max) {
+    if (max == null) {
+      max = min;
+      min = 0;
+    }
+    return min + Math.floor(Math.random() * (max - min + 1));
+  };
+
+  // A (possibly faster) way to get the current timestamp as an integer.
+  _.now = Date.now || function() {
+    return new Date().getTime();
+  };
+
+   // List of HTML entities for escaping.
+  var escapeMap = {
+    '&': '&amp;',
+    '<': '&lt;',
+    '>': '&gt;',
+    '"': '&quot;',
+    "'": '&#x27;',
+    '`': '&#x60;'
+  };
+  var unescapeMap = _.invert(escapeMap);
+
+  // Functions for escaping and unescaping strings to/from HTML interpolation.
+  var createEscaper = function(map) {
+    var escaper = function(match) {
+      return map[match];
+    };
+    // Regexes for identifying a key that needs to be escaped
+    var source = '(?:' + _.keys(map).join('|') + ')';
+    var testRegexp = RegExp(source);
+    var replaceRegexp = RegExp(source, 'g');
+    return function(string) {
+      string = string == null ? '' : '' + string;
+      return testRegexp.test(string) ? string.replace(replaceRegexp, escaper) : string;
+    };
+  };
+  _.escape = createEscaper(escapeMap);
+  _.unescape = createEscaper(unescapeMap);
+
+  // If the value of the named `property` is a function then invoke it with the
+  // `object` as context; otherwise, return it.
+  _.result = function(object, property, fallback) {
+    var value = object == null ? void 0 : object[property];
+    if (value === void 0) {
+      value = fallback;
+    }
+    return _.isFunction(value) ? value.call(object) : value;
+  };
+
+  // Generate a unique integer id (unique within the entire client session).
+  // Useful for temporary DOM ids.
+  var idCounter = 0;
+  _.uniqueId = function(prefix) {
+    var id = ++idCounter + '';
+    return prefix ? prefix + id : id;
+  };
+
+  // By default, Underscore uses ERB-style template delimiters, change the
+  // following template settings to use alternative delimiters.
+  _.templateSettings = {
+    evaluate    : /<%([\s\S]+?)%>/g,
+    interpolate : /<%=([\s\S]+?)%>/g,
+    escape      : /<%-([\s\S]+?)%>/g
+  };
+
+  // When customizing `templateSettings`, if you don't want to define an
+  // interpolation, evaluation or escaping regex, we need one that is
+  // guaranteed not to match.
+  var noMatch = /(.)^/;
+
+  // Certain characters need to be escaped so that they can be put into a
+  // string literal.
+  var escapes = {
+    "'":      "'",
+    '\\':     '\\',
+    '\r':     'r',
+    '\n':     'n',
+    '\u2028': 'u2028',
+    '\u2029': 'u2029'
+  };
+
+  var escaper = /\\|'|\r|\n|\u2028|\u2029/g;
+
+  var escapeChar = function(match) {
+    return '\\' + escapes[match];
+  };
+
+  // JavaScript micro-templating, similar to John Resig's implementation.
+  // Underscore templating handles arbitrary delimiters, preserves whitespace,
+  // and correctly escapes quotes within interpolated code.
+  // NB: `oldSettings` only exists for backwards compatibility.
+  _.template = function(text, settings, oldSettings) {
+    if (!settings && oldSettings) settings = oldSettings;
+    settings = _.defaults({}, settings, _.templateSettings);
+
+    // Combine delimiters into one regular expression via alternation.
+    var matcher = RegExp([
+      (settings.escape || noMatch).source,
+      (settings.interpolate || noMatch).source,
+      (settings.evaluate || noMatch).source
+    ].join('|') + '|$', 'g');
+
+    // Compile the template source, escaping string literals appropriately.
+    var index = 0;
+    var source = "__p+='";
+    text.replace(matcher, function(match, escape, interpolate, evaluate, offset) {
+      source += text.slice(index, offset).replace(escaper, escapeChar);
+      index = offset + match.length;
+
+      if (escape) {
+        source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'";
+      } else if (interpolate) {
+        source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'";
+      } else if (evaluate) {
+        source += "';\n" + evaluate + "\n__p+='";
+      }
+
+      // Adobe VMs need the match returned to produce the correct offest.
+      return match;
+    });
+    source += "';\n";
+
+    // If a variable is not specified, place data values in local scope.
+    if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n';
+
+    source = "var __t,__p='',__j=Array.prototype.join," +
+      "print=function(){__p+=__j.call(arguments,'');};\n" +
+      source + 'return __p;\n';
+
+    try {
+      var render = new Function(settings.variable || 'obj', '_', source);
+    } catch (e) {
+      e.source = source;
+      throw e;
+    }
+
+    var template = function(data) {
+      return render.call(this, data, _);
+    };
+
+    // Provide the compiled source as a convenience for precompilation.
+    var argument = settings.variable || 'obj';
+    template.source = 'function(' + argument + '){\n' + source + '}';
+
+    return template;
+  };
+
+  // Add a "chain" function. Start chaining a wrapped Underscore object.
+  _.chain = function(obj) {
+    var instance = _(obj);
+    instance._chain = true;
+    return instance;
+  };
+
+  // OOP
+  // ---------------
+  // If Underscore is called as a function, it returns a wrapped object that
+  // can be used OO-style. This wrapper holds altered versions of all the
+  // underscore functions. Wrapped objects may be chained.
+
+  // Helper function to continue chaining intermediate results.
+  var result = function(instance, obj) {
+    return instance._chain ? _(obj).chain() : obj;
+  };
+
+  // Add your own custom functions to the Underscore object.
+  _.mixin = function(obj) {
+    _.each(_.functions(obj), function(name) {
+      var func = _[name] = obj[name];
+      _.prototype[name] = function() {
+        var args = [this._wrapped];
+        push.apply(args, arguments);
+        return result(this, func.apply(_, args));
+      };
+    });
+  };
+
+  // Add all of the Underscore functions to the wrapper object.
+  _.mixin(_);
+
+  // Add all mutator Array functions to the wrapper.
+  _.each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
+    var method = ArrayProto[name];
+    _.prototype[name] = function() {
+      var obj = this._wrapped;
+      method.apply(obj, arguments);
+      if ((name === 'shift' || name === 'splice') && obj.length === 0) delete obj[0];
+      return result(this, obj);
+    };
+  });
+
+  // Add all accessor Array functions to the wrapper.
+  _.each(['concat', 'join', 'slice'], function(name) {
+    var method = ArrayProto[name];
+    _.prototype[name] = function() {
+      return result(this, method.apply(this._wrapped, arguments));
+    };
+  });
+
+  // Extracts the result from a wrapped and chained object.
+  _.prototype.value = function() {
+    return this._wrapped;
+  };
+
+  // Provide unwrapping proxy for some methods used in engine operations
+  // such as arithmetic and JSON stringification.
+  _.prototype.valueOf = _.prototype.toJSON = _.prototype.value;
+
+  _.prototype.toString = function() {
+    return '' + this._wrapped;
+  };
+
+  // AMD registration happens at the end for compatibility with AMD loaders
+  // that may not enforce next-turn semantics on modules. Even though general
+  // practice for AMD registration is to be anonymous, underscore registers
+  // as a named module because, like jQuery, it is a base library that is
+  // popular enough to be bundled in a third party lib, but not be part of
+  // an AMD load request. Those cases could generate an error when an
+  // anonymous define() is called outside of a loader request.
+  if (typeof define === 'function' && define.amd) {
+    define('underscore', [], function() {
+      return _;
+    });
+  }
+}.call(this));
+
+},{}],26:[function(require,module,exports){
+arguments[4][19][0].apply(exports,arguments)
+},{"dup":19}],27:[function(require,module,exports){
+module.exports = function isBuffer(arg) {
+  return arg && typeof arg === 'object'
+    && typeof arg.copy === 'function'
+    && typeof arg.fill === 'function'
+    && typeof arg.readUInt8 === 'function';
+}
+},{}],28:[function(require,module,exports){
+(function (process,global){
+// Copyright Joyent, Inc. and other Node contributors.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a
+// copy of this software and associated documentation files (the
+// "Software"), to deal in the Software without restriction, including
+// without limitation the rights to use, copy, modify, merge, publish,
+// distribute, sublicense, and/or sell copies of the Software, and to permit
+// persons to whom the Software is furnished to do so, subject to the
+// following conditions:
+//
+// The above copyright notice and this permission notice shall be included
+// in all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+// USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+var formatRegExp = /%[sdj%]/g;
+exports.format = function(f) {
+  if (!isString(f)) {
+    var objects = [];
+    for (var i = 0; i < arguments.length; i++) {
+      objects.push(inspect(arguments[i]));
+    }
+    return objects.join(' ');
+  }
+
+  var i = 1;
+  var args = arguments;
+  var len = args.length;
+  var str = String(f).replace(formatRegExp, function(x) {
+    if (x === '%%') return '%';
+    if (i >= len) return x;
+    switch (x) {
+      case '%s': return String(args[i++]);
+      case '%d': return Number(args[i++]);
+      case '%j':
+        try {
+          return JSON.stringify(args[i++]);
+        } catch (_) {
+          return '[Circular]';
+        }
+      default:
+        return x;
+    }
+  });
+  for (var x = args[i]; i < len; x = args[++i]) {
+    if (isNull(x) || !isObject(x)) {
+      str += ' ' + x;
+    } else {
+      str += ' ' + inspect(x);
+    }
+  }
+  return str;
+};
+
+
+// Mark that a method should not be used.
+// Returns a modified function which warns once by default.
+// If --no-deprecation is set, then it is a no-op.
+exports.deprecate = function(fn, msg) {
+  // Allow for deprecating things in the process of starting up.
+  if (isUndefined(global.process)) {
+    return function() {
+      return exports.deprecate(fn, msg).apply(this, arguments);
+    };
+  }
+
+  if (process.noDeprecation === true) {
+    return fn;
+  }
+
+  var warned = false;
+  function deprecated() {
+    if (!warned) {
+      if (process.throwDeprecation) {
+        throw new Error(msg);
+      } else if (process.traceDeprecation) {
+        console.trace(msg);
+      } else {
+        console.error(msg);
+      }
+      warned = true;
+    }
+    return fn.apply(this, arguments);
+  }
+
+  return deprecated;
+};
+
+
+var debugs = {};
+var debugEnviron;
+exports.debuglog = function(set) {
+  if (isUndefined(debugEnviron))
+    debugEnviron = process.env.NODE_DEBUG || '';
+  set = set.toUpperCase();
+  if (!debugs[set]) {
+    if (new RegExp('\\b' + set + '\\b', 'i').test(debugEnviron)) {
+      var pid = process.pid;
+      debugs[set] = function() {
+        var msg = exports.format.apply(exports, arguments);
+        console.error('%s %d: %s', set, pid, msg);
+      };
+    } else {
+      debugs[set] = function() {};
+    }
+  }
+  return debugs[set];
+};
+
+
+/**
+ * Echos the value of a value. Trys to print the value out
+ * in the best way possible given the different types.
+ *
+ * @param {Object} obj The object to print out.
+ * @param {Object} opts Optional options object that alters the output.
+ */
+/* legacy: obj, showHidden, depth, colors*/
+function inspect(obj, opts) {
+  // default options
+  var ctx = {
+    seen: [],
+    stylize: stylizeNoColor
+  };
+  // legacy...
+  if (arguments.length >= 3) ctx.depth = arguments[2];
+  if (arguments.length >= 4) ctx.colors = arguments[3];
+  if (isBoolean(opts)) {
+    // legacy...
+    ctx.showHidden = opts;
+  } else if (opts) {
+    // got an "options" object
+    exports._extend(ctx, opts);
+  }
+  // set default options
+  if (isUndefined(ctx.showHidden)) ctx.showHidden = false;
+  if (isUndefined(ctx.depth)) ctx.depth = 2;
+  if (isUndefined(ctx.colors)) ctx.colors = false;
+  if (isUndefined(ctx.customInspect)) ctx.customInspect = true;
+  if (ctx.colors) ctx.stylize = stylizeWithColor;
+  return formatValue(ctx, obj, ctx.depth);
+}
+exports.inspect = inspect;
+
+
+// http://en.wikipedia.org/wiki/ANSI_escape_code#graphics
+inspect.colors = {
+  'bold' : [1, 22],
+  'italic' : [3, 23],
+  'underline' : [4, 24],
+  'inverse' : [7, 27],
+  'white' : [37, 39],
+  'grey' : [90, 39],
+  'black' : [30, 39],
+  'blue' : [34, 39],
+  'cyan' : [36, 39],
+  'green' : [32, 39],
+  'magenta' : [35, 39],
+  'red' : [31, 39],
+  'yellow' : [33, 39]
+};
+
+// Don't use 'blue' not visible on cmd.exe
+inspect.styles = {
+  'special': 'cyan',
+  'number': 'yellow',
+  'boolean': 'yellow',
+  'undefined': 'grey',
+  'null': 'bold',
+  'string': 'green',
+  'date': 'magenta',
+  // "name": intentionally not styling
+  'regexp': 'red'
+};
+
+
+function stylizeWithColor(str, styleType) {
+  var style = inspect.styles[styleType];
+
+  if (style) {
+    return '\u001b[' + inspect.colors[style][0] + 'm' + str +
+           '\u001b[' + inspect.colors[style][1] + 'm';
+  } else {
+    return str;
+  }
+}
+
+
+function stylizeNoColor(str, styleType) {
+  return str;
+}
+
+
+function arrayToHash(array) {
+  var hash = {};
+
+  array.forEach(function(val, idx) {
+    hash[val] = true;
+  });
+
+  return hash;
+}
+
+
+function formatValue(ctx, value, recurseTimes) {
+  // Provide a hook for user-specified inspect functions.
+  // Check that value is an object with an inspect function on it
+  if (ctx.customInspect &&
+      value &&
+      isFunction(value.inspect) &&
+      // Filter out the util module, it's inspect function is special
+      value.inspect !== exports.inspect &&
+      // Also filter out any prototype objects using the circular check.
+      !(value.constructor && value.constructor.prototype === value)) {
+    var ret = value.inspect(recurseTimes, ctx);
+    if (!isString(ret)) {
+      ret = formatValue(ctx, ret, recurseTimes);
+    }
+    return ret;
+  }
+
+  // Primitive types cannot have properties
+  var primitive = formatPrimitive(ctx, value);
+  if (primitive) {
+    return primitive;
+  }
+
+  // Look up the keys of the object.
+  var keys = Object.keys(value);
+  var visibleKeys = arrayToHash(keys);
+
+  if (ctx.showHidden) {
+    keys = Object.getOwnPropertyNames(value);
+  }
+
+  // IE doesn't make error fields non-enumerable
+  // http://msdn.microsoft.com/en-us/library/ie/dww52sbt(v=vs.94).aspx
+  if (isError(value)
+      && (keys.indexOf('message') >= 0 || keys.indexOf('description') >= 0)) {
+    return formatError(value);
+  }
+
+  // Some type of object without properties can be shortcutted.
+  if (keys.length === 0) {
+    if (isFunction(value)) {
+      var name = value.name ? ': ' + value.name : '';
+      return ctx.stylize('[Function' + name + ']', 'special');
+    }
+    if (isRegExp(value)) {
+      return ctx.stylize(RegExp.prototype.toString.call(value), 'regexp');
+    }
+    if (isDate(value)) {
+      return ctx.stylize(Date.prototype.toString.call(value), 'date');
+    }
+    if (isError(value)) {
+      return formatError(value);
+    }
+  }
+
+  var base = '', array = false, braces = ['{', '}'];
+
+  // Make Array say that they are Array
+  if (isArray(value)) {
+    array = true;
+    braces = ['[', ']'];
+  }
+
+  // Make functions say that they are functions
+  if (isFunction(value)) {
+    var n = value.name ? ': ' + value.name : '';
+    base = ' [Function' + n + ']';
+  }
+
+  // Make RegExps say that they are RegExps
+  if (isRegExp(value)) {
+    base = ' ' + RegExp.prototype.toString.call(value);
+  }
+
+  // Make dates with properties first say the date
+  if (isDate(value)) {
+    base = ' ' + Date.prototype.toUTCString.call(value);
+  }
+
+  // Make error with message first say the error
+  if (isError(value)) {
+    base = ' ' + formatError(value);
+  }
+
+  if (keys.length === 0 && (!array || value.length == 0)) {
+    return braces[0] + base + braces[1];
+  }
+
+  if (recurseTimes < 0) {
+    if (isRegExp(value)) {
+      return ctx.stylize(RegExp.prototype.toString.call(value), 'regexp');
+    } else {
+      return ctx.stylize('[Object]', 'special');
+    }
+  }
+
+  ctx.seen.push(value);
+
+  var output;
+  if (array) {
+    output = formatArray(ctx, value, recurseTimes, visibleKeys, keys);
+  } else {
+    output = keys.map(function(key) {
+      return formatProperty(ctx, value, recurseTimes, visibleKeys, key, array);
+    });
+  }
+
+  ctx.seen.pop();
+
+  return reduceToSingleString(output, base, braces);
+}
+
+
+function formatPrimitive(ctx, value) {
+  if (isUndefined(value))
+    return ctx.stylize('undefined', 'undefined');
+  if (isString(value)) {
+    var simple = '\'' + JSON.stringify(value).replace(/^"|"$/g, '')
+                                             .replace(/'/g, "\\'")
+                                             .replace(/\\"/g, '"') + '\'';
+    return ctx.stylize(simple, 'string');
+  }
+  if (isNumber(value))
+    return ctx.stylize('' + value, 'number');
+  if (isBoolean(value))
+    return ctx.stylize('' + value, 'boolean');
+  // For some reason typeof null is "object", so special case here.
+  if (isNull(value))
+    return ctx.stylize('null', 'null');
+}
+
+
+function formatError(value) {
+  return '[' + Error.prototype.toString.call(value) + ']';
+}
+
+
+function formatArray(ctx, value, recurseTimes, visibleKeys, keys) {
+  var output = [];
+  for (var i = 0, l = value.length; i < l; ++i) {
+    if (hasOwnProperty(value, String(i))) {
+      output.push(formatProperty(ctx, value, recurseTimes, visibleKeys,
+          String(i), true));
+    } else {
+      output.push('');
+    }
+  }
+  keys.forEach(function(key) {
+    if (!key.match(/^\d+$/)) {
+      output.push(formatProperty(ctx, value, recurseTimes, visibleKeys,
+          key, true));
+    }
+  });
+  return output;
+}
+
+
+function formatProperty(ctx, value, recurseTimes, visibleKeys, key, array) {
+  var name, str, desc;
+  desc = Object.getOwnPropertyDescriptor(value, key) || { value: value[key] };
+  if (desc.get) {
+    if (desc.set) {
+      str = ctx.stylize('[Getter/Setter]', 'special');
+    } else {
+      str = ctx.stylize('[Getter]', 'special');
+    }
+  } else {
+    if (desc.set) {
+      str = ctx.stylize('[Setter]', 'special');
+    }
+  }
+  if (!hasOwnProperty(visibleKeys, key)) {
+    name = '[' + key + ']';
+  }
+  if (!str) {
+    if (ctx.seen.indexOf(desc.value) < 0) {
+      if (isNull(recurseTimes)) {
+        str = formatValue(ctx, desc.value, null);
+      } else {
+        str = formatValue(ctx, desc.value, recurseTimes - 1);
+      }
+      if (str.indexOf('\n') > -1) {
+        if (array) {
+          str = str.split('\n').map(function(line) {
+            return '  ' + line;
+          }).join('\n').substr(2);
+        } else {
+          str = '\n' + str.split('\n').map(function(line) {
+            return '   ' + line;
+          }).join('\n');
+        }
+      }
+    } else {
+      str = ctx.stylize('[Circular]', 'special');
+    }
+  }
+  if (isUndefined(name)) {
+    if (array && key.match(/^\d+$/)) {
+      return str;
+    }
+    name = JSON.stringify('' + key);
+    if (name.match(/^"([a-zA-Z_][a-zA-Z_0-9]*)"$/)) {
+      name = name.substr(1, name.length - 2);
+      name = ctx.stylize(name, 'name');
+    } else {
+      name = name.replace(/'/g, "\\'")
+                 .replace(/\\"/g, '"')
+                 .replace(/(^"|"$)/g, "'");
+      name = ctx.stylize(name, 'string');
+    }
+  }
+
+  return name + ': ' + str;
+}
+
+
+function reduceToSingleString(output, base, braces) {
+  var numLinesEst = 0;
+  var length = output.reduce(function(prev, cur) {
+    numLinesEst++;
+    if (cur.indexOf('\n') >= 0) numLinesEst++;
+    return prev + cur.replace(/\u001b\[\d\d?m/g, '').length + 1;
+  }, 0);
+
+  if (length > 60) {
+    return braces[0] +
+           (base === '' ? '' : base + '\n ') +
+           ' ' +
+           output.join(',\n  ') +
+           ' ' +
+           braces[1];
+  }
+
+  return braces[0] + base + ' ' + output.join(', ') + ' ' + braces[1];
+}
+
+
+// NOTE: These type checking functions intentionally don't use `instanceof`
+// because it is fragile and can be easily faked with `Object.create()`.
+function isArray(ar) {
+  return Array.isArray(ar);
+}
+exports.isArray = isArray;
+
+function isBoolean(arg) {
+  return typeof arg === 'boolean';
+}
+exports.isBoolean = isBoolean;
+
+function isNull(arg) {
+  return arg === null;
+}
+exports.isNull = isNull;
+
+function isNullOrUndefined(arg) {
+  return arg == null;
+}
+exports.isNullOrUndefined = isNullOrUndefined;
+
+function isNumber(arg) {
+  return typeof arg === 'number';
+}
+exports.isNumber = isNumber;
+
+function isString(arg) {
+  return typeof arg === 'string';
+}
+exports.isString = isString;
+
+function isSymbol(arg) {
+  return typeof arg === 'symbol';
+}
+exports.isSymbol = isSymbol;
+
+function isUndefined(arg) {
+  return arg === void 0;
+}
+exports.isUndefined = isUndefined;
+
+function isRegExp(re) {
+  return isObject(re) && objectToString(re) === '[object RegExp]';
+}
+exports.isRegExp = isRegExp;
+
+function isObject(arg) {
+  return typeof arg === 'object' && arg !== null;
+}
+exports.isObject = isObject;
+
+function isDate(d) {
+  return isObject(d) && objectToString(d) === '[object Date]';
+}
+exports.isDate = isDate;
+
+function isError(e) {
+  return isObject(e) &&
+      (objectToString(e) === '[object Error]' || e instanceof Error);
+}
+exports.isError = isError;
+
+function isFunction(arg) {
+  return typeof arg === 'function';
+}
+exports.isFunction = isFunction;
+
+function isPrimitive(arg) {
+  return arg === null ||
+         typeof arg === 'boolean' ||
+         typeof arg === 'number' ||
+         typeof arg === 'string' ||
+         typeof arg === 'symbol' ||  // ES6 symbol
+         typeof arg === 'undefined';
+}
+exports.isPrimitive = isPrimitive;
+
+exports.isBuffer = require('./support/isBuffer');
+
+function objectToString(o) {
+  return Object.prototype.toString.call(o);
+}
+
+
+function pad(n) {
+  return n < 10 ? '0' + n.toString(10) : n.toString(10);
+}
+
+
+var months = ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep',
+              'Oct', 'Nov', 'Dec'];
+
+// 26 Feb 16:19:34
+function timestamp() {
+  var d = new Date();
+  var time = [pad(d.getHours()),
+              pad(d.getMinutes()),
+              pad(d.getSeconds())].join(':');
+  return [d.getDate(), months[d.getMonth()], time].join(' ');
+}
+
+
+// log is just a thin wrapper to console.log that prepends a timestamp
+exports.log = function() {
+  console.log('%s - %s', timestamp(), exports.format.apply(exports, arguments));
+};
+
+
+/**
+ * Inherit the prototype methods from one constructor into another.
+ *
+ * The Function.prototype.inherits from lang.js rewritten as a standalone
+ * function (not on Function.prototype). NOTE: If this file is to be loaded
+ * during bootstrapping this function needs to be rewritten using some native
+ * functions as prototype setup using normal JavaScript does not work as
+ * expected during bootstrapping (see mirror.js in r114903).
+ *
+ * @param {function} ctor Constructor function which needs to inherit the
+ *     prototype.
+ * @param {function} superCtor Constructor function to inherit prototype from.
+ */
+exports.inherits = require('inherits');
+
+exports._extend = function(origin, add) {
+  // Don't do anything if add isn't an object
+  if (!add || !isObject(add)) return origin;
+
+  var keys = Object.keys(add);
+  var i = keys.length;
+  while (i--) {
+    origin[keys[i]] = add[keys[i]];
+  }
+  return origin;
+};
+
+function hasOwnProperty(obj, prop) {
+  return Object.prototype.hasOwnProperty.call(obj, prop);
+}
+
+}).call(this,require('_process'),typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
+},{"./support/isBuffer":27,"_process":24,"inherits":26}],29:[function(require,module,exports){
+// Returns a wrapper function that returns a wrapped callback
+// The wrapper function should do some stuff, and return a
+// presumably different callback function.
+// This makes sure that own properties are retained, so that
+// decorations and such are not lost along the way.
+module.exports = wrappy
+function wrappy (fn, cb) {
+  if (fn && cb) return wrappy(fn)(cb)
+
+  if (typeof fn !== 'function')
+    throw new TypeError('need wrapper function')
+
+  Object.keys(fn).forEach(function (k) {
+    wrapper[k] = fn[k]
+  })
+
+  return wrapper
+
+  function wrapper() {
+    var args = new Array(arguments.length)
+    for (var i = 0; i < args.length; i++) {
+      args[i] = arguments[i]
+    }
+    var ret = fn.apply(this, args)
+    var cb = args[args.length-1]
+    if (typeof ret === 'function' && ret !== cb) {
+      Object.keys(cb).forEach(function (k) {
+        ret[k] = cb[k]
+      })
+    }
+    return ret
+  }
+}
+
+},{}]},{},[7])(7)
+});
\ No newline at end of file
diff --git a/docs/htmls/assets/javascripts/workers/search.2c215733.min.js b/docs/htmls/assets/javascripts/workers/search.2c215733.min.js
new file mode 100644
index 0000000..6e2e3ea
--- /dev/null
+++ b/docs/htmls/assets/javascripts/workers/search.2c215733.min.js
@@ -0,0 +1,42 @@
+"use strict";(()=>{var xe=Object.create;var G=Object.defineProperty,ve=Object.defineProperties,Se=Object.getOwnPropertyDescriptor,Te=Object.getOwnPropertyDescriptors,Qe=Object.getOwnPropertyNames,J=Object.getOwnPropertySymbols,Ee=Object.getPrototypeOf,Z=Object.prototype.hasOwnProperty,be=Object.prototype.propertyIsEnumerable;var K=Math.pow,X=(t,e,r)=>e in t?G(t,e,{enumerable:!0,configurable:!0,writable:!0,value:r}):t[e]=r,_=(t,e)=>{for(var r in e||(e={}))Z.call(e,r)&&X(t,r,e[r]);if(J)for(var r of J(e))be.call(e,r)&&X(t,r,e[r]);return t},B=(t,e)=>ve(t,Te(e));var Le=(t,e)=>()=>(e||t((e={exports:{}}).exports,e),e.exports);var we=(t,e,r,n)=>{if(e&&typeof e=="object"||typeof e=="function")for(let i of Qe(e))!Z.call(t,i)&&i!==r&&G(t,i,{get:()=>e[i],enumerable:!(n=Se(e,i))||n.enumerable});return t};var Pe=(t,e,r)=>(r=t!=null?xe(Ee(t)):{},we(e||!t||!t.__esModule?G(r,"default",{value:t,enumerable:!0}):r,t));var W=(t,e,r)=>new Promise((n,i)=>{var s=u=>{try{a(r.next(u))}catch(c){i(c)}},o=u=>{try{a(r.throw(u))}catch(c){i(c)}},a=u=>u.done?n(u.value):Promise.resolve(u.value).then(s,o);a((r=r.apply(t,e)).next())});var re=Le((ee,te)=>{/**
+ * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9
+ * Copyright (C) 2020 Oliver Nightingale
+ * @license MIT
+ */(function(){var t=function(e){var r=new t.Builder;return r.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),r.searchPipeline.add(t.stemmer),e.call(r,r),r.build()};t.version="2.3.9";/*!
+ * lunr.utils
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.utils={},t.utils.warn=(function(e){return function(r){e.console&&console.warn&&console.warn(r)}})(this),t.utils.asString=function(e){return e==null?"":e.toString()},t.utils.clone=function(e){if(e==null)return e;for(var r=Object.create(null),n=Object.keys(e),i=0;i<n.length;i++){var s=n[i],o=e[s];if(Array.isArray(o)){r[s]=o.slice();continue}if(typeof o=="string"||typeof o=="number"||typeof o=="boolean"){r[s]=o;continue}throw new TypeError("clone is not deep and does not support nested objects")}return r},t.FieldRef=function(e,r,n){this.docRef=e,this.fieldName=r,this._stringValue=n},t.FieldRef.joiner="/",t.FieldRef.fromString=function(e){var r=e.indexOf(t.FieldRef.joiner);if(r===-1)throw"malformed field ref string";var n=e.slice(0,r),i=e.slice(r+1);return new t.FieldRef(i,n,e)},t.FieldRef.prototype.toString=function(){return this._stringValue==null&&(this._stringValue=this.fieldName+t.FieldRef.joiner+this.docRef),this._stringValue};/*!
+ * lunr.Set
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.Set=function(e){if(this.elements=Object.create(null),e){this.length=e.length;for(var r=0;r<this.length;r++)this.elements[e[r]]=!0}else this.length=0},t.Set.complete={intersect:function(e){return e},union:function(){return this},contains:function(){return!0}},t.Set.empty={intersect:function(){return this},union:function(e){return e},contains:function(){return!1}},t.Set.prototype.contains=function(e){return!!this.elements[e]},t.Set.prototype.intersect=function(e){var r,n,i,s=[];if(e===t.Set.complete)return this;if(e===t.Set.empty)return e;this.length<e.length?(r=this,n=e):(r=e,n=this),i=Object.keys(r.elements);for(var o=0;o<i.length;o++){var a=i[o];a in n.elements&&s.push(a)}return new t.Set(s)},t.Set.prototype.union=function(e){return e===t.Set.complete?t.Set.complete:e===t.Set.empty?this:new t.Set(Object.keys(this.elements).concat(Object.keys(e.elements)))},t.idf=function(e,r){var n=0;for(var i in e)i!="_index"&&(n+=Object.keys(e[i]).length);var s=(r-n+.5)/(n+.5);return Math.log(1+Math.abs(s))},t.Token=function(e,r){this.str=e||"",this.metadata=r||{}},t.Token.prototype.toString=function(){return this.str},t.Token.prototype.update=function(e){return this.str=e(this.str,this.metadata),this},t.Token.prototype.clone=function(e){return e=e||function(r){return r},new t.Token(e(this.str,this.metadata),this.metadata)};/*!
+ * lunr.tokenizer
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.tokenizer=function(e,r){if(e==null||e==null)return[];if(Array.isArray(e))return e.map(function(g){return new t.Token(t.utils.asString(g).toLowerCase(),t.utils.clone(r))});for(var n=e.toString().toLowerCase(),i=n.length,s=[],o=0,a=0;o<=i;o++){var u=n.charAt(o),c=o-a;if(u.match(t.tokenizer.separator)||o==i){if(c>0){var f=t.utils.clone(r)||{};f.position=[a,c],f.index=s.length,s.push(new t.Token(n.slice(a,o),f))}a=o+1}}return s},t.tokenizer.separator=/[\s\-]+/;/*!
+ * lunr.Pipeline
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.Pipeline=function(){this._stack=[]},t.Pipeline.registeredFunctions=Object.create(null),t.Pipeline.registerFunction=function(e,r){r in this.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+r),e.label=r,t.Pipeline.registeredFunctions[e.label]=e},t.Pipeline.warnIfFunctionNotRegistered=function(e){var r=e.label&&e.label in this.registeredFunctions;r||t.utils.warn(`Function is not registered with pipeline. This may cause problems when serialising the index.
+`,e)},t.Pipeline.load=function(e){var r=new t.Pipeline;return e.forEach(function(n){var i=t.Pipeline.registeredFunctions[n];if(i)r.add(i);else throw new Error("Cannot load unregistered function: "+n)}),r},t.Pipeline.prototype.add=function(){var e=Array.prototype.slice.call(arguments);e.forEach(function(r){t.Pipeline.warnIfFunctionNotRegistered(r),this._stack.push(r)},this)},t.Pipeline.prototype.after=function(e,r){t.Pipeline.warnIfFunctionNotRegistered(r);var n=this._stack.indexOf(e);if(n==-1)throw new Error("Cannot find existingFn");n=n+1,this._stack.splice(n,0,r)},t.Pipeline.prototype.before=function(e,r){t.Pipeline.warnIfFunctionNotRegistered(r);var n=this._stack.indexOf(e);if(n==-1)throw new Error("Cannot find existingFn");this._stack.splice(n,0,r)},t.Pipeline.prototype.remove=function(e){var r=this._stack.indexOf(e);r!=-1&&this._stack.splice(r,1)},t.Pipeline.prototype.run=function(e){for(var r=this._stack.length,n=0;n<r;n++){for(var i=this._stack[n],s=[],o=0;o<e.length;o++){var a=i(e[o],o,e);if(!(a==null||a===""))if(Array.isArray(a))for(var u=0;u<a.length;u++)s.push(a[u]);else s.push(a)}e=s}return e},t.Pipeline.prototype.runString=function(e,r){var n=new t.Token(e,r);return this.run([n]).map(function(i){return i.toString()})},t.Pipeline.prototype.reset=function(){this._stack=[]},t.Pipeline.prototype.toJSON=function(){return this._stack.map(function(e){return t.Pipeline.warnIfFunctionNotRegistered(e),e.label})};/*!
+ * lunr.Vector
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.Vector=function(e){this._magnitude=0,this.elements=e||[]},t.Vector.prototype.positionForIndex=function(e){if(this.elements.length==0)return 0;for(var r=0,n=this.elements.length/2,i=n-r,s=Math.floor(i/2),o=this.elements[s*2];i>1&&(o<e&&(r=s),o>e&&(n=s),o!=e);)i=n-r,s=r+Math.floor(i/2),o=this.elements[s*2];if(o==e||o>e)return s*2;if(o<e)return(s+1)*2},t.Vector.prototype.insert=function(e,r){this.upsert(e,r,function(){throw"duplicate index"})},t.Vector.prototype.upsert=function(e,r,n){this._magnitude=0;var i=this.positionForIndex(e);this.elements[i]==e?this.elements[i+1]=n(this.elements[i+1],r):this.elements.splice(i,0,e,r)},t.Vector.prototype.magnitude=function(){if(this._magnitude)return this._magnitude;for(var e=0,r=this.elements.length,n=1;n<r;n+=2){var i=this.elements[n];e+=i*i}return this._magnitude=Math.sqrt(e)},t.Vector.prototype.dot=function(e){for(var r=0,n=this.elements,i=e.elements,s=n.length,o=i.length,a=0,u=0,c=0,f=0;c<s&&f<o;)a=n[c],u=i[f],a<u?c+=2:a>u?f+=2:a==u&&(r+=n[c+1]*i[f+1],c+=2,f+=2);return r},t.Vector.prototype.similarity=function(e){return this.dot(e)/this.magnitude()||0},t.Vector.prototype.toArray=function(){for(var e=new Array(this.elements.length/2),r=1,n=0;r<this.elements.length;r+=2,n++)e[n]=this.elements[r];return e},t.Vector.prototype.toJSON=function(){return this.elements};/*!
+ * lunr.stemmer
+ * Copyright (C) 2020 Oliver Nightingale
+ * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt
+ */t.stemmer=(function(){var e={ational:"ate",tional:"tion",enci:"ence",anci:"ance",izer:"ize",bli:"ble",alli:"al",entli:"ent",eli:"e",ousli:"ous",ization:"ize",ation:"ate",ator:"ate",alism:"al",iveness:"ive",fulness:"ful",ousness:"ous",aliti:"al",iviti:"ive",biliti:"ble",logi:"log"},r={icate:"ic",ative:"",alize:"al",iciti:"ic",ical:"ic",ful:"",ness:""},n="[^aeiou]",i="[aeiouy]",s=n+"[^aeiouy]*",o=i+"[aeiou]*",a="^("+s+")?"+o+s,u="^("+s+")?"+o+s+"("+o+")?$",c="^("+s+")?"+o+s+o+s,f="^("+s+")?"+i,g=new RegExp(a),l=new RegExp(c),m=new RegExp(u),x=new RegExp(f),v=/^(.+?)(ss|i)es$/,d=/^(.+?)([^s])s$/,y=/^(.+?)eed$/,b=/^(.+?)(ed|ing)$/,E=/.$/,w=/(at|bl|iz)$/,R=new RegExp("([^aeiouylsz])\\1$"),j=new RegExp("^"+s+i+"[^aeiouwxy]$"),C=/^(.+?[^aeiou])y$/,D=/^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/,N=/^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/,M=/^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/,V=/^(.+?)(s|t)(ion)$/,P=/^(.+?)e$/,z=/ll$/,$=new RegExp("^"+s+i+"[^aeiouwxy]$"),A=function(h){var S,k,L,p,T,O,F;if(h.length<3)return h;if(L=h.substr(0,1),L=="y"&&(h=L.toUpperCase()+h.substr(1)),p=v,T=d,p.test(h)?h=h.replace(p,"$1$2"):T.test(h)&&(h=h.replace(T,"$1$2")),p=y,T=b,p.test(h)){var Q=p.exec(h);p=g,p.test(Q[1])&&(p=E,h=h.replace(p,""))}else if(T.test(h)){var Q=T.exec(h);S=Q[1],T=x,T.test(S)&&(h=S,T=w,O=R,F=j,T.test(h)?h=h+"e":O.test(h)?(p=E,h=h.replace(p,"")):F.test(h)&&(h=h+"e"))}if(p=C,p.test(h)){var Q=p.exec(h);S=Q[1],h=S+"i"}if(p=D,p.test(h)){var Q=p.exec(h);S=Q[1],k=Q[2],p=g,p.test(S)&&(h=S+e[k])}if(p=N,p.test(h)){var Q=p.exec(h);S=Q[1],k=Q[2],p=g,p.test(S)&&(h=S+r[k])}if(p=M,T=V,p.test(h)){var Q=p.exec(h);S=Q[1],p=l,p.test(S)&&(h=S)}else if(T.test(h)){var Q=T.exec(h);S=Q[1]+Q[2],T=l,T.test(S)&&(h=S)}if(p=P,p.test(h)){var Q=p.exec(h);S=Q[1],p=l,T=m,O=$,(p.test(S)||T.test(S)&&!O.test(S))&&(h=S)}return p=z,T=l,p.test(h)&&T.test(h)&&(p=E,h=h.replace(p,"")),L=="y"&&(h=L.toLowerCase()+h.substr(1)),h};return function(I){return I.update(A)}})(),t.Pipeline.registerFunction(t.stemmer,"stemmer");/*!
+ * lunr.stopWordFilter
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.generateStopWordFilter=function(e){var r=e.reduce(function(n,i){return n[i]=i,n},{});return function(n){if(n&&r[n.toString()]!==n.toString())return n}},t.stopWordFilter=t.generateStopWordFilter(["a","able","about","across","after","all","almost","also","am","among","an","and","any","are","as","at","be","because","been","but","by","can","cannot","could","dear","did","do","does","either","else","ever","every","for","from","get","got","had","has","have","he","her","hers","him","his","how","however","i","if","in","into","is","it","its","just","least","let","like","likely","may","me","might","most","must","my","neither","no","nor","not","of","off","often","on","only","or","other","our","own","rather","said","say","says","she","should","since","so","some","than","that","the","their","them","then","there","these","they","this","tis","to","too","twas","us","wants","was","we","were","what","when","where","which","while","who","whom","why","will","with","would","yet","you","your"]),t.Pipeline.registerFunction(t.stopWordFilter,"stopWordFilter");/*!
+ * lunr.trimmer
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.trimmer=function(e){return e.update(function(r){return r.replace(/^\W+/,"").replace(/\W+$/,"")})},t.Pipeline.registerFunction(t.trimmer,"trimmer");/*!
+ * lunr.TokenSet
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.TokenSet=function(){this.final=!1,this.edges={},this.id=t.TokenSet._nextId,t.TokenSet._nextId+=1},t.TokenSet._nextId=1,t.TokenSet.fromArray=function(e){for(var r=new t.TokenSet.Builder,n=0,i=e.length;n<i;n++)r.insert(e[n]);return r.finish(),r.root},t.TokenSet.fromClause=function(e){return"editDistance"in e?t.TokenSet.fromFuzzyString(e.term,e.editDistance):t.TokenSet.fromString(e.term)},t.TokenSet.fromFuzzyString=function(e,r){for(var n=new t.TokenSet,i=[{node:n,editsRemaining:r,str:e}];i.length;){var s=i.pop();if(s.str.length>0){var o=s.str.charAt(0),a;o in s.node.edges?a=s.node.edges[o]:(a=new t.TokenSet,s.node.edges[o]=a),s.str.length==1&&(a.final=!0),i.push({node:a,editsRemaining:s.editsRemaining,str:s.str.slice(1)})}if(s.editsRemaining!=0){if("*"in s.node.edges)var u=s.node.edges["*"];else{var u=new t.TokenSet;s.node.edges["*"]=u}if(s.str.length==0&&(u.final=!0),i.push({node:u,editsRemaining:s.editsRemaining-1,str:s.str}),s.str.length>1&&i.push({node:s.node,editsRemaining:s.editsRemaining-1,str:s.str.slice(1)}),s.str.length==1&&(s.node.final=!0),s.str.length>=1){if("*"in s.node.edges)var c=s.node.edges["*"];else{var c=new t.TokenSet;s.node.edges["*"]=c}s.str.length==1&&(c.final=!0),i.push({node:c,editsRemaining:s.editsRemaining-1,str:s.str.slice(1)})}if(s.str.length>1){var f=s.str.charAt(0),g=s.str.charAt(1),l;g in s.node.edges?l=s.node.edges[g]:(l=new t.TokenSet,s.node.edges[g]=l),s.str.length==1&&(l.final=!0),i.push({node:l,editsRemaining:s.editsRemaining-1,str:f+s.str.slice(2)})}}}return n},t.TokenSet.fromString=function(e){for(var r=new t.TokenSet,n=r,i=0,s=e.length;i<s;i++){var o=e[i],a=i==s-1;if(o=="*")r.edges[o]=r,r.final=a;else{var u=new t.TokenSet;u.final=a,r.edges[o]=u,r=u}}return n},t.TokenSet.prototype.toArray=function(){for(var e=[],r=[{prefix:"",node:this}];r.length;){var n=r.pop(),i=Object.keys(n.node.edges),s=i.length;n.node.final&&(n.prefix.charAt(0),e.push(n.prefix));for(var o=0;o<s;o++){var a=i[o];r.push({prefix:n.prefix.concat(a),node:n.node.edges[a]})}}return e},t.TokenSet.prototype.toString=function(){if(this._str)return this._str;for(var e=this.final?"1":"0",r=Object.keys(this.edges).sort(),n=r.length,i=0;i<n;i++){var s=r[i],o=this.edges[s];e=e+s+o.id}return e},t.TokenSet.prototype.intersect=function(e){for(var r=new t.TokenSet,n=void 0,i=[{qNode:e,output:r,node:this}];i.length;){n=i.pop();for(var s=Object.keys(n.qNode.edges),o=s.length,a=Object.keys(n.node.edges),u=a.length,c=0;c<o;c++)for(var f=s[c],g=0;g<u;g++){var l=a[g];if(l==f||f=="*"){var m=n.node.edges[l],x=n.qNode.edges[f],v=m.final&&x.final,d=void 0;l in n.output.edges?(d=n.output.edges[l],d.final=d.final||v):(d=new t.TokenSet,d.final=v,n.output.edges[l]=d),i.push({qNode:x,output:d,node:m})}}}return r},t.TokenSet.Builder=function(){this.previousWord="",this.root=new t.TokenSet,this.uncheckedNodes=[],this.minimizedNodes={}},t.TokenSet.Builder.prototype.insert=function(e){var r,n=0;if(e<this.previousWord)throw new Error("Out of order word insertion");for(var i=0;i<e.length&&i<this.previousWord.length&&e[i]==this.previousWord[i];i++)n++;this.minimize(n),this.uncheckedNodes.length==0?r=this.root:r=this.uncheckedNodes[this.uncheckedNodes.length-1].child;for(var i=n;i<e.length;i++){var s=new t.TokenSet,o=e[i];r.edges[o]=s,this.uncheckedNodes.push({parent:r,char:o,child:s}),r=s}r.final=!0,this.previousWord=e},t.TokenSet.Builder.prototype.finish=function(){this.minimize(0)},t.TokenSet.Builder.prototype.minimize=function(e){for(var r=this.uncheckedNodes.length-1;r>=e;r--){var n=this.uncheckedNodes[r],i=n.child.toString();i in this.minimizedNodes?n.parent.edges[n.char]=this.minimizedNodes[i]:(n.child._str=i,this.minimizedNodes[i]=n.child),this.uncheckedNodes.pop()}};/*!
+ * lunr.Index
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.Index=function(e){this.invertedIndex=e.invertedIndex,this.fieldVectors=e.fieldVectors,this.tokenSet=e.tokenSet,this.fields=e.fields,this.pipeline=e.pipeline},t.Index.prototype.search=function(e){return this.query(function(r){var n=new t.QueryParser(e,r);n.parse()})},t.Index.prototype.query=function(e){for(var r=new t.Query(this.fields),n=Object.create(null),i=Object.create(null),s=Object.create(null),o=Object.create(null),a=Object.create(null),u=0;u<this.fields.length;u++)i[this.fields[u]]=new t.Vector;e.call(r,r);for(var u=0;u<r.clauses.length;u++){var c=r.clauses[u],f=null,g=t.Set.empty;c.usePipeline?f=this.pipeline.runString(c.term,{fields:c.fields}):f=[c.term];for(var l=0;l<f.length;l++){var m=f[l];c.term=m;var x=t.TokenSet.fromClause(c),v=this.tokenSet.intersect(x).toArray();if(v.length===0&&c.presence===t.Query.presence.REQUIRED){for(var d=0;d<c.fields.length;d++){var y=c.fields[d];o[y]=t.Set.empty}break}for(var b=0;b<v.length;b++)for(var E=v[b],w=this.invertedIndex[E],R=w._index,d=0;d<c.fields.length;d++){var y=c.fields[d],j=w[y],C=Object.keys(j),D=E+"/"+y,N=new t.Set(C);if(c.presence==t.Query.presence.REQUIRED&&(g=g.union(N),o[y]===void 0&&(o[y]=t.Set.complete)),c.presence==t.Query.presence.PROHIBITED){a[y]===void 0&&(a[y]=t.Set.empty),a[y]=a[y].union(N);continue}if(i[y].upsert(R,c.boost,function(ye,me){return ye+me}),!s[D]){for(var M=0;M<C.length;M++){var V=C[M],P=new t.FieldRef(V,y),z=j[V],$;($=n[P])===void 0?n[P]=new t.MatchData(E,y,z):$.add(E,y,z)}s[D]=!0}}}if(c.presence===t.Query.presence.REQUIRED)for(var d=0;d<c.fields.length;d++){var y=c.fields[d];o[y]=o[y].intersect(g)}}for(var A=t.Set.complete,I=t.Set.empty,u=0;u<this.fields.length;u++){var y=this.fields[u];o[y]&&(A=A.intersect(o[y])),a[y]&&(I=I.union(a[y]))}var h=Object.keys(n),S=[],k=Object.create(null);if(r.isNegated()){h=Object.keys(this.fieldVectors);for(var u=0;u<h.length;u++){var P=h[u],L=t.FieldRef.fromString(P);n[P]=new t.MatchData}}for(var u=0;u<h.length;u++){var L=t.FieldRef.fromString(h[u]),p=L.docRef;if(A.contains(p)&&!I.contains(p)){var T=this.fieldVectors[L],O=i[L.fieldName].similarity(T),F;if((F=k[p])!==void 0)F.score+=O,F.matchData.combine(n[L]);else{var Q={ref:p,score:O,matchData:n[L]};k[p]=Q,S.push(Q)}}}return S.sort(function(pe,ge){return ge.score-pe.score})},t.Index.prototype.toJSON=function(){var e=Object.keys(this.invertedIndex).sort().map(function(n){return[n,this.invertedIndex[n]]},this),r=Object.keys(this.fieldVectors).map(function(n){return[n,this.fieldVectors[n].toJSON()]},this);return{version:t.version,fields:this.fields,fieldVectors:r,invertedIndex:e,pipeline:this.pipeline.toJSON()}},t.Index.load=function(e){var r={},n={},i=e.fieldVectors,s=Object.create(null),o=e.invertedIndex,a=new t.TokenSet.Builder,u=t.Pipeline.load(e.pipeline);e.version!=t.version&&t.utils.warn("Version mismatch when loading serialised index. Current version of lunr '"+t.version+"' does not match serialized index '"+e.version+"'");for(var c=0;c<i.length;c++){var f=i[c],g=f[0],l=f[1];n[g]=new t.Vector(l)}for(var c=0;c<o.length;c++){var f=o[c],m=f[0],x=f[1];a.insert(m),s[m]=x}return a.finish(),r.fields=e.fields,r.fieldVectors=n,r.invertedIndex=s,r.tokenSet=a.root,r.pipeline=u,new t.Index(r)};/*!
+ * lunr.Builder
+ * Copyright (C) 2020 Oliver Nightingale
+ */t.Builder=function(){this._ref="id",this._fields=Object.create(null),this._documents=Object.create(null),this.invertedIndex=Object.create(null),this.fieldTermFrequencies={},this.fieldLengths={},this.tokenizer=t.tokenizer,this.pipeline=new t.Pipeline,this.searchPipeline=new t.Pipeline,this.documentCount=0,this._b=.75,this._k1=1.2,this.termIndex=0,this.metadataWhitelist=[]},t.Builder.prototype.ref=function(e){this._ref=e},t.Builder.prototype.field=function(e,r){if(/\//.test(e))throw new RangeError("Field '"+e+"' contains illegal character '/'");this._fields[e]=r||{}},t.Builder.prototype.b=function(e){e<0?this._b=0:e>1?this._b=1:this._b=e},t.Builder.prototype.k1=function(e){this._k1=e},t.Builder.prototype.add=function(e,r){var n=e[this._ref],i=Object.keys(this._fields);this._documents[n]=r||{},this.documentCount+=1;for(var s=0;s<i.length;s++){var o=i[s],a=this._fields[o].extractor,u=a?a(e):e[o],c=this.tokenizer(u,{fields:[o]}),f=this.pipeline.run(c),g=new t.FieldRef(n,o),l=Object.create(null);this.fieldTermFrequencies[g]=l,this.fieldLengths[g]=0,this.fieldLengths[g]+=f.length;for(var m=0;m<f.length;m++){var x=f[m];if(l[x]==null&&(l[x]=0),l[x]+=1,this.invertedIndex[x]==null){var v=Object.create(null);v._index=this.termIndex,this.termIndex+=1;for(var d=0;d<i.length;d++)v[i[d]]=Object.create(null);this.invertedIndex[x]=v}this.invertedIndex[x][o][n]==null&&(this.invertedIndex[x][o][n]=Object.create(null));for(var y=0;y<this.metadataWhitelist.length;y++){var b=this.metadataWhitelist[y],E=x.metadata[b];this.invertedIndex[x][o][n][b]==null&&(this.invertedIndex[x][o][n][b]=[]),this.invertedIndex[x][o][n][b].push(E)}}}},t.Builder.prototype.calculateAverageFieldLengths=function(){for(var e=Object.keys(this.fieldLengths),r=e.length,n={},i={},s=0;s<r;s++){var o=t.FieldRef.fromString(e[s]),a=o.fieldName;i[a]||(i[a]=0),i[a]+=1,n[a]||(n[a]=0),n[a]+=this.fieldLengths[o]}for(var u=Object.keys(this._fields),s=0;s<u.length;s++){var c=u[s];n[c]=n[c]/i[c]}this.averageFieldLength=n},t.Builder.prototype.createFieldVectors=function(){for(var e={},r=Object.keys(this.fieldTermFrequencies),n=r.length,i=Object.create(null),s=0;s<n;s++){for(var o=t.FieldRef.fromString(r[s]),a=o.fieldName,u=this.fieldLengths[o],c=new t.Vector,f=this.fieldTermFrequencies[o],g=Object.keys(f),l=g.length,m=this._fields[a].boost||1,x=this._documents[o.docRef].boost||1,v=0;v<l;v++){var d=g[v],y=f[d],b=this.invertedIndex[d]._index,E,w,R;i[d]===void 0?(E=t.idf(this.invertedIndex[d],this.documentCount),i[d]=E):E=i[d],w=E*((this._k1+1)*y)/(this._k1*(1-this._b+this._b*(u/this.averageFieldLength[a]))+y),w*=m,w*=x,R=Math.round(w*1e3)/1e3,c.insert(b,R)}e[o]=c}this.fieldVectors=e},t.Builder.prototype.createTokenSet=function(){this.tokenSet=t.TokenSet.fromArray(Object.keys(this.invertedIndex).sort())},t.Builder.prototype.build=function(){return this.calculateAverageFieldLengths(),this.createFieldVectors(),this.createTokenSet(),new t.Index({invertedIndex:this.invertedIndex,fieldVectors:this.fieldVectors,tokenSet:this.tokenSet,fields:Object.keys(this._fields),pipeline:this.searchPipeline})},t.Builder.prototype.use=function(e){var r=Array.prototype.slice.call(arguments,1);r.unshift(this),e.apply(this,r)},t.MatchData=function(e,r,n){for(var i=Object.create(null),s=Object.keys(n||{}),o=0;o<s.length;o++){var a=s[o];i[a]=n[a].slice()}this.metadata=Object.create(null),e!==void 0&&(this.metadata[e]=Object.create(null),this.metadata[e][r]=i)},t.MatchData.prototype.combine=function(e){for(var r=Object.keys(e.metadata),n=0;n<r.length;n++){var i=r[n],s=Object.keys(e.metadata[i]);this.metadata[i]==null&&(this.metadata[i]=Object.create(null));for(var o=0;o<s.length;o++){var a=s[o],u=Object.keys(e.metadata[i][a]);this.metadata[i][a]==null&&(this.metadata[i][a]=Object.create(null));for(var c=0;c<u.length;c++){var 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+
diff --git a/docs/htmls/assets/javascripts/workers/search.2c215733.min.js.map b/docs/htmls/assets/javascripts/workers/search.2c215733.min.js.map
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@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["node_modules/lunr/lunr.js", "src/templates/assets/javascripts/integrations/search/worker/main/index.ts", "src/templates/assets/javascripts/browser/element/_/index.ts", "src/templates/assets/javascripts/polyfills/index.ts", "src/templates/assets/javascripts/integrations/search/config/index.ts", "src/templates/assets/javascripts/integrations/search/internal/_/index.ts", "src/templates/assets/javascripts/integrations/search/internal/extract/index.ts", "src/templates/assets/javascripts/integrations/search/internal/highlight/index.ts", "src/templates/assets/javascripts/integrations/search/internal/tokenize/index.ts", "src/templates/assets/javascripts/integrations/search/query/transform/index.ts", "src/templates/assets/javascripts/integrations/search/query/_/index.ts", "src/templates/assets/javascripts/integrations/search/query/segment/index.ts", "src/templates/assets/javascripts/integrations/search/_/index.ts"],
+  "sourcesContent": ["/**\n * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9\n * Copyright (C) 2020 Oliver Nightingale\n * @license MIT\n */\n\n;(function(){\n\n/**\n * A convenience function for configuring and constructing\n * a new lunr Index.\n *\n * A lunr.Builder instance is created and the pipeline setup\n * with a trimmer, stop word filter and stemmer.\n *\n * This builder object is yielded to the configuration function\n * that is passed as a parameter, allowing the list of fields\n * and other builder parameters to be customised.\n *\n * All documents _must_ be added within the passed config function.\n *\n * @example\n * var idx = lunr(function () {\n *   this.field('title')\n *   this.field('body')\n *   this.ref('id')\n *\n *   documents.forEach(function (doc) {\n *     this.add(doc)\n *   }, this)\n * })\n *\n * @see {@link lunr.Builder}\n * @see {@link lunr.Pipeline}\n * @see {@link lunr.trimmer}\n * @see {@link lunr.stopWordFilter}\n * @see {@link lunr.stemmer}\n * @namespace {function} lunr\n */\nvar lunr = function (config) {\n  var builder = new lunr.Builder\n\n  builder.pipeline.add(\n    lunr.trimmer,\n    lunr.stopWordFilter,\n    lunr.stemmer\n  )\n\n  builder.searchPipeline.add(\n    lunr.stemmer\n  )\n\n  config.call(builder, builder)\n  return builder.build()\n}\n\nlunr.version = \"2.3.9\"\n/*!\n * lunr.utils\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A namespace containing utils for the rest of the lunr library\n * @namespace lunr.utils\n */\nlunr.utils = {}\n\n/**\n * Print a warning message to the console.\n *\n * @param {String} message The message to be printed.\n * @memberOf lunr.utils\n * @function\n */\nlunr.utils.warn = (function (global) {\n  /* eslint-disable no-console */\n  return function (message) {\n    if (global.console && console.warn) {\n      console.warn(message)\n    }\n  }\n  /* eslint-enable no-console */\n})(this)\n\n/**\n * Convert an object to a string.\n *\n * In the case of `null` and `undefined` the function returns\n * the empty string, in all other cases the result of calling\n * `toString` on the passed object is returned.\n *\n * @param {Any} obj The object to convert to a string.\n * @return {String} string representation of the passed object.\n * @memberOf lunr.utils\n */\nlunr.utils.asString = function (obj) {\n  if (obj === void 0 || obj === null) {\n    return \"\"\n  } else {\n    return obj.toString()\n  }\n}\n\n/**\n * Clones an object.\n *\n * Will create a copy of an existing object such that any mutations\n * on the copy cannot affect the original.\n *\n * Only shallow objects are supported, passing a nested object to this\n * function will cause a TypeError.\n *\n * Objects with primitives, and arrays of primitives are supported.\n *\n * @param {Object} obj The object to clone.\n * @return {Object} a clone of the passed object.\n * @throws {TypeError} when a nested object is passed.\n * @memberOf Utils\n */\nlunr.utils.clone = function (obj) {\n  if (obj === null || obj === undefined) {\n    return obj\n  }\n\n  var clone = Object.create(null),\n      keys = Object.keys(obj)\n\n  for (var i = 0; i < keys.length; i++) {\n    var key = keys[i],\n        val = obj[key]\n\n    if (Array.isArray(val)) {\n      clone[key] = val.slice()\n      continue\n    }\n\n    if (typeof val === 'string' ||\n        typeof val === 'number' ||\n        typeof val === 'boolean') {\n      clone[key] = val\n      continue\n    }\n\n    throw new TypeError(\"clone is not deep and does not support nested objects\")\n  }\n\n  return clone\n}\nlunr.FieldRef = function (docRef, fieldName, stringValue) {\n  this.docRef = docRef\n  this.fieldName = fieldName\n  this._stringValue = stringValue\n}\n\nlunr.FieldRef.joiner = \"/\"\n\nlunr.FieldRef.fromString = function (s) {\n  var n = s.indexOf(lunr.FieldRef.joiner)\n\n  if (n === -1) {\n    throw \"malformed field ref string\"\n  }\n\n  var fieldRef = s.slice(0, n),\n      docRef = s.slice(n + 1)\n\n  return new lunr.FieldRef (docRef, fieldRef, s)\n}\n\nlunr.FieldRef.prototype.toString = function () {\n  if (this._stringValue == undefined) {\n    this._stringValue = this.fieldName + lunr.FieldRef.joiner + this.docRef\n  }\n\n  return this._stringValue\n}\n/*!\n * lunr.Set\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A lunr set.\n *\n * @constructor\n */\nlunr.Set = function (elements) {\n  this.elements = Object.create(null)\n\n  if (elements) {\n    this.length = elements.length\n\n    for (var i = 0; i < this.length; i++) {\n      this.elements[elements[i]] = true\n    }\n  } else {\n    this.length = 0\n  }\n}\n\n/**\n * A complete set that contains all elements.\n *\n * @static\n * @readonly\n * @type {lunr.Set}\n */\nlunr.Set.complete = {\n  intersect: function (other) {\n    return other\n  },\n\n  union: function () {\n    return this\n  },\n\n  contains: function () {\n    return true\n  }\n}\n\n/**\n * An empty set that contains no elements.\n *\n * @static\n * @readonly\n * @type {lunr.Set}\n */\nlunr.Set.empty = {\n  intersect: function () {\n    return this\n  },\n\n  union: function (other) {\n    return other\n  },\n\n  contains: function () {\n    return false\n  }\n}\n\n/**\n * Returns true if this set contains the specified object.\n *\n * @param {object} object - Object whose presence in this set is to be tested.\n * @returns {boolean} - True if this set contains the specified object.\n */\nlunr.Set.prototype.contains = function (object) {\n  return !!this.elements[object]\n}\n\n/**\n * Returns a new set containing only the elements that are present in both\n * this set and the specified set.\n *\n * @param {lunr.Set} other - set to intersect with this set.\n * @returns {lunr.Set} a new set that is the intersection of this and the specified set.\n */\n\nlunr.Set.prototype.intersect = function (other) {\n  var a, b, elements, intersection = []\n\n  if (other === lunr.Set.complete) {\n    return this\n  }\n\n  if (other === lunr.Set.empty) {\n    return other\n  }\n\n  if (this.length < other.length) {\n    a = this\n    b = other\n  } else {\n    a = other\n    b = this\n  }\n\n  elements = Object.keys(a.elements)\n\n  for (var i = 0; i < elements.length; i++) {\n    var element = elements[i]\n    if (element in b.elements) {\n      intersection.push(element)\n    }\n  }\n\n  return new lunr.Set (intersection)\n}\n\n/**\n * Returns a new set combining the elements of this and the specified set.\n *\n * @param {lunr.Set} other - set to union with this set.\n * @return {lunr.Set} a new set that is the union of this and the specified set.\n */\n\nlunr.Set.prototype.union = function (other) {\n  if (other === lunr.Set.complete) {\n    return lunr.Set.complete\n  }\n\n  if (other === lunr.Set.empty) {\n    return this\n  }\n\n  return new lunr.Set(Object.keys(this.elements).concat(Object.keys(other.elements)))\n}\n/**\n * A function to calculate the inverse document frequency for\n * a posting. This is shared between the builder and the index\n *\n * @private\n * @param {object} posting - The posting for a given term\n * @param {number} documentCount - The total number of documents.\n */\nlunr.idf = function (posting, documentCount) {\n  var documentsWithTerm = 0\n\n  for (var fieldName in posting) {\n    if (fieldName == '_index') continue // Ignore the term index, its not a field\n    documentsWithTerm += Object.keys(posting[fieldName]).length\n  }\n\n  var x = (documentCount - documentsWithTerm + 0.5) / (documentsWithTerm + 0.5)\n\n  return Math.log(1 + Math.abs(x))\n}\n\n/**\n * A token wraps a string representation of a token\n * as it is passed through the text processing pipeline.\n *\n * @constructor\n * @param {string} [str=''] - The string token being wrapped.\n * @param {object} [metadata={}] - Metadata associated with this token.\n */\nlunr.Token = function (str, metadata) {\n  this.str = str || \"\"\n  this.metadata = metadata || {}\n}\n\n/**\n * Returns the token string that is being wrapped by this object.\n *\n * @returns {string}\n */\nlunr.Token.prototype.toString = function () {\n  return this.str\n}\n\n/**\n * A token update function is used when updating or optionally\n * when cloning a token.\n *\n * @callback lunr.Token~updateFunction\n * @param {string} str - The string representation of the token.\n * @param {Object} metadata - All metadata associated with this token.\n */\n\n/**\n * Applies the given function to the wrapped string token.\n *\n * @example\n * token.update(function (str, metadata) {\n *   return str.toUpperCase()\n * })\n *\n * @param {lunr.Token~updateFunction} fn - A function to apply to the token string.\n * @returns {lunr.Token}\n */\nlunr.Token.prototype.update = function (fn) {\n  this.str = fn(this.str, this.metadata)\n  return this\n}\n\n/**\n * Creates a clone of this token. Optionally a function can be\n * applied to the cloned token.\n *\n * @param {lunr.Token~updateFunction} [fn] - An optional function to apply to the cloned token.\n * @returns {lunr.Token}\n */\nlunr.Token.prototype.clone = function (fn) {\n  fn = fn || function (s) { return s }\n  return new lunr.Token (fn(this.str, this.metadata), this.metadata)\n}\n/*!\n * lunr.tokenizer\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A function for splitting a string into tokens ready to be inserted into\n * the search index. Uses `lunr.tokenizer.separator` to split strings, change\n * the value of this property to change how strings are split into tokens.\n *\n * This tokenizer will convert its parameter to a string by calling `toString` and\n * then will split this string on the character in `lunr.tokenizer.separator`.\n * Arrays will have their elements converted to strings and wrapped in a lunr.Token.\n *\n * Optional metadata can be passed to the tokenizer, this metadata will be cloned and\n * added as metadata to every token that is created from the object to be tokenized.\n *\n * @static\n * @param {?(string|object|object[])} obj - The object to convert into tokens\n * @param {?object} metadata - Optional metadata to associate with every token\n * @returns {lunr.Token[]}\n * @see {@link lunr.Pipeline}\n */\nlunr.tokenizer = function (obj, metadata) {\n  if (obj == null || obj == undefined) {\n    return []\n  }\n\n  if (Array.isArray(obj)) {\n    return obj.map(function (t) {\n      return new lunr.Token(\n        lunr.utils.asString(t).toLowerCase(),\n        lunr.utils.clone(metadata)\n      )\n    })\n  }\n\n  var str = obj.toString().toLowerCase(),\n      len = str.length,\n      tokens = []\n\n  for (var sliceEnd = 0, sliceStart = 0; sliceEnd <= len; sliceEnd++) {\n    var char = str.charAt(sliceEnd),\n        sliceLength = sliceEnd - sliceStart\n\n    if ((char.match(lunr.tokenizer.separator) || sliceEnd == len)) {\n\n      if (sliceLength > 0) {\n        var tokenMetadata = lunr.utils.clone(metadata) || {}\n        tokenMetadata[\"position\"] = [sliceStart, sliceLength]\n        tokenMetadata[\"index\"] = tokens.length\n\n        tokens.push(\n          new lunr.Token (\n            str.slice(sliceStart, sliceEnd),\n            tokenMetadata\n          )\n        )\n      }\n\n      sliceStart = sliceEnd + 1\n    }\n\n  }\n\n  return tokens\n}\n\n/**\n * The separator used to split a string into tokens. Override this property to change the behaviour of\n * `lunr.tokenizer` behaviour when tokenizing strings. By default this splits on whitespace and hyphens.\n *\n * @static\n * @see lunr.tokenizer\n */\nlunr.tokenizer.separator = /[\\s\\-]+/\n/*!\n * lunr.Pipeline\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.Pipelines maintain an ordered list of functions to be applied to all\n * tokens in documents entering the search index and queries being ran against\n * the index.\n *\n * An instance of lunr.Index created with the lunr shortcut will contain a\n * pipeline with a stop word filter and an English language stemmer. Extra\n * functions can be added before or after either of these functions or these\n * default functions can be removed.\n *\n * When run the pipeline will call each function in turn, passing a token, the\n * index of that token in the original list of all tokens and finally a list of\n * all the original tokens.\n *\n * The output of functions in the pipeline will be passed to the next function\n * in the pipeline. To exclude a token from entering the index the function\n * should return undefined, the rest of the pipeline will not be called with\n * this token.\n *\n * For serialisation of pipelines to work, all functions used in an instance of\n * a pipeline should be registered with lunr.Pipeline. Registered functions can\n * then be loaded. If trying to load a serialised pipeline that uses functions\n * that are not registered an error will be thrown.\n *\n * If not planning on serialising the pipeline then registering pipeline functions\n * is not necessary.\n *\n * @constructor\n */\nlunr.Pipeline = function () {\n  this._stack = []\n}\n\nlunr.Pipeline.registeredFunctions = Object.create(null)\n\n/**\n * A pipeline function maps lunr.Token to lunr.Token. A lunr.Token contains the token\n * string as well as all known metadata. A pipeline function can mutate the token string\n * or mutate (or add) metadata for a given token.\n *\n * A pipeline function can indicate that the passed token should be discarded by returning\n * null, undefined or an empty string. This token will not be passed to any downstream pipeline\n * functions and will not be added to the index.\n *\n * Multiple tokens can be returned by returning an array of tokens. Each token will be passed\n * to any downstream pipeline functions and all will returned tokens will be added to the index.\n *\n * Any number of pipeline functions may be chained together using a lunr.Pipeline.\n *\n * @interface lunr.PipelineFunction\n * @param {lunr.Token} token - A token from the document being processed.\n * @param {number} i - The index of this token in the complete list of tokens for this document/field.\n * @param {lunr.Token[]} tokens - All tokens for this document/field.\n * @returns {(?lunr.Token|lunr.Token[])}\n */\n\n/**\n * Register a function with the pipeline.\n *\n * Functions that are used in the pipeline should be registered if the pipeline\n * needs to be serialised, or a serialised pipeline needs to be loaded.\n *\n * Registering a function does not add it to a pipeline, functions must still be\n * added to instances of the pipeline for them to be used when running a pipeline.\n *\n * @param {lunr.PipelineFunction} fn - The function to check for.\n * @param {String} label - The label to register this function with\n */\nlunr.Pipeline.registerFunction = function (fn, label) {\n  if (label in this.registeredFunctions) {\n    lunr.utils.warn('Overwriting existing registered function: ' + label)\n  }\n\n  fn.label = label\n  lunr.Pipeline.registeredFunctions[fn.label] = fn\n}\n\n/**\n * Warns if the function is not registered as a Pipeline function.\n *\n * @param {lunr.PipelineFunction} fn - The function to check for.\n * @private\n */\nlunr.Pipeline.warnIfFunctionNotRegistered = function (fn) {\n  var isRegistered = fn.label && (fn.label in this.registeredFunctions)\n\n  if (!isRegistered) {\n    lunr.utils.warn('Function is not registered with pipeline. This may cause problems when serialising the index.\\n', fn)\n  }\n}\n\n/**\n * Loads a previously serialised pipeline.\n *\n * All functions to be loaded must already be registered with lunr.Pipeline.\n * If any function from the serialised data has not been registered then an\n * error will be thrown.\n *\n * @param {Object} serialised - The serialised pipeline to load.\n * @returns {lunr.Pipeline}\n */\nlunr.Pipeline.load = function (serialised) {\n  var pipeline = new lunr.Pipeline\n\n  serialised.forEach(function (fnName) {\n    var fn = lunr.Pipeline.registeredFunctions[fnName]\n\n    if (fn) {\n      pipeline.add(fn)\n    } else {\n      throw new Error('Cannot load unregistered function: ' + fnName)\n    }\n  })\n\n  return pipeline\n}\n\n/**\n * Adds new functions to the end of the pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction[]} functions - Any number of functions to add to the pipeline.\n */\nlunr.Pipeline.prototype.add = function () {\n  var fns = Array.prototype.slice.call(arguments)\n\n  fns.forEach(function (fn) {\n    lunr.Pipeline.warnIfFunctionNotRegistered(fn)\n    this._stack.push(fn)\n  }, this)\n}\n\n/**\n * Adds a single function after a function that already exists in the\n * pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.\n * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.\n */\nlunr.Pipeline.prototype.after = function (existingFn, newFn) {\n  lunr.Pipeline.warnIfFunctionNotRegistered(newFn)\n\n  var pos = this._stack.indexOf(existingFn)\n  if (pos == -1) {\n    throw new Error('Cannot find existingFn')\n  }\n\n  pos = pos + 1\n  this._stack.splice(pos, 0, newFn)\n}\n\n/**\n * Adds a single function before a function that already exists in the\n * pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.\n * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.\n */\nlunr.Pipeline.prototype.before = function (existingFn, newFn) {\n  lunr.Pipeline.warnIfFunctionNotRegistered(newFn)\n\n  var pos = this._stack.indexOf(existingFn)\n  if (pos == -1) {\n    throw new Error('Cannot find existingFn')\n  }\n\n  this._stack.splice(pos, 0, newFn)\n}\n\n/**\n * Removes a function from the pipeline.\n *\n * @param {lunr.PipelineFunction} fn The function to remove from the pipeline.\n */\nlunr.Pipeline.prototype.remove = function (fn) {\n  var pos = this._stack.indexOf(fn)\n  if (pos == -1) {\n    return\n  }\n\n  this._stack.splice(pos, 1)\n}\n\n/**\n * Runs the current list of functions that make up the pipeline against the\n * passed tokens.\n *\n * @param {Array} tokens The tokens to run through the pipeline.\n * @returns {Array}\n */\nlunr.Pipeline.prototype.run = function (tokens) {\n  var stackLength = this._stack.length\n\n  for (var i = 0; i < stackLength; i++) {\n    var fn = this._stack[i]\n    var memo = []\n\n    for (var j = 0; j < tokens.length; j++) {\n      var result = fn(tokens[j], j, tokens)\n\n      if (result === null || result === void 0 || result === '') continue\n\n      if (Array.isArray(result)) {\n        for (var k = 0; k < result.length; k++) {\n          memo.push(result[k])\n        }\n      } else {\n        memo.push(result)\n      }\n    }\n\n    tokens = memo\n  }\n\n  return tokens\n}\n\n/**\n * Convenience method for passing a string through a pipeline and getting\n * strings out. This method takes care of wrapping the passed string in a\n * token and mapping the resulting tokens back to strings.\n *\n * @param {string} str - The string to pass through the pipeline.\n * @param {?object} metadata - Optional metadata to associate with the token\n * passed to the pipeline.\n * @returns {string[]}\n */\nlunr.Pipeline.prototype.runString = function (str, metadata) {\n  var token = new lunr.Token (str, metadata)\n\n  return this.run([token]).map(function (t) {\n    return t.toString()\n  })\n}\n\n/**\n * Resets the pipeline by removing any existing processors.\n *\n */\nlunr.Pipeline.prototype.reset = function () {\n  this._stack = []\n}\n\n/**\n * Returns a representation of the pipeline ready for serialisation.\n *\n * Logs a warning if the function has not been registered.\n *\n * @returns {Array}\n */\nlunr.Pipeline.prototype.toJSON = function () {\n  return this._stack.map(function (fn) {\n    lunr.Pipeline.warnIfFunctionNotRegistered(fn)\n\n    return fn.label\n  })\n}\n/*!\n * lunr.Vector\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A vector is used to construct the vector space of documents and queries. These\n * vectors support operations to determine the similarity between two documents or\n * a document and a query.\n *\n * Normally no parameters are required for initializing a vector, but in the case of\n * loading a previously dumped vector the raw elements can be provided to the constructor.\n *\n * For performance reasons vectors are implemented with a flat array, where an elements\n * index is immediately followed by its value. E.g. [index, value, index, value]. This\n * allows the underlying array to be as sparse as possible and still offer decent\n * performance when being used for vector calculations.\n *\n * @constructor\n * @param {Number[]} [elements] - The flat list of element index and element value pairs.\n */\nlunr.Vector = function (elements) {\n  this._magnitude = 0\n  this.elements = elements || []\n}\n\n\n/**\n * Calculates the position within the vector to insert a given index.\n *\n * This is used internally by insert and upsert. If there are duplicate indexes then\n * the position is returned as if the value for that index were to be updated, but it\n * is the callers responsibility to check whether there is a duplicate at that index\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @returns {Number}\n */\nlunr.Vector.prototype.positionForIndex = function (index) {\n  // For an empty vector the tuple can be inserted at the beginning\n  if (this.elements.length == 0) {\n    return 0\n  }\n\n  var start = 0,\n      end = this.elements.length / 2,\n      sliceLength = end - start,\n      pivotPoint = Math.floor(sliceLength / 2),\n      pivotIndex = this.elements[pivotPoint * 2]\n\n  while (sliceLength > 1) {\n    if (pivotIndex < index) {\n      start = pivotPoint\n    }\n\n    if (pivotIndex > index) {\n      end = pivotPoint\n    }\n\n    if (pivotIndex == index) {\n      break\n    }\n\n    sliceLength = end - start\n    pivotPoint = start + Math.floor(sliceLength / 2)\n    pivotIndex = this.elements[pivotPoint * 2]\n  }\n\n  if (pivotIndex == index) {\n    return pivotPoint * 2\n  }\n\n  if (pivotIndex > index) {\n    return pivotPoint * 2\n  }\n\n  if (pivotIndex < index) {\n    return (pivotPoint + 1) * 2\n  }\n}\n\n/**\n * Inserts an element at an index within the vector.\n *\n * Does not allow duplicates, will throw an error if there is already an entry\n * for this index.\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @param {Number} val - The value to be inserted into the vector.\n */\nlunr.Vector.prototype.insert = function (insertIdx, val) {\n  this.upsert(insertIdx, val, function () {\n    throw \"duplicate index\"\n  })\n}\n\n/**\n * Inserts or updates an existing index within the vector.\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @param {Number} val - The value to be inserted into the vector.\n * @param {function} fn - A function that is called for updates, the existing value and the\n * requested value are passed as arguments\n */\nlunr.Vector.prototype.upsert = function (insertIdx, val, fn) {\n  this._magnitude = 0\n  var position = this.positionForIndex(insertIdx)\n\n  if (this.elements[position] == insertIdx) {\n    this.elements[position + 1] = fn(this.elements[position + 1], val)\n  } else {\n    this.elements.splice(position, 0, insertIdx, val)\n  }\n}\n\n/**\n * Calculates the magnitude of this vector.\n *\n * @returns {Number}\n */\nlunr.Vector.prototype.magnitude = function () {\n  if (this._magnitude) return this._magnitude\n\n  var sumOfSquares = 0,\n      elementsLength = this.elements.length\n\n  for (var i = 1; i < elementsLength; i += 2) {\n    var val = this.elements[i]\n    sumOfSquares += val * val\n  }\n\n  return this._magnitude = Math.sqrt(sumOfSquares)\n}\n\n/**\n * Calculates the dot product of this vector and another vector.\n *\n * @param {lunr.Vector} otherVector - The vector to compute the dot product with.\n * @returns {Number}\n */\nlunr.Vector.prototype.dot = function (otherVector) {\n  var dotProduct = 0,\n      a = this.elements, b = otherVector.elements,\n      aLen = a.length, bLen = b.length,\n      aVal = 0, bVal = 0,\n      i = 0, j = 0\n\n  while (i < aLen && j < bLen) {\n    aVal = a[i], bVal = b[j]\n    if (aVal < bVal) {\n      i += 2\n    } else if (aVal > bVal) {\n      j += 2\n    } else if (aVal == bVal) {\n      dotProduct += a[i + 1] * b[j + 1]\n      i += 2\n      j += 2\n    }\n  }\n\n  return dotProduct\n}\n\n/**\n * Calculates the similarity between this vector and another vector.\n *\n * @param {lunr.Vector} otherVector - The other vector to calculate the\n * similarity with.\n * @returns {Number}\n */\nlunr.Vector.prototype.similarity = function (otherVector) {\n  return this.dot(otherVector) / this.magnitude() || 0\n}\n\n/**\n * Converts the vector to an array of the elements within the vector.\n *\n * @returns {Number[]}\n */\nlunr.Vector.prototype.toArray = function () {\n  var output = new Array (this.elements.length / 2)\n\n  for (var i = 1, j = 0; i < this.elements.length; i += 2, j++) {\n    output[j] = this.elements[i]\n  }\n\n  return output\n}\n\n/**\n * A JSON serializable representation of the vector.\n *\n * @returns {Number[]}\n */\nlunr.Vector.prototype.toJSON = function () {\n  return this.elements\n}\n/* eslint-disable */\n/*!\n * lunr.stemmer\n * Copyright (C) 2020 Oliver Nightingale\n * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt\n */\n\n/**\n * lunr.stemmer is an english language stemmer, this is a JavaScript\n * implementation of the PorterStemmer taken from http://tartarus.org/~martin\n *\n * @static\n * @implements {lunr.PipelineFunction}\n * @param {lunr.Token} token - The string to stem\n * @returns {lunr.Token}\n * @see {@link lunr.Pipeline}\n * @function\n */\nlunr.stemmer = (function(){\n  var step2list = {\n      \"ational\" : \"ate\",\n      \"tional\" : \"tion\",\n      \"enci\" : \"ence\",\n      \"anci\" : \"ance\",\n      \"izer\" : \"ize\",\n      \"bli\" : \"ble\",\n      \"alli\" : \"al\",\n      \"entli\" : \"ent\",\n      \"eli\" : \"e\",\n      \"ousli\" : \"ous\",\n      \"ization\" : \"ize\",\n      \"ation\" : \"ate\",\n      \"ator\" : \"ate\",\n      \"alism\" : \"al\",\n      \"iveness\" : \"ive\",\n      \"fulness\" : \"ful\",\n      \"ousness\" : \"ous\",\n      \"aliti\" : \"al\",\n      \"iviti\" : \"ive\",\n      \"biliti\" : \"ble\",\n      \"logi\" : \"log\"\n    },\n\n    step3list = {\n      \"icate\" : \"ic\",\n      \"ative\" : \"\",\n      \"alize\" : \"al\",\n      \"iciti\" : \"ic\",\n      \"ical\" : \"ic\",\n      \"ful\" : \"\",\n      \"ness\" : \"\"\n    },\n\n    c = \"[^aeiou]\",          // consonant\n    v = \"[aeiouy]\",          // vowel\n    C = c + \"[^aeiouy]*\",    // consonant sequence\n    V = v + \"[aeiou]*\",      // vowel sequence\n\n    mgr0 = \"^(\" + C + \")?\" + V + C,               // [C]VC... is m>0\n    meq1 = \"^(\" + C + \")?\" + V + C + \"(\" + V + \")?$\",  // [C]VC[V] is m=1\n    mgr1 = \"^(\" + C + \")?\" + V + C + V + C,       // [C]VCVC... is m>1\n    s_v = \"^(\" + C + \")?\" + v;                   // vowel in stem\n\n  var re_mgr0 = new RegExp(mgr0);\n  var re_mgr1 = new RegExp(mgr1);\n  var re_meq1 = new RegExp(meq1);\n  var re_s_v = new RegExp(s_v);\n\n  var re_1a = /^(.+?)(ss|i)es$/;\n  var re2_1a = /^(.+?)([^s])s$/;\n  var re_1b = /^(.+?)eed$/;\n  var re2_1b = /^(.+?)(ed|ing)$/;\n  var re_1b_2 = /.$/;\n  var re2_1b_2 = /(at|bl|iz)$/;\n  var re3_1b_2 = new RegExp(\"([^aeiouylsz])\\\\1$\");\n  var re4_1b_2 = new RegExp(\"^\" + C + v + \"[^aeiouwxy]$\");\n\n  var re_1c = /^(.+?[^aeiou])y$/;\n  var re_2 = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;\n\n  var re_3 = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;\n\n  var re_4 = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;\n  var re2_4 = /^(.+?)(s|t)(ion)$/;\n\n  var re_5 = /^(.+?)e$/;\n  var re_5_1 = /ll$/;\n  var re3_5 = new RegExp(\"^\" + C + v + \"[^aeiouwxy]$\");\n\n  var porterStemmer = function porterStemmer(w) {\n    var stem,\n      suffix,\n      firstch,\n      re,\n      re2,\n      re3,\n      re4;\n\n    if (w.length < 3) { return w; }\n\n    firstch = w.substr(0,1);\n    if (firstch == \"y\") {\n      w = firstch.toUpperCase() + w.substr(1);\n    }\n\n    // Step 1a\n    re = re_1a\n    re2 = re2_1a;\n\n    if (re.test(w)) { w = w.replace(re,\"$1$2\"); }\n    else if (re2.test(w)) { w = w.replace(re2,\"$1$2\"); }\n\n    // Step 1b\n    re = re_1b;\n    re2 = re2_1b;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      re = re_mgr0;\n      if (re.test(fp[1])) {\n        re = re_1b_2;\n        w = w.replace(re,\"\");\n      }\n    } else if (re2.test(w)) {\n      var fp = re2.exec(w);\n      stem = fp[1];\n      re2 = re_s_v;\n      if (re2.test(stem)) {\n        w = stem;\n        re2 = re2_1b_2;\n        re3 = re3_1b_2;\n        re4 = re4_1b_2;\n        if (re2.test(w)) { w = w + \"e\"; }\n        else if (re3.test(w)) { re = re_1b_2; w = w.replace(re,\"\"); }\n        else if (re4.test(w)) { w = w + \"e\"; }\n      }\n    }\n\n    // Step 1c - replace suffix y or Y by i if preceded by a non-vowel which is not the first letter of the word (so cry -> cri, by -> by, say -> say)\n    re = re_1c;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      stem = fp[1];\n      w = stem + \"i\";\n    }\n\n    // Step 2\n    re = re_2;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      stem = fp[1];\n      suffix = fp[2];\n      re = re_mgr0;\n      if (re.test(stem)) {\n        w = stem + step2list[suffix];\n      }\n    }\n\n    // Step 3\n    re = re_3;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      stem = fp[1];\n      suffix = fp[2];\n      re = re_mgr0;\n      if (re.test(stem)) {\n        w = stem + step3list[suffix];\n      }\n    }\n\n    // Step 4\n    re = re_4;\n    re2 = re2_4;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      stem = fp[1];\n      re = re_mgr1;\n      if (re.test(stem)) {\n        w = stem;\n      }\n    } else if (re2.test(w)) {\n      var fp = re2.exec(w);\n      stem = fp[1] + fp[2];\n      re2 = re_mgr1;\n      if (re2.test(stem)) {\n        w = stem;\n      }\n    }\n\n    // Step 5\n    re = re_5;\n    if (re.test(w)) {\n      var fp = re.exec(w);\n      stem = fp[1];\n      re = re_mgr1;\n      re2 = re_meq1;\n      re3 = re3_5;\n      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) {\n        w = stem;\n      }\n    }\n\n    re = re_5_1;\n    re2 = re_mgr1;\n    if (re.test(w) && re2.test(w)) {\n      re = re_1b_2;\n      w = w.replace(re,\"\");\n    }\n\n    // and turn initial Y back to y\n\n    if (firstch == \"y\") {\n      w = firstch.toLowerCase() + w.substr(1);\n    }\n\n    return w;\n  };\n\n  return function (token) {\n    return token.update(porterStemmer);\n  }\n})();\n\nlunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer')\n/*!\n * lunr.stopWordFilter\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.generateStopWordFilter builds a stopWordFilter function from the provided\n * list of stop words.\n *\n * The built in lunr.stopWordFilter is built using this generator and can be used\n * to generate custom stopWordFilters for applications or non English languages.\n *\n * @function\n * @param {Array} token The token to pass through the filter\n * @returns {lunr.PipelineFunction}\n * @see lunr.Pipeline\n * @see lunr.stopWordFilter\n */\nlunr.generateStopWordFilter = function (stopWords) {\n  var words = stopWords.reduce(function (memo, stopWord) {\n    memo[stopWord] = stopWord\n    return memo\n  }, {})\n\n  return function (token) {\n    if (token && words[token.toString()] !== token.toString()) return token\n  }\n}\n\n/**\n * lunr.stopWordFilter is an English language stop word list filter, any words\n * contained in the list will not be passed through the filter.\n *\n * This is intended to be used in the Pipeline. If the token does not pass the\n * filter then undefined will be returned.\n *\n * @function\n * @implements {lunr.PipelineFunction}\n * @params {lunr.Token} token - A token to check for being a stop word.\n * @returns {lunr.Token}\n * @see {@link lunr.Pipeline}\n */\nlunr.stopWordFilter = lunr.generateStopWordFilter([\n  'a',\n  'able',\n  'about',\n  'across',\n  'after',\n  'all',\n  'almost',\n  'also',\n  'am',\n  'among',\n  'an',\n  'and',\n  'any',\n  'are',\n  'as',\n  'at',\n  'be',\n  'because',\n  'been',\n  'but',\n  'by',\n  'can',\n  'cannot',\n  'could',\n  'dear',\n  'did',\n  'do',\n  'does',\n  'either',\n  'else',\n  'ever',\n  'every',\n  'for',\n  'from',\n  'get',\n  'got',\n  'had',\n  'has',\n  'have',\n  'he',\n  'her',\n  'hers',\n  'him',\n  'his',\n  'how',\n  'however',\n  'i',\n  'if',\n  'in',\n  'into',\n  'is',\n  'it',\n  'its',\n  'just',\n  'least',\n  'let',\n  'like',\n  'likely',\n  'may',\n  'me',\n  'might',\n  'most',\n  'must',\n  'my',\n  'neither',\n  'no',\n  'nor',\n  'not',\n  'of',\n  'off',\n  'often',\n  'on',\n  'only',\n  'or',\n  'other',\n  'our',\n  'own',\n  'rather',\n  'said',\n  'say',\n  'says',\n  'she',\n  'should',\n  'since',\n  'so',\n  'some',\n  'than',\n  'that',\n  'the',\n  'their',\n  'them',\n  'then',\n  'there',\n  'these',\n  'they',\n  'this',\n  'tis',\n  'to',\n  'too',\n  'twas',\n  'us',\n  'wants',\n  'was',\n  'we',\n  'were',\n  'what',\n  'when',\n  'where',\n  'which',\n  'while',\n  'who',\n  'whom',\n  'why',\n  'will',\n  'with',\n  'would',\n  'yet',\n  'you',\n  'your'\n])\n\nlunr.Pipeline.registerFunction(lunr.stopWordFilter, 'stopWordFilter')\n/*!\n * lunr.trimmer\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.trimmer is a pipeline function for trimming non word\n * characters from the beginning and end of tokens before they\n * enter the index.\n *\n * This implementation may not work correctly for non latin\n * characters and should either be removed or adapted for use\n * with languages with non-latin characters.\n *\n * @static\n * @implements {lunr.PipelineFunction}\n * @param {lunr.Token} token The token to pass through the filter\n * @returns {lunr.Token}\n * @see lunr.Pipeline\n */\nlunr.trimmer = function (token) {\n  return token.update(function (s) {\n    return s.replace(/^\\W+/, '').replace(/\\W+$/, '')\n  })\n}\n\nlunr.Pipeline.registerFunction(lunr.trimmer, 'trimmer')\n/*!\n * lunr.TokenSet\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A token set is used to store the unique list of all tokens\n * within an index. Token sets are also used to represent an\n * incoming query to the index, this query token set and index\n * token set are then intersected to find which tokens to look\n * up in the inverted index.\n *\n * A token set can hold multiple tokens, as in the case of the\n * index token set, or it can hold a single token as in the\n * case of a simple query token set.\n *\n * Additionally token sets are used to perform wildcard matching.\n * Leading, contained and trailing wildcards are supported, and\n * from this edit distance matching can also be provided.\n *\n * Token sets are implemented as a minimal finite state automata,\n * where both common prefixes and suffixes are shared between tokens.\n * This helps to reduce the space used for storing the token set.\n *\n * @constructor\n */\nlunr.TokenSet = function () {\n  this.final = false\n  this.edges = {}\n  this.id = lunr.TokenSet._nextId\n  lunr.TokenSet._nextId += 1\n}\n\n/**\n * Keeps track of the next, auto increment, identifier to assign\n * to a new tokenSet.\n *\n * TokenSets require a unique identifier to be correctly minimised.\n *\n * @private\n */\nlunr.TokenSet._nextId = 1\n\n/**\n * Creates a TokenSet instance from the given sorted array of words.\n *\n * @param {String[]} arr - A sorted array of strings to create the set from.\n * @returns {lunr.TokenSet}\n * @throws Will throw an error if the input array is not sorted.\n */\nlunr.TokenSet.fromArray = function (arr) {\n  var builder = new lunr.TokenSet.Builder\n\n  for (var i = 0, len = arr.length; i < len; i++) {\n    builder.insert(arr[i])\n  }\n\n  builder.finish()\n  return builder.root\n}\n\n/**\n * Creates a token set from a query clause.\n *\n * @private\n * @param {Object} clause - A single clause from lunr.Query.\n * @param {string} clause.term - The query clause term.\n * @param {number} [clause.editDistance] - The optional edit distance for the term.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.fromClause = function (clause) {\n  if ('editDistance' in clause) {\n    return lunr.TokenSet.fromFuzzyString(clause.term, clause.editDistance)\n  } else {\n    return lunr.TokenSet.fromString(clause.term)\n  }\n}\n\n/**\n * Creates a token set representing a single string with a specified\n * edit distance.\n *\n * Insertions, deletions, substitutions and transpositions are each\n * treated as an edit distance of 1.\n *\n * Increasing the allowed edit distance will have a dramatic impact\n * on the performance of both creating and intersecting these TokenSets.\n * It is advised to keep the edit distance less than 3.\n *\n * @param {string} str - The string to create the token set from.\n * @param {number} editDistance - The allowed edit distance to match.\n * @returns {lunr.Vector}\n */\nlunr.TokenSet.fromFuzzyString = function (str, editDistance) {\n  var root = new lunr.TokenSet\n\n  var stack = [{\n    node: root,\n    editsRemaining: editDistance,\n    str: str\n  }]\n\n  while (stack.length) {\n    var frame = stack.pop()\n\n    // no edit\n    if (frame.str.length > 0) {\n      var char = frame.str.charAt(0),\n          noEditNode\n\n      if (char in frame.node.edges) {\n        noEditNode = frame.node.edges[char]\n      } else {\n        noEditNode = new lunr.TokenSet\n        frame.node.edges[char] = noEditNode\n      }\n\n      if (frame.str.length == 1) {\n        noEditNode.final = true\n      }\n\n      stack.push({\n        node: noEditNode,\n        editsRemaining: frame.editsRemaining,\n        str: frame.str.slice(1)\n      })\n    }\n\n    if (frame.editsRemaining == 0) {\n      continue\n    }\n\n    // insertion\n    if (\"*\" in frame.node.edges) {\n      var insertionNode = frame.node.edges[\"*\"]\n    } else {\n      var insertionNode = new lunr.TokenSet\n      frame.node.edges[\"*\"] = insertionNode\n    }\n\n    if (frame.str.length == 0) {\n      insertionNode.final = true\n    }\n\n    stack.push({\n      node: insertionNode,\n      editsRemaining: frame.editsRemaining - 1,\n      str: frame.str\n    })\n\n    // deletion\n    // can only do a deletion if we have enough edits remaining\n    // and if there are characters left to delete in the string\n    if (frame.str.length > 1) {\n      stack.push({\n        node: frame.node,\n        editsRemaining: frame.editsRemaining - 1,\n        str: frame.str.slice(1)\n      })\n    }\n\n    // deletion\n    // just removing the last character from the str\n    if (frame.str.length == 1) {\n      frame.node.final = true\n    }\n\n    // substitution\n    // can only do a substitution if we have enough edits remaining\n    // and if there are characters left to substitute\n    if (frame.str.length >= 1) {\n      if (\"*\" in frame.node.edges) {\n        var substitutionNode = frame.node.edges[\"*\"]\n      } else {\n        var substitutionNode = new lunr.TokenSet\n        frame.node.edges[\"*\"] = substitutionNode\n      }\n\n      if (frame.str.length == 1) {\n        substitutionNode.final = true\n      }\n\n      stack.push({\n        node: substitutionNode,\n        editsRemaining: frame.editsRemaining - 1,\n        str: frame.str.slice(1)\n      })\n    }\n\n    // transposition\n    // can only do a transposition if there are edits remaining\n    // and there are enough characters to transpose\n    if (frame.str.length > 1) {\n      var charA = frame.str.charAt(0),\n          charB = frame.str.charAt(1),\n          transposeNode\n\n      if (charB in frame.node.edges) {\n        transposeNode = frame.node.edges[charB]\n      } else {\n        transposeNode = new lunr.TokenSet\n        frame.node.edges[charB] = transposeNode\n      }\n\n      if (frame.str.length == 1) {\n        transposeNode.final = true\n      }\n\n      stack.push({\n        node: transposeNode,\n        editsRemaining: frame.editsRemaining - 1,\n        str: charA + frame.str.slice(2)\n      })\n    }\n  }\n\n  return root\n}\n\n/**\n * Creates a TokenSet from a string.\n *\n * The string may contain one or more wildcard characters (*)\n * that will allow wildcard matching when intersecting with\n * another TokenSet.\n *\n * @param {string} str - The string to create a TokenSet from.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.fromString = function (str) {\n  var node = new lunr.TokenSet,\n      root = node\n\n  /*\n   * Iterates through all characters within the passed string\n   * appending a node for each character.\n   *\n   * When a wildcard character is found then a self\n   * referencing edge is introduced to continually match\n   * any number of any characters.\n   */\n  for (var i = 0, len = str.length; i < len; i++) {\n    var char = str[i],\n        final = (i == len - 1)\n\n    if (char == \"*\") {\n      node.edges[char] = node\n      node.final = final\n\n    } else {\n      var next = new lunr.TokenSet\n      next.final = final\n\n      node.edges[char] = next\n      node = next\n    }\n  }\n\n  return root\n}\n\n/**\n * Converts this TokenSet into an array of strings\n * contained within the TokenSet.\n *\n * This is not intended to be used on a TokenSet that\n * contains wildcards, in these cases the results are\n * undefined and are likely to cause an infinite loop.\n *\n * @returns {string[]}\n */\nlunr.TokenSet.prototype.toArray = function () {\n  var words = []\n\n  var stack = [{\n    prefix: \"\",\n    node: this\n  }]\n\n  while (stack.length) {\n    var frame = stack.pop(),\n        edges = Object.keys(frame.node.edges),\n        len = edges.length\n\n    if (frame.node.final) {\n      /* In Safari, at this point the prefix is sometimes corrupted, see:\n       * https://github.com/olivernn/lunr.js/issues/279 Calling any\n       * String.prototype method forces Safari to \"cast\" this string to what\n       * it's supposed to be, fixing the bug. */\n      frame.prefix.charAt(0)\n      words.push(frame.prefix)\n    }\n\n    for (var i = 0; i < len; i++) {\n      var edge = edges[i]\n\n      stack.push({\n        prefix: frame.prefix.concat(edge),\n        node: frame.node.edges[edge]\n      })\n    }\n  }\n\n  return words\n}\n\n/**\n * Generates a string representation of a TokenSet.\n *\n * This is intended to allow TokenSets to be used as keys\n * in objects, largely to aid the construction and minimisation\n * of a TokenSet. As such it is not designed to be a human\n * friendly representation of the TokenSet.\n *\n * @returns {string}\n */\nlunr.TokenSet.prototype.toString = function () {\n  // NOTE: Using Object.keys here as this.edges is very likely\n  // to enter 'hash-mode' with many keys being added\n  //\n  // avoiding a for-in loop here as it leads to the function\n  // being de-optimised (at least in V8). From some simple\n  // benchmarks the performance is comparable, but allowing\n  // V8 to optimize may mean easy performance wins in the future.\n\n  if (this._str) {\n    return this._str\n  }\n\n  var str = this.final ? '1' : '0',\n      labels = Object.keys(this.edges).sort(),\n      len = labels.length\n\n  for (var i = 0; i < len; i++) {\n    var label = labels[i],\n        node = this.edges[label]\n\n    str = str + label + node.id\n  }\n\n  return str\n}\n\n/**\n * Returns a new TokenSet that is the intersection of\n * this TokenSet and the passed TokenSet.\n *\n * This intersection will take into account any wildcards\n * contained within the TokenSet.\n *\n * @param {lunr.TokenSet} b - An other TokenSet to intersect with.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.prototype.intersect = function (b) {\n  var output = new lunr.TokenSet,\n      frame = undefined\n\n  var stack = [{\n    qNode: b,\n    output: output,\n    node: this\n  }]\n\n  while (stack.length) {\n    frame = stack.pop()\n\n    // NOTE: As with the #toString method, we are using\n    // Object.keys and a for loop instead of a for-in loop\n    // as both of these objects enter 'hash' mode, causing\n    // the function to be de-optimised in V8\n    var qEdges = Object.keys(frame.qNode.edges),\n        qLen = qEdges.length,\n        nEdges = Object.keys(frame.node.edges),\n        nLen = nEdges.length\n\n    for (var q = 0; q < qLen; q++) {\n      var qEdge = qEdges[q]\n\n      for (var n = 0; n < nLen; n++) {\n        var nEdge = nEdges[n]\n\n        if (nEdge == qEdge || qEdge == '*') {\n          var node = frame.node.edges[nEdge],\n              qNode = frame.qNode.edges[qEdge],\n              final = node.final && qNode.final,\n              next = undefined\n\n          if (nEdge in frame.output.edges) {\n            // an edge already exists for this character\n            // no need to create a new node, just set the finality\n            // bit unless this node is already final\n            next = frame.output.edges[nEdge]\n            next.final = next.final || final\n\n          } else {\n            // no edge exists yet, must create one\n            // set the finality bit and insert it\n            // into the output\n            next = new lunr.TokenSet\n            next.final = final\n            frame.output.edges[nEdge] = next\n          }\n\n          stack.push({\n            qNode: qNode,\n            output: next,\n            node: node\n          })\n        }\n      }\n    }\n  }\n\n  return output\n}\nlunr.TokenSet.Builder = function () {\n  this.previousWord = \"\"\n  this.root = new lunr.TokenSet\n  this.uncheckedNodes = []\n  this.minimizedNodes = {}\n}\n\nlunr.TokenSet.Builder.prototype.insert = function (word) {\n  var node,\n      commonPrefix = 0\n\n  if (word < this.previousWord) {\n    throw new Error (\"Out of order word insertion\")\n  }\n\n  for (var i = 0; i < word.length && i < this.previousWord.length; i++) {\n    if (word[i] != this.previousWord[i]) break\n    commonPrefix++\n  }\n\n  this.minimize(commonPrefix)\n\n  if (this.uncheckedNodes.length == 0) {\n    node = this.root\n  } else {\n    node = this.uncheckedNodes[this.uncheckedNodes.length - 1].child\n  }\n\n  for (var i = commonPrefix; i < word.length; i++) {\n    var nextNode = new lunr.TokenSet,\n        char = word[i]\n\n    node.edges[char] = nextNode\n\n    this.uncheckedNodes.push({\n      parent: node,\n      char: char,\n      child: nextNode\n    })\n\n    node = nextNode\n  }\n\n  node.final = true\n  this.previousWord = word\n}\n\nlunr.TokenSet.Builder.prototype.finish = function () {\n  this.minimize(0)\n}\n\nlunr.TokenSet.Builder.prototype.minimize = function (downTo) {\n  for (var i = this.uncheckedNodes.length - 1; i >= downTo; i--) {\n    var node = this.uncheckedNodes[i],\n        childKey = node.child.toString()\n\n    if (childKey in this.minimizedNodes) {\n      node.parent.edges[node.char] = this.minimizedNodes[childKey]\n    } else {\n      // Cache the key for this node since\n      // we know it can't change anymore\n      node.child._str = childKey\n\n      this.minimizedNodes[childKey] = node.child\n    }\n\n    this.uncheckedNodes.pop()\n  }\n}\n/*!\n * lunr.Index\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * An index contains the built index of all documents and provides a query interface\n * to the index.\n *\n * Usually instances of lunr.Index will not be created using this constructor, instead\n * lunr.Builder should be used to construct new indexes, or lunr.Index.load should be\n * used to load previously built and serialized indexes.\n *\n * @constructor\n * @param {Object} attrs - The attributes of the built search index.\n * @param {Object} attrs.invertedIndex - An index of term/field to document reference.\n * @param {Object<string, lunr.Vector>} attrs.fieldVectors - Field vectors\n * @param {lunr.TokenSet} attrs.tokenSet - An set of all corpus tokens.\n * @param {string[]} attrs.fields - The names of indexed document fields.\n * @param {lunr.Pipeline} attrs.pipeline - The pipeline to use for search terms.\n */\nlunr.Index = function (attrs) {\n  this.invertedIndex = attrs.invertedIndex\n  this.fieldVectors = attrs.fieldVectors\n  this.tokenSet = attrs.tokenSet\n  this.fields = attrs.fields\n  this.pipeline = attrs.pipeline\n}\n\n/**\n * A result contains details of a document matching a search query.\n * @typedef {Object} lunr.Index~Result\n * @property {string} ref - The reference of the document this result represents.\n * @property {number} score - A number between 0 and 1 representing how similar this document is to the query.\n * @property {lunr.MatchData} matchData - Contains metadata about this match including which term(s) caused the match.\n */\n\n/**\n * Although lunr provides the ability to create queries using lunr.Query, it also provides a simple\n * query language which itself is parsed into an instance of lunr.Query.\n *\n * For programmatically building queries it is advised to directly use lunr.Query, the query language\n * is best used for human entered text rather than program generated text.\n *\n * At its simplest queries can just be a single term, e.g. `hello`, multiple terms are also supported\n * and will be combined with OR, e.g `hello world` will match documents that contain either 'hello'\n * or 'world', though those that contain both will rank higher in the results.\n *\n * Wildcards can be included in terms to match one or more unspecified characters, these wildcards can\n * be inserted anywhere within the term, and more than one wildcard can exist in a single term. Adding\n * wildcards will increase the number of documents that will be found but can also have a negative\n * impact on query performance, especially with wildcards at the beginning of a term.\n *\n * Terms can be restricted to specific fields, e.g. `title:hello`, only documents with the term\n * hello in the title field will match this query. Using a field not present in the index will lead\n * to an error being thrown.\n *\n * Modifiers can also be added to terms, lunr supports edit distance and boost modifiers on terms. A term\n * boost will make documents matching that term score higher, e.g. `foo^5`. Edit distance is also supported\n * to provide fuzzy matching, e.g. 'hello~2' will match documents with hello with an edit distance of 2.\n * Avoid large values for edit distance to improve query performance.\n *\n * Each term also supports a presence modifier. By default a term's presence in document is optional, however\n * this can be changed to either required or prohibited. For a term's presence to be required in a document the\n * term should be prefixed with a '+', e.g. `+foo bar` is a search for documents that must contain 'foo' and\n * optionally contain 'bar'. Conversely a leading '-' sets the terms presence to prohibited, i.e. it must not\n * appear in a document, e.g. `-foo bar` is a search for documents that do not contain 'foo' but may contain 'bar'.\n *\n * To escape special characters the backslash character '\\' can be used, this allows searches to include\n * characters that would normally be considered modifiers, e.g. `foo\\~2` will search for a term \"foo~2\" instead\n * of attempting to apply a boost of 2 to the search term \"foo\".\n *\n * @typedef {string} lunr.Index~QueryString\n * @example <caption>Simple single term query</caption>\n * hello\n * @example <caption>Multiple term query</caption>\n * hello world\n * @example <caption>term scoped to a field</caption>\n * title:hello\n * @example <caption>term with a boost of 10</caption>\n * hello^10\n * @example <caption>term with an edit distance of 2</caption>\n * hello~2\n * @example <caption>terms with presence modifiers</caption>\n * -foo +bar baz\n */\n\n/**\n * Performs a search against the index using lunr query syntax.\n *\n * Results will be returned sorted by their score, the most relevant results\n * will be returned first.  For details on how the score is calculated, please see\n * the {@link https://lunrjs.com/guides/searching.html#scoring|guide}.\n *\n * For more programmatic querying use lunr.Index#query.\n *\n * @param {lunr.Index~QueryString} queryString - A string containing a lunr query.\n * @throws {lunr.QueryParseError} If the passed query string cannot be parsed.\n * @returns {lunr.Index~Result[]}\n */\nlunr.Index.prototype.search = function (queryString) {\n  return this.query(function (query) {\n    var parser = new lunr.QueryParser(queryString, query)\n    parser.parse()\n  })\n}\n\n/**\n * A query builder callback provides a query object to be used to express\n * the query to perform on the index.\n *\n * @callback lunr.Index~queryBuilder\n * @param {lunr.Query} query - The query object to build up.\n * @this lunr.Query\n */\n\n/**\n * Performs a query against the index using the yielded lunr.Query object.\n *\n * If performing programmatic queries against the index, this method is preferred\n * over lunr.Index#search so as to avoid the additional query parsing overhead.\n *\n * A query object is yielded to the supplied function which should be used to\n * express the query to be run against the index.\n *\n * Note that although this function takes a callback parameter it is _not_ an\n * asynchronous operation, the callback is just yielded a query object to be\n * customized.\n *\n * @param {lunr.Index~queryBuilder} fn - A function that is used to build the query.\n * @returns {lunr.Index~Result[]}\n */\nlunr.Index.prototype.query = function (fn) {\n  // for each query clause\n  // * process terms\n  // * expand terms from token set\n  // * find matching documents and metadata\n  // * get document vectors\n  // * score documents\n\n  var query = new lunr.Query(this.fields),\n      matchingFields = Object.create(null),\n      queryVectors = Object.create(null),\n      termFieldCache = Object.create(null),\n      requiredMatches = Object.create(null),\n      prohibitedMatches = Object.create(null)\n\n  /*\n   * To support field level boosts a query vector is created per\n   * field. An empty vector is eagerly created to support negated\n   * queries.\n   */\n  for (var i = 0; i < this.fields.length; i++) {\n    queryVectors[this.fields[i]] = new lunr.Vector\n  }\n\n  fn.call(query, query)\n\n  for (var i = 0; i < query.clauses.length; i++) {\n    /*\n     * Unless the pipeline has been disabled for this term, which is\n     * the case for terms with wildcards, we need to pass the clause\n     * term through the search pipeline. A pipeline returns an array\n     * of processed terms. Pipeline functions may expand the passed\n     * term, which means we may end up performing multiple index lookups\n     * for a single query term.\n     */\n    var clause = query.clauses[i],\n        terms = null,\n        clauseMatches = lunr.Set.empty\n\n    if (clause.usePipeline) {\n      terms = this.pipeline.runString(clause.term, {\n        fields: clause.fields\n      })\n    } else {\n      terms = [clause.term]\n    }\n\n    for (var m = 0; m < terms.length; m++) {\n      var term = terms[m]\n\n      /*\n       * Each term returned from the pipeline needs to use the same query\n       * clause object, e.g. the same boost and or edit distance. The\n       * simplest way to do this is to re-use the clause object but mutate\n       * its term property.\n       */\n      clause.term = term\n\n      /*\n       * From the term in the clause we create a token set which will then\n       * be used to intersect the indexes token set to get a list of terms\n       * to lookup in the inverted index\n       */\n      var termTokenSet = lunr.TokenSet.fromClause(clause),\n          expandedTerms = this.tokenSet.intersect(termTokenSet).toArray()\n\n      /*\n       * If a term marked as required does not exist in the tokenSet it is\n       * impossible for the search to return any matches. We set all the field\n       * scoped required matches set to empty and stop examining any further\n       * clauses.\n       */\n      if (expandedTerms.length === 0 && clause.presence === lunr.Query.presence.REQUIRED) {\n        for (var k = 0; k < clause.fields.length; k++) {\n          var field = clause.fields[k]\n          requiredMatches[field] = lunr.Set.empty\n        }\n\n        break\n      }\n\n      for (var j = 0; j < expandedTerms.length; j++) {\n        /*\n         * For each term get the posting and termIndex, this is required for\n         * building the query vector.\n         */\n        var expandedTerm = expandedTerms[j],\n            posting = this.invertedIndex[expandedTerm],\n            termIndex = posting._index\n\n        for (var k = 0; k < clause.fields.length; k++) {\n          /*\n           * For each field that this query term is scoped by (by default\n           * all fields are in scope) we need to get all the document refs\n           * that have this term in that field.\n           *\n           * The posting is the entry in the invertedIndex for the matching\n           * term from above.\n           */\n          var field = clause.fields[k],\n              fieldPosting = posting[field],\n              matchingDocumentRefs = Object.keys(fieldPosting),\n              termField = expandedTerm + \"/\" + field,\n              matchingDocumentsSet = new lunr.Set(matchingDocumentRefs)\n\n          /*\n           * if the presence of this term is required ensure that the matching\n           * documents are added to the set of required matches for this clause.\n           *\n           */\n          if (clause.presence == lunr.Query.presence.REQUIRED) {\n            clauseMatches = clauseMatches.union(matchingDocumentsSet)\n\n            if (requiredMatches[field] === undefined) {\n              requiredMatches[field] = lunr.Set.complete\n            }\n          }\n\n          /*\n           * if the presence of this term is prohibited ensure that the matching\n           * documents are added to the set of prohibited matches for this field,\n           * creating that set if it does not yet exist.\n           */\n          if (clause.presence == lunr.Query.presence.PROHIBITED) {\n            if (prohibitedMatches[field] === undefined) {\n              prohibitedMatches[field] = lunr.Set.empty\n            }\n\n            prohibitedMatches[field] = prohibitedMatches[field].union(matchingDocumentsSet)\n\n            /*\n             * Prohibited matches should not be part of the query vector used for\n             * similarity scoring and no metadata should be extracted so we continue\n             * to the next field\n             */\n            continue\n          }\n\n          /*\n           * The query field vector is populated using the termIndex found for\n           * the term and a unit value with the appropriate boost applied.\n           * Using upsert because there could already be an entry in the vector\n           * for the term we are working with. In that case we just add the scores\n           * together.\n           */\n          queryVectors[field].upsert(termIndex, clause.boost, function (a, b) { return a + b })\n\n          /**\n           * If we've already seen this term, field combo then we've already collected\n           * the matching documents and metadata, no need to go through all that again\n           */\n          if (termFieldCache[termField]) {\n            continue\n          }\n\n          for (var l = 0; l < matchingDocumentRefs.length; l++) {\n            /*\n             * All metadata for this term/field/document triple\n             * are then extracted and collected into an instance\n             * of lunr.MatchData ready to be returned in the query\n             * results\n             */\n            var matchingDocumentRef = matchingDocumentRefs[l],\n                matchingFieldRef = new lunr.FieldRef (matchingDocumentRef, field),\n                metadata = fieldPosting[matchingDocumentRef],\n                fieldMatch\n\n            if ((fieldMatch = matchingFields[matchingFieldRef]) === undefined) {\n              matchingFields[matchingFieldRef] = new lunr.MatchData (expandedTerm, field, metadata)\n            } else {\n              fieldMatch.add(expandedTerm, field, metadata)\n            }\n\n          }\n\n          termFieldCache[termField] = true\n        }\n      }\n    }\n\n    /**\n     * If the presence was required we need to update the requiredMatches field sets.\n     * We do this after all fields for the term have collected their matches because\n     * the clause terms presence is required in _any_ of the fields not _all_ of the\n     * fields.\n     */\n    if (clause.presence === lunr.Query.presence.REQUIRED) {\n      for (var k = 0; k < clause.fields.length; k++) {\n        var field = clause.fields[k]\n        requiredMatches[field] = requiredMatches[field].intersect(clauseMatches)\n      }\n    }\n  }\n\n  /**\n   * Need to combine the field scoped required and prohibited\n   * matching documents into a global set of required and prohibited\n   * matches\n   */\n  var allRequiredMatches = lunr.Set.complete,\n      allProhibitedMatches = lunr.Set.empty\n\n  for (var i = 0; i < this.fields.length; i++) {\n    var field = this.fields[i]\n\n    if (requiredMatches[field]) {\n      allRequiredMatches = allRequiredMatches.intersect(requiredMatches[field])\n    }\n\n    if (prohibitedMatches[field]) {\n      allProhibitedMatches = allProhibitedMatches.union(prohibitedMatches[field])\n    }\n  }\n\n  var matchingFieldRefs = Object.keys(matchingFields),\n      results = [],\n      matches = Object.create(null)\n\n  /*\n   * If the query is negated (contains only prohibited terms)\n   * we need to get _all_ fieldRefs currently existing in the\n   * index. This is only done when we know that the query is\n   * entirely prohibited terms to avoid any cost of getting all\n   * fieldRefs unnecessarily.\n   *\n   * Additionally, blank MatchData must be created to correctly\n   * populate the results.\n   */\n  if (query.isNegated()) {\n    matchingFieldRefs = Object.keys(this.fieldVectors)\n\n    for (var i = 0; i < matchingFieldRefs.length; i++) {\n      var matchingFieldRef = matchingFieldRefs[i]\n      var fieldRef = lunr.FieldRef.fromString(matchingFieldRef)\n      matchingFields[matchingFieldRef] = new lunr.MatchData\n    }\n  }\n\n  for (var i = 0; i < matchingFieldRefs.length; i++) {\n    /*\n     * Currently we have document fields that match the query, but we\n     * need to return documents. The matchData and scores are combined\n     * from multiple fields belonging to the same document.\n     *\n     * Scores are calculated by field, using the query vectors created\n     * above, and combined into a final document score using addition.\n     */\n    var fieldRef = lunr.FieldRef.fromString(matchingFieldRefs[i]),\n        docRef = fieldRef.docRef\n\n    if (!allRequiredMatches.contains(docRef)) {\n      continue\n    }\n\n    if (allProhibitedMatches.contains(docRef)) {\n      continue\n    }\n\n    var fieldVector = this.fieldVectors[fieldRef],\n        score = queryVectors[fieldRef.fieldName].similarity(fieldVector),\n        docMatch\n\n    if ((docMatch = matches[docRef]) !== undefined) {\n      docMatch.score += score\n      docMatch.matchData.combine(matchingFields[fieldRef])\n    } else {\n      var match = {\n        ref: docRef,\n        score: score,\n        matchData: matchingFields[fieldRef]\n      }\n      matches[docRef] = match\n      results.push(match)\n    }\n  }\n\n  /*\n   * Sort the results objects by score, highest first.\n   */\n  return results.sort(function (a, b) {\n    return b.score - a.score\n  })\n}\n\n/**\n * Prepares the index for JSON serialization.\n *\n * The schema for this JSON blob will be described in a\n * separate JSON schema file.\n *\n * @returns {Object}\n */\nlunr.Index.prototype.toJSON = function () {\n  var invertedIndex = Object.keys(this.invertedIndex)\n    .sort()\n    .map(function (term) {\n      return [term, this.invertedIndex[term]]\n    }, this)\n\n  var fieldVectors = Object.keys(this.fieldVectors)\n    .map(function (ref) {\n      return [ref, this.fieldVectors[ref].toJSON()]\n    }, this)\n\n  return {\n    version: lunr.version,\n    fields: this.fields,\n    fieldVectors: fieldVectors,\n    invertedIndex: invertedIndex,\n    pipeline: this.pipeline.toJSON()\n  }\n}\n\n/**\n * Loads a previously serialized lunr.Index\n *\n * @param {Object} serializedIndex - A previously serialized lunr.Index\n * @returns {lunr.Index}\n */\nlunr.Index.load = function (serializedIndex) {\n  var attrs = {},\n      fieldVectors = {},\n      serializedVectors = serializedIndex.fieldVectors,\n      invertedIndex = Object.create(null),\n      serializedInvertedIndex = serializedIndex.invertedIndex,\n      tokenSetBuilder = new lunr.TokenSet.Builder,\n      pipeline = lunr.Pipeline.load(serializedIndex.pipeline)\n\n  if (serializedIndex.version != lunr.version) {\n    lunr.utils.warn(\"Version mismatch when loading serialised index. Current version of lunr '\" + lunr.version + \"' does not match serialized index '\" + serializedIndex.version + \"'\")\n  }\n\n  for (var i = 0; i < serializedVectors.length; i++) {\n    var tuple = serializedVectors[i],\n        ref = tuple[0],\n        elements = tuple[1]\n\n    fieldVectors[ref] = new lunr.Vector(elements)\n  }\n\n  for (var i = 0; i < serializedInvertedIndex.length; i++) {\n    var tuple = serializedInvertedIndex[i],\n        term = tuple[0],\n        posting = tuple[1]\n\n    tokenSetBuilder.insert(term)\n    invertedIndex[term] = posting\n  }\n\n  tokenSetBuilder.finish()\n\n  attrs.fields = serializedIndex.fields\n\n  attrs.fieldVectors = fieldVectors\n  attrs.invertedIndex = invertedIndex\n  attrs.tokenSet = tokenSetBuilder.root\n  attrs.pipeline = pipeline\n\n  return new lunr.Index(attrs)\n}\n/*!\n * lunr.Builder\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.Builder performs indexing on a set of documents and\n * returns instances of lunr.Index ready for querying.\n *\n * All configuration of the index is done via the builder, the\n * fields to index, the document reference, the text processing\n * pipeline and document scoring parameters are all set on the\n * builder before indexing.\n *\n * @constructor\n * @property {string} _ref - Internal reference to the document reference field.\n * @property {string[]} _fields - Internal reference to the document fields to index.\n * @property {object} invertedIndex - The inverted index maps terms to document fields.\n * @property {object} documentTermFrequencies - Keeps track of document term frequencies.\n * @property {object} documentLengths - Keeps track of the length of documents added to the index.\n * @property {lunr.tokenizer} tokenizer - Function for splitting strings into tokens for indexing.\n * @property {lunr.Pipeline} pipeline - The pipeline performs text processing on tokens before indexing.\n * @property {lunr.Pipeline} searchPipeline - A pipeline for processing search terms before querying the index.\n * @property {number} documentCount - Keeps track of the total number of documents indexed.\n * @property {number} _b - A parameter to control field length normalization, setting this to 0 disabled normalization, 1 fully normalizes field lengths, the default value is 0.75.\n * @property {number} _k1 - A parameter to control how quickly an increase in term frequency results in term frequency saturation, the default value is 1.2.\n * @property {number} termIndex - A counter incremented for each unique term, used to identify a terms position in the vector space.\n * @property {array} metadataWhitelist - A list of metadata keys that have been whitelisted for entry in the index.\n */\nlunr.Builder = function () {\n  this._ref = \"id\"\n  this._fields = Object.create(null)\n  this._documents = Object.create(null)\n  this.invertedIndex = Object.create(null)\n  this.fieldTermFrequencies = {}\n  this.fieldLengths = {}\n  this.tokenizer = lunr.tokenizer\n  this.pipeline = new lunr.Pipeline\n  this.searchPipeline = new lunr.Pipeline\n  this.documentCount = 0\n  this._b = 0.75\n  this._k1 = 1.2\n  this.termIndex = 0\n  this.metadataWhitelist = []\n}\n\n/**\n * Sets the document field used as the document reference. Every document must have this field.\n * The type of this field in the document should be a string, if it is not a string it will be\n * coerced into a string by calling toString.\n *\n * The default ref is 'id'.\n *\n * The ref should _not_ be changed during indexing, it should be set before any documents are\n * added to the index. Changing it during indexing can lead to inconsistent results.\n *\n * @param {string} ref - The name of the reference field in the document.\n */\nlunr.Builder.prototype.ref = function (ref) {\n  this._ref = ref\n}\n\n/**\n * A function that is used to extract a field from a document.\n *\n * Lunr expects a field to be at the top level of a document, if however the field\n * is deeply nested within a document an extractor function can be used to extract\n * the right field for indexing.\n *\n * @callback fieldExtractor\n * @param {object} doc - The document being added to the index.\n * @returns {?(string|object|object[])} obj - The object that will be indexed for this field.\n * @example <caption>Extracting a nested field</caption>\n * function (doc) { return doc.nested.field }\n */\n\n/**\n * Adds a field to the list of document fields that will be indexed. Every document being\n * indexed should have this field. Null values for this field in indexed documents will\n * not cause errors but will limit the chance of that document being retrieved by searches.\n *\n * All fields should be added before adding documents to the index. Adding fields after\n * a document has been indexed will have no effect on already indexed documents.\n *\n * Fields can be boosted at build time. This allows terms within that field to have more\n * importance when ranking search results. Use a field boost to specify that matches within\n * one field are more important than other fields.\n *\n * @param {string} fieldName - The name of a field to index in all documents.\n * @param {object} attributes - Optional attributes associated with this field.\n * @param {number} [attributes.boost=1] - Boost applied to all terms within this field.\n * @param {fieldExtractor} [attributes.extractor] - Function to extract a field from a document.\n * @throws {RangeError} fieldName cannot contain unsupported characters '/'\n */\nlunr.Builder.prototype.field = function (fieldName, attributes) {\n  if (/\\//.test(fieldName)) {\n    throw new RangeError (\"Field '\" + fieldName + \"' contains illegal character '/'\")\n  }\n\n  this._fields[fieldName] = attributes || {}\n}\n\n/**\n * A parameter to tune the amount of field length normalisation that is applied when\n * calculating relevance scores. A value of 0 will completely disable any normalisation\n * and a value of 1 will fully normalise field lengths. The default is 0.75. Values of b\n * will be clamped to the range 0 - 1.\n *\n * @param {number} number - The value to set for this tuning parameter.\n */\nlunr.Builder.prototype.b = function (number) {\n  if (number < 0) {\n    this._b = 0\n  } else if (number > 1) {\n    this._b = 1\n  } else {\n    this._b = number\n  }\n}\n\n/**\n * A parameter that controls the speed at which a rise in term frequency results in term\n * frequency saturation. The default value is 1.2. Setting this to a higher value will give\n * slower saturation levels, a lower value will result in quicker saturation.\n *\n * @param {number} number - The value to set for this tuning parameter.\n */\nlunr.Builder.prototype.k1 = function (number) {\n  this._k1 = number\n}\n\n/**\n * Adds a document to the index.\n *\n * Before adding fields to the index the index should have been fully setup, with the document\n * ref and all fields to index already having been specified.\n *\n * The document must have a field name as specified by the ref (by default this is 'id') and\n * it should have all fields defined for indexing, though null or undefined values will not\n * cause errors.\n *\n * Entire documents can be boosted at build time. Applying a boost to a document indicates that\n * this document should rank higher in search results than other documents.\n *\n * @param {object} doc - The document to add to the index.\n * @param {object} attributes - Optional attributes associated with this document.\n * @param {number} [attributes.boost=1] - Boost applied to all terms within this document.\n */\nlunr.Builder.prototype.add = function (doc, attributes) {\n  var docRef = doc[this._ref],\n      fields = Object.keys(this._fields)\n\n  this._documents[docRef] = attributes || {}\n  this.documentCount += 1\n\n  for (var i = 0; i < fields.length; i++) {\n    var fieldName = fields[i],\n        extractor = this._fields[fieldName].extractor,\n        field = extractor ? extractor(doc) : doc[fieldName],\n        tokens = this.tokenizer(field, {\n          fields: [fieldName]\n        }),\n        terms = this.pipeline.run(tokens),\n        fieldRef = new lunr.FieldRef (docRef, fieldName),\n        fieldTerms = Object.create(null)\n\n    this.fieldTermFrequencies[fieldRef] = fieldTerms\n    this.fieldLengths[fieldRef] = 0\n\n    // store the length of this field for this document\n    this.fieldLengths[fieldRef] += terms.length\n\n    // calculate term frequencies for this field\n    for (var j = 0; j < terms.length; j++) {\n      var term = terms[j]\n\n      if (fieldTerms[term] == undefined) {\n        fieldTerms[term] = 0\n      }\n\n      fieldTerms[term] += 1\n\n      // add to inverted index\n      // create an initial posting if one doesn't exist\n      if (this.invertedIndex[term] == undefined) {\n        var posting = Object.create(null)\n        posting[\"_index\"] = this.termIndex\n        this.termIndex += 1\n\n        for (var k = 0; k < fields.length; k++) {\n          posting[fields[k]] = Object.create(null)\n        }\n\n        this.invertedIndex[term] = posting\n      }\n\n      // add an entry for this term/fieldName/docRef to the invertedIndex\n      if (this.invertedIndex[term][fieldName][docRef] == undefined) {\n        this.invertedIndex[term][fieldName][docRef] = Object.create(null)\n      }\n\n      // store all whitelisted metadata about this token in the\n      // inverted index\n      for (var l = 0; l < this.metadataWhitelist.length; l++) {\n        var metadataKey = this.metadataWhitelist[l],\n            metadata = term.metadata[metadataKey]\n\n        if (this.invertedIndex[term][fieldName][docRef][metadataKey] == undefined) {\n          this.invertedIndex[term][fieldName][docRef][metadataKey] = []\n        }\n\n        this.invertedIndex[term][fieldName][docRef][metadataKey].push(metadata)\n      }\n    }\n\n  }\n}\n\n/**\n * Calculates the average document length for this index\n *\n * @private\n */\nlunr.Builder.prototype.calculateAverageFieldLengths = function () {\n\n  var fieldRefs = Object.keys(this.fieldLengths),\n      numberOfFields = fieldRefs.length,\n      accumulator = {},\n      documentsWithField = {}\n\n  for (var i = 0; i < numberOfFields; i++) {\n    var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),\n        field = fieldRef.fieldName\n\n    documentsWithField[field] || (documentsWithField[field] = 0)\n    documentsWithField[field] += 1\n\n    accumulator[field] || (accumulator[field] = 0)\n    accumulator[field] += this.fieldLengths[fieldRef]\n  }\n\n  var fields = Object.keys(this._fields)\n\n  for (var i = 0; i < fields.length; i++) {\n    var fieldName = fields[i]\n    accumulator[fieldName] = accumulator[fieldName] / documentsWithField[fieldName]\n  }\n\n  this.averageFieldLength = accumulator\n}\n\n/**\n * Builds a vector space model of every document using lunr.Vector\n *\n * @private\n */\nlunr.Builder.prototype.createFieldVectors = function () {\n  var fieldVectors = {},\n      fieldRefs = Object.keys(this.fieldTermFrequencies),\n      fieldRefsLength = fieldRefs.length,\n      termIdfCache = Object.create(null)\n\n  for (var i = 0; i < fieldRefsLength; i++) {\n    var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),\n        fieldName = fieldRef.fieldName,\n        fieldLength = this.fieldLengths[fieldRef],\n        fieldVector = new lunr.Vector,\n        termFrequencies = this.fieldTermFrequencies[fieldRef],\n        terms = Object.keys(termFrequencies),\n        termsLength = terms.length\n\n\n    var fieldBoost = this._fields[fieldName].boost || 1,\n        docBoost = this._documents[fieldRef.docRef].boost || 1\n\n    for (var j = 0; j < termsLength; j++) {\n      var term = terms[j],\n          tf = termFrequencies[term],\n          termIndex = this.invertedIndex[term]._index,\n          idf, score, scoreWithPrecision\n\n      if (termIdfCache[term] === undefined) {\n        idf = lunr.idf(this.invertedIndex[term], this.documentCount)\n        termIdfCache[term] = idf\n      } else {\n        idf = termIdfCache[term]\n      }\n\n      score = idf * ((this._k1 + 1) * tf) / (this._k1 * (1 - this._b + this._b * (fieldLength / this.averageFieldLength[fieldName])) + tf)\n      score *= fieldBoost\n      score *= docBoost\n      scoreWithPrecision = Math.round(score * 1000) / 1000\n      // Converts 1.23456789 to 1.234.\n      // Reducing the precision so that the vectors take up less\n      // space when serialised. Doing it now so that they behave\n      // the same before and after serialisation. Also, this is\n      // the fastest approach to reducing a number's precision in\n      // JavaScript.\n\n      fieldVector.insert(termIndex, scoreWithPrecision)\n    }\n\n    fieldVectors[fieldRef] = fieldVector\n  }\n\n  this.fieldVectors = fieldVectors\n}\n\n/**\n * Creates a token set of all tokens in the index using lunr.TokenSet\n *\n * @private\n */\nlunr.Builder.prototype.createTokenSet = function () {\n  this.tokenSet = lunr.TokenSet.fromArray(\n    Object.keys(this.invertedIndex).sort()\n  )\n}\n\n/**\n * Builds the index, creating an instance of lunr.Index.\n *\n * This completes the indexing process and should only be called\n * once all documents have been added to the index.\n *\n * @returns {lunr.Index}\n */\nlunr.Builder.prototype.build = function () {\n  this.calculateAverageFieldLengths()\n  this.createFieldVectors()\n  this.createTokenSet()\n\n  return new lunr.Index({\n    invertedIndex: this.invertedIndex,\n    fieldVectors: this.fieldVectors,\n    tokenSet: this.tokenSet,\n    fields: Object.keys(this._fields),\n    pipeline: this.searchPipeline\n  })\n}\n\n/**\n * Applies a plugin to the index builder.\n *\n * A plugin is a function that is called with the index builder as its context.\n * Plugins can be used to customise or extend the behaviour of the index\n * in some way. A plugin is just a function, that encapsulated the custom\n * behaviour that should be applied when building the index.\n *\n * The plugin function will be called with the index builder as its argument, additional\n * arguments can also be passed when calling use. The function will be called\n * with the index builder as its context.\n *\n * @param {Function} plugin The plugin to apply.\n */\nlunr.Builder.prototype.use = function (fn) {\n  var args = Array.prototype.slice.call(arguments, 1)\n  args.unshift(this)\n  fn.apply(this, args)\n}\n/**\n * Contains and collects metadata about a matching document.\n * A single instance of lunr.MatchData is returned as part of every\n * lunr.Index~Result.\n *\n * @constructor\n * @param {string} term - The term this match data is associated with\n * @param {string} field - The field in which the term was found\n * @param {object} metadata - The metadata recorded about this term in this field\n * @property {object} metadata - A cloned collection of metadata associated with this document.\n * @see {@link lunr.Index~Result}\n */\nlunr.MatchData = function (term, field, metadata) {\n  var clonedMetadata = Object.create(null),\n      metadataKeys = Object.keys(metadata || {})\n\n  // Cloning the metadata to prevent the original\n  // being mutated during match data combination.\n  // Metadata is kept in an array within the inverted\n  // index so cloning the data can be done with\n  // Array#slice\n  for (var i = 0; i < metadataKeys.length; i++) {\n    var key = metadataKeys[i]\n    clonedMetadata[key] = metadata[key].slice()\n  }\n\n  this.metadata = Object.create(null)\n\n  if (term !== undefined) {\n    this.metadata[term] = Object.create(null)\n    this.metadata[term][field] = clonedMetadata\n  }\n}\n\n/**\n * An instance of lunr.MatchData will be created for every term that matches a\n * document. However only one instance is required in a lunr.Index~Result. This\n * method combines metadata from another instance of lunr.MatchData with this\n * objects metadata.\n *\n * @param {lunr.MatchData} otherMatchData - Another instance of match data to merge with this one.\n * @see {@link lunr.Index~Result}\n */\nlunr.MatchData.prototype.combine = function (otherMatchData) {\n  var terms = Object.keys(otherMatchData.metadata)\n\n  for (var i = 0; i < terms.length; i++) {\n    var term = terms[i],\n        fields = Object.keys(otherMatchData.metadata[term])\n\n    if (this.metadata[term] == undefined) {\n      this.metadata[term] = Object.create(null)\n    }\n\n    for (var j = 0; j < fields.length; j++) {\n      var field = fields[j],\n          keys = Object.keys(otherMatchData.metadata[term][field])\n\n      if (this.metadata[term][field] == undefined) {\n        this.metadata[term][field] = Object.create(null)\n      }\n\n      for (var k = 0; k < keys.length; k++) {\n        var key = keys[k]\n\n        if (this.metadata[term][field][key] == undefined) {\n          this.metadata[term][field][key] = otherMatchData.metadata[term][field][key]\n        } else {\n          this.metadata[term][field][key] = this.metadata[term][field][key].concat(otherMatchData.metadata[term][field][key])\n        }\n\n      }\n    }\n  }\n}\n\n/**\n * Add metadata for a term/field pair to this instance of match data.\n *\n * @param {string} term - The term this match data is associated with\n * @param {string} field - The field in which the term was found\n * @param {object} metadata - The metadata recorded about this term in this field\n */\nlunr.MatchData.prototype.add = function (term, field, metadata) {\n  if (!(term in this.metadata)) {\n    this.metadata[term] = Object.create(null)\n    this.metadata[term][field] = metadata\n    return\n  }\n\n  if (!(field in this.metadata[term])) {\n    this.metadata[term][field] = metadata\n    return\n  }\n\n  var metadataKeys = Object.keys(metadata)\n\n  for (var i = 0; i < metadataKeys.length; i++) {\n    var key = metadataKeys[i]\n\n    if (key in this.metadata[term][field]) {\n      this.metadata[term][field][key] = this.metadata[term][field][key].concat(metadata[key])\n    } else {\n      this.metadata[term][field][key] = metadata[key]\n    }\n  }\n}\n/**\n * A lunr.Query provides a programmatic way of defining queries to be performed\n * against a {@link lunr.Index}.\n *\n * Prefer constructing a lunr.Query using the {@link lunr.Index#query} method\n * so the query object is pre-initialized with the right index fields.\n *\n * @constructor\n * @property {lunr.Query~Clause[]} clauses - An array of query clauses.\n * @property {string[]} allFields - An array of all available fields in a lunr.Index.\n */\nlunr.Query = function (allFields) {\n  this.clauses = []\n  this.allFields = allFields\n}\n\n/**\n * Constants for indicating what kind of automatic wildcard insertion will be used when constructing a query clause.\n *\n * This allows wildcards to be added to the beginning and end of a term without having to manually do any string\n * concatenation.\n *\n * The wildcard constants can be bitwise combined to select both leading and trailing wildcards.\n *\n * @constant\n * @default\n * @property {number} wildcard.NONE - The term will have no wildcards inserted, this is the default behaviour\n * @property {number} wildcard.LEADING - Prepend the term with a wildcard, unless a leading wildcard already exists\n * @property {number} wildcard.TRAILING - Append a wildcard to the term, unless a trailing wildcard already exists\n * @see lunr.Query~Clause\n * @see lunr.Query#clause\n * @see lunr.Query#term\n * @example <caption>query term with trailing wildcard</caption>\n * query.term('foo', { wildcard: lunr.Query.wildcard.TRAILING })\n * @example <caption>query term with leading and trailing wildcard</caption>\n * query.term('foo', {\n *   wildcard: lunr.Query.wildcard.LEADING | lunr.Query.wildcard.TRAILING\n * })\n */\n\nlunr.Query.wildcard = new String (\"*\")\nlunr.Query.wildcard.NONE = 0\nlunr.Query.wildcard.LEADING = 1\nlunr.Query.wildcard.TRAILING = 2\n\n/**\n * Constants for indicating what kind of presence a term must have in matching documents.\n *\n * @constant\n * @enum {number}\n * @see lunr.Query~Clause\n * @see lunr.Query#clause\n * @see lunr.Query#term\n * @example <caption>query term with required presence</caption>\n * query.term('foo', { presence: lunr.Query.presence.REQUIRED })\n */\nlunr.Query.presence = {\n  /**\n   * Term's presence in a document is optional, this is the default value.\n   */\n  OPTIONAL: 1,\n\n  /**\n   * Term's presence in a document is required, documents that do not contain\n   * this term will not be returned.\n   */\n  REQUIRED: 2,\n\n  /**\n   * Term's presence in a document is prohibited, documents that do contain\n   * this term will not be returned.\n   */\n  PROHIBITED: 3\n}\n\n/**\n * A single clause in a {@link lunr.Query} contains a term and details on how to\n * match that term against a {@link lunr.Index}.\n *\n * @typedef {Object} lunr.Query~Clause\n * @property {string[]} fields - The fields in an index this clause should be matched against.\n * @property {number} [boost=1] - Any boost that should be applied when matching this clause.\n * @property {number} [editDistance] - Whether the term should have fuzzy matching applied, and how fuzzy the match should be.\n * @property {boolean} [usePipeline] - Whether the term should be passed through the search pipeline.\n * @property {number} [wildcard=lunr.Query.wildcard.NONE] - Whether the term should have wildcards appended or prepended.\n * @property {number} [presence=lunr.Query.presence.OPTIONAL] - The terms presence in any matching documents.\n */\n\n/**\n * Adds a {@link lunr.Query~Clause} to this query.\n *\n * Unless the clause contains the fields to be matched all fields will be matched. In addition\n * a default boost of 1 is applied to the clause.\n *\n * @param {lunr.Query~Clause} clause - The clause to add to this query.\n * @see lunr.Query~Clause\n * @returns {lunr.Query}\n */\nlunr.Query.prototype.clause = function (clause) {\n  if (!('fields' in clause)) {\n    clause.fields = this.allFields\n  }\n\n  if (!('boost' in clause)) {\n    clause.boost = 1\n  }\n\n  if (!('usePipeline' in clause)) {\n    clause.usePipeline = true\n  }\n\n  if (!('wildcard' in clause)) {\n    clause.wildcard = lunr.Query.wildcard.NONE\n  }\n\n  if ((clause.wildcard & lunr.Query.wildcard.LEADING) && (clause.term.charAt(0) != lunr.Query.wildcard)) {\n    clause.term = \"*\" + clause.term\n  }\n\n  if ((clause.wildcard & lunr.Query.wildcard.TRAILING) && (clause.term.slice(-1) != lunr.Query.wildcard)) {\n    clause.term = \"\" + clause.term + \"*\"\n  }\n\n  if (!('presence' in clause)) {\n    clause.presence = lunr.Query.presence.OPTIONAL\n  }\n\n  this.clauses.push(clause)\n\n  return this\n}\n\n/**\n * A negated query is one in which every clause has a presence of\n * prohibited. These queries require some special processing to return\n * the expected results.\n *\n * @returns boolean\n */\nlunr.Query.prototype.isNegated = function () {\n  for (var i = 0; i < this.clauses.length; i++) {\n    if (this.clauses[i].presence != lunr.Query.presence.PROHIBITED) {\n      return false\n    }\n  }\n\n  return true\n}\n\n/**\n * Adds a term to the current query, under the covers this will create a {@link lunr.Query~Clause}\n * to the list of clauses that make up this query.\n *\n * The term is used as is, i.e. no tokenization will be performed by this method. Instead conversion\n * to a token or token-like string should be done before calling this method.\n *\n * The term will be converted to a string by calling `toString`. Multiple terms can be passed as an\n * array, each term in the array will share the same options.\n *\n * @param {object|object[]} term - The term(s) to add to the query.\n * @param {object} [options] - Any additional properties to add to the query clause.\n * @returns {lunr.Query}\n * @see lunr.Query#clause\n * @see lunr.Query~Clause\n * @example <caption>adding a single term to a query</caption>\n * query.term(\"foo\")\n * @example <caption>adding a single term to a query and specifying search fields, term boost and automatic trailing wildcard</caption>\n * query.term(\"foo\", {\n *   fields: [\"title\"],\n *   boost: 10,\n *   wildcard: lunr.Query.wildcard.TRAILING\n * })\n * @example <caption>using lunr.tokenizer to convert a string to tokens before using them as terms</caption>\n * query.term(lunr.tokenizer(\"foo bar\"))\n */\nlunr.Query.prototype.term = function (term, options) {\n  if (Array.isArray(term)) {\n    term.forEach(function (t) { this.term(t, lunr.utils.clone(options)) }, this)\n    return this\n  }\n\n  var clause = options || {}\n  clause.term = term.toString()\n\n  this.clause(clause)\n\n  return this\n}\nlunr.QueryParseError = function (message, start, end) {\n  this.name = \"QueryParseError\"\n  this.message = message\n  this.start = start\n  this.end = end\n}\n\nlunr.QueryParseError.prototype = new Error\nlunr.QueryLexer = function (str) {\n  this.lexemes = []\n  this.str = str\n  this.length = str.length\n  this.pos = 0\n  this.start = 0\n  this.escapeCharPositions = []\n}\n\nlunr.QueryLexer.prototype.run = function () {\n  var state = lunr.QueryLexer.lexText\n\n  while (state) {\n    state = state(this)\n  }\n}\n\nlunr.QueryLexer.prototype.sliceString = function () {\n  var subSlices = [],\n      sliceStart = this.start,\n      sliceEnd = this.pos\n\n  for (var i = 0; i < this.escapeCharPositions.length; i++) {\n    sliceEnd = this.escapeCharPositions[i]\n    subSlices.push(this.str.slice(sliceStart, sliceEnd))\n    sliceStart = sliceEnd + 1\n  }\n\n  subSlices.push(this.str.slice(sliceStart, this.pos))\n  this.escapeCharPositions.length = 0\n\n  return subSlices.join('')\n}\n\nlunr.QueryLexer.prototype.emit = function (type) {\n  this.lexemes.push({\n    type: type,\n    str: this.sliceString(),\n    start: this.start,\n    end: this.pos\n  })\n\n  this.start = this.pos\n}\n\nlunr.QueryLexer.prototype.escapeCharacter = function () {\n  this.escapeCharPositions.push(this.pos - 1)\n  this.pos += 1\n}\n\nlunr.QueryLexer.prototype.next = function () {\n  if (this.pos >= this.length) {\n    return lunr.QueryLexer.EOS\n  }\n\n  var char = this.str.charAt(this.pos)\n  this.pos += 1\n  return char\n}\n\nlunr.QueryLexer.prototype.width = function () {\n  return this.pos - this.start\n}\n\nlunr.QueryLexer.prototype.ignore = function () {\n  if (this.start == this.pos) {\n    this.pos += 1\n  }\n\n  this.start = this.pos\n}\n\nlunr.QueryLexer.prototype.backup = function () {\n  this.pos -= 1\n}\n\nlunr.QueryLexer.prototype.acceptDigitRun = function () {\n  var char, charCode\n\n  do {\n    char = this.next()\n    charCode = char.charCodeAt(0)\n  } while (charCode > 47 && charCode < 58)\n\n  if (char != lunr.QueryLexer.EOS) {\n    this.backup()\n  }\n}\n\nlunr.QueryLexer.prototype.more = function () {\n  return this.pos < this.length\n}\n\nlunr.QueryLexer.EOS = 'EOS'\nlunr.QueryLexer.FIELD = 'FIELD'\nlunr.QueryLexer.TERM = 'TERM'\nlunr.QueryLexer.EDIT_DISTANCE = 'EDIT_DISTANCE'\nlunr.QueryLexer.BOOST = 'BOOST'\nlunr.QueryLexer.PRESENCE = 'PRESENCE'\n\nlunr.QueryLexer.lexField = function (lexer) {\n  lexer.backup()\n  lexer.emit(lunr.QueryLexer.FIELD)\n  lexer.ignore()\n  return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexTerm = function (lexer) {\n  if (lexer.width() > 1) {\n    lexer.backup()\n    lexer.emit(lunr.QueryLexer.TERM)\n  }\n\n  lexer.ignore()\n\n  if (lexer.more()) {\n    return lunr.QueryLexer.lexText\n  }\n}\n\nlunr.QueryLexer.lexEditDistance = function (lexer) {\n  lexer.ignore()\n  lexer.acceptDigitRun()\n  lexer.emit(lunr.QueryLexer.EDIT_DISTANCE)\n  return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexBoost = function (lexer) {\n  lexer.ignore()\n  lexer.acceptDigitRun()\n  lexer.emit(lunr.QueryLexer.BOOST)\n  return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexEOS = function (lexer) {\n  if (lexer.width() > 0) {\n    lexer.emit(lunr.QueryLexer.TERM)\n  }\n}\n\n// This matches the separator used when tokenising fields\n// within a document. These should match otherwise it is\n// not possible to search for some tokens within a document.\n//\n// It is possible for the user to change the separator on the\n// tokenizer so it _might_ clash with any other of the special\n// characters already used within the search string, e.g. :.\n//\n// This means that it is possible to change the separator in\n// such a way that makes some words unsearchable using a search\n// string.\nlunr.QueryLexer.termSeparator = lunr.tokenizer.separator\n\nlunr.QueryLexer.lexText = function (lexer) {\n  while (true) {\n    var char = lexer.next()\n\n    if (char == lunr.QueryLexer.EOS) {\n      return lunr.QueryLexer.lexEOS\n    }\n\n    // Escape character is '\\'\n    if (char.charCodeAt(0) == 92) {\n      lexer.escapeCharacter()\n      continue\n    }\n\n    if (char == \":\") {\n      return lunr.QueryLexer.lexField\n    }\n\n    if (char == \"~\") {\n      lexer.backup()\n      if (lexer.width() > 0) {\n        lexer.emit(lunr.QueryLexer.TERM)\n      }\n      return lunr.QueryLexer.lexEditDistance\n    }\n\n    if (char == \"^\") {\n      lexer.backup()\n      if (lexer.width() > 0) {\n        lexer.emit(lunr.QueryLexer.TERM)\n      }\n      return lunr.QueryLexer.lexBoost\n    }\n\n    // \"+\" indicates term presence is required\n    // checking for length to ensure that only\n    // leading \"+\" are considered\n    if (char == \"+\" && lexer.width() === 1) {\n      lexer.emit(lunr.QueryLexer.PRESENCE)\n      return lunr.QueryLexer.lexText\n    }\n\n    // \"-\" indicates term presence is prohibited\n    // checking for length to ensure that only\n    // leading \"-\" are considered\n    if (char == \"-\" && lexer.width() === 1) {\n      lexer.emit(lunr.QueryLexer.PRESENCE)\n      return lunr.QueryLexer.lexText\n    }\n\n    if (char.match(lunr.QueryLexer.termSeparator)) {\n      return lunr.QueryLexer.lexTerm\n    }\n  }\n}\n\nlunr.QueryParser = function (str, query) {\n  this.lexer = new lunr.QueryLexer (str)\n  this.query = query\n  this.currentClause = {}\n  this.lexemeIdx = 0\n}\n\nlunr.QueryParser.prototype.parse = function () {\n  this.lexer.run()\n  this.lexemes = this.lexer.lexemes\n\n  var state = lunr.QueryParser.parseClause\n\n  while (state) {\n    state = state(this)\n  }\n\n  return this.query\n}\n\nlunr.QueryParser.prototype.peekLexeme = function () {\n  return this.lexemes[this.lexemeIdx]\n}\n\nlunr.QueryParser.prototype.consumeLexeme = function () {\n  var lexeme = this.peekLexeme()\n  this.lexemeIdx += 1\n  return lexeme\n}\n\nlunr.QueryParser.prototype.nextClause = function () {\n  var completedClause = this.currentClause\n  this.query.clause(completedClause)\n  this.currentClause = {}\n}\n\nlunr.QueryParser.parseClause = function (parser) {\n  var lexeme = parser.peekLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  switch (lexeme.type) {\n    case lunr.QueryLexer.PRESENCE:\n      return lunr.QueryParser.parsePresence\n    case lunr.QueryLexer.FIELD:\n      return lunr.QueryParser.parseField\n    case lunr.QueryLexer.TERM:\n      return lunr.QueryParser.parseTerm\n    default:\n      var errorMessage = \"expected either a field or a term, found \" + lexeme.type\n\n      if (lexeme.str.length >= 1) {\n        errorMessage += \" with value '\" + lexeme.str + \"'\"\n      }\n\n      throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n}\n\nlunr.QueryParser.parsePresence = function (parser) {\n  var lexeme = parser.consumeLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  switch (lexeme.str) {\n    case \"-\":\n      parser.currentClause.presence = lunr.Query.presence.PROHIBITED\n      break\n    case \"+\":\n      parser.currentClause.presence = lunr.Query.presence.REQUIRED\n      break\n    default:\n      var errorMessage = \"unrecognised presence operator'\" + lexeme.str + \"'\"\n      throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  var nextLexeme = parser.peekLexeme()\n\n  if (nextLexeme == undefined) {\n    var errorMessage = \"expecting term or field, found nothing\"\n    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  switch (nextLexeme.type) {\n    case lunr.QueryLexer.FIELD:\n      return lunr.QueryParser.parseField\n    case lunr.QueryLexer.TERM:\n      return lunr.QueryParser.parseTerm\n    default:\n      var errorMessage = \"expecting term or field, found '\" + nextLexeme.type + \"'\"\n      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n  }\n}\n\nlunr.QueryParser.parseField = function (parser) {\n  var lexeme = parser.consumeLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  if (parser.query.allFields.indexOf(lexeme.str) == -1) {\n    var possibleFields = parser.query.allFields.map(function (f) { return \"'\" + f + \"'\" }).join(', '),\n        errorMessage = \"unrecognised field '\" + lexeme.str + \"', possible fields: \" + possibleFields\n\n    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  parser.currentClause.fields = [lexeme.str]\n\n  var nextLexeme = parser.peekLexeme()\n\n  if (nextLexeme == undefined) {\n    var errorMessage = \"expecting term, found nothing\"\n    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  switch (nextLexeme.type) {\n    case lunr.QueryLexer.TERM:\n      return lunr.QueryParser.parseTerm\n    default:\n      var errorMessage = \"expecting term, found '\" + nextLexeme.type + \"'\"\n      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n  }\n}\n\nlunr.QueryParser.parseTerm = function (parser) {\n  var lexeme = parser.consumeLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  parser.currentClause.term = lexeme.str.toLowerCase()\n\n  if (lexeme.str.indexOf(\"*\") != -1) {\n    parser.currentClause.usePipeline = false\n  }\n\n  var nextLexeme = parser.peekLexeme()\n\n  if (nextLexeme == undefined) {\n    parser.nextClause()\n    return\n  }\n\n  switch (nextLexeme.type) {\n    case lunr.QueryLexer.TERM:\n      parser.nextClause()\n      return lunr.QueryParser.parseTerm\n    case lunr.QueryLexer.FIELD:\n      parser.nextClause()\n      return lunr.QueryParser.parseField\n    case lunr.QueryLexer.EDIT_DISTANCE:\n      return lunr.QueryParser.parseEditDistance\n    case lunr.QueryLexer.BOOST:\n      return lunr.QueryParser.parseBoost\n    case lunr.QueryLexer.PRESENCE:\n      parser.nextClause()\n      return lunr.QueryParser.parsePresence\n    default:\n      var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n  }\n}\n\nlunr.QueryParser.parseEditDistance = function (parser) {\n  var lexeme = parser.consumeLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  var editDistance = parseInt(lexeme.str, 10)\n\n  if (isNaN(editDistance)) {\n    var errorMessage = \"edit distance must be numeric\"\n    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  parser.currentClause.editDistance = editDistance\n\n  var nextLexeme = parser.peekLexeme()\n\n  if (nextLexeme == undefined) {\n    parser.nextClause()\n    return\n  }\n\n  switch (nextLexeme.type) {\n    case lunr.QueryLexer.TERM:\n      parser.nextClause()\n      return lunr.QueryParser.parseTerm\n    case lunr.QueryLexer.FIELD:\n      parser.nextClause()\n      return lunr.QueryParser.parseField\n    case lunr.QueryLexer.EDIT_DISTANCE:\n      return lunr.QueryParser.parseEditDistance\n    case lunr.QueryLexer.BOOST:\n      return lunr.QueryParser.parseBoost\n    case lunr.QueryLexer.PRESENCE:\n      parser.nextClause()\n      return lunr.QueryParser.parsePresence\n    default:\n      var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n  }\n}\n\nlunr.QueryParser.parseBoost = function (parser) {\n  var lexeme = parser.consumeLexeme()\n\n  if (lexeme == undefined) {\n    return\n  }\n\n  var boost = parseInt(lexeme.str, 10)\n\n  if (isNaN(boost)) {\n    var errorMessage = \"boost must be numeric\"\n    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n  }\n\n  parser.currentClause.boost = boost\n\n  var nextLexeme = parser.peekLexeme()\n\n  if (nextLexeme == undefined) {\n    parser.nextClause()\n    return\n  }\n\n  switch (nextLexeme.type) {\n    case lunr.QueryLexer.TERM:\n      parser.nextClause()\n      return lunr.QueryParser.parseTerm\n    case lunr.QueryLexer.FIELD:\n      parser.nextClause()\n      return lunr.QueryParser.parseField\n    case lunr.QueryLexer.EDIT_DISTANCE:\n      return lunr.QueryParser.parseEditDistance\n    case lunr.QueryLexer.BOOST:\n      return lunr.QueryParser.parseBoost\n    case lunr.QueryLexer.PRESENCE:\n      parser.nextClause()\n      return lunr.QueryParser.parsePresence\n    default:\n      var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n  }\n}\n\n  /**\n   * export the module via AMD, CommonJS or as a browser global\n   * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js\n   */\n  ;(function (root, factory) {\n    if (typeof define === 'function' && define.amd) {\n      // AMD. Register as an anonymous module.\n      define(factory)\n    } else if (typeof exports === 'object') {\n      /**\n       * Node. Does not work with strict CommonJS, but\n       * only CommonJS-like enviroments that support module.exports,\n       * like Node.\n       */\n      module.exports = factory()\n    } else {\n      // Browser globals (root is window)\n      root.lunr = factory()\n    }\n  }(this, function () {\n    /**\n     * Just return a value to define the module export.\n     * This example returns an object, but the module\n     * can return a function as the exported value.\n     */\n    return lunr\n  }))\n})();\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport lunr from \"lunr\"\n\nimport { getElement } from \"~/browser/element/_\"\nimport \"~/polyfills\"\n\nimport { Search } from \"../../_\"\nimport { SearchConfig } from \"../../config\"\nimport {\n  SearchMessage,\n  SearchMessageType\n} from \"../message\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Add support for `iframe-worker` shim\n *\n * While `importScripts` is synchronous when executed inside of a web worker,\n * it's not possible to provide a synchronous shim implementation. The cool\n * thing is that awaiting a non-Promise will convert it into a Promise, so\n * extending the type definition to return a `Promise` shouldn't break anything.\n *\n * @see https://bit.ly/2PjDnXi - GitHub comment\n *\n * @param urls - Scripts to load\n *\n * @returns Promise resolving with no result\n */\ndeclare global {\n  function importScripts(...urls: string[]): Promise<void> | void\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nlet index: Search\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch (= import) multi-language support through `lunr-languages`\n *\n * This function automatically imports the stemmers necessary to process the\n * languages which are defined as part of the search configuration.\n *\n * If the worker runs inside of an `iframe` (when using `iframe-worker` as\n * a shim), the base URL for the stemmers to be loaded must be determined by\n * searching for the first `script` element with a `src` attribute, which will\n * contain the contents of this script.\n *\n * @param config - Search configuration\n *\n * @returns Promise resolving with no result\n */\nasync function setupSearchLanguages(\n  config: SearchConfig\n): Promise<void> {\n  let base = \"../lunr\"\n\n  /* Detect `iframe-worker` and fix base URL */\n  if (typeof parent !== \"undefined\" && \"IFrameWorker\" in parent) {\n    const worker = getElement<HTMLScriptElement>(\"script[src]\")\n    const [path] = worker.src.split(\"/worker\")\n\n    /* Prefix base with path */\n    base = base.replace(\"..\", path)\n  }\n\n  /* Add scripts for languages */\n  const scripts = []\n  for (const lang of config.lang) {\n    switch (lang) {\n\n      /* Add segmenter for Japanese */\n      case \"ja\":\n        scripts.push(`${base}/tinyseg.js`)\n        break\n\n      /* Add segmenter for Hindi and Thai */\n      case \"hi\":\n      case \"th\":\n        scripts.push(`${base}/wordcut.js`)\n        break\n    }\n\n    /* Add language support */\n    if (lang !== \"en\")\n      scripts.push(`${base}/min/lunr.${lang}.min.js`)\n  }\n\n  /* Add multi-language support */\n  if (config.lang.length > 1)\n    scripts.push(`${base}/min/lunr.multi.min.js`)\n\n  /* Load scripts synchronously */\n  if (scripts.length)\n    await importScripts(\n      `${base}/min/lunr.stemmer.support.min.js`,\n      ...scripts\n    )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Message handler\n *\n * @param message - Source message\n *\n * @returns Target message\n */\nexport async function handler(\n  message: SearchMessage\n): Promise<SearchMessage> {\n  switch (message.type) {\n\n    /* Search setup message */\n    case SearchMessageType.SETUP:\n      await setupSearchLanguages(message.data.config)\n      index = new Search(message.data)\n      return {\n        type: SearchMessageType.READY\n      }\n\n    /* Search query message */\n    case SearchMessageType.QUERY:\n      const query = message.data\n      try {\n        return {\n          type: SearchMessageType.RESULT,\n          data: index.search(query)\n        }\n\n      /* Return empty result in case of error */\n      } catch (err) {\n        console.warn(`Invalid query: ${query} \u2013 see https://bit.ly/2s3ChXG`)\n        console.warn(err)\n        return {\n          type: SearchMessageType.RESULT,\n          data: { items: [] }\n        }\n      }\n\n    /* All other messages */\n    default:\n      throw new TypeError(\"Invalid message type\")\n  }\n}\n\n/* ----------------------------------------------------------------------------\n * Worker\n * ------------------------------------------------------------------------- */\n\n/* Expose Lunr.js in global scope, or stemmers won't work */\nself.lunr = lunr\n\n/* Monkey-patch Lunr.js to mitigate https://t.ly/68TLq */\nlunr.utils.warn = console.warn\n\n/* Handle messages */\naddEventListener(\"message\", async ev => {\n  postMessage(await handler(ev.data))\n})\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve all elements matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Elements\n */\nexport function getElements<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T][]\n\nexport function getElements<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T[]\n\nexport function getElements<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T[] {\n  return Array.from(node.querySelectorAll<T>(selector))\n}\n\n/**\n * Retrieve an element matching a query selector or throw a reference error\n *\n * Note that this function assumes that the element is present. If unsure if an\n * element is existent, use the `getOptionalElement` function instead.\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element\n */\nexport function getElement<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T]\n\nexport function getElement<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T\n\nexport function getElement<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T {\n  const el = getOptionalElement<T>(selector, node)\n  if (typeof el === \"undefined\")\n    throw new ReferenceError(\n      `Missing element: expected \"${selector}\" to be present`\n    )\n\n  /* Return element */\n  return el\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Retrieve an optional element matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element or nothing\n */\nexport function getOptionalElement<T extends keyof HTMLElementTagNameMap>(\n  selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T] | undefined\n\nexport function getOptionalElement<T extends HTMLElement>(\n  selector: string, node?: ParentNode\n): T | undefined\n\nexport function getOptionalElement<T extends HTMLElement>(\n  selector: string, node: ParentNode = document\n): T | undefined {\n  return node.querySelector<T>(selector) || undefined\n}\n\n/**\n * Retrieve the currently active element\n *\n * @returns Element or nothing\n */\nexport function getActiveElement(): HTMLElement | undefined {\n  return (\n    document.activeElement?.shadowRoot?.activeElement as HTMLElement ??\n    document.activeElement as HTMLElement ??\n    undefined\n  )\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Polyfills\n * ------------------------------------------------------------------------- */\n\n/* Polyfill `Object.entries` */\nif (!Object.entries)\n  Object.entries = function (obj: object) {\n    const data: [string, string][] = []\n    for (const key of Object.keys(obj))\n      // @ts-expect-error - ignore property access warning\n      data.push([key, obj[key]])\n\n    /* Return entries */\n    return data\n  }\n\n/* Polyfill `Object.values` */\nif (!Object.values)\n  Object.values = function (obj: object) {\n    const data: string[] = []\n    for (const key of Object.keys(obj))\n      // @ts-expect-error - ignore property access warning\n      data.push(obj[key])\n\n    /* Return values */\n    return data\n  }\n\n/* ------------------------------------------------------------------------- */\n\n/* Polyfills for `Element` */\nif (typeof Element !== \"undefined\") {\n\n  /* Polyfill `Element.scrollTo` */\n  if (!Element.prototype.scrollTo)\n    Element.prototype.scrollTo = function (\n      x?: ScrollToOptions | number, y?: number\n    ): void {\n      if (typeof x === \"object\") {\n        this.scrollLeft = x.left!\n        this.scrollTop = x.top!\n      } else {\n        this.scrollLeft = x!\n        this.scrollTop = y!\n      }\n    }\n\n  /* Polyfill `Element.replaceWith` */\n  if (!Element.prototype.replaceWith)\n    Element.prototype.replaceWith = function (\n      ...nodes: Array<string | Node>\n    ): void {\n      const parent = this.parentNode\n      if (parent) {\n        if (nodes.length === 0)\n          parent.removeChild(this)\n\n        /* Replace children and create text nodes */\n        for (let i = nodes.length - 1; i >= 0; i--) {\n          let node = nodes[i]\n          if (typeof node === \"string\")\n            node = document.createTextNode(node)\n          else if (node.parentNode)\n            node.parentNode.removeChild(node)\n\n          /* Replace child or insert before previous sibling */\n          if (!i)\n            parent.replaceChild(node, this)\n          else\n            parent.insertBefore(this.previousSibling!, node)\n        }\n      }\n    }\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search field\n */\nexport interface SearchField {\n  boost?: number                       /* Field boost */\n}\n\n/**\n * Search configuration\n */\nexport interface SearchConfig {\n  lang: string[]                       /* Search languages */\n  separator: string                    /* Search separator */\n  pipeline: SearchPipelineFn[]         /* Search pipeline */\n  fields: Record<string, SearchField>  /* Search field */\n}\n\n/**\n * Search document\n */\nexport interface SearchDocument {\n  location: string                     /* Document location */\n  title: string                        /* Document title */\n  text: string                         /* Document text */\n  tags?: string[]                      /* Document tags */\n  boost?: number                       /* Document boost */\n  parent?: SearchDocument              /* Document parent */\n}\n\n/**\n * Search options\n */\nexport interface SearchOptions {\n  suggest: boolean                     /* Search suggestions */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nexport interface SearchIndex {\n  config: SearchConfig                 /* Search configuration */\n  docs: SearchDocument[]               /* Search documents */\n  options: SearchOptions               /* Search options */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search pipeline function\n */\ntype SearchPipelineFn =\n  | \"trimmer\"                          /* Trimmer */\n  | \"stopWordFilter\"                   /* Stop word filter */\n  | \"stemmer\"                          /* Stemmer */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search document map\n *\n * This function creates a mapping of URLs (including anchors) to the actual\n * articles and sections. It relies on the invariant that the search index is\n * ordered with the main article appearing before all sections with anchors.\n * If this is not the case, the logic music be changed.\n *\n * @param docs - Search documents\n *\n * @returns Search document map\n */\nexport function setupSearchDocumentMap(\n  docs: SearchDocument[]\n): Map<string, SearchDocument> {\n  const map = new Map<string, SearchDocument>()\n  for (const doc of docs) {\n    const [path] = doc.location.split(\"#\")\n\n    /* Add document article */\n    const article = map.get(path)\n    if (typeof article === \"undefined\") {\n      map.set(path, doc)\n\n      /* Add document section */\n    } else {\n      map.set(doc.location, doc)\n      doc.parent = article\n    }\n  }\n\n  /* Return search document map */\n  return map\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Visitor function\n *\n * @param start - Start offset\n * @param end - End offset\n */\ntype VisitorFn = (\n  start: number, end: number\n) => void\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Split a string using the given separator\n *\n * @param input - Input value\n * @param separator - Separator\n * @param fn - Visitor function\n */\nexport function split(\n  input: string, separator: RegExp, fn: VisitorFn\n): void {\n  separator = new RegExp(separator, \"g\")\n\n  /* Split string using separator */\n  let match: RegExpExecArray | null\n  let index = 0\n  do {\n    match = separator.exec(input)\n\n    /* Emit non-empty range */\n    const until = match?.index ?? input.length\n    if (index < until)\n      fn(index, until)\n\n    /* Update last index */\n    if (match) {\n      const [term] = match\n      index = match.index + term.length\n\n      /* Support zero-length lookaheads */\n      if (term.length === 0)\n        separator.lastIndex = match.index + 1\n    }\n  } while (match)\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Extraction type\n *\n * This type defines the possible values that are encoded into the first two\n * bits of a section that is part of the blocks of a tokenization table. There\n * are three types of interest: HTML opening and closing tags, as well as the\n * actual text content we need to extract for indexing.\n */\nexport const enum Extract {\n  TAG_OPEN  = 0,                       /* HTML opening tag */\n  TEXT      = 1,                       /* Text content */\n  TAG_CLOSE = 2                        /* HTML closing tag */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Visitor function\n *\n * @param block - Block index\n * @param type - Extraction type\n * @param start - Start offset\n * @param end - End offset\n */\ntype VisitorFn = (\n  block: number, type: Extract, start: number, end: number\n) => void\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Split a string into markup and text sections\n *\n * This function scans a string and divides it up into sections of markup and\n * text. For each section, it invokes the given visitor function with the block\n * index, extraction type, as well as start and end offsets. Using a visitor\n * function (= streaming data) is ideal for minimizing pressure on the GC.\n *\n * @param input - Input value\n * @param fn - Visitor function\n */\nexport function extract(\n  input: string, fn: VisitorFn\n): void {\n\n  let block = 0                        /* Current block */\n  let start = 0                        /* Current start offset */\n  let end = 0                          /* Current end offset */\n\n  /* Split string into sections */\n  for (let stack = 0; end < input.length; end++) {\n\n    /* Opening tag after non-empty section */\n    if (input.charAt(end) === \"<\" && end > start) {\n      fn(block, Extract.TEXT, start, start = end)\n\n    /* Closing tag */\n    } else if (input.charAt(end) === \">\") {\n      if (input.charAt(start + 1) === \"/\") {\n        if (--stack === 0)\n          fn(block++, Extract.TAG_CLOSE, start, end + 1)\n\n      /* Tag is not self-closing */\n      } else if (input.charAt(end - 1) !== \"/\") {\n        if (stack++ === 0)\n          fn(block, Extract.TAG_OPEN, start, end + 1)\n      }\n\n      /* New section */\n      start = end + 1\n    }\n  }\n\n  /* Add trailing section */\n  if (end > start)\n    fn(block, Extract.TEXT, start, end)\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Position table\n */\nexport type PositionTable = number[][]\n\n/**\n * Position\n */\nexport type Position = number\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Highlight all occurrences in a string\n *\n * This function receives a field's value (e.g. like `title` or `text`), it's\n * position table that was generated during indexing, and the positions found\n * when executing the query. It then highlights all occurrences, and returns\n * their concatenation. In case of multiple blocks, two are returned.\n *\n * @param input - Input value\n * @param table - Table for indexing\n * @param positions - Occurrences\n * @param full - Full results\n *\n * @returns Highlighted string value\n */\nexport function highlight(\n  input: string, table: PositionTable, positions: Position[], full = false\n): string {\n  return highlightAll([input], table, positions, full).pop()!\n}\n\n/**\n * Highlight all occurrences in a set of strings\n *\n * @param inputs - Input values\n * @param table - Table for indexing\n * @param positions - Occurrences\n * @param full - Full results\n *\n * @returns Highlighted string values\n */\nexport function highlightAll(\n  inputs: string[], table: PositionTable, positions: Position[], full = false\n): string[] {\n\n  /* Map blocks to input values */\n  const mapping = [0]\n  for (let t = 1; t < table.length; t++) {\n    const prev = table[t - 1]\n    const next = table[t]\n\n    /* Check if table points to new block */\n    const p = prev[prev.length - 1] >>> 2 & 0x3FF\n    const q = next[0]               >>> 12\n\n    /* Add block to mapping */\n    mapping.push(+(p > q) + mapping[mapping.length - 1])\n  }\n\n  /* Highlight strings one after another */\n  return inputs.map((input, i) => {\n    let cursor = 0\n\n    /* Map occurrences to blocks */\n    const blocks = new Map<number, number[]>()\n    for (const p of positions.sort((a, b) => a - b)) {\n      const index = p & 0xFFFFF\n      const block = p >>> 20\n      if (mapping[block] !== i)\n        continue\n\n      /* Ensure presence of block group */\n      let group = blocks.get(block)\n      if (typeof group === \"undefined\")\n        blocks.set(block, group = [])\n\n      /* Add index to group */\n      group.push(index)\n    }\n\n    /* Just return string, if no occurrences */\n    if (blocks.size === 0)\n      return input\n\n    /* Compute slices */\n    const slices: string[] = []\n    for (const [block, indexes] of blocks) {\n      const t = table[block]\n\n      /* Extract positions and length */\n      const start  = t[0]            >>> 12\n      const end    = t[t.length - 1] >>> 12\n      const length = t[t.length - 1] >>> 2 & 0x3FF\n\n      /* Add prefix, if full results are desired */\n      if (full && start > cursor)\n        slices.push(input.slice(cursor, start))\n\n      /* Extract and highlight slice */\n      let slice = input.slice(start, end + length)\n      for (const j of indexes.sort((a, b) => b - a)) {\n\n        /* Retrieve offset and length of match */\n        const p = (t[j] >>> 12) - start\n        const q = (t[j] >>> 2 & 0x3FF) + p\n\n        /* Wrap occurrence */\n        slice = [\n          slice.slice(0, p),\n          \"<mark>\",\n          slice.slice(p, q),\n          \"</mark>\",\n          slice.slice(q)\n        ].join(\"\")\n      }\n\n      /* Update cursor */\n      cursor = end + length\n\n      /* Append slice and abort if we have two */\n      if (slices.push(slice) === 2)\n        break\n    }\n\n    /* Add suffix, if full results are desired */\n    if (full && cursor < input.length)\n      slices.push(input.slice(cursor))\n\n    /* Return highlighted slices */\n    return slices.join(\"\")\n  })\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { split } from \"../_\"\nimport {\n  Extract,\n  extract\n} from \"../extract\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Split a string or set of strings into tokens\n *\n * This tokenizer supersedes the default tokenizer that is provided by Lunr.js,\n * as it is aware of HTML tags and allows for multi-character splitting.\n *\n * It takes the given inputs, splits each of them into markup and text sections,\n * tokenizes and segments (if necessary) each of them, and then indexes them in\n * a table by using a compact bit representation. Bitwise techniques are used\n * to write and read from the table during indexing and querying.\n *\n * @see https://bit.ly/3W3Xw4J - Search: better, faster, smaller\n *\n * @param input - Input value(s)\n *\n * @returns Tokens\n */\nexport function tokenize(\n  input?: string | string[]\n): lunr.Token[] {\n  const tokens: lunr.Token[] = []\n  if (typeof input === \"undefined\")\n    return tokens\n\n  /* Tokenize strings one after another */\n  const inputs = Array.isArray(input) ? input : [input]\n  for (let i = 0; i < inputs.length; i++) {\n    const table = lunr.tokenizer.table\n    const total = table.length\n\n    /* Split string into sections and tokenize content blocks */\n    extract(inputs[i], (block, type, start, end) => {\n      table[block += total] ||= []\n      switch (type) {\n\n        /* Handle markup */\n        case Extract.TAG_OPEN:\n        case Extract.TAG_CLOSE:\n          table[block].push(\n            start       << 12 |\n            end - start <<  2 |\n            type\n          )\n          break\n\n        /* Handle text content */\n        case Extract.TEXT:\n          const section = inputs[i].slice(start, end)\n          split(section, lunr.tokenizer.separator, (index, until) => {\n\n            /**\n             * Apply segmenter after tokenization. Note that the segmenter will\n             * also split words at word boundaries, which is not what we want,\n             * so we need to check if we can somehow mitigate this behavior.\n             */\n            if (typeof lunr.segmenter !== \"undefined\") {\n              const subsection = section.slice(index, until)\n              if (/^[MHIK]$/.test(lunr.segmenter.ctype_(subsection))) {\n                const segments = lunr.segmenter.segment(subsection)\n                for (let s = 0, l = 0; s < segments.length; s++) {\n\n                  /* Add block to section */\n                  table[block] ||= []\n                  table[block].push(\n                    start + index + l  << 12 |\n                    segments[s].length <<  2 |\n                    type\n                  )\n\n                  /* Add token with position */\n                  tokens.push(new lunr.Token(\n                    segments[s].toLowerCase(), {\n                      position: block << 20 | table[block].length - 1\n                    }\n                  ))\n\n                  /* Keep track of length */\n                  l += segments[s].length\n                }\n                return\n              }\n            }\n\n            /* Add block to section */\n            table[block].push(\n              start + index << 12 |\n              until - index <<  2 |\n              type\n            )\n\n            /* Add token with position */\n            tokens.push(new lunr.Token(\n              section.slice(index, until).toLowerCase(), {\n                position: block << 20 | table[block].length - 1\n              }\n            ))\n          })\n      }\n    })\n  }\n\n  /* Return tokens */\n  return tokens\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Visitor function\n *\n * @param value - String value\n *\n * @returns String term(s)\n */\ntype VisitorFn = (\n  value: string\n) => string | string[]\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Default transformation function\n *\n * 1. Trim excess whitespace from left and right.\n *\n * 2. Search for parts in quotation marks and prepend a `+` modifier to denote\n *    that the resulting document must contain all parts, converting the query\n *    to an `AND` query (as opposed to the default `OR` behavior). While users\n *    may expect parts enclosed in quotation marks to map to span queries, i.e.\n *    for which order is important, Lunr.js doesn't support them, so the best\n *    we can do is to convert the parts to an `AND` query.\n *\n * 3. Replace control characters which are not located at the beginning of the\n *    query or preceded by white space, or are not followed by a non-whitespace\n *    character or are at the end of the query string. Furthermore, filter\n *    unmatched quotation marks.\n *\n * 4. Split the query string at whitespace, then pass each part to the visitor\n *    function for tokenization, and append a wildcard to every resulting term\n *    that is not explicitly marked with a `+`, `-`, `~` or `^` modifier, since\n *    it ensures consistent and stable ranking when multiple terms are entered.\n *    Also, if a fuzzy or boost modifier are given, but no numeric value has\n *    been entered, default to 1 to not induce a query error.\n *\n * @param query - Query value\n * @param fn - Visitor function\n *\n * @returns Transformed query value\n */\nexport function transform(\n  query: string, fn: VisitorFn = term => term\n): string {\n  return query\n\n    /* => 1 */\n    .trim()\n\n    /* => 2 */\n    .split(/\"([^\"]+)\"/g)\n      .map((parts, index) => index & 1\n        ? parts.replace(/^\\b|^(?![^\\x00-\\x7F]|$)|\\s+/g, \" +\")\n        : parts\n      )\n      .join(\"\")\n\n    /* => 3 */\n    .replace(/\"|(?:^|\\s+)[*+\\-:^~]+(?=\\s+|$)/g, \"\")\n\n    /* => 4 */\n    .split(/\\s+/g)\n      .reduce((prev, term) => {\n        const next = fn(term)\n        return [...prev, ...Array.isArray(next) ? next : [next]]\n      }, [] as string[])\n      .map(term => /([~^]$)/.test(term) ? `${term}1` : term)\n      .map(term => /(^[+-]|[~^]\\d+$)/.test(term) ? term : `${term}*`)\n      .join(\" \")\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { split } from \"../../internal\"\nimport { transform } from \"../transform\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search query clause\n */\nexport interface SearchQueryClause {\n  presence: lunr.Query.presence        /* Clause presence */\n  term: string                         /* Clause term */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search query terms\n */\nexport type SearchQueryTerms = Record<string, boolean>\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Transform search query\n *\n * This function lexes the given search query and applies the transformation\n * function to each term, preserving markup like `+` and `-` modifiers.\n *\n * @param query - Search query\n *\n * @returns Search query\n */\nexport function transformSearchQuery(\n  query: string\n): string {\n\n  /* Split query terms with tokenizer */\n  return transform(query, part => {\n    const terms: string[] = []\n\n    /* Initialize lexer and analyze part */\n    const lexer = new lunr.QueryLexer(part)\n    lexer.run()\n\n    /* Extract and tokenize term from lexeme */\n    for (const { type, str: term, start, end } of lexer.lexemes)\n      switch (type) {\n\n        /* Hack: remove colon - see https://bit.ly/3wD3T3I */\n        case \"FIELD\":\n          if (![\"title\", \"text\", \"tags\"].includes(term))\n            part = [\n              part.slice(0, end),\n              \" \",\n              part.slice(end + 1)\n            ].join(\"\")\n          break\n\n        /* Tokenize term */\n        case \"TERM\":\n          split(term, lunr.tokenizer.separator, (...range) => {\n            terms.push([\n              part.slice(0, start),\n              term.slice(...range),\n              part.slice(end)\n            ].join(\"\"))\n          })\n      }\n\n    /* Return terms */\n    return terms\n  })\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Parse a search query for analysis\n *\n * Lunr.js itself has a bug where it doesn't detect or remove wildcards for\n * query clauses, so we must do this here.\n *\n * @see https://bit.ly/3DpTGtz - GitHub issue\n *\n * @param value - Query value\n *\n * @returns Search query clauses\n */\nexport function parseSearchQuery(\n  value: string\n): SearchQueryClause[] {\n  const query  = new lunr.Query([\"title\", \"text\", \"tags\"])\n  const parser = new lunr.QueryParser(value, query)\n\n  /* Parse Search query */\n  parser.parse()\n  for (const clause of query.clauses) {\n    clause.usePipeline = true\n\n    /* Handle leading wildcard */\n    if (clause.term.startsWith(\"*\")) {\n      clause.wildcard = lunr.Query.wildcard.LEADING\n      clause.term = clause.term.slice(1)\n    }\n\n    /* Handle trailing wildcard */\n    if (clause.term.endsWith(\"*\")) {\n      clause.wildcard = lunr.Query.wildcard.TRAILING\n      clause.term = clause.term.slice(0, -1)\n    }\n  }\n\n  /* Return query clauses */\n  return query.clauses\n}\n\n/**\n * Analyze the search query clauses in regard to the search terms found\n *\n * @param query - Search query clauses\n * @param terms - Search terms\n *\n * @returns Search query terms\n */\nexport function getSearchQueryTerms(\n  query: SearchQueryClause[], terms: string[]\n): SearchQueryTerms {\n  const clauses = new Set<SearchQueryClause>(query)\n\n  /* Match query clauses against terms */\n  const result: SearchQueryTerms = {}\n  for (let t = 0; t < terms.length; t++)\n    for (const clause of clauses)\n      if (terms[t].startsWith(clause.term)) {\n        result[clause.term] = true\n        clauses.delete(clause)\n      }\n\n  /* Annotate unmatched non-stopword query clauses */\n  for (const clause of clauses)\n    if (lunr.stopWordFilter?.(clause.term))\n      result[clause.term] = false\n\n  /* Return query terms */\n  return result\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Segment a search query using the inverted index\n *\n * This function implements a clever approach to text segmentation for Asian\n * languages, as it used the information already available in the search index.\n * The idea is to greedily segment the search query based on the tokens that are\n * already part of the index, as described in the linked issue.\n *\n * @see https://bit.ly/3lwjrk7 - GitHub issue\n *\n * @param query - Query value\n * @param index - Inverted index\n *\n * @returns Segmented query value\n */\nexport function segment(\n  query: string, index: object\n): Iterable<string> {\n  const segments = new Set<string>()\n\n  /* Segment search query */\n  const wordcuts = new Uint16Array(query.length)\n  for (let i = 0; i < query.length; i++)\n    for (let j = i + 1; j < query.length; j++) {\n      const value = query.slice(i, j)\n      if (value in index)\n        wordcuts[i] = j - i\n    }\n\n  /* Compute longest matches with minimum overlap */\n  const stack = [0]\n  for (let s = stack.length; s > 0;) {\n    const p = stack[--s]\n    for (let q = 1; q < wordcuts[p]; q++)\n      if (wordcuts[p + q] > wordcuts[p] - q) {\n        segments.add(query.slice(p, p + q))\n        stack[s++] = p + q\n      }\n\n    /* Continue at end of query string */\n    const q = p + wordcuts[p]\n    if (wordcuts[q] && q < query.length - 1)\n      stack[s++] = q\n\n    /* Add current segment */\n    segments.add(query.slice(p, q))\n  }\n\n  // @todo fix this case in the code block above, this is a hotfix\n  if (segments.has(\"\"))\n    return new Set([query])\n\n  /* Return segmented query value */\n  return segments\n}\n", "/*\n * Copyright (c) 2016-2025 Martin Donath <martin.donath@squidfunk.com>\n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n  SearchDocument,\n  SearchIndex,\n  SearchOptions,\n  setupSearchDocumentMap\n} from \"../config\"\nimport {\n  Position,\n  PositionTable,\n  highlight,\n  highlightAll,\n  tokenize\n} from \"../internal\"\nimport {\n  SearchQueryTerms,\n  getSearchQueryTerms,\n  parseSearchQuery,\n  segment,\n  transformSearchQuery\n} from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search item\n */\nexport interface SearchItem\n  extends SearchDocument\n{\n  score: number                        /* Score (relevance) */\n  terms: SearchQueryTerms              /* Search query terms */\n}\n\n/**\n * Search result\n */\nexport interface SearchResult {\n  items: SearchItem[][]                /* Search items */\n  suggest?: string[]                   /* Search suggestions */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create field extractor factory\n *\n * @param table - Position table map\n *\n * @returns Extractor factory\n */\nfunction extractor(table: Map<string, PositionTable>) {\n  return (name: keyof SearchDocument) => {\n    return (doc: SearchDocument) => {\n      if (typeof doc[name] === \"undefined\")\n        return undefined\n\n      /* Compute identifier and initialize table */\n      const id = [doc.location, name].join(\":\")\n      table.set(id, lunr.tokenizer.table = [])\n\n      /* Return field value */\n      return doc[name]\n    }\n  }\n}\n\n/**\n * Compute the difference of two lists of strings\n *\n * @param a - 1st list of strings\n * @param b - 2nd list of strings\n *\n * @returns Difference\n */\nfunction difference(a: string[], b: string[]): string[] {\n  const [x, y] = [new Set(a), new Set(b)]\n  return [\n    ...new Set([...x].filter(value => !y.has(value)))\n  ]\n}\n\n/* ----------------------------------------------------------------------------\n * Class\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nexport class Search {\n\n  /**\n   * Search document map\n   */\n  protected map: Map<string, SearchDocument>\n\n  /**\n   * Search options\n   */\n  protected options: SearchOptions\n\n  /**\n   * The underlying Lunr.js search index\n   */\n  protected index: lunr.Index\n\n  /**\n   * Internal position table map\n   */\n  protected table: Map<string, PositionTable>\n\n  /**\n   * Create the search integration\n   *\n   * @param data - Search index\n   */\n  public constructor({ config, docs, options }: SearchIndex) {\n    const field = extractor(this.table = new Map())\n\n    /* Set up document map and options */\n    this.map = setupSearchDocumentMap(docs)\n    this.options = options\n\n    /* Set up document index */\n    this.index = lunr(function () {\n      this.metadataWhitelist = [\"position\"]\n      this.b(0)\n\n      /* Set up (multi-)language support */\n      if (config.lang.length === 1 && config.lang[0] !== \"en\") {\n        // @ts-expect-error - namespace indexing not supported\n        this.use(lunr[config.lang[0]])\n      } else if (config.lang.length > 1) {\n        this.use(lunr.multiLanguage(...config.lang))\n      }\n\n      /* Set up custom tokenizer (must be after language setup) */\n      this.tokenizer = tokenize as typeof lunr.tokenizer\n      lunr.tokenizer.separator = new RegExp(config.separator)\n\n      /* Set up custom segmenter, if loaded */\n      lunr.segmenter = \"TinySegmenter\" in lunr\n        ? new lunr.TinySegmenter()\n        : undefined\n\n      /* Compute functions to be removed from the pipeline */\n      const fns = difference([\n        \"trimmer\", \"stopWordFilter\", \"stemmer\"\n      ], config.pipeline)\n\n      /* Remove functions from the pipeline for registered languages */\n      for (const lang of config.lang.map(language => (\n        // @ts-expect-error - namespace indexing not supported\n        language === \"en\" ? lunr : lunr[language]\n      )))\n        for (const fn of fns) {\n          this.pipeline.remove(lang[fn])\n          this.searchPipeline.remove(lang[fn])\n        }\n\n      /* Set up index reference */\n      this.ref(\"location\")\n\n      /* Set up index fields */\n      for (const [name, spec] of Object.entries(config.fields))\n        // @ts-expect-error - fix typings, if this proves to be a good idea\n        this.field(name, { ...spec, extractor: field(name) })\n\n      /* Add documents to index */\n      for (const doc of docs)\n        this.add(doc, { boost: doc.boost })\n    })\n  }\n\n  /**\n   * Search for matching documents\n   *\n   * @param query - Search query\n   *\n   * @returns Search result\n   */\n  public search(query: string): SearchResult {\n\n    // Experimental Chinese segmentation\n    query = query.replace(/\\p{sc=Han}+/gu, value => {\n      return [...segment(value, this.index.invertedIndex)]\n        .join(\"* \")\n    })\n\n    // @todo: move segmenter (above) into transformSearchQuery\n    query = transformSearchQuery(query)\n    if (!query)\n      return { items: [] }\n\n    /* Parse query to extract clauses for analysis */\n    const clauses = parseSearchQuery(query)\n      .filter(clause => (\n        clause.presence !== lunr.Query.presence.PROHIBITED\n      ))\n\n    /* Perform search and post-process results */\n    const groups = this.index.search(query)\n\n      /* Apply post-query boosts based on title and search query terms */\n      .reduce<SearchItem[]>((item, { ref, score, matchData }) => {\n        let doc = this.map.get(ref)\n        if (typeof doc !== \"undefined\") {\n\n          /* Shallow copy document */\n          doc = { ...doc }\n          if (doc.tags)\n            doc.tags = [...doc.tags]\n\n          /* Compute and analyze search query terms */\n          const terms = getSearchQueryTerms(\n            clauses,\n            Object.keys(matchData.metadata)\n          )\n\n          /* Highlight matches in fields */\n          for (const field of this.index.fields) {\n            if (typeof doc[field] === \"undefined\")\n              continue\n\n            /* Collect positions from matches */\n            const positions: Position[] = []\n            for (const match of Object.values(matchData.metadata))\n              if (typeof match[field] !== \"undefined\")\n                positions.push(...match[field].position)\n\n            /* Skip highlighting, if no positions were collected */\n            if (!positions.length)\n              continue\n\n            /* Load table and determine highlighting method */\n            const table = this.table.get([doc.location, field].join(\":\"))!\n            const fn = Array.isArray(doc[field])\n              ? highlightAll\n              : highlight\n\n            // @ts-expect-error - stop moaning, TypeScript!\n            doc[field] = fn(doc[field], table, positions, field !== \"text\")\n          }\n\n          /* Highlight title and text and apply post-query boosts */\n          const boost = +!doc.parent +\n            Object.values(terms)\n              .filter(t => t).length /\n            Object.keys(terms).length\n\n          /* Append item */\n          item.push({\n            ...doc,\n            score: score * (1 + boost ** 2),\n            terms\n          })\n        }\n        return item\n      }, [])\n\n      /* Sort search results again after applying boosts */\n      .sort((a, b) => b.score - a.score)\n\n      /* Group search results by article */\n      .reduce((items, result) => {\n        const doc = this.map.get(result.location)\n        if (typeof doc !== \"undefined\") {\n          const ref = doc.parent\n            ? doc.parent.location\n            : doc.location\n          items.set(ref, [...items.get(ref) || [], result])\n        }\n        return items\n      }, new Map<string, SearchItem[]>())\n\n    /* Ensure that every item set has an article */\n    for (const [ref, items] of groups)\n      if (!items.find(item => item.location === ref)) {\n        const doc = this.map.get(ref)!\n        items.push({ ...doc, score: 0, terms: {} })\n      }\n\n    /* Generate search suggestions, if desired */\n    let suggest: string[] | undefined\n    if (this.options.suggest) {\n      const titles = this.index.query(builder => {\n        for (const clause of clauses)\n          builder.term(clause.term, {\n            fields: [\"title\"],\n            presence: lunr.Query.presence.REQUIRED,\n            wildcard: lunr.Query.wildcard.TRAILING\n          })\n      })\n\n      /* Retrieve suggestions for best match */\n      suggest = titles.length\n        ? Object.keys(titles[0].matchData.metadata)\n        : []\n    }\n\n    /* Return search result */\n    return {\n      items: [...groups.values()],\n      ...typeof suggest !== \"undefined\" && { suggest }\n    }\n  }\n}\n"],
+  "mappings": 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diff --git a/docs/htmls/assets/stylesheets/palette.ab4e12ef.min.css b/docs/htmls/assets/stylesheets/palette.ab4e12ef.min.css
new file mode 100644
index 0000000..75aaf84
--- /dev/null
+++ b/docs/htmls/assets/stylesheets/palette.ab4e12ef.min.css
@@ -0,0 +1 @@
+@media screen{[data-md-color-scheme=slate]{--md-default-fg-color:hsla(var(--md-hue),15%,90%,0.82);--md-default-fg-color--light:hsla(var(--md-hue),15%,90%,0.56);--md-default-fg-color--lighter:hsla(var(--md-hue),15%,90%,0.32);--md-default-fg-color--lightest:hsla(var(--md-hue),15%,90%,0.12);--md-default-bg-color:hsla(var(--md-hue),15%,14%,1);--md-default-bg-color--light:hsla(var(--md-hue),15%,14%,0.54);--md-default-bg-color--lighter:hsla(var(--md-hue),15%,14%,0.26);--md-default-bg-color--lightest:hsla(var(--md-hue),15%,14%,0.07);--md-code-fg-color:hsla(var(--md-hue),18%,86%,0.82);--md-code-bg-color:hsla(var(--md-hue),15%,18%,1);--md-code-bg-color--light:hsla(var(--md-hue),15%,18%,0.9);--md-code-bg-color--lighter:hsla(var(--md-hue),15%,18%,0.54);--md-code-hl-color:#2977ff;--md-code-hl-color--light:#2977ff1a;--md-code-hl-number-color:#e6695b;--md-code-hl-special-color:#f06090;--md-code-hl-function-color:#c973d9;--md-code-hl-constant-color:#9383e2;--md-code-hl-keyword-color:#6791e0;--md-code-hl-string-color:#2fb170;--md-code-hl-name-color:var(--md-code-fg-color);--md-code-hl-operator-color:var(--md-default-fg-color--light);--md-code-hl-punctuation-color:var(--md-default-fg-color--light);--md-code-hl-comment-color:var(--md-default-fg-color--light);--md-code-hl-generic-color:var(--md-default-fg-color--light);--md-code-hl-variable-color:var(--md-default-fg-color--light);--md-typeset-color:var(--md-default-fg-color);--md-typeset-a-color:var(--md-primary-fg-color);--md-typeset-kbd-color:hsla(var(--md-hue),15%,90%,0.12);--md-typeset-kbd-accent-color:hsla(var(--md-hue),15%,90%,0.2);--md-typeset-kbd-border-color:hsla(var(--md-hue),15%,14%,1);--md-typeset-mark-color:#4287ff4d;--md-typeset-table-color:hsla(var(--md-hue),15%,95%,0.12);--md-typeset-table-color--light:hsla(var(--md-hue),15%,95%,0.035);--md-admonition-fg-color:var(--md-default-fg-color);--md-admonition-bg-color:var(--md-default-bg-color);--md-footer-bg-color:hsla(var(--md-hue),15%,10%,0.87);--md-footer-bg-color--dark:hsla(var(--md-hue),15%,8%,1);--md-shadow-z1:0 0.2rem 0.5rem #0000000d,0 0 0.05rem #0000001a;--md-shadow-z2:0 0.2rem 0.5rem #00000040,0 0 0.05rem #00000040;--md-shadow-z3:0 0.2rem 0.5rem #0006,0 0 0.05rem #00000059;color-scheme:dark}[data-md-color-scheme=slate] img[src$="#gh-light-mode-only"],[data-md-color-scheme=slate] 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diff --git a/docs/htmls/en/active_learning_workflow.html b/docs/htmls/en/active_learning_workflow.html
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+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
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+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#1-slurm-directives" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        1. SLURM Directives
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#2-basic-setup" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        2. Basic Setup
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#3-variable-definitions" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        3. Variable Definitions
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#4-check-required-files" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        4. Check Required Files
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#5-file-organization" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        5. File Organization
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#6-molecular-dynamics-simulation-submission" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        6. Molecular Dynamics Simulation Submission
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#7-monitoring-task-completion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        7. Monitoring Task Completion
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#8-analysis-and-filtering" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        8. Analysis and Filtering
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#9-sampling-methods" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        9. Sampling Methods
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#10-scf-calculations" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        10. SCF Calculations
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#11-prediction-step" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        11. Prediction Step
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
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+      <a href="polar_material_analysis.html" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
+  
+    Polar Material Analysis
+  
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+  
+  
+
+      </a>
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+
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+    GPUMDkit 教程
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+  
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+    
+  
+    快速入门
+  
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+  
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
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+  </span>
+  
+  
+
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+    </li>
+  
+
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
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+  
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+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
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+  
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+  
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
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+            
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
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+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#1-slurm-directives" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        1. SLURM Directives
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#2-basic-setup" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        2. Basic Setup
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#3-variable-definitions" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        3. Variable Definitions
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#4-check-required-files" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        4. Check Required Files
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#5-file-organization" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        5. File Organization
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#6-molecular-dynamics-simulation-submission" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        6. Molecular Dynamics Simulation Submission
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#7-monitoring-task-completion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        7. Monitoring Task Completion
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#8-analysis-and-filtering" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        8. Analysis and Filtering
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#9-sampling-methods" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        9. Sampling Methods
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#10-scf-calculations" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        10. SCF Calculations
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#11-prediction-step" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        11. Prediction Step
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🔁 Active Learning Workflow</h1>
+  <p style="text-align: justify;">This tutorial explains the steps and considerations involved in the <code>workflow_active_learning_dev.sh</code> script. The workflow is used to generate, select, and analyze molecular structures, followed by simulations and data collection.</p>
+</div>
+
+<h3 id="overview">Overview</h3>
+<p>This script is designed to handle molecular dynamics simulations, sampling, and SCF (self-consistent field) calculations for NEP. Below is a step-by-step guide explaining how the script works and what each part does.</p>
+<h3 id="1-slurm-directives">1. <strong>SLURM Directives</strong></h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>#!/bin/bash -l
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>#SBATCH -p intel-sc3,intel-sc3-32c
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>#SBATCH -q huge
+<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>#SBATCH -N 1
+<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a>#SBATCH -J workflow
+<a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a>#SBATCH -o workflow.log
+<a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a>#SBATCH --ntasks-per-node=1
+</code></pre></div>
+<p>The SLURM directives are used to define how the job will be submitted to the cluster:</p>
+<ul>
+<li><code>#SBATCH -p</code> defines the partition, in this case, it's <code>intel-sc3</code> and <code>intel-sc3-32c</code>.</li>
+<li><code>#SBATCH -q</code> specifies the queue, in this case, <code>huge</code>.</li>
+<li><code>#SBATCH -N</code> allocates 1 node for the job.</li>
+<li><code>#SBATCH -J</code> names the job <code>workflow</code>.</li>
+<li><code>#SBATCH -o</code> defines the output log file as <code>workflow.log</code>.</li>
+<li><code>--ntasks-per-node=1</code> specifies that only one task should run per node.</li>
+</ul>
+<p><strong><u>NOTE:</u></strong> If your machine does not have the SLURM environment, you can also run the script directly from the command line. For example:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>nohup bash workflow_active_learning_dev.sh &amp;&gt;workflow.log &amp;
+</code></pre></div>
+<h3 id="2-basic-setup">2. <strong>Basic Setup</strong></h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>cd $SLURM_SUBMIT_DIR 
+</code></pre></div>
+<p>Ensure the working directory is correct, and that all necessary files are present for the job.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  # Load the submit template
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>python_pynep=python  # Python executable for the deprecated pynep branch if needed
+</code></pre></div>
+<ul>
+<li><code>GPUMDkit_path</code> is the environment variable that stores the path for the <code>GPUMDkit</code> .</li>
+<li><code>python_pynep</code> points to the Python environment used for the deprecated <code>pynep</code>-related branch if needed.</li>
+</ul>
+<hr />
+<h3 id="3-variable-definitions">3. <strong>Variable Definitions</strong></h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>work_dir=${PWD}  # Set the working directory
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>prefix_name=LiF_iter01  # Prefix for calculations
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>min_dist=1.4  # Minimum atom distance
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a>box_limit=13  # Simulation box limit
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>max_fp_num=50  # Maximum number of single point calculations
+<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a>sample_method=pynep  # Sampling method (options: uniform, random, pynep)
+<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a>pynep_sample_dist=0.01  # Sampling distance for pynep
+</code></pre></div>
+<p>You can customize:</p>
+<ul>
+<li><code>prefix_name</code> to reflect the name of your current work.</li>
+<li><code>min_dist</code>, <code>box_limit</code>, and <code>max_fp_num</code> based on your own system.</li>
+<li><code>sample_method</code> (choose between <code>uniform</code>, <code>random</code>, or <code>pynep</code>).</li>
+<li><code>pynep_sample_dist</code> is the sampling distance for <code>pynep</code>.</li>
+</ul>
+<hr />
+<h3 id="4-check-required-files">4. <strong>Check Required Files</strong></h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ -f run.in ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>    # Check for the required files before proceeding.
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>else
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>    echo &quot;Please put nep.in nep.txt train.xyz run.in INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.&quot;
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>    exit 1
+<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>fi
+</code></pre></div>
+<p>Make sure the necessary files (<code>nep.txt</code>, <code>nep.in</code>, <code>train.xyz</code>, <code>run.in</code>, <code>INCAR</code>, <code>POTCAR</code>, <code>KPOINTS</code>) are available in the working directory. If any of these are missing, the script will terminate. <code>train.xyz</code> and <code>nep.txt</code> are used for <code>pynep</code> sampling, and <code>run.in</code> is the simulation parameters of MD in the current iteration.</p>
+<hr />
+<h3 id="5-file-organization">5. <strong>File Organization</strong></h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>mkdir 00.modev common
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>mv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>cp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev
+</code></pre></div>
+<p>The script organizes the working files into two folders:</p>
+<ul>
+<li><code>00.modev</code>: For molecular dynamics simulation.</li>
+<li><code>common</code>: For shared resources such as <code>nep.txt</code>, <code>run.in</code>, and the structure files, etc.</li>
+</ul>
+<hr />
+<h3 id="6-molecular-dynamics-simulation-submission">6. <strong>Molecular Dynamics Simulation Submission</strong></h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>submit_gpumd_array modev ${sample_struct_num}
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>sbatch submit.slurm
+</code></pre></div>
+<p>After preparing the input files, the script submits an array of molecular dynamics (MD) tasks using <code>submit_gpumd_array</code>.</p>
+<hr />
+<h3 id="7-monitoring-task-completion">7. <strong>Monitoring Task Completion</strong></h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>while true; do
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>    logs=$(find &quot;${work_dir}/00.modev/&quot; -type f -name log -path &quot;*/sample_*/log&quot;)
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>    finished_tasks_md=$(grep &quot;Finished running GPUMD.&quot; $logs | wc -l)
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>    error_tasks_md=$(grep &quot;Error&quot; $logs | wc -l)
+<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a>
+<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>    if [ &quot;$error_tasks_md&quot; -ne 0 ]; then
+<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a>        echo &quot;Error: MD simulation encountered an error.&quot;
+<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a>        exit 1
+<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a>    fi
+<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a>    if [ $finished_tasks_md -eq $sample_struct_num ]; then
+<a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a>        break
+<a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></a>    fi
+<a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a>    sleep 30
+<a id="__codelineno-8-14" name="__codelineno-8-14" href="#__codelineno-8-14"></a>done
+</code></pre></div>
+<p>The script continuously checks whether all MD tasks have finished by searching for a <code>Finished running GPUMD.</code> message in the logs. If an error is encountered, the script terminates.</p>
+<hr />
+<h3 id="8-analysis-and-filtering">8. <strong>Analysis and Filtering</strong></h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>mkdir ${work_dir}/01.select
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>...
+</code></pre></div>
+<p>In the <code>01.select</code> folder, all structures in the trajectory file <code>dump.xyz</code> during the MD process will be analyzed and filtered to avoid the generation of non-physical structures as much as possible. Specifically, the <code>get_min_dist.py</code>, <code>filter_structures_by_distance.py</code> and <code>filter_exyz_by_box.py</code> scripts will be employed to check whether there are situations where the distance between atoms is too close or the simulated box exceeds the limit value, and such structures will be filtered out.</p>
+<hr />
+<h3 id="9-sampling-methods">9. <strong>Sampling Methods</strong></h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>case $sample_method in
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>    &quot;uniform&quot;)
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>    &quot;random&quot;)
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a>    &quot;pynep&quot;)
+</code></pre></div>
+<p>The script supports three sampling methods: <code>uniform</code>, <code>random</code>, and <code>pynep</code>. It selects structures according to the chosen method and checks if the number exceeds <code>max_fp_num</code>, ensuring the final structure count is within limits.</p>
+<hr />
+<h3 id="10-scf-calculations">10. <strong>SCF Calculations</strong></h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>submit_vasp_array scf ${selected_struct_num} ${prefix_name}
+</code></pre></div>
+<p>After sampling, SCF calculations are submitted using <code>submit_vasp_array</code>. The process is similar to the MD submission, but for SCF calculations.</p>
+<hr />
+<h3 id="11-prediction-step">11. <strong>Prediction Step</strong></h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>submit_nep_prediction
+</code></pre></div>
+<p>The final step involves submitting the NEP prediction task to check  the accuracy of the NEP model. </p>
+<hr />
+<p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>
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diff --git a/docs/htmls/en/analyzer_scripts.html b/docs/htmls/en/analyzer_scripts.html
new file mode 100644
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+    Analyzer Scripts
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+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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+      <span class="md-nav__icon md-icon"></span>
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+      
+        <li class="md-nav__item">
+  <a href="#overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#composition-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Composition Analysis
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#property-range-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Property Range Analysis
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#minimum-distance-checks" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Minimum Distance Checks
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#filtering-structures" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Filtering Structures
+      
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+  
+    <nav class="md-nav" aria-label="Filtering Structures">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#filter-by-minimum-distance" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Filter by Minimum Distance
+      
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+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#filter-by-box-size" class="md-nav__link">
+    <span class="md-ellipsis">
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+        Filter by Box Size
+      
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+        
+          <li class="md-nav__item">
+  <a href="#filter-by-property-value" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+      
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+        
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+  <a href="#filter-by-pair-distance-range" class="md-nav__link">
+    <span class="md-ellipsis">
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+      
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+  <a href="#charge-balance-check" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Charge Balance Check
+      
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+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-commands" class="md-nav__link">
+    <span class="md-ellipsis">
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+      <a href="plot_scripts.html" class="md-nav__link">
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+      <a href="custom_commands.html" class="md-nav__link">
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+    
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+      <a href="polar_material_analysis.html" class="md-nav__link">
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+    Polar Material Analysis
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+    
+  
+    Contributing to GPUMDkit
+  
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+    GPUMDkit 教程
+  
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+    
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+    快速入门
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+      <a href="../zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
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+  </span>
+  
+  
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+    </li>
+  
+
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+            
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+  
+  
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+      <a href="../zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
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+  
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+      <a href="../zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
+  
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+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
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+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
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+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#composition-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Composition Analysis
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#property-range-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Property Range Analysis
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#minimum-distance-checks" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Minimum Distance Checks
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#filtering-structures" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Filtering Structures
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Filtering Structures">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#filter-by-minimum-distance" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Filter by Minimum Distance
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#filter-by-box-size" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Filter by Box Size
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#filter-by-property-value" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Filter by Property Value
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#filter-by-pair-distance-range" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Filter by Pair-Distance Range
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#charge-balance-check" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Charge Balance Check
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-commands" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example Commands
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
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+            
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+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🔍 Analyzer Scripts</h1>
+  <p style="text-align: justify;">Analyzer scripts provide structure statistics, distance checks, filters, and composition analysis for extxyz datasets.</p>
+</div>
+
+<p><strong>Script Location:</strong> <code>Scripts/analyzer/</code></p>
+<h2 id="overview">Overview</h2>
+<table>
+<thead>
+<tr>
+<th>Task</th>
+<th>Command</th>
+<th>Purpose</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>Composition</td>
+<td><code>gpumdkit.sh -analyze_comp train.xyz</code></td>
+<td>group structures by chemical composition</td>
+</tr>
+<tr>
+<td>Chemical species</td>
+<td><code>gpumdkit.sh -chem_species train.xyz</code></td>
+<td>list species in a file</td>
+</tr>
+<tr>
+<td>Property range</td>
+<td><code>gpumdkit.sh -range train.xyz force</code></td>
+<td>inspect energy/force/virial range</td>
+</tr>
+<tr>
+<td>Minimum distance</td>
+<td><code>gpumdkit.sh -min_dist dump.xyz</code></td>
+<td>fast distance check without PBC</td>
+</tr>
+<tr>
+<td>Minimum distance with PBC</td>
+<td><code>gpumdkit.sh -min_dist_pbc dump.xyz</code></td>
+<td>accurate distance check with PBC</td>
+</tr>
+<tr>
+<td>Charge balance</td>
+<td><code>gpumdkit.sh -cbc train.xyz</code></td>
+<td>oxidation-state balance check</td>
+</tr>
+<tr>
+<td>Distance filter</td>
+<td><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code></td>
+<td>remove structures with short contacts</td>
+</tr>
+<tr>
+<td>Box filter</td>
+<td><code>gpumdkit.sh -filter_box dump.xyz 13</code></td>
+<td>remove structures with too-large box edges</td>
+</tr>
+<tr>
+<td>Property filter</td>
+<td><code>gpumdkit.sh -filter_value train.xyz force 20</code></td>
+<td>filter by energy/force/virial threshold</td>
+</tr>
+<tr>
+<td>Pair-distance range</td>
+<td><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code></td>
+<td>extract structures by pair distance</td>
+</tr>
+</tbody>
+</table>
+<h2 id="composition-analysis">Composition Analysis</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
+</code></pre></div>
+<p>Example output:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>Index    Compositions           N atoms      Count
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>---------------------------------------------------
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>1        Li56O96Zr16La24        192          51
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>---------------------------------------------------
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>Enter index to export (e.g., &#39;1,2&#39;, &#39;2-3&#39;, &#39;all&#39;), or press Enter to skip:
+</code></pre></div>
+<p>This is useful when <code>train.xyz</code> contains structures from different systems or different cell sizes. You can export a subset by composition from the interactive prompt.</p>
+<h2 id="property-range-analysis">Property Range Analysis</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>energy
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>virial
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist
+</code></pre></div>
+<p>Use <code>hist</code> to show a histogram of the selected property.</p>
+<div align="center">
+  <img src="../../Gallery/range_force.png" alt="Force range histogram" width="52%" />
+</div>
+
+<h2 id="minimum-distance-checks">Minimum Distance Checks</h2>
+<p>Fast check without PBC:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist<span class="w"> </span>dump.xyz
+</code></pre></div>
+<p>Accurate check with PBC:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
+</code></pre></div>
+<p>Typical output:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>Minimum interatomic distances (with PBC):
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>+---------------------------+
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>| Atom Pair |  Distance (A) |
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>+---------------------------+
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>|   Li-Li   |     1.696     |
+<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>|   Li-O    |     1.587     |
+<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>|   O-O     |     2.355     |
+<a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a>+---------------------------+
+<a id="__codelineno-5-9" name="__codelineno-5-9" href="#__codelineno-5-9"></a>Overall min_distance: 1.587 A
+</code></pre></div>
+<p>The PBC version considers periodic boundary conditions.</p>
+<h2 id="filtering-structures">Filtering Structures</h2>
+<h3 id="filter-by-minimum-distance">Filter by Minimum Distance</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
+</code></pre></div>
+<p>This removes structures with any interatomic distance below <code>1.0 A</code>.</p>
+<h3 id="filter-by-box-size">Filter by Box Size</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
+</code></pre></div>
+<p>This filters structures by box-edge length.</p>
+<h3 id="filter-by-property-value">Filter by Property Value</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span><span class="m">20</span>
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>energy<span class="w"> </span><span class="m">5</span>
+</code></pre></div>
+<h3 id="filter-by-pair-distance-range">Filter by Pair-Distance Range</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-filter_range<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>.8<span class="w"> </span><span class="m">2</span>.0
+</code></pre></div>
+<p>This extracts structures where the Li-Li minimum distance is between <code>1.8 A</code> and <code>2.0 A</code>.</p>
+<h2 id="charge-balance-check">Charge Balance Check</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-cbc<span class="w"> </span>train.xyz
+</code></pre></div>
+<p>Outputs may include:</p>
+<ul>
+<li><code>balanced.xyz</code></li>
+<li><code>unbalanced.xyz</code></li>
+<li><code>indices.txt</code></li>
+</ul>
+<p>This is intended for systems where common oxidation states are meaningful.</p>
+<h2 id="example-commands">Example Commands</h2>
+<p>Property and distance checks:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>energy<span class="w"> </span>hist
+<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>train.xyz
+</code></pre></div>
+<p>Filtering examples:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>filtered_dist.xyz<span class="w"> </span><span class="m">13</span>
+</code></pre></div>
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diff --git a/docs/htmls/en/calculator_scripts.html b/docs/htmls/en/calculator_scripts.html
new file mode 100644
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+      <a href="format_conversion.html" class="md-nav__link">
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+      <a href="structure_sampling.html" class="md-nav__link">
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+    Structure Sampling
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+      <a href="workflow_scripts.html" class="md-nav__link">
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+    Workflow Scripts
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+    Calculator Scripts
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+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#ionic-conductivity" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Ionic Conductivity
+      
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+  </a>
+  
+    <nav class="md-nav" aria-label="Ionic Conductivity">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#required-and-optional-files" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Required and Optional Files
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#usage" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#example-output" class="md-nav__link">
+    <span class="md-ellipsis">
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+        Example Output
+      
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#mean-square-displacement" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Mean Square Displacement
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep-property-prediction" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP Property Prediction
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep-descriptors" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP Descriptors
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#density-of-atomistic-states" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Density of Atomistic States
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#neb-with-a-nep-model" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEB with a NEP Model
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#structure-minimization" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Structure Minimization
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#ferroelectric-and-polar-material-tools" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Ferroelectric and Polar Material Tools
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Ferroelectric and Polar Material Tools">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#build-neighbor-lists" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Build Neighbor Lists
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#calculate-displacements" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Calculate Displacements
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#average-a-structure" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Average a Structure
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#octahedral-tilt" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Octahedral Tilt
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#abo3-polarization" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        ABO3 Polarization
+      
+    </span>
+  </a>
+  
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+      
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+      <a href="analyzer_scripts.html" class="md-nav__link">
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+    
+  
+    Analyzer Scripts
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+  
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+      <a href="plot_scripts.html" class="md-nav__link">
+        
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+  
+    Plot Scripts
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+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="polar_material_analysis.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Polar Material Analysis
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="contributing_to_gpumdkit.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        
+          
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    简体中文
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    简体中文
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/index.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit 教程
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#ionic-conductivity" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Ionic Conductivity
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Ionic Conductivity">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#required-and-optional-files" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Required and Optional Files
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#usage" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#example-output" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example Output
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#mean-square-displacement" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Mean Square Displacement
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep-property-prediction" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP Property Prediction
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep-descriptors" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP Descriptors
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#density-of-atomistic-states" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Density of Atomistic States
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#neb-with-a-nep-model" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEB with a NEP Model
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#structure-minimization" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Structure Minimization
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#ferroelectric-and-polar-material-tools" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Ferroelectric and Polar Material Tools
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Ferroelectric and Polar Material Tools">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#build-neighbor-lists" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Build Neighbor Lists
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#calculate-displacements" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Calculate Displacements
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#average-a-structure" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Average a Structure
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#octahedral-tilt" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Octahedral Tilt
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#abo3-polarization" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        ABO3 Polarization
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🧮 Calculator Scripts</h1>
+  <p style="text-align: justify;">The calculator module contains scripts for computing properties from MD trajectories, NEP models, and structure files.</p>
+</div>
+
+<p><strong>Script Location:</strong> <code>Scripts/calculators/</code></p>
+<h2 id="overview">Overview</h2>
+<table>
+<thead>
+<tr>
+<th>Task</th>
+<th>Command</th>
+<th>Main Input</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>Ionic conductivity</td>
+<td><code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code></td>
+<td><code>msd.out</code>, <code>thermo.out</code>, <code>model.xyz</code></td>
+</tr>
+<tr>
+<td>MSD from trajectory</td>
+<td><code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code></td>
+<td>extxyz trajectory</td>
+</tr>
+<tr>
+<td>NEP prediction</td>
+<td><code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code></td>
+<td>extxyz + NEP model</td>
+</tr>
+<tr>
+<td>NEP descriptors</td>
+<td><code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code></td>
+<td>extxyz + NEP model</td>
+</tr>
+<tr>
+<td>DOAS</td>
+<td><code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code></td>
+<td>extxyz + NEP model</td>
+</tr>
+<tr>
+<td>NEB</td>
+<td><code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code></td>
+<td>initial/final structures</td>
+</tr>
+<tr>
+<td>Minimization</td>
+<td><code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code></td>
+<td>structure + NEP model</td>
+</tr>
+<tr>
+<td>Neighbor list</td>
+<td><code>gpumdkit.sh -calc nlist [args...]</code></td>
+<td>structure</td>
+</tr>
+<tr>
+<td>Displacement</td>
+<td><code>gpumdkit.sh -calc disp [args...]</code></td>
+<td>trajectory + neighbor list</td>
+</tr>
+<tr>
+<td>Average structure</td>
+<td><code>gpumdkit.sh -calc avg-struct [args...]</code></td>
+<td>trajectory</td>
+</tr>
+<tr>
+<td>Octahedral tilt</td>
+<td><code>gpumdkit.sh -calc oct-tilt [args...]</code></td>
+<td>trajectory + B-O neighbor list</td>
+</tr>
+<tr>
+<td>ABO3 polarization</td>
+<td><code>gpumdkit.sh -calc pol-abo3 [args...]</code></td>
+<td>trajectory + neighbor lists</td>
+</tr>
+</tbody>
+</table>
+<p>For a full command list:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>-h
+</code></pre></div>
+<p>The command-line help table looks like:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>|                                      CALCULATOR TOOLS                                                 |
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |
+<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a>| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |
+<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a>| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |
+<a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a>| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |
+<a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a>| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |
+<a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a>| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |
+<a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a>| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |
+<a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a>| nlist [script args...]                        Build neighbor lists                                    |
+<a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></a>| disp [script args...]                         Calculate displacement from trajectory                  |
+<a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a>| avg-struct [script args...]                   Calculate averaged structure                            |
+<a id="__codelineno-1-16" name="__codelineno-1-16" href="#__codelineno-1-16"></a>| oct-tilt [script args...]                     Calculate octahedral tilt                               |
+<a id="__codelineno-1-17" name="__codelineno-1-17" href="#__codelineno-1-17"></a>| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |
+<a id="__codelineno-1-18" name="__codelineno-1-18" href="#__codelineno-1-18"></a>+-------------------------------------------------------------------------------------------------------+
+</code></pre></div>
+<p>In interactive mode, choose <code>4) Calculators</code>. The menu is:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>|                     CALCULATOR TOOLS                     |
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>| 401) Calc ionic conductivity                             |
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>| 402) Calc properties by nep                              |
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>| 403) Calc descriptors of specific elements               |
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>| 404) Calc density of atomistic states (DOAS)             |
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>| 405) Calc nudged elastic band (NEB) by nep               |
+<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>| 406) Build neighbor list                                 |
+<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a>| 407) Calc displacement from trajectory                   |
+<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a>| 408) Calc averaged structure                             |
+<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a>| 409) Calc octahedral tilt                                |
+<a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a>| 410) Calc polarization for ABO3                          |
+<a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a>| 411) Minimize structure by nep                           |
+<a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a>| 412) Calc mean square displacement (MSD) from trajectory |
+<a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-17" name="__codelineno-2-17" href="#__codelineno-2-17"></a>| 000) Return to the main menu                             |
+<a id="__codelineno-2-18" name="__codelineno-2-18" href="#__codelineno-2-18"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-19" name="__codelineno-2-19" href="#__codelineno-2-19"></a>Input the function number:
+</code></pre></div>
+<h2 id="ionic-conductivity">Ionic Conductivity</h2>
+<p><code>calc_ion_conductivity.py</code> calculates ionic diffusivity and conductivity from <code>msd.out</code>.</p>
+<h3 id="required-and-optional-files">Required and Optional Files</h3>
+<table>
+<thead>
+<tr>
+<th>File</th>
+<th>Role</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>msd.out</code></td>
+<td>Required MSD data</td>
+</tr>
+<tr>
+<td><code>thermo.out</code></td>
+<td>Optional, used for automatic temperature detection</td>
+</tr>
+<tr>
+<td><code>model.xyz</code></td>
+<td>Optional, used for volume and ion-count detection</td>
+</tr>
+<tr>
+<td><code>run.in</code></td>
+<td>Optional, used to detect replication</td>
+</tr>
+</tbody>
+</table>
+<h3 id="usage">Usage</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>ionic-cond<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>
+</code></pre></div>
+<p>From interactive mode, choose <code>401</code>. You will see:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>| This function calls the script in calculators   |
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>| Script: calc_ion_conductivity.py                |
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a>| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a>Input &lt;element&gt; &lt;charge&gt; (eg. Li 1)
+<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a>------------&gt;&gt;
+</code></pre></div>
+<p>If automatic files are missing, the script will ask for temperature, volume, and ion count interactively.</p>
+<p>Interactive prompts in manual mode look like:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>Files &#39;thermo.out&#39; and &#39;model.xyz&#39; are not found.
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>Please provide the following values:
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>---------------------------&gt;
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>Enter average temperature (in K):
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>Enter system volume (in A^3):
+<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>Enter number of ions:
+</code></pre></div>
+<h3 id="example-output">Example Output</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>Diffusivity (D):
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>  D_x: 4.153e-07 cm^2/s
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>  D_y: 4.174e-07 cm^2/s
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>  D_z: 2.610e-07 cm^2/s
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a>  D_total: 3.646e-07 cm^2/s
+<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>------------------------------
+<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a>Ionic Conductivity:
+<a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a>  Sigma_x: 2.576e-02 mS/cm
+<a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a>  Sigma_y: 2.589e-02 mS/cm
+<a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a>  Sigma_z: 1.619e-02 mS/cm
+<a id="__codelineno-6-11" name="__codelineno-6-11" href="#__codelineno-6-11"></a>  Sigma_total: 2.261e-02 mS/cm
+</code></pre></div>
+<h2 id="mean-square-displacement">Mean Square Displacement</h2>
+<p><code>calc_msd.py</code> computes MSD directly from an extxyz trajectory.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">5000</span>
+</code></pre></div>
+<p>From interactive mode, choose <code>412</code>. You will see:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>  Optional argument: max_corr_steps (default: frame number)
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>Example: dump.xyz Li 10
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>------------&gt;&gt;
+</code></pre></div>
+<p>Arguments:</p>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>dump.xyz</code></td>
+<td>input trajectory</td>
+</tr>
+<tr>
+<td><code>Li</code></td>
+<td>target mobile species</td>
+</tr>
+<tr>
+<td><code>10</code></td>
+<td>time interval between frames, in fs</td>
+</tr>
+<tr>
+<td><code>5000</code></td>
+<td>optional maximum correlation steps</td>
+</tr>
+</tbody>
+</table>
+<p>Output:</p>
+<ul>
+<li><code>msd.out</code></li>
+</ul>
+<p>The beginning of <code>msd.out</code> is a text table with time and MSD columns. After generating it, use the plot commands below.</p>
+<p>You can then plot:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
+  <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
+</div>
+
+<h2 id="nep-property-prediction">NEP Property Prediction</h2>
+<p><code>calc_properties_with_nep.py</code> calculates energy, force, and stress for structures using a NEP model.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nep<span class="w"> </span>structures.xyz<span class="w"> </span>predictions.xyz<span class="w"> </span>nep.txt
+</code></pre></div>
+<p>This function is useful when you intentionally want to use a trained NEP model as a surrogate calculator. It should not be treated as a replacement for DFT unless the model quality has been carefully validated.</p>
+<h2 id="nep-descriptors">NEP Descriptors</h2>
+<p><code>calc_descriptors.py</code> extracts NEP descriptors for a selected element.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
+</code></pre></div>
+<p>Use cases:</p>
+<ul>
+<li>visualize chemical environments with PCA/UMAP;</li>
+<li>compare training and candidate structures;</li>
+<li>inspect whether new data expands descriptor space.</li>
+</ul>
+<p>Plot descriptors with:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/des_umap.png" alt="Descriptor UMAP" width="52%" />
+</div>
+
+<h2 id="density-of-atomistic-states">Density of Atomistic States</h2>
+<p><code>calc_doas.py</code> calculates density of atomistic states (DOAS), following the idea proposed by <a href="https://doi.org/10.1002/anie.202215544">Wang et al.</a>.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>doas<span class="w"> </span>structures.xyz<span class="w"> </span>nep.txt<span class="w"> </span>doas.out
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
+</code></pre></div>
+<p>The script:</p>
+<ol>
+<li>reads all structures;</li>
+<li>relaxes each structure with a NEP calculator;</li>
+<li>extracts per-atom energies;</li>
+<li>groups atomic energies by element;</li>
+<li>writes the grouped values to the output file.</li>
+</ol>
+<p>For very large systems, doing minimization and atomistic-energy extraction directly in GPUMD may be more efficient.</p>
+<div align="center">
+  <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
+</div>
+
+<h2 id="neb-with-a-nep-model">NEB with a NEP Model</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>neb<span class="w"> </span>initial.xyz<span class="w"> </span>final.xyz<span class="w"> </span><span class="m">9</span><span class="w"> </span>nep.txt
+</code></pre></div>
+<p>This runs a NEB calculation with <code>9</code> intermediate images. During execution, the script asks how atoms should be fixed:</p>
+<ul>
+<li><code>none</code>: no atoms fixed;</li>
+<li><code>index</code>: fix atoms by index;</li>
+<li><code>element</code>: fix all atoms of one element;</li>
+<li><code>position</code>: fix atoms inside a coordinate range.</li>
+</ul>
+<h2 id="structure-minimization">Structure Minimization</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>minimize<span class="w"> </span>POSCAR<span class="w"> </span>nep.txt<span class="w"> </span><span class="m">0</span>.01<span class="w"> </span><span class="m">1000</span>
+</code></pre></div>
+<p>Arguments:</p>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>POSCAR</code></td>
+<td>input structure, POSCAR/CONTCAR or extxyz</td>
+</tr>
+<tr>
+<td><code>nep.txt</code></td>
+<td>NEP model</td>
+</tr>
+<tr>
+<td><code>0.01</code></td>
+<td>optional force convergence threshold in eV/Ang</td>
+</tr>
+<tr>
+<td><code>1000</code></td>
+<td>optional maximum optimization steps</td>
+</tr>
+</tbody>
+</table>
+<p>Output:</p>
+<ul>
+<li><code>minimize.xyz</code></li>
+<li><code>minimize.log</code></li>
+</ul>
+<h2 id="ferroelectric-and-polar-material-tools">Ferroelectric and Polar Material Tools</h2>
+<p>The following tools are useful for perovskite and polar-material analysis. They require <code>ferrodispcalc</code>:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
+</code></pre></div>
+<p><code>ferrodispcalc</code> currently has no associated paper to cite.</p>
+<h3 id="build-neighbor-lists">Build Neighbor Lists</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+</code></pre></div>
+<p>This creates a neighbor-list file where each row stores one center atom and its nearest neighbor atoms.</p>
+<h3 id="calculate-displacements">Calculate Displacements</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+</code></pre></div>
+<p>Use <code>-l 0.2</code> to analyze the last 20% of frames. Use <code>-s</code>, <code>-t</code>, and <code>-p</code> if you want an explicit slice.</p>
+<h3 id="average-a-structure">Average a Structure</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+</code></pre></div>
+<p>This is useful before displacement or polarization analysis when a representative averaged structure is needed.</p>
+<h3 id="octahedral-tilt">Octahedral Tilt</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>octahedral_tilt.dat
+</code></pre></div>
+<p>The neighbor list should usually contain six B-O neighbors for each B-site center in an <code>ABO3</code>-like structure.</p>
+<h3 id="abo3-polarization">ABO3 Polarization</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-21-2" name="__codelineno-21-2" href="#__codelineno-21-2"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-o<span class="w"> </span>polarization.dat
+</code></pre></div>
+<p>The <code>--bec</code> values should be chosen according to your model or reference data. The tool is designed for <code>ABO3</code>-type local polarization analysis.</p>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
+            </div>
+          
+          
+<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
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+  <a href="#format-conversion" class="md-nav__link">
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+        <li class="md-nav__item">
+  <a href="#calculators" class="md-nav__link">
+    <span class="md-ellipsis">
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+      <a href="structure_sampling.html" class="md-nav__link">
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+  <span class="md-ellipsis">
+    
+  
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+  
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+            
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+        
+  
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+  <span class="md-ellipsis">
+    
+  
+    命令参考
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+  
+
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+
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+            
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+  <span class="md-ellipsis">
+    
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+    
+  
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+  
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+        
+  
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+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
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+  </span>
+  
+  
+
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+  
+
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+            
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+  
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
+              
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+  
+  
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+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
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+            
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+  
+  
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+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
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+  
+  
+  
+  
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+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+  
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+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
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+    </li>
+  
+
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
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+  </span>
+  
+  
+
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+    </li>
+  
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+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gpumdkitsh-h-output" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        gpumdkit.sh -h Output
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#main" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Main
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#format-conversion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Format Conversion
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#calculators" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Calculators
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#analyzers" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Analyzers
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#visualization" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Visualization
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#utilities" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Utilities
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>📋 Command Reference</h1>
+  <p style="text-align: justify;">This page lists the stable GPUMDkit command-line shortcuts. Interactive mode is available for workflows with many choices.</p>
+</div>
+
+<p>The source table is maintained in <code>docs/command_reference.tsv</code>.</p>
+<h2 id="gpumdkitsh-h-output"><code>gpumdkit.sh -h</code> Output</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>|                                          MAIN FUNCTIONS                                               |
+<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a>| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |
+<a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a>| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |
+<a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a>| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
+<a id="__codelineno-0-9" name="__codelineno-0-9" href="#__codelineno-0-9"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-10" name="__codelineno-0-10" href="#__codelineno-0-10"></a>|                                         FORMAT CONVERSION                                             |
+<a id="__codelineno-0-11" name="__codelineno-0-11" href="#__codelineno-0-11"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-12" name="__codelineno-0-12" href="#__codelineno-0-12"></a>| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |
+<a id="__codelineno-0-13" name="__codelineno-0-13" href="#__codelineno-0-13"></a>| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |
+<a id="__codelineno-0-14" name="__codelineno-0-14" href="#__codelineno-0-14"></a>| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |
+<a id="__codelineno-0-15" name="__codelineno-0-15" href="#__codelineno-0-15"></a>| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |
+<a id="__codelineno-0-16" name="__codelineno-0-16" href="#__codelineno-0-16"></a>| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |
+<a id="__codelineno-0-17" name="__codelineno-0-17" href="#__codelineno-0-17"></a>| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |
+<a id="__codelineno-0-18" name="__codelineno-0-18" href="#__codelineno-0-18"></a>| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
+<a id="__codelineno-0-19" name="__codelineno-0-19" href="#__codelineno-0-19"></a>| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
+<a id="__codelineno-0-20" name="__codelineno-0-20" href="#__codelineno-0-20"></a>| -frame_range  Extract frames by range         |                                                       |
+<a id="__codelineno-0-21" name="__codelineno-0-21" href="#__codelineno-0-21"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-22" name="__codelineno-0-22" href="#__codelineno-0-22"></a>|                                            ANALYSIS                                                   |
+<a id="__codelineno-0-23" name="__codelineno-0-23" href="#__codelineno-0-23"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-24" name="__codelineno-0-24" href="#__codelineno-0-24"></a>| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
+<a id="__codelineno-0-25" name="__codelineno-0-25" href="#__codelineno-0-25"></a>| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
+<a id="__codelineno-0-26" name="__codelineno-0-26" href="#__codelineno-0-26"></a>| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
+<a id="__codelineno-0-27" name="__codelineno-0-27" href="#__codelineno-0-27"></a>| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
+<a id="__codelineno-0-28" name="__codelineno-0-28" href="#__codelineno-0-28"></a>| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
+<a id="__codelineno-0-29" name="__codelineno-0-29" href="#__codelineno-0-29"></a>| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
+<a id="__codelineno-0-30" name="__codelineno-0-30" href="#__codelineno-0-30"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-31" name="__codelineno-0-31" href="#__codelineno-0-31"></a>| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |
+<a id="__codelineno-0-32" name="__codelineno-0-32" href="#__codelineno-0-32"></a>+-------------------------------------------------------------------------------------------------------+
+</code></pre></div>
+<h2 id="main">Main</h2>
+<table>
+<thead>
+<tr>
+<th>Command</th>
+<th>Syntax</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-h</code></td>
+<td><code>gpumdkit.sh -h</code></td>
+<td>Show general help</td>
+</tr>
+<tr>
+<td><code>-update</code></td>
+<td><code>gpumdkit.sh -update</code></td>
+<td>Update GPUMDkit</td>
+</tr>
+<tr>
+<td><code>-clean</code></td>
+<td><code>gpumdkit.sh -clean</code></td>
+<td>Clean extra files in the current directory</td>
+</tr>
+</tbody>
+</table>
+<h2 id="format-conversion">Format Conversion</h2>
+<table>
+<thead>
+<tr>
+<th>Command</th>
+<th>Syntax</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-out2xyz</code></td>
+<td><code>gpumdkit.sh -out2xyz &lt;dir&gt;</code></td>
+<td>OUTCAR to extxyz, shell version</td>
+</tr>
+<tr>
+<td><code>-out2exyz</code></td>
+<td><code>gpumdkit.sh -out2exyz &lt;dir&gt;</code></td>
+<td>OUTCAR to extxyz, Python version</td>
+</tr>
+<tr>
+<td><code>-cp2k2xyz</code></td>
+<td><code>gpumdkit.sh -cp2k2xyz</code></td>
+<td>CP2K output to xyz/extxyz</td>
+</tr>
+<tr>
+<td><code>-xdat2exyz</code></td>
+<td><code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code></td>
+<td>XDATCAR to extxyz</td>
+</tr>
+<tr>
+<td><code>-cif2pos</code></td>
+<td><code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code></td>
+<td>CIF to POSCAR/VASP</td>
+</tr>
+<tr>
+<td><code>-cif2exyz</code></td>
+<td><code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code></td>
+<td>CIF to extxyz</td>
+</tr>
+<tr>
+<td><code>-pos2exyz</code></td>
+<td><code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code></td>
+<td>POSCAR to extxyz</td>
+</tr>
+<tr>
+<td><code>-exyz2pos</code></td>
+<td><code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code></td>
+<td>extxyz frames to POSCAR files</td>
+</tr>
+<tr>
+<td><code>-pos2lmp</code></td>
+<td><code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code></td>
+<td>POSCAR to LAMMPS data</td>
+</tr>
+<tr>
+<td><code>-lmp2exyz</code></td>
+<td><code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code></td>
+<td>LAMMPS dump to extxyz</td>
+</tr>
+<tr>
+<td><code>-traj2exyz</code></td>
+<td><code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code></td>
+<td>ASE trajectory to extxyz</td>
+</tr>
+<tr>
+<td><code>-replicate</code></td>
+<td><code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code></td>
+<td>Replicate by cell factors</td>
+</tr>
+<tr>
+<td><code>-replicate</code></td>
+<td><code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code></td>
+<td>Replicate toward a target atom count</td>
+</tr>
+<tr>
+<td><code>-addgroup</code></td>
+<td><code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code></td>
+<td>Add GPUMD group labels</td>
+</tr>
+<tr>
+<td><code>-addweight</code></td>
+<td><code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code></td>
+<td>Add structure weights</td>
+</tr>
+<tr>
+<td><code>-get_frame</code></td>
+<td><code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code></td>
+<td>Extract one frame</td>
+</tr>
+<tr>
+<td><code>-clean_xyz</code></td>
+<td><code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code></td>
+<td>Remove extra extxyz properties</td>
+</tr>
+<tr>
+<td><code>-frame_range</code></td>
+<td><code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code></td>
+<td>Extract frames by fractional range</td>
+</tr>
+</tbody>
+</table>
+<h2 id="calculators">Calculators</h2>
+<table>
+<thead>
+<tr>
+<th>Command</th>
+<th>Syntax</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-calc ionic-cond</code></td>
+<td><code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code></td>
+<td>Ionic conductivity</td>
+</tr>
+<tr>
+<td><code>-calc nep</code></td>
+<td><code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code></td>
+<td>NEP property prediction</td>
+</tr>
+<tr>
+<td><code>-calc des</code></td>
+<td><code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code></td>
+<td>NEP descriptors</td>
+</tr>
+<tr>
+<td><code>-calc doas</code></td>
+<td><code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code></td>
+<td>Density of atomistic states</td>
+</tr>
+<tr>
+<td><code>-calc neb</code></td>
+<td><code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code></td>
+<td>NEB with a NEP model</td>
+</tr>
+<tr>
+<td><code>-calc minimize</code></td>
+<td><code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code></td>
+<td>Structure minimization</td>
+</tr>
+<tr>
+<td><code>-calc msd</code></td>
+<td><code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code></td>
+<td>MSD from trajectory</td>
+</tr>
+<tr>
+<td><code>-calc nlist</code></td>
+<td><code>gpumdkit.sh -calc nlist [args...]</code></td>
+<td>Neighbor lists</td>
+</tr>
+<tr>
+<td><code>-calc disp</code></td>
+<td><code>gpumdkit.sh -calc disp [args...]</code></td>
+<td>Displacements</td>
+</tr>
+<tr>
+<td><code>-calc avg-struct</code></td>
+<td><code>gpumdkit.sh -calc avg-struct [args...]</code></td>
+<td>Averaged structure</td>
+</tr>
+<tr>
+<td><code>-calc oct-tilt</code></td>
+<td><code>gpumdkit.sh -calc oct-tilt [args...]</code></td>
+<td>Octahedral tilt</td>
+</tr>
+<tr>
+<td><code>-calc pol-abo3</code></td>
+<td><code>gpumdkit.sh -calc pol-abo3 [args...]</code></td>
+<td>ABO3 local polarization</td>
+</tr>
+</tbody>
+</table>
+<h2 id="analyzers">Analyzers</h2>
+<table>
+<thead>
+<tr>
+<th>Command</th>
+<th>Syntax</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-range</code></td>
+<td><code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\|force\|virial&gt; [hist]</code></td>
+<td>Property range analysis</td>
+</tr>
+<tr>
+<td><code>-analyze_comp</code></td>
+<td><code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code></td>
+<td>Composition analysis</td>
+</tr>
+<tr>
+<td><code>-chem_species</code></td>
+<td><code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code></td>
+<td>Chemical species list</td>
+</tr>
+<tr>
+<td><code>-cbc</code></td>
+<td><code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code></td>
+<td>Charge-balance check</td>
+</tr>
+<tr>
+<td><code>-min_dist</code></td>
+<td><code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code></td>
+<td>Minimum distance without PBC</td>
+</tr>
+<tr>
+<td><code>-min_dist_pbc</code></td>
+<td><code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code></td>
+<td>Minimum distance with PBC</td>
+</tr>
+<tr>
+<td><code>-filter_dist</code></td>
+<td><code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code></td>
+<td>Distance filtering</td>
+</tr>
+<tr>
+<td><code>-filter_dist_pbc</code></td>
+<td><code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code></td>
+<td>PBC-aware distance filtering</td>
+</tr>
+<tr>
+<td><code>-filter_box</code></td>
+<td><code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code></td>
+<td>Box-edge filtering</td>
+</tr>
+<tr>
+<td><code>-filter_value</code></td>
+<td><code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code></td>
+<td>Property threshold filtering</td>
+</tr>
+<tr>
+<td><code>-filter_range</code></td>
+<td><code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code></td>
+<td>Element-pair distance range filtering</td>
+</tr>
+<tr>
+<td><code>-pda</code></td>
+<td><code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code></td>
+<td>Probability density analysis</td>
+</tr>
+</tbody>
+</table>
+<h2 id="visualization">Visualization</h2>
+<p>Use:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span><span class="o">[</span>options<span class="o">]</span>
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>-h
+</code></pre></div>
+<p>Common types include <code>train</code>, <code>prediction</code>, <code>thermo</code>, <code>msd</code>, <code>sdc</code>, <code>rdf</code>, <code>emd</code>, <code>nemd</code>, <code>hnemd</code>, <code>pdos</code>, and <code>plane-grid</code>.</p>
+<h2 id="utilities">Utilities</h2>
+<table>
+<thead>
+<tr>
+<th>Command</th>
+<th>Syntax</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-time</code></td>
+<td><code>gpumdkit.sh -time &lt;gpumd\|nep&gt;</code></td>
+<td>Monitor GPUMD or NEP progress</td>
+</tr>
+<tr>
+<td><code>-nep_modifier</code></td>
+<td><code>gpumdkit.sh -nep_modifier</code></td>
+<td>Modify NEP models interactively</td>
+</tr>
+<tr>
+<td><code>-pynep</code></td>
+<td><code>gpumdkit.sh -pynep</code></td>
+<td>Deprecated PyNEP FPS sampling</td>
+</tr>
+</tbody>
+</table>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
+            </div>
+          
+          
+<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
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diff --git a/docs/htmls/en/contributing_to_gpumdkit.html b/docs/htmls/en/contributing_to_gpumdkit.html
new file mode 100644
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+      <a href="quick_start.html" class="md-nav__link">
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+      <a href="command_reference.html" class="md-nav__link">
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+      <a href="format_conversion.html" class="md-nav__link">
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+      <a href="structure_sampling.html" class="md-nav__link">
+        
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+    Structure Sampling
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+      <a href="workflow_scripts.html" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Workflow Scripts
+  
+
+    
+  </span>
+  
+  
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+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="calculator_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Calculator Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="analyzer_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Analyzer Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="plot_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Plot Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="custom_commands.html" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Custom Commands
+  
+
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+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="active_learning_workflow.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Active Learning Workflow
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="polar_material_analysis.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Polar Material Analysis
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
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+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="contributing_to_gpumdkit.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#table-of-contents" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Table of Contents
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#development-restrictions-and-guidelines" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Development Restrictions and Guidelines
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Development Restrictions and Guidelines">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#language-requirements" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Language Requirements
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#modularity-and-reusability" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Modularity and Reusability
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#code-style" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Code Style
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#documentation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Documentation
+      
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+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#reporting-bugs" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Reporting Bugs
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#suggesting-features" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Suggesting Features
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#contributing-code" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Contributing Code
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Contributing Code">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#fork-and-clone-the-repository" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Fork and Clone the Repository
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#create-a-feature-branch" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Create a Feature Branch
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#making-changes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Making Changes
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Making Changes">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#interactive-mode-contributions" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive Mode Contributions
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#command-line-mode-contributions" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Command-Line Mode Contributions
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#updating-tab-completion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Updating Tab Completion
+      
+    </span>
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+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#code-style-and-best-practices" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Code Style and Best Practices
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#testing-your-changes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Testing Your Changes
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#commit-messages" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Commit Messages
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#push-and-open-a-pull-request" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Push and Open a Pull Request
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#questions-or-need-help" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Questions or Need Help?
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
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+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        
+          
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    简体中文
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    简体中文
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/index.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit 教程
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#table-of-contents" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Table of Contents
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#development-restrictions-and-guidelines" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Development Restrictions and Guidelines
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Development Restrictions and Guidelines">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#language-requirements" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Language Requirements
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#modularity-and-reusability" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Modularity and Reusability
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#code-style" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Code Style
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#documentation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Documentation
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#reporting-bugs" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Reporting Bugs
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#suggesting-features" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Suggesting Features
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#contributing-code" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Contributing Code
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Contributing Code">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#fork-and-clone-the-repository" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Fork and Clone the Repository
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#create-a-feature-branch" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Create a Feature Branch
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#making-changes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Making Changes
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Making Changes">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#interactive-mode-contributions" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive Mode Contributions
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#command-line-mode-contributions" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Command-Line Mode Contributions
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#updating-tab-completion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Updating Tab Completion
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#code-style-and-best-practices" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Code Style and Best Practices
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#testing-your-changes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Testing Your Changes
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#commit-messages" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Commit Messages
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#push-and-open-a-pull-request" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Push and Open a Pull Request
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#questions-or-need-help" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Questions or Need Help?
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🤝 Contributing to GPUMDkit</h1>
+  <p style="text-align: justify;">Thank you for your interest in contributing to <strong>GPUMDkit</strong>! We appreciate your time and effort in helping improve this toolkit.</p>
+</div>
+
+<p><code>GPUMDkit</code> is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.</p>
+<hr />
+<h2 id="table-of-contents">Table of Contents</h2>
+<ul>
+<li><a href="#development-restrictions-and-guidelines">Development Restrictions and Guidelines</a></li>
+<li><a href="#reporting-bugs">Reporting Bugs</a></li>
+<li><a href="#suggesting-features">Suggesting Features</a></li>
+<li><a href="#contributing-code">Contributing Code</a></li>
+<li><a href="#fork-and-clone-the-repository">Fork and Clone the Repository</a></li>
+<li><a href="#create-a-feature-branch">Create a Feature Branch</a></li>
+<li><a href="#making-changes">Making Changes</a><ul>
+<li><a href="#interactive-mode-contributions">Interactive Mode Contributions</a></li>
+<li><a href="#command-line-mode-contributions">Command-Line Mode Contributions</a></li>
+<li><a href="#updating-tab-completion">Updating Tab Completion</a></li>
+</ul>
+</li>
+<li><a href="#code-style-and-best-practices">Code Style and Best Practices</a></li>
+<li><a href="#testing-your-changes">Testing Your Changes</a></li>
+<li><a href="#commit-messages">Commit Messages</a></li>
+<li><a href="#push-and-open-a-pull-request">Push and Open a Pull Request</a></li>
+</ul>
+<hr />
+<h2 id="development-restrictions-and-guidelines">Development Restrictions and Guidelines</h2>
+<p>To maintain code quality and consistency across the project, please adhere to these guidelines:</p>
+<h3 id="language-requirements">Language Requirements</h3>
+<ul>
+<li><strong>All code should be written in English</strong>: This includes variable names, function names, comments, docstrings, commit messages, and documentation.</li>
+<li>While we understand that contributors come from diverse backgrounds, using English ensures that the codebase is accessible to the widest possible audience.</li>
+</ul>
+<h3 id="modularity-and-reusability">Modularity and Reusability</h3>
+<ul>
+<li><strong>Write modular and reusable code</strong>: Functions and scripts should be designed with flexibility in mind.</li>
+<li><strong>Prefer passing parameters over hardcoding values</strong>: Use function arguments, command-line parameters, or configuration files instead of hardcoded values. However, some filenames are required to be fixed by GPUMD and NEP programs (e.g., <code>train.xyz</code>, <code>thermo.out</code>), and these can be hardcoded as needed.</li>
+<li><strong>Example</strong>: 
+  <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="c1"># Good: accepts parameters</span>
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="k">function</span><span class="w"> </span>convert_file<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="w">    </span><span class="nb">local</span><span class="w"> </span><span class="nv">input_file</span><span class="o">=</span><span class="nv">$1</span>
+<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a><span class="w">    </span><span class="nb">local</span><span class="w"> </span><span class="nv">output_file</span><span class="o">=</span><span class="nv">$2</span>
+<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a><span class="w">    </span><span class="c1"># processing logic</span>
+<a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a><span class="o">}</span>
+<a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a>
+<a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a><span class="c1"># Avoid: hardcoded values (unless required by GPUMD/NEP)</span>
+<a id="__codelineno-0-9" name="__codelineno-0-9" href="#__codelineno-0-9"></a><span class="k">function</span><span class="w"> </span>convert_file<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-0-10" name="__codelineno-0-10" href="#__codelineno-0-10"></a><span class="w">    </span><span class="nb">local</span><span class="w"> </span><span class="nv">input_file</span><span class="o">=</span><span class="s2">&quot;hardcoded_input.xyz&quot;</span>
+<a id="__codelineno-0-11" name="__codelineno-0-11" href="#__codelineno-0-11"></a><span class="w">    </span><span class="c1"># processing logic</span>
+<a id="__codelineno-0-12" name="__codelineno-0-12" href="#__codelineno-0-12"></a><span class="o">}</span>
+</code></pre></div></li>
+</ul>
+<h3 id="code-style">Code Style</h3>
+<ul>
+<li>Write code that is clear and easy for others to maintain and modify.</li>
+<li>Use meaningful variable and function names.</li>
+<li>Add comments where necessary to explain complex logic.</li>
+</ul>
+<h3 id="documentation">Documentation</h3>
+<ul>
+<li>Ensure that help messages (e.g., <code>-h</code> flags) are clear and accurate.</li>
+<li>Documentation files in the <code>docs/</code> directory will be updated by the maintainers, so you generally don't need to modify them.</li>
+</ul>
+<hr />
+<h2 id="reporting-bugs">Reporting Bugs</h2>
+<p>If you encounter a bug, please help us fix it by reporting it through GitHub Issues:</p>
+<ol>
+<li><strong>Search existing issues</strong> to see if the bug has already been reported.</li>
+<li><strong>Open a new issue</strong> if it hasn't been reported yet: <a href="https://github.com/zhyan0603/GPUMDkit/issues/new">Create an Issue</a></li>
+<li><strong>Describe the problem in detail</strong> and provide test files if possible.</li>
+</ol>
+<p>You can also reach out to us through:
+- <strong>QQ Group</strong>: 825696376
+- <strong>Email</strong>: yanzihan@westlake.edu.cn
+- <strong>Script Developer</strong>: Contact the developer listed in the script header</p>
+<hr />
+<h2 id="suggesting-features">Suggesting Features</h2>
+<p>We welcome feature suggestions! To propose a new feature:</p>
+<ol>
+<li><strong>Search existing issues</strong> to see if someone has already suggested it.</li>
+<li><strong>Open a new feature request</strong>: <a href="https://github.com/zhyan0603/GPUMDkit/issues/new">Create a Feature Request</a> and mention @zhyan0603</li>
+<li><strong>Describe what you need</strong> clearly and explain how it would be useful.</li>
+</ol>
+<hr />
+<h2 id="contributing-code">Contributing Code</h2>
+<h3 id="fork-and-clone-the-repository">Fork and Clone the Repository</h3>
+<ol>
+<li>
+<p><strong>Fork the repository</strong> on GitHub by clicking the "Fork" button at the top right of the <a href="https://github.com/zhyan0603/GPUMDkit">repository page</a>.</p>
+</li>
+<li>
+<p><strong>Clone your fork</strong> to your local machine:</p>
+</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/YOUR_USERNAME/GPUMDkit.git
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
+</code></pre></div>
+<ol>
+<li><strong>Set up the upstream remote</strong> to keep your fork in sync:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>git<span class="w"> </span>remote<span class="w"> </span>add<span class="w"> </span>upstream<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
+</code></pre></div></li>
+</ol>
+<h3 id="create-a-feature-branch">Create a Feature Branch</h3>
+<p>Create a new branch for your changes:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># Create and checkout a new branch from main</span>
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>git<span class="w"> </span>checkout<span class="w"> </span>-b<span class="w"> </span>your-branch-name
+</code></pre></div>
+<p>Name your branch as you prefer.</p>
+<h3 id="making-changes">Making Changes</h3>
+<p>The structure of <code>GPUMDkit</code> consists of:
+- <strong><code>gpumdkit.sh</code></strong>: Main entry point (Bash script) handling both interactive menu mode and command-line mode
+- <strong><code>Scripts/</code></strong>: Python utility scripts organized by functionality
+  - <code>plt_scripts/</code>: Plotting scripts
+  - <code>calculators/</code>: Calculation utilities
+  - <code>format_conversion/</code>: Format conversion tools
+  - <code>workflow/</code>: Workflow automation
+  - <code>sample_structures/</code>: Structure sampling utilities
+  - <code>analyzer/</code>: Analysis tools
+  - <code>utils/</code>: Utility functions (including <code>completion.sh</code> for tab completion)
+- <strong><code>src/</code></strong>: Shell scripts containing menu functions for interactive mode
+  - <code>f1_format_conversions.sh</code>
+  - <code>f2_sample_structures.sh</code>
+  - <code>f3_workflows.sh</code>
+  - <code>f4_calculators.sh</code>
+  - <code>f5_analyzers.sh</code>
+  - <code>f6_plots.sh</code>
+  - <code>f7_utilities.sh</code>
+- <strong><code>docs/</code></strong>: Documentation files</p>
+<h4 id="interactive-mode-contributions">Interactive Mode Contributions</h4>
+<p>To add a new feature accessible through the interactive menu:</p>
+<ol>
+<li><strong>Create your implementation script</strong> in the appropriate <code>Scripts/</code> subdirectory:</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="c1"># Example: Add a new format conversion script</span>
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>touch<span class="w"> </span>Scripts/format_conversion/new_converter.py
+</code></pre></div>
+<ol>
+<li>
+<p><strong>Implement your functionality</strong> following the modularity guidelines (accept parameters, avoid hardcoding).</p>
+</li>
+<li>
+<p><strong>Add a wrapper function</strong> in the corresponding <code>src/</code> file:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="c1"># Example: Edit src/f1_format_conversions.sh</span>
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>vim<span class="w"> </span>src/f1_format_conversions.sh
+</code></pre></div></p>
+</li>
+</ol>
+<p>Add a new function:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="k">function</span><span class="w"> </span>f106_new_converter<span class="o">(){</span>
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Calling the script in Scripts/format_conversion |&quot;</span>
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Script: new_converter.py                        |&quot;</span>
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Developer: Your Name (your@email.com)           |&quot;</span>
+<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
+<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Input the required parameters:&quot;</span>
+<a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Example: input.xyz output.lmp&quot;</span>
+<a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ------------&gt;&gt;&quot;</span>
+<a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="s2">&quot; &quot;</span><span class="w"> </span>converter_params
+<a id="__codelineno-6-11" name="__codelineno-6-11" href="#__codelineno-6-11"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ---------------------------------------------------&quot;</span>
+<a id="__codelineno-6-12" name="__codelineno-6-12" href="#__codelineno-6-12"></a>python<span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/Scripts/format_conversion/new_converter.py<span class="w"> </span><span class="si">${</span><span class="nv">converter_params</span><span class="si">}</span>
+<a id="__codelineno-6-13" name="__codelineno-6-13" href="#__codelineno-6-13"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Code path: </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span><span class="s2">/Scripts/format_conversion/new_converter.py&quot;</span>
+<a id="__codelineno-6-14" name="__codelineno-6-14" href="#__codelineno-6-14"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ---------------------------------------------------&quot;</span>
+<a id="__codelineno-6-15" name="__codelineno-6-15" href="#__codelineno-6-15"></a><span class="o">}</span>
+</code></pre></div></p>
+<ol>
+<li>
+<p><strong>Update the menu display</strong> in <code>gpumdkit.sh</code>:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># Find the menu() function and update it if needed</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="c1"># Find the array_choice array and add your new choice number</span>
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="nv">array_choice</span><span class="o">=(</span>
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="w">    </span><span class="s2">&quot;0&quot;</span><span class="w"> </span><span class="s2">&quot;1&quot;</span><span class="w"> </span><span class="s2">&quot;101&quot;</span><span class="w"> </span><span class="s2">&quot;102&quot;</span><span class="w"> </span><span class="s2">&quot;103&quot;</span><span class="w"> </span><span class="s2">&quot;104&quot;</span><span class="w"> </span><span class="s2">&quot;105&quot;</span><span class="w"> </span><span class="s2">&quot;106&quot;</span><span class="w">  </span><span class="c1"># Added &quot;106&quot;</span>
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a><span class="w">    </span><span class="c1"># ... rest of choices</span>
+<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a><span class="o">)</span>
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>Add the case statement</strong> in <code>gpumdkit.sh</code>:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="c1"># In the main() function, find the appropriate case statement</span>
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a><span class="k">case</span><span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">choice</span><span class="p">:</span><span class="nv">0</span><span class="p">:</span><span class="nv">1</span><span class="si">}</span><span class="s2">&quot;</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a><span class="w">    </span><span class="c1"># ...</span>
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="w">    </span><span class="s2">&quot;1&quot;</span><span class="o">)</span>
+<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a><span class="w">        </span><span class="nb">source</span><span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/src/f1_format_conversions.sh
+<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a><span class="w">        </span><span class="k">case</span><span class="w"> </span><span class="nv">$choice</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="w">            </span><span class="s2">&quot;1&quot;</span><span class="o">)</span><span class="w"> </span>f1_format_conversion<span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a><span class="w">            </span><span class="s2">&quot;101&quot;</span><span class="o">)</span><span class="w"> </span>f101_out2xyz<span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a><span class="w">            </span><span class="c1"># ... existing cases ...</span>
+<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a><span class="w">            </span><span class="s2">&quot;106&quot;</span><span class="o">)</span><span class="w"> </span>f106_new_converter<span class="w"> </span><span class="p">;;</span><span class="w">  </span><span class="c1"># Add your case</span>
+<a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a><span class="w">        </span><span class="k">esac</span><span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></a><span class="w">    </span><span class="c1"># ...</span>
+<a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a><span class="k">esac</span>
+</code></pre></div></p>
+</li>
+</ol>
+<h4 id="command-line-mode-contributions">Command-Line Mode Contributions</h4>
+<p>To add a new command-line flag or subcommand:</p>
+<ol>
+<li>
+<p><strong>Create your implementation script</strong> in the appropriate <code>Scripts/</code> subdirectory:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="c1"># Example: Add a new analyzer script</span>
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>touch<span class="w"> </span>Scripts/analyzer/analyze_bonds.py
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>Implement your functionality</strong> with clear parameter requirements:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="c1"># Example: Scripts/analyzer/analyze_bonds.py</span>
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a><span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="k">def</span><span class="w"> </span><span class="nf">main</span><span class="p">():</span>
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">3</span><span class="p">:</span>
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;&quot;</span><span class="p">)</span>
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a>        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0&quot;</span><span class="p">)</span>
+<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>        <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
+<a id="__codelineno-10-9" name="__codelineno-10-9" href="#__codelineno-10-9"></a>
+<a id="__codelineno-10-10" name="__codelineno-10-10" href="#__codelineno-10-10"></a>    <span class="n">input_file</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<a id="__codelineno-10-11" name="__codelineno-10-11" href="#__codelineno-10-11"></a>    <span class="n">cutoff</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+<a id="__codelineno-10-12" name="__codelineno-10-12" href="#__codelineno-10-12"></a>
+<a id="__codelineno-10-13" name="__codelineno-10-13" href="#__codelineno-10-13"></a>    <span class="c1"># Your implementation here</span>
+<a id="__codelineno-10-14" name="__codelineno-10-14" href="#__codelineno-10-14"></a>
+<a id="__codelineno-10-15" name="__codelineno-10-15" href="#__codelineno-10-15"></a><span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
+<a id="__codelineno-10-16" name="__codelineno-10-16" href="#__codelineno-10-16"></a>    <span class="n">main</span><span class="p">()</span>
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>Add the command-line flag handler</strong> in <code>gpumdkit.sh</code>:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="c1"># Find the command-line parsing section (after line ~167)</span>
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="c1"># Add your new flag in the appropriate location</span>
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>
+<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a><span class="k">case</span><span class="w"> </span><span class="nv">$1</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="w">    </span><span class="c1"># ... existing cases ...</span>
+<a id="__codelineno-11-6" name="__codelineno-11-6" href="#__codelineno-11-6"></a><span class="w">    </span>-analyze_bonds<span class="o">)</span>
+<a id="__codelineno-11-7" name="__codelineno-11-7" href="#__codelineno-11-7"></a><span class="w">        </span><span class="k">if</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$3</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span>
+<a id="__codelineno-11-8" name="__codelineno-11-8" href="#__codelineno-11-8"></a><span class="w">            </span>python<span class="w"> </span><span class="si">${</span><span class="nv">analyzer_path</span><span class="si">}</span>/analyze_bonds.py<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$3</span><span class="s2">&quot;</span>
+<a id="__codelineno-11-9" name="__codelineno-11-9" href="#__codelineno-11-9"></a><span class="w">        </span><span class="k">else</span>
+<a id="__codelineno-11-10" name="__codelineno-11-10" href="#__codelineno-11-10"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;&quot;</span>
+<a id="__codelineno-11-11" name="__codelineno-11-11" href="#__codelineno-11-11"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0&quot;</span>
+<a id="__codelineno-11-12" name="__codelineno-11-12" href="#__codelineno-11-12"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Code path: </span><span class="si">${</span><span class="nv">analyzer_path</span><span class="si">}</span><span class="s2">/analyze_bonds.py&quot;</span>
+<a id="__codelineno-11-13" name="__codelineno-11-13" href="#__codelineno-11-13"></a><span class="w">            </span><span class="nb">exit</span><span class="w"> </span><span class="m">1</span>
+<a id="__codelineno-11-14" name="__codelineno-11-14" href="#__codelineno-11-14"></a><span class="w">        </span><span class="k">fi</span><span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-11-15" name="__codelineno-11-15" href="#__codelineno-11-15"></a><span class="w">    </span><span class="c1"># ... rest of cases ...</span>
+<a id="__codelineno-11-16" name="__codelineno-11-16" href="#__codelineno-11-16"></a><span class="k">esac</span>
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>Update the help information</strong> in <code>gpumdkit.sh</code>:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="c1"># Find the help_info_table() function and add your command</span>
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a><span class="k">function</span><span class="w"> </span>help_info_table<span class="o">(){</span>
+<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;+====================================== Analysis ===============================================+&quot;</span>
+<a id="__codelineno-12-4" name="__codelineno-12-4" href="#__codelineno-12-4"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |&quot;</span>
+<a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a><span class="w">    </span><span class="c1"># ... rest of help table ...</span>
+<a id="__codelineno-12-6" name="__codelineno-12-6" href="#__codelineno-12-6"></a><span class="o">}</span>
+</code></pre></div></p>
+</li>
+</ol>
+<h4 id="updating-tab-completion">Updating Tab Completion</h4>
+<p>When adding new command-line flags, update the tab completion script:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="c1"># Edit Scripts/utils/completion.sh</span>
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>vim<span class="w"> </span>Scripts/utils/completion.sh
+</code></pre></div>
+<p>Add your new flag to the <code>opts</code> variable:
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a><span class="c1"># Find the line with local opts=...</span>
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a><span class="nb">local</span><span class="w"> </span><span class="nv">opts</span><span class="o">=</span><span class="s2">&quot;-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ...&quot;</span>
+<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a><span class="c1">#                                                      ^^^^^^^^^^^^^^ Add your flag here</span>
+</code></pre></div></p>
+<p>If your flag accepts secondary options (like <code>-plt</code> or <code>-calc</code>), add a case for it:
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a><span class="k">case</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$prev</span><span class="s2">&quot;</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="w">    </span><span class="c1"># ... existing cases ...</span>
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a><span class="w">    </span>-analyze_bonds<span class="o">)</span>
+<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a><span class="w">        </span><span class="nv">COMPREPLY</span><span class="o">=(</span><span class="k">$(</span><span class="nb">compgen</span><span class="w"> </span>-f<span class="w"> </span>--<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$cur</span><span class="s2">&quot;</span><span class="k">)</span><span class="o">)</span><span class="w">  </span><span class="c1"># Complete with filenames</span>
+<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a><span class="w">        </span><span class="p">;;</span>
+<a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a><span class="w">    </span><span class="c1"># ... rest of cases ...</span>
+<a id="__codelineno-15-7" name="__codelineno-15-7" href="#__codelineno-15-7"></a><span class="k">esac</span>
+</code></pre></div></p>
+<h3 id="code-style-and-best-practices">Code Style and Best Practices</h3>
+<ul>
+<li><strong>Shell Scripts</strong>:</li>
+<li>Use <code>${variable}</code> for variable expansion</li>
+<li>
+<p>Write code that is clear and easy to maintain</p>
+</li>
+<li>
+<p><strong>Python Scripts</strong>:</p>
+</li>
+<li>Write clear, maintainable code</li>
+<li>Use meaningful variable names</li>
+</ul>
+<h3 id="testing-your-changes">Testing Your Changes</h3>
+<p>Before submitting your contribution:</p>
+<ol>
+<li>
+<p><strong>Test interactive mode</strong> (if applicable):
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a><span class="c1"># Navigate to your new feature and test it thoroughly</span>
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>Test command-line mode</strong> (if applicable):
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span><span class="o">[</span>arguments<span class="o">]</span>
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span>-h<span class="w">  </span><span class="c1"># Test help message</span>
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>Test tab completion</strong> (if you modified <code>completion.sh</code>):
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a><span class="nb">source</span><span class="w"> </span>Scripts/utils/completion.sh
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-&lt;TAB&gt;<span class="w">  </span><span class="c1"># Should show your new flag</span>
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>Test with various inputs</strong>:</p>
+</li>
+<li>Test with typical inputs</li>
+<li>Test with edge cases (empty files, large files, etc.)</li>
+<li>
+<p>Test error handling (missing files, invalid parameters)</p>
+</li>
+<li>
+<p><strong>Verify no regressions</strong>: Ensure existing functionality still works correctly.</p>
+</li>
+</ol>
+<h3 id="commit-messages">Commit Messages</h3>
+<p>Write clear, descriptive commit messages that explain what you changed. There are no strict format requirements - just make sure your message is understandable.</p>
+<h3 id="push-and-open-a-pull-request">Push and Open a Pull Request</h3>
+<ol>
+<li>
+<p><strong>Commit your changes</strong>:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>git<span class="w"> </span>add<span class="w"> </span>.
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>git<span class="w"> </span>commit<span class="w"> </span>-m<span class="w"> </span><span class="s2">&quot;your descriptive message&quot;</span>
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>Keep your branch updated</strong> with the upstream <code>main</code> branch:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>git<span class="w"> </span>fetch<span class="w"> </span>upstream
+<a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a>git<span class="w"> </span>rebase<span class="w"> </span>upstream/main
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>Push your branch</strong> to your fork:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>git<span class="w"> </span>push<span class="w"> </span>origin<span class="w"> </span>your-branch-name
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>Open a Pull Request</strong>:</p>
+</li>
+<li>Go to the <a href="https://github.com/zhyan0603/GPUMDkit">GPUMDkit repository</a></li>
+<li>Click "Pull Requests" → "New Pull Request"</li>
+<li>Set the base branch to <code>dev</code> for code review</li>
+<li>Set the compare branch to your feature branch</li>
+<li>
+<p>Fill in the PR description with:</p>
+<ul>
+<li><strong>Title</strong>: Brief description of changes</li>
+<li><strong>Description</strong>: Detailed explanation of what changed and why</li>
+<li><strong>Testing</strong>: Describe how you tested the changes</li>
+</ul>
+</li>
+<li>
+<p><strong>Respond to review feedback</strong>:</p>
+</li>
+<li>Be open to suggestions and constructive criticism</li>
+<li>Make requested changes promptly</li>
+<li>
+<p>Push additional commits to your branch (they'll automatically appear in the PR)</p>
+</li>
+<li>
+<p><strong>After approval</strong>: A maintainer will merge your PR.</p>
+</li>
+</ol>
+<hr />
+<h2 id="questions-or-need-help">Questions or Need Help?</h2>
+<p>If you have questions about contributing or need help with your contribution:</p>
+<ul>
+<li><strong>Open a discussion</strong>: Use <a href="https://github.com/zhyan0603/GPUMDkit/discussions">GitHub Discussions</a> for general questions</li>
+<li><strong>Ask in an issue</strong>: Comment on related issues for specific questions</li>
+<li><strong>Contact maintainers</strong>: Reach out to the core developers listed in the README</li>
+</ul>
+<hr />
+<p>Thank you again for contributing to <code>GPUMDkit</code>! Your efforts help make this toolkit better for the entire GPUMD and NEP community. 🚀</p>
+
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diff --git a/docs/htmls/en/custom_commands.html b/docs/htmls/en/custom_commands.html
new file mode 100644
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--- /dev/null
+++ b/docs/htmls/en/custom_commands.html
@@ -0,0 +1,1694 @@
+
+<!doctype html>
+<html lang="en" class="no-js">
+  <head>
+    
+      <meta charset="utf-8">
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+      
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+        <meta name="author" content="Zihan YAN">
+      
+      
+        <link rel="canonical" href="https://zhyan0603.github.io/GPUMDkit/en/custom_commands.html">
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+      <a href="analyzer_scripts.html" class="md-nav__link">
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+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
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+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#setup" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Setup
+      
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+  </a>
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+  <a href="#examples" class="md-nav__link">
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+      
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+  <a href="#command-with-required-arguments" class="md-nav__link">
+    <span class="md-ellipsis">
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+        Command with Required Arguments
+      
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+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#calling-an-external-script" class="md-nav__link">
+    <span class="md-ellipsis">
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+</li>
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+          <li class="md-nav__item">
+  <a href="#analysis-pipeline" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Analysis Pipeline
+      
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+  
+</li>
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+          <li class="md-nav__item">
+  <a href="#custom-workflow" class="md-nav__link">
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+      
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+  <a href="#tips" class="md-nav__link">
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+      <a href="active_learning_workflow.html" class="md-nav__link">
+        
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+    
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+      <a href="polar_material_analysis.html" class="md-nav__link">
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+    
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+      <a href="contributing_to_gpumdkit.html" class="md-nav__link">
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+    
+  
+    Contributing to GPUMDkit
+  
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+      <a href="../zh/index.html" class="md-nav__link">
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+    GPUMDkit 教程
+  
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+  
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+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
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+  
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+            
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
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+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
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+  
+
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+      <a href="../zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
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+  
+  
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+      <a href="../zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
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+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
+  
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+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  <a href="#setup" class="md-nav__link">
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+      
+        Setup
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+        
+          <li class="md-nav__item">
+  <a href="#simple-greeting" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Simple Greeting
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#command-with-required-arguments" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Command with Required Arguments
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#calling-an-external-script" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Calling an External Script
+      
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+        
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+  <a href="#analysis-pipeline" class="md-nav__link">
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+      
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+      
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+</li>
+        
+          <li class="md-nav__item">
+  <a href="#custom-workflow" class="md-nav__link">
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+      
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+                
+                  
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+  
+  
+
+
+<div align="center">
+  <h1>🔧 Custom Commands</h1>
+    <p style="text-align: justify;">GPUMDkit allows users to extend the command-line interface with <strong>custom commands</strong>. Define shortcuts for frequently used scripts in your <strong>~/.gpumdkit.in</strong> file.</p>
+</div>
+
+<h2 id="setup">Setup</h2>
+<p>Create or edit <code>~/.gpumdkit.in</code>:
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>vi<span class="w"> </span>~/.gpumdkit.in
+</code></pre></div></p>
+<p>Define custom functions with the <code>custom_</code> prefix.</p>
+<h2 id="examples">Examples</h2>
+<h3 id="simple-greeting">Simple Greeting</h3>
+<p>Write the following codes in your <code>~/.gpumdkit.in</code> </p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>custom_hello<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Hello, GPUMDkit user! This is a custom command.&quot;</span>
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Current GPUMDkit path: </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a><span class="o">}</span>
+</code></pre></div>
+<p>and run <code>gpumdkit.sh -hello</code>, you will see:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>Hello, GPUMDkit user! This is a custom command.
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>Current GPUMDkit path: /home/yanzihan/software/GPUMDkit
+</code></pre></div>
+<h3 id="command-with-required-arguments">Command with Required Arguments</h3>
+<p>For the following function:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>custom_greet<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a><span class="w">    </span><span class="nv">name</span><span class="o">=</span><span class="nv">$1</span>
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Hello, </span><span class="si">${</span><span class="nv">name</span><span class="si">}</span><span class="s2">!&quot;</span>
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="o">}</span>
+</code></pre></div>
+<p>and you can add a argument, for example: <code>gpumdkit.sh -greet Zihan</code>, then you will see:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>Hello, Zihan!
+</code></pre></div>
+<p><strong>Passing arguments</strong>: Use <code>"$@"</code> to forward all arguments safely. Use <code>${@:1}</code> when you need to refer to arguments starting from the first one. </p>
+<h3 id="calling-an-external-script">Calling an External Script</h3>
+<p>If you want to call an external script like <code>gpumdkit.sh</code>.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>custom_nepanalyse<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a><span class="w">    </span>python<span class="w"> </span>~/my_gpumd_tools/analyse_nep.py
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a><span class="o">}</span>
+</code></pre></div>
+<p>and run <code>gpumdkit.sh -nepanalyse</code></p>
+<h2 id="advanced-examples">Advanced Examples</h2>
+<h3 id="batch-processing">Batch Processing</h3>
+<p>Process multiple files:
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>custom_batch_plot<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="w">    </span><span class="k">for</span><span class="w"> </span>dir<span class="w"> </span><span class="k">in</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$@</span><span class="s2">&quot;</span><span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="w">        </span><span class="nb">cd</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$dir</span><span class="s2">&quot;</span>
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="w">        </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo<span class="w"> </span>save
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="w">        </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd<span class="w"> </span>save
+<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a><span class="w">        </span><span class="nb">cd</span><span class="w"> </span>..
+<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="w">    </span><span class="k">done</span>
+<a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a><span class="o">}</span>
+</code></pre></div></p>
+<p>Usage: <code>gpumdkit.sh -batch_plot dir1 dir2 dir3</code></p>
+<h3 id="analysis-pipeline">Analysis Pipeline</h3>
+<p>Combine multiple operations:
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>custom_analyze_training<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="w">    </span><span class="nv">xyz_file</span><span class="o">=</span><span class="nv">$1</span>
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Analyzing </span><span class="nv">$xyz_file</span><span class="s2">...&quot;</span>
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$xyz_file</span><span class="s2">&quot;</span><span class="w"> </span>force
+<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$xyz_file</span><span class="s2">&quot;</span>
+<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$xyz_file</span><span class="s2">&quot;</span>
+<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>
+<a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Analysis complete!&quot;</span>
+<a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a><span class="o">}</span>
+</code></pre></div></p>
+<p>Usage: <code>gpumdkit.sh -analyze_training train.xyz</code></p>
+<h3 id="custom-workflow">Custom Workflow</h3>
+<p>Automate common workflow:
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>custom_prep_training<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Preparing training data...&quot;</span>
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="w">    </span><span class="c1"># Convert VASP outputs</span>
+<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-out2xyz<span class="w"> </span>./
+<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>
+<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="w">    </span><span class="c1"># Filter outliers</span>
+<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span><span class="m">30</span>
+<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a>
+<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a><span class="w">    </span><span class="c1"># Check quality</span>
+<a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>filtered_force.xyz<span class="w"> </span>energy
+<a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></a>
+<a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Training data ready!&quot;</span>
+<a id="__codelineno-8-14" name="__codelineno-8-14" href="#__codelineno-8-14"></a><span class="o">}</span>
+</code></pre></div></p>
+<p>Usage: <code>gpumdkit.sh -prep_training</code></p>
+<h2 id="tips">Tips</h2>
+<ul>
+<li><strong>Use descriptive names</strong>: <code>custom_analyze_nep_training</code> is clearer than <code>custom_ant</code></li>
+<li><strong>Add help messages</strong>: Echo usage info when no arguments provided</li>
+<li><strong>Error handling</strong>: Check if required files exist before processing</li>
+<li><strong>Forward arguments safely</strong>: Use <code>"$@"</code> to preserve spaces and special characters</li>
+</ul>
+<hr />
+<p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>
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+      <a href="quick_start.html" class="md-nav__link">
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+    
+  
+    Format Conversion
+  
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+    
+  </span>
+  
+  
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+      <a href="format_conversion.html" class="md-nav__link md-nav__link--active">
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+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
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+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#interactive-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive Mode
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Interactive Mode">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#what-each-entry-does" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        What Each Entry Does
+      
+    </span>
+  </a>
+  
+</li>
+        
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+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#quick-command-reference" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Quick Command Reference
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#common-examples" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Common Examples
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Common Examples">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#convert-vasp-calculations-to-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Convert VASP calculations to extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#add-group-labels" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Add group labels
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#script-details" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Script Details
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Script Details">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#poscar-to-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        POSCAR to extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#extxyz-to-poscar" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        extxyz to POSCAR
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#lammps-dump-to-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        LAMMPS dump to extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#cif-conversion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        CIF conversion
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#add-weights" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Add weights
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#replicate-structures" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Replicate structures
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#extract-one-frame" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Extract one frame
+      
+    </span>
+  </a>
+  
+</li>
+        
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+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#common-mistakes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Common Mistakes
+      
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+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#notes" class="md-nav__link">
+    <span class="md-ellipsis">
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+      
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+      <a href="structure_sampling.html" class="md-nav__link">
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+      <a href="analyzer_scripts.html" class="md-nav__link">
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+      <a href="active_learning_workflow.html" class="md-nav__link">
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+    Contributing to GPUMDkit
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+    
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+    GPUMDkit 教程
+  
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+  
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+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
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+  
+  
+
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+    </li>
+  
+
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+            
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+      <a href="../zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#interactive-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive Mode
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Interactive Mode">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#what-each-entry-does" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        What Each Entry Does
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#quick-command-reference" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Quick Command Reference
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#common-examples" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Common Examples
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Common Examples">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#convert-vasp-calculations-to-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Convert VASP calculations to extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#add-group-labels" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Add group labels
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#script-details" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Script Details
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Script Details">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#poscar-to-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        POSCAR to extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#extxyz-to-poscar" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        extxyz to POSCAR
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#lammps-dump-to-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        LAMMPS dump to extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#cif-conversion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        CIF conversion
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#add-weights" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Add weights
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#replicate-structures" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Replicate structures
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#extract-one-frame" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Extract one frame
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#common-mistakes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Common Mistakes
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#notes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Notes
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🔄 Format Conversion</h1>
+  <p style="text-align: justify;">GPUMDkit contains utilities for converting common atomistic simulation formats, with extra handling for metadata such as group labels, weights, and frame extraction.</p>
+</div>
+
+<p><strong>Script Location:</strong> <code>Scripts/format_conversion/</code></p>
+<h2 id="overview">Overview</h2>
+<p>The format conversion module covers:</p>
+<ul>
+<li><strong>VASP</strong>: <code>POSCAR</code>, <code>CONTCAR</code>, <code>OUTCAR</code>, <code>XDATCAR</code></li>
+<li><strong>LAMMPS</strong>: data files and dump trajectories</li>
+<li><strong>CP2K</strong>: output logs, position, force, and cell files</li>
+<li><strong>ABACUS</strong>: SCF/MD logs</li>
+<li><strong>CIF</strong>: crystallographic structure files</li>
+<li><strong>ASE trajectory</strong>: <code>.traj</code></li>
+<li><strong>extxyz</strong>: a common structure format for GPUMD and NEP</li>
+</ul>
+<h2 id="interactive-mode">Interactive Mode</h2>
+<p>Open GPUMDkit:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh
+</code></pre></div>
+<p>Choose:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>1) Format Conversion
+</code></pre></div>
+<p>The format conversion menu is:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>+-------------------------------------------------------------+
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>|                   FORMAT CONVERSION TOOLS                   |
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>+-------------------------------------------------------------+
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>| 101) VASP to extxyz            106) Add group labels        |
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>| 102) MTP to extxyz             107) Add weight to extxyz    |
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>| 103) CP2K to extxyz            108) Extract frame extxyz    |
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>| 104) ABACUS to extxyz          109) Clean XYZ info          |
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>| 105) extxyz to POSCAR          110) Replicate structure     |
+<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>+-------------------------------------------------------------+
+<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a>| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |
+<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a>| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |
+<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a>| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |
+<a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a>| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|
+<a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a>+-------------------------------------------------------------+
+<a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a>| 000) Return to main menu                                    |
+<a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a>+-------------------------------------------------------------+
+<a id="__codelineno-2-17" name="__codelineno-2-17" href="#__codelineno-2-17"></a>Input the function number or converter keyword:
+</code></pre></div>
+<h3 id="what-each-entry-does">What Each Entry Does</h3>
+<table>
+<thead>
+<tr>
+<th>Entry</th>
+<th>Function</th>
+<th>When to Use</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>101</code></td>
+<td>VASP OUTCAR to extxyz, shell version</td>
+<td>convert VASP calculation directories</td>
+</tr>
+<tr>
+<td><code>102</code></td>
+<td>MTP cfg to extxyz</td>
+<td>convert MTP training data</td>
+</tr>
+<tr>
+<td><code>103</code></td>
+<td>CP2K to extxyz</td>
+<td>choose CP2K log/inp route or pos/frc/cell route</td>
+</tr>
+<tr>
+<td><code>104</code></td>
+<td>ABACUS to extxyz</td>
+<td>convert ABACUS SCF or MD output</td>
+</tr>
+<tr>
+<td><code>105</code></td>
+<td>extxyz to POSCAR</td>
+<td>write each extxyz frame as a POSCAR-style file</td>
+</tr>
+<tr>
+<td><code>106</code></td>
+<td>add group labels</td>
+<td>add atom group labels for GPUMD-related workflows</td>
+</tr>
+<tr>
+<td><code>107</code></td>
+<td>add weights</td>
+<td>assign training weights in extxyz</td>
+</tr>
+<tr>
+<td><code>108</code></td>
+<td>extract frame</td>
+<td>export one frame from an extxyz trajectory</td>
+</tr>
+<tr>
+<td><code>109</code></td>
+<td>clean XYZ info</td>
+<td>remove extra extxyz properties</td>
+</tr>
+<tr>
+<td><code>110</code></td>
+<td>replicate structure</td>
+<td>build supercells by factors or target atom count</td>
+</tr>
+<tr>
+<td><code>out2exyz</code></td>
+<td>OUTCAR to extxyz, Python version</td>
+<td>alternative VASP OUTCAR converter</td>
+</tr>
+<tr>
+<td><code>pos2exyz</code></td>
+<td>POSCAR to extxyz</td>
+<td>convert a single structure</td>
+</tr>
+<tr>
+<td><code>cif2pos</code></td>
+<td>CIF to POSCAR</td>
+<td>prepare VASP input from CIF</td>
+</tr>
+<tr>
+<td><code>cif2exyz</code></td>
+<td>CIF to extxyz</td>
+<td>prepare GPUMDkit input from CIF</td>
+</tr>
+<tr>
+<td><code>xdat2exyz</code></td>
+<td>XDATCAR to extxyz</td>
+<td>convert VASP MD trajectory</td>
+</tr>
+<tr>
+<td><code>pos2lmp</code></td>
+<td>POSCAR to LAMMPS data</td>
+<td>prepare LAMMPS input</td>
+</tr>
+<tr>
+<td><code>lmp2exyz</code></td>
+<td>LAMMPS dump to extxyz</td>
+<td>convert LAMMPS trajectory</td>
+</tr>
+<tr>
+<td><code>traj2exyz</code></td>
+<td>ASE traj to extxyz</td>
+<td>convert ASE trajectory</td>
+</tr>
+</tbody>
+</table>
+<h2 id="quick-command-reference">Quick Command Reference</h2>
+<table>
+<thead>
+<tr>
+<th>Source</th>
+<th>Target</th>
+<th>Command</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>OUTCAR directory</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -out2xyz &lt;dir&gt;</code></td>
+</tr>
+<tr>
+<td>OUTCAR directory</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -out2exyz &lt;dir&gt;</code></td>
+</tr>
+<tr>
+<td>POSCAR</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code></td>
+</tr>
+<tr>
+<td>extxyz</td>
+<td>POSCAR files</td>
+<td><code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code></td>
+</tr>
+<tr>
+<td>XDATCAR</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code></td>
+</tr>
+<tr>
+<td>POSCAR</td>
+<td>LAMMPS data</td>
+<td><code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code></td>
+</tr>
+<tr>
+<td>LAMMPS dump</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code></td>
+</tr>
+<tr>
+<td>CIF</td>
+<td>POSCAR</td>
+<td><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code></td>
+</tr>
+<tr>
+<td>CIF</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -cif2exyz input.cif model.xyz</code></td>
+</tr>
+<tr>
+<td>ASE traj</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -traj2exyz input.traj output.xyz</code></td>
+</tr>
+<tr>
+<td>extxyz</td>
+<td>clean extxyz</td>
+<td><code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code></td>
+</tr>
+</tbody>
+</table>
+<h2 id="common-examples">Common Examples</h2>
+<h3 id="convert-vasp-calculations-to-extxyz">Convert VASP calculations to extxyz</h3>
+<p>If each calculation directory contains an <code>OUTCAR</code>, run:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-out2xyz<span class="w"> </span>./vasp_results/
+</code></pre></div>
+<p>The shell version searches the target directory and converts VASP results into an extxyz file suitable for later analysis. If you prefer the Python implementation:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-out2exyz<span class="w"> </span>./vasp_results/
+</code></pre></div>
+<p>From interactive mode, choose <code>101</code>. You will see:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>| Calling the script in Scripts/format_conversion |
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>| Script: out2xyz.sh                              |
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>Input the directory containing OUTCARs
+<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>Example: ./
+<a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a>------------&gt;&gt;
+</code></pre></div>
+<h3 id="add-group-labels">Add group labels</h3>
+<p>Some GPUMD-related workflows use group labels for atom grouping, for example in species-specific MSD or diffusion calculations.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
+</code></pre></div>
+<p>This command reads the input structure and writes an extxyz file with group information.</p>
+<p>From interactive mode, choose <code>106</code>. You will see:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>| Calling the script in Scripts/format_conversion |
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>| Script: add_groups.py                           |
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a>Input &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...
+<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a>Example: POSCAR Li Y Cl
+<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>------------&gt;&gt;
+</code></pre></div>
+<h2 id="script-details">Script Details</h2>
+<h3 id="poscar-to-extxyz">POSCAR to extxyz</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+</code></pre></div>
+<p>Use this when you have a single VASP structure and want an extxyz output.</p>
+<p>Interactive keyword: <code>pos2exyz</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>Input &lt;POSCAR&gt; &lt;output.xyz&gt;
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>Example: POSCAR model.xyz
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>------------&gt;&gt;
+</code></pre></div>
+<h3 id="extxyz-to-poscar">extxyz to POSCAR</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-exyz2pos<span class="w"> </span>structures.xyz
+</code></pre></div>
+<p>This converts all frames in an extxyz file into <code>POSCAR_*.vasp</code> files. Frame indices are 0-based in most GPUMDkit scripts, but output filenames are meant for direct inspection and batch calculations.</p>
+<p>Interactive entry: <code>105</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>Input the name of extxyz
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>Example: ./train.xyz
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>------------&gt;&gt;
+</code></pre></div>
+<h3 id="lammps-dump-to-extxyz">LAMMPS dump to extxyz</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-lmp2exyz<span class="w"> </span>dump.lammpstrj<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
+</code></pre></div>
+<p>The element symbols must match the LAMMPS atom type IDs. For example, if type <code>1</code> is Li, type <code>2</code> is Y, and type <code>3</code> is Cl, the order should be <code>Li Y Cl</code>.</p>
+<p>Interactive keyword: <code>lmp2exyz</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>Example: dump.lammpstrj Li O
+<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>------------&gt;&gt;
+</code></pre></div>
+<h3 id="cif-conversion">CIF conversion</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-cif2pos<span class="w"> </span>input.cif<span class="w"> </span>POSCAR.vasp
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>gpumdkit.sh<span class="w"> </span>-cif2exyz<span class="w"> </span>input.cif<span class="w"> </span>model.xyz
+</code></pre></div>
+<p>Use <code>-cif2pos</code> if you want a VASP-style structure, and <code>-cif2exyz</code> if the next step is GPUMDkit analysis.</p>
+<h3 id="add-weights">Add weights</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-addweight<span class="w"> </span>train.xyz<span class="w"> </span>train_weighted.xyz<span class="w"> </span><span class="m">5</span>
+</code></pre></div>
+<p>This is useful when you want some structures to have a different training weight in a NEP dataset.</p>
+<h3 id="replicate-structures">Replicate structures</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-replicate<span class="w"> </span>POSCAR<span class="w"> </span>supercell.vasp<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span>
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-replicate<span class="w"> </span>POSCAR<span class="w"> </span>supercell.vasp<span class="w"> </span><span class="m">256</span>
+</code></pre></div>
+<p>The first form uses explicit replication factors. The second form tries to build a supercell close to a target atom count.</p>
+<h3 id="extract-one-frame">Extract one frame</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-get_frame<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1000</span>
+</code></pre></div>
+<p>This extracts frame index <code>1000</code> from an extxyz trajectory.</p>
+<h2 id="common-mistakes">Common Mistakes</h2>
+<table>
+<thead>
+<tr>
+<th>Problem</th>
+<th>What to Check</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>LAMMPS elements are wrong</td>
+<td>Check the element order passed after the dump file</td>
+</tr>
+<tr>
+<td>A trajectory has strange metadata</td>
+<td>Try <code>-clean_xyz input.xyz clean.xyz</code></td>
+</tr>
+<tr>
+<td>A converted structure looks shifted</td>
+<td>Inspect PBC/cell information in the source file</td>
+</tr>
+<tr>
+<td>Frame extraction gives the wrong structure</td>
+<td>Remember that frame indices are 0-based</td>
+</tr>
+</tbody>
+</table>
+<h2 id="notes">Notes</h2>
+<p>If a Python package required by a specific converter is missing, Python will report it when that converter is used.</p>
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+      <a href="../index.html" class="md-nav__link">
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+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit Tutorials
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="index.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit Tutorials
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#what-is-gpumdkit" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        What is GPUMDkit?
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#quick-start" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Quick Start
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Quick Start">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#installation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Installation
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#dependencies" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Dependencies
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#usage" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#tutorials" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Tutorials
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-convert-vasp-outcars" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example: Convert VASP OUTCARs
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-plot-nep-results" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example: Plot NEP Results
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-ionic-conductivity" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example: Ionic Conductivity
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#module-overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Module Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#links" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Links
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="quick_start.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Quick Start
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="command_reference.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Command Reference
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="format_conversion.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Format Conversion
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="structure_sampling.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Structure Sampling
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="workflow_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Workflow Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="calculator_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Calculator Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="analyzer_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Analyzer Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="plot_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Plot Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="custom_commands.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Custom Commands
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="active_learning_workflow.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Active Learning Workflow
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="polar_material_analysis.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Polar Material Analysis
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="contributing_to_gpumdkit.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
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+  
+  
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+    <li class="md-nav__item md-nav__item--nested">
+      
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+        
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    简体中文
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
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+    简体中文
+  
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+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/index.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit 教程
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
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+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
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+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
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+      
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+  
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+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#what-is-gpumdkit" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        What is GPUMDkit?
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#quick-start" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Quick Start
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Quick Start">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#installation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Installation
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#dependencies" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Dependencies
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#usage" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
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+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#tutorials" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Tutorials
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-convert-vasp-outcars" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example: Convert VASP OUTCARs
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-plot-nep-results" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example: Plot NEP Results
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-ionic-conductivity" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example: Ionic Conductivity
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#module-overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Module Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#links" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Links
+      
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+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>📚 GPUMDkit Tutorials</h1>
+  <p style="text-align: justify;">Welcome to <strong>GPUMDkit</strong>, a command-line toolkit for GPUMD and NEP.</p>
+</div>
+
+<h2 id="what-is-gpumdkit">What is GPUMDkit?</h2>
+<p>GPUMDkit streamlines common tasks in computational materials science:</p>
+<ul>
+<li><strong>Format Conversion</strong>: Convert between VASP, LAMMPS, CP2K, ABACUS, CIF, and extxyz formats</li>
+<li><strong>Visualization</strong>: Plotting tools for NEP training, MD simulations, and analysis</li>
+<li><strong>Calculators</strong>: Compute ionic conductivity, descriptors, MSD, NEB, and more</li>
+<li><strong>Analyzers</strong>: Structure validation, filtering, composition analysis</li>
+<li><strong>Workflows</strong>: Batch processing for DFT and MD simulations</li>
+<li><strong>Sampling</strong>: Structure selection using uniform, random, or FPS methods</li>
+</ul>
+<h2 id="quick-start">Quick Start</h2>
+<h3 id="installation">Installation</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="nb">source</span><span class="w"> </span>./install.sh
+</code></pre></div>
+<h3 id="dependencies">Dependencies</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>gpumdkit<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>gpumdkit
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>pip<span class="w"> </span>install<span class="w"> </span>neptrain<span class="w"> </span>dpdata<span class="w"> </span>calorine
+</code></pre></div>
+<h3 id="usage">Usage</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="c1"># Interactive mode</span>
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="c1"># Command-line mode</span>
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>gpumdkit.sh<span class="w"> </span>-&lt;option&gt;<span class="w"> </span><span class="o">[</span>args...<span class="o">]</span>
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a><span class="c1"># Get help</span>
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>gpumdkit.sh<span class="w"> </span>-h
+</code></pre></div>
+<h2 id="tutorials">Tutorials</h2>
+<table>
+<thead>
+<tr>
+<th>Tutorial</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><a href="quick_start.html">Quick Start</a></td>
+<td>Installation and first steps</td>
+</tr>
+<tr>
+<td><a href="command_reference.html">Command Reference</a></td>
+<td>One-page CLI and menu reference</td>
+</tr>
+<tr>
+<td><a href="format_conversion.html">Format Conversion</a></td>
+<td>Convert between file formats</td>
+</tr>
+<tr>
+<td><a href="calculator_scripts.html">Calculator Scripts</a></td>
+<td>Compute material properties</td>
+</tr>
+<tr>
+<td><a href="analyzer_scripts.html">Analyzer Scripts</a></td>
+<td>Structure analysis and validation</td>
+</tr>
+<tr>
+<td><a href="plot_scripts.html">Plot Scripts</a></td>
+<td>Plotting and visualization</td>
+</tr>
+<tr>
+<td><a href="workflow_scripts.html">Workflow Scripts</a></td>
+<td>Batch processing and automation</td>
+</tr>
+<tr>
+<td><a href="structure_sampling.html">Structure Sampling</a></td>
+<td>Structure selection methods</td>
+</tr>
+<tr>
+<td><a href="custom_commands.html">Custom Commands</a></td>
+<td>User-defined GPUMDkit shortcuts</td>
+</tr>
+<tr>
+<td><a href="active_learning_workflow.html">Active Learning Workflow</a></td>
+<td>Batch active-learning workflow notes</td>
+</tr>
+<tr>
+<td><a href="polar_material_analysis.html">Polar Material Analysis</a></td>
+<td>Ferroelectric and polarization tools</td>
+</tr>
+<tr>
+<td><a href="contributing_to_gpumdkit.html">Contributing to GPUMDkit</a></td>
+<td>Development notes</td>
+</tr>
+</tbody>
+</table>
+<h2 id="example-convert-vasp-outcars">Example: Convert VASP OUTCARs</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-out2xyz<span class="w"> </span>./vasp_results/
+</code></pre></div>
+<h2 id="example-plot-nep-results">Example: Plot NEP Results</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>prediction
+</code></pre></div>
+<h2 id="example-ionic-conductivity">Example: Ionic Conductivity</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>trajectory.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>ionic-cond<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+</code></pre></div>
+<h2 id="module-overview">Module Overview</h2>
+<table>
+<thead>
+<tr>
+<th>Module</th>
+<th>Menu</th>
+<th>CLI</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>Format Conversion</td>
+<td>1</td>
+<td><code>-out2xyz</code>, <code>-pos2exyz</code></td>
+<td>File conversion</td>
+</tr>
+<tr>
+<td>Sample Structures</td>
+<td>2</td>
+<td><code>-neptrain</code>, interactive menu</td>
+<td>Structure sampling</td>
+</tr>
+<tr>
+<td>Workflow</td>
+<td>3</td>
+<td>-</td>
+<td>Batch processing</td>
+</tr>
+<tr>
+<td>Calculators</td>
+<td>4</td>
+<td><code>-calc &lt;type&gt;</code></td>
+<td>Property calculations</td>
+</tr>
+<tr>
+<td>Analyzer</td>
+<td>5</td>
+<td><code>-range</code>, <code>-min_dist</code></td>
+<td>Structure analysis</td>
+</tr>
+<tr>
+<td>Visualization</td>
+<td>6</td>
+<td><code>-plt &lt;type&gt;</code></td>
+<td>Plotting tools</td>
+</tr>
+<tr>
+<td>Utilities</td>
+<td>7</td>
+<td><code>-time</code>, <code>-clean</code></td>
+<td>Utility functions</td>
+</tr>
+</tbody>
+</table>
+<h2 id="links">Links</h2>
+<ul>
+<li>GitHub: https://github.com/zhyan0603/GPUMDkit</li>
+<li>Documentation: https://zhyan0603.github.io/GPUMDkit/</li>
+</ul>
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+      <a href="format_conversion.html" class="md-nav__link">
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+      <a href="structure_sampling.html" class="md-nav__link">
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+      <a href="calculator_scripts.html" class="md-nav__link">
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+    Calculator Scripts
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+      <a href="analyzer_scripts.html" class="md-nav__link">
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+    Plot Scripts
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+      </a>
+      
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+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#quick-access" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Quick Access
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep-training-and-prediction" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP Training and Prediction
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="NEP Training and Prediction">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#training-results" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Training Results
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#prediction-results" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Prediction Results
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#traintest-comparison" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Train/Test Comparison
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#density-parity-plot" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Density Parity Plot
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#force-error-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Force Error Analysis
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#restart-parameters" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Restart Parameters
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#charge-and-born-effective-charge" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Charge and Born Effective Charge
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#molecular-dynamics-and-thermodynamics" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Molecular Dynamics and Thermodynamics
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Molecular Dynamics and Thermodynamics">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#thermodynamic-properties" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Thermodynamic Properties
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#radial-distribution-function" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Radial Distribution Function
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#velocity-autocorrelation-and-pdos" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Velocity Autocorrelation and PDOS
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#diffusion-and-ionic-transport" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Diffusion and Ionic Transport
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Diffusion and Ionic Transport">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#mean-square-displacement" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Mean Square Displacement
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#msd-for-all-species" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MSD for All Species
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#msd-convergence-check" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MSD Convergence Check
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#self-diffusion-coefficient" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Self-Diffusion Coefficient
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arrhenius-diffusivity" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arrhenius Diffusivity
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arrhenius-ionic-conductivity" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arrhenius Ionic Conductivity
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#heat-transport" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Heat Transport
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Heat Transport">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#emd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        EMD
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#nemd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEMD
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#hnemd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        HNEMD
+      
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+  
+</li>
+        
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+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#descriptor-dimer-and-extra-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Descriptor, Dimer, and Extra Analysis
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Descriptor, Dimer, and Extra Analysis">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#descriptor-visualization" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Descriptor Visualization
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#dimer-curve" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Dimer Curve
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#density-of-atomistic-states" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Density of Atomistic States
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#net-force-distribution" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Net Force Distribution
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#plane-grid-plot-for-polar-materials" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plane-Grid Plot for Polar Materials
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#quick-reference-table" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Quick Reference Table
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
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+      <a href="custom_commands.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Custom Commands
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
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+      <a href="active_learning_workflow.html" class="md-nav__link">
+        
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+  
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+    
+  
+    Active Learning Workflow
+  
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+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="polar_material_analysis.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Polar Material Analysis
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="contributing_to_gpumdkit.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+        </nav>
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+    <li class="md-nav__item md-nav__item--nested">
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        
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+    
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+  
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+      <a href="../zh/index.html" class="md-nav__link">
+        
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+    
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+    GPUMDkit 教程
+  
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+  
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+    </li>
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+
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+      <a href="../zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
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+  </span>
+  
+  
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+    </li>
+  
+
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+            
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+      <a href="../zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#quick-access" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Quick Access
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep-training-and-prediction" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP Training and Prediction
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="NEP Training and Prediction">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#training-results" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Training Results
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#prediction-results" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Prediction Results
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#traintest-comparison" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Train/Test Comparison
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#density-parity-plot" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Density Parity Plot
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#force-error-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Force Error Analysis
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#restart-parameters" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Restart Parameters
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#charge-and-born-effective-charge" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Charge and Born Effective Charge
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#molecular-dynamics-and-thermodynamics" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Molecular Dynamics and Thermodynamics
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Molecular Dynamics and Thermodynamics">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#thermodynamic-properties" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Thermodynamic Properties
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#radial-distribution-function" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Radial Distribution Function
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#velocity-autocorrelation-and-pdos" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Velocity Autocorrelation and PDOS
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#diffusion-and-ionic-transport" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Diffusion and Ionic Transport
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Diffusion and Ionic Transport">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#mean-square-displacement" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Mean Square Displacement
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#msd-for-all-species" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MSD for All Species
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#msd-convergence-check" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MSD Convergence Check
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#self-diffusion-coefficient" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Self-Diffusion Coefficient
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arrhenius-diffusivity" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arrhenius Diffusivity
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arrhenius-ionic-conductivity" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arrhenius Ionic Conductivity
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#heat-transport" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Heat Transport
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Heat Transport">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#emd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        EMD
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#nemd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEMD
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#hnemd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        HNEMD
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#descriptor-dimer-and-extra-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Descriptor, Dimer, and Extra Analysis
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Descriptor, Dimer, and Extra Analysis">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#descriptor-visualization" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Descriptor Visualization
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#dimer-curve" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Dimer Curve
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#density-of-atomistic-states" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Density of Atomistic States
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#net-force-distribution" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Net Force Distribution
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#plane-grid-plot-for-polar-materials" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plane-Grid Plot for Polar Materials
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#quick-reference-table" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Quick Reference Table
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>📊 Plot Scripts</h1>
+  <p style="text-align: justify;">The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators.</p>
+</div>
+
+<p><strong>Script Location:</strong> <code>Scripts/plt_scripts/</code></p>
+<h2 id="quick-access">Quick Access</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w">          </span><span class="c1"># show all plotting options</span>
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w">   </span><span class="c1"># generate a plot</span>
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>save
+<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>-h
+</code></pre></div>
+<h2 id="nep-training-and-prediction">NEP Training and Prediction</h2>
+<h3 id="training-results">Training Results</h3>
+<p><code>plt_train.py</code> visualizes NEP training progress, including loss curves and parity plots for energy, force, and virial/stress.</p>
+<p><strong>Input files:</strong></p>
+<ul>
+<li><code>loss.out</code></li>
+<li><code>energy_train.out</code></li>
+<li><code>force_train.out</code></li>
+<li><code>virial_train.out</code></li>
+</ul>
+<p><strong>Usage:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/train.png" alt="NEP training results" width="75%" />
+</div>
+
+<h3 id="prediction-results">Prediction Results</h3>
+<p><code>plt_prediction.py</code> visualizes prediction/test-set results.</p>
+<p><strong>Input files:</strong></p>
+<ul>
+<li><code>energy_test.out</code></li>
+<li><code>force_test.out</code></li>
+<li><code>virial_test.out</code></li>
+</ul>
+<p><strong>Usage:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>prediction
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/prediction.png" alt="NEP prediction results" width="75%" />
+</div>
+
+<h3 id="traintest-comparison">Train/Test Comparison</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train_test
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/train_test.png" alt="NEP train and test comparison" width="75%" />
+</div>
+
+<h3 id="density-parity-plot">Density Parity Plot</h3>
+<p>For large datasets, density-based parity plots are often easier to read than raw scatter plots.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>parity_density
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/parity_plot_density.png" alt="Parity density plot" width="70%" />
+</div>
+
+<h3 id="force-error-analysis">Force Error Analysis</h3>
+<p><code>plt_force_errors.py</code> plots force magnitude and angular errors following the analysis style proposed by <a href="https://doi.org/10.1038/s41524-023-01123-3">Liu et al.</a>.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>force_errors
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/force_errors.png" alt="Force error analysis" width="70%" />
+</div>
+
+<h3 id="restart-parameters">Restart Parameters</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>restart
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/nep_restart.png" alt="NEP restart parameters" width="60%" />
+</div>
+
+<h3 id="charge-and-born-effective-charge">Charge and Born Effective Charge</h3>
+<p>For qNEP charge output:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>charge
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/charge.png" alt="Charge distribution" width="45%" />
+</div>
+
+<p>For Born effective charge prediction:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>born_charge
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>bec
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/born_charge.png" alt="Born effective charge parity plot" width="45%" />
+</div>
+
+<h2 id="molecular-dynamics-and-thermodynamics">Molecular Dynamics and Thermodynamics</h2>
+<h3 id="thermodynamic-properties">Thermodynamic Properties</h3>
+<p><code>plt_thermo.py</code> reads <code>thermo.out</code> and plots temperature, potential energy, pressure, and other thermodynamic quantities.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo2
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo3
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/thermo.png" alt="Thermo plot" width="75%" />
+</div>
+
+<h3 id="radial-distribution-function">Radial Distribution Function</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf<span class="w"> </span>&lt;column&gt;
+</code></pre></div>
+<p>Full RDF output:</p>
+<div align="center">
+  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
+</div>
+
+<p>Single pair RDF:</p>
+<div align="center">
+  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
+</div>
+
+<h3 id="velocity-autocorrelation-and-pdos">Velocity Autocorrelation and PDOS</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos<span class="w"> </span>save
+</code></pre></div>
+<p><strong>Input files:</strong> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></p>
+<div align="center">
+  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
+</div>
+
+<p>Heat capacity output:</p>
+<div align="center">
+  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
+</div>
+
+<h2 id="diffusion-and-ionic-transport">Diffusion and Ionic Transport</h2>
+<h3 id="mean-square-displacement">Mean Square Displacement</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="Mean square displacement" width="48%" />
+</div>
+
+<h3 id="msd-for-all-species">MSD for All Species</h3>
+<p>Use this when <code>compute_msd</code> in <code>run.in</code> was configured with <code>all_groups</code>.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd_all<span class="w"> </span>msd.out<span class="w"> </span>Li<span class="w"> </span>P<span class="w"> </span>S
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/msd_all.png" alt="MSD for all species" width="48%" />
+</div>
+
+<h3 id="msd-convergence-check">MSD Convergence Check</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd_conv
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/msd_convergence.png" alt="MSD convergence" width="48%" />
+</div>
+
+<h3 id="self-diffusion-coefficient">Self-Diffusion Coefficient</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/sdc.png" alt="Self-diffusion coefficient" width="48%" />
+</div>
+
+<h3 id="arrhenius-diffusivity">Arrhenius Diffusivity</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_d
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>D
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/Arrhenius_D.png" alt="Arrhenius diffusivity" width="58%" />
+</div>
+
+<p>Example output:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>T: 300K, D_total: 1.001e-07 cm2/s
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>T: 350K, D_total: 4.184e-07 cm2/s
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>T: 400K, D_total: 1.027e-06 cm2/s
+<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a>Ea: 0.230 eV
+</code></pre></div>
+<h3 id="arrhenius-ionic-conductivity">Arrhenius Ionic Conductivity</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_sigma
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sigma
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/Arrhenius_sigma.png" alt="Arrhenius ionic conductivity" width="58%" />
+</div>
+
+<h2 id="heat-transport">Heat Transport</h2>
+<h3 id="emd">EMD</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>emd<span class="w"> </span>x
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/emd.png" alt="EMD thermal conductivity" width="72%" />
+</div>
+
+<h3 id="nemd">NEMD</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>nemd<span class="w"> </span><span class="o">[</span>real_length<span class="o">]</span><span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
+</code></pre></div>
+<p>Parameter notes:</p>
+<table>
+<thead>
+<tr>
+<th>Parameter</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>real_length</code></td>
+<td>real length of heat-transfer zone in nm; use <code>Auto</code> for automatic calculation</td>
+</tr>
+<tr>
+<td><code>scale_eff_size</code></td>
+<td>scale factor for effective cross-sectional area</td>
+</tr>
+<tr>
+<td><code>cutoff_freq</code></td>
+<td>cutoff frequency for SHC calculation in THz</td>
+</tr>
+<tr>
+<td><code>save</code></td>
+<td>optional flag to save the figure</td>
+</tr>
+</tbody>
+</table>
+<div align="center">
+  <img src="../../Gallery/nemd.png" alt="NEMD results" width="72%" />
+</div>
+
+<h3 id="hnemd">HNEMD</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>hnemd<span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/hnemd.png" alt="HNEMD results" width="72%" />
+</div>
+
+<h2 id="descriptor-dimer-and-extra-analysis">Descriptor, Dimer, and Extra Analysis</h2>
+<h3 id="descriptor-visualization">Descriptor Visualization</h3>
+<p>First calculate descriptors:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
+</code></pre></div>
+<p>Then visualize:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-23-1" name="__codelineno-23-1" href="#__codelineno-23-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
+<a id="__codelineno-23-2" name="__codelineno-23-2" href="#__codelineno-23-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/des_umap.png" alt="UMAP descriptor visualization" width="52%" />
+</div>
+
+<h3 id="dimer-curve">Dimer Curve</h3>
+<p><code>plt_dimer.py</code> places two atoms in a large cubic box and calculates energy/force as a function of dimer distance using a NEP model.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-24-1" name="__codelineno-24-1" href="#__codelineno-24-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span>nep.txt
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/dimer_nep.png" alt="Dimer NEP curve" width="45%" />
+  <img src="../../Gallery/dimer.png" alt="Dimer comparison" width="45%" />
+</div>
+
+<p><strong>Reference:</strong> <a href="https://doi.org/10.1021/acs.jcim.5c02335">J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</a></p>
+<h3 id="density-of-atomistic-states">Density of Atomistic States</h3>
+<p><code>plt_doas.py</code> plots the density of atomistic states proposed by <a href="https://doi.org/10.1002/anie.202215544">Wang et al.</a>.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-25-1" name="__codelineno-25-1" href="#__codelineno-25-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
+</div>
+
+<h3 id="net-force-distribution">Net Force Distribution</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-26-1" name="__codelineno-26-1" href="#__codelineno-26-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>net_force<span class="w"> </span>train.xyz
+</code></pre></div>
+<p><strong>Reference:</strong> <a href="https://arxiv.org/abs/2510.19774">arXiv:2510.19774</a></p>
+<div align="center">
+  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
+</div>
+
+<h2 id="plane-grid-plot-for-polar-materials">Plane-Grid Plot for Polar Materials</h2>
+<p>This workflow maps displacement or polarization data onto a grid and plots selected plane profiles.</p>
+<p>Typical upstream steps:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-27-1" name="__codelineno-27-1" href="#__codelineno-27-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span><span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
+<a id="__codelineno-27-2" name="__codelineno-27-2" href="#__codelineno-27-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Pb_Sr-O.dat<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+<a id="__codelineno-27-3" name="__codelineno-27-3" href="#__codelineno-27-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+</code></pre></div>
+<p>Plot:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-28-1" name="__codelineno-28-1" href="#__codelineno-28-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr
+<a id="__codelineno-28-2" name="__codelineno-28-2" href="#__codelineno-28-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span>
+</code></pre></div>
+<p>This function requires <code>ferrodispcalc</code>.</p>
+<h2 id="quick-reference-table">Quick Reference Table</h2>
+<table>
+<thead>
+<tr>
+<th>Command</th>
+<th>Input File(s)</th>
+<th>Purpose</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>train</code></td>
+<td><code>loss.out</code>, <code>*_train.out</code></td>
+<td>NEP training plots</td>
+</tr>
+<tr>
+<td><code>prediction</code></td>
+<td><code>*_test.out</code></td>
+<td>NEP prediction plots</td>
+</tr>
+<tr>
+<td><code>train_test</code></td>
+<td>train/test outputs</td>
+<td>combined parity plots</td>
+</tr>
+<tr>
+<td><code>thermo</code></td>
+<td><code>thermo.out</code></td>
+<td>thermodynamic properties</td>
+</tr>
+<tr>
+<td><code>msd</code></td>
+<td><code>msd.out</code></td>
+<td>mean square displacement</td>
+</tr>
+<tr>
+<td><code>sdc</code></td>
+<td><code>msd.out</code></td>
+<td>self-diffusion coefficient</td>
+</tr>
+<tr>
+<td><code>rdf</code></td>
+<td><code>rdf.out</code></td>
+<td>radial distribution function</td>
+</tr>
+<tr>
+<td><code>pdos</code></td>
+<td><code>dos.out</code>, <code>mvac.out</code></td>
+<td>VAC and PDOS</td>
+</tr>
+<tr>
+<td><code>emd</code></td>
+<td>EMD outputs</td>
+<td>EMD thermal conductivity</td>
+</tr>
+<tr>
+<td><code>nemd</code></td>
+<td>NEMD outputs</td>
+<td>NEMD thermal transport</td>
+</tr>
+<tr>
+<td><code>hnemd</code></td>
+<td>HNEMD outputs</td>
+<td>HNEMD thermal transport</td>
+</tr>
+<tr>
+<td><code>des</code></td>
+<td><code>descriptors.npy</code></td>
+<td>descriptor PCA/UMAP</td>
+</tr>
+<tr>
+<td><code>dimer</code></td>
+<td><code>nep.txt</code></td>
+<td>dimer energy/force curve</td>
+</tr>
+<tr>
+<td><code>doas</code></td>
+<td><code>doas.out</code></td>
+<td>density of atomistic states</td>
+</tr>
+<tr>
+<td><code>net_force</code></td>
+<td><code>train.xyz</code></td>
+<td>net force distribution</td>
+</tr>
+</tbody>
+</table>
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+
+
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+
+
+
+
+                
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diff --git a/docs/htmls/en/polar_material_analysis.html b/docs/htmls/en/polar_material_analysis.html
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+    
+  
+    Polar Material Analysis
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="polar_material_analysis.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Polar Material Analysis
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#dependency" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Dependency
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#interactive-mode-entry" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive mode entry
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#406-build-neighbor-list-calc_neighbor_listpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        406) Build neighbor list (calc_neighbor_list.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="406) Build neighbor list (calc_neighbor_list.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#usage" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arguments-complete" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments (complete)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#output-file" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output file
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#407-calc-displacement-from-trajectory-calc_displacementpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        407) Calc displacement from trajectory (calc_displacement.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="407) Calc displacement from trajectory (calc_displacement.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#usage_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arguments-complete_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments (complete)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#output-file_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output file
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#408-calc-averaged-structure-calc_averaged_structurepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        408) Calc averaged structure (calc_averaged_structure.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="408) Calc averaged structure (calc_averaged_structure.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#usage_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arguments-complete_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments (complete)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#output-file_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output file
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#409-calc-octahedral-tilt-calc_oct_tiltpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        409) Calc octahedral tilt (calc_oct_tilt.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="409) Calc octahedral tilt (calc_oct_tilt.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#usage_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arguments-complete_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments (complete)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#output-file_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output file
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#410-calc-polarization-for-abo3-calc_polarization_abo3py" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        410) Calc polarization for ABO3 (calc_polarization_abo3.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="410) Calc polarization for ABO3 (calc_polarization_abo3.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#usage_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arguments-complete_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments (complete)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#output-file_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output file
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plane-grid-visualization-plt_plane_gridpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plane-grid visualization (plt_plane_grid.py)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#output-files-at-a-glance" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output files at a glance
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#real-examples" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Real Examples
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Real Examples">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#temperature-driven-ferroelectric-to-paraelectric-phase-transition-for-pbtio3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#step-1-get-averaged-structures-from-the-last-half-of-each-trajectory" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 1: get averaged structures from the last half of each trajectory
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-2-build-neighbor-lists-from-modelxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 2: build neighbor lists from model.xyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-3-compute-displacement-and-polarization-for-each-temperature" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 3: compute displacement and polarization for each temperature
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-4-plot-displacement-and-polarization-maps-in-real-space" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 4: plot displacement and polarization maps in real space
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-5-build-a-temperature-order-parameter-curve" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 5: build a temperature-order-parameter curve
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#topological-structure-in-pbtio3srtio3-superlattice" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Topological structure in PbTiO3/SrTiO3 superlattice
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Topological structure in PbTiO3/SrTiO3 superlattice">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#step-1-build-an-averaged-structure-from-the-last-25-frames" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 1: build an averaged structure from the last 25% frames
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-2-build-the-ti-neighbor-list" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 2: build the Ti neighbor list
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-3-plot-the-plane-grid-map" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 3: plot the plane-grid map
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#other-systems" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Other Systems
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Other Systems">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#organic-inorganic-hybrid-ferroelectrics" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Organic-inorganic hybrid ferroelectrics
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#other-ferroelectric-families" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Other ferroelectric families
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+      </ul>
+    </nav>
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+      <a href="contributing_to_gpumdkit.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
+
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+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+        </nav>
+      
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+    
+  
+    简体中文
+  
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+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
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+  
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+      <a href="../zh/index.html" class="md-nav__link">
+        
+  
+  
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+    
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+    GPUMDkit 教程
+  
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+  </span>
+  
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+    </li>
+  
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+            
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+      <a href="../zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
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+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#dependency" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Dependency
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#interactive-mode-entry" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive mode entry
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#406-build-neighbor-list-calc_neighbor_listpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        406) Build neighbor list (calc_neighbor_list.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="406) Build neighbor list (calc_neighbor_list.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#usage" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arguments-complete" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments (complete)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#output-file" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output file
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#407-calc-displacement-from-trajectory-calc_displacementpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        407) Calc displacement from trajectory (calc_displacement.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="407) Calc displacement from trajectory (calc_displacement.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#usage_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arguments-complete_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments (complete)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#output-file_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output file
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#408-calc-averaged-structure-calc_averaged_structurepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        408) Calc averaged structure (calc_averaged_structure.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="408) Calc averaged structure (calc_averaged_structure.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#usage_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arguments-complete_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments (complete)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#output-file_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output file
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#409-calc-octahedral-tilt-calc_oct_tiltpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        409) Calc octahedral tilt (calc_oct_tilt.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="409) Calc octahedral tilt (calc_oct_tilt.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#usage_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arguments-complete_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments (complete)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#output-file_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output file
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#410-calc-polarization-for-abo3-calc_polarization_abo3py" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        410) Calc polarization for ABO3 (calc_polarization_abo3.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="410) Calc polarization for ABO3 (calc_polarization_abo3.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#usage_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Usage
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#arguments-complete_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Arguments (complete)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#output-file_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output file
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plane-grid-visualization-plt_plane_gridpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plane-grid visualization (plt_plane_grid.py)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#output-files-at-a-glance" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Output files at a glance
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#real-examples" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Real Examples
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Real Examples">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#temperature-driven-ferroelectric-to-paraelectric-phase-transition-for-pbtio3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#step-1-get-averaged-structures-from-the-last-half-of-each-trajectory" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 1: get averaged structures from the last half of each trajectory
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-2-build-neighbor-lists-from-modelxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 2: build neighbor lists from model.xyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-3-compute-displacement-and-polarization-for-each-temperature" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 3: compute displacement and polarization for each temperature
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-4-plot-displacement-and-polarization-maps-in-real-space" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 4: plot displacement and polarization maps in real space
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-5-build-a-temperature-order-parameter-curve" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 5: build a temperature-order-parameter curve
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#topological-structure-in-pbtio3srtio3-superlattice" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Topological structure in PbTiO3/SrTiO3 superlattice
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Topological structure in PbTiO3/SrTiO3 superlattice">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#step-1-build-an-averaged-structure-from-the-last-25-frames" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 1: build an averaged structure from the last 25% frames
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-2-build-the-ti-neighbor-list" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 2: build the Ti neighbor list
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#step-3-plot-the-plane-grid-map" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Step 3: plot the plane-grid map
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#other-systems" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Other Systems
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Other Systems">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#organic-inorganic-hybrid-ferroelectrics" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Organic-inorganic hybrid ferroelectrics
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#other-ferroelectric-families" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Other ferroelectric families
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🧲 Polar Material Analysis</h1>
+  <p style="text-align: justify;">This tutorial covers GPUMDkit calculator options <code>406-410</code> and the <code>plane-grid</code> plotting workflow.</p>
+</div>
+
+<p><strong>Script Location:</strong> <code>Scripts/calculators/</code> and <code>Scripts/plt_scripts/</code></p>
+<p>This tutorial includes both general and system-specific tools:</p>
+<ul>
+<li><code>nlist</code>, <code>disp</code>, and <code>avg-struct</code> are broadly useful for structure/trajectory analysis.</li>
+<li><code>oct-tilt</code> is for octahedral environments (requires 6 neighbors around each center).</li>
+<li><code>pol-abo3</code> is specific to <code>ABO3</code> polarization analysis.</li>
+</ul>
+<h2 id="dependency">Dependency</h2>
+<p>These scripts require <code>ferrodispcalc</code>:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
+</code></pre></div>
+<h2 id="interactive-mode-entry">Interactive mode entry</h2>
+<p>Options <code>406-410</code> are the core functions for this tutorial. The sections below explain when to use each one and how to run it.</p>
+<p>For full argument details, use:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-h
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-h
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-h
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-h
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-h
+<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-h
+</code></pre></div>
+<h2 id="406-build-neighbor-list-calc_neighbor_listpy">406) Build neighbor list (<code>calc_neighbor_list.py</code>)</h2>
+<p>Build neighbor lists for selected center and neighbor elements.</p>
+<p>When to use it:
+This is usually the first step before <code>disp</code>, <code>oct-tilt</code>, and <code>pol-abo3</code>, because those scripts read <code>nl-*.dat</code> neighbor files.</p>
+<h3 id="usage">Usage</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="c1"># Example 1: Ti-O nearest 6 neighbors for octahedral analysis</span>
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="c1"># Example 2: Pb/Sr-O nearest 12 neighbors for A-site centered analysis</span>
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
+</code></pre></div>
+<h3 id="arguments-complete">Arguments (complete)</h3>
+<ul>
+<li><code>-i, --input</code>:
+  Input structure file. Default: <code>model.xyz</code>.</li>
+<li><code>-x, --index</code>:
+  Frame index to read from input. Default: <code>0</code>.</li>
+<li><code>-c, --cutoff</code> (required):
+  Neighbor search cutoff (Angstrom).</li>
+<li><code>-n, --neighbor-num</code> (required):
+  Number of neighbors per center.</li>
+<li><code>-d, --defect</code>:
+  Defect mode. If enabled and neighbors are insufficient, missing slots are filled with the center index.</li>
+<li><code>-C, --center-elements</code> (required):
+  Center species list.</li>
+<li><code>-E, --neighbor-elements</code> (required):
+  Neighbor species list.</li>
+<li><code>-o, --output</code>:
+  Output file path. Default: <code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>.</li>
+</ul>
+<h3 id="output-file">Output file</h3>
+<ul>
+<li>Main output: neighbor list text file (for example <code>nl-Ti-O.dat</code>).</li>
+<li>The file is a 2D integer array with shape <code>(n_center, neighbor_num + 1)</code>. Each row corresponds to one center atom: the first column is the center index, and the remaining columns are its neighbor indices (all 1-based).</li>
+</ul>
+<h2 id="407-calc-displacement-from-trajectory-calc_displacementpy">407) Calc displacement from trajectory (<code>calc_displacement.py</code>)</h2>
+<p>Compute local displacement vectors from a trajectory/model and a neighbor list.</p>
+<h3 id="usage_1">Usage</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># Example 1: single-frame displacement from model.xyz</span>
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>disp_model.dat
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="c1"># Example 2: use the last 20% frames in movie.xyz</span>
+<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+</code></pre></div>
+<h3 id="arguments-complete_1">Arguments (complete)</h3>
+<ul>
+<li><code>-i, --input</code>:
+  Input xyz file. Default: <code>model.xyz</code>.</li>
+<li><code>-n, --neighbor-list</code> (required):
+  Neighbor list file from <code>nlist</code>.</li>
+<li><code>-o, --output</code>:
+  Output file. Default: <code>displacements.dat</code>.</li>
+<li><code>-s, --start</code>:
+  Slice start index. Default: <code>0</code>.</li>
+<li><code>-t, --stop</code>:
+  Slice stop index. Default: end.</li>
+<li><code>-p, --step</code>:
+  Slice step. Default: <code>1</code>.</li>
+<li><code>-l, --last</code>:
+  Select trailing frames.
+  Integer: last <code>N</code> frames.
+  <code>0 &lt; value &lt; 1</code>: last ratio of frames.</li>
+<li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
+</ul>
+<h3 id="output-file_1">Output file</h3>
+<ul>
+<li>Main output: <code>displacements.dat</code> (or your custom output name).</li>
+<li>The saved text file is a 2D array: for a single-frame input, its shape is <code>(n_center, 3)</code>; for a multi-frame input, it is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The three columns are <code>dx</code>, <code>dy</code>, and <code>dz</code> displacement components in Angstrom.</li>
+</ul>
+<h2 id="408-calc-averaged-structure-calc_averaged_structurepy">408) Calc averaged structure (<code>calc_averaged_structure.py</code>)</h2>
+<p>Generate one averaged structure from selected trajectory frames.
+Use this after equilibration. For a solid near equilibrium, average a frame window at the target temperature and analyze that representative structure instead of processing every snapshot.</p>
+<h3 id="usage_2">Usage</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="c1"># Example 1: average all frames</span>
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="c1"># Example 2: average selected frames (100:500:2)</span>
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-s<span class="w"> </span><span class="m">100</span><span class="w"> </span>-t<span class="w"> </span><span class="m">500</span><span class="w"> </span>-p<span class="w"> </span><span class="m">2</span><span class="w"> </span>-o<span class="w"> </span>avg_slice.xyz
+</code></pre></div>
+<h3 id="arguments-complete_2">Arguments (complete)</h3>
+<ul>
+<li><code>-i, --input</code>:
+  Input trajectory file. Default: <code>movie.xyz</code>.</li>
+<li><code>-o, --output</code>:
+  Output structure file. Default: <code>averaged_structure.xyz</code>.</li>
+<li><code>-s, --start</code>:
+  Slice start index. Default: <code>0</code>.</li>
+<li><code>-t, --stop</code>:
+  Slice stop index. Default: end.</li>
+<li><code>-p, --step</code>:
+  Slice step. Default: <code>1</code>.</li>
+<li><code>-l, --last</code>:
+  Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li>
+<li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
+</ul>
+<h3 id="output-file_2">Output file</h3>
+<ul>
+<li>Main output: averaged single-frame extxyz file.</li>
+<li>Position averaging applies MIC/PBC correction relative to the first selected frame.</li>
+</ul>
+<h2 id="409-calc-octahedral-tilt-calc_oct_tiltpy">409) Calc octahedral tilt (<code>calc_oct_tilt.py</code>)</h2>
+<p>Calculate octahedral tilt angles from a B-O neighbor list.
+This is commonly used to analyze octahedral rotation patterns in <code>ABO3</code> systems, such as <code>SrTiO3</code> and <code>PbZrO3</code>.</p>
+<h3 id="usage_3">Usage</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="c1"># Example 1: octahedral tilt of the TiO6 octahedra from a single frame</span>
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>oct_tilt_model.dat
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="c1"># Example 2: octahedral tilt of the TiO6 octahedra from the last 20% trajectory frames</span>
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>octahedral_tilt.dat
+</code></pre></div>
+<h3 id="arguments-complete_3">Arguments (complete)</h3>
+<ul>
+<li><code>-i, --input</code>:
+  Input xyz file. Default: <code>model.xyz</code>.</li>
+<li><code>-n, --neighbor-list</code> (required):
+  B-O neighbor list file.</li>
+<li><code>-o, --output</code>:
+  Output file. Default: <code>octahedral_tilt.dat</code>.</li>
+<li><code>-s, --start</code>:
+  Slice start index. Default: <code>0</code>.</li>
+<li><code>-t, --stop</code>:
+  Slice stop index. Default: end.</li>
+<li><code>-p, --step</code>:
+  Slice step. Default: <code>1</code>.</li>
+<li><code>-l, --last</code>:
+  Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li>
+<li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
+</ul>
+<h3 id="output-file_3">Output file</h3>
+<ul>
+<li>Main output: <code>octahedral_tilt.dat</code> (or custom name).</li>
+<li>The saved text file is a 2D array with three columns (<code>theta_x</code>, <code>theta_y</code>, <code>theta_z</code>, in degree): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code>.</li>
+</ul>
+<h2 id="410-calc-polarization-for-abo3-calc_polarization_abo3py">410) Calc polarization for ABO3 (<code>calc_polarization_abo3.py</code>)</h2>
+<p>Calculate local polarization vectors for <code>ABO3</code> systems.</p>
+<h3 id="usage_4">Usage</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="c1"># Example 1: single-frame ABO3 polarization</span>
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Sr</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-o<span class="w"> </span>polarization_model.dat
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="c1"># Example 2: trajectory polarization on a selected frame window</span>
+<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-s<span class="w"> </span><span class="m">200</span><span class="w"> </span>-t<span class="w"> </span><span class="m">600</span><span class="w"> </span>-p<span class="w"> </span><span class="m">5</span><span class="w"> </span>-o<span class="w"> </span>polarization_slice.dat
+</code></pre></div>
+<h3 id="arguments-complete_4">Arguments (complete)</h3>
+<ul>
+<li><code>-i, --input</code>:
+  Input xyz file. Default: <code>model.xyz</code>.</li>
+<li><code>--nl-ba</code> (required):
+  B-A neighbor list.</li>
+<li><code>--nl-bo</code> (required):
+  B-O neighbor list.</li>
+<li><code>-o, --output</code>:
+  Output file. Default: <code>polarization.dat</code>.</li>
+<li><code>--bec</code> (required):
+  Born effective charge terms in <code>Element=value</code> format.
+  Example: <code>Pb=2.5 Ti=4.0 O=-2.0</code>.</li>
+<li><code>-s, --start</code>:
+  Slice start index. Default: <code>0</code>.</li>
+<li><code>-t, --stop</code>:
+  Slice stop index. Default: end.</li>
+<li><code>-p, --step</code>:
+  Slice step. Default: <code>1</code>.</li>
+<li><code>-l, --last</code>:
+  Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li>
+<li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
+</ul>
+<p>Important checks:</p>
+<ul>
+<li><code>--bec</code> must include all element species in the input structure.</li>
+<li>Center atom indices in <code>--nl-ba</code> and <code>--nl-bo</code> must match.</li>
+</ul>
+<h3 id="output-file_4">Output file</h3>
+<ul>
+<li>Main output: <code>polarization.dat</code> (or custom name).</li>
+<li>The saved text file is a 2D array with three columns (<code>Px</code>, <code>Py</code>, <code>Pz</code>, in <code>C/m^2</code>): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The script prints a warning if the total Born charge is not balanced.</li>
+</ul>
+<h3 id="plane-grid-visualization-plt_plane_gridpy">Plane-grid visualization (<code>plt_plane_grid.py</code>)</h3>
+<p>You can visualize either <code>displacements.dat</code> or <code>polarization.dat</code>:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># Example 1: displacement map on Ti sites, first XY layer</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span>
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="c1"># Example 2: polarization map on Pb sites, XZ and YZ layers</span>
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>polarization.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span>--select-yz<span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">4</span>
+</code></pre></div>
+<p>Arguments (complete):</p>
+<ul>
+<li><code>-i, --input</code>:
+  Input xyz file for atomic layout and layering. Default: <code>model.xyz</code>.</li>
+<li><code>-d, --disp</code>:
+  Vector-field data file. Default: <code>displacements.dat</code>.</li>
+<li><code>-e, --elements</code> (required):
+  Center element symbols used to map vectors to lattice layers.</li>
+<li><code>-m, --tol</code>:
+  Layer tolerance for grid mapping. Default: <code>1.0</code>.</li>
+<li><code>-g, --target-size</code>:
+  Expected grid size as <code>nx ny nz</code>.</li>
+<li><code>-o, --save-dir</code>:
+  Figure output directory. Default: <code>plot</code>.</li>
+<li><code>-f, --frame</code>:
+  Frame index to visualize when vector data has multiple frames. Default: <code>0</code>.</li>
+<li><code>--select-xy</code>:
+  Selected XY layer indices.</li>
+<li><code>--select-xz</code>:
+  Selected XZ layer indices.</li>
+<li><code>--select-yz</code>:
+  Selected YZ layer indices.</li>
+</ul>
+<p>Output:</p>
+<ul>
+<li>Creates output directory if needed.</li>
+<li>Saves figures as <code>XY_*.png</code>, <code>XZ_*.png</code>, <code>YZ_*.png</code>.</li>
+</ul>
+<div align="center">
+    <img src="../Gallery/PTO_STO_superlattice.png" alt="PTO_STO" width="65%" />
+</div>
+
+<h2 id="output-files-at-a-glance">Output files at a glance</h2>
+<table>
+<thead>
+<tr>
+<th>Script</th>
+<th>Main output</th>
+<th>What it stores</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>calc_neighbor_list.py</code></td>
+<td><code>nl-*.dat</code></td>
+<td>1-based center index + neighbor indices</td>
+</tr>
+<tr>
+<td><code>calc_displacement.py</code></td>
+<td><code>*.dat</code></td>
+<td>Local displacement vectors (<code>dx dy dz</code>, Angstrom)</td>
+</tr>
+<tr>
+<td><code>calc_averaged_structure.py</code></td>
+<td><code>*.xyz</code></td>
+<td>One averaged structure</td>
+</tr>
+<tr>
+<td><code>calc_oct_tilt.py</code></td>
+<td><code>*.dat</code></td>
+<td>Octahedral tilt angles (<code>theta_x theta_y theta_z</code>, degree)</td>
+</tr>
+<tr>
+<td><code>calc_polarization_abo3.py</code></td>
+<td><code>*.dat</code></td>
+<td>Local polarization vectors (<code>Px Py Pz</code>, <code>C/m^2</code>)</td>
+</tr>
+<tr>
+<td><code>plt_plane_grid.py</code></td>
+<td><code>plot/*.png</code></td>
+<td>XY/XZ/YZ plane maps from vector-field data</td>
+</tr>
+</tbody>
+</table>
+<h2 id="real-examples">Real Examples</h2>
+<h3 id="temperature-driven-ferroelectric-to-paraelectric-phase-transition-for-pbtio3">Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3</h3>
+<p>Assume all files are in the current directory <code>./</code>:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>./
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>├── model.xyz
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>├── 300K.xyz
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>├── 350K.xyz
+<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a>├── 400K.xyz
+<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>├── ...
+<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a>└── 800K.xyz
+</code></pre></div>
+<p><code>model.xyz</code> is the initial structure used to run MD simulations. Each <code>TEMP K.xyz</code> is a trajectory at that temperature.</p>
+<h4 id="step-1-get-averaged-structures-from-the-last-half-of-each-trajectory">Step 1: get averaged structures from the last half of each trajectory</h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span>
+<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a><span class="k">done</span>
+</code></pre></div>
+<p>This writes <code>300K-avg.xyz</code>, <code>350K-avg.xyz</code>, ..., <code>800K-avg.xyz</code>.</p>
+<h4 id="step-2-build-neighbor-lists-from-modelxyz">Step 2: build neighbor lists from <code>model.xyz</code></h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="c1"># B-O list: for each Ti, find the nearest 6 O atoms</span>
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="c1"># A-O list: for each Pb, find the nearest 12 O atoms</span>
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Pb-O.dat
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a><span class="c1"># B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms</span>
+<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">5</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">8</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>Pb<span class="w"> </span>-o<span class="w"> </span>nl-Ti-Pb.dat
+</code></pre></div>
+<h4 id="step-3-compute-displacement-and-polarization-for-each-temperature">Step 3: compute displacement and polarization for each temperature</h4>
+<p>Use Born effective charges (BEC), not nominal ionic charges. For PbTiO3 in this example:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="n">PTO</span> <span class="o">=</span> <span class="p">{</span>
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>    <span class="s1">&#39;Pb&#39;</span><span class="p">:</span> <span class="mf">3.44</span><span class="p">,</span>
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>    <span class="s1">&#39;Ti&#39;</span><span class="p">:</span> <span class="mf">5.18</span><span class="p">,</span>
+<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a>    <span class="s1">&#39;O&#39;</span><span class="p">:</span> <span class="o">-</span><span class="p">(</span><span class="mf">3.44</span> <span class="o">+</span> <span class="mf">5.18</span><span class="p">)</span> <span class="o">/</span> <span class="mi">3</span>
+<a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="p">}</span>
+</code></pre></div>
+<p>You can obtain BEC from your own DFPT calculation or from literature values. Thus use following commands to compute local displacement and polarization:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span>
+<a id="__codelineno-12-4" name="__codelineno-12-4" href="#__codelineno-12-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a><span class="w">    </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">3</span>.44<span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">5</span>.18<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.8733333333<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span>
+<a id="__codelineno-12-6" name="__codelineno-12-6" href="#__codelineno-12-6"></a><span class="k">done</span>
+</code></pre></div>
+<h4 id="step-4-plot-displacement-and-polarization-maps-in-real-space">Step 4: plot displacement and polarization maps in real space</h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp&quot;</span>
+<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol&quot;</span>
+<a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a><span class="k">done</span>
+</code></pre></div>
+<h4 id="step-5-build-a-temperature-order-parameter-curve">Step 5: build a temperature-order-parameter curve</h4>
+<p>By analyzing the lattice of each temperature-averaged structure together with its polarization (<code>XX-pol.dat</code>), we can obtain the following figure:</p>
+<div align="center">
+    <img src="../Gallery/PTO-temp.png" alt="PTO-temp" width="65%" />
+</div>
+
+<p>The trend shows a clear phase transition around <code>600 K</code>, where the polarization vanishes.</p>
+<h3 id="topological-structure-in-pbtio3srtio3-superlattice">Topological structure in PbTiO3/SrTiO3 superlattice</h3>
+<p>Assume <code>movie.xyz</code> is the trajectory of the PbTiO3/SrTiO3 superlattice in the current directory.</p>
+<h4 id="step-1-build-an-averaged-structure-from-the-last-25-frames">Step 1: build an averaged structure from the last 25% frames</h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>model-avg.xyz
+</code></pre></div>
+<h4 id="step-2-build-the-ti-neighbor-list">Step 2: build the Ti neighbor list</h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+</code></pre></div>
+<h4 id="step-3-plot-the-plane-grid-map">Step 3: plot the plane-grid map</h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>disp-last25.dat
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-d<span class="w"> </span>disp-last25.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span>-o<span class="w"> </span>plot-topology
+</code></pre></div>
+<div align="center">
+    <img src="../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
+</div>
+
+<p>This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero. By analyzing how polarization varies around the vortex core, you can estimate the local dielectric response, but that is beyond the scope of this tutorial.</p>
+<p>Note: this figure uses a different colormap from the default GPUMDkit plotting style. The default output does not look exactly the same, but you can get this style with small plotting-script changes.</p>
+<h3 id="other-systems">Other Systems</h3>
+<h4 id="organic-inorganic-hybrid-ferroelectrics">Organic-inorganic hybrid ferroelectrics</h4>
+<p>In many organic-inorganic ferroelectrics, polarization is strongly tied to anisotropic molecular units. A practical way to track molecular orientation is to use bond vectors.</p>
+<p>For TMCM-CdCl3, you can use the C-Cl bond direction of the TMCM molecule as an orientation proxy, then use it to estimate the polarization state:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a><span class="c1"># Find the nearest Cl around each C (tune cutoff if needed)</span>
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">3</span><span class="w"> </span>-n<span class="w"> </span><span class="m">1</span><span class="w"> </span>-C<span class="w"> </span>C<span class="w"> </span>-E<span class="w"> </span>Cl<span class="w"> </span>-o<span class="w"> </span>nl-C-Cl.dat
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>
+<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a><span class="c1"># Compute C-Cl bond vectors from the trajectory</span>
+<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-C-Cl.dat<span class="w"> </span>-o<span class="w"> </span>ccl_vectors.dat
+</code></pre></div>
+<p><code>ccl_vectors.dat</code> can then be analyzed as an orientation order parameter. More details could be found at: Phys. Rev. Lett. 136, 016801</p>
+<h4 id="other-ferroelectric-families">Other ferroelectric families</h4>
+<p>Beyond <code>ABO3</code>, <code>ferrodispcalc</code> can be adapted to many ferroelectric systems, including nitrides, hafnia-based compounds, organic-inorganic hybrids, and some 2D ferroelectrics.</p>
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+  
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+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#1-prepare-a-python-environment" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        1. Prepare a Python Environment
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#2-install-gpumdkit" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        2. Install GPUMDkit
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#3-usage-modes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        3. Usage Modes
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="3. Usage Modes">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#interactive-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive Mode
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#command-line-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Command-Line Mode
+      
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+  
+</li>
+        
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#4-practical-examples" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        4. Practical Examples
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="4. Practical Examples">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#convert-poscar-to-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Convert POSCAR to extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#add-gpumd-group-labels" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Add GPUMD Group Labels
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plot-nep-training-results" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plot NEP Training Results
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plot-nep-test-results" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plot NEP Test Results
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plot-thermodynamic-data" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plot Thermodynamic Data
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plot-msd-and-self-diffusion-coefficient" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plot MSD and Self-Diffusion Coefficient
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#5-help" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        5. Help
+      
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+      <a href="command_reference.html" class="md-nav__link">
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+    Contributing to GPUMDkit
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+      <a href="../zh/index.html" class="md-nav__link">
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+    
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+    GPUMDkit 教程
+  
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+  
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+  
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+                
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+  
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+      <a href="../zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+                
+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#1-prepare-a-python-environment" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        1. Prepare a Python Environment
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#2-install-gpumdkit" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        2. Install GPUMDkit
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#3-usage-modes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        3. Usage Modes
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="3. Usage Modes">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#interactive-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive Mode
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#command-line-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Command-Line Mode
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#4-practical-examples" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        4. Practical Examples
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="4. Practical Examples">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#convert-poscar-to-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Convert POSCAR to extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#add-gpumd-group-labels" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Add GPUMD Group Labels
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plot-nep-training-results" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plot NEP Training Results
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plot-nep-test-results" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plot NEP Test Results
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plot-thermodynamic-data" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plot Thermodynamic Data
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plot-msd-and-self-diffusion-coefficient" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plot MSD and Self-Diffusion Coefficient
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#5-help" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        5. Help
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🚀 Quick Start</h1>
+  <p style="text-align: justify;">This page introduces the basic installation and several common commands. GPUMDkit can be used through the interactive menu or by direct command-line options.</p>
+</div>
+
+<h2 id="1-prepare-a-python-environment">1. Prepare a Python Environment</h2>
+<p>You can use a clean conda environment:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>gpumdkit<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>gpumdkit
+</code></pre></div>
+<p>Some optional functions use additional packages:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>pip<span class="w"> </span>install<span class="w"> </span>neptrain<span class="w"> </span>dpdata<span class="w"> </span>calorine
+</code></pre></div>
+<p>Other Python dependencies are loaded by the corresponding scripts. If a package is missing, Python will report it when that function is used.</p>
+<h2 id="2-install-gpumdkit">2. Install GPUMDkit</h2>
+<p>Clone the repository:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
+</code></pre></div>
+<p>Run the installer:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="nb">source</span><span class="w"> </span>./install.sh
+</code></pre></div>
+<p>The installer writes <code>GPUMDkit_path</code> and <code>PATH</code> settings to your shell configuration and loads them for the current shell. It writes to <code>~/.bashrc</code> by default; if the current shell is zsh, it writes to <code>~/.zshrc</code>. If an existing GPUMDkit path is found, the installer prints the old path and asks whether to replace it. Before changing the rc file, it creates a backup.</p>
+<p>Typical installation output:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>======================================================
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>  GPUMDkit Installation
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>======================================================
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a> [1/4] Detecting GPUMDkit directory...
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>       /path/to/GPUMDkit
+<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a> [2/4] Detecting shell configuration...
+<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a>       Target: /Users/you/.bashrc
+<a id="__codelineno-4-8" name="__codelineno-4-8" href="#__codelineno-4-8"></a>       Adding environment variables to /Users/you/.bashrc
+<a id="__codelineno-4-9" name="__codelineno-4-9" href="#__codelineno-4-9"></a>       Success: Environment variables added.
+<a id="__codelineno-4-10" name="__codelineno-4-10" href="#__codelineno-4-10"></a> [3/4] Setting executable permissions...
+<a id="__codelineno-4-11" name="__codelineno-4-11" href="#__codelineno-4-11"></a>       Added executable permission to gpumdkit.sh
+<a id="__codelineno-4-12" name="__codelineno-4-12" href="#__codelineno-4-12"></a> [4/4] Loading environment...
+<a id="__codelineno-4-13" name="__codelineno-4-13" href="#__codelineno-4-13"></a>
+<a id="__codelineno-4-14" name="__codelineno-4-14" href="#__codelineno-4-14"></a>======================================================
+<a id="__codelineno-4-15" name="__codelineno-4-15" href="#__codelineno-4-15"></a>  Installation Complete!  GPUMDkit is ready to use.
+<a id="__codelineno-4-16" name="__codelineno-4-16" href="#__codelineno-4-16"></a>======================================================
+</code></pre></div>
+<p>If GPUMDkit was installed before, you may see:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>Existing GPUMDkit configuration found.
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>Existing path(s):
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>  - /old/path/to/GPUMDkit
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>New path:
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>  - /new/path/to/GPUMDkit
+<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>
+<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>Replace the existing GPUMDkit configuration with the new path? [y/N]:
+</code></pre></div>
+<p>Check the command:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-h
+</code></pre></div>
+<p>The help table:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>|                                          MAIN FUNCTIONS                                               |
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a>| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |
+<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a>| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |
+<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
+<a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a>|                                         FORMAT CONVERSION                                             |
+<a id="__codelineno-7-11" name="__codelineno-7-11" href="#__codelineno-7-11"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a>| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |
+<a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a>| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |
+<a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a>| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |
+<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a>| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |
+<a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a>| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |
+<a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a>| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |
+<a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a>| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
+<a id="__codelineno-7-19" name="__codelineno-7-19" href="#__codelineno-7-19"></a>| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
+<a id="__codelineno-7-20" name="__codelineno-7-20" href="#__codelineno-7-20"></a>| -frame_range  Extract frames by range         |                                                       |
+<a id="__codelineno-7-21" name="__codelineno-7-21" href="#__codelineno-7-21"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-22" name="__codelineno-7-22" href="#__codelineno-7-22"></a>|                                            ANALYSIS                                                   |
+<a id="__codelineno-7-23" name="__codelineno-7-23" href="#__codelineno-7-23"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-24" name="__codelineno-7-24" href="#__codelineno-7-24"></a>| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
+<a id="__codelineno-7-25" name="__codelineno-7-25" href="#__codelineno-7-25"></a>| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
+<a id="__codelineno-7-26" name="__codelineno-7-26" href="#__codelineno-7-26"></a>| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
+<a id="__codelineno-7-27" name="__codelineno-7-27" href="#__codelineno-7-27"></a>| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
+<a id="__codelineno-7-28" name="__codelineno-7-28" href="#__codelineno-7-28"></a>| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
+<a id="__codelineno-7-29" name="__codelineno-7-29" href="#__codelineno-7-29"></a>| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
+<a id="__codelineno-7-30" name="__codelineno-7-30" href="#__codelineno-7-30"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-31" name="__codelineno-7-31" href="#__codelineno-7-31"></a>| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |
+<a id="__codelineno-7-32" name="__codelineno-7-32" href="#__codelineno-7-32"></a>+-------------------------------------------------------------------------------------------------------+
+</code></pre></div>
+<h2 id="3-usage-modes">3. Usage Modes</h2>
+<h3 id="interactive-mode">Interactive Mode</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh
+</code></pre></div>
+<p>Main menu:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>           ____ ____  _   _ __  __ ____  _    _ _
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>         | |  _| |_) | | | | |\/| | | | | |/ / | __|
+<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a>         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_
+<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
+<a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a>
+<a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a>          GPUMDkit Version 1.5.6 (dev) (2026-06-17)
+<a id="__codelineno-9-8" name="__codelineno-9-8" href="#__codelineno-9-8"></a>    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+<a id="__codelineno-9-9" name="__codelineno-9-9" href="#__codelineno-9-9"></a> Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA
+<a id="__codelineno-9-10" name="__codelineno-9-10" href="#__codelineno-9-10"></a>
+<a id="__codelineno-9-11" name="__codelineno-9-11" href="#__codelineno-9-11"></a> ---------------------- GPUMD ------------------------
+<a id="__codelineno-9-12" name="__codelineno-9-12" href="#__codelineno-9-12"></a> 1) Format Conversion          2) Sample Structures
+<a id="__codelineno-9-13" name="__codelineno-9-13" href="#__codelineno-9-13"></a> 3) Workflow                   4) Calculators
+<a id="__codelineno-9-14" name="__codelineno-9-14" href="#__codelineno-9-14"></a> 5) Analyzer                   6) Visualization
+<a id="__codelineno-9-15" name="__codelineno-9-15" href="#__codelineno-9-15"></a> 7) Utilities                  8) Developing...
+<a id="__codelineno-9-16" name="__codelineno-9-16" href="#__codelineno-9-16"></a> 0) Exit
+<a id="__codelineno-9-17" name="__codelineno-9-17" href="#__codelineno-9-17"></a> ------------&gt;&gt;
+<a id="__codelineno-9-18" name="__codelineno-9-18" href="#__codelineno-9-18"></a> Input the function number:
+</code></pre></div>
+<h3 id="command-line-mode">Command-Line Mode</h3>
+<p>Direct commands use fixed positional arguments:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+</code></pre></div>
+<p>For example:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+</code></pre></div>
+<p>means reading <code>POSCAR</code> and writing <code>model.xyz</code>.</p>
+<h2 id="4-practical-examples">4. Practical Examples</h2>
+<h3 id="convert-poscar-to-extxyz">Convert POSCAR to extxyz</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+</code></pre></div>
+<h3 id="add-gpumd-group-labels">Add GPUMD Group Labels</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
+</code></pre></div>
+<p>Group labels are used by some GPUMD-related workflows and analyses that need atom grouping, such as species-specific MSD or diffusion calculations.</p>
+<h3 id="plot-nep-training-results">Plot NEP Training Results</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/train.png" alt="NEP training results" width="72%" />
+</div>
+
+<h3 id="plot-nep-test-results">Plot NEP Test Results</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/prediction.png" alt="NEP test results" width="72%" />
+</div>
+
+<h3 id="plot-thermodynamic-data">Plot Thermodynamic Data</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/thermo.png" alt="Thermo plot" width="72%" />
+</div>
+
+<h3 id="plot-msd-and-self-diffusion-coefficient">Plot MSD and Self-Diffusion Coefficient</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
+  <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
+</div>
+
+<h2 id="5-help">5. Help</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-h
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>-h
+<a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>-h
+<a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train<span class="w"> </span>-h
+<a id="__codelineno-18-5" name="__codelineno-18-5" href="#__codelineno-18-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>-h
+</code></pre></div>
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+    Structure Sampling
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+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#interactive-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive Mode
+      
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+      
+        <li class="md-nav__item">
+  <a href="#uniform-and-random-sampling" class="md-nav__link">
+    <span class="md-ellipsis">
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+      
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+      
+        <li class="md-nav__item">
+  <a href="#farthest-point-sampling-with-neptrain" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Farthest Point Sampling with NepTrain
+      
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+      
+        <li class="md-nav__item">
+  <a href="#deprecated-pynep-fps" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+      
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+  </a>
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+</li>
+      
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+  <a href="#structure-perturbation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Structure Perturbation
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#force-deviation-selection" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Force-Deviation Selection
+      
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+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#frame-range-extraction" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Frame Range Extraction
+      
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+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-commands" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example Commands
+      
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+  
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+      
+        <li class="md-nav__item">
+  <a href="#common-mistakes" class="md-nav__link">
+    <span class="md-ellipsis">
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+      
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+      <a href="workflow_scripts.html" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Workflow Scripts
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+      <a href="calculator_scripts.html" class="md-nav__link">
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+    GPUMDkit 教程
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+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
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+  
+  
+
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+  
+
+              
+            
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+      <a href="../zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
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+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
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+  
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+  
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+      <a href="../zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
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+
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+            
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+                
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+      <a href="../zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+                
+  
+  
+  
+  
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+      <a href="../zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#interactive-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive Mode
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#uniform-and-random-sampling" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Uniform and Random Sampling
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#farthest-point-sampling-with-neptrain" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Farthest Point Sampling with NepTrain
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#deprecated-pynep-fps" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Deprecated PyNEP FPS
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#structure-perturbation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Structure Perturbation
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#force-deviation-selection" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Force-Deviation Selection
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#frame-range-extraction" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Frame Range Extraction
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-commands" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example Commands
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#common-mistakes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Common Mistakes
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>📦 Structure Sampling</h1>
+  <p style="text-align: justify;">Structure sampling is used to select, generate, or filter candidate configurations for NEP training and molecular dynamics workflows.</p>
+</div>
+
+<p><strong>Script Location:</strong> <code>Scripts/sample_structures/</code></p>
+<h2 id="interactive-mode">Interactive Mode</h2>
+<p>Sampling tasks are usually easier to run from the interactive menu:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh
+</code></pre></div>
+<p>Choose:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>2) Sample Structures
+</code></pre></div>
+<p>The menu is:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>+------------------------------------------------------+
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>|                 SAMPLE STRUCTURE TOOLS               |
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>+------------------------------------------------------+
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>| 201) Sample structures from extxyz                   |
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>| 202) PyNEP sampling [deprecated]                    |
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>| 203) FPS sampling by NepTrain [preferred]            |
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>| 204) Perturb structure                               |
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>| 205) Select max force deviation structs              |
+<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>+------------------------------------------------------+
+<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a>| 000) Return to the main menu                         |
+<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a>+------------------------------------------------------+
+<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a>Input the function number:
+</code></pre></div>
+<p>Available entries:</p>
+<table>
+<thead>
+<tr>
+<th>Menu</th>
+<th>Method</th>
+<th>Use Case</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>201</td>
+<td>Uniform/random sampling</td>
+<td>quick frame selection from a trajectory</td>
+</tr>
+<tr>
+<td>202</td>
+<td>PyNEP notice</td>
+<td>prints a notice; use <code>gpumdkit.sh -pynep</code> to run PyNEP</td>
+</tr>
+<tr>
+<td>203</td>
+<td>NepTrain FPS</td>
+<td>descriptor-based FPS with NepTrain</td>
+</tr>
+<tr>
+<td>204</td>
+<td>Perturb structure</td>
+<td>generate perturbed structures from POSCAR/CONTCAR</td>
+</tr>
+<tr>
+<td>205</td>
+<td>Force-deviation selection</td>
+<td>select structures with high model deviation</td>
+</tr>
+</tbody>
+</table>
+<h2 id="uniform-and-random-sampling">Uniform and Random Sampling</h2>
+<p>From interactive mode, choose <code>201</code>. You will see:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>[skip_num]: number of initial frames to skip, default value is 0
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>Sampling_method: &#39;uniform&#39; or &#39;random&#39;
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>Example: train.xyz uniform 50
+<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>------------&gt;&gt;
+</code></pre></div>
+<p>Example input:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>dump.xyz uniform 50
+</code></pre></div>
+<p>or:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>dump.xyz random 100 500
+</code></pre></div>
+<p>Arguments:</p>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>dump.xyz</code></td>
+<td>input trajectory</td>
+</tr>
+<tr>
+<td><code>uniform</code> / <code>random</code></td>
+<td>sampling method</td>
+</tr>
+<tr>
+<td><code>50</code> / <code>100</code></td>
+<td>number of selected structures</td>
+</tr>
+<tr>
+<td><code>500</code></td>
+<td>optional number of initial frames to skip</td>
+</tr>
+</tbody>
+</table>
+<p>Output:</p>
+<ul>
+<li><code>sampled_structures.xyz</code></li>
+</ul>
+<h2 id="farthest-point-sampling-with-neptrain">Farthest Point Sampling with NepTrain</h2>
+<p>This entry uses NepTrain descriptors for FPS.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
+</code></pre></div>
+<p>From interactive mode, choose <code>203</code>. You will see:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>Example: dump.xyz train.xyz nep.txt
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>------------&gt;&gt;
+</code></pre></div>
+<p>Inputs:</p>
+<table>
+<thead>
+<tr>
+<th>File</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>dump.xyz</code></td>
+<td>candidate structures</td>
+</tr>
+<tr>
+<td><code>train.xyz</code></td>
+<td>existing training set</td>
+</tr>
+<tr>
+<td><code>nep.txt</code></td>
+<td>current NEP model used to compute descriptors</td>
+</tr>
+</tbody>
+</table>
+<p>Outputs:</p>
+<ul>
+<li><code>selected.xyz</code></li>
+<li><code>select.png</code></li>
+<li><code>pca_sample.txt</code></li>
+<li><code>pca_train.txt</code></li>
+<li><code>pca_selected.txt</code></li>
+</ul>
+<p>During execution, choose one of two selection modes:</p>
+<ol>
+<li>select until the descriptor distance is below a threshold;</li>
+<li>select a specified number of structures.</li>
+</ol>
+<p>The script then prints a selection prompt:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>Choose selection method:
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>1) Select structures based on minimum distance
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>2) Select structures based on number of structures
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>------------&gt;&gt;
+</code></pre></div>
+<p>This function requires the <code>NepTrain</code> package. If you use this function, we recommend citing the NepTrain paper printed by the script.</p>
+<h2 id="deprecated-pynep-fps">Deprecated PyNEP FPS</h2>
+<p>PyNEP FPS is kept for compatibility, but it is only exposed through the direct <code>-pynep</code> entry:</p>
+<p>If you choose <code>202</code> from the interactive menu, it prints:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>+-------------------------------------------------+
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>| Function 202 is no longer supported here.       |
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>| PyNEP package is no longer actively maintained. |
+<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a>| Please use 203) NepTrain sampling instead.      |
+<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>| If you still need PyNEP compatibility, run:     |
+<a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a>|                 gpumdkit.sh -pynep              |
+<a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a>+-------------------------------------------------+
+</code></pre></div>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pynep
+</code></pre></div>
+<p>Then input:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>dump.xyz train.xyz nep.txt 8
+</code></pre></div>
+<p>This entry requires <code>pynep</code> and is kept for compatibility.</p>
+<h2 id="structure-perturbation">Structure Perturbation</h2>
+<p>Use perturbation when you want to generate initial structures around a known configuration.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>python<span class="w"> </span>Scripts/sample_structures/perturb_structure.py<span class="w"> </span>POSCAR<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">0</span>.03<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>uniform
+</code></pre></div>
+<p>From interactive mode, choose <code>204</code>. You will see:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>The default parameters for perturb are 20 0.03 0.2 uniform
+<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>Example: POSCAR 20 0.03 0.2 uniform
+<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a>------------&gt;&gt;
+</code></pre></div>
+<p>Arguments:</p>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>POSCAR</code></td>
+<td>input VASP structure</td>
+</tr>
+<tr>
+<td><code>20</code></td>
+<td>number of perturbed structures</td>
+</tr>
+<tr>
+<td><code>0.03</code></td>
+<td>cell perturbation fraction</td>
+</tr>
+<tr>
+<td><code>0.2</code></td>
+<td>atom perturbation distance in Angstrom</td>
+</tr>
+<tr>
+<td><code>uniform</code></td>
+<td>perturbation style: <code>normal</code>, <code>uniform</code>, or <code>const</code></td>
+</tr>
+</tbody>
+</table>
+<p>Output:</p>
+<ul>
+<li><code>POSCAR_01.vasp</code>, <code>POSCAR_02.vasp</code>, ...</li>
+</ul>
+<p>This function requires <code>dpdata</code>.</p>
+<h2 id="force-deviation-selection">Force-Deviation Selection</h2>
+<p>Use this together with the GPUMD <code>active</code> command. The <code>active</code> command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. <code>select_max_modev.py</code> selects structures with large force deviations from <code>active.out</code> and <code>active.xyz</code>, then writes them to <code>selected.xyz</code>.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>python<span class="w"> </span>Scripts/sample_structures/select_max_modev.py<span class="w"> </span><span class="m">200</span><span class="w"> </span><span class="m">0</span>.15
+</code></pre></div>
+<p>From interactive mode, choose <code>205</code>. You will see:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>+----------------------------------------------------+
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>| Select max force deviation structs from active.xyz |
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a>|     generated by the active command in gpumd.      |
+<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a>+----------------------------------------------------+
+<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a>Input &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)
+<a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a>------------&gt;&gt;
+</code></pre></div>
+<p>Arguments:</p>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>200</code></td>
+<td>maximum number of structures to keep</td>
+</tr>
+<tr>
+<td><code>0.15</code></td>
+<td>minimum force deviation threshold</td>
+</tr>
+</tbody>
+</table>
+<p>Required files:</p>
+<ul>
+<li><code>active.out</code></li>
+<li><code>active.xyz</code></li>
+</ul>
+<p>Output:</p>
+<ul>
+<li><code>selected.xyz</code></li>
+</ul>
+<h2 id="frame-range-extraction">Frame Range Extraction</h2>
+<p>Use this to extract a fraction of a trajectory:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>python<span class="w"> </span>Scripts/sample_structures/frame_range.py<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span>.8
+</code></pre></div>
+<p>This writes frames from 0% to 80% of the trajectory.</p>
+<h2 id="example-commands">Example Commands</h2>
+<p>An example sequence using several sampling-related tools:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
+</code></pre></div>
+<h2 id="common-mistakes">Common Mistakes</h2>
+<table>
+<thead>
+<tr>
+<th>Problem</th>
+<th>Recommendation</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>FPS selects too many similar structures</td>
+<td>increase the distance threshold or select fewer structures</td>
+</tr>
+<tr>
+<td>Perturbed structures are unphysical</td>
+<td>reduce <code>cell_pert</code> and <code>atom_pert</code>, then check minimum distances</td>
+</tr>
+<tr>
+<td><code>active.out</code> and <code>active.xyz</code> do not match</td>
+<td>regenerate both from the same GPUMD active run</td>
+</tr>
+<tr>
+<td>PCA plot looks strange</td>
+<td>check whether <code>nep.txt</code> matches the chemical species in both datasets</td>
+</tr>
+</tbody>
+</table>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
+            </div>
+          
+          
+<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
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diff --git a/docs/htmls/en/workflow_scripts.html b/docs/htmls/en/workflow_scripts.html
new file mode 100644
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+      <a href="structure_sampling.html" class="md-nav__link">
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+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#interactive-entry" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+      
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+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#scf-batch-pretreatment" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        SCF Batch Pretreatment
+      
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+  
+    <nav class="md-nav" aria-label="SCF Batch Pretreatment">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#vasp" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        VASP
+      
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+</li>
+        
+          <li class="md-nav__item">
+  <a href="#cp2k" class="md-nav__link">
+    <span class="md-ellipsis">
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+  
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+        
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#md-sampling-pretreatment" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+      
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+  </a>
+  
+    <nav class="md-nav" aria-label="MD Sampling Pretreatment">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gpumd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        GPUMD
+      
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+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#lammps" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        LAMMPS
+      
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+  
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#active-learning-style-workflow" class="md-nav__link">
+    <span class="md-ellipsis">
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+        Active-Learning Style Workflow
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#template-based-temperature-series" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Template-Based Temperature Series
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#practical-notes" class="md-nav__link">
+    <span class="md-ellipsis">
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+        Practical Notes
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+      <a href="active_learning_workflow.html" class="md-nav__link">
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+    Contributing to GPUMDkit
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+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
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+  
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+
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+  
+
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+            
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+      <a href="../zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
+              
+                
+  
+  
+  
+  
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+      <a href="../zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
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+                
+  
+  
+  
+  
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+      <a href="../zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+                
+  
+  
+  
+  
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+      <a href="../zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="../zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#interactive-entry" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive Entry
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#scf-batch-pretreatment" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        SCF Batch Pretreatment
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="SCF Batch Pretreatment">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#vasp" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        VASP
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#cp2k" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        CP2K
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#md-sampling-pretreatment" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MD Sampling Pretreatment
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="MD Sampling Pretreatment">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gpumd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        GPUMD
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#lammps" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        LAMMPS
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#active-learning-style-workflow" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Active-Learning Style Workflow
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#template-based-temperature-series" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Template-Based Temperature Series
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#practical-notes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Practical Notes
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🔧 Workflow Scripts</h1>
+  <p style="text-align: justify;">Workflow scripts automate repetitive preparation steps for DFT, MD, and NEP development.</p>
+</div>
+
+<p><strong>Script Location:</strong> <code>Scripts/workflow/</code></p>
+<h2 id="interactive-entry">Interactive Entry</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh
+</code></pre></div>
+<p>Choose:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>3) Workflow
+</code></pre></div>
+<p>Typical workflow menu:</p>
+<table>
+<thead>
+<tr>
+<th>Menu</th>
+<th>Workflow</th>
+<th>Purpose</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>301</td>
+<td>SCF batch pretreatment</td>
+<td>prepare single-point DFT calculations</td>
+</tr>
+<tr>
+<td>302</td>
+<td>MD sample batch pretreatment (GPUMD)</td>
+<td>prepare GPUMD sampling calculations</td>
+</tr>
+<tr>
+<td>303</td>
+<td>MD sample batch pretreatment (LAMMPS)</td>
+<td>prepare LAMMPS sampling calculations</td>
+</tr>
+</tbody>
+</table>
+<h2 id="scf-batch-pretreatment">SCF Batch Pretreatment</h2>
+<p>Use this when you have many structures and want to prepare single-point DFT calculations.</p>
+<h3 id="vasp">VASP</h3>
+<p>Interactive mode:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="c1"># choose 3 -&gt; 301 -&gt; VASP</span>
+</code></pre></div>
+<p>Before running, put structure files in the current directory. The script checks files in this order:</p>
+<ol>
+<li>if one or more <code>.vasp</code> files exist, it processes <code>.vasp</code> files;</li>
+<li>if both <code>.vasp</code> and <code>.xyz</code> files exist, it prints a notice and only processes <code>.vasp</code> files;</li>
+<li>if no <code>.vasp</code> file exists and one <code>.xyz</code> file exists, it converts that extxyz file to POSCAR files;</li>
+<li>if no <code>.vasp</code> file exists and multiple <code>.xyz</code> files exist, it asks you to choose one.</li>
+</ol>
+<p>Typical input directory before running:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>current directory/
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>├── POSCAR_1.vasp
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>├── POSCAR_2.vasp
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>└── POSCAR_3.vasp
+</code></pre></div>
+<p>or:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>current directory/
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>└── sampled.xyz
+</code></pre></div>
+<p>After running, the script creates:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>current directory/
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>├── struct_fp/
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>│   ├── POSCAR_1.vasp
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>│   ├── POSCAR_2.vasp
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>│   └── ...
+<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>├── fp/
+<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>├── &lt;prefix&gt;_1/
+<a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a>├── &lt;prefix&gt;_2/
+<a id="__codelineno-5-9" name="__codelineno-5-9" href="#__codelineno-5-9"></a>└── presub.sh
+</code></pre></div>
+<p>You must place <code>INCAR</code>, <code>POTCAR</code>, and <code>KPOINTS</code> in the generated <code>fp/</code> directory after the script creates it. The calculation folders link to files in <code>fp/</code>.</p>
+<p>The <code>prefix</code> you input during the workflow becomes the calculation folder prefix. When <code>out2xyz</code> is later used to extract results, the folder name is stored as <code>config_type</code> in the extxyz file, which makes it easier to trace where each structure came from.</p>
+<h3 id="cp2k">CP2K</h3>
+<p>CP2K SCF batch pretreatment is available from the workflow menu and can also be called directly:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="c1"># choose 3 -&gt; 301 -&gt; CP2K</span>
+</code></pre></div>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>python<span class="w"> </span>Scripts/workflow/scf_batch_pretreatment_cp2k.py<span class="w"> </span>train.xyz<span class="w"> </span>template.inp<span class="w"> </span>calc
+</code></pre></div>
+<p>The interactive wrapper asks for:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;
+</code></pre></div>
+<p>Example:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>dump.xyz template.inp H2O
+</code></pre></div>
+<p>The template should be configured to read coordinates from <code>pos.xyz</code>. A reference template is available at:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>Scripts/workflow/cp2k_template.inp
+</code></pre></div>
+<p>The script creates <code>&lt;prefix&gt;_&lt;index&gt;/</code> directories, writes <code>input.inp</code>, and writes <code>pos.xyz</code> for each structure.</p>
+<h2 id="md-sampling-pretreatment">MD Sampling Pretreatment</h2>
+<h3 id="gpumd">GPUMD</h3>
+<p>Interactive mode:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="c1"># choose 3 -&gt; 302</span>
+</code></pre></div>
+<p>Typical preparation:
+Before running, put <code>.vasp</code> files or one extxyz file in the current directory. The detection order is the same as the VASP SCF workflow: <code>.vasp</code> files are preferred; if multiple <code>.xyz</code> files are found without <code>.vasp</code>, the script asks you to choose one.</p>
+<p>Typical input directory:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>current directory/
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>├── POSCAR_1.vasp
+<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a>└── POSCAR_2.vasp
+</code></pre></div>
+<p>or:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>current directory/
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>└── dump.xyz
+</code></pre></div>
+<p>After running, the script creates:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>current directory/
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>├── struct_md/
+<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a>│   ├── model_1.xyz
+<a id="__codelineno-14-4" name="__codelineno-14-4" href="#__codelineno-14-4"></a>│   ├── model_2.xyz
+<a id="__codelineno-14-5" name="__codelineno-14-5" href="#__codelineno-14-5"></a>│   └── ...
+<a id="__codelineno-14-6" name="__codelineno-14-6" href="#__codelineno-14-6"></a>├── md/
+<a id="__codelineno-14-7" name="__codelineno-14-7" href="#__codelineno-14-7"></a>├── sample_1/
+<a id="__codelineno-14-8" name="__codelineno-14-8" href="#__codelineno-14-8"></a>├── sample_2/
+<a id="__codelineno-14-9" name="__codelineno-14-9" href="#__codelineno-14-9"></a>└── presub.sh
+</code></pre></div>
+<p>You must place <code>nep.txt</code> and <code>run_*.in</code> files in the generated <code>md/</code> directory. The script links <code>run_1.in</code> to <code>sample_1/run.in</code>, <code>run_2.in</code> to <code>sample_2/run.in</code>, and so on.</p>
+<h3 id="lammps">LAMMPS</h3>
+<p>Interactive mode:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="c1"># choose 3 -&gt; 303</span>
+</code></pre></div>
+<p>Typical preparation:
+Before running, put <code>.vasp</code> files or one extxyz file in the current directory. <code>.vasp</code> files are preferred when both formats exist.</p>
+<p>After running, the script creates LAMMPS data files in <code>struct_md/</code>, sample folders, and an <code>md/</code> directory:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>current directory/
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>├── struct_md/
+<a id="__codelineno-16-3" name="__codelineno-16-3" href="#__codelineno-16-3"></a>│   ├── lammps_1.data
+<a id="__codelineno-16-4" name="__codelineno-16-4" href="#__codelineno-16-4"></a>│   ├── lammps_2.data
+<a id="__codelineno-16-5" name="__codelineno-16-5" href="#__codelineno-16-5"></a>│   └── ...
+<a id="__codelineno-16-6" name="__codelineno-16-6" href="#__codelineno-16-6"></a>├── md/
+<a id="__codelineno-16-7" name="__codelineno-16-7" href="#__codelineno-16-7"></a>├── sample_1/
+<a id="__codelineno-16-8" name="__codelineno-16-8" href="#__codelineno-16-8"></a>├── sample_2/
+<a id="__codelineno-16-9" name="__codelineno-16-9" href="#__codelineno-16-9"></a>└── presub.sh
+</code></pre></div>
+<p>You must place <code>lmprun.in</code> and <code>nep.txt</code> in the generated <code>md/</code> directory.</p>
+<h2 id="active-learning-style-workflow">Active-Learning Style Workflow</h2>
+<p>A common NEP improvement loop is:</p>
+<ol>
+<li>run MD with the current <code>nep.txt</code>;</li>
+<li>collect <code>dump.xyz</code> or <code>active.xyz</code>;</li>
+<li>remove unphysical structures;</li>
+<li>select diverse or uncertain structures;</li>
+<li>run DFT single-point calculations;</li>
+<li>convert DFT results to extxyz;</li>
+<li>append new structures to <code>train.xyz</code>;</li>
+<li>retrain the NEP model.</li>
+</ol>
+<p>For the development active-learning script, see <a href="active_learning_workflow.html">Active Learning</a>.</p>
+<h2 id="template-based-temperature-series">Template-Based Temperature Series</h2>
+<p>For a simple temperature series, a shell loop is often enough:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a><span class="k">for</span><span class="w"> </span>temp<span class="w"> </span><span class="k">in</span><span class="w"> </span><span class="m">300</span><span class="w"> </span><span class="m">500</span><span class="w"> </span><span class="m">700</span><span class="w"> </span><span class="m">900</span><span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a><span class="w">    </span>mkdir<span class="w"> </span>-p<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K&quot;</span>
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a><span class="w">    </span>cp<span class="w"> </span>model.xyz<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/&quot;</span>
+<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a><span class="w">    </span>cp<span class="w"> </span>nep.txt<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/&quot;</span>
+<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a><span class="w">    </span>sed<span class="w"> </span><span class="s2">&quot;s/TEMPERATURE/</span><span class="nv">$temp</span><span class="s2">/g&quot;</span><span class="w"> </span>run_template.in<span class="w"> </span>&gt;<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/run.in&quot;</span>
+<a id="__codelineno-17-6" name="__codelineno-17-6" href="#__codelineno-17-6"></a><span class="k">done</span>
+</code></pre></div>
+<p>Then submit the generated folders according to your local cluster system.</p>
+<h2 id="practical-notes">Practical Notes</h2>
+<ul>
+<li>Workflow scripts are cluster- and template-dependent. Always test with a small number of structures first.</li>
+<li>Keep template files (<code>INCAR</code>, <code>KPOINTS</code>, <code>POTCAR</code>, <code>run.in</code>, CP2K inputs) under version control if possible.</li>
+<li>Check generated folders before submitting a large batch.</li>
+<li>Use analyzers and sampling scripts before expensive DFT calculations.</li>
+</ul>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
+            </div>
+          
+          
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+      
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+              <article class="md-content__inner md-typeset">
+                
+                  
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+
+  
+  
+
+
+<div align="center">
+  <h1>📚 GPUMDkit Documentation</h1>
+  <p style="text-align: justify;">A practical bilingual tutorial for GPUMDkit, covering installation, command-line tools, interactive workflows, plotting, and analysis utilities.</p>
+</div>
+
+<h2 id="language">Language</h2>
+<table>
+<thead>
+<tr>
+<th>Language</th>
+<th>Start Here</th>
+<th>Command Reference</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>English</td>
+<td><a href="en/index.html">GPUMDkit Tutorials</a></td>
+<td><a href="en/command_reference.html">Command Reference</a></td>
+</tr>
+<tr>
+<td>简体中文</td>
+<td><a href="zh/index.html">GPUMDkit 教程</a></td>
+<td><a href="zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html">命令参考</a></td>
+</tr>
+</tbody>
+</table>
+<h2 id="what-you-can-learn-here">What You Can Learn Here</h2>
+<p>This documentation is organized as a practical tutorial rather than only a command list. New users are encouraged to start from the overview and quick start pages, then move to the topic that matches their task.</p>
+<table>
+<thead>
+<tr>
+<th>Topic</th>
+<th>What it Covers</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>Quick Start</td>
+<td>Installation, environment setup, interactive mode, direct command mode</td>
+</tr>
+<tr>
+<td>Format Conversion</td>
+<td>VASP, LAMMPS, CP2K, ABACUS, CIF, extxyz, group labels, weights</td>
+</tr>
+<tr>
+<td>Sampling</td>
+<td>Uniform/random sampling, NepTrain FPS, perturbation, force-deviation selection</td>
+</tr>
+<tr>
+<td>Calculators</td>
+<td>MSD, ionic conductivity, NEP prediction, descriptors, DOAS, NEB, polarization tools</td>
+</tr>
+<tr>
+<td>Analyzers</td>
+<td>Composition checks, distance checks, filters, property range analysis</td>
+</tr>
+<tr>
+<td>Visualization</td>
+<td>NEP training plots, MD plots, transport plots, thermal transport plots, example figures</td>
+</tr>
+<tr>
+<td>Workflows</td>
+<td>Batch DFT/MD processing and active-learning style workflows</td>
+</tr>
+</tbody>
+</table>
+<p>For complex operations, use the interactive menu:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh
+</code></pre></div>
+<p>For common operations with fixed arguments, use direct command-line mode:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-h
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>-h
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>-h
+</code></pre></div>
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+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"],"fields":{"title":{"boost":1000.0},"text":{"boost":1.0},"tags":{"boost":1000000.0}}},"docs":[{"location":"index.html","title":"Home","text":"\ud83d\udcda GPUMDkit Documentation <p>A practical bilingual tutorial for GPUMDkit, covering installation, command-line tools, interactive workflows, plotting, and analysis utilities.</p>"},{"location":"index.html#language","title":"Language","text":"Language Start Here Command Reference English GPUMDkit Tutorials Command Reference \u7b80\u4f53\u4e2d\u6587 GPUMDkit \u6559\u7a0b \u547d\u4ee4\u53c2\u8003"},{"location":"index.html#what-you-can-learn-here","title":"What You Can Learn Here","text":"<p>This documentation is organized as a practical tutorial rather than only a command list. New users are encouraged to start from the overview and quick start pages, then move to the topic that matches their task.</p> Topic What it Covers Quick Start Installation, environment setup, interactive mode, direct command mode Format Conversion VASP, LAMMPS, CP2K, ABACUS, CIF, extxyz, group labels, weights Sampling Uniform/random sampling, NepTrain FPS, perturbation, force-deviation selection Calculators MSD, ionic conductivity, NEP prediction, descriptors, DOAS, NEB, polarization tools Analyzers Composition checks, distance checks, filters, property range analysis Visualization NEP training plots, MD plots, transport plots, thermal transport plots, example figures Workflows Batch DFT/MD processing and active-learning style workflows <p>For complex operations, use the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>For common operations with fixed arguments, use direct command-line mode:</p> <pre><code>gpumdkit.sh -h\ngpumdkit.sh -plt -h\ngpumdkit.sh -calc -h\n</code></pre>"},{"location":"en/index.html","title":"GPUMDkit Tutorials","text":"\ud83d\udcda GPUMDkit Tutorials <p>Welcome to GPUMDkit, a command-line toolkit for GPUMD and NEP.</p>"},{"location":"en/index.html#what-is-gpumdkit","title":"What is GPUMDkit?","text":"<p>GPUMDkit streamlines common tasks in computational materials science:</p> <ul> <li>Format Conversion: Convert between VASP, LAMMPS, CP2K, ABACUS, CIF, and extxyz formats</li> <li>Visualization: Plotting tools for NEP training, MD simulations, and analysis</li> <li>Calculators: Compute ionic conductivity, descriptors, MSD, NEB, and more</li> <li>Analyzers: Structure validation, filtering, composition analysis</li> <li>Workflows: Batch processing for DFT and MD simulations</li> <li>Sampling: Structure selection using uniform, random, or FPS methods</li> </ul>"},{"location":"en/index.html#quick-start","title":"Quick Start","text":""},{"location":"en/index.html#installation","title":"Installation","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"en/index.html#dependencies","title":"Dependencies","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"en/index.html#usage","title":"Usage","text":"<pre><code># Interactive mode\ngpumdkit.sh\n\n# Command-line mode\ngpumdkit.sh -&lt;option&gt; [args...]\n\n# Get help\ngpumdkit.sh -h\n</code></pre>"},{"location":"en/index.html#tutorials","title":"Tutorials","text":"Tutorial Description Quick Start Installation and first steps Command Reference One-page CLI and menu reference Format Conversion Convert between file formats Calculator Scripts Compute material properties Analyzer Scripts Structure analysis and validation Plot Scripts Plotting and visualization Workflow Scripts Batch processing and automation Structure Sampling Structure selection methods Custom Commands User-defined GPUMDkit shortcuts Active Learning Workflow Batch active-learning workflow notes Polar Material Analysis Ferroelectric and polarization tools Contributing to GPUMDkit Development notes"},{"location":"en/index.html#example-convert-vasp-outcars","title":"Example: Convert VASP OUTCARs","text":"<pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre>"},{"location":"en/index.html#example-plot-nep-results","title":"Example: Plot NEP Results","text":"<pre><code>gpumdkit.sh -plt train\ngpumdkit.sh -plt prediction\n</code></pre>"},{"location":"en/index.html#example-ionic-conductivity","title":"Example: Ionic Conductivity","text":"<pre><code>gpumdkit.sh -calc msd trajectory.xyz Li 10\ngpumdkit.sh -calc ionic-cond Li 1\ngpumdkit.sh -plt msd\n</code></pre>"},{"location":"en/index.html#module-overview","title":"Module Overview","text":"Module Menu CLI Description Format Conversion 1 <code>-out2xyz</code>, <code>-pos2exyz</code> File conversion Sample Structures 2 <code>-neptrain</code>, interactive menu Structure sampling Workflow 3 - Batch processing Calculators 4 <code>-calc &lt;type&gt;</code> Property calculations Analyzer 5 <code>-range</code>, <code>-min_dist</code> Structure analysis Visualization 6 <code>-plt &lt;type&gt;</code> Plotting tools Utilities 7 <code>-time</code>, <code>-clean</code> Utility functions"},{"location":"en/index.html#links","title":"Links","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>Documentation: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"en/active_learning_workflow.html","title":"Active Learning Workflow","text":"\ud83d\udd01 Active Learning Workflow <p>This tutorial explains the steps and considerations involved in the <code>workflow_active_learning_dev.sh</code> script. The workflow is used to generate, select, and analyze molecular structures, followed by simulations and data collection.</p>"},{"location":"en/active_learning_workflow.html#overview","title":"Overview","text":"<p>This script is designed to handle molecular dynamics simulations, sampling, and SCF (self-consistent field) calculations for NEP. Below is a step-by-step guide explaining how the script works and what each part does.</p>"},{"location":"en/active_learning_workflow.html#1-slurm-directives","title":"1. SLURM Directives","text":"<pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>The SLURM directives are used to define how the job will be submitted to the cluster:</p> <ul> <li><code>#SBATCH -p</code> defines the partition, in this case, it's <code>intel-sc3</code> and <code>intel-sc3-32c</code>.</li> <li><code>#SBATCH -q</code> specifies the queue, in this case, <code>huge</code>.</li> <li><code>#SBATCH -N</code> allocates 1 node for the job.</li> <li><code>#SBATCH -J</code> names the job <code>workflow</code>.</li> <li><code>#SBATCH -o</code> defines the output log file as <code>workflow.log</code>.</li> <li><code>--ntasks-per-node=1</code> specifies that only one task should run per node.</li> </ul> <p>NOTE: If your machine does not have the SLURM environment, you can also run the script directly from the command line. For example:</p> <pre><code>nohup bash workflow_active_learning_dev.sh &amp;&gt;workflow.log &amp;\n</code></pre>"},{"location":"en/active_learning_workflow.html#2-basic-setup","title":"2. Basic Setup","text":"<pre><code>cd $SLURM_SUBMIT_DIR \n</code></pre> <p>Ensure the working directory is correct, and that all necessary files are present for the job.</p> <pre><code>source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  # Load the submit template\npython_pynep=python  # Python executable for the deprecated pynep branch if needed\n</code></pre> <ul> <li><code>GPUMDkit_path</code> is the environment variable that stores the path for the <code>GPUMDkit</code> .</li> <li><code>python_pynep</code> points to the Python environment used for the deprecated <code>pynep</code>-related branch if needed.</li> </ul>"},{"location":"en/active_learning_workflow.html#3-variable-definitions","title":"3. Variable Definitions","text":"<pre><code>work_dir=${PWD}  # Set the working directory\nprefix_name=LiF_iter01  # Prefix for calculations\nmin_dist=1.4  # Minimum atom distance\nbox_limit=13  # Simulation box limit\nmax_fp_num=50  # Maximum number of single point calculations\nsample_method=pynep  # Sampling method (options: uniform, random, pynep)\npynep_sample_dist=0.01  # Sampling distance for pynep\n</code></pre> <p>You can customize:</p> <ul> <li><code>prefix_name</code> to reflect the name of your current work.</li> <li><code>min_dist</code>, <code>box_limit</code>, and <code>max_fp_num</code> based on your own system.</li> <li><code>sample_method</code> (choose between <code>uniform</code>, <code>random</code>, or <code>pynep</code>).</li> <li><code>pynep_sample_dist</code> is the sampling distance for <code>pynep</code>.</li> </ul>"},{"location":"en/active_learning_workflow.html#4-check-required-files","title":"4. Check Required Files","text":"<pre><code>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ -f run.in ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then\n    # Check for the required files before proceeding.\nelse\n    echo \"Please put nep.in nep.txt train.xyz run.in INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.\"\n    exit 1\nfi\n</code></pre> <p>Make sure the necessary files (<code>nep.txt</code>, <code>nep.in</code>, <code>train.xyz</code>, <code>run.in</code>, <code>INCAR</code>, <code>POTCAR</code>, <code>KPOINTS</code>) are available in the working directory. If any of these are missing, the script will terminate. <code>train.xyz</code> and <code>nep.txt</code> are used for <code>pynep</code> sampling, and <code>run.in</code> is the simulation parameters of MD in the current iteration.</p>"},{"location":"en/active_learning_workflow.html#5-file-organization","title":"5. File Organization","text":"<pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <p>The script organizes the working files into two folders:</p> <ul> <li><code>00.modev</code>: For molecular dynamics simulation.</li> <li><code>common</code>: For shared resources such as <code>nep.txt</code>, <code>run.in</code>, and the structure files, etc.</li> </ul>"},{"location":"en/active_learning_workflow.html#6-molecular-dynamics-simulation-submission","title":"6. Molecular Dynamics Simulation Submission","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>After preparing the input files, the script submits an array of molecular dynamics (MD) tasks using <code>submit_gpumd_array</code>.</p>"},{"location":"en/active_learning_workflow.html#7-monitoring-task-completion","title":"7. Monitoring Task Completion","text":"<pre><code>while true; do\n    logs=$(find \"${work_dir}/00.modev/\" -type f -name log -path \"*/sample_*/log\")\n    finished_tasks_md=$(grep \"Finished running GPUMD.\" $logs | wc -l)\n    error_tasks_md=$(grep \"Error\" $logs | wc -l)\n\n    if [ \"$error_tasks_md\" -ne 0 ]; then\n        echo \"Error: MD simulation encountered an error.\"\n        exit 1\n    fi\n    if [ $finished_tasks_md -eq $sample_struct_num ]; then\n        break\n    fi\n    sleep 30\ndone\n</code></pre> <p>The script continuously checks whether all MD tasks have finished by searching for a <code>Finished running GPUMD.</code> message in the logs. If an error is encountered, the script terminates.</p>"},{"location":"en/active_learning_workflow.html#8-analysis-and-filtering","title":"8. Analysis and Filtering","text":"<pre><code>mkdir ${work_dir}/01.select\n...\n</code></pre> <p>In the <code>01.select</code> folder, all structures in the trajectory file <code>dump.xyz</code> during the MD process will be analyzed and filtered to avoid the generation of non-physical structures as much as possible. Specifically, the <code>get_min_dist.py</code>, <code>filter_structures_by_distance.py</code> and <code>filter_exyz_by_box.py</code> scripts will be employed to check whether there are situations where the distance between atoms is too close or the simulated box exceeds the limit value, and such structures will be filtered out.</p>"},{"location":"en/active_learning_workflow.html#9-sampling-methods","title":"9. Sampling Methods","text":"<pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <p>The script supports three sampling methods: <code>uniform</code>, <code>random</code>, and <code>pynep</code>. It selects structures according to the chosen method and checks if the number exceeds <code>max_fp_num</code>, ensuring the final structure count is within limits.</p>"},{"location":"en/active_learning_workflow.html#10-scf-calculations","title":"10. SCF Calculations","text":"<pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>After sampling, SCF calculations are submitted using <code>submit_vasp_array</code>. The process is similar to the MD submission, but for SCF calculations.</p>"},{"location":"en/active_learning_workflow.html#11-prediction-step","title":"11. Prediction Step","text":"<pre><code>submit_nep_prediction\n</code></pre> <p>The final step involves submitting the NEP prediction task to check  the accuracy of the NEP model. </p> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/analyzer_scripts.html","title":"Analyzer Scripts","text":"\ud83d\udd0d Analyzer Scripts <p>Analyzer scripts provide structure statistics, distance checks, filters, and composition analysis for extxyz datasets.</p> <p>Script Location: <code>Scripts/analyzer/</code></p>"},{"location":"en/analyzer_scripts.html#overview","title":"Overview","text":"Task Command Purpose Composition <code>gpumdkit.sh -analyze_comp train.xyz</code> group structures by chemical composition Chemical species <code>gpumdkit.sh -chem_species train.xyz</code> list species in a file Property range <code>gpumdkit.sh -range train.xyz force</code> inspect energy/force/virial range Minimum distance <code>gpumdkit.sh -min_dist dump.xyz</code> fast distance check without PBC Minimum distance with PBC <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> accurate distance check with PBC Charge balance <code>gpumdkit.sh -cbc train.xyz</code> oxidation-state balance check Distance filter <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> remove structures with short contacts Box filter <code>gpumdkit.sh -filter_box dump.xyz 13</code> remove structures with too-large box edges Property filter <code>gpumdkit.sh -filter_value train.xyz force 20</code> filter by energy/force/virial threshold Pair-distance range <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> extract structures by pair distance"},{"location":"en/analyzer_scripts.html#composition-analysis","title":"Composition Analysis","text":"<pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>Example output:</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>This is useful when <code>train.xyz</code> contains structures from different systems or different cell sizes. You can export a subset by composition from the interactive prompt.</p>"},{"location":"en/analyzer_scripts.html#property-range-analysis","title":"Property Range Analysis","text":"<pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist\n</code></pre> <p>Use <code>hist</code> to show a histogram of the selected property.</p>"},{"location":"en/analyzer_scripts.html#minimum-distance-checks","title":"Minimum Distance Checks","text":"<p>Fast check without PBC:</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>Accurate check with PBC:</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>Typical output:</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (A) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 A\n</code></pre> <p>The PBC version considers periodic boundary conditions.</p>"},{"location":"en/analyzer_scripts.html#filtering-structures","title":"Filtering Structures","text":""},{"location":"en/analyzer_scripts.html#filter-by-minimum-distance","title":"Filter by Minimum Distance","text":"<pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>This removes structures with any interatomic distance below <code>1.0 A</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-box-size","title":"Filter by Box Size","text":"<pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>This filters structures by box-edge length.</p>"},{"location":"en/analyzer_scripts.html#filter-by-property-value","title":"Filter by Property Value","text":"<pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre>"},{"location":"en/analyzer_scripts.html#filter-by-pair-distance-range","title":"Filter by Pair-Distance Range","text":"<pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>This extracts structures where the Li-Li minimum distance is between <code>1.8 A</code> and <code>2.0 A</code>.</p>"},{"location":"en/analyzer_scripts.html#charge-balance-check","title":"Charge Balance Check","text":"<pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>Outputs may include:</p> <ul> <li><code>balanced.xyz</code></li> <li><code>unbalanced.xyz</code></li> <li><code>indices.txt</code></li> </ul> <p>This is intended for systems where common oxidation states are meaningful.</p>"},{"location":"en/analyzer_scripts.html#example-commands","title":"Example Commands","text":"<p>Property and distance checks:</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\ngpumdkit.sh -range train.xyz force hist\ngpumdkit.sh -range train.xyz energy hist\ngpumdkit.sh -min_dist_pbc train.xyz\n</code></pre> <p>Filtering examples:</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\ngpumdkit.sh -filter_box filtered_dist.xyz 13\n</code></pre>"},{"location":"en/calculator_scripts.html","title":"Calculator Scripts","text":"\ud83e\uddee Calculator Scripts <p>The calculator module contains scripts for computing properties from MD trajectories, NEP models, and structure files.</p> <p>Script Location: <code>Scripts/calculators/</code></p>"},{"location":"en/calculator_scripts.html#overview","title":"Overview","text":"Task Command Main Input Ionic conductivity <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>, <code>thermo.out</code>, <code>model.xyz</code> MSD from trajectory <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz trajectory NEP prediction <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP model NEP descriptors <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP model DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP model NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> initial/final structures Minimization <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> structure + NEP model Neighbor list <code>gpumdkit.sh -calc nlist [args...]</code> structure Displacement <code>gpumdkit.sh -calc disp [args...]</code> trajectory + neighbor list Average structure <code>gpumdkit.sh -calc avg-struct [args...]</code> trajectory Octahedral tilt <code>gpumdkit.sh -calc oct-tilt [args...]</code> trajectory + B-O neighbor list ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 [args...]</code> trajectory + neighbor lists <p>For a full command list:</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>The command-line help table looks like:</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>In interactive mode, choose <code>4) Calculators</code>. The menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"en/calculator_scripts.html#ionic-conductivity","title":"Ionic Conductivity","text":"<p><code>calc_ion_conductivity.py</code> calculates ionic diffusivity and conductivity from <code>msd.out</code>.</p>"},{"location":"en/calculator_scripts.html#required-and-optional-files","title":"Required and Optional Files","text":"File Role <code>msd.out</code> Required MSD data <code>thermo.out</code> Optional, used for automatic temperature detection <code>model.xyz</code> Optional, used for volume and ion-count detection <code>run.in</code> Optional, used to detect replication"},{"location":"en/calculator_scripts.html#usage","title":"Usage","text":"<pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>From interactive mode, choose <code>401</code>. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>If automatic files are missing, the script will ask for temperature, volume, and ion count interactively.</p> <p>Interactive prompts in manual mode look like:</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre>"},{"location":"en/calculator_scripts.html#example-output","title":"Example Output","text":"<pre><code>Diffusivity (D):\n  D_x: 4.153e-07 cm^2/s\n  D_y: 4.174e-07 cm^2/s\n  D_z: 2.610e-07 cm^2/s\n  D_total: 3.646e-07 cm^2/s\n------------------------------\nIonic Conductivity:\n  Sigma_x: 2.576e-02 mS/cm\n  Sigma_y: 2.589e-02 mS/cm\n  Sigma_z: 1.619e-02 mS/cm\n  Sigma_total: 2.261e-02 mS/cm\n</code></pre>"},{"location":"en/calculator_scripts.html#mean-square-displacement","title":"Mean Square Displacement","text":"<p><code>calc_msd.py</code> computes MSD directly from an extxyz trajectory.</p> <pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>From interactive mode, choose <code>412</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>Li</code> target mobile species <code>10</code> time interval between frames, in fs <code>5000</code> optional maximum correlation steps <p>Output:</p> <ul> <li><code>msd.out</code></li> </ul> <p>The beginning of <code>msd.out</code> is a text table with time and MSD columns. After generating it, use the plot commands below.</p> <p>You can then plot:</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-property-prediction","title":"NEP Property Prediction","text":"<p><code>calc_properties_with_nep.py</code> calculates energy, force, and stress for structures using a NEP model.</p> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>This function is useful when you intentionally want to use a trained NEP model as a surrogate calculator. It should not be treated as a replacement for DFT unless the model quality has been carefully validated.</p>"},{"location":"en/calculator_scripts.html#nep-descriptors","title":"NEP Descriptors","text":"<p><code>calc_descriptors.py</code> extracts NEP descriptors for a selected element.</p> <pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>Use cases:</p> <ul> <li>visualize chemical environments with PCA/UMAP;</li> <li>compare training and candidate structures;</li> <li>inspect whether new data expands descriptor space.</li> </ul> <p>Plot descriptors with:</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/calculator_scripts.html#density-of-atomistic-states","title":"Density of Atomistic States","text":"<p><code>calc_doas.py</code> calculates density of atomistic states (DOAS), following the idea proposed by Wang et al..</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>The script:</p> <ol> <li>reads all structures;</li> <li>relaxes each structure with a NEP calculator;</li> <li>extracts per-atom energies;</li> <li>groups atomic energies by element;</li> <li>writes the grouped values to the output file.</li> </ol> <p>For very large systems, doing minimization and atomistic-energy extraction directly in GPUMD may be more efficient.</p>"},{"location":"en/calculator_scripts.html#neb-with-a-nep-model","title":"NEB with a NEP Model","text":"<pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>This runs a NEB calculation with <code>9</code> intermediate images. During execution, the script asks how atoms should be fixed:</p> <ul> <li><code>none</code>: no atoms fixed;</li> <li><code>index</code>: fix atoms by index;</li> <li><code>element</code>: fix all atoms of one element;</li> <li><code>position</code>: fix atoms inside a coordinate range.</li> </ul>"},{"location":"en/calculator_scripts.html#structure-minimization","title":"Structure Minimization","text":"<pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input structure, POSCAR/CONTCAR or extxyz <code>nep.txt</code> NEP model <code>0.01</code> optional force convergence threshold in eV/Ang <code>1000</code> optional maximum optimization steps <p>Output:</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"en/calculator_scripts.html#ferroelectric-and-polar-material-tools","title":"Ferroelectric and Polar Material Tools","text":"<p>The following tools are useful for perovskite and polar-material analysis. They require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p><code>ferrodispcalc</code> currently has no associated paper to cite.</p>"},{"location":"en/calculator_scripts.html#build-neighbor-lists","title":"Build Neighbor Lists","text":"<pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre> <p>This creates a neighbor-list file where each row stores one center atom and its nearest neighbor atoms.</p>"},{"location":"en/calculator_scripts.html#calculate-displacements","title":"Calculate Displacements","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre> <p>Use <code>-l 0.2</code> to analyze the last 20% of frames. Use <code>-s</code>, <code>-t</code>, and <code>-p</code> if you want an explicit slice.</p>"},{"location":"en/calculator_scripts.html#average-a-structure","title":"Average a Structure","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>This is useful before displacement or polarization analysis when a representative averaged structure is needed.</p>"},{"location":"en/calculator_scripts.html#octahedral-tilt","title":"Octahedral Tilt","text":"<pre><code>gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre> <p>The neighbor list should usually contain six B-O neighbors for each B-site center in an <code>ABO3</code>-like structure.</p>"},{"location":"en/calculator_scripts.html#abo3-polarization","title":"ABO3 Polarization","text":"<pre><code>gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -o polarization.dat\n</code></pre> <p>The <code>--bec</code> values should be chosen according to your model or reference data. The tool is designed for <code>ABO3</code>-type local polarization analysis.</p>"},{"location":"en/command_reference.html","title":"Command Reference","text":"\ud83d\udccb Command Reference <p>This page lists the stable GPUMDkit command-line shortcuts. Interactive mode is available for workflows with many choices.</p> <p>The source table is maintained in <code>docs/command_reference.tsv</code>.</p>"},{"location":"en/command_reference.html#gpumdkitsh-h-output","title":"<code>gpumdkit.sh -h</code> Output","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |\n| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/command_reference.html#main","title":"Main","text":"Command Syntax Description <code>-h</code> <code>gpumdkit.sh -h</code> Show general help <code>-update</code> <code>gpumdkit.sh -update</code> Update GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> Clean extra files in the current directory"},{"location":"en/command_reference.html#format-conversion","title":"Format Conversion","text":"Command Syntax Description <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR to extxyz, shell version <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR to extxyz, Python version <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K output to xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR to extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF to POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF to extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR to extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz frames to POSCAR files <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR to LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump to extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory to extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> Replicate by cell factors <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> Replicate toward a target atom count <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> Add GPUMD group labels <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> Add structure weights <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> Extract one frame <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> Remove extra extxyz properties <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> Extract frames by fractional range"},{"location":"en/command_reference.html#calculators","title":"Calculators","text":"Command Syntax Description <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> Ionic conductivity <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP property prediction <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP descriptors <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> Density of atomistic states <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> NEB with a NEP model <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> Structure minimization <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> MSD from trajectory <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> Neighbor lists <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> Displacements <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> Averaged structure <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> Octahedral tilt <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 local polarization"},{"location":"en/command_reference.html#analyzers","title":"Analyzers","text":"Command Syntax Description <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> Property range analysis <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> Composition analysis <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> Chemical species list <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> Charge-balance check <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> Minimum distance without PBC <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> Minimum distance with PBC <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> Distance filtering <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> PBC-aware distance filtering <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> Box-edge filtering <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> Property threshold filtering <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> Element-pair distance range filtering <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> Probability density analysis"},{"location":"en/command_reference.html#visualization","title":"Visualization","text":"<p>Use:</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>Common types include <code>train</code>, <code>prediction</code>, <code>thermo</code>, <code>msd</code>, <code>sdc</code>, <code>rdf</code>, <code>emd</code>, <code>nemd</code>, <code>hnemd</code>, <code>pdos</code>, and <code>plane-grid</code>.</p>"},{"location":"en/command_reference.html#utilities","title":"Utilities","text":"Command Syntax Description <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> Monitor GPUMD or NEP progress <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> Modify NEP models interactively <code>-pynep</code> <code>gpumdkit.sh -pynep</code> Deprecated PyNEP FPS sampling"},{"location":"en/contributing_to_gpumdkit.html","title":"Contributing to GPUMDkit","text":"\ud83e\udd1d Contributing to GPUMDkit <p>Thank you for your interest in contributing to GPUMDkit! We appreciate your time and effort in helping improve this toolkit.</p> <p><code>GPUMDkit</code> is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.</p>"},{"location":"en/contributing_to_gpumdkit.html#table-of-contents","title":"Table of Contents","text":"<ul> <li>Development Restrictions and Guidelines</li> <li>Reporting Bugs</li> <li>Suggesting Features</li> <li>Contributing Code</li> <li>Fork and Clone the Repository</li> <li>Create a Feature Branch</li> <li>Making Changes<ul> <li>Interactive Mode Contributions</li> <li>Command-Line Mode Contributions</li> <li>Updating Tab Completion</li> </ul> </li> <li>Code Style and Best Practices</li> <li>Testing Your Changes</li> <li>Commit Messages</li> <li>Push and Open a Pull Request</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#development-restrictions-and-guidelines","title":"Development Restrictions and Guidelines","text":"<p>To maintain code quality and consistency across the project, please adhere to these guidelines:</p>"},{"location":"en/contributing_to_gpumdkit.html#language-requirements","title":"Language Requirements","text":"<ul> <li>All code should be written in English: This includes variable names, function names, comments, docstrings, commit messages, and documentation.</li> <li>While we understand that contributors come from diverse backgrounds, using English ensures that the codebase is accessible to the widest possible audience.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#modularity-and-reusability","title":"Modularity and Reusability","text":"<ul> <li>Write modular and reusable code: Functions and scripts should be designed with flexibility in mind.</li> <li>Prefer passing parameters over hardcoding values: Use function arguments, command-line parameters, or configuration files instead of hardcoded values. However, some filenames are required to be fixed by GPUMD and NEP programs (e.g., <code>train.xyz</code>, <code>thermo.out</code>), and these can be hardcoded as needed.</li> <li>Example:    <pre><code># Good: accepts parameters\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # processing logic\n}\n\n# Avoid: hardcoded values (unless required by GPUMD/NEP)\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # processing logic\n}\n</code></pre></li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#code-style","title":"Code Style","text":"<ul> <li>Write code that is clear and easy for others to maintain and modify.</li> <li>Use meaningful variable and function names.</li> <li>Add comments where necessary to explain complex logic.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#documentation","title":"Documentation","text":"<ul> <li>Ensure that help messages (e.g., <code>-h</code> flags) are clear and accurate.</li> <li>Documentation files in the <code>docs/</code> directory will be updated by the maintainers, so you generally don't need to modify them.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#reporting-bugs","title":"Reporting Bugs","text":"<p>If you encounter a bug, please help us fix it by reporting it through GitHub Issues:</p> <ol> <li>Search existing issues to see if the bug has already been reported.</li> <li>Open a new issue if it hasn't been reported yet: Create an Issue</li> <li>Describe the problem in detail and provide test files if possible.</li> </ol> <p>You can also reach out to us through: - QQ Group: 825696376 - Email: yanzihan@westlake.edu.cn - Script Developer: Contact the developer listed in the script header</p>"},{"location":"en/contributing_to_gpumdkit.html#suggesting-features","title":"Suggesting Features","text":"<p>We welcome feature suggestions! To propose a new feature:</p> <ol> <li>Search existing issues to see if someone has already suggested it.</li> <li>Open a new feature request: Create a Feature Request and mention @zhyan0603</li> <li>Describe what you need clearly and explain how it would be useful.</li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#contributing-code","title":"Contributing Code","text":""},{"location":"en/contributing_to_gpumdkit.html#fork-and-clone-the-repository","title":"Fork and Clone the Repository","text":"<ol> <li> <p>Fork the repository on GitHub by clicking the \"Fork\" button at the top right of the repository page.</p> </li> <li> <p>Clone your fork to your local machine:</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>Set up the upstream remote to keep your fork in sync:    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#create-a-feature-branch","title":"Create a Feature Branch","text":"<p>Create a new branch for your changes:</p> <pre><code># Create and checkout a new branch from main\ngit checkout -b your-branch-name\n</code></pre> <p>Name your branch as you prefer.</p>"},{"location":"en/contributing_to_gpumdkit.html#making-changes","title":"Making Changes","text":"<p>The structure of <code>GPUMDkit</code> consists of: - <code>gpumdkit.sh</code>: Main entry point (Bash script) handling both interactive menu mode and command-line mode - <code>Scripts/</code>: Python utility scripts organized by functionality   - <code>plt_scripts/</code>: Plotting scripts   - <code>calculators/</code>: Calculation utilities   - <code>format_conversion/</code>: Format conversion tools   - <code>workflow/</code>: Workflow automation   - <code>sample_structures/</code>: Structure sampling utilities   - <code>analyzer/</code>: Analysis tools   - <code>utils/</code>: Utility functions (including <code>completion.sh</code> for tab completion) - <code>src/</code>: Shell scripts containing menu functions for interactive mode   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>docs/</code>: Documentation files</p>"},{"location":"en/contributing_to_gpumdkit.html#interactive-mode-contributions","title":"Interactive Mode Contributions","text":"<p>To add a new feature accessible through the interactive menu:</p> <ol> <li>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:</li> </ol> <pre><code># Example: Add a new format conversion script\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>Implement your functionality following the modularity guidelines (accept parameters, avoid hardcoding).</p> </li> <li> <p>Add a wrapper function in the corresponding <code>src/</code> file:    <pre><code># Example: Edit src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>Add a new function:    <pre><code>function f106_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input the required parameters:\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -p \" \" converter_params\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py ${converter_params}\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>Update the menu display in <code>gpumdkit.sh</code>:    <pre><code># Find the menu() function and update it if needed\n# Find the array_choice array and add your new choice number\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\"  # Added \"106\"\n    # ... rest of choices\n)\n</code></pre></p> </li> <li> <p>Add the case statement in <code>gpumdkit.sh</code>:    <pre><code># In the main() function, find the appropriate case statement\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n            \"101\") f101_out2xyz ;;\n            # ... existing cases ...\n            \"106\") f106_new_converter ;;  # Add your case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#command-line-mode-contributions","title":"Command-Line Mode Contributions","text":"<p>To add a new command-line flag or subcommand:</p> <ol> <li> <p>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:    <pre><code># Example: Add a new analyzer script\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>Implement your functionality with clear parameter requirements:    <pre><code># Example: Scripts/analyzer/analyze_bonds.py\nimport sys\n\ndef main():\n    if len(sys.argv) != 3:\n        print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n        print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n        sys.exit(1)\n\n    input_file = sys.argv[1]\n    cutoff = float(sys.argv[2])\n\n    # Your implementation here\n\nif __name__ == \"__main__\":\n    main()\n</code></pre></p> </li> <li> <p>Add the command-line flag handler in <code>gpumdkit.sh</code>:    <pre><code># Find the command-line parsing section (after line ~167)\n# Add your new flag in the appropriate location\n\ncase $1 in\n    # ... existing cases ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py \"$2\" \"$3\"\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n            exit 1\n        fi ;;\n    # ... rest of cases ...\nesac\n</code></pre></p> </li> <li> <p>Update the help information in <code>gpumdkit.sh</code>:    <pre><code># Find the help_info_table() function and add your command\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... rest of help table ...\n}\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#updating-tab-completion","title":"Updating Tab Completion","text":"<p>When adding new command-line flags, update the tab completion script:</p> <pre><code># Edit Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>Add your new flag to the <code>opts</code> variable: <pre><code># Find the line with local opts=...\nlocal opts=\"-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ...\"\n#                                                      ^^^^^^^^^^^^^^ Add your flag here\n</code></pre></p> <p>If your flag accepts secondary options (like <code>-plt</code> or <code>-calc</code>), add a case for it: <pre><code>case \"$prev\" in\n    # ... existing cases ...\n    -analyze_bonds)\n        COMPREPLY=($(compgen -f -- \"$cur\"))  # Complete with filenames\n        ;;\n    # ... rest of cases ...\nesac\n</code></pre></p>"},{"location":"en/contributing_to_gpumdkit.html#code-style-and-best-practices","title":"Code Style and Best Practices","text":"<ul> <li>Shell Scripts:</li> <li>Use <code>${variable}</code> for variable expansion</li> <li> <p>Write code that is clear and easy to maintain</p> </li> <li> <p>Python Scripts:</p> </li> <li>Write clear, maintainable code</li> <li>Use meaningful variable names</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#testing-your-changes","title":"Testing Your Changes","text":"<p>Before submitting your contribution:</p> <ol> <li> <p>Test interactive mode (if applicable):    <pre><code>gpumdkit.sh\n# Navigate to your new feature and test it thoroughly\n</code></pre></p> </li> <li> <p>Test command-line mode (if applicable):    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # Test help message\n</code></pre></p> </li> <li> <p>Test tab completion (if you modified <code>completion.sh</code>):    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # Should show your new flag\n</code></pre></p> </li> <li> <p>Test with various inputs:</p> </li> <li>Test with typical inputs</li> <li>Test with edge cases (empty files, large files, etc.)</li> <li> <p>Test error handling (missing files, invalid parameters)</p> </li> <li> <p>Verify no regressions: Ensure existing functionality still works correctly.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#commit-messages","title":"Commit Messages","text":"<p>Write clear, descriptive commit messages that explain what you changed. There are no strict format requirements - just make sure your message is understandable.</p>"},{"location":"en/contributing_to_gpumdkit.html#push-and-open-a-pull-request","title":"Push and Open a Pull Request","text":"<ol> <li> <p>Commit your changes:    <pre><code>git add .\ngit commit -m \"your descriptive message\"\n</code></pre></p> </li> <li> <p>Keep your branch updated with the upstream <code>main</code> branch:    <pre><code>git fetch upstream\ngit rebase upstream/main\n</code></pre></p> </li> <li> <p>Push your branch to your fork:    <pre><code>git push origin your-branch-name\n</code></pre></p> </li> <li> <p>Open a Pull Request:</p> </li> <li>Go to the GPUMDkit repository</li> <li>Click \"Pull Requests\" \u2192 \"New Pull Request\"</li> <li>Set the base branch to <code>dev</code> for code review</li> <li>Set the compare branch to your feature branch</li> <li> <p>Fill in the PR description with:</p> <ul> <li>Title: Brief description of changes</li> <li>Description: Detailed explanation of what changed and why</li> <li>Testing: Describe how you tested the changes</li> </ul> </li> <li> <p>Respond to review feedback:</p> </li> <li>Be open to suggestions and constructive criticism</li> <li>Make requested changes promptly</li> <li> <p>Push additional commits to your branch (they'll automatically appear in the PR)</p> </li> <li> <p>After approval: A maintainer will merge your PR.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#questions-or-need-help","title":"Questions or Need Help?","text":"<p>If you have questions about contributing or need help with your contribution:</p> <ul> <li>Open a discussion: Use GitHub Discussions for general questions</li> <li>Ask in an issue: Comment on related issues for specific questions</li> <li>Contact maintainers: Reach out to the core developers listed in the README</li> </ul> <p>Thank you again for contributing to <code>GPUMDkit</code>! Your efforts help make this toolkit better for the entire GPUMD and NEP community. \ud83d\ude80</p>"},{"location":"en/custom_commands.html","title":"Custom Commands","text":"\ud83d\udd27 Custom Commands <p>GPUMDkit allows users to extend the command-line interface with custom commands. Define shortcuts for frequently used scripts in your ~/.gpumdkit.in file.</p>"},{"location":"en/custom_commands.html#setup","title":"Setup","text":"<p>Create or edit <code>~/.gpumdkit.in</code>: <pre><code>vi ~/.gpumdkit.in\n</code></pre></p> <p>Define custom functions with the <code>custom_</code> prefix.</p>"},{"location":"en/custom_commands.html#examples","title":"Examples","text":""},{"location":"en/custom_commands.html#simple-greeting","title":"Simple Greeting","text":"<p>Write the following codes in your <code>~/.gpumdkit.in</code> </p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>and run <code>gpumdkit.sh -hello</code>, you will see:</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"en/custom_commands.html#command-with-required-arguments","title":"Command with Required Arguments","text":"<p>For the following function:</p> <pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>and you can add a argument, for example: <code>gpumdkit.sh -greet Zihan</code>, then you will see:</p> <pre><code>Hello, Zihan!\n</code></pre> <p>Passing arguments: Use <code>\"$@\"</code> to forward all arguments safely. Use <code>${@:1}</code> when you need to refer to arguments starting from the first one. </p>"},{"location":"en/custom_commands.html#calling-an-external-script","title":"Calling an External Script","text":"<p>If you want to call an external script like <code>gpumdkit.sh</code>.</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>and run <code>gpumdkit.sh -nepanalyse</code></p>"},{"location":"en/custom_commands.html#advanced-examples","title":"Advanced Examples","text":""},{"location":"en/custom_commands.html#batch-processing","title":"Batch Processing","text":"<p>Process multiple files: <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -batch_plot dir1 dir2 dir3</code></p>"},{"location":"en/custom_commands.html#analysis-pipeline","title":"Analysis Pipeline","text":"<p>Combine multiple operations: <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -analyze_training train.xyz</code></p>"},{"location":"en/custom_commands.html#custom-workflow","title":"Custom Workflow","text":"<p>Automate common workflow: <pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    # Convert VASP outputs\n    gpumdkit.sh -out2xyz ./\n\n    # Filter outliers\n    gpumdkit.sh -filter_value train.xyz force 30\n\n    # Check quality\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -prep_training</code></p>"},{"location":"en/custom_commands.html#tips","title":"Tips","text":"<ul> <li>Use descriptive names: <code>custom_analyze_nep_training</code> is clearer than <code>custom_ant</code></li> <li>Add help messages: Echo usage info when no arguments provided</li> <li>Error handling: Check if required files exist before processing</li> <li>Forward arguments safely: Use <code>\"$@\"</code> to preserve spaces and special characters</li> </ul> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/format_conversion.html","title":"Format Conversion","text":"\ud83d\udd04 Format Conversion <p>GPUMDkit contains utilities for converting common atomistic simulation formats, with extra handling for metadata such as group labels, weights, and frame extraction.</p> <p>Script Location: <code>Scripts/format_conversion/</code></p>"},{"location":"en/format_conversion.html#overview","title":"Overview","text":"<p>The format conversion module covers:</p> <ul> <li>VASP: <code>POSCAR</code>, <code>CONTCAR</code>, <code>OUTCAR</code>, <code>XDATCAR</code></li> <li>LAMMPS: data files and dump trajectories</li> <li>CP2K: output logs, position, force, and cell files</li> <li>ABACUS: SCF/MD logs</li> <li>CIF: crystallographic structure files</li> <li>ASE trajectory: <code>.traj</code></li> <li>extxyz: a common structure format for GPUMD and NEP</li> </ul>"},{"location":"en/format_conversion.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>1) Format Conversion\n</code></pre> <p>The format conversion menu is:</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"en/format_conversion.html#what-each-entry-does","title":"What Each Entry Does","text":"Entry Function When to Use <code>101</code> VASP OUTCAR to extxyz, shell version convert VASP calculation directories <code>102</code> MTP cfg to extxyz convert MTP training data <code>103</code> CP2K to extxyz choose CP2K log/inp route or pos/frc/cell route <code>104</code> ABACUS to extxyz convert ABACUS SCF or MD output <code>105</code> extxyz to POSCAR write each extxyz frame as a POSCAR-style file <code>106</code> add group labels add atom group labels for GPUMD-related workflows <code>107</code> add weights assign training weights in extxyz <code>108</code> extract frame export one frame from an extxyz trajectory <code>109</code> clean XYZ info remove extra extxyz properties <code>110</code> replicate structure build supercells by factors or target atom count <code>out2exyz</code> OUTCAR to extxyz, Python version alternative VASP OUTCAR converter <code>pos2exyz</code> POSCAR to extxyz convert a single structure <code>cif2pos</code> CIF to POSCAR prepare VASP input from CIF <code>cif2exyz</code> CIF to extxyz prepare GPUMDkit input from CIF <code>xdat2exyz</code> XDATCAR to extxyz convert VASP MD trajectory <code>pos2lmp</code> POSCAR to LAMMPS data prepare LAMMPS input <code>lmp2exyz</code> LAMMPS dump to extxyz convert LAMMPS trajectory <code>traj2exyz</code> ASE traj to extxyz convert ASE trajectory"},{"location":"en/format_conversion.html#quick-command-reference","title":"Quick Command Reference","text":"Source Target Command OUTCAR directory extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR directory extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> extxyz POSCAR files <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"en/format_conversion.html#common-examples","title":"Common Examples","text":""},{"location":"en/format_conversion.html#convert-vasp-calculations-to-extxyz","title":"Convert VASP calculations to extxyz","text":"<p>If each calculation directory contains an <code>OUTCAR</code>, run:</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>The shell version searches the target directory and converts VASP results into an extxyz file suitable for later analysis. If you prefer the Python implementation:</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>From interactive mode, choose <code>101</code>. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#add-group-labels","title":"Add group labels","text":"<p>Some GPUMD-related workflows use group labels for atom grouping, for example in species-specific MSD or diffusion calculations.</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>This command reads the input structure and writes an extxyz file with group information.</p> <p>From interactive mode, choose <code>106</code>. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#script-details","title":"Script Details","text":""},{"location":"en/format_conversion.html#poscar-to-extxyz","title":"POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>Use this when you have a single VASP structure and want an extxyz output.</p> <p>Interactive keyword: <code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#extxyz-to-poscar","title":"extxyz to POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>This converts all frames in an extxyz file into <code>POSCAR_*.vasp</code> files. Frame indices are 0-based in most GPUMDkit scripts, but output filenames are meant for direct inspection and batch calculations.</p> <p>Interactive entry: <code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#lammps-dump-to-extxyz","title":"LAMMPS dump to extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>The element symbols must match the LAMMPS atom type IDs. For example, if type <code>1</code> is Li, type <code>2</code> is Y, and type <code>3</code> is Cl, the order should be <code>Li Y Cl</code>.</p> <p>Interactive keyword: <code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#cif-conversion","title":"CIF conversion","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>Use <code>-cif2pos</code> if you want a VASP-style structure, and <code>-cif2exyz</code> if the next step is GPUMDkit analysis.</p>"},{"location":"en/format_conversion.html#add-weights","title":"Add weights","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>This is useful when you want some structures to have a different training weight in a NEP dataset.</p>"},{"location":"en/format_conversion.html#replicate-structures","title":"Replicate structures","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>The first form uses explicit replication factors. The second form tries to build a supercell close to a target atom count.</p>"},{"location":"en/format_conversion.html#extract-one-frame","title":"Extract one frame","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>This extracts frame index <code>1000</code> from an extxyz trajectory.</p>"},{"location":"en/format_conversion.html#common-mistakes","title":"Common Mistakes","text":"Problem What to Check LAMMPS elements are wrong Check the element order passed after the dump file A trajectory has strange metadata Try <code>-clean_xyz input.xyz clean.xyz</code> A converted structure looks shifted Inspect PBC/cell information in the source file Frame extraction gives the wrong structure Remember that frame indices are 0-based"},{"location":"en/format_conversion.html#notes","title":"Notes","text":"<p>If a Python package required by a specific converter is missing, Python will report it when that converter is used.</p>"},{"location":"en/plot_scripts.html","title":"Plot Scripts","text":"\ud83d\udcca Plot Scripts <p>The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators.</p> <p>Script Location: <code>Scripts/plt_scripts/</code></p>"},{"location":"en/plot_scripts.html#quick-access","title":"Quick Access","text":"<pre><code>gpumdkit.sh -plt          # show all plotting options\ngpumdkit.sh -plt &lt;type&gt;   # generate a plot\ngpumdkit.sh -plt &lt;type&gt; save\ngpumdkit.sh -plt &lt;type&gt; -h\n</code></pre>"},{"location":"en/plot_scripts.html#nep-training-and-prediction","title":"NEP Training and Prediction","text":""},{"location":"en/plot_scripts.html#training-results","title":"Training Results","text":"<p><code>plt_train.py</code> visualizes NEP training progress, including loss curves and parity plots for energy, force, and virial/stress.</p> <p>Input files:</p> <ul> <li><code>loss.out</code></li> <li><code>energy_train.out</code></li> <li><code>force_train.out</code></li> <li><code>virial_train.out</code></li> </ul> <p>Usage:</p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/plot_scripts.html#prediction-results","title":"Prediction Results","text":"<p><code>plt_prediction.py</code> visualizes prediction/test-set results.</p> <p>Input files:</p> <ul> <li><code>energy_test.out</code></li> <li><code>force_test.out</code></li> <li><code>virial_test.out</code></li> </ul> <p>Usage:</p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test\n</code></pre>"},{"location":"en/plot_scripts.html#traintest-comparison","title":"Train/Test Comparison","text":"<pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"en/plot_scripts.html#density-parity-plot","title":"Density Parity Plot","text":"<p>For large datasets, density-based parity plots are often easier to read than raw scatter plots.</p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"en/plot_scripts.html#force-error-analysis","title":"Force Error Analysis","text":"<p><code>plt_force_errors.py</code> plots force magnitude and angular errors following the analysis style proposed by Liu et al..</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"en/plot_scripts.html#restart-parameters","title":"Restart Parameters","text":"<pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"en/plot_scripts.html#charge-and-born-effective-charge","title":"Charge and Born Effective Charge","text":"<p>For qNEP charge output:</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre> <p>For Born effective charge prediction:</p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec\n</code></pre>"},{"location":"en/plot_scripts.html#molecular-dynamics-and-thermodynamics","title":"Molecular Dynamics and Thermodynamics","text":""},{"location":"en/plot_scripts.html#thermodynamic-properties","title":"Thermodynamic Properties","text":"<p><code>plt_thermo.py</code> reads <code>thermo.out</code> and plots temperature, potential energy, pressure, and other thermodynamic quantities.</p> <pre><code>gpumdkit.sh -plt thermo\ngpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"en/plot_scripts.html#radial-distribution-function","title":"Radial Distribution Function","text":"<pre><code>gpumdkit.sh -plt rdf\ngpumdkit.sh -plt rdf &lt;column&gt;\n</code></pre> <p>Full RDF output:</p> <p>Single pair RDF:</p>"},{"location":"en/plot_scripts.html#velocity-autocorrelation-and-pdos","title":"Velocity Autocorrelation and PDOS","text":"<pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>Input files: <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></p> <p>Heat capacity output:</p>"},{"location":"en/plot_scripts.html#diffusion-and-ionic-transport","title":"Diffusion and Ionic Transport","text":""},{"location":"en/plot_scripts.html#mean-square-displacement","title":"Mean Square Displacement","text":"<pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"en/plot_scripts.html#msd-for-all-species","title":"MSD for All Species","text":"<p>Use this when <code>compute_msd</code> in <code>run.in</code> was configured with <code>all_groups</code>.</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"en/plot_scripts.html#msd-convergence-check","title":"MSD Convergence Check","text":"<pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"en/plot_scripts.html#self-diffusion-coefficient","title":"Self-Diffusion Coefficient","text":"<pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/plot_scripts.html#arrhenius-diffusivity","title":"Arrhenius Diffusivity","text":"<pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D\n</code></pre> <p>Example output:</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"en/plot_scripts.html#arrhenius-ionic-conductivity","title":"Arrhenius Ionic Conductivity","text":"<pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma\n</code></pre>"},{"location":"en/plot_scripts.html#heat-transport","title":"Heat Transport","text":""},{"location":"en/plot_scripts.html#emd","title":"EMD","text":"<pre><code>gpumdkit.sh -plt emd x\n</code></pre>"},{"location":"en/plot_scripts.html#nemd","title":"NEMD","text":"<pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre> <p>Parameter notes:</p> Parameter Meaning <code>real_length</code> real length of heat-transfer zone in nm; use <code>Auto</code> for automatic calculation <code>scale_eff_size</code> scale factor for effective cross-sectional area <code>cutoff_freq</code> cutoff frequency for SHC calculation in THz <code>save</code> optional flag to save the figure"},{"location":"en/plot_scripts.html#hnemd","title":"HNEMD","text":"<pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#descriptor-dimer-and-extra-analysis","title":"Descriptor, Dimer, and Extra Analysis","text":""},{"location":"en/plot_scripts.html#descriptor-visualization","title":"Descriptor Visualization","text":"<p>First calculate descriptors:</p> <pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>Then visualize:</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/plot_scripts.html#dimer-curve","title":"Dimer Curve","text":"<p><code>plt_dimer.py</code> places two atoms in a large cubic box and calculates energy/force as a function of dimer distance using a NEP model.</p> <pre><code>gpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>Reference: J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"en/plot_scripts.html#density-of-atomistic-states","title":"Density of Atomistic States","text":"<p><code>plt_doas.py</code> plots the density of atomistic states proposed by Wang et al..</p> <pre><code>gpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"en/plot_scripts.html#net-force-distribution","title":"Net Force Distribution","text":"<pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>Reference: arXiv:2510.19774</p>"},{"location":"en/plot_scripts.html#plane-grid-plot-for-polar-materials","title":"Plane-Grid Plot for Polar Materials","text":"<p>This workflow maps displacement or polarization data onto a grid and plots selected plane profiles.</p> <p>Typical upstream steps:</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>Plot:</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre> <p>This function requires <code>ferrodispcalc</code>.</p>"},{"location":"en/plot_scripts.html#quick-reference-table","title":"Quick Reference Table","text":"Command Input File(s) Purpose <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP training plots <code>prediction</code> <code>*_test.out</code> NEP prediction plots <code>train_test</code> train/test outputs combined parity plots <code>thermo</code> <code>thermo.out</code> thermodynamic properties <code>msd</code> <code>msd.out</code> mean square displacement <code>sdc</code> <code>msd.out</code> self-diffusion coefficient <code>rdf</code> <code>rdf.out</code> radial distribution function <code>pdos</code> <code>dos.out</code>, <code>mvac.out</code> VAC and PDOS <code>emd</code> EMD outputs EMD thermal conductivity <code>nemd</code> NEMD outputs NEMD thermal transport <code>hnemd</code> HNEMD outputs HNEMD thermal transport <code>des</code> <code>descriptors.npy</code> descriptor PCA/UMAP <code>dimer</code> <code>nep.txt</code> dimer energy/force curve <code>doas</code> <code>doas.out</code> density of atomistic states <code>net_force</code> <code>train.xyz</code> net force distribution"},{"location":"en/polar_material_analysis.html","title":"Polar Material Analysis","text":"\ud83e\uddf2 Polar Material Analysis <p>This tutorial covers GPUMDkit calculator options <code>406-410</code> and the <code>plane-grid</code> plotting workflow.</p> <p>Script Location: <code>Scripts/calculators/</code> and <code>Scripts/plt_scripts/</code></p> <p>This tutorial includes both general and system-specific tools:</p> <ul> <li><code>nlist</code>, <code>disp</code>, and <code>avg-struct</code> are broadly useful for structure/trajectory analysis.</li> <li><code>oct-tilt</code> is for octahedral environments (requires 6 neighbors around each center).</li> <li><code>pol-abo3</code> is specific to <code>ABO3</code> polarization analysis.</li> </ul>"},{"location":"en/polar_material_analysis.html#dependency","title":"Dependency","text":"<p>These scripts require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"en/polar_material_analysis.html#interactive-mode-entry","title":"Interactive mode entry","text":"<p>Options <code>406-410</code> are the core functions for this tutorial. The sections below explain when to use each one and how to run it.</p> <p>For full argument details, use:</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"en/polar_material_analysis.html#406-build-neighbor-list-calc_neighbor_listpy","title":"406) Build neighbor list (<code>calc_neighbor_list.py</code>)","text":"<p>Build neighbor lists for selected center and neighbor elements.</p> <p>When to use it: This is usually the first step before <code>disp</code>, <code>oct-tilt</code>, and <code>pol-abo3</code>, because those scripts read <code>nl-*.dat</code> neighbor files.</p>"},{"location":"en/polar_material_analysis.html#usage","title":"Usage","text":"<pre><code># Example 1: Ti-O nearest 6 neighbors for octahedral analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# Example 2: Pb/Sr-O nearest 12 neighbors for A-site centered analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input structure file. Default: <code>model.xyz</code>.</li> <li><code>-x, --index</code>:   Frame index to read from input. Default: <code>0</code>.</li> <li><code>-c, --cutoff</code> (required):   Neighbor search cutoff (Angstrom).</li> <li><code>-n, --neighbor-num</code> (required):   Number of neighbors per center.</li> <li><code>-d, --defect</code>:   Defect mode. If enabled and neighbors are insufficient, missing slots are filled with the center index.</li> <li><code>-C, --center-elements</code> (required):   Center species list.</li> <li><code>-E, --neighbor-elements</code> (required):   Neighbor species list.</li> <li><code>-o, --output</code>:   Output file path. Default: <code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file","title":"Output file","text":"<ul> <li>Main output: neighbor list text file (for example <code>nl-Ti-O.dat</code>).</li> <li>The file is a 2D integer array with shape <code>(n_center, neighbor_num + 1)</code>. Each row corresponds to one center atom: the first column is the center index, and the remaining columns are its neighbor indices (all 1-based).</li> </ul>"},{"location":"en/polar_material_analysis.html#407-calc-displacement-from-trajectory-calc_displacementpy","title":"407) Calc displacement from trajectory (<code>calc_displacement.py</code>)","text":"<p>Compute local displacement vectors from a trajectory/model and a neighbor list.</p>"},{"location":"en/polar_material_analysis.html#usage_1","title":"Usage","text":"<pre><code># Example 1: single-frame displacement from model.xyz\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# Example 2: use the last 20% frames in movie.xyz\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_1","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   Neighbor list file from <code>nlist</code>.</li> <li><code>-o, --output</code>:   Output file. Default: <code>displacements.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames.   Integer: last <code>N</code> frames.   <code>0 &lt; value &lt; 1</code>: last ratio of frames.</li> <li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_1","title":"Output file","text":"<ul> <li>Main output: <code>displacements.dat</code> (or your custom output name).</li> <li>The saved text file is a 2D array: for a single-frame input, its shape is <code>(n_center, 3)</code>; for a multi-frame input, it is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The three columns are <code>dx</code>, <code>dy</code>, and <code>dz</code> displacement components in Angstrom.</li> </ul>"},{"location":"en/polar_material_analysis.html#408-calc-averaged-structure-calc_averaged_structurepy","title":"408) Calc averaged structure (<code>calc_averaged_structure.py</code>)","text":"<p>Generate one averaged structure from selected trajectory frames. Use this after equilibration. For a solid near equilibrium, average a frame window at the target temperature and analyze that representative structure instead of processing every snapshot.</p>"},{"location":"en/polar_material_analysis.html#usage_2","title":"Usage","text":"<pre><code># Example 1: average all frames\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# Example 2: average selected frames (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_2","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input trajectory file. Default: <code>movie.xyz</code>.</li> <li><code>-o, --output</code>:   Output structure file. Default: <code>averaged_structure.xyz</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_2","title":"Output file","text":"<ul> <li>Main output: averaged single-frame extxyz file.</li> <li>Position averaging applies MIC/PBC correction relative to the first selected frame.</li> </ul>"},{"location":"en/polar_material_analysis.html#409-calc-octahedral-tilt-calc_oct_tiltpy","title":"409) Calc octahedral tilt (<code>calc_oct_tilt.py</code>)","text":"<p>Calculate octahedral tilt angles from a B-O neighbor list. This is commonly used to analyze octahedral rotation patterns in <code>ABO3</code> systems, such as <code>SrTiO3</code> and <code>PbZrO3</code>.</p>"},{"location":"en/polar_material_analysis.html#usage_3","title":"Usage","text":"<pre><code># Example 1: octahedral tilt of the TiO6 octahedra from a single frame\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# Example 2: octahedral tilt of the TiO6 octahedra from the last 20% trajectory frames\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_3","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   B-O neighbor list file.</li> <li><code>-o, --output</code>:   Output file. Default: <code>octahedral_tilt.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_3","title":"Output file","text":"<ul> <li>Main output: <code>octahedral_tilt.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>theta_x</code>, <code>theta_y</code>, <code>theta_z</code>, in degree): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#410-calc-polarization-for-abo3-calc_polarization_abo3py","title":"410) Calc polarization for ABO3 (<code>calc_polarization_abo3.py</code>)","text":"<p>Calculate local polarization vectors for <code>ABO3</code> systems.</p>"},{"location":"en/polar_material_analysis.html#usage_4","title":"Usage","text":"<pre><code># Example 1: single-frame ABO3 polarization\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# Example 2: trajectory polarization on a selected frame window\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_4","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>--nl-ba</code> (required):   B-A neighbor list.</li> <li><code>--nl-bo</code> (required):   B-O neighbor list.</li> <li><code>-o, --output</code>:   Output file. Default: <code>polarization.dat</code>.</li> <li><code>--bec</code> (required):   Born effective charge terms in <code>Element=value</code> format.   Example: <code>Pb=2.5 Ti=4.0 O=-2.0</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul> <p>Important checks:</p> <ul> <li><code>--bec</code> must include all element species in the input structure.</li> <li>Center atom indices in <code>--nl-ba</code> and <code>--nl-bo</code> must match.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_4","title":"Output file","text":"<ul> <li>Main output: <code>polarization.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>Px</code>, <code>Py</code>, <code>Pz</code>, in <code>C/m^2</code>): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The script prints a warning if the total Born charge is not balanced.</li> </ul>"},{"location":"en/polar_material_analysis.html#plane-grid-visualization-plt_plane_gridpy","title":"Plane-grid visualization (<code>plt_plane_grid.py</code>)","text":"<p>You can visualize either <code>displacements.dat</code> or <code>polarization.dat</code>:</p> <pre><code># Example 1: displacement map on Ti sites, first XY layer\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# Example 2: polarization map on Pb sites, XZ and YZ layers\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>Arguments (complete):</p> <ul> <li><code>-i, --input</code>:   Input xyz file for atomic layout and layering. Default: <code>model.xyz</code>.</li> <li><code>-d, --disp</code>:   Vector-field data file. Default: <code>displacements.dat</code>.</li> <li><code>-e, --elements</code> (required):   Center element symbols used to map vectors to lattice layers.</li> <li><code>-m, --tol</code>:   Layer tolerance for grid mapping. Default: <code>1.0</code>.</li> <li><code>-g, --target-size</code>:   Expected grid size as <code>nx ny nz</code>.</li> <li><code>-o, --save-dir</code>:   Figure output directory. Default: <code>plot</code>.</li> <li><code>-f, --frame</code>:   Frame index to visualize when vector data has multiple frames. Default: <code>0</code>.</li> <li><code>--select-xy</code>:   Selected XY layer indices.</li> <li><code>--select-xz</code>:   Selected XZ layer indices.</li> <li><code>--select-yz</code>:   Selected YZ layer indices.</li> </ul> <p>Output:</p> <ul> <li>Creates output directory if needed.</li> <li>Saves figures as <code>XY_*.png</code>, <code>XZ_*.png</code>, <code>YZ_*.png</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-files-at-a-glance","title":"Output files at a glance","text":"Script Main output What it stores <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based center index + neighbor indices <code>calc_displacement.py</code> <code>*.dat</code> Local displacement vectors (<code>dx dy dz</code>, Angstrom) <code>calc_averaged_structure.py</code> <code>*.xyz</code> One averaged structure <code>calc_oct_tilt.py</code> <code>*.dat</code> Octahedral tilt angles (<code>theta_x theta_y theta_z</code>, degree) <code>calc_polarization_abo3.py</code> <code>*.dat</code> Local polarization vectors (<code>Px Py Pz</code>, <code>C/m^2</code>) <code>plt_plane_grid.py</code> <code>plot/*.png</code> XY/XZ/YZ plane maps from vector-field data"},{"location":"en/polar_material_analysis.html#real-examples","title":"Real Examples","text":""},{"location":"en/polar_material_analysis.html#temperature-driven-ferroelectric-to-paraelectric-phase-transition-for-pbtio3","title":"Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3","text":"<p>Assume all files are in the current directory <code>./</code>:</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> is the initial structure used to run MD simulations. Each <code>TEMP K.xyz</code> is a trajectory at that temperature.</p>"},{"location":"en/polar_material_analysis.html#step-1-get-averaged-structures-from-the-last-half-of-each-trajectory","title":"Step 1: get averaged structures from the last half of each trajectory","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>This writes <code>300K-avg.xyz</code>, <code>350K-avg.xyz</code>, ..., <code>800K-avg.xyz</code>.</p>"},{"location":"en/polar_material_analysis.html#step-2-build-neighbor-lists-from-modelxyz","title":"Step 2: build neighbor lists from <code>model.xyz</code>","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-compute-displacement-and-polarization-for-each-temperature","title":"Step 3: compute displacement and polarization for each temperature","text":"<p>Use Born effective charges (BEC), not nominal ionic charges. For PbTiO3 in this example:</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>You can obtain BEC from your own DFPT calculation or from literature values. Thus use following commands to compute local displacement and polarization:</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-4-plot-displacement-and-polarization-maps-in-real-space","title":"Step 4: plot displacement and polarization maps in real space","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-5-build-a-temperature-order-parameter-curve","title":"Step 5: build a temperature-order-parameter curve","text":"<p>By analyzing the lattice of each temperature-averaged structure together with its polarization (<code>XX-pol.dat</code>), we can obtain the following figure:</p> <p>The trend shows a clear phase transition around <code>600 K</code>, where the polarization vanishes.</p>"},{"location":"en/polar_material_analysis.html#topological-structure-in-pbtio3srtio3-superlattice","title":"Topological structure in PbTiO3/SrTiO3 superlattice","text":"<p>Assume <code>movie.xyz</code> is the trajectory of the PbTiO3/SrTiO3 superlattice in the current directory.</p>"},{"location":"en/polar_material_analysis.html#step-1-build-an-averaged-structure-from-the-last-25-frames","title":"Step 1: build an averaged structure from the last 25% frames","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-2-build-the-ti-neighbor-list","title":"Step 2: build the Ti neighbor list","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-plot-the-plane-grid-map","title":"Step 3: plot the plane-grid map","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero. By analyzing how polarization varies around the vortex core, you can estimate the local dielectric response, but that is beyond the scope of this tutorial.</p> <p>Note: this figure uses a different colormap from the default GPUMDkit plotting style. The default output does not look exactly the same, but you can get this style with small plotting-script changes.</p>"},{"location":"en/polar_material_analysis.html#other-systems","title":"Other Systems","text":""},{"location":"en/polar_material_analysis.html#organic-inorganic-hybrid-ferroelectrics","title":"Organic-inorganic hybrid ferroelectrics","text":"<p>In many organic-inorganic ferroelectrics, polarization is strongly tied to anisotropic molecular units. A practical way to track molecular orientation is to use bond vectors.</p> <p>For TMCM-CdCl3, you can use the C-Cl bond direction of the TMCM molecule as an orientation proxy, then use it to estimate the polarization state:</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p><code>ccl_vectors.dat</code> can then be analyzed as an orientation order parameter. More details could be found at: Phys. Rev. Lett. 136, 016801</p>"},{"location":"en/polar_material_analysis.html#other-ferroelectric-families","title":"Other ferroelectric families","text":"<p>Beyond <code>ABO3</code>, <code>ferrodispcalc</code> can be adapted to many ferroelectric systems, including nitrides, hafnia-based compounds, organic-inorganic hybrids, and some 2D ferroelectrics.</p>"},{"location":"en/quick_start.html","title":"Quick Start","text":"\ud83d\ude80 Quick Start <p>This page introduces the basic installation and several common commands. GPUMDkit can be used through the interactive menu or by direct command-line options.</p>"},{"location":"en/quick_start.html#1-prepare-a-python-environment","title":"1. Prepare a Python Environment","text":"<p>You can use a clean conda environment:</p> <pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>Some optional functions use additional packages:</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>Other Python dependencies are loaded by the corresponding scripts. If a package is missing, Python will report it when that function is used.</p>"},{"location":"en/quick_start.html#2-install-gpumdkit","title":"2. Install GPUMDkit","text":"<p>Clone the repository:</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <p>Run the installer:</p> <pre><code>source ./install.sh\n</code></pre> <p>The installer writes <code>GPUMDkit_path</code> and <code>PATH</code> settings to your shell configuration and loads them for the current shell. It writes to <code>~/.bashrc</code> by default; if the current shell is zsh, it writes to <code>~/.zshrc</code>. If an existing GPUMDkit path is found, the installer prints the old path and asks whether to replace it. Before changing the rc file, it creates a backup.</p> <p>Typical installation output:</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>If GPUMDkit was installed before, you may see:</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre> <p>Check the command:</p> <pre><code>gpumdkit.sh -h\n</code></pre> <p>The help table:</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |\n| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/quick_start.html#3-usage-modes","title":"3. Usage Modes","text":""},{"location":"en/quick_start.html#interactive-mode","title":"Interactive Mode","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>Main menu:</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre>"},{"location":"en/quick_start.html#command-line-mode","title":"Command-Line Mode","text":"<p>Direct commands use fixed positional arguments:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -plt thermo\n</code></pre> <p>For example:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>means reading <code>POSCAR</code> and writing <code>model.xyz</code>.</p>"},{"location":"en/quick_start.html#4-practical-examples","title":"4. Practical Examples","text":""},{"location":"en/quick_start.html#convert-poscar-to-extxyz","title":"Convert POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"en/quick_start.html#add-gpumd-group-labels","title":"Add GPUMD Group Labels","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>Group labels are used by some GPUMD-related workflows and analyses that need atom grouping, such as species-specific MSD or diffusion calculations.</p>"},{"location":"en/quick_start.html#plot-nep-training-results","title":"Plot NEP Training Results","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/quick_start.html#plot-nep-test-results","title":"Plot NEP Test Results","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"en/quick_start.html#plot-thermodynamic-data","title":"Plot Thermodynamic Data","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/quick_start.html#plot-msd-and-self-diffusion-coefficient","title":"Plot MSD and Self-Diffusion Coefficient","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/quick_start.html#5-help","title":"5. Help","text":"<pre><code>gpumdkit.sh -h\ngpumdkit.sh -plt -h\ngpumdkit.sh -calc -h\ngpumdkit.sh -plt train -h\ngpumdkit.sh -calc msd -h\n</code></pre>"},{"location":"en/structure_sampling.html","title":"Structure Sampling","text":"\ud83d\udce6 Structure Sampling <p>Structure sampling is used to select, generate, or filter candidate configurations for NEP training and molecular dynamics workflows.</p> <p>Script Location: <code>Scripts/sample_structures/</code></p>"},{"location":"en/structure_sampling.html#interactive-mode","title":"Interactive Mode","text":"<p>Sampling tasks are usually easier to run from the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>2) Sample Structures\n</code></pre> <p>The menu is:</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Method Use Case 201 Uniform/random sampling quick frame selection from a trajectory 202 PyNEP notice prints a notice; use <code>gpumdkit.sh -pynep</code> to run PyNEP 203 NepTrain FPS descriptor-based FPS with NepTrain 204 Perturb structure generate perturbed structures from POSCAR/CONTCAR 205 Force-deviation selection select structures with high model deviation"},{"location":"en/structure_sampling.html#uniform-and-random-sampling","title":"Uniform and Random Sampling","text":"<p>From interactive mode, choose <code>201</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>Example input:</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>or:</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>uniform</code> / <code>random</code> sampling method <code>50</code> / <code>100</code> number of selected structures <code>500</code> optional number of initial frames to skip <p>Output:</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#farthest-point-sampling-with-neptrain","title":"Farthest Point Sampling with NepTrain","text":"<p>This entry uses NepTrain descriptors for FPS.</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>From interactive mode, choose <code>203</code>. You will see:</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>Inputs:</p> File Meaning <code>dump.xyz</code> candidate structures <code>train.xyz</code> existing training set <code>nep.txt</code> current NEP model used to compute descriptors <p>Outputs:</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>During execution, choose one of two selection modes:</p> <ol> <li>select until the descriptor distance is below a threshold;</li> <li>select a specified number of structures.</li> </ol> <p>The script then prints a selection prompt:</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>This function requires the <code>NepTrain</code> package. If you use this function, we recommend citing the NepTrain paper printed by the script.</p>"},{"location":"en/structure_sampling.html#deprecated-pynep-fps","title":"Deprecated PyNEP FPS","text":"<p>PyNEP FPS is kept for compatibility, but it is only exposed through the direct <code>-pynep</code> entry:</p> <p>If you choose <code>202</code> from the interactive menu, it prints:</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre> <pre><code>gpumdkit.sh -pynep\n</code></pre> <p>Then input:</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>This entry requires <code>pynep</code> and is kept for compatibility.</p>"},{"location":"en/structure_sampling.html#structure-perturbation","title":"Structure Perturbation","text":"<p>Use perturbation when you want to generate initial structures around a known configuration.</p> <pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>From interactive mode, choose <code>204</code>. You will see:</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input VASP structure <code>20</code> number of perturbed structures <code>0.03</code> cell perturbation fraction <code>0.2</code> atom perturbation distance in Angstrom <code>uniform</code> perturbation style: <code>normal</code>, <code>uniform</code>, or <code>const</code> <p>Output:</p> <ul> <li><code>POSCAR_01.vasp</code>, <code>POSCAR_02.vasp</code>, ...</li> </ul> <p>This function requires <code>dpdata</code>.</p>"},{"location":"en/structure_sampling.html#force-deviation-selection","title":"Force-Deviation Selection","text":"<p>Use this together with the GPUMD <code>active</code> command. The <code>active</code> command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. <code>select_max_modev.py</code> selects structures with large force deviations from <code>active.out</code> and <code>active.xyz</code>, then writes them to <code>selected.xyz</code>.</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>From interactive mode, choose <code>205</code>. You will see:</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>200</code> maximum number of structures to keep <code>0.15</code> minimum force deviation threshold <p>Required files:</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>Output:</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#frame-range-extraction","title":"Frame Range Extraction","text":"<p>Use this to extract a fraction of a trajectory:</p> <pre><code>python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>This writes frames from 0% to 80% of the trajectory.</p>"},{"location":"en/structure_sampling.html#example-commands","title":"Example Commands","text":"<p>An example sequence using several sampling-related tools:</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"en/structure_sampling.html#common-mistakes","title":"Common Mistakes","text":"Problem Recommendation FPS selects too many similar structures increase the distance threshold or select fewer structures Perturbed structures are unphysical reduce <code>cell_pert</code> and <code>atom_pert</code>, then check minimum distances <code>active.out</code> and <code>active.xyz</code> do not match regenerate both from the same GPUMD active run PCA plot looks strange check whether <code>nep.txt</code> matches the chemical species in both datasets"},{"location":"en/workflow_scripts.html","title":"Workflow Scripts","text":"\ud83d\udd27 Workflow Scripts <p>Workflow scripts automate repetitive preparation steps for DFT, MD, and NEP development.</p> <p>Script Location: <code>Scripts/workflow/</code></p>"},{"location":"en/workflow_scripts.html#interactive-entry","title":"Interactive Entry","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>3) Workflow\n</code></pre> <p>Typical workflow menu:</p> Menu Workflow Purpose 301 SCF batch pretreatment prepare single-point DFT calculations 302 MD sample batch pretreatment (GPUMD) prepare GPUMD sampling calculations 303 MD sample batch pretreatment (LAMMPS) prepare LAMMPS sampling calculations"},{"location":"en/workflow_scripts.html#scf-batch-pretreatment","title":"SCF Batch Pretreatment","text":"<p>Use this when you have many structures and want to prepare single-point DFT calculations.</p>"},{"location":"en/workflow_scripts.html#vasp","title":"VASP","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>Before running, put structure files in the current directory. The script checks files in this order:</p> <ol> <li>if one or more <code>.vasp</code> files exist, it processes <code>.vasp</code> files;</li> <li>if both <code>.vasp</code> and <code>.xyz</code> files exist, it prints a notice and only processes <code>.vasp</code> files;</li> <li>if no <code>.vasp</code> file exists and one <code>.xyz</code> file exists, it converts that extxyz file to POSCAR files;</li> <li>if no <code>.vasp</code> file exists and multiple <code>.xyz</code> files exist, it asks you to choose one.</li> </ol> <p>Typical input directory before running:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>INCAR</code>, <code>POTCAR</code>, and <code>KPOINTS</code> in the generated <code>fp/</code> directory after the script creates it. The calculation folders link to files in <code>fp/</code>.</p> <p>The <code>prefix</code> you input during the workflow becomes the calculation folder prefix. When <code>out2xyz</code> is later used to extract results, the folder name is stored as <code>config_type</code> in the extxyz file, which makes it easier to trace where each structure came from.</p>"},{"location":"en/workflow_scripts.html#cp2k","title":"CP2K","text":"<p>CP2K SCF batch pretreatment is available from the workflow menu and can also be called directly:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>The interactive wrapper asks for:</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>Example:</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>The template should be configured to read coordinates from <code>pos.xyz</code>. A reference template is available at:</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>The script creates <code>&lt;prefix&gt;_&lt;index&gt;/</code> directories, writes <code>input.inp</code>, and writes <code>pos.xyz</code> for each structure.</p>"},{"location":"en/workflow_scripts.html#md-sampling-pretreatment","title":"MD Sampling Pretreatment","text":""},{"location":"en/workflow_scripts.html#gpumd","title":"GPUMD","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 302\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. The detection order is the same as the VASP SCF workflow: <code>.vasp</code> files are preferred; if multiple <code>.xyz</code> files are found without <code>.vasp</code>, the script asks you to choose one.</p> <p>Typical input directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>nep.txt</code> and <code>run_*.in</code> files in the generated <code>md/</code> directory. The script links <code>run_1.in</code> to <code>sample_1/run.in</code>, <code>run_2.in</code> to <code>sample_2/run.in</code>, and so on.</p>"},{"location":"en/workflow_scripts.html#lammps","title":"LAMMPS","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 303\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. <code>.vasp</code> files are preferred when both formats exist.</p> <p>After running, the script creates LAMMPS data files in <code>struct_md/</code>, sample folders, and an <code>md/</code> directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>lmprun.in</code> and <code>nep.txt</code> in the generated <code>md/</code> directory.</p>"},{"location":"en/workflow_scripts.html#active-learning-style-workflow","title":"Active-Learning Style Workflow","text":"<p>A common NEP improvement loop is:</p> <ol> <li>run MD with the current <code>nep.txt</code>;</li> <li>collect <code>dump.xyz</code> or <code>active.xyz</code>;</li> <li>remove unphysical structures;</li> <li>select diverse or uncertain structures;</li> <li>run DFT single-point calculations;</li> <li>convert DFT results to extxyz;</li> <li>append new structures to <code>train.xyz</code>;</li> <li>retrain the NEP model.</li> </ol> <p>For the development active-learning script, see Active Learning.</p>"},{"location":"en/workflow_scripts.html#template-based-temperature-series","title":"Template-Based Temperature Series","text":"<p>For a simple temperature series, a shell loop is often enough:</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>Then submit the generated folders according to your local cluster system.</p>"},{"location":"en/workflow_scripts.html#practical-notes","title":"Practical Notes","text":"<ul> <li>Workflow scripts are cluster- and template-dependent. Always test with a small number of structures first.</li> <li>Keep template files (<code>INCAR</code>, <code>KPOINTS</code>, <code>POTCAR</code>, <code>run.in</code>, CP2K inputs) under version control if possible.</li> <li>Check generated folders before submitting a large batch.</li> <li>Use analyzers and sampling scripts before expensive DFT calculations.</li> </ul>"},{"location":"zh/index.html","title":"GPUMDkit \u6559\u7a0b","text":"\ud83d\udcda GPUMDkit \u6559\u7a0b <p>\u6b22\u8fce\u4f7f\u7528 GPUMDkit\uff0c\u8fd9\u662f\u4e00\u4e2a\u9762\u5411 GPUMD \u548c NEP \u7684\u547d\u4ee4\u884c\u5de5\u5177\u5305\u3002</p>"},{"location":"zh/index.html#gpumdkit","title":"\u4ec0\u4e48\u662f GPUMDkit\uff1f","text":"<p>GPUMDkit \u7b80\u5316\u4e86\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u7684\u5e38\u89c1\u4efb\u52a1\uff1a</p> <ul> <li>\u683c\u5f0f\u8f6c\u6362\uff1a\u5728 VASP\u3001LAMMPS\u3001CP2K\u3001ABACUS\u3001CIF \u548c extxyz \u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362</li> <li>\u53ef\u89c6\u5316\uff1a\u7528\u4e8e NEP \u8bad\u7ec3\u3001MD \u6a21\u62df\u548c\u5206\u6790\u7684\u7ed8\u56fe\u5de5\u5177</li> <li>\u8ba1\u7b97\u5668\uff1a\u8ba1\u7b97\u79bb\u5b50\u7535\u5bfc\u7387\u3001\u63cf\u8ff0\u7b26\u3001MSD\u3001NEB \u7b49</li> <li>\u5206\u6790\u5de5\u5177\uff1a\u7ed3\u6784\u9a8c\u8bc1\u3001\u8fc7\u6ee4\u3001\u6210\u5206\u5206\u6790</li> <li>\u5de5\u4f5c\u6d41\uff1aDFT \u548c MD \u6a21\u62df\u7684\u6279\u5904\u7406</li> <li>\u7ed3\u6784\u91c7\u6837\uff1a\u4f7f\u7528\u5747\u5300\u3001\u968f\u673a\u6216 FPS \u65b9\u6cd5\u9009\u62e9\u7ed3\u6784</li> </ul>"},{"location":"zh/index.html#_1","title":"\u5feb\u901f\u5f00\u59cb","text":""},{"location":"zh/index.html#_2","title":"\u5b89\u88c5","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"zh/index.html#_3","title":"\u4f9d\u8d56","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"zh/index.html#_4","title":"\u4f7f\u7528\u65b9\u6cd5","text":"<pre><code># \u4ea4\u4e92\u6a21\u5f0f\ngpumdkit.sh\n\n# \u547d\u4ee4\u884c\u6a21\u5f0f\ngpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n\n# \u83b7\u53d6\u5e2e\u52a9\ngpumdkit.sh -h\n</code></pre>"},{"location":"zh/index.html#_5","title":"\u6559\u7a0b\u5217\u8868","text":"\u6559\u7a0b \u63cf\u8ff0 \u5feb\u901f\u5165\u95e8 \u5b89\u88c5\u548c\u7b2c\u4e00\u6b65 \u547d\u4ee4\u53c2\u8003 \u5e38\u7528 CLI \u548c\u83dc\u5355\u5165\u53e3\u901f\u67e5 \u683c\u5f0f\u8f6c\u6362 \u5728\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362 \u8ba1\u7b97\u5668\u811a\u672c \u8ba1\u7b97\u6750\u6599\u5c5e\u6027 \u5206\u6790\u5de5\u5177 \u7ed3\u6784\u5206\u6790\u548c\u9a8c\u8bc1 \u7ed8\u56fe\u811a\u672c \u7ed8\u56fe\u548c\u53ef\u89c6\u5316 \u5de5\u4f5c\u6d41\u811a\u672c \u6279\u5904\u7406\u548c\u81ea\u52a8\u5316 \u7ed3\u6784\u91c7\u6837 \u7ed3\u6784\u9009\u62e9\u65b9\u6cd5 \u81ea\u5b9a\u4e49\u547d\u4ee4 \u7528\u6237\u81ea\u5b9a\u4e49 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 \u6279\u91cf\u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\u8bf4\u660e \u6781\u6027\u6750\u6599\u5206\u6790 \u94c1\u7535\u548c\u6781\u5316\u76f8\u5173\u5de5\u5177 \u8d21\u732e\u6307\u5357 \u5f00\u53d1\u548c\u8d21\u732e\u8bf4\u660e"},{"location":"zh/index.html#vasp-outcar","title":"\u793a\u4f8b\uff1a\u8f6c\u6362 VASP OUTCAR","text":"<pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre>"},{"location":"zh/index.html#nep","title":"\u793a\u4f8b\uff1a\u7ed8\u5236 NEP \u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt train\ngpumdkit.sh -plt prediction\n</code></pre>"},{"location":"zh/index.html#_6","title":"\u793a\u4f8b\uff1a\u79bb\u5b50\u7535\u5bfc\u7387","text":"<pre><code>gpumdkit.sh -calc msd trajectory.xyz Li 10\ngpumdkit.sh -calc ionic-cond Li 1\ngpumdkit.sh -plt msd\n</code></pre>"},{"location":"zh/index.html#_7","title":"\u6a21\u5757\u6982\u89c8","text":"\u6a21\u5757 \u83dc\u5355 CLI \u63cf\u8ff0 \u683c\u5f0f\u8f6c\u6362 1 <code>-out2xyz</code>, <code>-pos2exyz</code> \u6587\u4ef6\u8f6c\u6362 \u7ed3\u6784\u91c7\u6837 2 <code>-neptrain</code>\u3001\u4ea4\u4e92\u83dc\u5355 \u7ed3\u6784\u91c7\u6837 \u5de5\u4f5c\u6d41 3 - \u6279\u5904\u7406 \u8ba1\u7b97\u5668 4 <code>-calc &lt;\u7c7b\u578b&gt;</code> \u5c5e\u6027\u8ba1\u7b97 \u5206\u6790\u5de5\u5177 5 <code>-range</code>, <code>-min_dist</code> \u7ed3\u6784\u5206\u6790 \u53ef\u89c6\u5316 6 <code>-plt &lt;\u7c7b\u578b&gt;</code> \u7ed8\u56fe\u5de5\u5177 \u5b9e\u7528\u5de5\u5177 7 <code>-time</code>, <code>-clean</code> \u5b9e\u7528\u529f\u80fd"},{"location":"zh/index.html#_8","title":"\u94fe\u63a5","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>\u6587\u6863: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html","title":"\u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41","text":"\ud83d\udd01 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 <p><code>workflow_active_learning_dev.sh</code> \u7528\u4e8e\u7ec4\u7ec7\u4e00\u8f6e NEP \u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\uff1a\u8fd0\u884c GPUMD \u5206\u5b50\u52a8\u529b\u5b66\u3001\u7b5b\u9009\u7ed3\u6784\u3001\u62bd\u6837\u3001\u63d0\u4ea4\u7b2c\u4e00\u6027\u539f\u7406\u8ba1\u7b97\uff0c\u5e76\u8fdb\u884c NEP \u9884\u6d4b\u68c0\u67e5\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#_1","title":"\u6982\u89c8","text":"<p>\u8be5\u811a\u672c\u7528\u4e8e\u5904\u7406 NEP \u4e3b\u52a8\u5b66\u4e60\u4e2d\u5e38\u89c1\u7684\u4e00\u8f6e\u6d41\u7a0b\uff1a\u8fd0\u884c\u5206\u5b50\u52a8\u529b\u5b66\u3001\u7b5b\u9009\u7ed3\u6784\u3001\u62bd\u6837\u3001\u63d0\u4ea4 SCF \u8ba1\u7b97\uff0c\u5e76\u6574\u7406\u540e\u7eed prediction \u68c0\u67e5\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#1-slurm","title":"1. SLURM \u8bbe\u7f6e","text":"<p>\u811a\u672c\u5f00\u5934\u5305\u542b\u96c6\u7fa4\u63d0\u4ea4\u53c2\u6570\uff0c\u4f8b\u5982\uff1a</p> <pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>\u8fd9\u4e9b\u53c2\u6570\u9700\u8981\u6839\u636e\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u4fee\u6539\u3002\u5982\u679c\u6ca1\u6709 SLURM \u73af\u5883\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u540e\u53f0\u8fd0\u884c\uff1a</p> <pre><code>nohup bash workflow_active_learning_dev.sh &gt; workflow.log 2&gt;&amp;1 &amp;\n</code></pre>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#2","title":"2. \u57fa\u672c\u8bbe\u7f6e","text":"<p>\u811a\u672c\u4f1a\u8fdb\u5165\u63d0\u4ea4\u76ee\u5f55\uff0c\u5e76\u52a0\u8f7d\u63d0\u4ea4\u6a21\u677f\uff1a</p> <pre><code>cd $SLURM_SUBMIT_DIR\nsource ${GPUMDkit_path}/Scripts/workflow/submit_template.sh\npython_pynep=python\n</code></pre> <ul> <li><code>GPUMDkit_path</code> \u662f\u5b89\u88c5\u811a\u672c\u5199\u5165\u7684 GPUMDkit \u8def\u5f84\u3002</li> <li><code>python_pynep</code> \u4ec5\u7528\u4e8e\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#3","title":"3. \u4e3b\u8981\u53d8\u91cf","text":"<p>\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u9002\u5408\u5df2\u7ecf\u6709\u521d\u59cb <code>nep.txt</code>\u3001<code>nep.in</code>\u3001<code>train.xyz</code> \u548c GPUMD/DFT \u8f93\u5165\u6587\u4ef6\uff0c\u5e76\u5e0c\u671b\u5728\u96c6\u7fa4\u4e0a\u81ea\u52a8\u6269\u5c55\u8bad\u7ec3\u96c6\u7684\u60c5\u51b5\u3002</p> <p>\u811a\u672c\u5f00\u5934\u901a\u5e38\u9700\u8981\u6839\u636e\u4f53\u7cfb\u4fee\u6539\uff1a</p> <pre><code>work_dir=${PWD}\nprefix_name=LiF_iter01\nmin_dist=1.4\nbox_limit=13\nmax_fp_num=50\nsample_method=pynep\npynep_sample_dist=0.01\n</code></pre> <ul> <li><code>prefix_name</code> \u7528\u4e8e\u547d\u540d\u672c\u8f6e\u8ba1\u7b97\u3002</li> <li><code>min_dist</code> \u548c <code>box_limit</code> \u7528\u4e8e\u8fc7\u6ee4\u660e\u663e\u4e0d\u5408\u7406\u7684\u7ed3\u6784\u3002</li> <li><code>max_fp_num</code> \u63a7\u5236\u6700\u591a\u63d0\u4ea4\u591a\u5c11\u4e2a\u5355\u70b9\u8ba1\u7b97\u3002</li> <li><code>sample_method</code> \u53ef\u9009 <code>uniform</code>\u3001<code>random</code> \u6216 <code>pynep</code>\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#4","title":"4. \u68c0\u67e5\u8f93\u5165\u6587\u4ef6","text":"<p>\u5e38\u89c1\u8f93\u5165\u5305\u62ec\uff1a</p> <ul> <li><code>nep.txt</code></li> <li><code>nep.in</code></li> <li><code>train.xyz</code></li> <li><code>run.in</code></li> <li><code>INCAR</code></li> <li><code>POTCAR</code></li> <li><code>KPOINTS</code></li> <li>\u521d\u59cb\u91c7\u6837\u7ed3\u6784\u6587\u4ef6\uff0c\u4f8b\u5982 <code>sample_struct.xyz</code></li> </ul> <p>\u811a\u672c\u4f1a\u628a\u516c\u5171\u8f93\u5165\u79fb\u52a8\u5230 <code>common/</code>\uff0c\u5e76\u521b\u5efa <code>00.modev/</code>\u3001<code>01.select/</code> \u7b49\u5de5\u4f5c\u76ee\u5f55\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#5","title":"5. \u6587\u4ef6\u7ec4\u7ec7","text":"<p>\u811a\u672c\u4f1a\u521b\u5efa\u516c\u5171\u8f93\u5165\u76ee\u5f55\u548c MD \u76ee\u5f55\uff1a</p> <pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <ul> <li><code>00.modev</code>\uff1a\u7528\u4e8e\u8fd0\u884c GPUMD MD \u91c7\u6837\u3002</li> <li><code>common</code>\uff1a\u4fdd\u5b58 <code>nep.txt</code>\u3001<code>run.in</code>\u3001\u7ed3\u6784\u6587\u4ef6\u548c DFT \u8f93\u5165\u6587\u4ef6\u7b49\u516c\u5171\u8d44\u6e90\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#6-md","title":"6. \u63d0\u4ea4 MD \u4efb\u52a1","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>\u811a\u672c\u4f1a\u901a\u8fc7\u63d0\u4ea4\u6a21\u677f\u521b\u5efa\u6570\u7ec4\u4efb\u52a1\u3002\u4e0d\u540c\u96c6\u7fa4\u4e0a\u7684\u63d0\u4ea4\u547d\u4ee4\u548c\u6a21\u677f\u53ef\u80fd\u9700\u8981\u81ea\u5df1\u4fee\u6539\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#7","title":"7. \u68c0\u67e5\u4efb\u52a1\u5b8c\u6210","text":"<p>\u811a\u672c\u4f1a\u6301\u7eed\u68c0\u67e5 <code>00.modev/</code> \u4e0b\u5404\u4e2a <code>sample_*/log</code> \u6587\u4ef6\uff0c\u786e\u8ba4\u662f\u5426\u51fa\u73b0\uff1a</p> <pre><code>Finished running GPUMD.\n</code></pre> <p>\u5982\u679c\u53d1\u73b0 <code>Error</code>\uff0c\u811a\u672c\u4f1a\u505c\u6b62\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#8","title":"8. \u5206\u6790\u548c\u8fc7\u6ee4\u7ed3\u6784","text":"<p>MD \u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u8fdb\u5165 <code>01.select</code>\uff0c\u5bf9 <code>dump.xyz</code> \u4e2d\u7684\u7ed3\u6784\u8fdb\u884c\u7b5b\u9009\u3002\u5e38\u89c1\u68c0\u67e5\u5305\u62ec\uff1a</p> <ul> <li>\u6700\u5c0f\u539f\u5b50\u8ddd\u79bb\uff1b</li> <li>\u6a21\u62df\u76d2\u5b50\u8fb9\u957f\uff1b</li> <li>\u7ed3\u6784\u6570\u91cf\u662f\u5426\u8d85\u8fc7 <code>max_fp_num</code>\u3002</li> </ul> <p>\u8fd9\u4e9b\u6b65\u9aa4\u4f1a\u8c03\u7528 analyzer \u548c sample_structures \u4e2d\u7684\u811a\u672c\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#9","title":"9. \u62bd\u6837\u65b9\u6cd5","text":"<p>\u811a\u672c\u6839\u636e <code>sample_method</code> \u9009\u62e9\u62bd\u6837\u65b9\u5f0f\uff1a</p> <pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <ul> <li><code>uniform</code>\uff1a\u5747\u5300\u62bd\u5e27\uff1b</li> <li><code>random</code>\uff1a\u968f\u673a\u62bd\u5e27\uff1b</li> <li><code>pynep</code>\uff1a\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#10-scf","title":"10. \u63d0\u4ea4 SCF \u8ba1\u7b97","text":"<p>\u62bd\u6837\u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u63d0\u4ea4 VASP \u5355\u70b9\u8ba1\u7b97\uff1a</p> <pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>\u8fd9\u91cc\u7684 <code>prefix_name</code> \u4f1a\u7528\u4e8e\u8ba1\u7b97\u76ee\u5f55\u547d\u540d\uff0c\u4e5f\u65b9\u4fbf\u540e\u7eed\u8ffd\u8e2a\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#11-prediction","title":"11. Prediction \u6b65\u9aa4","text":"<p>\u6700\u540e\u811a\u672c\u4f1a\u63d0\u4ea4 NEP prediction\uff0c\u7528\u4e8e\u68c0\u67e5\u5f53\u524d\u6a21\u578b\u5728\u65b0\u589e\u7ed3\u6784\u4e0a\u7684\u8bef\u5dee\u3002</p> <p>\u8fd9\u4e2a\u811a\u672c\u548c\u8ba1\u7b97\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u4f7f\u7528\u524d\u5efa\u8bae\u5148\u7528\u5c0f\u4f53\u7cfb\u6216\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u4e00\u8f6e\uff0c\u5e76\u68c0\u67e5\u63d0\u4ea4\u6a21\u677f\u3001\u8def\u5f84\u548c\u8f93\u5165\u6587\u4ef6\u662f\u5426\u7b26\u5408\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html","title":"\u5206\u6790\u5de5\u5177","text":"\ud83d\udd0d \u5206\u6790\u5de5\u5177 <p>\u5206\u6790\u5de5\u5177\u7528\u4e8e\u5bf9 extxyz \u6570\u636e\u96c6\u8fdb\u884c\u7ed3\u6784\u7edf\u8ba1\u3001\u8ddd\u79bb\u68c0\u67e5\u3001\u8fc7\u6ee4\u548c\u7ec4\u5206\u5206\u6790\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/analyzer/</code></p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_1","title":"\u529f\u80fd\u6982\u89c8","text":"\u4efb\u52a1 \u547d\u4ee4 \u7528\u9014 \u7ec4\u5206\u5206\u6790 <code>gpumdkit.sh -analyze_comp train.xyz</code> \u6309\u5316\u5b66\u7ec4\u5206\u7edf\u8ba1\u7ed3\u6784 \u5143\u7d20\u5217\u8868 <code>gpumdkit.sh -chem_species train.xyz</code> \u67e5\u770b\u6587\u4ef6\u4e2d\u6709\u54ea\u4e9b\u5143\u7d20 \u6027\u8d28\u8303\u56f4 <code>gpumdkit.sh -range train.xyz force</code> \u68c0\u67e5\u80fd\u91cf/\u529b/virial \u8303\u56f4 \u6700\u5c0f\u8ddd\u79bb <code>gpumdkit.sh -min_dist dump.xyz</code> \u5feb\u901f\u68c0\u67e5\uff0c\u4e0d\u8003\u8651 PBC PBC \u6700\u5c0f\u8ddd\u79bb <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> \u8003\u8651 PBC \u7684\u8ddd\u79bb\u68c0\u67e5 \u7535\u8377\u5e73\u8861 <code>gpumdkit.sh -cbc train.xyz</code> \u68c0\u67e5\u5e38\u89c1\u6c27\u5316\u6001\u662f\u5426\u5e73\u8861 \u8ddd\u79bb\u8fc7\u6ee4 <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> \u5220\u9664\u77ed\u8ddd\u79bb\u7ed3\u6784 \u76d2\u5b50\u8fc7\u6ee4 <code>gpumdkit.sh -filter_box dump.xyz 13</code> \u5220\u9664\u76d2\u5b50\u8fb9\u957f\u8fc7\u5927\u7684\u7ed3\u6784 \u6570\u503c\u8fc7\u6ee4 <code>gpumdkit.sh -filter_value train.xyz force 20</code> \u6309\u6027\u8d28\u9608\u503c\u8fc7\u6ee4 \u5143\u7d20\u5bf9\u8ddd\u79bb <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> \u6309\u5143\u7d20\u5bf9\u8ddd\u79bb\u8303\u56f4\u63d0\u53d6"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_2","title":"\u7ec4\u5206\u5206\u6790","text":"<pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>\u793a\u4f8b\u8f93\u51fa\uff1a</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>\u5982\u679c\u4e00\u4e2a <code>train.xyz</code> \u4e2d\u6df7\u5408\u4e86\u591a\u4e2a\u4f53\u7cfb\u6216\u4e0d\u540c\u8d85\u80de\uff0c\u8fd9\u4e2a\u529f\u80fd\u5f88\u6709\u7528\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#virial","title":"\u80fd\u91cf/\u529b/virial \u8303\u56f4","text":"<pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist\n</code></pre> <p>\u4f7f\u7528 <code>hist</code> \u53ef\u4ee5\u753b\u51fa\u6240\u9009\u6027\u8d28\u7684\u76f4\u65b9\u56fe\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_3","title":"\u6700\u5c0f\u8ddd\u79bb\u68c0\u67e5","text":"<p>\u5feb\u901f\u7248\u672c\uff1a</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>\u8003\u8651 PBC \u7684\u7248\u672c\uff1a</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>PBC \u7248\u672c\u4f1a\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_4","title":"\u7ed3\u6784\u8fc7\u6ee4","text":"<p>\u6309\u6700\u5c0f\u8ddd\u79bb\u8fc7\u6ee4\uff1a</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>\u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4\uff1a</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>\u6309\u6027\u8d28\u503c\u8fc7\u6ee4\uff1a</p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\n</code></pre> <p>\u6309\u5143\u7d20\u5bf9\u8ddd\u79bb\u8303\u56f4\u63d0\u53d6\uff1a</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_5","title":"\u7535\u8377\u5e73\u8861\u68c0\u67e5","text":"<pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>\u53ef\u80fd\u8f93\u51fa\uff1a</p> <ul> <li><code>balanced.xyz</code></li> <li><code>unbalanced.xyz</code></li> <li><code>indices.txt</code></li> </ul> <p>\u8fd9\u4e2a\u529f\u80fd\u9002\u5408\u5e38\u89c1\u6c27\u5316\u6001\u6709\u610f\u4e49\u7684\u79bb\u5b50\u6750\u6599\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_6","title":"\u793a\u4f8b\u547d\u4ee4","text":"<p>\u6027\u8d28\u548c\u8ddd\u79bb\u68c0\u67e5\uff1a</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\ngpumdkit.sh -range train.xyz force hist\ngpumdkit.sh -range train.xyz energy hist\ngpumdkit.sh -min_dist_pbc train.xyz\n</code></pre> <p>\u8fc7\u6ee4\u793a\u4f8b\uff1a</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\ngpumdkit.sh -filter_box filtered_dist.xyz 13\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html","title":"\u547d\u4ee4\u53c2\u8003","text":"\ud83d\udccb \u547d\u4ee4\u53c2\u8003 <p>\u672c\u9875\u5217\u51fa GPUMDkit \u7a33\u5b9a\u7684\u547d\u4ee4\u884c\u5feb\u6377\u5165\u53e3\u3002\u5bf9\u4e8e\u53c2\u6570\u8f83\u591a\u3001\u9700\u8981\u9009\u62e9\u7684\u4efb\u52a1\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528\u4ea4\u4e92\u6a21\u5f0f\u3002</p> <p>\u6e90\u8868\u7ef4\u62a4\u5728 <code>docs/command_reference.tsv</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#gpumdkitsh-h","title":"<code>gpumdkit.sh -h</code> \u8f93\u51fa","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |\n| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_1","title":"\u4e3b\u547d\u4ee4","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-h</code> <code>gpumdkit.sh -h</code> \u663e\u793a\u901a\u7528\u5e2e\u52a9 <code>-update</code> <code>gpumdkit.sh -update</code> \u66f4\u65b0 GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> \u6e05\u7406\u5f53\u524d\u76ee\u5f55\u4e2d\u7684\u5197\u4f59\u6587\u4ef6"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_2","title":"\u683c\u5f0f\u8f6c\u6362","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K \u8f93\u51fa\u8f6c xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR \u8f6c extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF \u8f6c POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF \u8f6c extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR \u8f6c extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz \u591a\u5e27\u8f6c POSCAR \u6587\u4ef6 <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR \u8f6c LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump \u8f6c extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory \u8f6c extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> \u6309\u6676\u80de\u500d\u6570\u6269\u80de <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> \u6309\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> \u6dfb\u52a0 GPUMD group \u6807\u7b7e <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> \u6dfb\u52a0\u7ed3\u6784\u6743\u91cd <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> \u63d0\u53d6\u5355\u5e27 <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> \u6e05\u7406 extxyz \u5197\u4f59\u5c5e\u6027 <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> \u6309\u6bd4\u4f8b\u8303\u56f4\u63d0\u53d6\u5e27"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_3","title":"\u8ba1\u7b97\u5668","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> \u79bb\u5b50\u7535\u5bfc\u7387 <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP \u6027\u8d28\u9884\u6d4b <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP \u63cf\u8ff0\u7b26 <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u57fa\u4e8e NEP \u7684 NEB <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784\u4f18\u5316 <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> \u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> \u90bb\u5c45\u5217\u8868 <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> \u4f4d\u79fb <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> \u5e73\u5747\u7ed3\u6784 <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> \u516b\u9762\u4f53\u503e\u659c <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 \u5c40\u57df\u6781\u5316"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_4","title":"\u5206\u6790\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> \u6027\u8d28\u8303\u56f4\u5206\u6790 <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> \u6210\u5206\u5206\u6790 <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> \u5143\u7d20\u5217\u8868 <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> \u7535\u8377\u5e73\u8861\u68c0\u67e5 <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> \u65e0 PBC \u6700\u5c0f\u8ddd\u79bb <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> \u5e26 PBC \u6700\u5c0f\u8ddd\u79bb <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u5e26 PBC \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> \u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4 <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> \u6027\u8d28\u9608\u503c\u8fc7\u6ee4 <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> \u5143\u7d20\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4 <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> \u6982\u7387\u5bc6\u5ea6\u5206\u6790"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_5","title":"\u53ef\u89c6\u5316","text":"<p>\u4f7f\u7528\uff1a</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>\u5e38\u7528\u7c7b\u578b\u5305\u62ec <code>train</code>\u3001<code>prediction</code>\u3001<code>thermo</code>\u3001<code>msd</code>\u3001<code>sdc</code>\u3001<code>rdf</code>\u3001<code>emd</code>\u3001<code>nemd</code>\u3001<code>hnemd</code>\u3001<code>pdos</code> \u548c <code>plane-grid</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_6","title":"\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> \u76d1\u63a7 GPUMD \u6216 NEP \u8fdb\u5ea6 <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> \u4ea4\u4e92\u5f0f\u4fee\u6539 NEP \u6a21\u578b <code>-pynep</code> <code>gpumdkit.sh -pynep</code> \u5df2\u5f03\u7528\u7684 PyNEP FPS \u91c7\u6837"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html","title":"\u5de5\u4f5c\u6d41\u811a\u672c","text":"\ud83d\udd27 \u5de5\u4f5c\u6d41\u811a\u672c <p>\u5de5\u4f5c\u6d41\u811a\u672c\u7528\u4e8e\u81ea\u52a8\u5316\u91cd\u590d\u6027\u7684 DFT\u3001MD \u548c NEP \u6570\u636e\u51c6\u5907\u6b65\u9aa4\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_1","title":"\u4ea4\u4e92\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>3) Workflow\n</code></pre> <p>\u5e38\u89c1\u83dc\u5355\uff1a</p> \u83dc\u5355 \u5de5\u4f5c\u6d41 \u7528\u9014 301 SCF batch pretreatment \u51c6\u5907 DFT \u5355\u70b9\u8ba1\u7b97 302 MD sample batch pretreatment (GPUMD) \u51c6\u5907 GPUMD \u91c7\u6837\u8ba1\u7b97 303 MD sample batch pretreatment (LAMMPS) \u51c6\u5907 LAMMPS \u91c7\u6837\u8ba1\u7b97"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#scf","title":"SCF \u6279\u5904\u7406\u9884\u5904\u7406","text":"<p>\u9002\u7528\u4e8e\u5df2\u6709\u591a\u4e2a\u7ed3\u6784\uff0c\u9700\u8981\u51c6\u5907\u7b2c\u4e00\u6027\u539f\u7406\u5355\u70b9\u8ba1\u7b97\u7684\u60c5\u51b5\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#vasp","title":"VASP","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a\u7ed3\u6784\u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u811a\u672c\u6309\u4ee5\u4e0b\u987a\u5e8f\u68c0\u6d4b\uff1a</p> <ol> <li>\u5982\u679c\u5b58\u5728\u4e00\u4e2a\u6216\u591a\u4e2a <code>.vasp</code> \u6587\u4ef6\uff0c\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c <code>.vasp</code> \u548c <code>.xyz</code> \u540c\u65f6\u5b58\u5728\uff0c\u4f1a\u6253\u5370\u63d0\u793a\uff0c\u5e76\u53ea\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u53ea\u6709\u4e00\u4e2a <code>.xyz</code>\uff0c\u4f1a\u628a\u8fd9\u4e2a extxyz \u8f6c\u4e3a POSCAR \u6587\u4ef6\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</li> </ol> <p>\u8fd0\u884c\u524d\u7684\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>fp/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u7528\u6237\u628a <code>INCAR</code>\u3001<code>POTCAR</code>\u3001<code>KPOINTS</code> \u653e\u5230 <code>fp/</code> \u4e2d\uff0c\u8ba1\u7b97\u76ee\u5f55\u4f1a\u94fe\u63a5\u8fd9\u91cc\u7684\u6587\u4ef6\u3002</p> <p>\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u8f93\u5165\u7684 <code>prefix</code> \u4f1a\u4f5c\u4e3a\u8ba1\u7b97\u6587\u4ef6\u5939\u540d\u524d\u7f00\u3002\u540e\u7eed\u4f7f\u7528 <code>out2xyz</code> \u63d0\u53d6\u7ed3\u679c\u65f6\uff0c\u6587\u4ef6\u5939\u540d\u4f1a\u4f5c\u4e3a <code>config_type</code> \u5199\u5165 extxyz\uff0c\u4fbf\u4e8e\u4e4b\u540e\u68c0\u67e5\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#cp2k","title":"CP2K","text":"<p>CP2K \u53ef\u4ee5\u4ece\u4ea4\u4e92\u83dc\u5355\u8fdb\u5165\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u547d\u4ee4\u884c\u8c03\u7528\uff1a</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4f1a\u8981\u6c42\u8f93\u5165\uff1a</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>CP2K \u6a21\u677f\u5e94\u8bbe\u7f6e\u4e3a\u4ece <code>pos.xyz</code> \u8bfb\u53d6\u5750\u6807\u3002\u53c2\u8003\u6a21\u677f\u5728\uff1a</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>\u811a\u672c\u4f1a\u4e3a\u6bcf\u4e2a\u7ed3\u6784\u751f\u6210 <code>&lt;prefix&gt;_&lt;index&gt;/</code> \u76ee\u5f55\uff0c\u5e76\u5199\u5165 <code>input.inp</code> \u548c <code>pos.xyz</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#md","title":"MD \u91c7\u6837\u9884\u5904\u7406","text":""},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#gpumd","title":"GPUMD","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 302\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u68c0\u6d4b\u987a\u5e8f\u4e0e VASP SCF \u9884\u5904\u7406\u4e00\u81f4\uff1a\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</p> <p>\u8fd0\u884c\u524d\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>md/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>nep.txt</code> \u548c <code>run_*.in</code> \u653e\u5165 <code>md/</code>\u3002\u4f8b\u5982 <code>run_1.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_1/run.in</code>\uff0c<code>run_2.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_2/run.in</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#lammps","title":"LAMMPS","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 303\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\uff1b\u4e24\u79cd\u683c\u5f0f\u540c\u65f6\u5b58\u5728\u65f6\u4f18\u5148\u5904\u7406 <code>.vasp</code>\u3002</p> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>lmprun.in</code> \u548c <code>nep.txt</code> \u653e\u5230 <code>md/</code> \u4e2d\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_2","title":"\u4e3b\u52a8\u5b66\u4e60\u5f0f\u6d41\u7a0b","text":"<p>\u5e38\u89c1 NEP \u6570\u636e\u8fed\u4ee3\u6d41\u7a0b\uff1a</p> <ol> <li>\u4f7f\u7528\u5f53\u524d <code>nep.txt</code> \u8fd0\u884c MD\uff1b</li> <li>\u6536\u96c6 <code>dump.xyz</code> \u6216 <code>active.xyz</code>\uff1b</li> <li>\u5220\u9664\u660e\u663e\u4e0d\u5408\u7406\u7ed3\u6784\uff1b</li> <li>\u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\uff1b</li> <li>\u8fd0\u884c DFT \u5355\u70b9\uff1b</li> <li>\u5c06 DFT \u7ed3\u679c\u8f6c\u6362\u4e3a extxyz\uff1b</li> <li>\u8ffd\u52a0\u5230 <code>train.xyz</code>\uff1b</li> <li>\u91cd\u65b0\u8bad\u7ec3 NEP\u3002</li> </ol> <p>\u66f4\u5b8c\u6574\u7684\u5f00\u53d1\u7248\u4e3b\u52a8\u5b66\u4e60\u811a\u672c\u8bf4\u660e\u89c1 \u4e3b\u52a8\u5b66\u4e60\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_3","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u5de5\u4f5c\u6d41\u811a\u672c\u548c\u96c6\u7fa4\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u6279\u91cf\u63d0\u4ea4\u524d\u5148\u7528\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u3002</li> <li>\u6a21\u677f\u6587\u4ef6\u5982 <code>INCAR</code>\u3001<code>KPOINTS</code>\u3001<code>POTCAR</code>\u3001<code>run.in</code> \u5e94\u4ed4\u7ec6\u68c0\u67e5\u3002</li> <li>\u6279\u91cf DFT \u524d\u5148\u7528\u5206\u6790\u548c\u91c7\u6837\u811a\u672c\u6e05\u7406\u5019\u9009\u7ed3\u6784\u3002</li> </ul>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html","title":"\u5feb\u901f\u5165\u95e8","text":"\ud83d\ude80 \u5feb\u901f\u5165\u95e8 <p>\u672c\u9875\u4ecb\u7ecd GPUMDkit \u7684\u57fa\u672c\u5b89\u88c5\u65b9\u5f0f\u548c\u51e0\u4e2a\u5e38\u7528\u547d\u4ee4\u3002GPUMDkit \u65e2\u53ef\u4ee5\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u4f7f\u7528\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u901a\u8fc7\u547d\u4ee4\u884c\u9009\u9879\u8c03\u7528\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#1-python","title":"1. \u51c6\u5907 Python \u73af\u5883","text":"<p>\u53ef\u4ee5\u4f7f\u7528\u5e72\u51c0\u7684 conda \u73af\u5883\uff1a</p> <pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>\u90e8\u5206\u53ef\u9009\u529f\u80fd\u9700\u8981\u989d\u5916\u4f9d\u8d56\uff1a</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>\u5176\u4ed6 Python \u4f9d\u8d56\u7531\u5bf9\u5e94\u811a\u672c\u5728\u8fd0\u884c\u65f6\u5bfc\u5165\u3002\u5982\u679c\u7f3a\u5c11\u67d0\u4e2a\u5305\uff0c\u4f7f\u7528\u5bf9\u5e94\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u63d0\u793a\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#2-gpumdkit","title":"2. \u5b89\u88c5 GPUMDkit","text":"<p>\u514b\u9686\u4ed3\u5e93\uff1a</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <p>\u8fd0\u884c\u5b89\u88c5\u811a\u672c\uff1a</p> <pre><code>source ./install.sh\n</code></pre> <p>\u5b89\u88c5\u811a\u672c\u4f1a\u5199\u5165 <code>GPUMDkit_path</code> \u548c <code>PATH</code> \u8bbe\u7f6e\uff0c\u5e76\u5728\u5f53\u524d shell \u4e2d\u52a0\u8f7d\u3002\u9ed8\u8ba4\u5199\u5165 <code>~/.bashrc</code>\uff1b\u5982\u679c\u5f53\u524d shell \u662f zsh\uff0c\u5219\u5199\u5165 <code>~/.zshrc</code>\u3002\u5982\u679c\u68c0\u6d4b\u5230\u5df2\u6709 GPUMDkit \u8def\u5f84\uff0c\u5b89\u88c5\u811a\u672c\u4f1a\u6253\u5370\u65e7\u8def\u5f84\u5e76\u8be2\u95ee\u662f\u5426\u66ff\u6362\uff1b\u4fee\u6539 rc \u6587\u4ef6\u524d\u4f1a\u5148\u521b\u5efa\u5907\u4efd\u3002</p> <p>\u5178\u578b\u5b89\u88c5\u8f93\u51fa\uff1a</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>\u5982\u679c\u4e4b\u524d\u5df2\u7ecf\u5b89\u88c5\u8fc7 GPUMDkit\uff0c\u53ef\u80fd\u4f1a\u770b\u5230\uff1a</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre> <p>\u68c0\u67e5\u547d\u4ee4\uff1a</p> <pre><code>gpumdkit.sh -h\n</code></pre> <p>\u5e2e\u52a9\u8868\uff1a</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |\n| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#3","title":"3. \u4f7f\u7528\u65b9\u5f0f","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_1","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u4e3b\u83dc\u5355\uff1a</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_2","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<p>\u76f4\u63a5\u547d\u4ee4\u4f7f\u7528\u56fa\u5b9a\u7684\u4f4d\u7f6e\u53c2\u6570\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -plt thermo\n</code></pre> <p>\u4f8b\u5982\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>\u8868\u793a\u8bfb\u53d6 <code>POSCAR</code>\uff0c\u5199\u51fa <code>model.xyz</code>\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#4","title":"4. \u5b9e\u9645\u4f8b\u5b50","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#gpumd-group","title":"\u6dfb\u52a0 GPUMD group \u6807\u7b7e","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>group \u6807\u7b7e\u7528\u4e8e\u4e00\u4e9b\u9700\u8981\u539f\u5b50\u5206\u7ec4\u7684 GPUMD \u76f8\u5173\u6d41\u7a0b\u548c\u5206\u6790\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep","title":"\u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep_1","title":"\u7ed8\u5236 NEP \u6d4b\u8bd5\u96c6\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_3","title":"\u7ed8\u5236\u70ed\u529b\u5b66\u91cf","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#msd","title":"\u7ed8\u5236 MSD \u548c\u81ea\u6269\u6563\u7cfb\u6570","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#5","title":"5. \u83b7\u53d6\u5e2e\u52a9","text":"<pre><code>gpumdkit.sh -h\ngpumdkit.sh -plt -h\ngpumdkit.sh -calc -h\ngpumdkit.sh -plt train -h\ngpumdkit.sh -calc msd -h\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html","title":"\u6781\u6027\u6750\u6599\u5206\u6790","text":"\ud83e\uddf2 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u672c\u6559\u7a0b\u4ecb\u7ecd GPUMDkit \u4e2d\u8ba1\u7b97\u5668\u9009\u9879 <code>406-410</code>\uff0c\u4ee5\u53ca <code>plane-grid</code> \u7ed8\u56fe\u6d41\u7a0b\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code> \u548c <code>Scripts/plt_scripts/</code></p> <p>\u672c\u6559\u7a0b\u5305\u542b\u901a\u7528\u5de5\u5177\u548c\u4f53\u7cfb\u76f8\u5173\u5de5\u5177\uff1a</p> <ul> <li><code>nlist</code>\u3001<code>disp</code> \u548c <code>avg-struct</code> \u53ef\u5e7f\u6cdb\u7528\u4e8e\u7ed3\u6784\u548c\u8f68\u8ff9\u5206\u6790\u3002</li> <li><code>oct-tilt</code> \u7528\u4e8e\u516b\u9762\u4f53\u73af\u5883\u5206\u6790\uff0c\u9700\u8981\u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u5468\u56f4\u6709 6 \u4e2a\u8fd1\u90bb\u3002</li> <li><code>pol-abo3</code> \u4e13\u7528\u4e8e <code>ABO3</code> \u4f53\u7cfb\u7684\u6781\u5316\u5206\u6790\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_1","title":"\u4f9d\u8d56","text":"<p>\u8fd9\u4e9b\u811a\u672c\u9700\u8981 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_2","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<p>\u9009\u9879 <code>406-410</code> \u662f\u672c\u6559\u7a0b\u4e2d\u7684\u6838\u5fc3\u529f\u80fd\u3002\u4e0b\u9762\u5404\u8282\u4f1a\u8bf4\u660e\u6bcf\u4e2a\u529f\u80fd\u7684\u7528\u9014\u548c\u8fd0\u884c\u65b9\u5f0f\u3002</p> <p>\u5b8c\u6574\u53c2\u6570\u8bf4\u660e\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u547d\u4ee4\u67e5\u770b\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#406-calc_neighbor_listpy","title":"406) \u6784\u5efa\u8fd1\u90bb\u5217\u8868 (<code>calc_neighbor_list.py</code>)","text":"<p>\u4e3a\u6307\u5b9a\u4e2d\u5fc3\u5143\u7d20\u548c\u8fd1\u90bb\u5143\u7d20\u6784\u5efa\u8fd1\u90bb\u5217\u8868\u3002</p> <p>\u4f7f\u7528\u573a\u666f\uff1a \u8fd9\u901a\u5e38\u662f\u8fd0\u884c <code>disp</code>\u3001<code>oct-tilt</code> \u548c <code>pol-abo3</code> \u4e4b\u524d\u7684\u7b2c\u4e00\u6b65\uff0c\u56e0\u4e3a\u8fd9\u4e9b\u811a\u672c\u4f1a\u8bfb\u53d6 <code>nl-*.dat</code> \u8fd1\u90bb\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_3","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4e3a\u516b\u9762\u4f53\u5206\u6790\u6784\u5efa Ti-O \u6700\u8fd1 6 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# \u793a\u4f8b 2\uff1a\u4e3a A \u4f4d\u4e2d\u5fc3\u5206\u6790\u6784\u5efa Pb/Sr-O \u6700\u8fd1 12 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_4","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-x, --index</code>\uff1a   \u4ece\u8f93\u5165\u6587\u4ef6\u4e2d\u8bfb\u53d6\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-c, --cutoff</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u641c\u7d22\u622a\u65ad\u8ddd\u79bb\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> <li><code>-n, --neighbor-num</code>\uff08\u5fc5\u9700\uff09\uff1a   \u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u7684\u8fd1\u90bb\u6570\u91cf\u3002</li> <li><code>-d, --defect</code>\uff1a   \u7f3a\u9677\u6a21\u5f0f\u3002\u542f\u7528\u540e\uff0c\u5982\u679c\u8fd1\u90bb\u6570\u91cf\u4e0d\u8db3\uff0c\u7f3a\u5931\u4f4d\u7f6e\u4f1a\u7528\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u586b\u5145\u3002</li> <li><code>-C, --center-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u4e2d\u5fc3\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-E, --neighbor-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u8def\u5f84\u3002\u9ed8\u8ba4\u503c\uff1a<code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_5","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u8fd1\u90bb\u5217\u8868\u6587\u672c\u6587\u4ef6\uff0c\u4f8b\u5982 <code>nl-Ti-O.dat</code>\u3002</li> <li>\u6587\u4ef6\u662f\u4e00\u4e2a\u4e8c\u7ef4\u6574\u6570\u6570\u7ec4\uff0c\u5f62\u72b6\u4e3a <code>(n_center, neighbor_num + 1)</code>\u3002\u6bcf\u4e00\u884c\u5bf9\u5e94\u4e00\u4e2a\u4e2d\u5fc3\u539f\u5b50\uff1a\u7b2c\u4e00\u5217\u662f\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\uff0c\u540e\u7eed\u5217\u662f\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7\uff0c\u6240\u6709\u7f16\u53f7\u5747\u4e3a 1-based\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#407-calc_displacementpy","title":"407) \u4ece\u8f68\u8ff9\u8ba1\u7b97\u4f4d\u79fb (<code>calc_displacement.py</code>)","text":"<p>\u6839\u636e\u8f68\u8ff9\u6216\u6a21\u578b\u7ed3\u6784\u4ee5\u53ca\u8fd1\u90bb\u5217\u8868\uff0c\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_6","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece model.xyz \u8ba1\u7b97\u5355\u5e27\u4f4d\u79fb\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4f7f\u7528 movie.xyz \u7684\u6700\u540e 20% \u5e27\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_7","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7531 <code>nlist</code> \u751f\u6210\u7684\u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u90e8\u5206\u5e27\u3002   \u6574\u6570\u8868\u793a\u6700\u540e <code>N</code> \u5e27\uff1b   <code>0 &lt; value &lt; 1</code> \u8868\u793a\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_8","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>displacements.dat</code>\uff0c\u6216\u4f60\u6307\u5b9a\u7684\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e8c\u7ef4\u6570\u7ec4\uff1a\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u4e09\u5217\u5206\u522b\u4e3a <code>dx</code>\u3001<code>dy</code> \u548c <code>dz</code> \u4f4d\u79fb\u5206\u91cf\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#408-calc_averaged_structurepy","title":"408) \u8ba1\u7b97\u5e73\u5747\u7ed3\u6784 (<code>calc_averaged_structure.py</code>)","text":"<p>\u4ece\u9009\u5b9a\u8f68\u8ff9\u5e27\u751f\u6210\u4e00\u4e2a\u5e73\u5747\u7ed3\u6784\u3002 \u901a\u5e38\u53ef\u5728\u4f53\u7cfb\u5e73\u8861\u540e\u4f7f\u7528\uff1a\u5bf9\u4e8e\u63a5\u8fd1\u5e73\u8861\u7684\u56fa\u4f53\uff0c\u53ef\u4ee5\u5bf9\u76ee\u6807\u6e29\u5ea6\u4e0b\u7684\u4e00\u6bb5\u8f68\u8ff9\u53d6\u5e73\u5747\uff0c\u5e76\u5206\u6790\u8be5\u4ee3\u8868\u6027\u7ed3\u6784\uff0c\u800c\u4e0d\u662f\u9010\u5e27\u5904\u7406\u6bcf\u4e2a snapshot\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_9","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5e73\u5747\u6240\u6709\u5e27\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# \u793a\u4f8b 2\uff1a\u5e73\u5747\u9009\u5b9a\u5e27\u8303\u56f4 (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_10","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u8f68\u8ff9\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>movie.xyz</code>\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>averaged_structure.xyz</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_11","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u5355\u5e27\u5e73\u5747\u7ed3\u6784 extxyz \u6587\u4ef6\u3002</li> <li>\u4f4d\u7f6e\u5e73\u5747\u4f1a\u76f8\u5bf9\u4e8e\u6240\u9009\u7b2c\u4e00\u5e27\u8fdb\u884c MIC/PBC \u4fee\u6b63\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#409-calc_oct_tiltpy","title":"409) \u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c (<code>calc_oct_tilt.py</code>)","text":"<p>\u6839\u636e B-O \u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c\u89d2\u3002 \u8be5\u529f\u80fd\u5e38\u7528\u4e8e\u5206\u6790 <code>ABO3</code> \u4f53\u7cfb\u4e2d\u7684\u516b\u9762\u4f53\u8f6c\u52a8\u6a21\u5f0f\uff0c\u4f8b\u5982 <code>SrTiO3</code> \u548c <code>PbZrO3</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_12","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece\u5355\u5e27\u7ed3\u6784\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4ece\u8f68\u8ff9\u6700\u540e 20% \u5e27\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_13","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>octahedral_tilt.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_14","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>octahedral_tilt.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>theta_x</code>\u3001<code>theta_y</code>\u3001<code>theta_z</code>\uff0c\u5355\u4f4d\u4e3a degree\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#410-abo3-calc_polarization_abo3py","title":"410) \u8ba1\u7b97 ABO3 \u4f53\u7cfb\u6781\u5316 (<code>calc_polarization_abo3.py</code>)","text":"<p>\u8ba1\u7b97 <code>ABO3</code> \u4f53\u7cfb\u7684\u5c40\u57df\u6781\u5316\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_15","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5355\u5e27 ABO3 \u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# \u793a\u4f8b 2\uff1a\u9009\u5b9a\u8f68\u8ff9\u5e27\u8303\u56f4\u4e0a\u7684\u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_16","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>--nl-ba</code>\uff08\u5fc5\u9700\uff09\uff1a   B-A \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>--nl-bo</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>polarization.dat</code>\u3002</li> <li><code>--bec</code>\uff08\u5fc5\u9700\uff09\uff1a   Born \u6709\u6548\u7535\u8377\u9879\uff0c\u683c\u5f0f\u4e3a <code>Element=value</code>\u3002   \u793a\u4f8b\uff1a<code>Pb=2.5 Ti=4.0 O=-2.0</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul> <p>\u91cd\u8981\u68c0\u67e5\uff1a</p> <ul> <li><code>--bec</code> \u5fc5\u987b\u5305\u542b\u8f93\u5165\u7ed3\u6784\u4e2d\u7684\u6240\u6709\u5143\u7d20\u79cd\u7c7b\u3002</li> <li><code>--nl-ba</code> \u548c <code>--nl-bo</code> \u4e2d\u7684\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u5fc5\u987b\u5339\u914d\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_17","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>polarization.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>Px</code>\u3001<code>Py</code>\u3001<code>Pz</code>\uff0c\u5355\u4f4d\u4e3a <code>C/m^2</code>\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u5982\u679c\u603b Born \u7535\u8377\u4e0d\u5e73\u8861\uff0c\u811a\u672c\u4f1a\u6253\u5370 warning\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#plane-grid-plt_plane_gridpy","title":"Plane-grid \u53ef\u89c6\u5316 (<code>plt_plane_grid.py</code>)","text":"<p>\u4f60\u53ef\u4ee5\u53ef\u89c6\u5316 <code>displacements.dat</code> \u6216 <code>polarization.dat</code>\uff1a</p> <pre><code># \u793a\u4f8b 1\uff1aTi \u4f4d\u70b9\u4e0a\u7684\u4f4d\u79fb\u56fe\uff0c\u9009\u62e9\u7b2c\u4e00\u4e2a XY \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# \u793a\u4f8b 2\uff1aPb \u4f4d\u70b9\u4e0a\u7684\u6781\u5316\u56fe\uff0c\u9009\u62e9 XZ \u548c YZ \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>\u53c2\u6570\uff08\u5b8c\u6574\uff09\uff1a</p> <ul> <li><code>-i, --input</code>\uff1a   \u7528\u4e8e\u539f\u5b50\u5e03\u5c40\u548c\u5206\u5c42\u7684\u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-d, --disp</code>\uff1a   \u77e2\u91cf\u573a\u6570\u636e\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-e, --elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7528\u4e8e\u5c06\u77e2\u91cf\u6620\u5c04\u5230\u6676\u683c\u5c42\u4e0a\u7684\u4e2d\u5fc3\u5143\u7d20\u7b26\u53f7\u3002</li> <li><code>-m, --tol</code>\uff1a   \u7f51\u683c\u6620\u5c04\u7684\u5c42\u5bb9\u5dee\u3002\u9ed8\u8ba4\u503c\uff1a<code>1.0</code>\u3002</li> <li><code>-g, --target-size</code>\uff1a   \u671f\u671b\u7f51\u683c\u5927\u5c0f\uff0c\u683c\u5f0f\u4e3a <code>nx ny nz</code>\u3002</li> <li><code>-o, --save-dir</code>\uff1a   \u56fe\u7247\u8f93\u51fa\u76ee\u5f55\u3002\u9ed8\u8ba4\u503c\uff1a<code>plot</code>\u3002</li> <li><code>-f, --frame</code>\uff1a   \u5f53\u77e2\u91cf\u6570\u636e\u5305\u542b\u591a\u5e27\u65f6\uff0c\u8981\u53ef\u89c6\u5316\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>--select-xy</code>\uff1a   \u9009\u5b9a\u7684 XY \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-xz</code>\uff1a   \u9009\u5b9a\u7684 XZ \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-yz</code>\uff1a   \u9009\u5b9a\u7684 YZ \u5c42\u7f16\u53f7\u3002</li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li>\u5982\u679c\u9700\u8981\uff0c\u4f1a\u521b\u5efa\u8f93\u51fa\u76ee\u5f55\u3002</li> <li>\u56fe\u7247\u4fdd\u5b58\u4e3a <code>XY_*.png</code>\u3001<code>XZ_*.png</code>\u3001<code>YZ_*.png</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_18","title":"\u8f93\u51fa\u6587\u4ef6\u4e00\u89c8","text":"\u811a\u672c \u4e3b\u8981\u8f93\u51fa \u4fdd\u5b58\u5185\u5bb9 <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based \u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u548c\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7 <code>calc_displacement.py</code> <code>*.dat</code> \u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\uff08<code>dx dy dz</code>\uff0cAngstrom\uff09 <code>calc_averaged_structure.py</code> <code>*.xyz</code> \u4e00\u4e2a\u5e73\u5747\u7ed3\u6784 <code>calc_oct_tilt.py</code> <code>*.dat</code> \u516b\u9762\u4f53\u503e\u8f6c\u89d2\uff08<code>theta_x theta_y theta_z</code>\uff0cdegree\uff09 <code>calc_polarization_abo3.py</code> <code>*.dat</code> \u5c40\u57df\u6781\u5316\u77e2\u91cf\uff08<code>Px Py Pz</code>\uff0c<code>C/m^2</code>\uff09 <code>plt_plane_grid.py</code> <code>plot/*.png</code> \u6839\u636e\u77e2\u91cf\u573a\u6570\u636e\u7ed8\u5236\u7684 XY/XZ/YZ \u5e73\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_19","title":"\u771f\u5b9e\u6848\u4f8b","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3-","title":"PbTiO3 \u7684\u6e29\u5ea6\u9a71\u52a8\u94c1\u7535-\u987a\u7535\u76f8\u53d8","text":"<p>\u5047\u8bbe\u6240\u6709\u6587\u4ef6\u90fd\u4f4d\u4e8e\u5f53\u524d\u76ee\u5f55 <code>./</code>\uff1a</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> \u662f\u7528\u4e8e\u8fdb\u884c MD \u6a21\u62df\u7684\u521d\u59cb\u7ed3\u6784\u3002\u6bcf\u4e2a <code>TEMP K.xyz</code> \u662f\u5bf9\u5e94\u6e29\u5ea6\u4e0b\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1","title":"\u7b2c 1 \u6b65\uff1a\u4ece\u6bcf\u6761\u8f68\u8ff9\u7684\u540e\u534a\u6bb5\u5f97\u5230\u5e73\u5747\u7ed3\u6784","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>\u8fd9\u4f1a\u5199\u51fa <code>300K-avg.xyz</code>\u3001<code>350K-avg.xyz</code>\u3001...\u3001<code>800K-avg.xyz</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-modelxyz","title":"\u7b2c 2 \u6b65\uff1a\u57fa\u4e8e <code>model.xyz</code> \u6784\u5efa\u8fd1\u90bb\u5217\u8868","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3","title":"\u7b2c 3 \u6b65\uff1a\u4e3a\u6bcf\u4e2a\u6e29\u5ea6\u8ba1\u7b97\u4f4d\u79fb\u548c\u6781\u5316","text":"<p>\u8fd9\u91cc\u4f7f\u7528 Born \u6709\u6548\u7535\u8377\uff08BEC\uff09\uff0c\u4e0d\u662f\u540d\u4e49\u79bb\u5b50\u7535\u8377\u3002\u5bf9\u4e8e\u672c\u4f8b\u4e2d\u7684 PbTiO3\uff1a</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>\u4f60\u53ef\u4ee5\u4ece\u81ea\u5df1\u7684 DFPT \u8ba1\u7b97\u6216\u6587\u732e\u4e2d\u83b7\u5f97 BEC\u3002\u56e0\u6b64\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u548c\u6781\u5316\uff1a</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#4","title":"\u7b2c 4 \u6b65\uff1a\u7ed8\u5236\u5b9e\u7a7a\u95f4\u4f4d\u79fb\u548c\u6781\u5316\u56fe","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#5-","title":"\u7b2c 5 \u6b65\uff1a\u6784\u5efa\u6e29\u5ea6-\u5e8f\u53c2\u91cf\u66f2\u7ebf","text":"<p>\u7ed3\u5408\u6bcf\u4e2a\u6e29\u5ea6\u5e73\u5747\u7ed3\u6784\u7684\u6676\u683c\u4fe1\u606f\u548c\u6781\u5316\u6587\u4ef6\uff08<code>XX-pol.dat</code>\uff09\u8fdb\u884c\u5206\u6790\uff0c\u53ef\u4ee5\u5f97\u5230\u5982\u4e0b\u56fe\uff1a</p> <p>\u8be5\u8d8b\u52bf\u663e\u793a\u5728\u7ea6 <code>600 K</code> \u9644\u8fd1\u53d1\u751f\u660e\u663e\u76f8\u53d8\uff0c\u6b64\u65f6\u6781\u5316\u6d88\u5931\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3srtio3","title":"PbTiO3/SrTiO3 \u8d85\u6676\u683c\u4e2d\u7684\u62d3\u6251\u7ed3\u6784","text":"<p>\u5047\u8bbe <code>movie.xyz</code> \u662f\u5f53\u524d\u76ee\u5f55\u4e0b PbTiO3/SrTiO3 \u8d85\u6676\u683c\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1-25","title":"\u7b2c 1 \u6b65\uff1a\u4f7f\u7528\u6700\u540e 25% \u5e27\u6784\u5efa\u5e73\u5747\u7ed3\u6784","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-ti","title":"\u7b2c 2 \u6b65\uff1a\u6784\u5efa Ti \u8fd1\u90bb\u5217\u8868","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3-plane-grid","title":"\u7b2c 3 \u6b65\uff1a\u7ed8\u5236 plane-grid \u56fe","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>\u8fd9\u4f1a\u5f97\u5230\u4e0e\u524d\u9762\u5c55\u793a\u76f8\u4f3c\u7684\u56fe\u3002\u5728 PTO \u533a\u57df\u53ef\u4ee5\u770b\u5230\u7c7b\u4f3c\u6da1\u65cb\u7684\u6781\u5316\u56fe\u6837\uff0c\u800c STO \u533a\u57df\u7684\u6781\u5316\u63a5\u8fd1\u4e8e\u96f6\u3002\u901a\u8fc7\u5206\u6790\u6da1\u65cb\u6838\u9644\u8fd1\u6781\u5316\u7684\u53d8\u5316\uff0c\u53ef\u4ee5\u4f30\u8ba1\u5c40\u57df\u4ecb\u7535\u54cd\u5e94\uff0c\u4f46\u8fd9\u8d85\u51fa\u4e86\u672c\u6559\u7a0b\u8303\u56f4\u3002</p> <p>\u6ce8\u610f\uff1a\u8be5\u56fe\u4f7f\u7528\u7684 colormap \u4e0e GPUMDkit \u9ed8\u8ba4\u7ed8\u56fe\u98ce\u683c\u4e0d\u540c\u3002\u9ed8\u8ba4\u8f93\u51fa\u4e0d\u4f1a\u4e0e\u56fe\u4e2d\u5b8c\u5168\u4e00\u81f4\uff0c\u4f46\u53ef\u4ee5\u901a\u8fc7\u5c11\u91cf\u4fee\u6539\u7ed8\u56fe\u811a\u672c\u83b7\u5f97\u8fd9\u79cd\u98ce\u683c\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_20","title":"\u5176\u4ed6\u4f53\u7cfb","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#-","title":"\u6709\u673a-\u65e0\u673a\u6742\u5316\u94c1\u7535\u4f53","text":"<p>\u5728\u8bb8\u591a\u6709\u673a-\u65e0\u673a\u94c1\u7535\u4f53\u4e2d\uff0c\u6781\u5316\u4e0e\u5404\u5411\u5f02\u6027\u7684\u5206\u5b50\u5355\u5143\u5bc6\u5207\u76f8\u5173\u3002\u8ddf\u8e2a\u5206\u5b50\u53d6\u5411\u7684\u4e00\u79cd\u5b9e\u7528\u65b9\u6cd5\u662f\u4f7f\u7528\u952e\u77e2\u91cf\u3002</p> <p>\u5bf9\u4e8e TMCM-CdCl3\uff0c\u53ef\u4ee5\u4f7f\u7528 TMCM \u5206\u5b50\u4e2d\u7684 C-Cl \u952e\u65b9\u5411\u4f5c\u4e3a\u53d6\u5411\u4ee3\u7406\uff0c\u5e76\u636e\u6b64\u4f30\u8ba1\u6781\u5316\u6001\uff1a</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p>\u968f\u540e\u53ef\u4ee5\u628a <code>ccl_vectors.dat</code> \u4f5c\u4e3a\u53d6\u5411\u5e8f\u53c2\u91cf\u8fdb\u884c\u5206\u6790\u3002\u66f4\u591a\u7ec6\u8282\u53ef\u53c2\u8003\uff1aPhys. Rev. Lett. 136, 016801\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_21","title":"\u5176\u4ed6\u94c1\u7535\u6750\u6599\u5bb6\u65cf","text":"<p>\u9664 <code>ABO3</code> \u5916\uff0c<code>ferrodispcalc</code> \u4e5f\u53ef\u4ee5\u9002\u914d\u8bb8\u591a\u94c1\u7535\u4f53\u7cfb\uff0c\u5305\u62ec\u6c2e\u5316\u7269\u3001\u6c27\u5316\u94ea\u57fa\u5316\u5408\u7269\u3001\u6709\u673a-\u65e0\u673a\u6742\u5316\u4f53\u7cfb\u4ee5\u53ca\u90e8\u5206\u4e8c\u7ef4\u94c1\u7535\u6750\u6599\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html","title":"\u683c\u5f0f\u8f6c\u6362","text":"\ud83d\udd04 \u683c\u5f0f\u8f6c\u6362 <p>\u683c\u5f0f\u8f6c\u6362\u6a21\u5757\u7528\u4e8e\u5728\u5e38\u89c1\u539f\u5b50\u6a21\u62df\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362\uff0c\u540c\u65f6\u63d0\u4f9b group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u5e27\u63d0\u53d6\u7b49\u5143\u6570\u636e\u5904\u7406\u529f\u80fd\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/format_conversion/</code></p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_1","title":"\u652f\u6301\u7684\u683c\u5f0f","text":"<ul> <li>VASP\uff1a<code>POSCAR</code>\u3001<code>CONTCAR</code>\u3001<code>OUTCAR</code>\u3001<code>XDATCAR</code></li> <li>LAMMPS\uff1adata \u6587\u4ef6\u548c dump \u8f68\u8ff9</li> <li>CP2K\uff1a\u8f93\u51fa log\u3001\u5750\u6807\u3001\u529b\u548c\u6676\u80de\u6587\u4ef6</li> <li>ABACUS\uff1aSCF/MD \u8f93\u51fa</li> <li>CIF\uff1a\u6676\u4f53\u7ed3\u6784\u6587\u4ef6</li> <li>ASE trajectory\uff1a<code>.traj</code></li> <li>extxyz\uff1aGPUMD \u548c NEP \u5e38\u7528\u7684\u7ed3\u6784\u683c\u5f0f</li> </ul>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_2","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>1) Format Conversion\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_3","title":"\u6bcf\u4e2a\u5165\u53e3\u7684\u4f5c\u7528","text":"\u5165\u53e3 \u529f\u80fd \u9002\u7528\u573a\u666f <code>101</code> VASP OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c \u6279\u91cf\u8f6c\u6362 VASP \u8ba1\u7b97\u76ee\u5f55 <code>102</code> MTP cfg \u8f6c extxyz \u8f6c\u6362 MTP \u6570\u636e <code>103</code> CP2K \u8f6c extxyz \u53ef\u9009\u62e9 log/inp \u8def\u7ebf\u6216 pos/frc/cell \u8def\u7ebf <code>104</code> ABACUS \u8f6c extxyz \u8f6c\u6362 ABACUS SCF \u6216 MD \u8f93\u51fa <code>105</code> extxyz \u8f6c POSCAR \u5c06 extxyz \u6bcf\u4e00\u5e27\u5199\u6210 POSCAR <code>106</code> \u6dfb\u52a0 group \u6807\u7b7e \u4e3a GPUMD \u76f8\u5173\u6d41\u7a0b\u6dfb\u52a0\u539f\u5b50\u5206\u7ec4\u6807\u7b7e <code>107</code> \u6dfb\u52a0\u6743\u91cd \u4fee\u6539\u8bad\u7ec3\u96c6\u7ed3\u6784\u6743\u91cd <code>108</code> \u63d0\u53d6\u5355\u5e27 \u4ece extxyz \u8f68\u8ff9\u5bfc\u51fa\u67d0\u4e00\u5e27 <code>109</code> \u6e05\u7406 XYZ \u4fe1\u606f \u5220\u9664\u591a\u4f59 extxyz \u5c5e\u6027 <code>110</code> \u6269\u80de \u6309\u500d\u6570\u6216\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>out2exyz</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c VASP OUTCAR \u8f6c\u6362\u7684\u53e6\u4e00\u4e2a\u5165\u53e3 <code>pos2exyz</code> POSCAR \u8f6c extxyz \u8f6c\u6362\u5355\u4e2a\u7ed3\u6784 <code>cif2pos</code> CIF \u8f6c POSCAR \u4ece CIF \u51c6\u5907 VASP \u8f93\u5165 <code>cif2exyz</code> CIF \u8f6c extxyz \u4ece CIF \u51c6\u5907 GPUMDkit \u8f93\u5165 <code>xdat2exyz</code> XDATCAR \u8f6c extxyz \u8f6c\u6362 VASP MD \u8f68\u8ff9 <code>pos2lmp</code> POSCAR \u8f6c LAMMPS data \u51c6\u5907 LAMMPS \u8f93\u5165 <code>lmp2exyz</code> LAMMPS dump \u8f6c extxyz \u8f6c\u6362 LAMMPS \u8f68\u8ff9 <code>traj2exyz</code> ASE traj \u8f6c extxyz \u8f6c\u6362 ASE \u8f68\u8ff9"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_4","title":"\u5feb\u901f\u547d\u4ee4\u8868","text":"\u6765\u6e90 \u76ee\u6807 \u547d\u4ee4 OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz POSCAR model.xyz</code> extxyz POSCAR \u6587\u4ef6 <code>gpumdkit.sh -exyz2pos train.xyz</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_5","title":"\u5e38\u89c1\u4f8b\u5b50","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#vasp","title":"\u8f6c\u6362 VASP \u7ed3\u679c","text":"<p>\u5982\u679c\u6bcf\u4e2a\u8ba1\u7b97\u76ee\u5f55\u4e0b\u90fd\u6709 <code>OUTCAR</code>\uff1a</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>\u4e5f\u53ef\u4ee5\u4f7f\u7528 Python \u7248\u672c\uff1a</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>\u5728\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>101</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#group","title":"\u6dfb\u52a0 group \u6807\u7b7e","text":"<p>\u4e00\u4e9b GPUMD \u76f8\u5173\u6d41\u7a0b\u4f1a\u4f7f\u7528 group \u6807\u7b7e\u8fdb\u884c\u539f\u5b50\u5206\u7ec4\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>\u8be5\u547d\u4ee4\u8bfb\u53d6\u8f93\u5165\u7ed3\u6784\uff0c\u5e76\u5199\u51fa\u5e26 group \u4fe1\u606f\u7684 extxyz \u6587\u4ef6\u3002</p> <p>\u5728\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>106</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_6","title":"\u5e38\u7528\u811a\u672c\u8bf4\u660e","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>\u9002\u5408\u628a\u5355\u4e2a VASP \u7ed3\u6784\u8f6c\u6210 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz-poscar","title":"extxyz \u8f6c POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>\u4f1a\u5c06 extxyz \u4e2d\u6240\u6709\u5e27\u8f6c\u6362\u6210 <code>POSCAR_*.vasp</code> \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3\uff1a<code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#lammps-dump-extxyz","title":"LAMMPS dump \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>\u5143\u7d20\u987a\u5e8f\u5fc5\u987b\u5bf9\u5e94 LAMMPS \u4e2d\u7684 atom type ID\u3002\u4f8b\u5982 type 1 \u662f Li\u3001type 2 \u662f Y\u3001type 3 \u662f Cl\uff0c\u5219\u8f93\u5165 <code>Li Y Cl</code>\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#cif","title":"CIF \u8f6c\u6362","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>\u5982\u679c\u540e\u7eed\u9700\u8981 VASP \u8ba1\u7b97\uff0c\u4f7f\u7528 <code>-cif2pos</code>\uff1b\u5982\u679c\u540e\u7eed\u8981\u8fdb\u5165 GPUMDkit \u5206\u6790\uff0c\u4f7f\u7528 <code>-cif2exyz</code>\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_7","title":"\u6dfb\u52a0\u6743\u91cd","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>\u7528\u4e8e\u7ed9\u8bad\u7ec3\u96c6\u7ed3\u6784\u6dfb\u52a0\u6216\u4fee\u6539\u6743\u91cd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_8","title":"\u6269\u80de","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>\u7b2c\u4e00\u79cd\u6309\u6676\u80de\u500d\u6570\u6269\u80de\uff0c\u7b2c\u4e8c\u79cd\u6309\u76ee\u6807\u539f\u5b50\u6570\u81ea\u52a8\u9009\u62e9\u6269\u80de\u65b9\u5f0f\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_9","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae LAMMPS \u8f6c\u6362\u540e\u5143\u7d20\u4e0d\u5bf9 \u68c0\u67e5 dump \u6587\u4ef6\u540e\u7684\u5143\u7d20\u987a\u5e8f extxyz \u5143\u6570\u636e\u592a\u591a \u4f7f\u7528 <code>-clean_xyz input.xyz clean.xyz</code> \u63d0\u53d6\u5e27\u4e0d\u5bf9 \u6ce8\u610f\u5e27\u7d22\u5f15\u901a\u5e38\u4ece 0 \u5f00\u59cb"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_10","title":"\u8bf4\u660e","text":"<p>\u5982\u679c\u67d0\u4e2a\u8f6c\u6362\u811a\u672c\u7f3a\u5c11\u6240\u9700 Python \u5305\uff0c\u8fd0\u884c\u8be5\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u76f8\u5e94\u63d0\u793a\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html","title":"\u7ed3\u6784\u91c7\u6837","text":"\ud83d\udce6 \u7ed3\u6784\u91c7\u6837 <p>\u7ed3\u6784\u91c7\u6837\u7528\u4e8e\u4ece\u8f68\u8ff9\u4e2d\u9009\u62e9\u5019\u9009\u7ed3\u6784\u3001\u751f\u6210\u6270\u52a8\u7ed3\u6784\uff0c\u6216\u6839\u636e\u6a21\u578b\u504f\u5dee\u6311\u9009\u503c\u5f97\u8fdb\u4e00\u6b65\u8ba1\u7b97\u7684\u7ed3\u6784\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/sample_structures/</code></p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_1","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>2) Sample Structures\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u65b9\u6cd5 \u7528\u9014 201 uniform/random \u4ece\u8f68\u8ff9\u4e2d\u5747\u5300\u6216\u968f\u673a\u62bd\u5e27 202 PyNEP notice \u53ea\u6253\u5370\u63d0\u793a\uff1b\u771f\u6b63\u8fd0\u884c PyNEP \u8bf7\u7528 <code>gpumdkit.sh -pynep</code> 203 NepTrain FPS \u4f7f\u7528 NepTrain \u63cf\u8ff0\u7b26\u7684 FPS \u91c7\u6837 204 perturb \u4ece POSCAR/CONTCAR \u751f\u6210\u6270\u52a8\u7ed3\u6784 205 force deviation \u4ece active learning \u8f93\u51fa\u4e2d\u9009\u62e9\u9ad8\u504f\u5dee\u7ed3\u6784"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_2","title":"\u5747\u5300/\u968f\u673a\u91c7\u6837","text":"<p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>201</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>\u4f8b\u5982\u8f93\u5165\uff1a</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>\u6216\uff1a</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>uniform</code> / <code>random</code> \u91c7\u6837\u65b9\u6cd5 <code>50</code> / <code>100</code> \u91c7\u6837\u7ed3\u6784\u6570 <code>500</code> \u53ef\u9009\uff0c\u8df3\u8fc7\u524d 500 \u5e27 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#neptrain-fps","title":"NepTrain FPS","text":"<p>NepTrain \u7248\u672c\u7684 FPS\uff1a</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>203</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u5165\uff1a</p> \u6587\u4ef6 \u542b\u4e49 <code>dump.xyz</code> \u5019\u9009\u7ed3\u6784 <code>train.xyz</code> \u5f53\u524d\u8bad\u7ec3\u96c6 <code>nep.txt</code> \u7528\u4e8e\u8ba1\u7b97\u63cf\u8ff0\u7b26\u7684 NEP \u6a21\u578b <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>\u8fd0\u884c\u65f6\u53ef\u4ee5\u9009\u62e9\u6309\u6700\u5c0f\u8ddd\u79bb\u9608\u503c\u91c7\u6837\uff0c\u6216\u6307\u5b9a\u91c7\u6837\u7ed3\u6784\u6570\u3002\u811a\u672c\u968f\u540e\u4f1a\u6253\u5370\uff1a</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>NepTrain</code>\uff0c\u8fd0\u884c\u65f6\u4f1a\u63d0\u793a\u76f8\u5173\u5f15\u7528\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep","title":"PyNEP \u65e7\u5165\u53e3","text":"<p>PyNEP FPS \u4ecd\u7136\u4fdd\u7559\u517c\u5bb9\uff0c\u4f46\u53ea\u901a\u8fc7 <code>-pynep</code> \u5165\u53e3\u8c03\u7528\uff1a</p> <p>\u5982\u679c\u5728\u4ea4\u4e92\u83dc\u5355\u4e2d\u9009\u62e9 <code>202</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre> <pre><code>gpumdkit.sh -pynep\n</code></pre> <p>\u968f\u540e\u8f93\u5165\uff1a</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u8fd9\u4e2a\u5165\u53e3\u9700\u8981 <code>pynep</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_3","title":"\u7ed3\u6784\u6270\u52a8","text":"<pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>204</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>POSCAR</code> \u8f93\u5165\u7ed3\u6784 <code>20</code> \u751f\u6210\u7ed3\u6784\u6570 <code>0.03</code> \u6676\u80de\u6270\u52a8\u6bd4\u4f8b <code>0.2</code> \u539f\u5b50\u6270\u52a8\u8ddd\u79bb\uff0c\u5355\u4f4d Angstrom <code>uniform</code> \u6270\u52a8\u65b9\u5f0f\uff0c\u53ef\u9009 <code>normal</code>\u3001<code>uniform</code>\u3001<code>const</code> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>POSCAR_01.vasp</code>\u3001<code>POSCAR_02.vasp</code> \u7b49</li> </ul> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>dpdata</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_4","title":"\u6700\u5927\u529b\u504f\u5dee\u7ed3\u6784\u9009\u62e9","text":"<p>\u8be5\u529f\u80fd\u9700\u8981\u914d\u5408 GPUMD \u7684 <code>active</code> \u547d\u4ee4\u4f7f\u7528\u3002<code>active</code> \u901a\u8fc7\u59d4\u5458\u4f1a\u8bc4\u5ba1\u673a\u5236\uff0c\u8ba9\u591a\u6761\u52bf\u51fd\u6570\u5bf9\u540c\u4e00\u7ed3\u6784\u8fdb\u884c\u9884\u6d4b\uff0c\u5e76\u8bb0\u5f55\u6bcf\u4e2a\u7ed3\u6784\u7684\u6700\u5927\u529b\u504f\u5dee\u3002<code>select_max_modev.py</code> \u4f1a\u4ece <code>active.out</code> \u548c <code>active.xyz</code> \u4e2d\u9009\u62e9\u529b\u504f\u5dee\u8f83\u5927\u7684\u7ed3\u6784\uff0c\u5199\u5165 <code>selected.xyz</code>\u3002</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>205</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>\u9700\u8981\u5f53\u524d\u76ee\u5f55\u4e0b\u6709\uff1a</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_5","title":"\u793a\u4f8b\u547d\u4ee4","text":"<pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_6","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae FPS \u9009\u51fa\u592a\u591a\u76f8\u4f3c\u7ed3\u6784 \u8c03\u5927\u8ddd\u79bb\u9608\u503c\u6216\u9650\u5236\u6700\u5927\u9009\u62e9\u6570 \u6270\u52a8\u7ed3\u6784\u4e0d\u5408\u7406 \u51cf\u5c0f <code>cell_pert</code> \u548c <code>atom_pert</code> <code>active.out</code> \u548c <code>active.xyz</code> \u4e0d\u5339\u914d \u786e\u4fdd\u6765\u81ea\u540c\u4e00\u6b21 GPUMD active \u8fd0\u884c PCA \u56fe\u5f02\u5e38 \u68c0\u67e5 <code>nep.txt</code> \u662f\u5426\u548c\u4e24\u4e2a\u6570\u636e\u96c6\u5143\u7d20\u4e00\u81f4"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html","title":"\u7ed8\u56fe\u811a\u672c","text":"\ud83d\udcca \u7ed8\u56fe\u811a\u672c <p>\u7ed8\u56fe\u6a21\u5757\u7528\u4e8e\u53ef\u89c6\u5316 GPUMD\u3001NEP \u548c GPUMDkit \u8ba1\u7b97\u5668\u4ea7\u751f\u7684\u6570\u636e\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/plt_scripts/</code></p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_1","title":"\u5feb\u901f\u5165\u53e3","text":"<pre><code>gpumdkit.sh -plt\ngpumdkit.sh -plt &lt;type&gt;\ngpumdkit.sh -plt &lt;type&gt; save\ngpumdkit.sh -plt &lt;type&gt; -h\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u8bad\u7ec3\u4e0e\u9884\u6d4b","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_2","title":"\u8bad\u7ec3\u7ed3\u679c","text":"<p>\u8bfb\u53d6 <code>loss.out</code>\u3001<code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code>\uff0c\u7ed8\u5236 loss \u548c\u80fd\u91cf/\u529b/virial \u7684 parity plot\u3002</p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_3","title":"\u9884\u6d4b\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_4","title":"\u8bad\u7ec3/\u6d4b\u8bd5\u96c6\u5bf9\u6bd4","text":"<pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#parity-plot","title":"\u5bc6\u5ea6 parity plot","text":"<p>\u5927\u6570\u636e\u96c6\u6563\u70b9\u592a\u5bc6\u65f6\uff0c\u5bc6\u5ea6\u56fe\u66f4\u5bb9\u6613\u89c2\u5bdf\u8bef\u5dee\u5206\u5e03\uff1a</p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_5","title":"\u529b\u8bef\u5dee\u5206\u6790","text":"<p><code>plt_force_errors.py</code> \u53c2\u8003 Liu et al. \u7684\u65b9\u5f0f\u5206\u6790\u529b\u5927\u5c0f\u8bef\u5dee\u548c\u89d2\u5ea6\u8bef\u5dee\u3002</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#born","title":"\u7535\u8377\u548c Born \u6709\u6548\u7535\u8377","text":"<pre><code>gpumdkit.sh -plt charge\ngpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#md","title":"MD \u548c\u7ed3\u6784\u5206\u6790\u7ed8\u56fe","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_6","title":"\u70ed\u529b\u5b66\u91cf","text":"<pre><code>gpumdkit.sh -plt thermo\ngpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#rdf","title":"RDF","text":"<pre><code>gpumdkit.sh -plt rdf\ngpumdkit.sh -plt rdf &lt;column&gt;\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#vac-pdos","title":"VAC \u548c PDOS","text":"<pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>\u8f93\u5165\u6587\u4ef6\u901a\u5e38\u5305\u62ec <code>model.xyz</code>\u3001<code>run.in</code>\u3001<code>dos.out</code>\u3001<code>mvac.out</code>\u3002</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_7","title":"\u6269\u6563\u548c\u79bb\u5b50\u8f93\u8fd0","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\ngpumdkit.sh -plt msd_conv\ngpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt arrhenius_sigma\n</code></pre> <p>Arrhenius \u56fe\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_8","title":"\u70ed\u8f93\u8fd0","text":"<pre><code>gpumdkit.sh -plt emd x\ngpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\ngpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#dimer","title":"\u63cf\u8ff0\u7b26\u3001Dimer \u548c\u5176\u4ed6\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_9","title":"\u63cf\u8ff0\u7b26\u53ef\u89c6\u5316","text":"<pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#dimer_1","title":"Dimer \u66f2\u7ebf","text":"<pre><code>gpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>Reference: J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#doas","title":"DOAS","text":"<pre><code>gpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#net-force","title":"Net force","text":"<pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>Reference: arXiv:2510.19774</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_10","title":"\u5feb\u901f\u8868","text":"\u547d\u4ee4 \u8f93\u5165\u6587\u4ef6 \u7528\u9014 <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP \u8bad\u7ec3\u7ed3\u679c <code>prediction</code> <code>*_test.out</code> NEP \u9884\u6d4b\u7ed3\u679c <code>thermo</code> <code>thermo.out</code> \u70ed\u529b\u5b66\u91cf <code>msd</code> <code>msd.out</code> \u5747\u65b9\u4f4d\u79fb <code>sdc</code> <code>msd.out</code> \u81ea\u6269\u6563\u7cfb\u6570 <code>rdf</code> <code>rdf.out</code> \u5f84\u5411\u5206\u5e03\u51fd\u6570 <code>pdos</code> <code>dos.out</code>, <code>mvac.out</code> VAC \u548c PDOS <code>emd</code>/<code>nemd</code>/<code>hnemd</code> \u70ed\u8f93\u8fd0\u8f93\u51fa \u70ed\u5bfc\u7387\u5206\u6790 <code>des</code> <code>descriptors.npy</code> \u63cf\u8ff0\u7b26\u964d\u7ef4 <code>dimer</code> <code>nep.txt</code> \u4e8c\u805a\u4f53\u80fd\u91cf/\u529b\u66f2\u7ebf <code>doas</code> <code>doas.out</code> \u539f\u5b50\u6001\u5bc6\u5ea6"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html","title":"\u81ea\u5b9a\u4e49\u547d\u4ee4","text":"\ud83d\udd27 \u81ea\u5b9a\u4e49\u547d\u4ee4 <p>GPUMDkit \u652f\u6301\u4ece ~/.gpumdkit.in \u52a0\u8f7d\u81ea\u5b9a\u4e49\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u628a\u5e38\u7528\u811a\u672c\u6216\u5de5\u4f5c\u6d41\u5c01\u88c5\u6210 <code>custom_</code> \u5f00\u5934\u7684 Bash \u51fd\u6570\uff0c\u7136\u540e\u901a\u8fc7 <code>gpumdkit.sh -\u547d\u4ee4\u540d</code> \u8c03\u7528\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_1","title":"\u8bbe\u7f6e","text":"<p>\u7f16\u8f91\u914d\u7f6e\u6587\u4ef6\uff1a</p> <pre><code>vi ~/.gpumdkit.in\n</code></pre> <p>\u81ea\u5b9a\u4e49\u51fd\u6570\u9700\u8981\u4f7f\u7528 <code>custom_</code> \u524d\u7f00\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_2","title":"\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_3","title":"\u7b80\u5355\u95ee\u5019","text":"<p>\u5728 <code>~/.gpumdkit.in</code> \u4e2d\u5199\u5165\uff1a</p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>\u7136\u540e\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -hello\n</code></pre> <p>\u4f60\u4f1a\u770b\u5230\u7c7b\u4f3c\u8f93\u51fa\uff1a</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_4","title":"\u5e26\u5fc5\u9700\u53c2\u6570\u7684\u547d\u4ee4","text":"<pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -greet Zihan\n</code></pre> <p>\u8f93\u51fa\uff1a</p> <pre><code>Hello, Zihan!\n</code></pre> <p>\u4f20\u9012\u53c2\u6570\u65f6\uff0c\u53ef\u4ee5\u7528 <code>\"$@\"</code> \u5b89\u5168\u5730\u8f6c\u53d1\u6240\u6709\u53c2\u6570\uff1b\u5982\u679c\u9700\u8981\u4ece\u7b2c\u4e00\u4e2a\u53c2\u6570\u5f00\u59cb\u5f15\u7528\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528 <code>${@:1}</code>\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_5","title":"\u8c03\u7528\u5916\u90e8\u811a\u672c","text":"<p>\u5982\u679c\u5e0c\u671b\u50cf\u8c03\u7528 GPUMDkit \u5185\u7f6e\u547d\u4ee4\u4e00\u6837\u8c03\u7528\u81ea\u5df1\u7684\u811a\u672c\uff1a</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -nepanalyse\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_6","title":"\u8fdb\u9636\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_7","title":"\u6279\u5904\u7406\u7ed8\u56fe","text":"<p>\u5bf9\u591a\u4e2a\u76ee\u5f55\u6279\u91cf\u7ed8\u56fe\uff1a</p> <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -batch_plot dir1 dir2 dir3\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_8","title":"\u8bad\u7ec3\u96c6\u5206\u6790\u6d41\u7a0b","text":"<p>\u628a\u591a\u4e2a\u5206\u6790\u547d\u4ee4\u7ec4\u5408\u6210\u4e00\u4e2a\u5165\u53e3\uff1a</p> <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -analyze_training train.xyz\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_9","title":"\u81ea\u5b9a\u4e49\u6570\u636e\u51c6\u5907\u6d41\u7a0b","text":"<pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    gpumdkit.sh -out2xyz ./\n    gpumdkit.sh -filter_value train.xyz force 30\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -prep_training\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_10","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u547d\u4ee4\u540d\u5c3d\u91cf\u6e05\u695a\uff0c\u4f8b\u5982 <code>custom_analyze_training</code> \u6bd4 <code>custom_at</code> \u66f4\u5bb9\u6613\u7ef4\u62a4\u3002</li> <li>\u5bf9\u9700\u8981\u53c2\u6570\u7684\u547d\u4ee4\uff0c\u5efa\u8bae\u5728\u53c2\u6570\u4e3a\u7a7a\u65f6\u6253\u5370\u7528\u6cd5\u63d0\u793a\u3002</li> <li>\u8c03\u7528\u5916\u90e8\u811a\u672c\u65f6\uff0c\u5c3d\u91cf\u7528 <code>\"$@\"</code> \u4fdd\u7559\u53c2\u6570\u4e2d\u7684\u7a7a\u683c\u548c\u7279\u6b8a\u5b57\u7b26\u3002</li> <li>\u6279\u5904\u7406\u76ee\u5f55\u65f6\uff0c\u6ce8\u610f\u4f7f\u7528 <code>cd \"$dir\"</code>\uff0c\u907f\u514d\u8def\u5f84\u4e2d\u6709\u7a7a\u683c\u65f6\u51fa\u9519\u3002</li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html","title":"\u8ba1\u7b97\u5668\u811a\u672c","text":"\ud83e\uddee \u8ba1\u7b97\u5668\u811a\u672c <p>\u8ba1\u7b97\u5668\u6a21\u5757\u7528\u4e8e\u4ece MD \u8f68\u8ff9\u3001NEP \u6a21\u578b\u548c\u7ed3\u6784\u6587\u4ef6\u4e2d\u8ba1\u7b97\u6750\u6599\u6027\u8d28\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code></p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_1","title":"\u529f\u80fd\u6982\u89c8","text":"\u4efb\u52a1 \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u79bb\u5b50\u7535\u5bfc\u7387 <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>\u3001<code>thermo.out</code>\u3001<code>model.xyz</code> MSD <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz \u8f68\u8ff9 NEP \u9884\u6d4b <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP \u6a21\u578b NEP \u63cf\u8ff0\u7b26 <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP \u6a21\u578b DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP \u6a21\u578b NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u521d\u672b\u6001\u7ed3\u6784 \u7ed3\u6784\u4f18\u5316 <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784 + NEP \u6a21\u578b \u90bb\u5c45\u5217\u8868 <code>gpumdkit.sh -calc nlist [args...]</code> \u7ed3\u6784 \u4f4d\u79fb <code>gpumdkit.sh -calc disp [args...]</code> \u8f68\u8ff9 + \u90bb\u5c45\u5217\u8868 \u5e73\u5747\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct [args...]</code> \u8f68\u8ff9 \u516b\u9762\u4f53\u503e\u8f6c <code>gpumdkit.sh -calc oct-tilt [args...]</code> \u8f68\u8ff9 + B-O \u90bb\u5c45\u5217\u8868 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 [args...]</code> \u8f68\u8ff9 + \u90bb\u5c45\u5217\u8868 <p>\u67e5\u770b\u5b8c\u6574\u5e2e\u52a9\uff1a</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>\u547d\u4ee4\u884c\u5e2e\u52a9\u8868\u7c7b\u4f3c\uff1a</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>4) Calculators</code>\uff0c\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_2","title":"\u79bb\u5b50\u7535\u5bfc\u7387","text":"<pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>401</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>\u5e38\u7528\u8f93\u5165\u6587\u4ef6\uff1a</p> \u6587\u4ef6 \u4f5c\u7528 <code>msd.out</code> \u5fc5\u9700\uff0cMSD \u6570\u636e <code>thermo.out</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u6e29\u5ea6 <code>model.xyz</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u4f53\u79ef\u548c\u79bb\u5b50\u6570 <code>run.in</code> \u53ef\u9009\uff0c\u8bc6\u522b\u6269\u80de\u4fe1\u606f <p>\u5982\u679c\u7f3a\u5c11\u81ea\u52a8\u8bc6\u522b\u6240\u9700\u6587\u4ef6\uff0c\u811a\u672c\u4f1a\u4ea4\u4e92\u5f0f\u8be2\u95ee\u6e29\u5ea6\u3001\u4f53\u79ef\u548c\u79bb\u5b50\u6570\u3002</p> <p>\u624b\u52a8\u6a21\u5f0f\u7684\u63d0\u793a\u7c7b\u4f3c\uff1a</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#msd","title":"\u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD","text":"<pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>412</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>Li</code> \u76ee\u6807\u6269\u6563\u5143\u7d20 <code>10</code> \u5e27\u95f4\u9694\uff0c\u5355\u4f4d fs <code>5000</code> \u53ef\u9009\uff0c\u6700\u5927\u76f8\u5173\u6b65\u6570 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>msd.out</code></li> </ul> <p>\u968f\u540e\u53ef\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u9884\u6d4b\u6027\u8d28","text":"<pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>\u8be5\u529f\u80fd\u4f7f\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8ba1\u7b97\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u3002\u53ea\u6709\u5f53\u4f60\u786e\u8ba4\u6a21\u578b\u8d28\u91cf\u53ef\u9760\uff0c\u5e76\u660e\u786e\u5e0c\u671b\u4f7f\u7528 NEP \u4f5c\u4e3a\u66ff\u4ee3\u8ba1\u7b97\u5668\u65f6\uff0c\u624d\u5efa\u8bae\u4f7f\u7528\u5b83\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep_1","title":"NEP \u63cf\u8ff0\u7b26","text":"<pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>\u7528\u9014\u5305\u62ec\uff1a</p> <ul> <li>\u7528 PCA/UMAP \u53ef\u89c6\u5316\u5c40\u57df\u73af\u5883\uff1b</li> <li>\u6bd4\u8f83\u8bad\u7ec3\u96c6\u548c\u5019\u9009\u7ed3\u6784\uff1b</li> <li>\u5224\u65ad\u65b0\u6570\u636e\u662f\u5426\u6269\u5c55\u4e86\u63cf\u8ff0\u7b26\u7a7a\u95f4\u3002</li> </ul> <p>\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#doas","title":"DOAS","text":"<p><code>calc_doas.py</code> \u7528\u4e8e\u8ba1\u7b97 Wang et al. \u63d0\u51fa\u7684 density of atomistic states\u3002</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>\u811a\u672c\u4f1a\uff1a</p> <ol> <li>\u8bfb\u53d6\u6240\u6709\u7ed3\u6784\uff1b</li> <li>\u4f7f\u7528 NEP \u8fdb\u884c\u7ed3\u6784\u4f18\u5316\uff1b</li> <li>\u63d0\u53d6\u6bcf\u4e2a\u539f\u5b50\u7684\u80fd\u91cf\uff1b</li> <li>\u6309\u5143\u7d20\u5206\u7ec4\u8f93\u51fa\uff1b</li> <li>\u7528\u7ed8\u56fe\u811a\u672c\u53ef\u89c6\u5316\u5206\u5e03\u3002</li> </ol>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#neb","title":"NEB \u548c\u7ed3\u6784\u4f18\u5316","text":"<p>NEB\uff1a</p> <pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>\u7ed3\u6784\u4f18\u5316\uff1a</p> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>\u8f93\u51fa\u5305\u62ec\uff1a</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_3","title":"\u94c1\u7535\u548c\u6781\u6027\u6750\u6599\u5de5\u5177","text":"<p>\u8fd9\u4e9b\u5de5\u5177\u9700\u8981 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p><code>ferrodispcalc</code> \u76ee\u524d\u6ca1\u6709\u9700\u8981\u989d\u5916\u5f15\u7528\u7684\u8bba\u6587\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_4","title":"\u90bb\u5c45\u5217\u8868","text":"<pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_5","title":"\u4f4d\u79fb","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_6","title":"\u5e73\u5747\u7ed3\u6784","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_7","title":"\u516b\u9762\u4f53\u503e\u8f6c","text":"<pre><code>gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#abo3","title":"ABO3 \u5c40\u57df\u6781\u5316","text":"<pre><code>gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -o polarization.dat\n</code></pre> <p><code>--bec</code> \u5e94\u6839\u636e\u4f60\u7684\u4f53\u7cfb\u6216\u53c2\u8003\u6570\u636e\u8bbe\u7f6e\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html","title":"\u8d21\u732e\u6307\u5357","text":"\ud83e\udd1d \u8d21\u732e\u6307\u5357 <p>\u611f\u8c22\u4f60\u6709\u5174\u8da3\u4e3a GPUMDkit \u505a\u8d21\u732e\u3002\u6211\u4eec\u975e\u5e38\u611f\u8c22\u4f60\u613f\u610f\u82b1\u65f6\u95f4\u548c\u7cbe\u529b\u5e2e\u52a9\u6539\u8fdb\u8fd9\u4e2a\u5de5\u5177\u5305\u3002</p> <p><code>GPUMDkit</code> \u662f\u4e00\u4e2a\u5f00\u6e90\u8f6f\u4ef6\u5305\u3002\u65e0\u8bba\u662f\u4fee\u590d bug\u3001\u6dfb\u52a0\u65b0\u529f\u80fd\u3001\u6539\u8fdb\u6587\u6863\uff0c\u8fd8\u662f\u63d0\u51fa\u4f7f\u7528\u5efa\u8bae\uff0c\u6211\u4eec\u90fd\u6b22\u8fce\u793e\u533a\u8d21\u732e\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_1","title":"\u76ee\u5f55","text":"<ul> <li>\u5f00\u53d1\u9650\u5236\u548c\u6307\u5357</li> <li>\u62a5\u544a Bug</li> <li>\u63d0\u51fa\u529f\u80fd\u5efa\u8bae</li> <li>\u8d21\u732e\u4ee3\u7801</li> <li>Fork \u5e76\u514b\u9686\u4ed3\u5e93</li> <li>\u521b\u5efa\u529f\u80fd\u5206\u652f</li> <li>\u8fdb\u884c\u4fee\u6539</li> <li>\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e</li> <li>\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e</li> <li>\u66f4\u65b0 Tab \u8865\u5168</li> <li>\u4ee3\u7801\u98ce\u683c\u548c\u6700\u4f73\u5b9e\u8df5</li> <li>\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539</li> <li>\u63d0\u4ea4\u4fe1\u606f</li> <li>\u63a8\u9001\u5e76\u6253\u5f00 Pull Request</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_2","title":"\u5f00\u53d1\u9650\u5236\u548c\u6307\u5357","text":"<p>\u4e3a\u4e86\u4fdd\u6301\u9879\u76ee\u4ee3\u7801\u8d28\u91cf\u548c\u4e00\u81f4\u6027\uff0c\u8bf7\u9075\u5b88\u4ee5\u4e0b\u6307\u5357\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_3","title":"\u8bed\u8a00\u8981\u6c42","text":"<ul> <li>\u6240\u6709\u4ee3\u7801\u5e94\u4f7f\u7528\u82f1\u6587\u7f16\u5199\uff1a\u5305\u62ec\u53d8\u91cf\u540d\u3001\u51fd\u6570\u540d\u3001\u6ce8\u91ca\u3001docstring\u3001\u63d0\u4ea4\u4fe1\u606f\u548c\u6587\u6863\u3002</li> <li>\u6211\u4eec\u7406\u89e3\u8d21\u732e\u8005\u53ef\u80fd\u6765\u81ea\u4e0d\u540c\u80cc\u666f\uff0c\u4f46\u4f7f\u7528\u82f1\u6587\u53ef\u4ee5\u8ba9\u4ee3\u7801\u5e93\u5bf9\u66f4\u5e7f\u6cdb\u7684\u7528\u6237\u4fdd\u6301\u53ef\u8bfb\u548c\u53ef\u7ef4\u62a4\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_4","title":"\u6a21\u5757\u5316\u548c\u53ef\u590d\u7528\u6027","text":"<ul> <li>\u7f16\u5199\u6a21\u5757\u5316\u3001\u53ef\u590d\u7528\u7684\u4ee3\u7801\uff1a\u51fd\u6570\u548c\u811a\u672c\u5e94\u5c3d\u91cf\u5177\u6709\u7075\u6d3b\u6027\u3002</li> <li>\u4f18\u5148\u901a\u8fc7\u53c2\u6570\u4f20\u9012\u4fe1\u606f\uff0c\u907f\u514d\u786c\u7f16\u7801\uff1a\u4f7f\u7528\u51fd\u6570\u53c2\u6570\u3001\u547d\u4ee4\u884c\u53c2\u6570\u6216\u914d\u7f6e\u6587\u4ef6\uff0c\u800c\u4e0d\u662f\u628a\u6570\u503c\u76f4\u63a5\u5199\u6b7b\u3002\u4e0d\u8fc7\uff0c\u67d0\u4e9b\u6587\u4ef6\u540d\u662f GPUMD \u548c NEP \u7a0b\u5e8f\u56fa\u5b9a\u8981\u6c42\u7684\uff0c\u4f8b\u5982 <code>train.xyz</code>\u3001<code>thermo.out</code>\uff0c\u8fd9\u7c7b\u60c5\u51b5\u53ef\u4ee5\u6309\u9700\u8981\u4fdd\u7559\u56fa\u5b9a\u6587\u4ef6\u540d\u3002</li> <li>\u793a\u4f8b\uff1a</li> </ul> <pre><code># Good: accepts parameters\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # processing logic\n}\n\n# Avoid: hardcoded values (unless required by GPUMD/NEP)\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # processing logic\n}\n</code></pre>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_5","title":"\u4ee3\u7801\u98ce\u683c","text":"<ul> <li>\u7f16\u5199\u6e05\u6670\u3001\u6613\u4e8e\u4ed6\u4eba\u7ef4\u62a4\u548c\u4fee\u6539\u7684\u4ee3\u7801\u3002</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u540d\u548c\u51fd\u6570\u540d\u3002</li> <li>\u5728\u5fc5\u8981\u65f6\u6dfb\u52a0\u6ce8\u91ca\uff0c\u89e3\u91ca\u590d\u6742\u903b\u8f91\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_6","title":"\u6587\u6863","text":"<ul> <li>\u786e\u4fdd\u5e2e\u52a9\u4fe1\u606f\uff08\u4f8b\u5982 <code>-h</code> \u53c2\u6570\uff09\u6e05\u6670\u3001\u51c6\u786e\u3002</li> <li><code>docs/</code> \u76ee\u5f55\u4e2d\u7684\u6587\u6863\u901a\u5e38\u7531\u7ef4\u62a4\u8005\u66f4\u65b0\uff0c\u56e0\u6b64\u4e00\u822c\u4e0d\u9700\u8981\u8d21\u732e\u8005\u76f4\u63a5\u4fee\u6539\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#bug","title":"\u62a5\u544a Bug","text":"<p>\u5982\u679c\u4f60\u9047\u5230 bug\uff0c\u8bf7\u901a\u8fc7 GitHub Issues \u5e2e\u52a9\u6211\u4eec\u5b9a\u4f4d\u548c\u4fee\u590d\uff1a</p> <ol> <li>\u5148\u641c\u7d22\u5df2\u6709 issue\uff0c\u786e\u8ba4\u8fd9\u4e2a bug \u662f\u5426\u5df2\u7ecf\u88ab\u62a5\u544a\u8fc7\u3002</li> <li>\u5982\u679c\u8fd8\u6ca1\u6709\u62a5\u544a\uff0c\u8bf7\u521b\u5efa\u65b0 issue\uff1aCreate an Issue</li> <li>\u8be6\u7ec6\u63cf\u8ff0\u95ee\u9898\uff0c\u5982\u679c\u53ef\u4ee5\uff0c\u8bf7\u63d0\u4f9b\u6d4b\u8bd5\u6587\u4ef6\u3002</li> </ol> <p>\u4f60\u4e5f\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u65b9\u5f0f\u8054\u7cfb\u6211\u4eec\uff1a</p> <ul> <li>QQ \u7fa4\uff1a825696376</li> <li>Email\uff1ayanzihan@westlake.edu.cn</li> <li>\u811a\u672c\u5f00\u53d1\u8005\uff1a\u8054\u7cfb\u811a\u672c\u6587\u4ef6\u5934\u90e8\u5217\u51fa\u7684\u5f00\u53d1\u8005</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_7","title":"\u63d0\u51fa\u529f\u80fd\u5efa\u8bae","text":"<p>\u6211\u4eec\u6b22\u8fce\u65b0\u7684\u529f\u80fd\u5efa\u8bae\u3002\u63d0\u51fa\u65b0\u529f\u80fd\u65f6\uff0c\u53ef\u4ee5\u6309\u4ee5\u4e0b\u65b9\u5f0f\u8fdb\u884c\uff1a</p> <ol> <li>\u5148\u641c\u7d22\u5df2\u6709 issue\uff0c\u786e\u8ba4\u662f\u5426\u5df2\u7ecf\u6709\u4eba\u63d0\u51fa\u8fc7\u7c7b\u4f3c\u5efa\u8bae\u3002</li> <li>\u521b\u5efa\u65b0\u7684\u529f\u80fd\u8bf7\u6c42\uff1aCreate a Feature Request\uff0c\u5e76\u63d0\u53ca @zhyan0603\u3002</li> <li>\u6e05\u695a\u63cf\u8ff0\u4f60\u7684\u9700\u6c42\uff0c\u5e76\u8bf4\u660e\u5b83\u4e3a\u4ec0\u4e48\u6709\u7528\u3002</li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_8","title":"\u8d21\u732e\u4ee3\u7801","text":""},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#fork","title":"Fork \u5e76\u514b\u9686\u4ed3\u5e93","text":"<ol> <li> <p>\u5728 GitHub \u7684 GPUMDkit \u4ed3\u5e93\u9875\u9762\u53f3\u4e0a\u89d2\u70b9\u51fb \"Fork\"\uff0c\u5c06\u4ed3\u5e93 fork \u5230\u81ea\u5df1\u7684\u8d26\u53f7\u4e0b\u3002</p> </li> <li> <p>\u5c06\u4f60\u7684 fork \u514b\u9686\u5230\u672c\u5730\uff1a</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>\u8bbe\u7f6e upstream remote\uff0c\u65b9\u4fbf\u548c\u4e3b\u4ed3\u5e93\u4fdd\u6301\u540c\u6b65\uff1a</li> </ol> <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_9","title":"\u521b\u5efa\u529f\u80fd\u5206\u652f","text":"<p>\u4e3a\u4f60\u7684\u4fee\u6539\u521b\u5efa\u4e00\u4e2a\u65b0\u5206\u652f\uff1a</p> <pre><code># Create and checkout a new branch from main\ngit checkout -b your-branch-name\n</code></pre> <p>\u5206\u652f\u540d\u53ef\u4ee5\u6309\u4f60\u7684\u4e60\u60ef\u547d\u540d\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_10","title":"\u8fdb\u884c\u4fee\u6539","text":"<p><code>GPUMDkit</code> \u7684\u7ed3\u6784\u5305\u62ec\uff1a</p> <ul> <li><code>gpumdkit.sh</code>\uff1a\u4e3b\u5165\u53e3 Bash \u811a\u672c\uff0c\u8d1f\u8d23\u4ea4\u4e92\u83dc\u5355\u6a21\u5f0f\u548c\u547d\u4ee4\u884c\u6a21\u5f0f\u3002</li> <li><code>Scripts/</code>\uff1a\u6309\u529f\u80fd\u5206\u7c7b\u7ec4\u7ec7\u7684 Python \u5de5\u5177\u811a\u672c\u3002</li> <li><code>plt_scripts/</code>\uff1a\u7ed8\u56fe\u811a\u672c</li> <li><code>calculators/</code>\uff1a\u8ba1\u7b97\u5de5\u5177</li> <li><code>format_conversion/</code>\uff1a\u683c\u5f0f\u8f6c\u6362\u5de5\u5177</li> <li><code>workflow/</code>\uff1a\u5de5\u4f5c\u6d41\u81ea\u52a8\u5316</li> <li><code>sample_structures/</code>\uff1a\u7ed3\u6784\u91c7\u6837\u5de5\u5177</li> <li><code>analyzer/</code>\uff1a\u5206\u6790\u5de5\u5177</li> <li><code>utils/</code>\uff1a\u5b9e\u7528\u51fd\u6570\uff0c\u5305\u62ec\u7528\u4e8e Tab \u8865\u5168\u7684 <code>completion.sh</code></li> <li><code>src/</code>\uff1a\u5305\u542b\u4ea4\u4e92\u6a21\u5f0f\u83dc\u5355\u51fd\u6570\u7684 Shell \u811a\u672c\u3002</li> <li><code>f1_format_conversions.sh</code></li> <li><code>f2_sample_structures.sh</code></li> <li><code>f3_workflows.sh</code></li> <li><code>f4_calculators.sh</code></li> <li><code>f5_analyzers.sh</code></li> <li><code>f6_plots.sh</code></li> <li><code>f7_utilities.sh</code></li> <li><code>docs/</code>\uff1a\u6587\u6863\u6587\u4ef6\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_11","title":"\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e","text":"<p>\u5982\u679c\u8981\u6dfb\u52a0\u4e00\u4e2a\u53ef\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u8bbf\u95ee\u7684\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u5728\u5408\u9002\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a</li> </ol> <pre><code># Example: Add a new format conversion script\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u5e76\u9075\u5faa\u6a21\u5757\u5316\u6307\u5357\uff1a\u63a5\u53d7\u53c2\u6570\uff0c\u907f\u514d\u4e0d\u5fc5\u8981\u7684\u786c\u7f16\u7801\u3002</p> </li> <li> <p>\u5728\u5bf9\u5e94\u7684 <code>src/</code> \u6587\u4ef6\u4e2d\u6dfb\u52a0\u5305\u88c5\u51fd\u6570\uff1a</p> </li> </ol> <pre><code># Example: Edit src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre> <p>\u6dfb\u52a0\u4e00\u4e2a\u65b0\u51fd\u6570\uff1a</p> <pre><code>function f106_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input the required parameters:\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -p \" \" converter_params\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py ${converter_params}\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre> <ol> <li>\u66f4\u65b0 <code>gpumdkit.sh</code> \u4e2d\u7684\u83dc\u5355\u663e\u793a\uff1a</li> </ol> <pre><code># Find the menu() function and update it if needed\n# Find the array_choice array and add your new choice number\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\"  # Added \"106\"\n    # ... rest of choices\n)\n</code></pre> <ol> <li>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0 case \u5206\u652f\uff1a</li> </ol> <pre><code># In the main() function, find the appropriate case statement\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n            \"101\") f101_out2xyz ;;\n            # ... existing cases ...\n            \"106\") f106_new_converter ;;  # Add your case\n        esac ;;\n    # ...\nesac\n</code></pre>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_12","title":"\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e","text":"<p>\u5982\u679c\u8981\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c flag \u6216\u5b50\u547d\u4ee4\uff1a</p> <ol> <li>\u5728\u5408\u9002\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a</li> </ol> <pre><code># Example: Add a new analyzer script\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre> <ol> <li>\u5b9e\u73b0\u529f\u80fd\uff0c\u5e76\u660e\u786e\u53c2\u6570\u8981\u6c42\uff1a</li> </ol> <pre><code># Example: Scripts/analyzer/analyze_bonds.py\nimport sys\n\ndef main():\n    if len(sys.argv) != 3:\n        print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n        print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n        sys.exit(1)\n\n    input_file = sys.argv[1]\n    cutoff = float(sys.argv[2])\n\n    # Your implementation here\n\nif __name__ == \"__main__\":\n    main()\n</code></pre> <ol> <li>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0\u547d\u4ee4\u884c flag \u5904\u7406\u903b\u8f91\uff1a</li> </ol> <pre><code># Find the command-line parsing section (after line ~167)\n# Add your new flag in the appropriate location\n\ncase $1 in\n    # ... existing cases ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py \"$2\" \"$3\"\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n            exit 1\n        fi ;;\n    # ... rest of cases ...\nesac\n</code></pre> <ol> <li>\u66f4\u65b0 <code>gpumdkit.sh</code> \u4e2d\u7684\u5e2e\u52a9\u4fe1\u606f\uff1a</li> </ol> <pre><code># Find the help_info_table() function and add your command\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... rest of help table ...\n}\n</code></pre>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#tab","title":"\u66f4\u65b0 Tab \u8865\u5168","text":"<p>\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c flag \u65f6\uff0c\u8bf7\u66f4\u65b0 Tab \u8865\u5168\u811a\u672c\uff1a</p> <pre><code># Edit Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>\u5c06\u65b0\u7684 flag \u52a0\u5165 <code>opts</code> \u53d8\u91cf\uff1a</p> <pre><code># Find the line with local opts=...\nlocal opts=\"-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ...\"\n#                                                      ^^^^^^^^^^^^^^ Add your flag here\n</code></pre> <p>\u5982\u679c\u8fd9\u4e2a flag \u63a5\u53d7\u4e8c\u7ea7\u9009\u9879\uff0c\u4f8b\u5982 <code>-plt</code> \u6216 <code>-calc</code>\uff0c\u4e5f\u9700\u8981\u4e3a\u5b83\u6dfb\u52a0\u5bf9\u5e94\u7684 <code>case</code> \u5206\u652f\uff1a</p> <pre><code>case \"$prev\" in\n    # ... existing cases ...\n    -analyze_bonds)\n        COMPREPLY=($(compgen -f -- \"$cur\"))  # Complete with filenames\n        ;;\n    # ... rest of cases ...\nesac\n</code></pre>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_13","title":"\u4ee3\u7801\u98ce\u683c\u548c\u6700\u4f73\u5b9e\u8df5","text":"<ul> <li>Shell \u811a\u672c\uff1a</li> <li>\u4f7f\u7528 <code>${variable}</code> \u8fdb\u884c\u53d8\u91cf\u5c55\u5f00\u3002</li> <li> <p>\u7f16\u5199\u6e05\u6670\u3001\u6613\u7ef4\u62a4\u7684\u4ee3\u7801\u3002</p> </li> <li> <p>Python \u811a\u672c\uff1a</p> </li> <li>\u7f16\u5199\u6e05\u6670\u3001\u53ef\u7ef4\u62a4\u7684\u4ee3\u7801\u3002</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u540d\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_14","title":"\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539","text":"<p>\u63d0\u4ea4\u8d21\u732e\u524d\uff0c\u8bf7\u8fdb\u884c\u6d4b\u8bd5\uff1a</p> <ol> <li>\u6d4b\u8bd5\u4ea4\u4e92\u6a21\u5f0f\uff08\u5982\u679c\u9002\u7528\uff09\uff1a</li> </ol> <pre><code>gpumdkit.sh\n# Navigate to your new feature and test it thoroughly\n</code></pre> <ol> <li>\u6d4b\u8bd5\u547d\u4ee4\u884c\u6a21\u5f0f\uff08\u5982\u679c\u9002\u7528\uff09\uff1a</li> </ol> <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # Test help message\n</code></pre> <ol> <li>\u6d4b\u8bd5 Tab \u8865\u5168\uff08\u5982\u679c\u4fee\u6539\u4e86 <code>completion.sh</code>\uff09\uff1a</li> </ol> <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # Should show your new flag\n</code></pre> <ol> <li> <p>\u4f7f\u7528\u4e0d\u540c\u8f93\u5165\u6d4b\u8bd5\uff1a</p> </li> <li> <p>\u6d4b\u8bd5\u5e38\u89c4\u8f93\u5165\u3002</p> </li> <li>\u6d4b\u8bd5\u8fb9\u754c\u60c5\u51b5\uff0c\u4f8b\u5982\u7a7a\u6587\u4ef6\u3001\u5927\u6587\u4ef6\u7b49\u3002</li> <li> <p>\u6d4b\u8bd5\u9519\u8bef\u5904\u7406\uff0c\u4f8b\u5982\u7f3a\u5c11\u6587\u4ef6\u3001\u53c2\u6570\u65e0\u6548\u7b49\u3002</p> </li> <li> <p>\u786e\u8ba4\u6ca1\u6709\u56de\u5f52\u95ee\u9898\uff1a\u786e\u4fdd\u5df2\u6709\u529f\u80fd\u4ecd\u7136\u53ef\u4ee5\u6b63\u5e38\u5de5\u4f5c\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_15","title":"\u63d0\u4ea4\u4fe1\u606f","text":"<p>\u63d0\u4ea4\u4fe1\u606f\u5e94\u6e05\u695a\u3001\u5177\u4f53\uff0c\u8bf4\u660e\u4f60\u4fee\u6539\u4e86\u4ec0\u4e48\u3002\u4e0d\u8981\u6c42\u4e25\u683c\u683c\u5f0f\uff0c\u4f46\u9700\u8981\u8ba9\u4ed6\u4eba\u80fd\u591f\u7406\u89e3\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#pull-request","title":"\u63a8\u9001\u5e76\u6253\u5f00 Pull Request","text":"<ol> <li>\u63d0\u4ea4\u4f60\u7684\u4fee\u6539\uff1a</li> </ol> <pre><code>git add .\ngit commit -m \"your descriptive message\"\n</code></pre> <ol> <li>\u8ba9\u4f60\u7684\u5206\u652f\u4e0e upstream <code>main</code> \u5206\u652f\u4fdd\u6301\u540c\u6b65\uff1a</li> </ol> <pre><code>git fetch upstream\ngit rebase upstream/main\n</code></pre> <ol> <li>\u5c06\u5206\u652f\u63a8\u9001\u5230\u4f60\u7684 fork\uff1a</li> </ol> <pre><code>git push origin your-branch-name\n</code></pre> <ol> <li> <p>\u6253\u5f00 Pull Request\uff1a</p> </li> <li> <p>\u8fdb\u5165 GPUMDkit repository\u3002</p> </li> <li>\u70b9\u51fb \"Pull Requests\" -&gt; \"New Pull Request\"\u3002</li> <li>\u5c06 base branch \u8bbe\u7f6e\u4e3a <code>dev</code>\uff0c\u7528\u4e8e\u4ee3\u7801\u5ba1\u67e5\u3002</li> <li>\u5c06 compare branch \u8bbe\u7f6e\u4e3a\u4f60\u7684\u529f\u80fd\u5206\u652f\u3002</li> <li> <p>\u586b\u5199 PR \u63cf\u8ff0\uff0c\u5305\u62ec\uff1a</p> <ul> <li>Title\uff1a\u7b80\u8981\u63cf\u8ff0\u4fee\u6539\u5185\u5bb9\u3002</li> <li>Description\uff1a\u8be6\u7ec6\u8bf4\u660e\u4fee\u6539\u4e86\u4ec0\u4e48\u4ee5\u53ca\u4e3a\u4ec0\u4e48\u4fee\u6539\u3002</li> <li>Testing\uff1a\u8bf4\u660e\u4f60\u5982\u4f55\u6d4b\u8bd5\u8fd9\u4e9b\u4fee\u6539\u3002</li> </ul> </li> <li> <p>\u56de\u5e94\u5ba1\u67e5\u610f\u89c1\uff1a</p> </li> <li> <p>\u63a5\u53d7\u5efa\u8bae\u548c\u5efa\u8bbe\u6027\u610f\u89c1\u3002</p> </li> <li>\u53ca\u65f6\u5b8c\u6210\u8981\u6c42\u7684\u4fee\u6539\u3002</li> <li> <p>\u5c06\u989d\u5916\u63d0\u4ea4\u63a8\u9001\u5230\u4f60\u7684\u5206\u652f\uff0c\u5b83\u4eec\u4f1a\u81ea\u52a8\u663e\u793a\u5728 PR \u4e2d\u3002</p> </li> <li> <p>\u5ba1\u67e5\u901a\u8fc7\u540e\uff1a\u7ef4\u62a4\u8005\u4f1a\u5408\u5e76\u4f60\u7684 PR\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_16","title":"\u6709\u95ee\u9898\u6216\u9700\u8981\u5e2e\u52a9\uff1f","text":"<p>\u5982\u679c\u4f60\u5bf9\u8d21\u732e\u6d41\u7a0b\u6709\u7591\u95ee\uff0c\u6216\u9700\u8981\u5e2e\u52a9\uff1a</p> <ul> <li>\u6253\u5f00\u8ba8\u8bba\uff1a\u4e00\u822c\u95ee\u9898\u53ef\u4ee5\u4f7f\u7528 GitHub Discussions\u3002</li> <li>\u5728 issue \u4e2d\u63d0\u95ee\uff1a\u4e0e\u5177\u4f53\u95ee\u9898\u76f8\u5173\u7684\u5185\u5bb9\u53ef\u4ee5\u5728\u5bf9\u5e94 issue \u4e0b\u8bc4\u8bba\u3002</li> <li>\u8054\u7cfb\u7ef4\u62a4\u8005\uff1a\u8054\u7cfb README \u4e2d\u5217\u51fa\u7684\u6838\u5fc3\u5f00\u53d1\u8005\u3002</li> </ul> <p>\u518d\u6b21\u611f\u8c22\u4f60\u4e3a <code>GPUMDkit</code> \u505a\u8d21\u732e\u3002\u4f60\u7684\u5de5\u4f5c\u4f1a\u5e2e\u52a9\u6574\u4e2a GPUMD \u548c NEP \u793e\u533a\u66f4\u597d\u5730\u4f7f\u7528\u8fd9\u4e2a\u5de5\u5177\u5305\u3002</p>"}]}
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diff --git a/docs/htmls/sitemap.xml b/docs/htmls/sitemap.xml
new file mode 100644
index 0000000..82522c9
--- /dev/null
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@@ -0,0 +1,111 @@
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+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/index.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/en/index.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/en/active_learning_workflow.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/en/analyzer_scripts.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/en/calculator_scripts.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/en/command_reference.html</loc>
+         <lastmod>2026-06-28</lastmod>
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+    <url>
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+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
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+    </url>
+    <url>
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+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
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+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
+         <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html</loc>
+         <lastmod>2026-06-28</lastmod>
+    </url>
+    <url>
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+    </url>
+</urlset>
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diff --git a/docs/htmls/zh/index.html b/docs/htmls/zh/index.html
new file mode 100644
index 0000000..e0b8e55
--- /dev/null
+++ b/docs/htmls/zh/index.html
@@ -0,0 +1,1777 @@
+
+<!doctype html>
+<html lang="en" class="no-js">
+  <head>
+    
+      <meta charset="utf-8">
+      <meta name="viewport" content="width=device-width,initial-scale=1">
+      
+        <meta name="description" content="Tutorials for GPUMDkit.">
+      
+      
+        <meta name="author" content="Zihan YAN">
+      
+      
+        <link rel="canonical" href="https://zhyan0603.github.io/GPUMDkit/zh/index.html">
+      
+      
+        <link rel="prev" href="../en/contributing_to_gpumdkit.html">
+      
+      
+        <link rel="next" href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html">
+      
+      
+        
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+      <a href="../en/format_conversion.html" class="md-nav__link">
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+      <a href="../en/structure_sampling.html" class="md-nav__link">
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+      <a href="../en/workflow_scripts.html" class="md-nav__link">
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+      <a href="../en/calculator_scripts.html" class="md-nav__link">
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+      <a href="../en/analyzer_scripts.html" class="md-nav__link">
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+      <a href="../en/plot_scripts.html" class="md-nav__link">
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+      <a href="../en/custom_commands.html" class="md-nav__link">
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+      <a href="../en/active_learning_workflow.html" class="md-nav__link">
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+    
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+      <a href="../en/polar_material_analysis.html" class="md-nav__link">
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+    
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+  
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+  </span>
+  
+  
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+
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+            
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+      <a href="../en/contributing_to_gpumdkit.html" class="md-nav__link">
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+    
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+    Contributing to GPUMDkit
+  
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+  
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+    
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+          <ul class="md-nav__list" data-md-scrollfix>
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+      
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+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit 教程
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="index.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit 教程
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gpumdkit" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        什么是 GPUMDkit？
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        快速开始
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="快速开始">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        安装
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        依赖
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        使用方法
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        教程列表
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#vasp-outcar" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例：转换 VASP OUTCAR
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例：绘制 NEP 结果
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例：离子电导率
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        模块概览
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        链接
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
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+            
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+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gpumdkit" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        什么是 GPUMDkit？
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        快速开始
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="快速开始">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        安装
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        依赖
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        使用方法
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        教程列表
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#vasp-outcar" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例：转换 VASP OUTCAR
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例：绘制 NEP 结果
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例：离子电导率
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        模块概览
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        链接
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>📚 GPUMDkit 教程</h1>
+  <p style="text-align: justify;">欢迎使用 <strong>GPUMDkit</strong>，这是一个面向 GPUMD 和 NEP 的命令行工具包。</p>
+</div>
+
+<h2 id="gpumdkit">什么是 GPUMDkit？</h2>
+<p>GPUMDkit 简化了计算材料科学中的常见任务：</p>
+<ul>
+<li><strong>格式转换</strong>：在 VASP、LAMMPS、CP2K、ABACUS、CIF 和 extxyz 格式之间转换</li>
+<li><strong>可视化</strong>：用于 NEP 训练、MD 模拟和分析的绘图工具</li>
+<li><strong>计算器</strong>：计算离子电导率、描述符、MSD、NEB 等</li>
+<li><strong>分析工具</strong>：结构验证、过滤、成分分析</li>
+<li><strong>工作流</strong>：DFT 和 MD 模拟的批处理</li>
+<li><strong>结构采样</strong>：使用均匀、随机或 FPS 方法选择结构</li>
+</ul>
+<h2 id="_1">快速开始</h2>
+<h3 id="_2">安装</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="nb">source</span><span class="w"> </span>./install.sh
+</code></pre></div>
+<h3 id="_3">依赖</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>gpumdkit<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>gpumdkit
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>pip<span class="w"> </span>install<span class="w"> </span>neptrain<span class="w"> </span>dpdata<span class="w"> </span>calorine
+</code></pre></div>
+<h3 id="_4">使用方法</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="c1"># 交互模式</span>
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="c1"># 命令行模式</span>
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>gpumdkit.sh<span class="w"> </span>-&lt;选项&gt;<span class="w"> </span><span class="o">[</span>参数...<span class="o">]</span>
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a><span class="c1"># 获取帮助</span>
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>gpumdkit.sh<span class="w"> </span>-h
+</code></pre></div>
+<h2 id="_5">教程列表</h2>
+<table>
+<thead>
+<tr>
+<th>教程</th>
+<th>描述</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><a href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html">快速入门</a></td>
+<td>安装和第一步</td>
+</tr>
+<tr>
+<td><a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html">命令参考</a></td>
+<td>常用 CLI 和菜单入口速查</td>
+</tr>
+<tr>
+<td><a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html">格式转换</a></td>
+<td>在文件格式之间转换</td>
+</tr>
+<tr>
+<td><a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html">计算器脚本</a></td>
+<td>计算材料属性</td>
+</tr>
+<tr>
+<td><a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html">分析工具</a></td>
+<td>结构分析和验证</td>
+</tr>
+<tr>
+<td><a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html">绘图脚本</a></td>
+<td>绘图和可视化</td>
+</tr>
+<tr>
+<td><a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html">工作流脚本</a></td>
+<td>批处理和自动化</td>
+</tr>
+<tr>
+<td><a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html">结构采样</a></td>
+<td>结构选择方法</td>
+</tr>
+<tr>
+<td><a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html">自定义命令</a></td>
+<td>用户自定义 GPUMDkit 快捷命令</td>
+</tr>
+<tr>
+<td><a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html">主动学习工作流</a></td>
+<td>批量主动学习流程说明</td>
+</tr>
+<tr>
+<td><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
+<td>铁电和极化相关工具</td>
+</tr>
+<tr>
+<td><a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html">贡献指南</a></td>
+<td>开发和贡献说明</td>
+</tr>
+</tbody>
+</table>
+<h2 id="vasp-outcar">示例：转换 VASP OUTCAR</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-out2xyz<span class="w"> </span>./vasp_results/
+</code></pre></div>
+<h2 id="nep">示例：绘制 NEP 结果</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>prediction
+</code></pre></div>
+<h2 id="_6">示例：离子电导率</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>trajectory.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>ionic-cond<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+</code></pre></div>
+<h2 id="_7">模块概览</h2>
+<table>
+<thead>
+<tr>
+<th>模块</th>
+<th>菜单</th>
+<th>CLI</th>
+<th>描述</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>格式转换</td>
+<td>1</td>
+<td><code>-out2xyz</code>, <code>-pos2exyz</code></td>
+<td>文件转换</td>
+</tr>
+<tr>
+<td>结构采样</td>
+<td>2</td>
+<td><code>-neptrain</code>、交互菜单</td>
+<td>结构采样</td>
+</tr>
+<tr>
+<td>工作流</td>
+<td>3</td>
+<td>-</td>
+<td>批处理</td>
+</tr>
+<tr>
+<td>计算器</td>
+<td>4</td>
+<td><code>-calc &lt;类型&gt;</code></td>
+<td>属性计算</td>
+</tr>
+<tr>
+<td>分析工具</td>
+<td>5</td>
+<td><code>-range</code>, <code>-min_dist</code></td>
+<td>结构分析</td>
+</tr>
+<tr>
+<td>可视化</td>
+<td>6</td>
+<td><code>-plt &lt;类型&gt;</code></td>
+<td>绘图工具</td>
+</tr>
+<tr>
+<td>实用工具</td>
+<td>7</td>
+<td><code>-time</code>, <code>-clean</code></td>
+<td>实用功能</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_8">链接</h2>
+<ul>
+<li>GitHub: https://github.com/zhyan0603/GPUMDkit</li>
+<li>文档: https://zhyan0603.github.io/GPUMDkit/</li>
+</ul>
+
+
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diff --git "a/docs/htmls/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.html" "b/docs/htmls/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.html"
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+      <a href="../en/structure_sampling.html" class="md-nav__link">
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+      <a href="../en/workflow_scripts.html" class="md-nav__link">
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+      <a href="../en/active_learning_workflow.html" class="md-nav__link">
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+    
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+      <a href="../en/polar_material_analysis.html" class="md-nav__link">
+        
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+    
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+    Polar Material Analysis
+  
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+  </span>
+  
+  
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+      </a>
+    </li>
+  
+
+              
+            
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+      <a href="../en/contributing_to_gpumdkit.html" class="md-nav__link">
+        
+  
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+    
+  
+    Contributing to GPUMDkit
+  
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+  
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+    </li>
+  
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+              
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+    
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+          </label>
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+        
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+    
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+    GPUMDkit 教程
+  
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+  </span>
+  
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+
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+    </li>
+  
+
+              
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
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+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
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+      <a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        概览
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#1-slurm" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        1. SLURM 设置
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        2. 基本设置
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        3. 主要变量
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        4. 检查输入文件
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        5. 文件组织
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#6-md" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        6. 提交 MD 任务
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        7. 检查任务完成
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        8. 分析和过滤结构
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        9. 抽样方法
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#10-scf" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        10. 提交 SCF 计算
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#11-prediction" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        11. Prediction 步骤
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
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+      <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
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+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
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+  
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+
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+    </li>
+  
+
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+      
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+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
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+            
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+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        概览
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#1-slurm" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        1. SLURM 设置
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        2. 基本设置
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        3. 主要变量
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        4. 检查输入文件
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        5. 文件组织
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#6-md" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        6. 提交 MD 任务
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        7. 检查任务完成
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        8. 分析和过滤结构
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        9. 抽样方法
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#10-scf" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        10. 提交 SCF 计算
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#11-prediction" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        11. Prediction 步骤
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🔁 主动学习工作流</h1>
+  <p style="text-align: justify;"><code>workflow_active_learning_dev.sh</code> 用于组织一轮 NEP 主动学习流程：运行 GPUMD 分子动力学、筛选结构、抽样、提交第一性原理计算，并进行 NEP 预测检查。</p>
+</div>
+
+<h3 id="_1">概览</h3>
+<p>该脚本用于处理 NEP 主动学习中常见的一轮流程：运行分子动力学、筛选结构、抽样、提交 SCF 计算，并整理后续 prediction 检查。</p>
+<h2 id="1-slurm">1. SLURM 设置</h2>
+<p>脚本开头包含集群提交参数，例如：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="ch">#!/bin/bash -l</span>
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="c1">#SBATCH -p intel-sc3,intel-sc3-32c</span>
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="c1">#SBATCH -q huge</span>
+<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a><span class="c1">#SBATCH -N 1</span>
+<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a><span class="c1">#SBATCH -J workflow</span>
+<a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a><span class="c1">#SBATCH -o workflow.log</span>
+<a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a><span class="c1">#SBATCH --ntasks-per-node=1</span>
+</code></pre></div>
+<p>这些参数需要根据自己的集群环境修改。如果没有 SLURM 环境，也可以直接后台运行：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>nohup<span class="w"> </span>bash<span class="w"> </span>workflow_active_learning_dev.sh<span class="w"> </span>&gt;<span class="w"> </span>workflow.log<span class="w"> </span><span class="m">2</span>&gt;<span class="p">&amp;</span><span class="m">1</span><span class="w"> </span><span class="p">&amp;</span>
+</code></pre></div>
+<h2 id="2">2. 基本设置</h2>
+<p>脚本会进入提交目录，并加载提交模板：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="nb">cd</span><span class="w"> </span><span class="nv">$SLURM_SUBMIT_DIR</span>
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="nb">source</span><span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/Scripts/workflow/submit_template.sh
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a><span class="nv">python_pynep</span><span class="o">=</span>python
+</code></pre></div>
+<ul>
+<li><code>GPUMDkit_path</code> 是安装脚本写入的 GPUMDkit 路径。</li>
+<li><code>python_pynep</code> 仅用于旧的 PyNEP 兼容分支。</li>
+</ul>
+<h2 id="3">3. 主要变量</h2>
+<p>这个工作流适合已经有初始 <code>nep.txt</code>、<code>nep.in</code>、<code>train.xyz</code> 和 GPUMD/DFT 输入文件，并希望在集群上自动扩展训练集的情况。</p>
+<p>脚本开头通常需要根据体系修改：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="nv">work_dir</span><span class="o">=</span><span class="si">${</span><span class="nv">PWD</span><span class="si">}</span>
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a><span class="nv">prefix_name</span><span class="o">=</span>LiF_iter01
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a><span class="nv">min_dist</span><span class="o">=</span><span class="m">1</span>.4
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="nv">box_limit</span><span class="o">=</span><span class="m">13</span>
+<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a><span class="nv">max_fp_num</span><span class="o">=</span><span class="m">50</span>
+<a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a><span class="nv">sample_method</span><span class="o">=</span>pynep
+<a id="__codelineno-3-7" name="__codelineno-3-7" href="#__codelineno-3-7"></a><span class="nv">pynep_sample_dist</span><span class="o">=</span><span class="m">0</span>.01
+</code></pre></div>
+<ul>
+<li><code>prefix_name</code> 用于命名本轮计算。</li>
+<li><code>min_dist</code> 和 <code>box_limit</code> 用于过滤明显不合理的结构。</li>
+<li><code>max_fp_num</code> 控制最多提交多少个单点计算。</li>
+<li><code>sample_method</code> 可选 <code>uniform</code>、<code>random</code> 或 <code>pynep</code>。</li>
+</ul>
+<h2 id="4">4. 检查输入文件</h2>
+<p>常见输入包括：</p>
+<ul>
+<li><code>nep.txt</code></li>
+<li><code>nep.in</code></li>
+<li><code>train.xyz</code></li>
+<li><code>run.in</code></li>
+<li><code>INCAR</code></li>
+<li><code>POTCAR</code></li>
+<li><code>KPOINTS</code></li>
+<li>初始采样结构文件，例如 <code>sample_struct.xyz</code></li>
+</ul>
+<p>脚本会把公共输入移动到 <code>common/</code>，并创建 <code>00.modev/</code>、<code>01.select/</code> 等工作目录。</p>
+<h2 id="5">5. 文件组织</h2>
+<p>脚本会创建公共输入目录和 MD 目录：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>mkdir<span class="w"> </span><span class="m">00</span>.modev<span class="w"> </span>common
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>mv<span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/<span class="o">{</span>nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR<span class="o">}</span><span class="w"> </span>./common
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>cp<span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/common/<span class="nv">$sample_xyz_file</span><span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/00.modev
+</code></pre></div>
+<ul>
+<li><code>00.modev</code>：用于运行 GPUMD MD 采样。</li>
+<li><code>common</code>：保存 <code>nep.txt</code>、<code>run.in</code>、结构文件和 DFT 输入文件等公共资源。</li>
+</ul>
+<h2 id="6-md">6. 提交 MD 任务</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>submit_gpumd_array<span class="w"> </span>modev<span class="w"> </span><span class="si">${</span><span class="nv">sample_struct_num</span><span class="si">}</span>
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>sbatch<span class="w"> </span>submit.slurm
+</code></pre></div>
+<p>脚本会通过提交模板创建数组任务。不同集群上的提交命令和模板可能需要自己修改。</p>
+<h2 id="7">7. 检查任务完成</h2>
+<p>脚本会持续检查 <code>00.modev/</code> 下各个 <code>sample_*/log</code> 文件，确认是否出现：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>Finished<span class="w"> </span>running<span class="w"> </span>GPUMD.
+</code></pre></div>
+<p>如果发现 <code>Error</code>，脚本会停止。</p>
+<h2 id="8">8. 分析和过滤结构</h2>
+<p>MD 完成后，脚本会进入 <code>01.select</code>，对 <code>dump.xyz</code> 中的结构进行筛选。常见检查包括：</p>
+<ul>
+<li>最小原子距离；</li>
+<li>模拟盒子边长；</li>
+<li>结构数量是否超过 <code>max_fp_num</code>。</li>
+</ul>
+<p>这些步骤会调用 analyzer 和 sample_structures 中的脚本。</p>
+<h2 id="9">9. 抽样方法</h2>
+<p>脚本根据 <code>sample_method</code> 选择抽样方式：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="k">case</span><span class="w"> </span><span class="nv">$sample_method</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="w">    </span><span class="s2">&quot;uniform&quot;</span><span class="o">)</span>
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="w">    </span><span class="s2">&quot;random&quot;</span><span class="o">)</span>
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="w">    </span><span class="s2">&quot;pynep&quot;</span><span class="o">)</span>
+</code></pre></div>
+<ul>
+<li><code>uniform</code>：均匀抽帧；</li>
+<li><code>random</code>：随机抽帧；</li>
+<li><code>pynep</code>：旧的 PyNEP 兼容分支。</li>
+</ul>
+<h2 id="10-scf">10. 提交 SCF 计算</h2>
+<p>抽样完成后，脚本会提交 VASP 单点计算：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>submit_vasp_array<span class="w"> </span>scf<span class="w"> </span><span class="si">${</span><span class="nv">selected_struct_num</span><span class="si">}</span><span class="w"> </span><span class="si">${</span><span class="nv">prefix_name</span><span class="si">}</span>
+</code></pre></div>
+<p>这里的 <code>prefix_name</code> 会用于计算目录命名，也方便后续追踪结构来源。</p>
+<h2 id="11-prediction">11. Prediction 步骤</h2>
+<p>最后脚本会提交 NEP prediction，用于检查当前模型在新增结构上的误差。</p>
+<hr />
+<p>这个脚本和计算环境强相关，正式使用前建议先用小体系或少量结构测试一轮，并检查提交模板、路径和输入文件是否符合自己的集群环境。</p>
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diff --git "a/docs/htmls/zh/\345\210\206\346\236\220\345\267\245\345\205\267.html" "b/docs/htmls/zh/\345\210\206\346\236\220\345\267\245\345\205\267.html"
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+  <span class="md-ellipsis">
+    
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+    命令参考
+  
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+  
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+
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+    
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+  <span class="md-ellipsis">
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+  
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+  <span class="md-ellipsis">
+    
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+  
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+  
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+      </a>
+      
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+  
+  
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+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        功能概览
+      
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+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        组分分析
+      
+    </span>
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+      
+        <li class="md-nav__item">
+  <a href="#virial" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        能量/力/virial 范围
+      
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+  
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+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
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+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        结构过滤
+      
+    </span>
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+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        电荷平衡检查
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
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+        示例命令
+      
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
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+  
+
+              
+            
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+  
+  
+  
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+    自定义命令
+  
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+  
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
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+  
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
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+  </span>
+  
+  
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+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
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+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        功能概览
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        组分分析
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#virial" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        能量/力/virial 范围
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        最小距离检查
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        结构过滤
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        电荷平衡检查
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
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+        示例命令
+      
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+</li>
+      
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+                </div>
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+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🔍 分析工具</h1>
+  <p style="text-align: justify;">分析工具用于对 extxyz 数据集进行结构统计、距离检查、过滤和组分分析。</p>
+</div>
+
+<p><strong>脚本位置：</strong> <code>Scripts/analyzer/</code></p>
+<h2 id="_1">功能概览</h2>
+<table>
+<thead>
+<tr>
+<th>任务</th>
+<th>命令</th>
+<th>用途</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>组分分析</td>
+<td><code>gpumdkit.sh -analyze_comp train.xyz</code></td>
+<td>按化学组分统计结构</td>
+</tr>
+<tr>
+<td>元素列表</td>
+<td><code>gpumdkit.sh -chem_species train.xyz</code></td>
+<td>查看文件中有哪些元素</td>
+</tr>
+<tr>
+<td>性质范围</td>
+<td><code>gpumdkit.sh -range train.xyz force</code></td>
+<td>检查能量/力/virial 范围</td>
+</tr>
+<tr>
+<td>最小距离</td>
+<td><code>gpumdkit.sh -min_dist dump.xyz</code></td>
+<td>快速检查，不考虑 PBC</td>
+</tr>
+<tr>
+<td>PBC 最小距离</td>
+<td><code>gpumdkit.sh -min_dist_pbc dump.xyz</code></td>
+<td>考虑 PBC 的距离检查</td>
+</tr>
+<tr>
+<td>电荷平衡</td>
+<td><code>gpumdkit.sh -cbc train.xyz</code></td>
+<td>检查常见氧化态是否平衡</td>
+</tr>
+<tr>
+<td>距离过滤</td>
+<td><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code></td>
+<td>删除短距离结构</td>
+</tr>
+<tr>
+<td>盒子过滤</td>
+<td><code>gpumdkit.sh -filter_box dump.xyz 13</code></td>
+<td>删除盒子边长过大的结构</td>
+</tr>
+<tr>
+<td>数值过滤</td>
+<td><code>gpumdkit.sh -filter_value train.xyz force 20</code></td>
+<td>按性质阈值过滤</td>
+</tr>
+<tr>
+<td>元素对距离</td>
+<td><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code></td>
+<td>按元素对距离范围提取</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_2">组分分析</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
+</code></pre></div>
+<p>示例输出：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>Index    Compositions           N atoms      Count
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>---------------------------------------------------
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>1        Li56O96Zr16La24        192          51
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>---------------------------------------------------
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>Enter index to export (e.g., &#39;1,2&#39;, &#39;2-3&#39;, &#39;all&#39;), or press Enter to skip:
+</code></pre></div>
+<p>如果一个 <code>train.xyz</code> 中混合了多个体系或不同超胞，这个功能很有用。</p>
+<h2 id="virial">能量/力/virial 范围</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>energy
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>virial
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist
+</code></pre></div>
+<p>使用 <code>hist</code> 可以画出所选性质的直方图。</p>
+<div align="center">
+  <img src="../../Gallery/range_force.png" alt="Force range histogram" width="52%" />
+</div>
+
+<h2 id="_3">最小距离检查</h2>
+<p>快速版本：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist<span class="w"> </span>dump.xyz
+</code></pre></div>
+<p>考虑 PBC 的版本：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
+</code></pre></div>
+<p>PBC 版本会考虑周期性边界条件。</p>
+<h2 id="_4">结构过滤</h2>
+<p>按最小距离过滤：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
+</code></pre></div>
+<p>按盒子大小过滤：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
+</code></pre></div>
+<p>按性质值过滤：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span><span class="m">20</span>
+</code></pre></div>
+<p>按元素对距离范围提取：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-filter_range<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>.8<span class="w"> </span><span class="m">2</span>.0
+</code></pre></div>
+<h2 id="_5">电荷平衡检查</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-cbc<span class="w"> </span>train.xyz
+</code></pre></div>
+<p>可能输出：</p>
+<ul>
+<li><code>balanced.xyz</code></li>
+<li><code>unbalanced.xyz</code></li>
+<li><code>indices.txt</code></li>
+</ul>
+<p>这个功能适合常见氧化态有意义的离子材料。</p>
+<h2 id="_6">示例命令</h2>
+<p>性质和距离检查：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>energy<span class="w"> </span>hist
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>train.xyz
+</code></pre></div>
+<p>过滤示例：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>filtered_dist.xyz<span class="w"> </span><span class="m">13</span>
+</code></pre></div>
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diff --git "a/docs/htmls/zh/\345\221\275\344\273\244\345\217\202\350\200\203.html" "b/docs/htmls/zh/\345\221\275\344\273\244\345\217\202\350\200\203.html"
new file mode 100644
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+++ "b/docs/htmls/zh/\345\221\275\344\273\244\345\217\202\350\200\203.html"
@@ -0,0 +1,1856 @@
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+      <a href="../en/index.html" class="md-nav__link">
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+    <li class="md-nav__item">
+      <a href="../en/quick_start.html" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
+  
+    Quick Start
+  
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+  </span>
+  
+  
+
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+    </li>
+  
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+    <li class="md-nav__item">
+      <a href="../en/command_reference.html" class="md-nav__link">
+        
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+    
+  
+    Command Reference
+  
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+  
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+    </li>
+  
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+  
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+    <li class="md-nav__item">
+      <a href="../en/format_conversion.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Format Conversion
+  
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+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
+              
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/structure_sampling.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Structure Sampling
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/workflow_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Workflow Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/calculator_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Calculator Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/analyzer_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Analyzer Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/plot_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Plot Scripts
+  
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+  </span>
+  
+  
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+    </li>
+  
+
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../en/custom_commands.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Custom Commands
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/active_learning_workflow.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Active Learning Workflow
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/polar_material_analysis.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Polar Material Analysis
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/contributing_to_gpumdkit.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
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+    
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+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        
+          
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    简体中文
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    简体中文
+  
+
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+          <ul class="md-nav__list" data-md-scrollfix>
+            
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+  
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+  
+  
+    <li class="md-nav__item">
+      <a href="index.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit 教程
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gpumdkitsh-h" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        gpumdkit.sh -h 输出
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        主命令
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        格式转换
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        计算器
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        分析工具
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        可视化
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        工具
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gpumdkitsh-h" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        gpumdkit.sh -h 输出
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        主命令
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        格式转换
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        计算器
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        分析工具
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        可视化
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        工具
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>📋 命令参考</h1>
+  <p style="text-align: justify;">本页列出 GPUMDkit 稳定的命令行快捷入口。对于参数较多、需要选择的任务，也可以使用交互模式。</p>
+</div>
+
+<p>源表维护在 <code>docs/command_reference.tsv</code>。</p>
+<h2 id="gpumdkitsh-h"><code>gpumdkit.sh -h</code> 输出</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>|                                          MAIN FUNCTIONS                                               |
+<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a>| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |
+<a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a>| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |
+<a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a>| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
+<a id="__codelineno-0-9" name="__codelineno-0-9" href="#__codelineno-0-9"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-10" name="__codelineno-0-10" href="#__codelineno-0-10"></a>|                                         FORMAT CONVERSION                                             |
+<a id="__codelineno-0-11" name="__codelineno-0-11" href="#__codelineno-0-11"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-12" name="__codelineno-0-12" href="#__codelineno-0-12"></a>| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |
+<a id="__codelineno-0-13" name="__codelineno-0-13" href="#__codelineno-0-13"></a>| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |
+<a id="__codelineno-0-14" name="__codelineno-0-14" href="#__codelineno-0-14"></a>| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |
+<a id="__codelineno-0-15" name="__codelineno-0-15" href="#__codelineno-0-15"></a>| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |
+<a id="__codelineno-0-16" name="__codelineno-0-16" href="#__codelineno-0-16"></a>| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |
+<a id="__codelineno-0-17" name="__codelineno-0-17" href="#__codelineno-0-17"></a>| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |
+<a id="__codelineno-0-18" name="__codelineno-0-18" href="#__codelineno-0-18"></a>| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
+<a id="__codelineno-0-19" name="__codelineno-0-19" href="#__codelineno-0-19"></a>| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
+<a id="__codelineno-0-20" name="__codelineno-0-20" href="#__codelineno-0-20"></a>| -frame_range  Extract frames by range         |                                                       |
+<a id="__codelineno-0-21" name="__codelineno-0-21" href="#__codelineno-0-21"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-22" name="__codelineno-0-22" href="#__codelineno-0-22"></a>|                                            ANALYSIS                                                   |
+<a id="__codelineno-0-23" name="__codelineno-0-23" href="#__codelineno-0-23"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-24" name="__codelineno-0-24" href="#__codelineno-0-24"></a>| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
+<a id="__codelineno-0-25" name="__codelineno-0-25" href="#__codelineno-0-25"></a>| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
+<a id="__codelineno-0-26" name="__codelineno-0-26" href="#__codelineno-0-26"></a>| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
+<a id="__codelineno-0-27" name="__codelineno-0-27" href="#__codelineno-0-27"></a>| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
+<a id="__codelineno-0-28" name="__codelineno-0-28" href="#__codelineno-0-28"></a>| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
+<a id="__codelineno-0-29" name="__codelineno-0-29" href="#__codelineno-0-29"></a>| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
+<a id="__codelineno-0-30" name="__codelineno-0-30" href="#__codelineno-0-30"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-0-31" name="__codelineno-0-31" href="#__codelineno-0-31"></a>| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |
+<a id="__codelineno-0-32" name="__codelineno-0-32" href="#__codelineno-0-32"></a>+-------------------------------------------------------------------------------------------------------+
+</code></pre></div>
+<h2 id="_1">主命令</h2>
+<table>
+<thead>
+<tr>
+<th>命令</th>
+<th>语法</th>
+<th>说明</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-h</code></td>
+<td><code>gpumdkit.sh -h</code></td>
+<td>显示通用帮助</td>
+</tr>
+<tr>
+<td><code>-update</code></td>
+<td><code>gpumdkit.sh -update</code></td>
+<td>更新 GPUMDkit</td>
+</tr>
+<tr>
+<td><code>-clean</code></td>
+<td><code>gpumdkit.sh -clean</code></td>
+<td>清理当前目录中的冗余文件</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_2">格式转换</h2>
+<table>
+<thead>
+<tr>
+<th>命令</th>
+<th>语法</th>
+<th>说明</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-out2xyz</code></td>
+<td><code>gpumdkit.sh -out2xyz &lt;dir&gt;</code></td>
+<td>OUTCAR 转 extxyz，shell 版本</td>
+</tr>
+<tr>
+<td><code>-out2exyz</code></td>
+<td><code>gpumdkit.sh -out2exyz &lt;dir&gt;</code></td>
+<td>OUTCAR 转 extxyz，Python 版本</td>
+</tr>
+<tr>
+<td><code>-cp2k2xyz</code></td>
+<td><code>gpumdkit.sh -cp2k2xyz</code></td>
+<td>CP2K 输出转 xyz/extxyz</td>
+</tr>
+<tr>
+<td><code>-xdat2exyz</code></td>
+<td><code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code></td>
+<td>XDATCAR 转 extxyz</td>
+</tr>
+<tr>
+<td><code>-cif2pos</code></td>
+<td><code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code></td>
+<td>CIF 转 POSCAR/VASP</td>
+</tr>
+<tr>
+<td><code>-cif2exyz</code></td>
+<td><code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code></td>
+<td>CIF 转 extxyz</td>
+</tr>
+<tr>
+<td><code>-pos2exyz</code></td>
+<td><code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code></td>
+<td>POSCAR 转 extxyz</td>
+</tr>
+<tr>
+<td><code>-exyz2pos</code></td>
+<td><code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code></td>
+<td>extxyz 多帧转 POSCAR 文件</td>
+</tr>
+<tr>
+<td><code>-pos2lmp</code></td>
+<td><code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code></td>
+<td>POSCAR 转 LAMMPS data</td>
+</tr>
+<tr>
+<td><code>-lmp2exyz</code></td>
+<td><code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code></td>
+<td>LAMMPS dump 转 extxyz</td>
+</tr>
+<tr>
+<td><code>-traj2exyz</code></td>
+<td><code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code></td>
+<td>ASE trajectory 转 extxyz</td>
+</tr>
+<tr>
+<td><code>-replicate</code></td>
+<td><code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code></td>
+<td>按晶胞倍数扩胞</td>
+</tr>
+<tr>
+<td><code>-replicate</code></td>
+<td><code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code></td>
+<td>按目标原子数扩胞</td>
+</tr>
+<tr>
+<td><code>-addgroup</code></td>
+<td><code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code></td>
+<td>添加 GPUMD group 标签</td>
+</tr>
+<tr>
+<td><code>-addweight</code></td>
+<td><code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code></td>
+<td>添加结构权重</td>
+</tr>
+<tr>
+<td><code>-get_frame</code></td>
+<td><code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code></td>
+<td>提取单帧</td>
+</tr>
+<tr>
+<td><code>-clean_xyz</code></td>
+<td><code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code></td>
+<td>清理 extxyz 冗余属性</td>
+</tr>
+<tr>
+<td><code>-frame_range</code></td>
+<td><code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code></td>
+<td>按比例范围提取帧</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_3">计算器</h2>
+<table>
+<thead>
+<tr>
+<th>命令</th>
+<th>语法</th>
+<th>说明</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-calc ionic-cond</code></td>
+<td><code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code></td>
+<td>离子电导率</td>
+</tr>
+<tr>
+<td><code>-calc nep</code></td>
+<td><code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code></td>
+<td>NEP 性质预测</td>
+</tr>
+<tr>
+<td><code>-calc des</code></td>
+<td><code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code></td>
+<td>NEP 描述符</td>
+</tr>
+<tr>
+<td><code>-calc doas</code></td>
+<td><code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code></td>
+<td>原子态密度</td>
+</tr>
+<tr>
+<td><code>-calc neb</code></td>
+<td><code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code></td>
+<td>基于 NEP 的 NEB</td>
+</tr>
+<tr>
+<td><code>-calc minimize</code></td>
+<td><code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code></td>
+<td>结构优化</td>
+</tr>
+<tr>
+<td><code>-calc msd</code></td>
+<td><code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code></td>
+<td>从轨迹计算 MSD</td>
+</tr>
+<tr>
+<td><code>-calc nlist</code></td>
+<td><code>gpumdkit.sh -calc nlist [args...]</code></td>
+<td>邻居列表</td>
+</tr>
+<tr>
+<td><code>-calc disp</code></td>
+<td><code>gpumdkit.sh -calc disp [args...]</code></td>
+<td>位移</td>
+</tr>
+<tr>
+<td><code>-calc avg-struct</code></td>
+<td><code>gpumdkit.sh -calc avg-struct [args...]</code></td>
+<td>平均结构</td>
+</tr>
+<tr>
+<td><code>-calc oct-tilt</code></td>
+<td><code>gpumdkit.sh -calc oct-tilt [args...]</code></td>
+<td>八面体倾斜</td>
+</tr>
+<tr>
+<td><code>-calc pol-abo3</code></td>
+<td><code>gpumdkit.sh -calc pol-abo3 [args...]</code></td>
+<td>ABO3 局域极化</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_4">分析工具</h2>
+<table>
+<thead>
+<tr>
+<th>命令</th>
+<th>语法</th>
+<th>说明</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-range</code></td>
+<td><code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\|force\|virial&gt; [hist]</code></td>
+<td>性质范围分析</td>
+</tr>
+<tr>
+<td><code>-analyze_comp</code></td>
+<td><code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code></td>
+<td>成分分析</td>
+</tr>
+<tr>
+<td><code>-chem_species</code></td>
+<td><code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code></td>
+<td>元素列表</td>
+</tr>
+<tr>
+<td><code>-cbc</code></td>
+<td><code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code></td>
+<td>电荷平衡检查</td>
+</tr>
+<tr>
+<td><code>-min_dist</code></td>
+<td><code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code></td>
+<td>无 PBC 最小距离</td>
+</tr>
+<tr>
+<td><code>-min_dist_pbc</code></td>
+<td><code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code></td>
+<td>带 PBC 最小距离</td>
+</tr>
+<tr>
+<td><code>-filter_dist</code></td>
+<td><code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code></td>
+<td>距离过滤</td>
+</tr>
+<tr>
+<td><code>-filter_dist_pbc</code></td>
+<td><code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code></td>
+<td>带 PBC 距离过滤</td>
+</tr>
+<tr>
+<td><code>-filter_box</code></td>
+<td><code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code></td>
+<td>盒子边长过滤</td>
+</tr>
+<tr>
+<td><code>-filter_value</code></td>
+<td><code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code></td>
+<td>性质阈值过滤</td>
+</tr>
+<tr>
+<td><code>-filter_range</code></td>
+<td><code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code></td>
+<td>元素对距离范围过滤</td>
+</tr>
+<tr>
+<td><code>-pda</code></td>
+<td><code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code></td>
+<td>概率密度分析</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_5">可视化</h2>
+<p>使用：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span><span class="o">[</span>options<span class="o">]</span>
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>-h
+</code></pre></div>
+<p>常用类型包括 <code>train</code>、<code>prediction</code>、<code>thermo</code>、<code>msd</code>、<code>sdc</code>、<code>rdf</code>、<code>emd</code>、<code>nemd</code>、<code>hnemd</code>、<code>pdos</code> 和 <code>plane-grid</code>。</p>
+<h2 id="_6">工具</h2>
+<table>
+<thead>
+<tr>
+<th>命令</th>
+<th>语法</th>
+<th>说明</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>-time</code></td>
+<td><code>gpumdkit.sh -time &lt;gpumd\|nep&gt;</code></td>
+<td>监控 GPUMD 或 NEP 进度</td>
+</tr>
+<tr>
+<td><code>-nep_modifier</code></td>
+<td><code>gpumdkit.sh -nep_modifier</code></td>
+<td>交互式修改 NEP 模型</td>
+</tr>
+<tr>
+<td><code>-pynep</code></td>
+<td><code>gpumdkit.sh -pynep</code></td>
+<td>已弃用的 PyNEP FPS 采样</td>
+</tr>
+</tbody>
+</table>
+
+
+
+
+
+
+
+
+
+
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+      <a href="../en/quick_start.html" class="md-nav__link">
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+      <a href="../en/command_reference.html" class="md-nav__link">
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+      <a href="../en/format_conversion.html" class="md-nav__link">
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+      <a href="../en/structure_sampling.html" class="md-nav__link">
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+      <a href="../en/workflow_scripts.html" class="md-nav__link">
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+    Workflow Scripts
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+      <a href="../en/calculator_scripts.html" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
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+    Calculator Scripts
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+      <a href="../en/analyzer_scripts.html" class="md-nav__link">
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+      <a href="../en/plot_scripts.html" class="md-nav__link">
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+      <a href="../en/custom_commands.html" class="md-nav__link">
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+    
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+    Custom Commands
+  
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+      <a href="../en/active_learning_workflow.html" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
+  
+    Active Learning Workflow
+  
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+  </span>
+  
+  
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+    </li>
+  
+
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+            
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+      <a href="../en/polar_material_analysis.html" class="md-nav__link">
+        
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+    
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+    Polar Material Analysis
+  
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+  </span>
+  
+  
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+    </li>
+  
+
+              
+            
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+      <a href="../en/contributing_to_gpumdkit.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
+
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+  </span>
+  
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+
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+    </li>
+  
+
+              
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+        </nav>
+      
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+        
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    简体中文
+  
+
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+  
+  
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+          </label>
+        
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+  
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+    <li class="md-nav__item">
+      <a href="index.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit 教程
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
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+      <a href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互入口
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#scf" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        SCF 批处理预处理
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="SCF 批处理预处理">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#vasp" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        VASP
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#cp2k" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        CP2K
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#md" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MD 采样预处理
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="MD 采样预处理">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gpumd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        GPUMD
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#lammps" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        LAMMPS
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        主动学习式流程
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        使用建议
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互入口
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#scf" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        SCF 批处理预处理
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="SCF 批处理预处理">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#vasp" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        VASP
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#cp2k" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        CP2K
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#md" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MD 采样预处理
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="MD 采样预处理">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gpumd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        GPUMD
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#lammps" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        LAMMPS
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        主动学习式流程
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        使用建议
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🔧 工作流脚本</h1>
+  <p style="text-align: justify;">工作流脚本用于自动化重复性的 DFT、MD 和 NEP 数据准备步骤。</p>
+</div>
+
+<p><strong>脚本位置：</strong> <code>Scripts/workflow/</code></p>
+<h2 id="_1">交互入口</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh
+</code></pre></div>
+<p>选择：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>3) Workflow
+</code></pre></div>
+<p>常见菜单：</p>
+<table>
+<thead>
+<tr>
+<th>菜单</th>
+<th>工作流</th>
+<th>用途</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>301</td>
+<td>SCF batch pretreatment</td>
+<td>准备 DFT 单点计算</td>
+</tr>
+<tr>
+<td>302</td>
+<td>MD sample batch pretreatment (GPUMD)</td>
+<td>准备 GPUMD 采样计算</td>
+</tr>
+<tr>
+<td>303</td>
+<td>MD sample batch pretreatment (LAMMPS)</td>
+<td>准备 LAMMPS 采样计算</td>
+</tr>
+</tbody>
+</table>
+<h2 id="scf">SCF 批处理预处理</h2>
+<p>适用于已有多个结构，需要准备第一性原理单点计算的情况。</p>
+<h3 id="vasp">VASP</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="c1"># 选择 3 -&gt; 301 -&gt; VASP</span>
+</code></pre></div>
+<p>运行前，把结构文件放在当前目录。脚本按以下顺序检测：</p>
+<ol>
+<li>如果存在一个或多个 <code>.vasp</code> 文件，优先处理 <code>.vasp</code>；</li>
+<li>如果 <code>.vasp</code> 和 <code>.xyz</code> 同时存在，会打印提示，并只处理 <code>.vasp</code>；</li>
+<li>如果没有 <code>.vasp</code> 且只有一个 <code>.xyz</code>，会把这个 extxyz 转为 POSCAR 文件；</li>
+<li>如果没有 <code>.vasp</code> 且存在多个 <code>.xyz</code>，会让用户选择一个。</li>
+</ol>
+<p>运行前的典型目录：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>current directory/
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>├── POSCAR_1.vasp
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>├── POSCAR_2.vasp
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>└── POSCAR_3.vasp
+</code></pre></div>
+<p>或：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>current directory/
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>└── sampled.xyz
+</code></pre></div>
+<p>运行后脚本会创建：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>current directory/
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>├── struct_fp/
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>│   ├── POSCAR_1.vasp
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>│   ├── POSCAR_2.vasp
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>│   └── ...
+<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>├── fp/
+<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>├── &lt;prefix&gt;_1/
+<a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a>├── &lt;prefix&gt;_2/
+<a id="__codelineno-5-9" name="__codelineno-5-9" href="#__codelineno-5-9"></a>└── presub.sh
+</code></pre></div>
+<p><code>fp/</code> 是脚本自动创建的。脚本结束后，需要用户把 <code>INCAR</code>、<code>POTCAR</code>、<code>KPOINTS</code> 放到 <code>fp/</code> 中，计算目录会链接这里的文件。</p>
+<p>运行过程中输入的 <code>prefix</code> 会作为计算文件夹名前缀。后续使用 <code>out2xyz</code> 提取结果时，文件夹名会作为 <code>config_type</code> 写入 extxyz，便于之后检查结构来源。</p>
+<h3 id="cp2k">CP2K</h3>
+<p>CP2K 可以从交互菜单进入，也可以直接命令行调用：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="c1"># 选择 3 -&gt; 301 -&gt; CP2K</span>
+</code></pre></div>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>python<span class="w"> </span>Scripts/workflow/scf_batch_pretreatment_cp2k.py<span class="w"> </span>train.xyz<span class="w"> </span>template.inp<span class="w"> </span>calc
+</code></pre></div>
+<p>交互模式会要求输入：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;
+</code></pre></div>
+<p>示例：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>dump.xyz template.inp H2O
+</code></pre></div>
+<p>CP2K 模板应设置为从 <code>pos.xyz</code> 读取坐标。参考模板在：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>Scripts/workflow/cp2k_template.inp
+</code></pre></div>
+<p>脚本会为每个结构生成 <code>&lt;prefix&gt;_&lt;index&gt;/</code> 目录，并写入 <code>input.inp</code> 和 <code>pos.xyz</code>。</p>
+<h2 id="md">MD 采样预处理</h2>
+<h3 id="gpumd">GPUMD</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="c1"># 选择 3 -&gt; 302</span>
+</code></pre></div>
+<p>运行前，把 <code>.vasp</code> 文件或一个 extxyz 文件放在当前目录。检测顺序与 VASP SCF 预处理一致：优先处理 <code>.vasp</code>；如果没有 <code>.vasp</code> 且存在多个 <code>.xyz</code>，会让用户选择一个。</p>
+<p>运行前典型目录：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>current directory/
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>├── POSCAR_1.vasp
+<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a>└── POSCAR_2.vasp
+</code></pre></div>
+<p>或：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>current directory/
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>└── dump.xyz
+</code></pre></div>
+<p>运行后脚本会创建：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>current directory/
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>├── struct_md/
+<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a>│   ├── model_1.xyz
+<a id="__codelineno-14-4" name="__codelineno-14-4" href="#__codelineno-14-4"></a>│   ├── model_2.xyz
+<a id="__codelineno-14-5" name="__codelineno-14-5" href="#__codelineno-14-5"></a>│   └── ...
+<a id="__codelineno-14-6" name="__codelineno-14-6" href="#__codelineno-14-6"></a>├── md/
+<a id="__codelineno-14-7" name="__codelineno-14-7" href="#__codelineno-14-7"></a>├── sample_1/
+<a id="__codelineno-14-8" name="__codelineno-14-8" href="#__codelineno-14-8"></a>├── sample_2/
+<a id="__codelineno-14-9" name="__codelineno-14-9" href="#__codelineno-14-9"></a>└── presub.sh
+</code></pre></div>
+<p><code>md/</code> 是脚本自动创建的。脚本结束后，需要把 <code>nep.txt</code> 和 <code>run_*.in</code> 放入 <code>md/</code>。例如 <code>run_1.in</code> 会链接到 <code>sample_1/run.in</code>，<code>run_2.in</code> 会链接到 <code>sample_2/run.in</code>。</p>
+<h3 id="lammps">LAMMPS</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="c1"># 选择 3 -&gt; 303</span>
+</code></pre></div>
+<p>运行前，把 <code>.vasp</code> 文件或一个 extxyz 文件放在当前目录；两种格式同时存在时优先处理 <code>.vasp</code>。</p>
+<p>运行后脚本会创建：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>current directory/
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>├── struct_md/
+<a id="__codelineno-16-3" name="__codelineno-16-3" href="#__codelineno-16-3"></a>│   ├── lammps_1.data
+<a id="__codelineno-16-4" name="__codelineno-16-4" href="#__codelineno-16-4"></a>│   ├── lammps_2.data
+<a id="__codelineno-16-5" name="__codelineno-16-5" href="#__codelineno-16-5"></a>│   └── ...
+<a id="__codelineno-16-6" name="__codelineno-16-6" href="#__codelineno-16-6"></a>├── md/
+<a id="__codelineno-16-7" name="__codelineno-16-7" href="#__codelineno-16-7"></a>├── sample_1/
+<a id="__codelineno-16-8" name="__codelineno-16-8" href="#__codelineno-16-8"></a>├── sample_2/
+<a id="__codelineno-16-9" name="__codelineno-16-9" href="#__codelineno-16-9"></a>└── presub.sh
+</code></pre></div>
+<p>脚本结束后，需要把 <code>lmprun.in</code> 和 <code>nep.txt</code> 放到 <code>md/</code> 中。</p>
+<h2 id="_2">主动学习式流程</h2>
+<p>常见 NEP 数据迭代流程：</p>
+<ol>
+<li>使用当前 <code>nep.txt</code> 运行 MD；</li>
+<li>收集 <code>dump.xyz</code> 或 <code>active.xyz</code>；</li>
+<li>删除明显不合理结构；</li>
+<li>选择多样性高或偏差大的结构；</li>
+<li>运行 DFT 单点；</li>
+<li>将 DFT 结果转换为 extxyz；</li>
+<li>追加到 <code>train.xyz</code>；</li>
+<li>重新训练 NEP。</li>
+</ol>
+<p>更完整的开发版主动学习脚本说明见 <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html">主动学习</a>。</p>
+<h2 id="_3">使用建议</h2>
+<ul>
+<li>工作流脚本和集群环境强相关，正式批量提交前先用少量结构测试。</li>
+<li>模板文件如 <code>INCAR</code>、<code>KPOINTS</code>、<code>POTCAR</code>、<code>run.in</code> 应仔细检查。</li>
+<li>批量 DFT 前先用分析和采样脚本清理候选结构。</li>
+</ul>
+
+
+
+
+
+
+
+
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+
+
+                
+              </article>
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diff --git "a/docs/htmls/zh/\345\277\253\351\200\237\345\205\245\351\227\250.html" "b/docs/htmls/zh/\345\277\253\351\200\237\345\205\245\351\227\250.html"
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+      <a href="../en/format_conversion.html" class="md-nav__link">
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+      <a href="../en/structure_sampling.html" class="md-nav__link">
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+      <a href="../en/workflow_scripts.html" class="md-nav__link">
+        
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+    
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+    Workflow Scripts
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+      <a href="../en/calculator_scripts.html" class="md-nav__link">
+        
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+    
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+      <a href="../en/analyzer_scripts.html" class="md-nav__link">
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+      <a href="../en/plot_scripts.html" class="md-nav__link">
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+    
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+      <a href="../en/custom_commands.html" class="md-nav__link">
+        
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+    
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+  
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+      <a href="../en/active_learning_workflow.html" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
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+  
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+  </span>
+  
+  
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+    </li>
+  
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+      <a href="../en/polar_material_analysis.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Polar Material Analysis
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+      <a href="../en/contributing_to_gpumdkit.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
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+  </span>
+  
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+
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+    </li>
+  
+
+              
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+        </nav>
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+            
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+    
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+      <a href="index.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit 教程
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+      
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+      
+      
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+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#1-python" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        1. 准备 Python 环境
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#2-gpumdkit" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        2. 安装 GPUMDkit
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        3. 使用方式
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="3. 使用方式">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互模式
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        命令行模式
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        4. 实际例子
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="4. 实际例子">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#poscar-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        POSCAR 转 extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gpumd-group" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        添加 GPUMD group 标签
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#nep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        绘制 NEP 训练结果
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#nep_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        绘制 NEP 测试集结果
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        绘制热力学量
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#msd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        绘制 MSD 和自扩散系数
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        5. 获取帮助
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#1-python" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        1. 准备 Python 环境
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#2-gpumdkit" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        2. 安装 GPUMDkit
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        3. 使用方式
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="3. 使用方式">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互模式
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        命令行模式
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        4. 实际例子
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="4. 实际例子">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#poscar-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        POSCAR 转 extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gpumd-group" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        添加 GPUMD group 标签
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#nep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        绘制 NEP 训练结果
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#nep_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        绘制 NEP 测试集结果
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        绘制热力学量
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#msd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        绘制 MSD 和自扩散系数
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        5. 获取帮助
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🚀 快速入门</h1>
+  <p style="text-align: justify;">本页介绍 GPUMDkit 的基本安装方式和几个常用命令。GPUMDkit 既可以通过交互菜单使用，也可以直接通过命令行选项调用。</p>
+</div>
+
+<h2 id="1-python">1. 准备 Python 环境</h2>
+<p>可以使用干净的 conda 环境：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>gpumdkit<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>gpumdkit
+</code></pre></div>
+<p>部分可选功能需要额外依赖：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>pip<span class="w"> </span>install<span class="w"> </span>neptrain<span class="w"> </span>dpdata<span class="w"> </span>calorine
+</code></pre></div>
+<p>其他 Python 依赖由对应脚本在运行时导入。如果缺少某个包，使用对应功能时 Python 会给出提示。</p>
+<h2 id="2-gpumdkit">2. 安装 GPUMDkit</h2>
+<p>克隆仓库：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
+</code></pre></div>
+<p>运行安装脚本：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="nb">source</span><span class="w"> </span>./install.sh
+</code></pre></div>
+<p>安装脚本会写入 <code>GPUMDkit_path</code> 和 <code>PATH</code> 设置，并在当前 shell 中加载。默认写入 <code>~/.bashrc</code>；如果当前 shell 是 zsh，则写入 <code>~/.zshrc</code>。如果检测到已有 GPUMDkit 路径，安装脚本会打印旧路径并询问是否替换；修改 rc 文件前会先创建备份。</p>
+<p>典型安装输出：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>======================================================
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>  GPUMDkit Installation
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>======================================================
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a> [1/4] Detecting GPUMDkit directory...
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>       /path/to/GPUMDkit
+<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a> [2/4] Detecting shell configuration...
+<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a>       Target: /Users/you/.bashrc
+<a id="__codelineno-4-8" name="__codelineno-4-8" href="#__codelineno-4-8"></a>       Adding environment variables to /Users/you/.bashrc
+<a id="__codelineno-4-9" name="__codelineno-4-9" href="#__codelineno-4-9"></a>       Success: Environment variables added.
+<a id="__codelineno-4-10" name="__codelineno-4-10" href="#__codelineno-4-10"></a> [3/4] Setting executable permissions...
+<a id="__codelineno-4-11" name="__codelineno-4-11" href="#__codelineno-4-11"></a>       Added executable permission to gpumdkit.sh
+<a id="__codelineno-4-12" name="__codelineno-4-12" href="#__codelineno-4-12"></a> [4/4] Loading environment...
+<a id="__codelineno-4-13" name="__codelineno-4-13" href="#__codelineno-4-13"></a>
+<a id="__codelineno-4-14" name="__codelineno-4-14" href="#__codelineno-4-14"></a>======================================================
+<a id="__codelineno-4-15" name="__codelineno-4-15" href="#__codelineno-4-15"></a>  Installation Complete!  GPUMDkit is ready to use.
+<a id="__codelineno-4-16" name="__codelineno-4-16" href="#__codelineno-4-16"></a>======================================================
+</code></pre></div>
+<p>如果之前已经安装过 GPUMDkit，可能会看到：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>Existing GPUMDkit configuration found.
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>Existing path(s):
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>  - /old/path/to/GPUMDkit
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>New path:
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>  - /new/path/to/GPUMDkit
+<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>
+<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>Replace the existing GPUMDkit configuration with the new path? [y/N]:
+</code></pre></div>
+<p>检查命令：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-h
+</code></pre></div>
+<p>帮助表：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>|                                          MAIN FUNCTIONS                                               |
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a>| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |
+<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a>| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |
+<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
+<a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a>|                                         FORMAT CONVERSION                                             |
+<a id="__codelineno-7-11" name="__codelineno-7-11" href="#__codelineno-7-11"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a>| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |
+<a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a>| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |
+<a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a>| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |
+<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a>| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |
+<a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a>| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |
+<a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a>| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |
+<a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a>| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
+<a id="__codelineno-7-19" name="__codelineno-7-19" href="#__codelineno-7-19"></a>| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
+<a id="__codelineno-7-20" name="__codelineno-7-20" href="#__codelineno-7-20"></a>| -frame_range  Extract frames by range         |                                                       |
+<a id="__codelineno-7-21" name="__codelineno-7-21" href="#__codelineno-7-21"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-22" name="__codelineno-7-22" href="#__codelineno-7-22"></a>|                                            ANALYSIS                                                   |
+<a id="__codelineno-7-23" name="__codelineno-7-23" href="#__codelineno-7-23"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-24" name="__codelineno-7-24" href="#__codelineno-7-24"></a>| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
+<a id="__codelineno-7-25" name="__codelineno-7-25" href="#__codelineno-7-25"></a>| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
+<a id="__codelineno-7-26" name="__codelineno-7-26" href="#__codelineno-7-26"></a>| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
+<a id="__codelineno-7-27" name="__codelineno-7-27" href="#__codelineno-7-27"></a>| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
+<a id="__codelineno-7-28" name="__codelineno-7-28" href="#__codelineno-7-28"></a>| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
+<a id="__codelineno-7-29" name="__codelineno-7-29" href="#__codelineno-7-29"></a>| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
+<a id="__codelineno-7-30" name="__codelineno-7-30" href="#__codelineno-7-30"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-7-31" name="__codelineno-7-31" href="#__codelineno-7-31"></a>| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |
+<a id="__codelineno-7-32" name="__codelineno-7-32" href="#__codelineno-7-32"></a>+-------------------------------------------------------------------------------------------------------+
+</code></pre></div>
+<h2 id="3">3. 使用方式</h2>
+<h3 id="_1">交互模式</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh
+</code></pre></div>
+<p>主菜单：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>           ____ ____  _   _ __  __ ____  _    _ _
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>         | |  _| |_) | | | | |\/| | | | | |/ / | __|
+<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a>         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_
+<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
+<a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a>
+<a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a>          GPUMDkit Version 1.5.6 (dev) (2026-06-17)
+<a id="__codelineno-9-8" name="__codelineno-9-8" href="#__codelineno-9-8"></a>    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+<a id="__codelineno-9-9" name="__codelineno-9-9" href="#__codelineno-9-9"></a> Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA
+<a id="__codelineno-9-10" name="__codelineno-9-10" href="#__codelineno-9-10"></a>
+<a id="__codelineno-9-11" name="__codelineno-9-11" href="#__codelineno-9-11"></a> ---------------------- GPUMD ------------------------
+<a id="__codelineno-9-12" name="__codelineno-9-12" href="#__codelineno-9-12"></a> 1) Format Conversion          2) Sample Structures
+<a id="__codelineno-9-13" name="__codelineno-9-13" href="#__codelineno-9-13"></a> 3) Workflow                   4) Calculators
+<a id="__codelineno-9-14" name="__codelineno-9-14" href="#__codelineno-9-14"></a> 5) Analyzer                   6) Visualization
+<a id="__codelineno-9-15" name="__codelineno-9-15" href="#__codelineno-9-15"></a> 7) Utilities                  8) Developing...
+<a id="__codelineno-9-16" name="__codelineno-9-16" href="#__codelineno-9-16"></a> 0) Exit
+<a id="__codelineno-9-17" name="__codelineno-9-17" href="#__codelineno-9-17"></a> ------------&gt;&gt;
+<a id="__codelineno-9-18" name="__codelineno-9-18" href="#__codelineno-9-18"></a> Input the function number:
+</code></pre></div>
+<h3 id="_2">命令行模式</h3>
+<p>直接命令使用固定的位置参数：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+</code></pre></div>
+<p>例如：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+</code></pre></div>
+<p>表示读取 <code>POSCAR</code>，写出 <code>model.xyz</code>。</p>
+<h2 id="4">4. 实际例子</h2>
+<h3 id="poscar-extxyz">POSCAR 转 extxyz</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+</code></pre></div>
+<h3 id="gpumd-group">添加 GPUMD group 标签</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
+</code></pre></div>
+<p>group 标签用于一些需要原子分组的 GPUMD 相关流程和分析，例如特定元素的 MSD 或扩散性质计算。</p>
+<h3 id="nep">绘制 NEP 训练结果</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/train.png" alt="NEP training results" width="72%" />
+</div>
+
+<h3 id="nep_1">绘制 NEP 测试集结果</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/prediction.png" alt="NEP test results" width="72%" />
+</div>
+
+<h3 id="_3">绘制热力学量</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/thermo.png" alt="Thermo plot" width="72%" />
+</div>
+
+<h3 id="msd">绘制 MSD 和自扩散系数</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
+  <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
+</div>
+
+<h2 id="5">5. 获取帮助</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-h
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>-h
+<a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>-h
+<a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train<span class="w"> </span>-h
+<a id="__codelineno-18-5" name="__codelineno-18-5" href="#__codelineno-18-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>-h
+</code></pre></div>
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+      <a href="../en/active_learning_workflow.html" class="md-nav__link">
+        
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+      <a href="../en/polar_material_analysis.html" class="md-nav__link">
+        
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+    
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+    Polar Material Analysis
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+      <a href="../en/contributing_to_gpumdkit.html" class="md-nav__link">
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+    Contributing to GPUMDkit
+  
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+        
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+    
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+    GPUMDkit 教程
+  
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+  
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+  
+
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
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+  
+    <li class="md-nav__item">
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        依赖
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互模式入口
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#406-calc_neighbor_listpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        406) 构建近邻列表 (calc_neighbor_list.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="406) 构建近邻列表 (calc_neighbor_list.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        用法
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        参数（完整）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#407-calc_displacementpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        407) 从轨迹计算位移 (calc_displacement.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="407) 从轨迹计算位移 (calc_displacement.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        用法
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        参数（完整）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#408-calc_averaged_structurepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        408) 计算平均结构 (calc_averaged_structure.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="408) 计算平均结构 (calc_averaged_structure.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        用法
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        参数（完整）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_11" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#409-calc_oct_tiltpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        409) 计算八面体倾转 (calc_oct_tilt.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="409) 计算八面体倾转 (calc_oct_tilt.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        用法
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        参数（完整）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_14" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#410-abo3-calc_polarization_abo3py" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        410) 计算 ABO3 体系极化 (calc_polarization_abo3.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="410) 计算 ABO3 体系极化 (calc_polarization_abo3.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        用法
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_16" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        参数（完整）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_17" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plane-grid-plt_plane_gridpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plane-grid 可视化 (plt_plane_grid.py)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_18" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件一览
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_19" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        真实案例
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="真实案例">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#pbtio3-" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        PbTiO3 的温度驱动铁电-顺电相变
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="PbTiO3 的温度驱动铁电-顺电相变">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 1 步：从每条轨迹的后半段得到平均结构
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#2-modelxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 2 步：基于 model.xyz 构建近邻列表
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 3 步：为每个温度计算位移和极化
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 4 步：绘制实空间位移和极化图
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#5-" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 5 步：构建温度-序参量曲线
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#pbtio3srtio3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        PbTiO3/SrTiO3 超晶格中的拓扑结构
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="PbTiO3/SrTiO3 超晶格中的拓扑结构">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#1-25" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 1 步：使用最后 25% 帧构建平均结构
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#2-ti" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 2 步：构建 Ti 近邻列表
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#3-plane-grid" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 3 步：绘制 plane-grid 图
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_20" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        其他体系
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="其他体系">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#-" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        有机-无机杂化铁电体
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_21" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        其他铁电材料家族
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        依赖
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互模式入口
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#406-calc_neighbor_listpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        406) 构建近邻列表 (calc_neighbor_list.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="406) 构建近邻列表 (calc_neighbor_list.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        用法
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        参数（完整）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#407-calc_displacementpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        407) 从轨迹计算位移 (calc_displacement.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="407) 从轨迹计算位移 (calc_displacement.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        用法
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        参数（完整）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#408-calc_averaged_structurepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        408) 计算平均结构 (calc_averaged_structure.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="408) 计算平均结构 (calc_averaged_structure.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        用法
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        参数（完整）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_11" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#409-calc_oct_tiltpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        409) 计算八面体倾转 (calc_oct_tilt.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="409) 计算八面体倾转 (calc_oct_tilt.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        用法
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        参数（完整）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_14" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#410-abo3-calc_polarization_abo3py" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        410) 计算 ABO3 体系极化 (calc_polarization_abo3.py)
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="410) 计算 ABO3 体系极化 (calc_polarization_abo3.py)">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        用法
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_16" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        参数（完整）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_17" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plane-grid-plt_plane_gridpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Plane-grid 可视化 (plt_plane_grid.py)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_18" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        输出文件一览
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_19" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        真实案例
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="真实案例">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#pbtio3-" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        PbTiO3 的温度驱动铁电-顺电相变
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="PbTiO3 的温度驱动铁电-顺电相变">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 1 步：从每条轨迹的后半段得到平均结构
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#2-modelxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 2 步：基于 model.xyz 构建近邻列表
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 3 步：为每个温度计算位移和极化
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 4 步：绘制实空间位移和极化图
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#5-" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 5 步：构建温度-序参量曲线
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#pbtio3srtio3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        PbTiO3/SrTiO3 超晶格中的拓扑结构
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="PbTiO3/SrTiO3 超晶格中的拓扑结构">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#1-25" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 1 步：使用最后 25% 帧构建平均结构
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#2-ti" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 2 步：构建 Ti 近邻列表
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#3-plane-grid" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        第 3 步：绘制 plane-grid 图
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_20" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        其他体系
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="其他体系">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#-" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        有机-无机杂化铁电体
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_21" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        其他铁电材料家族
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🧲 极性材料分析</h1>
+  <p style="text-align: justify;">本教程介绍 GPUMDkit 中计算器选项 <code>406-410</code>，以及 <code>plane-grid</code> 绘图流程。</p>
+</div>
+
+<p><strong>脚本位置：</strong> <code>Scripts/calculators/</code> 和 <code>Scripts/plt_scripts/</code></p>
+<p>本教程包含通用工具和体系相关工具：</p>
+<ul>
+<li><code>nlist</code>、<code>disp</code> 和 <code>avg-struct</code> 可广泛用于结构和轨迹分析。</li>
+<li><code>oct-tilt</code> 用于八面体环境分析，需要每个中心原子周围有 6 个近邻。</li>
+<li><code>pol-abo3</code> 专用于 <code>ABO3</code> 体系的极化分析。</li>
+</ul>
+<h2 id="_1">依赖</h2>
+<p>这些脚本需要 <code>ferrodispcalc</code>：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
+</code></pre></div>
+<h2 id="_2">交互模式入口</h2>
+<p>选项 <code>406-410</code> 是本教程中的核心功能。下面各节会说明每个功能的用途和运行方式。</p>
+<p>完整参数说明可以通过以下命令查看：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-h
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-h
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-h
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-h
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-h
+<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-h
+</code></pre></div>
+<h2 id="406-calc_neighbor_listpy">406) 构建近邻列表 (<code>calc_neighbor_list.py</code>)</h2>
+<p>为指定中心元素和近邻元素构建近邻列表。</p>
+<p>使用场景：
+这通常是运行 <code>disp</code>、<code>oct-tilt</code> 和 <code>pol-abo3</code> 之前的第一步，因为这些脚本会读取 <code>nl-*.dat</code> 近邻文件。</p>
+<h3 id="_3">用法</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="c1"># 示例 1：为八面体分析构建 Ti-O 最近 6 个近邻</span>
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="c1"># 示例 2：为 A 位中心分析构建 Pb/Sr-O 最近 12 个近邻</span>
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
+</code></pre></div>
+<h3 id="_4">参数（完整）</h3>
+<ul>
+<li><code>-i, --input</code>：
+  输入结构文件。默认值：<code>model.xyz</code>。</li>
+<li><code>-x, --index</code>：
+  从输入文件中读取的帧编号。默认值：<code>0</code>。</li>
+<li><code>-c, --cutoff</code>（必需）：
+  近邻搜索截断距离，单位为 Angstrom。</li>
+<li><code>-n, --neighbor-num</code>（必需）：
+  每个中心原子的近邻数量。</li>
+<li><code>-d, --defect</code>：
+  缺陷模式。启用后，如果近邻数量不足，缺失位置会用中心原子编号填充。</li>
+<li><code>-C, --center-elements</code>（必需）：
+  中心元素列表。</li>
+<li><code>-E, --neighbor-elements</code>（必需）：
+  近邻元素列表。</li>
+<li><code>-o, --output</code>：
+  输出文件路径。默认值：<code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>。</li>
+</ul>
+<h3 id="_5">输出文件</h3>
+<ul>
+<li>主要输出：近邻列表文本文件，例如 <code>nl-Ti-O.dat</code>。</li>
+<li>文件是一个二维整数数组，形状为 <code>(n_center, neighbor_num + 1)</code>。每一行对应一个中心原子：第一列是中心原子编号，后续列是近邻原子编号，所有编号均为 1-based。</li>
+</ul>
+<h2 id="407-calc_displacementpy">407) 从轨迹计算位移 (<code>calc_displacement.py</code>)</h2>
+<p>根据轨迹或模型结构以及近邻列表，计算局域位移矢量。</p>
+<h3 id="_6">用法</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># 示例 1：从 model.xyz 计算单帧位移</span>
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>disp_model.dat
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="c1"># 示例 2：使用 movie.xyz 的最后 20% 帧</span>
+<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+</code></pre></div>
+<h3 id="_7">参数（完整）</h3>
+<ul>
+<li><code>-i, --input</code>：
+  输入 xyz 文件。默认值：<code>model.xyz</code>。</li>
+<li><code>-n, --neighbor-list</code>（必需）：
+  由 <code>nlist</code> 生成的近邻列表文件。</li>
+<li><code>-o, --output</code>：
+  输出文件。默认值：<code>displacements.dat</code>。</li>
+<li><code>-s, --start</code>：
+  切片起始帧。默认值：<code>0</code>。</li>
+<li><code>-t, --stop</code>：
+  切片终止帧。默认值：到末尾。</li>
+<li><code>-p, --step</code>：
+  切片步长。默认值：<code>1</code>。</li>
+<li><code>-l, --last</code>：
+  选择末尾部分帧。
+  整数表示最后 <code>N</code> 帧；
+  <code>0 &lt; value &lt; 1</code> 表示最后一部分比例的帧。</li>
+<li><code>--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
+</ul>
+<h3 id="_8">输出文件</h3>
+<ul>
+<li>主要输出：<code>displacements.dat</code>，或你指定的输出文件名。</li>
+<li>保存的文本文件是二维数组：对于单帧输入，形状为 <code>(n_center, 3)</code>；对于多帧输入，形状为 <code>(n_selected_frame * n_center, 3)</code>，按帧优先顺序排列。三列分别为 <code>dx</code>、<code>dy</code> 和 <code>dz</code> 位移分量，单位为 Angstrom。</li>
+</ul>
+<h2 id="408-calc_averaged_structurepy">408) 计算平均结构 (<code>calc_averaged_structure.py</code>)</h2>
+<p>从选定轨迹帧生成一个平均结构。
+通常可在体系平衡后使用：对于接近平衡的固体，可以对目标温度下的一段轨迹取平均，并分析该代表性结构，而不是逐帧处理每个 snapshot。</p>
+<h3 id="_9">用法</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="c1"># 示例 1：平均所有帧</span>
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="c1"># 示例 2：平均选定帧范围 (100:500:2)</span>
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-s<span class="w"> </span><span class="m">100</span><span class="w"> </span>-t<span class="w"> </span><span class="m">500</span><span class="w"> </span>-p<span class="w"> </span><span class="m">2</span><span class="w"> </span>-o<span class="w"> </span>avg_slice.xyz
+</code></pre></div>
+<h3 id="_10">参数（完整）</h3>
+<ul>
+<li><code>-i, --input</code>：
+  输入轨迹文件。默认值：<code>movie.xyz</code>。</li>
+<li><code>-o, --output</code>：
+  输出结构文件。默认值：<code>averaged_structure.xyz</code>。</li>
+<li><code>-s, --start</code>：
+  切片起始帧。默认值：<code>0</code>。</li>
+<li><code>-t, --stop</code>：
+  切片终止帧。默认值：到末尾。</li>
+<li><code>-p, --step</code>：
+  切片步长。默认值：<code>1</code>。</li>
+<li><code>-l, --last</code>：
+  选择末尾帧，可以是最后 <code>N</code> 帧或最后一部分比例的帧。</li>
+<li><code>--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
+</ul>
+<h3 id="_11">输出文件</h3>
+<ul>
+<li>主要输出：单帧平均结构 extxyz 文件。</li>
+<li>位置平均会相对于所选第一帧进行 MIC/PBC 修正。</li>
+</ul>
+<h2 id="409-calc_oct_tiltpy">409) 计算八面体倾转 (<code>calc_oct_tilt.py</code>)</h2>
+<p>根据 B-O 近邻列表计算八面体倾转角。
+该功能常用于分析 <code>ABO3</code> 体系中的八面体转动模式，例如 <code>SrTiO3</code> 和 <code>PbZrO3</code>。</p>
+<h3 id="_12">用法</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="c1"># 示例 1：从单帧结构计算 TiO6 八面体倾转</span>
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>oct_tilt_model.dat
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="c1"># 示例 2：从轨迹最后 20% 帧计算 TiO6 八面体倾转</span>
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>octahedral_tilt.dat
+</code></pre></div>
+<h3 id="_13">参数（完整）</h3>
+<ul>
+<li><code>-i, --input</code>：
+  输入 xyz 文件。默认值：<code>model.xyz</code>。</li>
+<li><code>-n, --neighbor-list</code>（必需）：
+  B-O 近邻列表文件。</li>
+<li><code>-o, --output</code>：
+  输出文件。默认值：<code>octahedral_tilt.dat</code>。</li>
+<li><code>-s, --start</code>：
+  切片起始帧。默认值：<code>0</code>。</li>
+<li><code>-t, --stop</code>：
+  切片终止帧。默认值：到末尾。</li>
+<li><code>-p, --step</code>：
+  切片步长。默认值：<code>1</code>。</li>
+<li><code>-l, --last</code>：
+  选择末尾帧，可以是最后 <code>N</code> 帧或最后一部分比例的帧。</li>
+<li><code>--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
+</ul>
+<h3 id="_14">输出文件</h3>
+<ul>
+<li>主要输出：<code>octahedral_tilt.dat</code>，或自定义输出文件名。</li>
+<li>保存的文本文件是三列二维数组，分别为 <code>theta_x</code>、<code>theta_y</code>、<code>theta_z</code>，单位为 degree。对于单帧输入，形状为 <code>(n_center, 3)</code>；对于多帧输入，形状为 <code>(n_selected_frame * n_center, 3)</code>。</li>
+</ul>
+<h2 id="410-abo3-calc_polarization_abo3py">410) 计算 ABO3 体系极化 (<code>calc_polarization_abo3.py</code>)</h2>
+<p>计算 <code>ABO3</code> 体系的局域极化矢量。</p>
+<h3 id="_15">用法</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="c1"># 示例 1：单帧 ABO3 极化</span>
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Sr</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-o<span class="w"> </span>polarization_model.dat
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="c1"># 示例 2：选定轨迹帧范围上的极化</span>
+<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-s<span class="w"> </span><span class="m">200</span><span class="w"> </span>-t<span class="w"> </span><span class="m">600</span><span class="w"> </span>-p<span class="w"> </span><span class="m">5</span><span class="w"> </span>-o<span class="w"> </span>polarization_slice.dat
+</code></pre></div>
+<h3 id="_16">参数（完整）</h3>
+<ul>
+<li><code>-i, --input</code>：
+  输入 xyz 文件。默认值：<code>model.xyz</code>。</li>
+<li><code>--nl-ba</code>（必需）：
+  B-A 近邻列表。</li>
+<li><code>--nl-bo</code>（必需）：
+  B-O 近邻列表。</li>
+<li><code>-o, --output</code>：
+  输出文件。默认值：<code>polarization.dat</code>。</li>
+<li><code>--bec</code>（必需）：
+  Born 有效电荷项，格式为 <code>Element=value</code>。
+  示例：<code>Pb=2.5 Ti=4.0 O=-2.0</code>。</li>
+<li><code>-s, --start</code>：
+  切片起始帧。默认值：<code>0</code>。</li>
+<li><code>-t, --stop</code>：
+  切片终止帧。默认值：到末尾。</li>
+<li><code>-p, --step</code>：
+  切片步长。默认值：<code>1</code>。</li>
+<li><code>-l, --last</code>：
+  选择末尾帧，可以是最后 <code>N</code> 帧或最后一部分比例的帧。</li>
+<li><code>--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
+</ul>
+<p>重要检查：</p>
+<ul>
+<li><code>--bec</code> 必须包含输入结构中的所有元素种类。</li>
+<li><code>--nl-ba</code> 和 <code>--nl-bo</code> 中的中心原子编号必须匹配。</li>
+</ul>
+<h3 id="_17">输出文件</h3>
+<ul>
+<li>主要输出：<code>polarization.dat</code>，或自定义输出文件名。</li>
+<li>保存的文本文件是三列二维数组，分别为 <code>Px</code>、<code>Py</code>、<code>Pz</code>，单位为 <code>C/m^2</code>。对于单帧输入，形状为 <code>(n_center, 3)</code>；对于多帧输入，形状为 <code>(n_selected_frame * n_center, 3)</code>，按帧优先顺序排列。如果总 Born 电荷不平衡，脚本会打印 warning。</li>
+</ul>
+<h3 id="plane-grid-plt_plane_gridpy">Plane-grid 可视化 (<code>plt_plane_grid.py</code>)</h3>
+<p>你可以可视化 <code>displacements.dat</code> 或 <code>polarization.dat</code>：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># 示例 1：Ti 位点上的位移图，选择第一个 XY 层</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span>
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="c1"># 示例 2：Pb 位点上的极化图，选择 XZ 和 YZ 层</span>
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>polarization.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span>--select-yz<span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">4</span>
+</code></pre></div>
+<p>参数（完整）：</p>
+<ul>
+<li><code>-i, --input</code>：
+  用于原子布局和分层的输入 xyz 文件。默认值：<code>model.xyz</code>。</li>
+<li><code>-d, --disp</code>：
+  矢量场数据文件。默认值：<code>displacements.dat</code>。</li>
+<li><code>-e, --elements</code>（必需）：
+  用于将矢量映射到晶格层上的中心元素符号。</li>
+<li><code>-m, --tol</code>：
+  网格映射的层容差。默认值：<code>1.0</code>。</li>
+<li><code>-g, --target-size</code>：
+  期望网格大小，格式为 <code>nx ny nz</code>。</li>
+<li><code>-o, --save-dir</code>：
+  图片输出目录。默认值：<code>plot</code>。</li>
+<li><code>-f, --frame</code>：
+  当矢量数据包含多帧时，要可视化的帧编号。默认值：<code>0</code>。</li>
+<li><code>--select-xy</code>：
+  选定的 XY 层编号。</li>
+<li><code>--select-xz</code>：
+  选定的 XZ 层编号。</li>
+<li><code>--select-yz</code>：
+  选定的 YZ 层编号。</li>
+</ul>
+<p>输出：</p>
+<ul>
+<li>如果需要，会创建输出目录。</li>
+<li>图片保存为 <code>XY_*.png</code>、<code>XZ_*.png</code>、<code>YZ_*.png</code>。</li>
+</ul>
+<div align="center">
+    <img src="../Gallery/PTO_STO_superlattice.png" alt="PTO_STO" width="65%" />
+</div>
+
+<h2 id="_18">输出文件一览</h2>
+<table>
+<thead>
+<tr>
+<th>脚本</th>
+<th>主要输出</th>
+<th>保存内容</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>calc_neighbor_list.py</code></td>
+<td><code>nl-*.dat</code></td>
+<td>1-based 中心原子编号和近邻原子编号</td>
+</tr>
+<tr>
+<td><code>calc_displacement.py</code></td>
+<td><code>*.dat</code></td>
+<td>局域位移矢量（<code>dx dy dz</code>，Angstrom）</td>
+</tr>
+<tr>
+<td><code>calc_averaged_structure.py</code></td>
+<td><code>*.xyz</code></td>
+<td>一个平均结构</td>
+</tr>
+<tr>
+<td><code>calc_oct_tilt.py</code></td>
+<td><code>*.dat</code></td>
+<td>八面体倾转角（<code>theta_x theta_y theta_z</code>，degree）</td>
+</tr>
+<tr>
+<td><code>calc_polarization_abo3.py</code></td>
+<td><code>*.dat</code></td>
+<td>局域极化矢量（<code>Px Py Pz</code>，<code>C/m^2</code>）</td>
+</tr>
+<tr>
+<td><code>plt_plane_grid.py</code></td>
+<td><code>plot/*.png</code></td>
+<td>根据矢量场数据绘制的 XY/XZ/YZ 平面图</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_19">真实案例</h2>
+<h3 id="pbtio3-">PbTiO3 的温度驱动铁电-顺电相变</h3>
+<p>假设所有文件都位于当前目录 <code>./</code>：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>./
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>├── model.xyz
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>├── 300K.xyz
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>├── 350K.xyz
+<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a>├── 400K.xyz
+<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>├── ...
+<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a>└── 800K.xyz
+</code></pre></div>
+<p><code>model.xyz</code> 是用于进行 MD 模拟的初始结构。每个 <code>TEMP K.xyz</code> 是对应温度下的轨迹。</p>
+<h4 id="1">第 1 步：从每条轨迹的后半段得到平均结构</h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span>
+<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a><span class="k">done</span>
+</code></pre></div>
+<p>这会写出 <code>300K-avg.xyz</code>、<code>350K-avg.xyz</code>、...、<code>800K-avg.xyz</code>。</p>
+<h4 id="2-modelxyz">第 2 步：基于 <code>model.xyz</code> 构建近邻列表</h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="c1"># B-O list: for each Ti, find the nearest 6 O atoms</span>
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="c1"># A-O list: for each Pb, find the nearest 12 O atoms</span>
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Pb-O.dat
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a><span class="c1"># B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms</span>
+<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">5</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">8</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>Pb<span class="w"> </span>-o<span class="w"> </span>nl-Ti-Pb.dat
+</code></pre></div>
+<h4 id="3">第 3 步：为每个温度计算位移和极化</h4>
+<p>这里使用 Born 有效电荷（BEC），不是名义离子电荷。对于本例中的 PbTiO3：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="n">PTO</span> <span class="o">=</span> <span class="p">{</span>
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>    <span class="s1">&#39;Pb&#39;</span><span class="p">:</span> <span class="mf">3.44</span><span class="p">,</span>
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>    <span class="s1">&#39;Ti&#39;</span><span class="p">:</span> <span class="mf">5.18</span><span class="p">,</span>
+<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a>    <span class="s1">&#39;O&#39;</span><span class="p">:</span> <span class="o">-</span><span class="p">(</span><span class="mf">3.44</span> <span class="o">+</span> <span class="mf">5.18</span><span class="p">)</span> <span class="o">/</span> <span class="mi">3</span>
+<a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="p">}</span>
+</code></pre></div>
+<p>你可以从自己的 DFPT 计算或文献中获得 BEC。因此，可以使用以下命令计算局域位移和极化：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span>
+<a id="__codelineno-12-4" name="__codelineno-12-4" href="#__codelineno-12-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a><span class="w">    </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">3</span>.44<span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">5</span>.18<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.8733333333<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span>
+<a id="__codelineno-12-6" name="__codelineno-12-6" href="#__codelineno-12-6"></a><span class="k">done</span>
+</code></pre></div>
+<h4 id="4">第 4 步：绘制实空间位移和极化图</h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp&quot;</span>
+<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol&quot;</span>
+<a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a><span class="k">done</span>
+</code></pre></div>
+<h4 id="5-">第 5 步：构建温度-序参量曲线</h4>
+<p>结合每个温度平均结构的晶格信息和极化文件（<code>XX-pol.dat</code>）进行分析，可以得到如下图：</p>
+<div align="center">
+    <img src="../Gallery/PTO-temp.png" alt="PTO-temp" width="65%" />
+</div>
+
+<p>该趋势显示在约 <code>600 K</code> 附近发生明显相变，此时极化消失。</p>
+<h3 id="pbtio3srtio3">PbTiO3/SrTiO3 超晶格中的拓扑结构</h3>
+<p>假设 <code>movie.xyz</code> 是当前目录下 PbTiO3/SrTiO3 超晶格的轨迹。</p>
+<h4 id="1-25">第 1 步：使用最后 25% 帧构建平均结构</h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>model-avg.xyz
+</code></pre></div>
+<h4 id="2-ti">第 2 步：构建 Ti 近邻列表</h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+</code></pre></div>
+<h4 id="3-plane-grid">第 3 步：绘制 plane-grid 图</h4>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>disp-last25.dat
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-d<span class="w"> </span>disp-last25.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span>-o<span class="w"> </span>plot-topology
+</code></pre></div>
+<div align="center">
+    <img src="../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
+</div>
+
+<p>这会得到与前面展示相似的图。在 PTO 区域可以看到类似涡旋的极化图样，而 STO 区域的极化接近于零。通过分析涡旋核附近极化的变化，可以估计局域介电响应，但这超出了本教程范围。</p>
+<p>注意：该图使用的 colormap 与 GPUMDkit 默认绘图风格不同。默认输出不会与图中完全一致，但可以通过少量修改绘图脚本获得这种风格。</p>
+<h3 id="_20">其他体系</h3>
+<h4 id="-">有机-无机杂化铁电体</h4>
+<p>在许多有机-无机铁电体中，极化与各向异性的分子单元密切相关。跟踪分子取向的一种实用方法是使用键矢量。</p>
+<p>对于 TMCM-CdCl3，可以使用 TMCM 分子中的 C-Cl 键方向作为取向代理，并据此估计极化态：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a><span class="c1"># Find the nearest Cl around each C (tune cutoff if needed)</span>
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">3</span><span class="w"> </span>-n<span class="w"> </span><span class="m">1</span><span class="w"> </span>-C<span class="w"> </span>C<span class="w"> </span>-E<span class="w"> </span>Cl<span class="w"> </span>-o<span class="w"> </span>nl-C-Cl.dat
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>
+<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a><span class="c1"># Compute C-Cl bond vectors from the trajectory</span>
+<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-C-Cl.dat<span class="w"> </span>-o<span class="w"> </span>ccl_vectors.dat
+</code></pre></div>
+<p>随后可以把 <code>ccl_vectors.dat</code> 作为取向序参量进行分析。更多细节可参考：Phys. Rev. Lett. 136, 016801。</p>
+<h4 id="_21">其他铁电材料家族</h4>
+<p>除 <code>ABO3</code> 外，<code>ferrodispcalc</code> 也可以适配许多铁电体系，包括氮化物、氧化铪基化合物、有机-无机杂化体系以及部分二维铁电材料。</p>
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+      <a href="../en/index.html" class="md-nav__link">
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+    GPUMDkit Tutorials
+  
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+  
+    <li class="md-nav__item">
+      <a href="../en/quick_start.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Quick Start
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
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+  
+    <li class="md-nav__item">
+      <a href="../en/command_reference.html" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Command Reference
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/format_conversion.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Format Conversion
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/structure_sampling.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Structure Sampling
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/workflow_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Workflow Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/calculator_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Calculator Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/analyzer_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Analyzer Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/plot_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Plot Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/custom_commands.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Custom Commands
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/active_learning_workflow.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Active Learning Workflow
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/polar_material_analysis.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Polar Material Analysis
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/contributing_to_gpumdkit.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        
+          
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    简体中文
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    简体中文
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="index.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit 教程
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        支持的格式
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互模式
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="交互模式">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        每个入口的作用
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        快速命令表
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        常见例子
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="常见例子">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#vasp" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        转换 VASP 结果
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#group" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        添加 group 标签
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        常用脚本说明
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="常用脚本说明">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#poscar-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        POSCAR 转 extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#extxyz-poscar" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        extxyz 转 POSCAR
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#lammps-dump-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        LAMMPS dump 转 extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#cif" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        CIF 转换
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        添加权重
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        扩胞
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        常见问题
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        说明
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        支持的格式
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互模式
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="交互模式">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        每个入口的作用
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        快速命令表
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        常见例子
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="常见例子">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#vasp" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        转换 VASP 结果
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#group" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        添加 group 标签
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        常用脚本说明
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="常用脚本说明">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#poscar-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        POSCAR 转 extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#extxyz-poscar" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        extxyz 转 POSCAR
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#lammps-dump-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        LAMMPS dump 转 extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#cif" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        CIF 转换
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        添加权重
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        扩胞
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        常见问题
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        说明
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🔄 格式转换</h1>
+  <p style="text-align: justify;">格式转换模块用于在常见原子模拟文件格式之间转换，同时提供 group 标签、权重、帧提取等元数据处理功能。</p>
+</div>
+
+<p><strong>脚本位置：</strong> <code>Scripts/format_conversion/</code></p>
+<h2 id="_1">支持的格式</h2>
+<ul>
+<li><strong>VASP</strong>：<code>POSCAR</code>、<code>CONTCAR</code>、<code>OUTCAR</code>、<code>XDATCAR</code></li>
+<li><strong>LAMMPS</strong>：data 文件和 dump 轨迹</li>
+<li><strong>CP2K</strong>：输出 log、坐标、力和晶胞文件</li>
+<li><strong>ABACUS</strong>：SCF/MD 输出</li>
+<li><strong>CIF</strong>：晶体结构文件</li>
+<li><strong>ASE trajectory</strong>：<code>.traj</code></li>
+<li><strong>extxyz</strong>：GPUMD 和 NEP 常用的结构格式</li>
+</ul>
+<h2 id="_2">交互模式</h2>
+<p>打开 GPUMDkit：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh
+</code></pre></div>
+<p>选择：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>1) Format Conversion
+</code></pre></div>
+<p>菜单如下：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>+-------------------------------------------------------------+
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>|                   FORMAT CONVERSION TOOLS                   |
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>+-------------------------------------------------------------+
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>| 101) VASP to extxyz            106) Add group labels        |
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>| 102) MTP to extxyz             107) Add weight to extxyz    |
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>| 103) CP2K to extxyz            108) Extract frame extxyz    |
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>| 104) ABACUS to extxyz          109) Clean XYZ info          |
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>| 105) extxyz to POSCAR          110) Replicate structure     |
+<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>+-------------------------------------------------------------+
+<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a>| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |
+<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a>| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |
+<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a>| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |
+<a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a>| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|
+<a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a>+-------------------------------------------------------------+
+<a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a>| 000) Return to main menu                                    |
+<a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a>+-------------------------------------------------------------+
+<a id="__codelineno-2-17" name="__codelineno-2-17" href="#__codelineno-2-17"></a>Input the function number or converter keyword:
+</code></pre></div>
+<h3 id="_3">每个入口的作用</h3>
+<table>
+<thead>
+<tr>
+<th>入口</th>
+<th>功能</th>
+<th>适用场景</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>101</code></td>
+<td>VASP OUTCAR 转 extxyz，shell 版本</td>
+<td>批量转换 VASP 计算目录</td>
+</tr>
+<tr>
+<td><code>102</code></td>
+<td>MTP cfg 转 extxyz</td>
+<td>转换 MTP 数据</td>
+</tr>
+<tr>
+<td><code>103</code></td>
+<td>CP2K 转 extxyz</td>
+<td>可选择 log/inp 路线或 pos/frc/cell 路线</td>
+</tr>
+<tr>
+<td><code>104</code></td>
+<td>ABACUS 转 extxyz</td>
+<td>转换 ABACUS SCF 或 MD 输出</td>
+</tr>
+<tr>
+<td><code>105</code></td>
+<td>extxyz 转 POSCAR</td>
+<td>将 extxyz 每一帧写成 POSCAR</td>
+</tr>
+<tr>
+<td><code>106</code></td>
+<td>添加 group 标签</td>
+<td>为 GPUMD 相关流程添加原子分组标签</td>
+</tr>
+<tr>
+<td><code>107</code></td>
+<td>添加权重</td>
+<td>修改训练集结构权重</td>
+</tr>
+<tr>
+<td><code>108</code></td>
+<td>提取单帧</td>
+<td>从 extxyz 轨迹导出某一帧</td>
+</tr>
+<tr>
+<td><code>109</code></td>
+<td>清理 XYZ 信息</td>
+<td>删除多余 extxyz 属性</td>
+</tr>
+<tr>
+<td><code>110</code></td>
+<td>扩胞</td>
+<td>按倍数或目标原子数扩胞</td>
+</tr>
+<tr>
+<td><code>out2exyz</code></td>
+<td>OUTCAR 转 extxyz，Python 版本</td>
+<td>VASP OUTCAR 转换的另一个入口</td>
+</tr>
+<tr>
+<td><code>pos2exyz</code></td>
+<td>POSCAR 转 extxyz</td>
+<td>转换单个结构</td>
+</tr>
+<tr>
+<td><code>cif2pos</code></td>
+<td>CIF 转 POSCAR</td>
+<td>从 CIF 准备 VASP 输入</td>
+</tr>
+<tr>
+<td><code>cif2exyz</code></td>
+<td>CIF 转 extxyz</td>
+<td>从 CIF 准备 GPUMDkit 输入</td>
+</tr>
+<tr>
+<td><code>xdat2exyz</code></td>
+<td>XDATCAR 转 extxyz</td>
+<td>转换 VASP MD 轨迹</td>
+</tr>
+<tr>
+<td><code>pos2lmp</code></td>
+<td>POSCAR 转 LAMMPS data</td>
+<td>准备 LAMMPS 输入</td>
+</tr>
+<tr>
+<td><code>lmp2exyz</code></td>
+<td>LAMMPS dump 转 extxyz</td>
+<td>转换 LAMMPS 轨迹</td>
+</tr>
+<tr>
+<td><code>traj2exyz</code></td>
+<td>ASE traj 转 extxyz</td>
+<td>转换 ASE 轨迹</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_4">快速命令表</h2>
+<table>
+<thead>
+<tr>
+<th>来源</th>
+<th>目标</th>
+<th>命令</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>OUTCAR 目录</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -out2xyz &lt;dir&gt;</code></td>
+</tr>
+<tr>
+<td>OUTCAR 目录</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -out2exyz &lt;dir&gt;</code></td>
+</tr>
+<tr>
+<td>POSCAR</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -pos2exyz POSCAR model.xyz</code></td>
+</tr>
+<tr>
+<td>extxyz</td>
+<td>POSCAR 文件</td>
+<td><code>gpumdkit.sh -exyz2pos train.xyz</code></td>
+</tr>
+<tr>
+<td>XDATCAR</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code></td>
+</tr>
+<tr>
+<td>POSCAR</td>
+<td>LAMMPS data</td>
+<td><code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code></td>
+</tr>
+<tr>
+<td>LAMMPS dump</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code></td>
+</tr>
+<tr>
+<td>CIF</td>
+<td>POSCAR</td>
+<td><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code></td>
+</tr>
+<tr>
+<td>CIF</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -cif2exyz input.cif model.xyz</code></td>
+</tr>
+<tr>
+<td>ASE traj</td>
+<td>extxyz</td>
+<td><code>gpumdkit.sh -traj2exyz input.traj output.xyz</code></td>
+</tr>
+</tbody>
+</table>
+<h2 id="_5">常见例子</h2>
+<h3 id="vasp">转换 VASP 结果</h3>
+<p>如果每个计算目录下都有 <code>OUTCAR</code>：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-out2xyz<span class="w"> </span>./vasp_results/
+</code></pre></div>
+<p>也可以使用 Python 版本：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-out2exyz<span class="w"> </span>./vasp_results/
+</code></pre></div>
+<p>在交互模式中选择 <code>101</code>，会看到：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>| Calling the script in Scripts/format_conversion |
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>| Script: out2xyz.sh                              |
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>Input the directory containing OUTCARs
+<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>Example: ./
+<a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a>------------&gt;&gt;
+</code></pre></div>
+<h3 id="group">添加 group 标签</h3>
+<p>一些 GPUMD 相关流程会使用 group 标签进行原子分组，例如特定元素的 MSD 或扩散性质计算。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
+</code></pre></div>
+<p>该命令读取输入结构，并写出带 group 信息的 extxyz 文件。</p>
+<p>在交互模式中选择 <code>106</code>，会看到：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>| Calling the script in Scripts/format_conversion |
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>| Script: add_groups.py                           |
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a>Input &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...
+<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a>Example: POSCAR Li Y Cl
+<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>------------&gt;&gt;
+</code></pre></div>
+<h2 id="_6">常用脚本说明</h2>
+<h3 id="poscar-extxyz">POSCAR 转 extxyz</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+</code></pre></div>
+<p>适合把单个 VASP 结构转成 extxyz 文件。</p>
+<p>交互模式关键词：<code>pos2exyz</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>Input &lt;POSCAR&gt; &lt;output.xyz&gt;
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>Example: POSCAR model.xyz
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>------------&gt;&gt;
+</code></pre></div>
+<h3 id="extxyz-poscar">extxyz 转 POSCAR</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-exyz2pos<span class="w"> </span>structures.xyz
+</code></pre></div>
+<p>会将 extxyz 中所有帧转换成 <code>POSCAR_*.vasp</code> 文件。</p>
+<p>交互模式入口：<code>105</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>Input the name of extxyz
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>Example: ./train.xyz
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>------------&gt;&gt;
+</code></pre></div>
+<h3 id="lammps-dump-extxyz">LAMMPS dump 转 extxyz</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-lmp2exyz<span class="w"> </span>dump.lammpstrj<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
+</code></pre></div>
+<p>元素顺序必须对应 LAMMPS 中的 atom type ID。例如 type 1 是 Li、type 2 是 Y、type 3 是 Cl，则输入 <code>Li Y Cl</code>。</p>
+<p>交互模式关键词：<code>lmp2exyz</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>Example: dump.lammpstrj Li O
+<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>------------&gt;&gt;
+</code></pre></div>
+<h3 id="cif">CIF 转换</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-cif2pos<span class="w"> </span>input.cif<span class="w"> </span>POSCAR.vasp
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>gpumdkit.sh<span class="w"> </span>-cif2exyz<span class="w"> </span>input.cif<span class="w"> </span>model.xyz
+</code></pre></div>
+<p>如果后续需要 VASP 计算，使用 <code>-cif2pos</code>；如果后续要进入 GPUMDkit 分析，使用 <code>-cif2exyz</code>。</p>
+<h3 id="_7">添加权重</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-addweight<span class="w"> </span>train.xyz<span class="w"> </span>train_weighted.xyz<span class="w"> </span><span class="m">5</span>
+</code></pre></div>
+<p>用于给训练集结构添加或修改权重。</p>
+<h3 id="_8">扩胞</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-replicate<span class="w"> </span>POSCAR<span class="w"> </span>supercell.vasp<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span>
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-replicate<span class="w"> </span>POSCAR<span class="w"> </span>supercell.vasp<span class="w"> </span><span class="m">256</span>
+</code></pre></div>
+<p>第一种按晶胞倍数扩胞，第二种按目标原子数自动选择扩胞方式。</p>
+<h2 id="_9">常见问题</h2>
+<table>
+<thead>
+<tr>
+<th>问题</th>
+<th>建议</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>LAMMPS 转换后元素不对</td>
+<td>检查 dump 文件后的元素顺序</td>
+</tr>
+<tr>
+<td>extxyz 元数据太多</td>
+<td>使用 <code>-clean_xyz input.xyz clean.xyz</code></td>
+</tr>
+<tr>
+<td>提取帧不对</td>
+<td>注意帧索引通常从 0 开始</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_10">说明</h2>
+<p>如果某个转换脚本缺少所需 Python 包，运行该功能时 Python 会给出相应提示。</p>
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+      <a href="../en/active_learning_workflow.html" class="md-nav__link">
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+      <a href="../en/polar_material_analysis.html" class="md-nav__link">
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+  
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+
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+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
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+  
+  
+
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+  
+
+              
+            
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+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
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+    <li class="md-nav__item md-nav__item--active">
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+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
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+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互模式入口
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        均匀/随机采样
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#neptrain-fps" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NepTrain FPS
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#pynep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        PyNEP 旧入口
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        结构扰动
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        最大力偏差结构选择
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例命令
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        常见问题
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
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+            
+              
+                
+  
+  
+  
+  
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+      <a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
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+      <a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+                
+  
+  
+  
+  
+    <li class="md-nav__item">
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互模式入口
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        均匀/随机采样
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#neptrain-fps" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NepTrain FPS
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#pynep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        PyNEP 旧入口
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        结构扰动
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        最大力偏差结构选择
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例命令
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        常见问题
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>📦 结构采样</h1>
+  <p style="text-align: justify;">结构采样用于从轨迹中选择候选结构、生成扰动结构，或根据模型偏差挑选值得进一步计算的结构。</p>
+</div>
+
+<p><strong>脚本位置：</strong> <code>Scripts/sample_structures/</code></p>
+<h2 id="_1">交互模式入口</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh
+</code></pre></div>
+<p>选择：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>2) Sample Structures
+</code></pre></div>
+<p>菜单如下：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>+------------------------------------------------------+
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>|                 SAMPLE STRUCTURE TOOLS               |
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>+------------------------------------------------------+
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>| 201) Sample structures from extxyz                   |
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>| 202) PyNEP sampling [deprecated]                    |
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>| 203) FPS sampling by NepTrain [preferred]            |
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>| 204) Perturb structure                               |
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>| 205) Select max force deviation structs              |
+<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>+------------------------------------------------------+
+<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a>| 000) Return to the main menu                         |
+<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a>+------------------------------------------------------+
+<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a>Input the function number:
+</code></pre></div>
+<p>常用功能：</p>
+<table>
+<thead>
+<tr>
+<th>菜单</th>
+<th>方法</th>
+<th>用途</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>201</td>
+<td>uniform/random</td>
+<td>从轨迹中均匀或随机抽帧</td>
+</tr>
+<tr>
+<td>202</td>
+<td>PyNEP notice</td>
+<td>只打印提示；真正运行 PyNEP 请用 <code>gpumdkit.sh -pynep</code></td>
+</tr>
+<tr>
+<td>203</td>
+<td>NepTrain FPS</td>
+<td>使用 NepTrain 描述符的 FPS 采样</td>
+</tr>
+<tr>
+<td>204</td>
+<td>perturb</td>
+<td>从 POSCAR/CONTCAR 生成扰动结构</td>
+</tr>
+<tr>
+<td>205</td>
+<td>force deviation</td>
+<td>从 active learning 输出中选择高偏差结构</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_2">均匀/随机采样</h2>
+<p>交互模式选择 <code>201</code>，会看到：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>[skip_num]: number of initial frames to skip, default value is 0
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>Sampling_method: &#39;uniform&#39; or &#39;random&#39;
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>Example: train.xyz uniform 50
+<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>------------&gt;&gt;
+</code></pre></div>
+<p>例如输入：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>dump.xyz uniform 50
+</code></pre></div>
+<p>或：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>dump.xyz random 100 500
+</code></pre></div>
+<p>参数含义：</p>
+<table>
+<thead>
+<tr>
+<th>参数</th>
+<th>含义</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>dump.xyz</code></td>
+<td>输入轨迹</td>
+</tr>
+<tr>
+<td><code>uniform</code> / <code>random</code></td>
+<td>采样方法</td>
+</tr>
+<tr>
+<td><code>50</code> / <code>100</code></td>
+<td>采样结构数</td>
+</tr>
+<tr>
+<td><code>500</code></td>
+<td>可选，跳过前 500 帧</td>
+</tr>
+</tbody>
+</table>
+<p>输出：</p>
+<ul>
+<li><code>sampled_structures.xyz</code></li>
+</ul>
+<h2 id="neptrain-fps">NepTrain FPS</h2>
+<p>NepTrain 版本的 FPS：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
+</code></pre></div>
+<p>交互模式选择 <code>203</code>，会看到：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>Example: dump.xyz train.xyz nep.txt
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>------------&gt;&gt;
+</code></pre></div>
+<p>输入：</p>
+<table>
+<thead>
+<tr>
+<th>文件</th>
+<th>含义</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>dump.xyz</code></td>
+<td>候选结构</td>
+</tr>
+<tr>
+<td><code>train.xyz</code></td>
+<td>当前训练集</td>
+</tr>
+<tr>
+<td><code>nep.txt</code></td>
+<td>用于计算描述符的 NEP 模型</td>
+</tr>
+</tbody>
+</table>
+<p>输出：</p>
+<ul>
+<li><code>selected.xyz</code></li>
+<li><code>select.png</code></li>
+<li><code>pca_sample.txt</code></li>
+<li><code>pca_train.txt</code></li>
+<li><code>pca_selected.txt</code></li>
+</ul>
+<p>运行时可以选择按最小距离阈值采样，或指定采样结构数。脚本随后会打印：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>Choose selection method:
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>1) Select structures based on minimum distance
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>2) Select structures based on number of structures
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>------------&gt;&gt;
+</code></pre></div>
+<p>该功能需要 <code>NepTrain</code>，运行时会提示相关引用。</p>
+<h2 id="pynep">PyNEP 旧入口</h2>
+<p>PyNEP FPS 仍然保留兼容，但只通过 <code>-pynep</code> 入口调用：</p>
+<p>如果在交互菜单中选择 <code>202</code>，会看到：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>+-------------------------------------------------+
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>| Function 202 is no longer supported here.       |
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>| PyNEP package is no longer actively maintained. |
+<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a>| Please use 203) NepTrain sampling instead.      |
+<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>| If you still need PyNEP compatibility, run:     |
+<a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a>|                 gpumdkit.sh -pynep              |
+<a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a>+-------------------------------------------------+
+</code></pre></div>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pynep
+</code></pre></div>
+<p>随后输入：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>dump.xyz train.xyz nep.txt 8
+</code></pre></div>
+<p>这个入口需要 <code>pynep</code>。</p>
+<h2 id="_3">结构扰动</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>python<span class="w"> </span>Scripts/sample_structures/perturb_structure.py<span class="w"> </span>POSCAR<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">0</span>.03<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>uniform
+</code></pre></div>
+<p>交互模式选择 <code>204</code>，会看到：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>The default parameters for perturb are 20 0.03 0.2 uniform
+<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>Example: POSCAR 20 0.03 0.2 uniform
+<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a>------------&gt;&gt;
+</code></pre></div>
+<p>参数含义：</p>
+<table>
+<thead>
+<tr>
+<th>参数</th>
+<th>含义</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>POSCAR</code></td>
+<td>输入结构</td>
+</tr>
+<tr>
+<td><code>20</code></td>
+<td>生成结构数</td>
+</tr>
+<tr>
+<td><code>0.03</code></td>
+<td>晶胞扰动比例</td>
+</tr>
+<tr>
+<td><code>0.2</code></td>
+<td>原子扰动距离，单位 Angstrom</td>
+</tr>
+<tr>
+<td><code>uniform</code></td>
+<td>扰动方式，可选 <code>normal</code>、<code>uniform</code>、<code>const</code></td>
+</tr>
+</tbody>
+</table>
+<p>输出：</p>
+<ul>
+<li><code>POSCAR_01.vasp</code>、<code>POSCAR_02.vasp</code> 等</li>
+</ul>
+<p>该功能需要 <code>dpdata</code>。</p>
+<h2 id="_4">最大力偏差结构选择</h2>
+<p>该功能需要配合 GPUMD 的 <code>active</code> 命令使用。<code>active</code> 通过委员会评审机制，让多条势函数对同一结构进行预测，并记录每个结构的最大力偏差。<code>select_max_modev.py</code> 会从 <code>active.out</code> 和 <code>active.xyz</code> 中选择力偏差较大的结构，写入 <code>selected.xyz</code>。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>python<span class="w"> </span>Scripts/sample_structures/select_max_modev.py<span class="w"> </span><span class="m">200</span><span class="w"> </span><span class="m">0</span>.15
+</code></pre></div>
+<p>交互模式选择 <code>205</code>，会看到：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>+----------------------------------------------------+
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>| Select max force deviation structs from active.xyz |
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a>|     generated by the active command in gpumd.      |
+<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a>+----------------------------------------------------+
+<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a>Input &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)
+<a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a>------------&gt;&gt;
+</code></pre></div>
+<p>需要当前目录下有：</p>
+<ul>
+<li><code>active.out</code></li>
+<li><code>active.xyz</code></li>
+</ul>
+<p>输出：</p>
+<ul>
+<li><code>selected.xyz</code></li>
+</ul>
+<h2 id="_5">示例命令</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
+<a id="__codelineno-16-3" name="__codelineno-16-3" href="#__codelineno-16-3"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
+</code></pre></div>
+<h2 id="_6">常见问题</h2>
+<table>
+<thead>
+<tr>
+<th>问题</th>
+<th>建议</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>FPS 选出太多相似结构</td>
+<td>调大距离阈值或限制最大选择数</td>
+</tr>
+<tr>
+<td>扰动结构不合理</td>
+<td>减小 <code>cell_pert</code> 和 <code>atom_pert</code></td>
+</tr>
+<tr>
+<td><code>active.out</code> 和 <code>active.xyz</code> 不匹配</td>
+<td>确保来自同一次 GPUMD active 运行</td>
+</tr>
+<tr>
+<td>PCA 图异常</td>
+<td>检查 <code>nep.txt</code> 是否和两个数据集元素一致</td>
+</tr>
+</tbody>
+</table>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
+            </div>
+          
+          
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diff --git "a/docs/htmls/zh/\347\273\230\345\233\276\350\204\232\346\234\254.html" "b/docs/htmls/zh/\347\273\230\345\233\276\350\204\232\346\234\254.html"
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+      <a href="../en/quick_start.html" class="md-nav__link">
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+      <a href="../en/command_reference.html" class="md-nav__link">
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+      <a href="../en/format_conversion.html" class="md-nav__link">
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+    Format Conversion
+  
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+      <a href="../en/structure_sampling.html" class="md-nav__link">
+        
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+    Structure Sampling
+  
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+      <a href="../en/workflow_scripts.html" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Workflow Scripts
+  
+
+    
+  </span>
+  
+  
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+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
+    <li class="md-nav__item">
+      <a href="../en/calculator_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Calculator Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
+    <li class="md-nav__item">
+      <a href="../en/analyzer_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Analyzer Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/plot_scripts.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Plot Scripts
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/custom_commands.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Custom Commands
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/active_learning_workflow.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Active Learning Workflow
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/polar_material_analysis.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Polar Material Analysis
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../en/contributing_to_gpumdkit.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Contributing to GPUMDkit
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
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+  
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+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        
+          
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+            
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    简体中文
+  
+
+    
+  </span>
+  
+  
+
+            <span class="md-nav__icon md-icon"></span>
+          </label>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            
+  
+    简体中文
+  
+
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="index.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    GPUMDkit 教程
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        快速入口
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP 训练与预测
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="NEP 训练与预测">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        训练结果
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        预测结果
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        训练/测试集对比
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#parity-plot" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        密度 parity plot
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        力误差分析
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#born" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        电荷和 Born 有效电荷
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#md" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MD 和结构分析绘图
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="MD 和结构分析绘图">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        热力学量
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#rdf" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        RDF
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#vac-pdos" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        VAC 和 PDOS
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        扩散和离子输运
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        热输运
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#dimer" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        描述符、Dimer 和其他分析
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="描述符、Dimer 和其他分析">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        描述符可视化
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#dimer_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Dimer 曲线
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#doas" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        DOAS
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#net-force" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Net force
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        快速表
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        快速入口
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP 训练与预测
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="NEP 训练与预测">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        训练结果
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        预测结果
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        训练/测试集对比
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#parity-plot" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        密度 parity plot
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        力误差分析
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#born" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        电荷和 Born 有效电荷
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#md" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MD 和结构分析绘图
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="MD 和结构分析绘图">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        热力学量
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#rdf" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        RDF
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#vac-pdos" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        VAC 和 PDOS
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        扩散和离子输运
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        热输运
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#dimer" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        描述符、Dimer 和其他分析
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="描述符、Dimer 和其他分析">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        描述符可视化
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#dimer_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Dimer 曲线
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#doas" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        DOAS
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#net-force" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Net force
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        快速表
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>📊 绘图脚本</h1>
+  <p style="text-align: justify;">绘图模块用于可视化 GPUMD、NEP 和 GPUMDkit 计算器产生的数据。</p>
+</div>
+
+<p><strong>脚本位置：</strong> <code>Scripts/plt_scripts/</code></p>
+<h2 id="_1">快速入口</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-plt
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>save
+<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>-h
+</code></pre></div>
+<h2 id="nep">NEP 训练与预测</h2>
+<h3 id="_2">训练结果</h3>
+<p>读取 <code>loss.out</code>、<code>energy_train.out</code>、<code>force_train.out</code>、<code>virial_train.out</code>，绘制 loss 和能量/力/virial 的 parity plot。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/train.png" alt="NEP training results" width="75%" />
+</div>
+
+<h3 id="_3">预测结果</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>prediction
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/prediction.png" alt="NEP prediction results" width="75%" />
+</div>
+
+<h3 id="_4">训练/测试集对比</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train_test
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/train_test.png" alt="NEP train and test comparison" width="75%" />
+</div>
+
+<h3 id="parity-plot">密度 parity plot</h3>
+<p>大数据集散点太密时，密度图更容易观察误差分布：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>parity_density
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/parity_plot_density.png" alt="Parity density plot" width="70%" />
+</div>
+
+<h3 id="_5">力误差分析</h3>
+<p><code>plt_force_errors.py</code> 参考 <a href="https://doi.org/10.1038/s41524-023-01123-3">Liu et al.</a> 的方式分析力大小误差和角度误差。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>force_errors
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/force_errors.png" alt="Force error analysis" width="70%" />
+</div>
+
+<h3 id="born">电荷和 Born 有效电荷</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>charge
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>born_charge
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>bec
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/charge.png" alt="Charge distribution" width="45%" />
+  <img src="../../Gallery/born_charge.png" alt="Born effective charge parity plot" width="45%" />
+</div>
+
+<h2 id="md">MD 和结构分析绘图</h2>
+<h3 id="_6">热力学量</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo2
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo3
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/thermo.png" alt="Thermo plot" width="75%" />
+</div>
+
+<h3 id="rdf">RDF</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf<span class="w"> </span>&lt;column&gt;
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
+  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
+</div>
+
+<h3 id="vac-pdos">VAC 和 PDOS</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos<span class="w"> </span>save
+</code></pre></div>
+<p>输入文件通常包括 <code>model.xyz</code>、<code>run.in</code>、<code>dos.out</code>、<code>mvac.out</code>。</p>
+<div align="center">
+  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
+  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
+</div>
+
+<h2 id="_7">扩散和离子输运</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd_conv
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_d
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_sigma
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="Mean square displacement" width="45%" />
+  <img src="../../Gallery/sdc.png" alt="Self-diffusion coefficient" width="45%" />
+</div>
+
+<p>Arrhenius 图：</p>
+<div align="center">
+  <img src="../../Gallery/Arrhenius_D.png" alt="Arrhenius diffusivity" width="55%" />
+  <img src="../../Gallery/Arrhenius_sigma.png" alt="Arrhenius ionic conductivity" width="55%" />
+</div>
+
+<h2 id="_8">热输运</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>emd<span class="w"> </span>x
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>nemd<span class="w"> </span><span class="o">[</span>real_length<span class="o">]</span><span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>hnemd<span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/emd.png" alt="EMD thermal conductivity" width="70%" />
+  <img src="../../Gallery/nemd.png" alt="NEMD results" width="70%" />
+  <img src="../../Gallery/hnemd.png" alt="HNEMD results" width="70%" />
+</div>
+
+<h2 id="dimer">描述符、Dimer 和其他分析</h2>
+<h3 id="_9">描述符可视化</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
+<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/des_umap.png" alt="UMAP descriptor visualization" width="52%" />
+</div>
+
+<h3 id="dimer_1">Dimer 曲线</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span>nep.txt
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/dimer_nep.png" alt="Dimer NEP curve" width="45%" />
+  <img src="../../Gallery/dimer.png" alt="Dimer comparison" width="45%" />
+</div>
+
+<p><strong>Reference:</strong> <a href="https://doi.org/10.1021/acs.jcim.5c02335">J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</a></p>
+<h3 id="doas">DOAS</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
+</div>
+
+<h3 id="net-force">Net force</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>net_force<span class="w"> </span>train.xyz
+</code></pre></div>
+<p><strong>Reference:</strong> <a href="https://arxiv.org/abs/2510.19774">arXiv:2510.19774</a></p>
+<div align="center">
+  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
+</div>
+
+<h2 id="_10">快速表</h2>
+<table>
+<thead>
+<tr>
+<th>命令</th>
+<th>输入文件</th>
+<th>用途</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>train</code></td>
+<td><code>loss.out</code>, <code>*_train.out</code></td>
+<td>NEP 训练结果</td>
+</tr>
+<tr>
+<td><code>prediction</code></td>
+<td><code>*_test.out</code></td>
+<td>NEP 预测结果</td>
+</tr>
+<tr>
+<td><code>thermo</code></td>
+<td><code>thermo.out</code></td>
+<td>热力学量</td>
+</tr>
+<tr>
+<td><code>msd</code></td>
+<td><code>msd.out</code></td>
+<td>均方位移</td>
+</tr>
+<tr>
+<td><code>sdc</code></td>
+<td><code>msd.out</code></td>
+<td>自扩散系数</td>
+</tr>
+<tr>
+<td><code>rdf</code></td>
+<td><code>rdf.out</code></td>
+<td>径向分布函数</td>
+</tr>
+<tr>
+<td><code>pdos</code></td>
+<td><code>dos.out</code>, <code>mvac.out</code></td>
+<td>VAC 和 PDOS</td>
+</tr>
+<tr>
+<td><code>emd</code>/<code>nemd</code>/<code>hnemd</code></td>
+<td>热输运输出</td>
+<td>热导率分析</td>
+</tr>
+<tr>
+<td><code>des</code></td>
+<td><code>descriptors.npy</code></td>
+<td>描述符降维</td>
+</tr>
+<tr>
+<td><code>dimer</code></td>
+<td><code>nep.txt</code></td>
+<td>二聚体能量/力曲线</td>
+</tr>
+<tr>
+<td><code>doas</code></td>
+<td><code>doas.out</code></td>
+<td>原子态密度</td>
+</tr>
+</tbody>
+</table>
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              </article>
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+      <a href="../en/structure_sampling.html" class="md-nav__link">
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+      <a href="../en/plot_scripts.html" class="md-nav__link">
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+      <a href="../en/custom_commands.html" class="md-nav__link">
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+      <a href="../en/active_learning_workflow.html" class="md-nav__link">
+        
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+    
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+    Active Learning Workflow
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+      <a href="../en/polar_material_analysis.html" class="md-nav__link">
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+    Polar Material Analysis
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+      <a href="../en/contributing_to_gpumdkit.html" class="md-nav__link">
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+    
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+    Contributing to GPUMDkit
+  
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+  
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+      <a href="index.html" class="md-nav__link">
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+    
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+    GPUMDkit 教程
+  
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+    
+  </span>
+  
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+
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+    </li>
+  
+
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
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+  
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+      <a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
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+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        设置
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="示例">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        简单问候
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        带必需参数的命令
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        调用外部脚本
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        进阶示例
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="进阶示例">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        批处理绘图
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        训练集分析流程
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        自定义数据准备流程
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        使用建议
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
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+                
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+  
+  
+  
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+      <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        设置
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="示例">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        简单问候
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        带必需参数的命令
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        调用外部脚本
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        进阶示例
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="进阶示例">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        批处理绘图
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        训练集分析流程
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        自定义数据准备流程
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        使用建议
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🔧 自定义命令</h1>
+  <p style="text-align: justify;">GPUMDkit 支持从 <strong>~/.gpumdkit.in</strong> 加载自定义命令。你可以把常用脚本或工作流封装成 <code>custom_</code> 开头的 Bash 函数，然后通过 <code>gpumdkit.sh -命令名</code> 调用。</p>
+</div>
+
+<h2 id="_1">设置</h2>
+<p>编辑配置文件：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>vi<span class="w"> </span>~/.gpumdkit.in
+</code></pre></div>
+<p>自定义函数需要使用 <code>custom_</code> 前缀。</p>
+<h2 id="_2">示例</h2>
+<h3 id="_3">简单问候</h3>
+<p>在 <code>~/.gpumdkit.in</code> 中写入：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>custom_hello<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Hello, GPUMDkit user! This is a custom command.&quot;</span>
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Current GPUMDkit path: </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a><span class="o">}</span>
+</code></pre></div>
+<p>然后运行：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-hello
+</code></pre></div>
+<p>你会看到类似输出：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>Hello, GPUMDkit user! This is a custom command.
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>Current GPUMDkit path: /home/yanzihan/software/GPUMDkit
+</code></pre></div>
+<h3 id="_4">带必需参数的命令</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>custom_greet<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a><span class="w">    </span><span class="nv">name</span><span class="o">=</span><span class="nv">$1</span>
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Hello, </span><span class="si">${</span><span class="nv">name</span><span class="si">}</span><span class="s2">!&quot;</span>
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="o">}</span>
+</code></pre></div>
+<p>运行：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-greet<span class="w"> </span>Zihan
+</code></pre></div>
+<p>输出：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>Hello, Zihan!
+</code></pre></div>
+<p>传递参数时，可以用 <code>"$@"</code> 安全地转发所有参数；如果需要从第一个参数开始引用，也可以使用 <code>${@:1}</code>。</p>
+<h3 id="_5">调用外部脚本</h3>
+<p>如果希望像调用 GPUMDkit 内置命令一样调用自己的脚本：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>custom_nepanalyse<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="w">    </span>python<span class="w"> </span>~/my_gpumd_tools/analyse_nep.py
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="o">}</span>
+</code></pre></div>
+<p>运行：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-nepanalyse
+</code></pre></div>
+<h2 id="_6">进阶示例</h2>
+<h3 id="_7">批处理绘图</h3>
+<p>对多个目录批量绘图：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>custom_batch_plot<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a><span class="w">    </span><span class="k">for</span><span class="w"> </span>dir<span class="w"> </span><span class="k">in</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$@</span><span class="s2">&quot;</span><span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a><span class="w">        </span><span class="nb">cd</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$dir</span><span class="s2">&quot;</span>
+<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a><span class="w">        </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo<span class="w"> </span>save
+<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a><span class="w">        </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd<span class="w"> </span>save
+<a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a><span class="w">        </span><span class="nb">cd</span><span class="w"> </span>..
+<a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a><span class="w">    </span><span class="k">done</span>
+<a id="__codelineno-9-8" name="__codelineno-9-8" href="#__codelineno-9-8"></a><span class="o">}</span>
+</code></pre></div>
+<p>用法：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-batch_plot<span class="w"> </span>dir1<span class="w"> </span>dir2<span class="w"> </span>dir3
+</code></pre></div>
+<h3 id="_8">训练集分析流程</h3>
+<p>把多个分析命令组合成一个入口：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>custom_analyze_training<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="w">    </span><span class="nv">xyz_file</span><span class="o">=</span><span class="nv">$1</span>
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Analyzing </span><span class="nv">$xyz_file</span><span class="s2">...&quot;</span>
+<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a>
+<a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$xyz_file</span><span class="s2">&quot;</span><span class="w"> </span>force
+<a id="__codelineno-11-6" name="__codelineno-11-6" href="#__codelineno-11-6"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$xyz_file</span><span class="s2">&quot;</span>
+<a id="__codelineno-11-7" name="__codelineno-11-7" href="#__codelineno-11-7"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$xyz_file</span><span class="s2">&quot;</span>
+<a id="__codelineno-11-8" name="__codelineno-11-8" href="#__codelineno-11-8"></a>
+<a id="__codelineno-11-9" name="__codelineno-11-9" href="#__codelineno-11-9"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Analysis complete!&quot;</span>
+<a id="__codelineno-11-10" name="__codelineno-11-10" href="#__codelineno-11-10"></a><span class="o">}</span>
+</code></pre></div>
+<p>用法：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-analyze_training<span class="w"> </span>train.xyz
+</code></pre></div>
+<h3 id="_9">自定义数据准备流程</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>custom_prep_training<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Preparing training data...&quot;</span>
+<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>
+<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-out2xyz<span class="w"> </span>./
+<a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span><span class="m">30</span>
+<a id="__codelineno-13-6" name="__codelineno-13-6" href="#__codelineno-13-6"></a><span class="w">    </span>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>filtered_force.xyz<span class="w"> </span>energy
+<a id="__codelineno-13-7" name="__codelineno-13-7" href="#__codelineno-13-7"></a>
+<a id="__codelineno-13-8" name="__codelineno-13-8" href="#__codelineno-13-8"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Training data ready!&quot;</span>
+<a id="__codelineno-13-9" name="__codelineno-13-9" href="#__codelineno-13-9"></a><span class="o">}</span>
+</code></pre></div>
+<p>用法：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-prep_training
+</code></pre></div>
+<h2 id="_10">使用建议</h2>
+<ul>
+<li>命令名尽量清楚，例如 <code>custom_analyze_training</code> 比 <code>custom_at</code> 更容易维护。</li>
+<li>对需要参数的命令，建议在参数为空时打印用法提示。</li>
+<li>调用外部脚本时，尽量用 <code>"$@"</code> 保留参数中的空格和特殊字符。</li>
+<li>批处理目录时，注意使用 <code>cd "$dir"</code>，避免路径中有空格时出错。</li>
+</ul>
+
+
+
+
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+
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+              </article>
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diff --git "a/docs/htmls/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.html" "b/docs/htmls/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.html"
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+      <a href="../en/custom_commands.html" class="md-nav__link">
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+      <a href="../en/active_learning_workflow.html" class="md-nav__link">
+        
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+    
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+  
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+      <a href="../en/polar_material_analysis.html" class="md-nav__link">
+        
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+    
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+    Polar Material Analysis
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+      <a href="../en/contributing_to_gpumdkit.html" class="md-nav__link">
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+    Contributing to GPUMDkit
+  
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+  
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+    GPUMDkit 教程
+  
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+  
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    快速入门
+  
+
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+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
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+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
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+      <a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
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+      <a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    结构采样
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
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+      <a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
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+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html" class="md-nav__link md-nav__link--active">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        功能概览
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        离子电导率
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#msd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        从轨迹计算 MSD
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP 预测性质
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP 描述符
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#doas" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        DOAS
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#neb" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEB 和结构优化
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        铁电和极性材料工具
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="铁电和极性材料工具">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        邻居列表
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        位移
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        平均结构
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        八面体倾转
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#abo3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        ABO3 局域极化
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
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+    </li>
+  
+
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    分析工具
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    绘图脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
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+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    贡献指南
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        功能概览
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        离子电导率
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#msd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        从轨迹计算 MSD
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP 预测性质
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#nep_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP 描述符
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#doas" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        DOAS
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#neb" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEB 和结构优化
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        铁电和极性材料工具
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="铁电和极性材料工具">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        邻居列表
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        位移
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        平均结构
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        八面体倾转
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#abo3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        ABO3 局域极化
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🧮 计算器脚本</h1>
+  <p style="text-align: justify;">计算器模块用于从 MD 轨迹、NEP 模型和结构文件中计算材料性质。</p>
+</div>
+
+<p><strong>脚本位置：</strong> <code>Scripts/calculators/</code></p>
+<h2 id="_1">功能概览</h2>
+<table>
+<thead>
+<tr>
+<th>任务</th>
+<th>命令</th>
+<th>主要输入</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>离子电导率</td>
+<td><code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code></td>
+<td><code>msd.out</code>、<code>thermo.out</code>、<code>model.xyz</code></td>
+</tr>
+<tr>
+<td>MSD</td>
+<td><code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code></td>
+<td>extxyz 轨迹</td>
+</tr>
+<tr>
+<td>NEP 预测</td>
+<td><code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code></td>
+<td>extxyz + NEP 模型</td>
+</tr>
+<tr>
+<td>NEP 描述符</td>
+<td><code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code></td>
+<td>extxyz + NEP 模型</td>
+</tr>
+<tr>
+<td>DOAS</td>
+<td><code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code></td>
+<td>extxyz + NEP 模型</td>
+</tr>
+<tr>
+<td>NEB</td>
+<td><code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code></td>
+<td>初末态结构</td>
+</tr>
+<tr>
+<td>结构优化</td>
+<td><code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code></td>
+<td>结构 + NEP 模型</td>
+</tr>
+<tr>
+<td>邻居列表</td>
+<td><code>gpumdkit.sh -calc nlist [args...]</code></td>
+<td>结构</td>
+</tr>
+<tr>
+<td>位移</td>
+<td><code>gpumdkit.sh -calc disp [args...]</code></td>
+<td>轨迹 + 邻居列表</td>
+</tr>
+<tr>
+<td>平均结构</td>
+<td><code>gpumdkit.sh -calc avg-struct [args...]</code></td>
+<td>轨迹</td>
+</tr>
+<tr>
+<td>八面体倾转</td>
+<td><code>gpumdkit.sh -calc oct-tilt [args...]</code></td>
+<td>轨迹 + B-O 邻居列表</td>
+</tr>
+<tr>
+<td>ABO3 极化</td>
+<td><code>gpumdkit.sh -calc pol-abo3 [args...]</code></td>
+<td>轨迹 + 邻居列表</td>
+</tr>
+</tbody>
+</table>
+<p>查看完整帮助：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>-h
+</code></pre></div>
+<p>命令行帮助表类似：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>|                                      CALCULATOR TOOLS                                                 |
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>+-------------------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |
+<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a>| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |
+<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a>| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |
+<a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a>| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |
+<a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a>| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |
+<a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a>| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |
+<a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a>| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |
+<a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a>| nlist [script args...]                        Build neighbor lists                                    |
+<a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></a>| disp [script args...]                         Calculate displacement from trajectory                  |
+<a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a>| avg-struct [script args...]                   Calculate averaged structure                            |
+<a id="__codelineno-1-16" name="__codelineno-1-16" href="#__codelineno-1-16"></a>| oct-tilt [script args...]                     Calculate octahedral tilt                               |
+<a id="__codelineno-1-17" name="__codelineno-1-17" href="#__codelineno-1-17"></a>| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |
+<a id="__codelineno-1-18" name="__codelineno-1-18" href="#__codelineno-1-18"></a>+-------------------------------------------------------------------------------------------------------+
+</code></pre></div>
+<p>交互模式中选择 <code>4) Calculators</code>，菜单如下：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>|                     CALCULATOR TOOLS                     |
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>| 401) Calc ionic conductivity                             |
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>| 402) Calc properties by nep                              |
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>| 403) Calc descriptors of specific elements               |
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>| 404) Calc density of atomistic states (DOAS)             |
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>| 405) Calc nudged elastic band (NEB) by nep               |
+<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>| 406) Build neighbor list                                 |
+<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a>| 407) Calc displacement from trajectory                   |
+<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a>| 408) Calc averaged structure                             |
+<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a>| 409) Calc octahedral tilt                                |
+<a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a>| 410) Calc polarization for ABO3                          |
+<a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a>| 411) Minimize structure by nep                           |
+<a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a>| 412) Calc mean square displacement (MSD) from trajectory |
+<a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-17" name="__codelineno-2-17" href="#__codelineno-2-17"></a>| 000) Return to the main menu                             |
+<a id="__codelineno-2-18" name="__codelineno-2-18" href="#__codelineno-2-18"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-19" name="__codelineno-2-19" href="#__codelineno-2-19"></a>Input the function number:
+</code></pre></div>
+<h2 id="_2">离子电导率</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>ionic-cond<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>
+</code></pre></div>
+<p>交互模式选择 <code>401</code>，会看到：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>| This function calls the script in calculators   |
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>| Script: calc_ion_conductivity.py                |
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a>| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>&gt;-------------------------------------------------&lt;
+<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a>Input &lt;element&gt; &lt;charge&gt; (eg. Li 1)
+<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a>------------&gt;&gt;
+</code></pre></div>
+<p>常用输入文件：</p>
+<table>
+<thead>
+<tr>
+<th>文件</th>
+<th>作用</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>msd.out</code></td>
+<td>必需，MSD 数据</td>
+</tr>
+<tr>
+<td><code>thermo.out</code></td>
+<td>可选，自动读取温度</td>
+</tr>
+<tr>
+<td><code>model.xyz</code></td>
+<td>可选，自动读取体积和离子数</td>
+</tr>
+<tr>
+<td><code>run.in</code></td>
+<td>可选，识别扩胞信息</td>
+</tr>
+</tbody>
+</table>
+<p>如果缺少自动识别所需文件，脚本会交互式询问温度、体积和离子数。</p>
+<p>手动模式的提示类似：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>Files &#39;thermo.out&#39; and &#39;model.xyz&#39; are not found.
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>Please provide the following values:
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>---------------------------&gt;
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>Enter average temperature (in K):
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>Enter system volume (in A^3):
+<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>Enter number of ions:
+</code></pre></div>
+<h2 id="msd">从轨迹计算 MSD</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">5000</span>
+</code></pre></div>
+<p>交互模式选择 <code>412</code>，会看到：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>  Optional argument: max_corr_steps (default: frame number)
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>Example: dump.xyz Li 10
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>------------&gt;&gt;
+</code></pre></div>
+<p>参数含义：</p>
+<table>
+<thead>
+<tr>
+<th>参数</th>
+<th>含义</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>dump.xyz</code></td>
+<td>输入轨迹</td>
+</tr>
+<tr>
+<td><code>Li</code></td>
+<td>目标扩散元素</td>
+</tr>
+<tr>
+<td><code>10</code></td>
+<td>帧间隔，单位 fs</td>
+</tr>
+<tr>
+<td><code>5000</code></td>
+<td>可选，最大相关步数</td>
+</tr>
+</tbody>
+</table>
+<p>输出：</p>
+<ul>
+<li><code>msd.out</code></li>
+</ul>
+<p>随后可绘图：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
+  <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
+</div>
+
+<h2 id="nep">NEP 预测性质</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nep<span class="w"> </span>structures.xyz<span class="w"> </span>predictions.xyz<span class="w"> </span>nep.txt
+</code></pre></div>
+<p>该功能使用训练好的 NEP 模型计算能量、力和应力。只有当你确认模型质量可靠，并明确希望使用 NEP 作为替代计算器时，才建议使用它。</p>
+<h2 id="nep_1">NEP 描述符</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
+</code></pre></div>
+<p>用途包括：</p>
+<ul>
+<li>用 PCA/UMAP 可视化局域环境；</li>
+<li>比较训练集和候选结构；</li>
+<li>判断新数据是否扩展了描述符空间。</li>
+</ul>
+<p>绘图：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/des_umap.png" alt="Descriptor UMAP" width="52%" />
+</div>
+
+<h2 id="doas">DOAS</h2>
+<p><code>calc_doas.py</code> 用于计算 <a href="https://doi.org/10.1002/anie.202215544">Wang et al.</a> 提出的 density of atomistic states。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>doas<span class="w"> </span>structures.xyz<span class="w"> </span>nep.txt<span class="w"> </span>doas.out
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
+</code></pre></div>
+<p>脚本会：</p>
+<ol>
+<li>读取所有结构；</li>
+<li>使用 NEP 进行结构优化；</li>
+<li>提取每个原子的能量；</li>
+<li>按元素分组输出；</li>
+<li>用绘图脚本可视化分布。</li>
+</ol>
+<div align="center">
+  <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
+</div>
+
+<h2 id="neb">NEB 和结构优化</h2>
+<p>NEB：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>neb<span class="w"> </span>initial.xyz<span class="w"> </span>final.xyz<span class="w"> </span><span class="m">9</span><span class="w"> </span>nep.txt
+</code></pre></div>
+<p>结构优化：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>minimize<span class="w"> </span>POSCAR<span class="w"> </span>nep.txt<span class="w"> </span><span class="m">0</span>.01<span class="w"> </span><span class="m">1000</span>
+</code></pre></div>
+<p>输出包括：</p>
+<ul>
+<li><code>minimize.xyz</code></li>
+<li><code>minimize.log</code></li>
+</ul>
+<h2 id="_3">铁电和极性材料工具</h2>
+<p>这些工具需要 <code>ferrodispcalc</code>：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
+</code></pre></div>
+<p><code>ferrodispcalc</code> 目前没有需要额外引用的论文。</p>
+<h3 id="_4">邻居列表</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+</code></pre></div>
+<h3 id="_5">位移</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+</code></pre></div>
+<h3 id="_6">平均结构</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+</code></pre></div>
+<h3 id="_7">八面体倾转</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>octahedral_tilt.dat
+</code></pre></div>
+<h3 id="abo3">ABO3 局域极化</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-o<span class="w"> </span>polarization.dat
+</code></pre></div>
+<p><code>--bec</code> 应根据你的体系或参考数据设置。</p>
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+    GPUMDkit 教程
+  
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+    
+  
+    快速入门
+  
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+  
+
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+      <a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    命令参考
+  
+
+    
+  </span>
+  
+  
+
+      </a>
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+  
+
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+            
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    格式转换
+  
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+  
+  
+
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+  
+
+              
+            
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
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+  
+
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+  
+
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+  
+
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    工作流脚本
+  
+
+    
+  </span>
+  
+  
+
+      </a>
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+  
+
+              
+            
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+  
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+  <span class="md-ellipsis">
+    
+  
+    计算器脚本
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+
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+  
+
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+    分析工具
+  
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+
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+
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+    
+  
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+  
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+
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+
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+  
+  <span class="md-ellipsis">
+    
+  
+    自定义命令
+  
+
+    
+  </span>
+  
+  
+
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+
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    主动学习工作流
+  
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+  
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+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    极性材料分析
+  
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+  </span>
+  
+  
+
+      </a>
+    </li>
+  
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+  <span class="md-ellipsis">
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+    贡献指南
+  
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+
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+  
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+    <label class="md-nav__title" for="__toc">
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+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        目录
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        开发限制和指南
+      
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+  
+    <nav class="md-nav" aria-label="开发限制和指南">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        语言要求
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        模块化和可复用性
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        代码风格
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        文档
+      
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+      
+        <li class="md-nav__item">
+  <a href="#bug" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        报告 Bug
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        提出功能建议
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        贡献代码
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="贡献代码">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#fork" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Fork 并克隆仓库
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        创建功能分支
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        进行修改
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="进行修改">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_11" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互模式贡献
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        命令行模式贡献
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#tab" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        更新 Tab 补全
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        代码风格和最佳实践
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_14" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        测试你的修改
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        提交信息
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#pull-request" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        推送并打开 Pull Request
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_16" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        有问题或需要帮助？
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        目录
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        开发限制和指南
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="开发限制和指南">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        语言要求
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        模块化和可复用性
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        代码风格
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        文档
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#bug" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        报告 Bug
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        提出功能建议
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        贡献代码
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="贡献代码">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#fork" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Fork 并克隆仓库
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        创建功能分支
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        进行修改
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="进行修改">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_11" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互模式贡献
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        命令行模式贡献
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#tab" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        更新 Tab 补全
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        代码风格和最佳实践
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_14" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        测试你的修改
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        提交信息
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#pull-request" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        推送并打开 Pull Request
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_16" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        有问题或需要帮助？
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+
+  
+  
+
+
+<div align="center">
+  <h1>🤝 贡献指南</h1>
+  <p style="text-align: justify;">感谢你有兴趣为 <strong>GPUMDkit</strong> 做贡献。我们非常感谢你愿意花时间和精力帮助改进这个工具包。</p>
+</div>
+
+<p><code>GPUMDkit</code> 是一个开源软件包。无论是修复 bug、添加新功能、改进文档，还是提出使用建议，我们都欢迎社区贡献。</p>
+<hr />
+<h2 id="_1">目录</h2>
+<ul>
+<li>开发限制和指南</li>
+<li>报告 Bug</li>
+<li>提出功能建议</li>
+<li>贡献代码</li>
+<li>Fork 并克隆仓库</li>
+<li>创建功能分支</li>
+<li>进行修改</li>
+<li>交互模式贡献</li>
+<li>命令行模式贡献</li>
+<li>更新 Tab 补全</li>
+<li>代码风格和最佳实践</li>
+<li>测试你的修改</li>
+<li>提交信息</li>
+<li>推送并打开 Pull Request</li>
+</ul>
+<hr />
+<h2 id="_2">开发限制和指南</h2>
+<p>为了保持项目代码质量和一致性，请遵守以下指南。</p>
+<h3 id="_3">语言要求</h3>
+<ul>
+<li><strong>所有代码应使用英文编写</strong>：包括变量名、函数名、注释、docstring、提交信息和文档。</li>
+<li>我们理解贡献者可能来自不同背景，但使用英文可以让代码库对更广泛的用户保持可读和可维护。</li>
+</ul>
+<h3 id="_4">模块化和可复用性</h3>
+<ul>
+<li><strong>编写模块化、可复用的代码</strong>：函数和脚本应尽量具有灵活性。</li>
+<li><strong>优先通过参数传递信息，避免硬编码</strong>：使用函数参数、命令行参数或配置文件，而不是把数值直接写死。不过，某些文件名是 GPUMD 和 NEP 程序固定要求的，例如 <code>train.xyz</code>、<code>thermo.out</code>，这类情况可以按需要保留固定文件名。</li>
+<li><strong>示例</strong>：</li>
+</ul>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="c1"># Good: accepts parameters</span>
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="k">function</span><span class="w"> </span>convert_file<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="w">    </span><span class="nb">local</span><span class="w"> </span><span class="nv">input_file</span><span class="o">=</span><span class="nv">$1</span>
+<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a><span class="w">    </span><span class="nb">local</span><span class="w"> </span><span class="nv">output_file</span><span class="o">=</span><span class="nv">$2</span>
+<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a><span class="w">    </span><span class="c1"># processing logic</span>
+<a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a><span class="o">}</span>
+<a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a>
+<a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a><span class="c1"># Avoid: hardcoded values (unless required by GPUMD/NEP)</span>
+<a id="__codelineno-0-9" name="__codelineno-0-9" href="#__codelineno-0-9"></a><span class="k">function</span><span class="w"> </span>convert_file<span class="o">()</span><span class="w"> </span><span class="o">{</span>
+<a id="__codelineno-0-10" name="__codelineno-0-10" href="#__codelineno-0-10"></a><span class="w">    </span><span class="nb">local</span><span class="w"> </span><span class="nv">input_file</span><span class="o">=</span><span class="s2">&quot;hardcoded_input.xyz&quot;</span>
+<a id="__codelineno-0-11" name="__codelineno-0-11" href="#__codelineno-0-11"></a><span class="w">    </span><span class="c1"># processing logic</span>
+<a id="__codelineno-0-12" name="__codelineno-0-12" href="#__codelineno-0-12"></a><span class="o">}</span>
+</code></pre></div>
+<h3 id="_5">代码风格</h3>
+<ul>
+<li>编写清晰、易于他人维护和修改的代码。</li>
+<li>使用有意义的变量名和函数名。</li>
+<li>在必要时添加注释，解释复杂逻辑。</li>
+</ul>
+<h3 id="_6">文档</h3>
+<ul>
+<li>确保帮助信息（例如 <code>-h</code> 参数）清晰、准确。</li>
+<li><code>docs/</code> 目录中的文档通常由维护者更新，因此一般不需要贡献者直接修改。</li>
+</ul>
+<hr />
+<h2 id="bug">报告 Bug</h2>
+<p>如果你遇到 bug，请通过 GitHub Issues 帮助我们定位和修复：</p>
+<ol>
+<li><strong>先搜索已有 issue</strong>，确认这个 bug 是否已经被报告过。</li>
+<li><strong>如果还没有报告，请创建新 issue</strong>：<a href="https://github.com/zhyan0603/GPUMDkit/issues/new">Create an Issue</a></li>
+<li><strong>详细描述问题</strong>，如果可以，请提供测试文件。</li>
+</ol>
+<p>你也可以通过以下方式联系我们：</p>
+<ul>
+<li><strong>QQ 群</strong>：825696376</li>
+<li><strong>Email</strong>：yanzihan@westlake.edu.cn</li>
+<li><strong>脚本开发者</strong>：联系脚本文件头部列出的开发者</li>
+</ul>
+<hr />
+<h2 id="_7">提出功能建议</h2>
+<p>我们欢迎新的功能建议。提出新功能时，可以按以下方式进行：</p>
+<ol>
+<li><strong>先搜索已有 issue</strong>，确认是否已经有人提出过类似建议。</li>
+<li><strong>创建新的功能请求</strong>：<a href="https://github.com/zhyan0603/GPUMDkit/issues/new">Create a Feature Request</a>，并提及 @zhyan0603。</li>
+<li><strong>清楚描述你的需求</strong>，并说明它为什么有用。</li>
+</ol>
+<hr />
+<h2 id="_8">贡献代码</h2>
+<h3 id="fork">Fork 并克隆仓库</h3>
+<ol>
+<li>
+<p>在 GitHub 的 <a href="https://github.com/zhyan0603/GPUMDkit">GPUMDkit 仓库页面</a>右上角点击 "Fork"，将仓库 fork 到自己的账号下。</p>
+</li>
+<li>
+<p>将你的 fork 克隆到本地：</p>
+</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/YOUR_USERNAME/GPUMDkit.git
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
+</code></pre></div>
+<ol>
+<li>设置 upstream remote，方便和主仓库保持同步：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>git<span class="w"> </span>remote<span class="w"> </span>add<span class="w"> </span>upstream<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
+</code></pre></div>
+<h3 id="_9">创建功能分支</h3>
+<p>为你的修改创建一个新分支：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># Create and checkout a new branch from main</span>
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>git<span class="w"> </span>checkout<span class="w"> </span>-b<span class="w"> </span>your-branch-name
+</code></pre></div>
+<p>分支名可以按你的习惯命名。</p>
+<h3 id="_10">进行修改</h3>
+<p><code>GPUMDkit</code> 的结构包括：</p>
+<ul>
+<li><strong><code>gpumdkit.sh</code></strong>：主入口 Bash 脚本，负责交互菜单模式和命令行模式。</li>
+<li><strong><code>Scripts/</code></strong>：按功能分类组织的 Python 工具脚本。</li>
+<li><code>plt_scripts/</code>：绘图脚本</li>
+<li><code>calculators/</code>：计算工具</li>
+<li><code>format_conversion/</code>：格式转换工具</li>
+<li><code>workflow/</code>：工作流自动化</li>
+<li><code>sample_structures/</code>：结构采样工具</li>
+<li><code>analyzer/</code>：分析工具</li>
+<li><code>utils/</code>：实用函数，包括用于 Tab 补全的 <code>completion.sh</code></li>
+<li><strong><code>src/</code></strong>：包含交互模式菜单函数的 Shell 脚本。</li>
+<li><code>f1_format_conversions.sh</code></li>
+<li><code>f2_sample_structures.sh</code></li>
+<li><code>f3_workflows.sh</code></li>
+<li><code>f4_calculators.sh</code></li>
+<li><code>f5_analyzers.sh</code></li>
+<li><code>f6_plots.sh</code></li>
+<li><code>f7_utilities.sh</code></li>
+<li><strong><code>docs/</code></strong>：文档文件。</li>
+</ul>
+<h4 id="_11">交互模式贡献</h4>
+<p>如果要添加一个可通过交互菜单访问的新功能：</p>
+<ol>
+<li><strong>在合适的 <code>Scripts/</code> 子目录中创建实现脚本</strong>：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="c1"># Example: Add a new format conversion script</span>
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>touch<span class="w"> </span>Scripts/format_conversion/new_converter.py
+</code></pre></div>
+<ol>
+<li>
+<p><strong>实现你的功能</strong>，并遵循模块化指南：接受参数，避免不必要的硬编码。</p>
+</li>
+<li>
+<p><strong>在对应的 <code>src/</code> 文件中添加包装函数</strong>：</p>
+</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="c1"># Example: Edit src/f1_format_conversions.sh</span>
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>vim<span class="w"> </span>src/f1_format_conversions.sh
+</code></pre></div>
+<p>添加一个新函数：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="k">function</span><span class="w"> </span>f106_new_converter<span class="o">(){</span>
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Calling the script in Scripts/format_conversion |&quot;</span>
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Script: new_converter.py                        |&quot;</span>
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Developer: Your Name (your@email.com)           |&quot;</span>
+<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
+<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Input the required parameters:&quot;</span>
+<a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Example: input.xyz output.lmp&quot;</span>
+<a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ------------&gt;&gt;&quot;</span>
+<a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="s2">&quot; &quot;</span><span class="w"> </span>converter_params
+<a id="__codelineno-6-11" name="__codelineno-6-11" href="#__codelineno-6-11"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ---------------------------------------------------&quot;</span>
+<a id="__codelineno-6-12" name="__codelineno-6-12" href="#__codelineno-6-12"></a>python<span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/Scripts/format_conversion/new_converter.py<span class="w"> </span><span class="si">${</span><span class="nv">converter_params</span><span class="si">}</span>
+<a id="__codelineno-6-13" name="__codelineno-6-13" href="#__codelineno-6-13"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Code path: </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span><span class="s2">/Scripts/format_conversion/new_converter.py&quot;</span>
+<a id="__codelineno-6-14" name="__codelineno-6-14" href="#__codelineno-6-14"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ---------------------------------------------------&quot;</span>
+<a id="__codelineno-6-15" name="__codelineno-6-15" href="#__codelineno-6-15"></a><span class="o">}</span>
+</code></pre></div>
+<ol>
+<li><strong>更新 <code>gpumdkit.sh</code> 中的菜单显示</strong>：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># Find the menu() function and update it if needed</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="c1"># Find the array_choice array and add your new choice number</span>
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="nv">array_choice</span><span class="o">=(</span>
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="w">    </span><span class="s2">&quot;0&quot;</span><span class="w"> </span><span class="s2">&quot;1&quot;</span><span class="w"> </span><span class="s2">&quot;101&quot;</span><span class="w"> </span><span class="s2">&quot;102&quot;</span><span class="w"> </span><span class="s2">&quot;103&quot;</span><span class="w"> </span><span class="s2">&quot;104&quot;</span><span class="w"> </span><span class="s2">&quot;105&quot;</span><span class="w"> </span><span class="s2">&quot;106&quot;</span><span class="w">  </span><span class="c1"># Added &quot;106&quot;</span>
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a><span class="w">    </span><span class="c1"># ... rest of choices</span>
+<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a><span class="o">)</span>
+</code></pre></div>
+<ol>
+<li><strong>在 <code>gpumdkit.sh</code> 中添加 case 分支</strong>：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="c1"># In the main() function, find the appropriate case statement</span>
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a><span class="k">case</span><span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">choice</span><span class="p">:</span><span class="nv">0</span><span class="p">:</span><span class="nv">1</span><span class="si">}</span><span class="s2">&quot;</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a><span class="w">    </span><span class="c1"># ...</span>
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="w">    </span><span class="s2">&quot;1&quot;</span><span class="o">)</span>
+<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a><span class="w">        </span><span class="nb">source</span><span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/src/f1_format_conversions.sh
+<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a><span class="w">        </span><span class="k">case</span><span class="w"> </span><span class="nv">$choice</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="w">            </span><span class="s2">&quot;1&quot;</span><span class="o">)</span><span class="w"> </span>f1_format_conversion<span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a><span class="w">            </span><span class="s2">&quot;101&quot;</span><span class="o">)</span><span class="w"> </span>f101_out2xyz<span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a><span class="w">            </span><span class="c1"># ... existing cases ...</span>
+<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a><span class="w">            </span><span class="s2">&quot;106&quot;</span><span class="o">)</span><span class="w"> </span>f106_new_converter<span class="w"> </span><span class="p">;;</span><span class="w">  </span><span class="c1"># Add your case</span>
+<a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a><span class="w">        </span><span class="k">esac</span><span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></a><span class="w">    </span><span class="c1"># ...</span>
+<a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a><span class="k">esac</span>
+</code></pre></div>
+<h4 id="_12">命令行模式贡献</h4>
+<p>如果要添加新的命令行 flag 或子命令：</p>
+<ol>
+<li><strong>在合适的 <code>Scripts/</code> 子目录中创建实现脚本</strong>：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="c1"># Example: Add a new analyzer script</span>
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>touch<span class="w"> </span>Scripts/analyzer/analyze_bonds.py
+</code></pre></div>
+<ol>
+<li><strong>实现功能，并明确参数要求</strong>：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="c1"># Example: Scripts/analyzer/analyze_bonds.py</span>
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a><span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="k">def</span><span class="w"> </span><span class="nf">main</span><span class="p">():</span>
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">3</span><span class="p">:</span>
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;&quot;</span><span class="p">)</span>
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a>        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0&quot;</span><span class="p">)</span>
+<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>        <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
+<a id="__codelineno-10-9" name="__codelineno-10-9" href="#__codelineno-10-9"></a>
+<a id="__codelineno-10-10" name="__codelineno-10-10" href="#__codelineno-10-10"></a>    <span class="n">input_file</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<a id="__codelineno-10-11" name="__codelineno-10-11" href="#__codelineno-10-11"></a>    <span class="n">cutoff</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+<a id="__codelineno-10-12" name="__codelineno-10-12" href="#__codelineno-10-12"></a>
+<a id="__codelineno-10-13" name="__codelineno-10-13" href="#__codelineno-10-13"></a>    <span class="c1"># Your implementation here</span>
+<a id="__codelineno-10-14" name="__codelineno-10-14" href="#__codelineno-10-14"></a>
+<a id="__codelineno-10-15" name="__codelineno-10-15" href="#__codelineno-10-15"></a><span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
+<a id="__codelineno-10-16" name="__codelineno-10-16" href="#__codelineno-10-16"></a>    <span class="n">main</span><span class="p">()</span>
+</code></pre></div>
+<ol>
+<li><strong>在 <code>gpumdkit.sh</code> 中添加命令行 flag 处理逻辑</strong>：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="c1"># Find the command-line parsing section (after line ~167)</span>
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="c1"># Add your new flag in the appropriate location</span>
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>
+<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a><span class="k">case</span><span class="w"> </span><span class="nv">$1</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="w">    </span><span class="c1"># ... existing cases ...</span>
+<a id="__codelineno-11-6" name="__codelineno-11-6" href="#__codelineno-11-6"></a><span class="w">    </span>-analyze_bonds<span class="o">)</span>
+<a id="__codelineno-11-7" name="__codelineno-11-7" href="#__codelineno-11-7"></a><span class="w">        </span><span class="k">if</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$3</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span>
+<a id="__codelineno-11-8" name="__codelineno-11-8" href="#__codelineno-11-8"></a><span class="w">            </span>python<span class="w"> </span><span class="si">${</span><span class="nv">analyzer_path</span><span class="si">}</span>/analyze_bonds.py<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$3</span><span class="s2">&quot;</span>
+<a id="__codelineno-11-9" name="__codelineno-11-9" href="#__codelineno-11-9"></a><span class="w">        </span><span class="k">else</span>
+<a id="__codelineno-11-10" name="__codelineno-11-10" href="#__codelineno-11-10"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;&quot;</span>
+<a id="__codelineno-11-11" name="__codelineno-11-11" href="#__codelineno-11-11"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0&quot;</span>
+<a id="__codelineno-11-12" name="__codelineno-11-12" href="#__codelineno-11-12"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Code path: </span><span class="si">${</span><span class="nv">analyzer_path</span><span class="si">}</span><span class="s2">/analyze_bonds.py&quot;</span>
+<a id="__codelineno-11-13" name="__codelineno-11-13" href="#__codelineno-11-13"></a><span class="w">            </span><span class="nb">exit</span><span class="w"> </span><span class="m">1</span>
+<a id="__codelineno-11-14" name="__codelineno-11-14" href="#__codelineno-11-14"></a><span class="w">        </span><span class="k">fi</span><span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-11-15" name="__codelineno-11-15" href="#__codelineno-11-15"></a><span class="w">    </span><span class="c1"># ... rest of cases ...</span>
+<a id="__codelineno-11-16" name="__codelineno-11-16" href="#__codelineno-11-16"></a><span class="k">esac</span>
+</code></pre></div>
+<ol>
+<li><strong>更新 <code>gpumdkit.sh</code> 中的帮助信息</strong>：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="c1"># Find the help_info_table() function and add your command</span>
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a><span class="k">function</span><span class="w"> </span>help_info_table<span class="o">(){</span>
+<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;+====================================== Analysis ===============================================+&quot;</span>
+<a id="__codelineno-12-4" name="__codelineno-12-4" href="#__codelineno-12-4"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |&quot;</span>
+<a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a><span class="w">    </span><span class="c1"># ... rest of help table ...</span>
+<a id="__codelineno-12-6" name="__codelineno-12-6" href="#__codelineno-12-6"></a><span class="o">}</span>
+</code></pre></div>
+<h4 id="tab">更新 Tab 补全</h4>
+<p>添加新的命令行 flag 时，请更新 Tab 补全脚本：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="c1"># Edit Scripts/utils/completion.sh</span>
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>vim<span class="w"> </span>Scripts/utils/completion.sh
+</code></pre></div>
+<p>将新的 flag 加入 <code>opts</code> 变量：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a><span class="c1"># Find the line with local opts=...</span>
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a><span class="nb">local</span><span class="w"> </span><span class="nv">opts</span><span class="o">=</span><span class="s2">&quot;-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ...&quot;</span>
+<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a><span class="c1">#                                                      ^^^^^^^^^^^^^^ Add your flag here</span>
+</code></pre></div>
+<p>如果这个 flag 接受二级选项，例如 <code>-plt</code> 或 <code>-calc</code>，也需要为它添加对应的 <code>case</code> 分支：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a><span class="k">case</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$prev</span><span class="s2">&quot;</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="w">    </span><span class="c1"># ... existing cases ...</span>
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a><span class="w">    </span>-analyze_bonds<span class="o">)</span>
+<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a><span class="w">        </span><span class="nv">COMPREPLY</span><span class="o">=(</span><span class="k">$(</span><span class="nb">compgen</span><span class="w"> </span>-f<span class="w"> </span>--<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$cur</span><span class="s2">&quot;</span><span class="k">)</span><span class="o">)</span><span class="w">  </span><span class="c1"># Complete with filenames</span>
+<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a><span class="w">        </span><span class="p">;;</span>
+<a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a><span class="w">    </span><span class="c1"># ... rest of cases ...</span>
+<a id="__codelineno-15-7" name="__codelineno-15-7" href="#__codelineno-15-7"></a><span class="k">esac</span>
+</code></pre></div>
+<h3 id="_13">代码风格和最佳实践</h3>
+<ul>
+<li><strong>Shell 脚本</strong>：</li>
+<li>使用 <code>${variable}</code> 进行变量展开。</li>
+<li>
+<p>编写清晰、易维护的代码。</p>
+</li>
+<li>
+<p><strong>Python 脚本</strong>：</p>
+</li>
+<li>编写清晰、可维护的代码。</li>
+<li>使用有意义的变量名。</li>
+</ul>
+<h3 id="_14">测试你的修改</h3>
+<p>提交贡献前，请进行测试：</p>
+<ol>
+<li><strong>测试交互模式</strong>（如果适用）：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a><span class="c1"># Navigate to your new feature and test it thoroughly</span>
+</code></pre></div>
+<ol>
+<li><strong>测试命令行模式</strong>（如果适用）：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span><span class="o">[</span>arguments<span class="o">]</span>
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span>-h<span class="w">  </span><span class="c1"># Test help message</span>
+</code></pre></div>
+<ol>
+<li><strong>测试 Tab 补全</strong>（如果修改了 <code>completion.sh</code>）：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a><span class="nb">source</span><span class="w"> </span>Scripts/utils/completion.sh
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-&lt;TAB&gt;<span class="w">  </span><span class="c1"># Should show your new flag</span>
+</code></pre></div>
+<ol>
+<li>
+<p><strong>使用不同输入测试</strong>：</p>
+</li>
+<li>
+<p>测试常规输入。</p>
+</li>
+<li>测试边界情况，例如空文件、大文件等。</li>
+<li>
+<p>测试错误处理，例如缺少文件、参数无效等。</p>
+</li>
+<li>
+<p><strong>确认没有回归问题</strong>：确保已有功能仍然可以正常工作。</p>
+</li>
+</ol>
+<h3 id="_15">提交信息</h3>
+<p>提交信息应清楚、具体，说明你修改了什么。不要求严格格式，但需要让他人能够理解。</p>
+<h3 id="pull-request">推送并打开 Pull Request</h3>
+<ol>
+<li><strong>提交你的修改</strong>：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>git<span class="w"> </span>add<span class="w"> </span>.
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>git<span class="w"> </span>commit<span class="w"> </span>-m<span class="w"> </span><span class="s2">&quot;your descriptive message&quot;</span>
+</code></pre></div>
+<ol>
+<li><strong>让你的分支与 upstream <code>main</code> 分支保持同步</strong>：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>git<span class="w"> </span>fetch<span class="w"> </span>upstream
+<a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a>git<span class="w"> </span>rebase<span class="w"> </span>upstream/main
+</code></pre></div>
+<ol>
+<li><strong>将分支推送到你的 fork</strong>：</li>
+</ol>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>git<span class="w"> </span>push<span class="w"> </span>origin<span class="w"> </span>your-branch-name
+</code></pre></div>
+<ol>
+<li>
+<p><strong>打开 Pull Request</strong>：</p>
+</li>
+<li>
+<p>进入 <a href="https://github.com/zhyan0603/GPUMDkit">GPUMDkit repository</a>。</p>
+</li>
+<li>点击 "Pull Requests" -&gt; "New Pull Request"。</li>
+<li>将 base branch 设置为 <code>dev</code>，用于代码审查。</li>
+<li>将 compare branch 设置为你的功能分支。</li>
+<li>
+<p>填写 PR 描述，包括：</p>
+<ul>
+<li><strong>Title</strong>：简要描述修改内容。</li>
+<li><strong>Description</strong>：详细说明修改了什么以及为什么修改。</li>
+<li><strong>Testing</strong>：说明你如何测试这些修改。</li>
+</ul>
+</li>
+<li>
+<p><strong>回应审查意见</strong>：</p>
+</li>
+<li>
+<p>接受建议和建设性意见。</p>
+</li>
+<li>及时完成要求的修改。</li>
+<li>
+<p>将额外提交推送到你的分支，它们会自动显示在 PR 中。</p>
+</li>
+<li>
+<p><strong>审查通过后</strong>：维护者会合并你的 PR。</p>
+</li>
+</ol>
+<hr />
+<h2 id="_16">有问题或需要帮助？</h2>
+<p>如果你对贡献流程有疑问，或需要帮助：</p>
+<ul>
+<li><strong>打开讨论</strong>：一般问题可以使用 <a href="https://github.com/zhyan0603/GPUMDkit/discussions">GitHub Discussions</a>。</li>
+<li><strong>在 issue 中提问</strong>：与具体问题相关的内容可以在对应 issue 下评论。</li>
+<li><strong>联系维护者</strong>：联系 README 中列出的核心开发者。</li>
+</ul>
+<hr />
+<p>再次感谢你为 <code>GPUMDkit</code> 做贡献。你的工作会帮助整个 GPUMD 和 NEP 社区更好地使用这个工具包。</p>
+
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+      <script id="__config" type="application/json">{"annotate": null, "base": "..", "features": ["content.code.copy", "navigation.top", "search.suggest", "search.highlight"], "search": "../assets/javascripts/workers/search.2c215733.min.js", "tags": null, "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": null}</script>
+    
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+      
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+</html>
\ No newline at end of file
diff --git a/docs/index.html b/docs/index.html
index f762b4b..c8d114c 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -28,7 +28,7 @@
         <button class="mobile-menu-btn" style="display: none;">☰</button>
         <nav class="nav-links">
             <a href="index.html" class="nav-item">Home</a>
-            <a href="htmls/tutorials.html" class="nav-item">Documentation</a>
+            <a href="htmls/index.html" class="nav-item">Documentation</a>
             <a href="gallery.html" class="nav-item">Gallery</a>
             <a href="publications.html" class="nav-item">Publications</a>            
             <!-- <a href="https://github.com/zhyan0603/GPUMDkit" class="nav-item">Join Us</a> -->
@@ -340,7 +340,7 @@ <h4 class="paper-title-modern">GPUMDkit: A User-Friendly Toolkit for GPUMD and N
                 <div class="footer-column">
                     <h4>Quick Links</h4>
                     <ul>
-                        <li><a href="htmls/tutorials.html">Documentation</a></li>
+                        <li><a href="htmls/index.html">Documentation</a></li>
                         <li><a href="gallery.html">Gallery</a></li>
                         <li><a href="publications.html">Publications</a></li>
                         <li><a href="https://github.com/zhyan0603/GPUMDkit/archive/refs/heads/main.zip">Download</a></li>
@@ -386,4 +386,4 @@ <h4>GPUMD ecosystem</h4>
     <script src="js/publications.js"></script>
     <script src="js/ui-interactions.js"></script>
 </body>
-</html>
\ No newline at end of file
+</html>
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
index 58b5f40..78f7ac1 100644
--- a/docs/mkdocs.yml
+++ b/docs/mkdocs.yml
@@ -52,17 +52,35 @@ plugins:
       lang: en
 
 nav:
-  - Home: tutorials.md
-  - Plot Scripts: plot_scripts.md
-  - Format Conversion: format_conversion.md
-  - Sample Structures: sample_structures.md
-  - Workflow: workflow.md
-  - Calculators: calculators.md
-  - Analyzers: analyzer.md
-  - Custom Commands: custom_commands.md
-  - Active Learning Workflow: workflow_active_learning.md
-  - Polar Material Analysis: polar_material_analysis.md
-  - Contributing: contributing.md
+  - Home: index.md
+  - English:
+    - GPUMDkit Tutorials: en/index.md
+    - Quick Start: en/quick_start.md
+    - Command Reference: en/command_reference.md
+    - Format Conversion: en/format_conversion.md
+    - Structure Sampling: en/structure_sampling.md
+    - Workflow Scripts: en/workflow_scripts.md
+    - Calculator Scripts: en/calculator_scripts.md
+    - Analyzer Scripts: en/analyzer_scripts.md
+    - Plot Scripts: en/plot_scripts.md
+    - Custom Commands: en/custom_commands.md
+    - Active Learning Workflow: en/active_learning_workflow.md
+    - Polar Material Analysis: en/polar_material_analysis.md
+    - Contributing to GPUMDkit: en/contributing_to_gpumdkit.md
+  - 简体中文:
+    - GPUMDkit 教程: zh/index.md
+    - 快速入门: zh/快速入门.md
+    - 命令参考: zh/命令参考.md
+    - 格式转换: zh/格式转换.md
+    - 结构采样: zh/结构采样.md
+    - 工作流脚本: zh/工作流脚本.md
+    - 计算器脚本: zh/计算器脚本.md
+    - 分析工具: zh/分析工具.md
+    - 绘图脚本: zh/绘图脚本.md
+    - 自定义命令: zh/自定义命令.md
+    - 主动学习工作流: zh/主动学习工作流.md
+    - 极性材料分析: zh/极性材料分析.md
+    - 贡献指南: zh/贡献指南.md
 
 extra:
   social:
@@ -80,4 +98,4 @@ extra:
       name: ResearchGate
     - icon: fontawesome/brands/orcid
       link: https://orcid.org/0000-0002-8911-6549
-      name: ORCID
\ No newline at end of file
+      name: ORCID
diff --git a/docs/publications.html b/docs/publications.html
index 4f331aa..6aa1aea 100644
--- a/docs/publications.html
+++ b/docs/publications.html
@@ -99,7 +99,7 @@
         <button class="mobile-menu-btn" style="display: none;">☰</button>
         <nav class="nav-links">
             <a href="index.html" class="nav-item">Home</a>            
-            <a href="htmls/tutorials.html" class="nav-item">Documentation</a>
+            <a href="htmls/index.html" class="nav-item">Documentation</a>
             <a href="gallery.html" class="nav-item">Gallery</a>
             <a href="publications.html" class="nav-item" style="color: var(--text-gpumd);">Publications</a>
             <!-- <a href="https://github.com/zhyan0603/GPUMDkit" class="nav-item">Join Us</a> -->
@@ -120,7 +120,7 @@
                 <div class="footer-column">
                     <h4>Quick Links</h4>
                     <ul>
-                        <li><a href="htmls/tutorials.html">Documentation</a></li>
+                        <li><a href="htmls/index.html">Documentation</a></li>
                         <li><a href="gallery.html">Gallery</a></li>
                         <li><a href="publications.html">Publications</a></li>
                         <li><a href="https://github.com/zhyan0603/GPUMDkit/archive/refs/heads/main.zip">Download</a></li>
diff --git a/docs/script.js b/docs/script.js
index 607ced4..5be0d05 100644
--- a/docs/script.js
+++ b/docs/script.js
@@ -6,7 +6,7 @@ const mainContentText = `
          | |_| |  __/| |_| | |  | | |_| |   <| | |_
           \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
 
-          GPUMDkit Version 1.5.5 (dev) (2026-05-16)
+          GPUMDkit Version 1.5.6 (dev) (2026-06-17)
     Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
  Main Contributors: Denan LI, Xin WU, Zhoulin LIU & Chen HUA
 
@@ -57,7 +57,7 @@ const logsCommand2 = `
 `;
 
 const helpContentText = ` +-------------------------------------------------------------------------------------------------------+
-|                          GPUMDkit 1.5.5 (dev) (2026-05-16) Command Help                               |
+|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
 +-------------------------------------------------------------------------------------------------------+
 |                                          MAIN FUNCTIONS                                               |
 +-------------------------------------------------------------------------------------------------------+
@@ -84,13 +84,13 @@ const helpContentText = ` +-----------------------------------------------------
 | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
 | -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-| -pynep        FPS sampling by PyNEP           | -filter_box        Filter by box-edge length          |
+| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
 +-------------------------------------------------------------------------------------------------------+
 | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
 +-------------------------------------------------------------------------------------------------------+`;
 
 const plotContentText = `  +-----------------------------------------------------------------------------------------------+
- |                     GPUMDkit 1.5.5 (dev) (2026-05-16) PLOT & VISUALIZATION TOOLS              |
+ |                     GPUMDkit 1.5.6 (dev) (2026-06-17) PLOT & VISUALIZATION TOOLS              |
  +-----------------------------------------------------------------------------------------------+
  |  Usage: gpumdkit.sh -plt <type>                        Help: gpumdkit.sh -plt <type> -h       |
  +-----------------------------------------------------------------------------------------------+
@@ -476,4 +476,4 @@ function typeLogsTerminal() {
     contentEl.appendChild(cmdDiv3);
 }
 
-window.addEventListener('load', init);
\ No newline at end of file
+window.addEventListener('load', init);
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index d2afdae..dcb759f 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -29,7 +29,7 @@
          <lastmod>2025-12-28</lastmod>
     </url>
     <url>
-         <loc>https://zhyan0603.github.io/GPUMDkit/htmls/tutorials.html</loc>
+         <loc>https://zhyan0603.github.io/GPUMDkit/htmls/index.html</loc>
          <lastmod>2025-12-28</lastmod>
     </url>
     <url>
@@ -40,4 +40,4 @@
          <loc>https://zhyan0603.github.io/GPUMDkit/htmls/workflow_active_learning.html</loc>
          <lastmod>2025-12-28</lastmod>
     </url>  
-</urlset>
\ No newline at end of file
+</urlset>
diff --git a/docs/tutorials/analyzer.md b/docs/tutorials/analyzer.md
deleted file mode 100644
index ec4480c..0000000
--- a/docs/tutorials/analyzer.md
+++ /dev/null
@@ -1,610 +0,0 @@
-<div align="center">
-  <h1>🔍 Analyzer Scripts</h1>
-    <p style="text-align: justify;">This directory (Scripts/analyzer/) contains analysis tools for structure files, simulation data, and dataset quality control. These scripts help validate, filter, and understand molecular dynamics data and training sets.</p>
-</div>
-
-**Script Location:** `Scripts/analyzer/`
-
-This section covers the analyzer tools in GPUMDkit (Interactive Mode - Option 5).
-
-The analyzer scripts provide functionality for:
-
-- Energy, force, and virial range analysis
-- Minimum distance calculations (with/without periodic boundary conditions)
-- Structure filtering by various criteria (distance, box size, property values)
-- Composition analysis of multi-component systems
-- Time estimation for GPUMD and NEP calculations
-- Dataset quality checks and outlier detection
-
-## Interactive Mode
-
-```bash
-gpumdkit.sh
-# Select: 5) Analyzer
-```
-
-You'll see the following menu:
-
-```
- +------------------------------------------------------+
- |                    ANALYZER TOOLS                    |
- +------------------------------------------------------+
- | 501) Analyze composition of extxyz                   |
- | 502) Find outliers of extxyz                         |
- | 503) Analyze chemical species of extxyz              |
- | 504) Check charge balance of extxyz                  |
- | 505) Analyze energy/force/virial range               |
- | 506) Filter structures by minimum distance           |
- | 507) Get minimum interatomic distance                |
- | 508) Probability density analysis                    |
- +------------------------------------------------------+
- | 000) Return to the main menu                         |
- +------------------------------------------------------+
- Input the function number:
-```
-
-for `501`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in analyzer      |
- | Script: analyze_composition.py                  |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <input.xyz> you want to analyze
- Examp: train.xyz
- ------------>>
-```
-
-for `502`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in analyzer      |
- | Script: find_outliers.py                        |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input the threshold of RMSE to identify outliers
- ---------------------------------------------------
- Enter energy RMSE threshold (meV/atom): 1
- Enter force RMSE threshold (meV/Å): 60
- Enter stress RMSE threshold (GPa): 0.03
-```
-
-for `503`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in analyzer      |
- | Script: analyze_chem_species.py                 |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <input.xyz> you want to analyze
- Example: train.xyz
- ------------>>
-```
-
-for `504`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in analyzer      |
- | Script: charge_balance_check.py                 |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <input.xyz> you want to analyze
- Examp: train.xyz
- ------------>>
-```
-
-for `505`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in analyzer      |
- | Script: energy_force_virial_analyzer.py         |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <input.xyz> and property (energy/force/virial)
- Example: train.xyz force
- ------------>>
-```
-
-for `506`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in analyzer      |
- | Script: filter_structures_by_distance.py        |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <input.xyz> and <min_dist>
- Example: dump.xyz 1.5
- ------------>>
-```
-
-for `507`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in analyzer      |
- | Script: get_min_dist.py / get_min_dist_pbc.py   |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <input.xyz> you want to analyze
- Example: dump.xyz
- ------------>>
-```
-
-for `508`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in analyzer      |
- | Script: probability_density_analysis.py         |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <ref_struct> <trajectory_file> <species> <interval>
- Example: LLZO.vasp dump.xyz Li 0.25
- ------------>>
-```
-
-Follow the prompts to complete the function.
-
-## Command-Line Mode
-
-```bash
-gpumdkit.sh -range <file.xyz> <property>
-gpumdkit.sh -min_dist <file.xyz>
-gpumdkit.sh -min_dist_pbc <file.xyz>
-gpumdkit.sh -filter_value <file.xyz> <property> <threshold>
-gpumdkit.sh -filter_dist <file.xyz> <min_dist>
-gpumdkit.sh -filter_box <file.xyz> <box_limit>
-gpumdkit.sh -analyze_comp <file.xyz>
-gpumdkit.sh -time gpumd
-gpumdkit.sh -time nep
-```
-
----
-
-## Scripts
-
-### analyze_composition.py
-
----
-
-This script analyze the composition of your `extxyz` file.
-
-#### Usage
-
-```
-python analyze_composition.py <extxyz>
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -analyze_comp train.xyz
-```
-
-#### Output
-
-```
- Calling script by Zihan YAN
- Code path: /d/Westlake/GPUMD/Gpumdkit/Scripts/analyzer/analyze_composition.py
- Index    Compositions           N atoms      Count
- ---------------------------------------------------
- 1        Li56O96Zr16La24        192          51
- ---------------------------------------------------
- Enter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:
-```
-
-
-
-### charge_balance_check.py
-
----
-
-This script can be used to check the charge balance status of your `extxyz` file.
-
-#### Usage
-
-```
-python charge_balance_check.py <extxyz>
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -cbc train.xyz
-```
-
-#### Output
-
-```
- Calling script by Zihan YAN
-Computing compositions: 100%|████████████████████████████████████████████████████████████████████| 51/51 [00:03<00:00, 13.03it/s]
-Checking oxidation states: 100%|████████████████████████████████████████████████████████████████████| 1/1 [00:03<00:00,  3.67s/it]
-```
-
-Finally, you will get a `balanced.xyz` and `indices.txt` file.
-
-
-
-### energy_force_virial_analyzer.py
-
----
-
-This script calculates and visualizes the range of properties (such as energy, forces, and virial) from the `extxyz` file.
-
-#### Usage
-
-The script requires at least two arguments:
-
-- The filename of the `extxyz` file.
-- The name of the property to analyze (`energy`, `force`, or `virial`).
-
-An optional third argument (`hist`) can be provided to generate a histogram plot of the values.
-
-```
-python energy_force_virial_analyzer.py <filename> <property> [hist]
-```
-
-#### Example
-
-```sh
-python energy_force_virial_analyzer.py train.xyz force
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -range train.xyz force
-```
-
-#### Output
-
-```
-Force range: 0.03210566767721861 to 9.230115912468435
-```
-
-If you add the `[hist]` option, it will calculate the range of forces and display a histogram:
-
-```sh
-python energy_force_virial_analyzer.py train.xyz force hist
-```
-
-<div align="center">
-<img src="../Gallery/range_force.png" width = "50%" />
-</div>
-
-
-
-
-### filter_dist_range.py
-
----
-
-This script is used to extract the structures with specified `min_dist`.
-
-#### Usage
-
-```
-python filter_dist_range.py <input.xyz> <element1> <element2> <min_dist> <max_dist>
-```
-
-#### Example
-
-```sh
-python filter_dist_range.py dump.xyz Li Li 1.8 2.0
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -filter_range dump.xyz Li Li 1.9 2.0
-```
-
-This means you need to extract the structures with the `min_dist` of Li-Li in the range of 1.8-2.0 in `dump.xyz` file. Finally, the `filtered_Li_Li_1.8_2.0.xyz` file will be generated.
-
-
-
-### get_min_dist.py
-
----
-
-This script is used to calculate the min_dist of the structures.
-
-#### Usage
-
-```
-python get_min_dist.py <extxyz_file>
-```
-
-#### Example
-
-```sh
-python get_min_dist.py dump.xyz
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -min_dist dump.xyz
-```
-
-#### Output
-
-```
- Calling script by Zihan YAN
- Code path: /d/Westlake/GPUMD/Gpumdkit/Scripts/analyzer/get_min_dist.py
- +---------------------------+
- |   PBC ignored for speed   |
- | use -min_dist_pbc for PBC |
- +---------------------------+
- Minimum interatomic distances:
- +---------------------------+
- | Atom Pair |  Distance (Å) |
- +---------------------------+
- |   Li-Li   |     1.696     |
- |   Li-La   |     2.498     |
- |   Li-Zr   |     2.506     |
- |   Li-O    |     1.587     |
- |   La-La   |     3.463     |
- |   La-Zr   |     3.243     |
- |   La-O    |     2.043     |
- |   Zr-Zr   |     5.060     |
- |   Zr-O    |     1.867     |
- |   O-O     |     2.480     |
- +---------------------------+
- Overall min_distance: 1.587 Å
-```
-
-NOTE: This script is fast because it does not take into account periodic boundary conditions (PBC), but in some cases it can be problematic.
-
-
-
-### get_min_dist_pbc.py
-
----
-
-This script is used to calculate the min_dist of the structures considering the PBC.
-
-#### Usage
-
-```
-python get_min_dist_pbc.py <extxyz_file>
-```
-
-#### Example
-
-```sh
-python get_min_dist_pbc.py dump.xyz
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -min_dist_pbc dump.xyz
-```
-
-#### Output
-
-```
- Calling script by Zihan YAN
- Code path: /d/Westlake/GPUMD/Gpumdkit/Scripts/analyzer/get_min_dist_pbc.py
- Minimum interatomic distances (with PBC):
- +---------------------------+
- | Atom Pair |  Distance (Å) |
- +---------------------------+
- |   Li-Li   |     1.696     |
- |   Li-La   |     2.498     |
- |   Li-Zr   |     2.477     |
- |   Li-O    |     1.587     |
- |   La-La   |     3.463     |
- |   La-Zr   |     3.210     |
- |   La-O    |     2.043     |
- |   Zr-Zr   |     5.060     |
- |   Zr-O    |     1.867     |
- |   O-O     |     2.355     |
- +---------------------------+
- Overall min_distance: 1.587 Å
-```
-
-
-
-### find_outliers.py
-
----
-
-This script is used to find outliers in training data based on RMSE thresholds for energy, force, and stress.
-
-#### Usage
-
-```sh
-python find_outliers.py
-```
-
-#### Interactive Mode
-
-```
- Input the function number:
- 5
- ------------>>
- 501) Analyze composition of extxyz
- 502) Find outliers of extxyz
- 000) Return to the main menu
- ------------>>
- Input the function number:
- 502
- >-------------------------------------------------<
- | This function calls the script in analyzer      |
- | Script: find_outliers.py                        |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input the threshold of RMSE to identify outliers
- ---------------------------------------------------
- Enter energy RMSE threshold (meV/atom): 1
- Enter force RMSE threshold (meV/Å): 60
- Enter stress RMSE threshold (GPa): 0.03
-```
-
-After that, you will get `selected.xyz`, `remained.xyz`, and `slected_remained.png`
-
-
-
-### filter_exyz_by_value.py
-
----
-
-This script filter the structures by min_dist.
-
-#### Usage
-
-```sh
-python filter_exyz_by_value.py <extxyz_file> <min_dist>
-```
-
-#### Example
-
-```sh
-python filter_exyz_by_value.py dump.xyz 1.4
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -filter_value dump.xyz 1.4
-```
-
-
-
-### filter_exyz_by_box.py
-
----
-
-This script filter the structures by box limit.
-
-#### Usage
-
-```
-python filter_exyz_by_box.py <extxyz_file> <min_dist>
-```
-
-#### Example
-
-```
-python filter_exyz_by_box.py dump.xyz 20
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -filter_box dump.xyz 20
-```
-
-
-
-### filter_exyz_by_value.py
-
----
-
-This script filter the structures by specified value.
-
-#### Usage
-
-```
-python filter_exyz_by_value.py <extxyz_file> <property> <threshold>
-```
-
-- `<extxyz_file>`: The path to the input `extxyz` file.
-- `<property>`: Filtering property: `energy`, `force`, or `virial`
-- `<threshold>`: Threshold value for filtering
-
-#### Example
-
-```
-python filter_exyz_by_value.py train.xyz force 20
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -filter_value train.xyz force 20
-```
-
-This command will filter out the structure in `train.xyz` with a force greater than 20 eV/angstrom.
-
-
-
-### time_consuming_gpumd.sh
-
----
-
-This script calculates the remaining time for GPUMD.
-
-#### Usage
-
-```
-bash time_consuming_gpumd.sh
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -time gpumd
-```
-
-#### Output
-
-```
- ----------------- System Information ----------------
- total frames: 1050000
- -----------------------------------------------------
- Current Frame  Speed (steps/s)   Total Time       Time Left       Estimated End
- -------------   -------------   -------------   -------------   -----------------
-     13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04
-     14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56
-     15000          199.94        1h 27m 31s      1h 26m 16s    2025-12-27 19:03:56
-```
-
-
-
-### time_consuming_nep.sh
-
----
-
-This script calculates the remaining time for nep.
-
-#### Usage
-
-```
-bash time_consuming_nep.sh
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -time nep
-```
-
-#### Output
-
-```
-+-----------------+-----------+-----------------+---------------------+
-|       Step      | Time Diff |    Time Left    |    Finish Time      |
-+-----------------+-----------+-----------------+---------------------+
-| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |
-| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |
-| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |
-| 7000            | 2 s       | 0 h 31 m 0 s    | 2025-10-23 15:49:44 |
-| 7100            | 3 s       | 0 h 46 m 27 s   | 2025-10-23 16:05:14 |
-```
-
-## Contributing
-
-To add new analyzer scripts, see [CONTRIBUTING.md](contributing.md) for detailed guidelines.
-
----
-
-Thank you for using GPUMDkit! If you have questions or need assistance with analyzer scripts, please open an issue on our [GitHub repository](https://github.com/zhyan0603/GPUMDkit/issues) or contact Zihan YAN (yanzihan@westlake.edu.cn).
diff --git a/docs/tutorials/calculators.md b/docs/tutorials/calculators.md
deleted file mode 100644
index c47302c..0000000
--- a/docs/tutorials/calculators.md
+++ /dev/null
@@ -1,446 +0,0 @@
-<div align="center">
-  <h1>🧮 Calculators</h1>
-    <p style="text-align: justify;">This directory (Scripts/calculators/) contains computational tools for calculating various material properties using NEP models and analyzing simulation data.</p>
-</div>
-
-**Script Location:** `Scripts/calculators/`
-
-This section covers the calculator tools in GPUMDkit (Interactive Mode - Option 4).
-
-The calculator scripts provide functionality for:
-
-- Ionic conductivity and diffusivity calculations
-- Property predictions using NEP models
-- Descriptor calculations for PCA or UMAP analysis
-- Density of atomistic states (DOAS)
-- Nudged elastic band (NEB) calculations
-- Radial distribution function (RDF) calculations
-
-## Interactive Mode
-
-```bash
-gpumdkit.sh
-# Select: 4) Calculators
-```
-
-You'll see the following menu:
-
-```
- +----------------------------------------------------------+
- |                     CALCULATOR TOOLS                     |
- +----------------------------------------------------------+
- | 401) Calc ionic conductivity                             |
- | 402) Calc properties by nep                              |
- | 403) Calc descriptors of specific elements               |
- | 404) Calc density of atomistic states (DOAS)             |
- | 405) Calc nudged elastic band (NEB) by nep               |
- | 406) Build neighbor list                                 |
- | 407) Calc displacement from trajectory                   |
- | 408) Calc averaged structure                             |
- | 409) Calc octahedral tilt                                |
- | 410) Calc polarization for ABO3                          |
- | 411) Minimize structure by nep                           |
- | 412) Calc mean square displacement (MSD) from trajectory |
- +----------------------------------------------------------+
- | 000) Return to the main menu                             |
- +----------------------------------------------------------+
- Input the function number:
-```
-
-for `401`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in calculators   |
- | Script: calc_ion_conductivity.py                |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <element> <charge> (eg. Li 1)
- ------------>>
-```
-
-for `402`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in calculators   |
- | Script: calc_properties_with_nep.py             |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <input.xyz> <output.xyz> <nep_model>
- Examp: input.xyz output.xyz nep.txt
- ------------>>
-```
-
-for `403`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in calculators   |
- | Script: calc_descriptors.py                     |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <input.xyz> <output.npy> <nep_model> <element>
- Examp: train.xyz des_Li.npy nep.txt Li
- ------------>>
-```
-
-for `404`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in calculators   |
- | Script: calc_doas.py                            |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <input.xyz> <nep_model> <output_file>
- Examp: dump.xyz nep.txt doas.out
- ------------>>
-```
-
-for `405`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in calculators   |
- | Script: neb_calculation.py                      |
- | Developer: Zhoulin LIU (1776627910@qq.com)      |
- >-------------------------------------------------<
- Input <initial_struct> <final_struct> <n_image> <nep_model>
- Examp: IS.xyz FS.xyz 5 nep.txt
- ------------>>
-```
-
-for `406-410`:
-
-See https://gpumdkit.cn/htmls/polar_material_analysis.html for details
-
-for `411`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in calculators   |
- | Script: minimize_structure_by_nep.py            |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <structure_file> <nep.txt> [fmax=0.01] [max_steps=1000]
- Supported structure formats: POSCAR, .xyz
- Optional arguments:
-  fmax: Force convergence threshold in eV/Ang (default: 0.01)
-  max_steps: Maximum number of optimization steps (default: 1000)
- Example: POSCAR nep.txt 0.01 1000
- ------------>>
-```
-
-for `412`:
-
-```
- >-------------------------------------------------<
- | This function calls the script in calculators   |
- | Script: calc_msd.py                             |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]
-   Optional argument: max_corr_steps (default: frame number)
- Example: dump.xyz Li 10
- ------------>>
-```
-
-Follow the prompts to complete the function.
-
-## Command-Line Mode
-
-```bash
-gpumdkit.sh -calc ionic-cond <element> <charge>
-gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>
-gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>
-gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>
-```
-
----
-
-## Scripts
-
-### calc_ion_conductivity.py
-
-Calculates ionic diffusivity and conductivity from mean square displacement (MSD) data.
-
-#### Input Files
-- `msd.out` - MSD data from GPUMD (required)
-- `thermo.out` - Temperature data (optional, for automatic temperature detection)
-- `model.xyz` - Structure file (optional, for automatic volume/atom count detection)
-- `run.in` - MD input file (optional, for replicate detection)
-
-#### Usage
-
-**Command-line mode:**
-
-```bash
-gpumdkit.sh -calc ionic-cond <element> <charge>
-```
-
-**Direct execution:**
-```bash
-python calc_ion_conductivity.py <element> <charge>
-```
-
-#### Parameters
-- `<element>`: Chemical species symbol (e.g., Li, Na, O)
-- `<charge>`: Formal charge of the ion (e.g., 1 for Li⁺, -2 for O²⁻)
-
-#### Examples
-
-**Automatic mode** (with thermo.out and model.xyz present):
-
-```bash
-gpumdkit.sh -calc ionic-cond Li 1
-```
-
-**Manual input mode** (if files not found):
-```bash
-gpumdkit.sh -calc ionic-cond Li 1
-# Script will prompt:
-Files 'thermo.out' and 'model.xyz' are not found.
-Please provide the following values:
---------------------------->
-Enter average temperature (in K): 800
-Enter system volume (in Å^3): 16785
-Enter number of ions: 448
-```
-
-#### Output
-
-```
-Diffusivity (D):
-  D_x: 4.153e-07 cm^2/s
-  D_y: 4.174e-07 cm^2/s
-  D_z: 2.610e-07 cm^2/s
-  D_total: 3.646e-07 cm^2/s
-------------------------------
-Ionic Conductivity:
-  Sigma_x: 2.576e-02 mS/cm
-  Sigma_y: 2.589e-02 mS/cm
-  Sigma_z: 1.619e-02 mS/cm
-  Sigma_total: 2.261e-02 mS/cm
-```
-
----
-
-### calc_properties_with_nep.py
-
-Calculates energies, forces, and stresses for structures using a NEP model. You can provide a clean extxyz file and use a `nep.txt` to label the reference values for energies, forces, and stresses. 
-
-***Note that you must know what you are doing and this is not a substitute for DFT calculations.***
-
-Unless you have a well-trained NEP model and you want to use it as a DFT surrogate, you probably shouldn't use this feature. See [this article](https://doi.org/10.1021/acs.jcim.5c02335) if you are interesting in it.
-
-#### Input Files
-- A clean structure file in `extxyz` format with energy, force, and virial/stress. 
-
-  (use `gpumdkit.sh -clean_xyz train.xyz` to remove the original values)
-
-- NEP model file (nep.txt)
-
-#### Usage
-
-**Command-line mode:**
-```bash
-gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>
-```
-
-**Direct execution:**
-```bash
-python calc_properties_with_nep.py <input.xyz> <output.xyz> <nep.txt>
-```
-
-#### Example
-
-```bash
-# Predict properties for a test set
-gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
-```
-
-#### Requirements
-- Python package: `calorine` 
-
-```bash
-pip install calorine
-```
-
----
-
-### calc_descriptors.py
-
-Calculates descriptors for the specific species, which can be used for dimensionality reduction and structure analysis.
-
-#### Usage
-
-**Command-line mode:**
-```bash
-gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>
-```
-
-**Direct execution:**
-```bash
-python calc_descriptors.py <input.xyz> <output.npy> <nep.txt> <element>
-```
-
-#### Parameters
-- `<input.xyz>`: Input structure file
-- `<output.npy>`: Output `npy` file with high-dimensional descriptors
-- `<nep.txt>`: NEP model file
-- `<element>`: Target element for descriptor calculations
-
-#### Examples
-
-```bash
-# Calculate descriptors using UMAP
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-```
-
-#### Output
-- NumPy array file (.npy) containing descriptor vectors
-- Can be visualized using `gpumdkit.sh -plt des`
-
-#### Applications
-- **Training set analysis**: Check if training data covers configuration space
-- **Model comparison**: Compare descriptor distributions across different models
-
-#### Reference
-See [arXiv:2504.15925](https://doi.org/10.48550/arXiv.2504.15925) if you are interesting in it.
-
----
-
-### calc_doas.py
-
-Calculates the [density of atomistic states (DOAS)](https://doi.org/10.1002/anie.202215544) by optimizing structures and computing per-atom energies.
-
-#### Usage
-
-**Command-line mode:**
-```bash
-gpumdkit.sh -calc doas <input.xyz> <nep.txt> <doas.out>
-```
-
-**Direct execution:**
-```bash
-python calc_doas.py <input.xyz> <nep.txt> <doas.out>
-```
-
-#### Parameters
-- `<input.xyz>`: Input structure file
-- `<nep.txt>`: NEP model file for structure optimization and atomistic-energies calculation
-- `<output.txt>`: Output file with grouped atomic energies by element
-
-#### Example
-
-```bash
-# Calculate DOAS
-gpumdkit.sh -calc doas structures.xyz nep.txt doas.out
-
-# Visualize results
-gpumdkit.sh -plt doas doas.txt <species>
-gpumdkit.sh -plt doas doas.txt Li
-```
-
-#### Process
-1. Reads all structures from input file
-2. Optimizes each structure using NEP (BFGS, fmax=0.05 eV/Å)
-3. Extracts per-atom energies from optimized structures
-4. Groups energies by element type
-5. Outputs distribution for each element
-
-You can also do the `minimize` and atomistic energy calculations in `gpumd`, which is prefered for large-scale structures.
-
----
-
-### neb_calculation.py
-
-Performs nudged elastic band (NEB) calculations to find minimum energy pathways between initial and final states.
-
-#### Usage
-
-**Direct execution only:**
-```bash
-python neb_calculation.py <initial.xyz> <final.xyz> <n_images> <nep.txt>
-```
-
-#### Parameters
-- `<initial.xyz>`: Initial structure file
-- `<final.xyz>`: Final structure file
-- `<n_images>`: Number of intermediate images
-- `<nep.txt>`: NEP model for energy/force calculations
-
-#### Example
-
-```bash
-# Calculate Li migration pathway with 9 intermediate images
-python neb_calculation.py init.xyz fin.xyz 9 nep.txt
-```
-
-#### Interactive Options
-```
- Input the function number:
- 4
- ------------>>
- 401) Calc ionic conductivity
- 402) Calc properties by nep
- 403) Calc descriptors of specific elements
- 404) Calc density of atomistic states (DOAS)
- 405) Calc nudged elastic band (NEB) by nep
- 000) Return to the main menu
- ------------>>
- Input the function number:
- 405
- >-------------------------------------------------<
- | This function calls the script in calculators   |
- | Script: neb_calculation.py                      |
- | Developer: Zhoulin LIU (1776627910@qq.com)      |
- >-------------------------------------------------<
- Input <initial_struct> <final_struct> <n_image> <nep_model>
- Examp: IS.xyz FS.xyz 5 nep.txt
- ------------>>
-```
-
----
-
-### rdf_calculator_ovito.py
-
-Calculates radial distribution function (RDF) using OVITO's analysis tools.
-
-#### Usage
-
-**Direct execution:**
-```bash
-python rdf_calculator_ovito.py <input.xyz> <cutoff> <bins>
-```
-
-#### Parameters
-- `<input.xyz>`: Input structure file (can be single frame or trajectory)
-- `<cutoff>`: Maximum distance for RDF calculation (Angstroms)
-- `<bins>`: Number of histogram bins for RDF
-
-#### Example
-
-```bash
-# Calculate RDF with 6 Å cutoff and 400 bins
-python rdf_calculator_ovito.py trajectory.xyz 6.0 400
-```
-
-#### Visualization
-After calculation:
-```bash
-gpumdkit.sh -plt rdf    
-```
-
-**Note**: It is recommended to use the `compute_rdf` command in `gpumd`.
-
----
-
-## Contributing
-
-See [CONTRIBUTING.md](contributing.md) for detailed guidelines.
-
----
-
-Thank you for using GPUMDkit! If you have questions or need assistance with calculator scripts, please open an issue on our [GitHub repository](https://github.com/zhyan0603/GPUMDkit/issues) or contact Zihan YAN (yanzihan@westlake.edu.cn).
diff --git a/docs/tutorials/workflow_active_learning.md b/docs/tutorials/en/active_learning_workflow.md
similarity index 90%
rename from docs/tutorials/workflow_active_learning.md
rename to docs/tutorials/en/active_learning_workflow.md
index 56a0742..c1e7056 100644
--- a/docs/tutorials/workflow_active_learning.md
+++ b/docs/tutorials/en/active_learning_workflow.md
@@ -1,6 +1,7 @@
-## Tutorial for workflow_active_learning_dev.sh
-
-This tutorial explains the steps and considerations involved in `workflow_active_learning_dev.sh` script. The workflow is used to generate, select, and analyze molecular structures, followed by simulations and data collection.
+<div align="center">
+  <h1>🔁 Active Learning Workflow</h1>
+  <p style="text-align: justify;">This tutorial explains the steps and considerations involved in the <code>workflow_active_learning_dev.sh</code> script. The workflow is used to generate, select, and analyze molecular structures, followed by simulations and data collection.</p>
+</div>
 
 ### Overview
 
@@ -30,7 +31,7 @@ The SLURM directives are used to define how the job will be submitted to the clu
 **<u>NOTE:</u>** If your machine does not have the SLURM environment, you can also run the script directly from the command line. For example:
 
 ```
-nohup bash workflow_activate_learning_dev.sh &>workflow.log &
+nohup bash workflow_active_learning_dev.sh &>workflow.log &
 ```
 
 ### 2. **Basic Setup**
@@ -43,11 +44,11 @@ Ensure the working directory is correct, and that all necessary files are presen
 
 ```
 source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  # Load the submit template
-python_pynep=/storage/zhuyizhouLab/yanzhihan/soft/conda/envs/gpumd/bin/python  # Python executable
+python_pynep=python  # Python executable for the deprecated pynep branch if needed
 ```
 
 - `GPUMDkit_path` is the environment variable that stores the path for the `GPUMDkit` .
-- `python_pynep` points to the Python environment needed for `pynep`-related scripts.
+- `python_pynep` points to the Python environment used for the deprecated `pynep`-related branch if needed.
 
 ------
 
@@ -183,4 +184,3 @@ The final step involves submitting the NEP prediction task to check  the accurac
 ---
 
 Thank you for using `GPUMDkit`! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).
-
diff --git a/docs/tutorials/en/analyzer_scripts.md b/docs/tutorials/en/analyzer_scripts.md
new file mode 100644
index 0000000..3a9f3aa
--- /dev/null
+++ b/docs/tutorials/en/analyzer_scripts.md
@@ -0,0 +1,149 @@
+<div align="center">
+  <h1>🔍 Analyzer Scripts</h1>
+  <p style="text-align: justify;">Analyzer scripts provide structure statistics, distance checks, filters, and composition analysis for extxyz datasets.</p>
+</div>
+
+**Script Location:** `Scripts/analyzer/`
+
+## Overview
+
+| Task | Command | Purpose |
+|------|---------|---------|
+| Composition | `gpumdkit.sh -analyze_comp train.xyz` | group structures by chemical composition |
+| Chemical species | `gpumdkit.sh -chem_species train.xyz` | list species in a file |
+| Property range | `gpumdkit.sh -range train.xyz force` | inspect energy/force/virial range |
+| Minimum distance | `gpumdkit.sh -min_dist dump.xyz` | fast distance check without PBC |
+| Minimum distance with PBC | `gpumdkit.sh -min_dist_pbc dump.xyz` | accurate distance check with PBC |
+| Charge balance | `gpumdkit.sh -cbc train.xyz` | oxidation-state balance check |
+| Distance filter | `gpumdkit.sh -filter_dist_pbc dump.xyz 1.0` | remove structures with short contacts |
+| Box filter | `gpumdkit.sh -filter_box dump.xyz 13` | remove structures with too-large box edges |
+| Property filter | `gpumdkit.sh -filter_value train.xyz force 20` | filter by energy/force/virial threshold |
+| Pair-distance range | `gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0` | extract structures by pair distance |
+
+## Composition Analysis
+
+```bash
+gpumdkit.sh -analyze_comp train.xyz
+```
+
+Example output:
+
+```text
+Index    Compositions           N atoms      Count
+---------------------------------------------------
+1        Li56O96Zr16La24        192          51
+---------------------------------------------------
+Enter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:
+```
+
+This is useful when `train.xyz` contains structures from different systems or different cell sizes. You can export a subset by composition from the interactive prompt.
+
+## Property Range Analysis
+
+```bash
+gpumdkit.sh -range train.xyz force
+gpumdkit.sh -range train.xyz energy
+gpumdkit.sh -range train.xyz virial
+gpumdkit.sh -range train.xyz force hist
+```
+
+Use `hist` to show a histogram of the selected property.
+
+<div align="center">
+  <img src="../../Gallery/range_force.png" alt="Force range histogram" width="52%" />
+</div>
+
+## Minimum Distance Checks
+
+Fast check without PBC:
+
+```bash
+gpumdkit.sh -min_dist dump.xyz
+```
+
+Accurate check with PBC:
+
+```bash
+gpumdkit.sh -min_dist_pbc dump.xyz
+```
+
+Typical output:
+
+```text
+Minimum interatomic distances (with PBC):
++---------------------------+
+| Atom Pair |  Distance (A) |
++---------------------------+
+|   Li-Li   |     1.696     |
+|   Li-O    |     1.587     |
+|   O-O     |     2.355     |
++---------------------------+
+Overall min_distance: 1.587 A
+```
+
+The PBC version considers periodic boundary conditions.
+
+## Filtering Structures
+
+### Filter by Minimum Distance
+
+```bash
+gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
+```
+
+This removes structures with any interatomic distance below `1.0 A`.
+
+### Filter by Box Size
+
+```bash
+gpumdkit.sh -filter_box dump.xyz 13
+```
+
+This filters structures by box-edge length.
+
+### Filter by Property Value
+
+```bash
+gpumdkit.sh -filter_value train.xyz force 20
+gpumdkit.sh -filter_value train.xyz energy 5
+```
+
+### Filter by Pair-Distance Range
+
+```bash
+gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0
+```
+
+This extracts structures where the Li-Li minimum distance is between `1.8 A` and `2.0 A`.
+
+## Charge Balance Check
+
+```bash
+gpumdkit.sh -cbc train.xyz
+```
+
+Outputs may include:
+
+- `balanced.xyz`
+- `unbalanced.xyz`
+- `indices.txt`
+
+This is intended for systems where common oxidation states are meaningful.
+
+## Example Commands
+
+Property and distance checks:
+
+```bash
+gpumdkit.sh -analyze_comp train.xyz
+gpumdkit.sh -range train.xyz force hist
+gpumdkit.sh -range train.xyz energy hist
+gpumdkit.sh -min_dist_pbc train.xyz
+```
+
+Filtering examples:
+
+```bash
+gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
+gpumdkit.sh -filter_box filtered_dist.xyz 13
+```
diff --git a/docs/tutorials/en/calculator_scripts.md b/docs/tutorials/en/calculator_scripts.md
new file mode 100644
index 0000000..e4cd732
--- /dev/null
+++ b/docs/tutorials/en/calculator_scripts.md
@@ -0,0 +1,323 @@
+<div align="center">
+  <h1>🧮 Calculator Scripts</h1>
+  <p style="text-align: justify;">The calculator module contains scripts for computing properties from MD trajectories, NEP models, and structure files.</p>
+</div>
+
+**Script Location:** `Scripts/calculators/`
+
+## Overview
+
+| Task | Command | Main Input |
+|------|---------|------------|
+| Ionic conductivity | `gpumdkit.sh -calc ionic-cond <element> <charge>` | `msd.out`, `thermo.out`, `model.xyz` |
+| MSD from trajectory | `gpumdkit.sh -calc msd <trajectory.xyz> <element> <dt_fs>` | extxyz trajectory |
+| NEP prediction | `gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>` | extxyz + NEP model |
+| NEP descriptors | `gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>` | extxyz + NEP model |
+| DOAS | `gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>` | extxyz + NEP model |
+| NEB | `gpumdkit.sh -calc neb <initial.xyz> <final.xyz> <n_images> <nep.txt>` | initial/final structures |
+| Minimization | `gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]` | structure + NEP model |
+| Neighbor list | `gpumdkit.sh -calc nlist [args...]` | structure |
+| Displacement | `gpumdkit.sh -calc disp [args...]` | trajectory + neighbor list |
+| Average structure | `gpumdkit.sh -calc avg-struct [args...]` | trajectory |
+| Octahedral tilt | `gpumdkit.sh -calc oct-tilt [args...]` | trajectory + B-O neighbor list |
+| ABO3 polarization | `gpumdkit.sh -calc pol-abo3 [args...]` | trajectory + neighbor lists |
+
+For a full command list:
+
+```bash
+gpumdkit.sh -calc -h
+```
+
+The command-line help table looks like:
+
+```text
++-------------------------------------------------------------------------------------------------------+
+|                                      CALCULATOR TOOLS                                                 |
++-------------------------------------------------------------------------------------------------------+
+| Usage: gpumdkit.sh -calc <type> [args...]                                                             |
++-------------------------------------------------------------------------------------------------------+
+| ionic-cond <element> <charge>                 Calculate ionic conductivity from MSD data              |
+| nep <input.xyz> <output.xyz> <nep_model>      Calculate energy/force/virial with a NEP model          |
+| des <input.xyz> <output.npy> <nep_model> <el> Calculate NEP descriptors for one element               |
+| doas <input.xyz> <nep_model> <output.txt>     Calculate density of atomistic states                   |
+| neb <initial.xyz> <final.xyz> <n_images> <nep> Run NEB calculation with a NEP model                   |
+| minimize <structure> <nep_model> [fmax] [n]   Minimize a structure with a NEP model                   |
+| msd <trajectory.xyz> <element> <dt_fs> [n]    Calculate MSD from an extxyz trajectory                 |
+| nlist [script args...]                        Build neighbor lists                                    |
+| disp [script args...]                         Calculate displacement from trajectory                  |
+| avg-struct [script args...]                   Calculate averaged structure                            |
+| oct-tilt [script args...]                     Calculate octahedral tilt                               |
+| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |
++-------------------------------------------------------------------------------------------------------+
+```
+
+In interactive mode, choose `4) Calculators`. The menu is:
+
+```text
++----------------------------------------------------------+
+|                     CALCULATOR TOOLS                     |
++----------------------------------------------------------+
+| 401) Calc ionic conductivity                             |
+| 402) Calc properties by nep                              |
+| 403) Calc descriptors of specific elements               |
+| 404) Calc density of atomistic states (DOAS)             |
+| 405) Calc nudged elastic band (NEB) by nep               |
+| 406) Build neighbor list                                 |
+| 407) Calc displacement from trajectory                   |
+| 408) Calc averaged structure                             |
+| 409) Calc octahedral tilt                                |
+| 410) Calc polarization for ABO3                          |
+| 411) Minimize structure by nep                           |
+| 412) Calc mean square displacement (MSD) from trajectory |
++----------------------------------------------------------+
+| 000) Return to the main menu                             |
++----------------------------------------------------------+
+Input the function number:
+```
+
+## Ionic Conductivity
+
+`calc_ion_conductivity.py` calculates ionic diffusivity and conductivity from `msd.out`.
+
+### Required and Optional Files
+
+| File | Role |
+|------|------|
+| `msd.out` | Required MSD data |
+| `thermo.out` | Optional, used for automatic temperature detection |
+| `model.xyz` | Optional, used for volume and ion-count detection |
+| `run.in` | Optional, used to detect replication |
+
+### Usage
+
+```bash
+gpumdkit.sh -calc ionic-cond Li 1
+```
+
+From interactive mode, choose `401`. You will see:
+
+```text
+>-------------------------------------------------<
+| This function calls the script in calculators   |
+| Script: calc_ion_conductivity.py                |
+| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
+>-------------------------------------------------<
+Input <element> <charge> (eg. Li 1)
+------------>>
+```
+
+If automatic files are missing, the script will ask for temperature, volume, and ion count interactively.
+
+Interactive prompts in manual mode look like:
+
+```text
+Files 'thermo.out' and 'model.xyz' are not found.
+Please provide the following values:
+--------------------------->
+Enter average temperature (in K):
+Enter system volume (in A^3):
+Enter number of ions:
+```
+
+### Example Output
+
+```text
+Diffusivity (D):
+  D_x: 4.153e-07 cm^2/s
+  D_y: 4.174e-07 cm^2/s
+  D_z: 2.610e-07 cm^2/s
+  D_total: 3.646e-07 cm^2/s
+------------------------------
+Ionic Conductivity:
+  Sigma_x: 2.576e-02 mS/cm
+  Sigma_y: 2.589e-02 mS/cm
+  Sigma_z: 1.619e-02 mS/cm
+  Sigma_total: 2.261e-02 mS/cm
+```
+
+## Mean Square Displacement
+
+`calc_msd.py` computes MSD directly from an extxyz trajectory.
+
+```bash
+gpumdkit.sh -calc msd dump.xyz Li 10
+gpumdkit.sh -calc msd dump.xyz Li 10 5000
+```
+
+From interactive mode, choose `412`. You will see:
+
+```text
+Input <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]
+  Optional argument: max_corr_steps (default: frame number)
+Example: dump.xyz Li 10
+------------>>
+```
+
+Arguments:
+
+| Argument | Meaning |
+|----------|---------|
+| `dump.xyz` | input trajectory |
+| `Li` | target mobile species |
+| `10` | time interval between frames, in fs |
+| `5000` | optional maximum correlation steps |
+
+Output:
+
+- `msd.out`
+
+The beginning of `msd.out` is a text table with time and MSD columns. After generating it, use the plot commands below.
+
+You can then plot:
+
+```bash
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+```
+
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
+  <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
+</div>
+
+## NEP Property Prediction
+
+`calc_properties_with_nep.py` calculates energy, force, and stress for structures using a NEP model.
+
+```bash
+gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
+```
+
+This function is useful when you intentionally want to use a trained NEP model as a surrogate calculator. It should not be treated as a replacement for DFT unless the model quality has been carefully validated.
+
+## NEP Descriptors
+
+`calc_descriptors.py` extracts NEP descriptors for a selected element.
+
+```bash
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+```
+
+Use cases:
+
+- visualize chemical environments with PCA/UMAP;
+- compare training and candidate structures;
+- inspect whether new data expands descriptor space.
+
+Plot descriptors with:
+
+```bash
+gpumdkit.sh -plt des pca
+gpumdkit.sh -plt des umap
+```
+
+<div align="center">
+  <img src="../../Gallery/des_umap.png" alt="Descriptor UMAP" width="52%" />
+</div>
+
+## Density of Atomistic States
+
+`calc_doas.py` calculates density of atomistic states (DOAS), following the idea proposed by [Wang et al.](https://doi.org/10.1002/anie.202215544).
+
+```bash
+gpumdkit.sh -calc doas structures.xyz nep.txt doas.out
+gpumdkit.sh -plt doas doas.out Li
+```
+
+The script:
+
+1. reads all structures;
+2. relaxes each structure with a NEP calculator;
+3. extracts per-atom energies;
+4. groups atomic energies by element;
+5. writes the grouped values to the output file.
+
+For very large systems, doing minimization and atomistic-energy extraction directly in GPUMD may be more efficient.
+
+<div align="center">
+  <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
+</div>
+
+## NEB with a NEP Model
+
+```bash
+gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt
+```
+
+This runs a NEB calculation with `9` intermediate images. During execution, the script asks how atoms should be fixed:
+
+- `none`: no atoms fixed;
+- `index`: fix atoms by index;
+- `element`: fix all atoms of one element;
+- `position`: fix atoms inside a coordinate range.
+
+## Structure Minimization
+
+```bash
+gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
+```
+
+Arguments:
+
+| Argument | Meaning |
+|----------|---------|
+| `POSCAR` | input structure, POSCAR/CONTCAR or extxyz |
+| `nep.txt` | NEP model |
+| `0.01` | optional force convergence threshold in eV/Ang |
+| `1000` | optional maximum optimization steps |
+
+Output:
+
+- `minimize.xyz`
+- `minimize.log`
+
+## Ferroelectric and Polar Material Tools
+
+The following tools are useful for perovskite and polar-material analysis. They require `ferrodispcalc`:
+
+```bash
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
+```
+
+`ferrodispcalc` currently has no associated paper to cite.
+
+### Build Neighbor Lists
+
+```bash
+gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat
+```
+
+This creates a neighbor-list file where each row stores one center atom and its nearest neighbor atoms.
+
+### Calculate Displacements
+
+```bash
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat
+```
+
+Use `-l 0.2` to analyze the last 20% of frames. Use `-s`, `-t`, and `-p` if you want an explicit slice.
+
+### Average a Structure
+
+```bash
+gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz
+```
+
+This is useful before displacement or polarization analysis when a representative averaged structure is needed.
+
+### Octahedral Tilt
+
+```bash
+gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat
+```
+
+The neighbor list should usually contain six B-O neighbors for each B-site center in an `ABO3`-like structure.
+
+### ABO3 Polarization
+
+```bash
+gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \
+  --bec Pb=2 Ti=4.0 O=-2.0 -o polarization.dat
+```
+
+The `--bec` values should be chosen according to your model or reference data. The tool is designed for `ABO3`-type local polarization analysis.
diff --git a/docs/tutorials/en/command_reference.md b/docs/tutorials/en/command_reference.md
new file mode 100644
index 0000000..f4aa1ea
--- /dev/null
+++ b/docs/tutorials/en/command_reference.md
@@ -0,0 +1,127 @@
+<div align="center">
+  <h1>📋 Command Reference</h1>
+  <p style="text-align: justify;">This page lists the stable GPUMDkit command-line shortcuts. Interactive mode is available for workflows with many choices.</p>
+</div>
+
+The source table is maintained in `docs/command_reference.tsv`.
+
+## `gpumdkit.sh -h` Output
+
+```text
++-------------------------------------------------------------------------------------------------------+
+|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
++-------------------------------------------------------------------------------------------------------+
+|                                          MAIN FUNCTIONS                                               |
++-------------------------------------------------------------------------------------------------------+
+| -h            Show this help table            | -plt <type>        Plot and visualization tools       |
+| -calc <type>  Calculator tools                | -time <gpumd|nep>  Time-consuming analyzer            |
+| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
++-------------------------------------------------------------------------------------------------------+
+|                                         FORMAT CONVERSION                                             |
++-------------------------------------------------------------------------------------------------------+
+| -out2xyz      OUTCAR -> extxyz (shell)        | -out2exyz          OUTCAR -> extxyz (python)          |
+| -cp2k2xyz     CP2K log -> xyz                 | -xdat2exyz         XDATCAR -> extxyz                  |
+| -cif2pos      cif -> POSCAR                   | -cif2exyz          cif -> extxyz                      |
+| -pos2exyz     POSCAR -> extxyz                | -exyz2pos          extxyz -> POSCAR                   |
+| -pos2lmp      POSCAR -> LAMMPS data           | -lmp2exyz          LAMMPS dump -> extxyz              |
+| -traj2exyz    ASE traj -> extxyz              | -replicate         Replicate structure                |
+| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
+| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
+| -frame_range  Extract frames by range         |                                                       |
++-------------------------------------------------------------------------------------------------------+
+|                                            ANALYSIS                                                   |
++-------------------------------------------------------------------------------------------------------+
+| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
+| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
+| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
+| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
+| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
+| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
++-------------------------------------------------------------------------------------------------------+
+| Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
++-------------------------------------------------------------------------------------------------------+
+```
+
+## Main
+
+| Command | Syntax | Description |
+|---|---|---|
+| `-h` | `gpumdkit.sh -h` | Show general help |
+| `-update` | `gpumdkit.sh -update` | Update GPUMDkit |
+| `-clean` | `gpumdkit.sh -clean` | Clean extra files in the current directory |
+
+## Format Conversion
+
+| Command | Syntax | Description |
+|---|---|---|
+| `-out2xyz` | `gpumdkit.sh -out2xyz <dir>` | OUTCAR to extxyz, shell version |
+| `-out2exyz` | `gpumdkit.sh -out2exyz <dir>` | OUTCAR to extxyz, Python version |
+| `-cp2k2xyz` | `gpumdkit.sh -cp2k2xyz` | CP2K output to xyz/extxyz |
+| `-xdat2exyz` | `gpumdkit.sh -xdat2exyz <XDATCAR> <output.xyz>` | XDATCAR to extxyz |
+| `-cif2pos` | `gpumdkit.sh -cif2pos <input.cif> <output.vasp>` | CIF to POSCAR/VASP |
+| `-cif2exyz` | `gpumdkit.sh -cif2exyz <input.cif> <output.xyz>` | CIF to extxyz |
+| `-pos2exyz` | `gpumdkit.sh -pos2exyz <POSCAR> <output.xyz>` | POSCAR to extxyz |
+| `-exyz2pos` | `gpumdkit.sh -exyz2pos <input.xyz>` | extxyz frames to POSCAR files |
+| `-pos2lmp` | `gpumdkit.sh -pos2lmp <POSCAR> <output.data>` | POSCAR to LAMMPS data |
+| `-lmp2exyz` | `gpumdkit.sh -lmp2exyz <dump> <element...>` | LAMMPS dump to extxyz |
+| `-traj2exyz` | `gpumdkit.sh -traj2exyz <input.traj> <output.xyz>` | ASE trajectory to extxyz |
+| `-replicate` | `gpumdkit.sh -replicate <input> <output> a b c` | Replicate by cell factors |
+| `-replicate` | `gpumdkit.sh -replicate <input> <output> <target_num>` | Replicate toward a target atom count |
+| `-addgroup` | `gpumdkit.sh -addgroup <POSCAR> <element...>` | Add GPUMD group labels |
+| `-addweight` | `gpumdkit.sh -addweight <input.xyz> <output.xyz> <weight>` | Add structure weights |
+| `-get_frame` | `gpumdkit.sh -get_frame <input.xyz> <frame_index>` | Extract one frame |
+| `-clean_xyz` | `gpumdkit.sh -clean_xyz <input.xyz> <output.xyz>` | Remove extra extxyz properties |
+| `-frame_range` | `gpumdkit.sh -frame_range <input.xyz> <start_frac> <end_frac>` | Extract frames by fractional range |
+
+## Calculators
+
+| Command | Syntax | Description |
+|---|---|---|
+| `-calc ionic-cond` | `gpumdkit.sh -calc ionic-cond <element> <charge>` | Ionic conductivity |
+| `-calc nep` | `gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>` | NEP property prediction |
+| `-calc des` | `gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>` | NEP descriptors |
+| `-calc doas` | `gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>` | Density of atomistic states |
+| `-calc neb` | `gpumdkit.sh -calc neb <initial.xyz> <final.xyz> <n_images> <nep.txt>` | NEB with a NEP model |
+| `-calc minimize` | `gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]` | Structure minimization |
+| `-calc msd` | `gpumdkit.sh -calc msd <trajectory.xyz> <element> <dt_fs> [max_corr_steps]` | MSD from trajectory |
+| `-calc nlist` | `gpumdkit.sh -calc nlist [args...]` | Neighbor lists |
+| `-calc disp` | `gpumdkit.sh -calc disp [args...]` | Displacements |
+| `-calc avg-struct` | `gpumdkit.sh -calc avg-struct [args...]` | Averaged structure |
+| `-calc oct-tilt` | `gpumdkit.sh -calc oct-tilt [args...]` | Octahedral tilt |
+| `-calc pol-abo3` | `gpumdkit.sh -calc pol-abo3 [args...]` | ABO3 local polarization |
+
+## Analyzers
+
+| Command | Syntax | Description |
+|---|---|---|
+| `-range` | `gpumdkit.sh -range <input.xyz> <energy\|force\|virial> [hist]` | Property range analysis |
+| `-analyze_comp` | `gpumdkit.sh -analyze_comp <input.xyz>` | Composition analysis |
+| `-chem_species` | `gpumdkit.sh -chem_species <input.xyz>` | Chemical species list |
+| `-cbc` | `gpumdkit.sh -cbc <input.xyz>` | Charge-balance check |
+| `-min_dist` | `gpumdkit.sh -min_dist <input.xyz>` | Minimum distance without PBC |
+| `-min_dist_pbc` | `gpumdkit.sh -min_dist_pbc <input.xyz>` | Minimum distance with PBC |
+| `-filter_dist` | `gpumdkit.sh -filter_dist <input.xyz> <min_dist>` | Distance filtering |
+| `-filter_dist_pbc` | `gpumdkit.sh -filter_dist_pbc <input.xyz> <min_dist>` | PBC-aware distance filtering |
+| `-filter_box` | `gpumdkit.sh -filter_box <input.xyz> <edge_limit>` | Box-edge filtering |
+| `-filter_value` | `gpumdkit.sh -filter_value <input.xyz> <property> <threshold>` | Property threshold filtering |
+| `-filter_range` | `gpumdkit.sh -filter_range <input.xyz> <element1> <element2> <min_dist> <max_dist>` | Element-pair distance range filtering |
+| `-pda` | `gpumdkit.sh -pda <ref_struct> <trajectory.xyz> <species> <interval>` | Probability density analysis |
+
+## Visualization
+
+Use:
+
+```bash
+gpumdkit.sh -plt <type> [options]
+gpumdkit.sh -plt -h
+```
+
+Common types include `train`, `prediction`, `thermo`, `msd`, `sdc`, `rdf`, `emd`, `nemd`, `hnemd`, `pdos`, and `plane-grid`.
+
+## Utilities
+
+| Command | Syntax | Description |
+|---|---|---|
+| `-time` | `gpumdkit.sh -time <gpumd\|nep>` | Monitor GPUMD or NEP progress |
+| `-nep_modifier` | `gpumdkit.sh -nep_modifier` | Modify NEP models interactively |
+| `-pynep` | `gpumdkit.sh -pynep` | Deprecated PyNEP FPS sampling |
diff --git a/docs/tutorials/contributing.md b/docs/tutorials/en/contributing_to_gpumdkit.md
similarity index 96%
rename from docs/tutorials/contributing.md
rename to docs/tutorials/en/contributing_to_gpumdkit.md
index 3dcc6ba..e279a2d 100644
--- a/docs/tutorials/contributing.md
+++ b/docs/tutorials/en/contributing_to_gpumdkit.md
@@ -1,6 +1,9 @@
-# Contributing to GPUMDkit
+<div align="center">
+  <h1>🤝 Contributing to GPUMDkit</h1>
+  <p style="text-align: justify;">Thank you for your interest in contributing to <strong>GPUMDkit</strong>! We appreciate your time and effort in helping improve this toolkit.</p>
+</div>
 
-Thank you for your interest in contributing to `GPUMDkit`! We appreciate your time and effort in helping improve this toolkit. `GPUMDkit` is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.
+`GPUMDkit` is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.
 
 ---
 
@@ -137,6 +140,8 @@ The structure of `GPUMDkit` consists of:
   - `f3_workflows.sh`
   - `f4_calculators.sh`
   - `f5_analyzers.sh`
+  - `f6_plots.sh`
+  - `f7_utilities.sh`
 - **`docs/`**: Documentation files
 
 #### Interactive Mode Contributions
@@ -167,7 +172,7 @@ To add a new feature accessible through the interactive menu:
    echo " | Developer: Your Name (your@email.com)           |"
    echo " >-------------------------------------------------<"
    echo " Input the required parameters:"
-   echo " Examp: input.xyz output.lmp"
+   echo " Example: input.xyz output.lmp"
    echo " ------------>>"
    read -p " " converter_params
    echo " ---------------------------------------------------"
diff --git a/docs/tutorials/custom_commands.md b/docs/tutorials/en/custom_commands.md
similarity index 100%
rename from docs/tutorials/custom_commands.md
rename to docs/tutorials/en/custom_commands.md
diff --git a/docs/tutorials/en/format_conversion.md b/docs/tutorials/en/format_conversion.md
new file mode 100644
index 0000000..08fa3a2
--- /dev/null
+++ b/docs/tutorials/en/format_conversion.md
@@ -0,0 +1,242 @@
+<div align="center">
+  <h1>🔄 Format Conversion</h1>
+  <p style="text-align: justify;">GPUMDkit contains utilities for converting common atomistic simulation formats, with extra handling for metadata such as group labels, weights, and frame extraction.</p>
+</div>
+
+**Script Location:** `Scripts/format_conversion/`
+
+## Overview
+
+The format conversion module covers:
+
+- **VASP**: `POSCAR`, `CONTCAR`, `OUTCAR`, `XDATCAR`
+- **LAMMPS**: data files and dump trajectories
+- **CP2K**: output logs, position, force, and cell files
+- **ABACUS**: SCF/MD logs
+- **CIF**: crystallographic structure files
+- **ASE trajectory**: `.traj`
+- **extxyz**: a common structure format for GPUMD and NEP
+
+## Interactive Mode
+
+Open GPUMDkit:
+
+```bash
+gpumdkit.sh
+```
+
+Choose:
+
+```text
+1) Format Conversion
+```
+
+The format conversion menu is:
+
+```text
++-------------------------------------------------------------+
+|                   FORMAT CONVERSION TOOLS                   |
++-------------------------------------------------------------+
+| 101) VASP to extxyz            106) Add group labels        |
+| 102) MTP to extxyz             107) Add weight to extxyz    |
+| 103) CP2K to extxyz            108) Extract frame extxyz    |
+| 104) ABACUS to extxyz          109) Clean XYZ info          |
+| 105) extxyz to POSCAR          110) Replicate structure     |
++-------------------------------------------------------------+
+| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |
+| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |
+| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |
+| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|
++-------------------------------------------------------------+
+| 000) Return to main menu                                    |
++-------------------------------------------------------------+
+Input the function number or converter keyword:
+```
+
+### What Each Entry Does
+
+| Entry | Function | When to Use |
+|-------|----------|-------------|
+| `101` | VASP OUTCAR to extxyz, shell version | convert VASP calculation directories |
+| `102` | MTP cfg to extxyz | convert MTP training data |
+| `103` | CP2K to extxyz | choose CP2K log/inp route or pos/frc/cell route |
+| `104` | ABACUS to extxyz | convert ABACUS SCF or MD output |
+| `105` | extxyz to POSCAR | write each extxyz frame as a POSCAR-style file |
+| `106` | add group labels | add atom group labels for GPUMD-related workflows |
+| `107` | add weights | assign training weights in extxyz |
+| `108` | extract frame | export one frame from an extxyz trajectory |
+| `109` | clean XYZ info | remove extra extxyz properties |
+| `110` | replicate structure | build supercells by factors or target atom count |
+| `out2exyz` | OUTCAR to extxyz, Python version | alternative VASP OUTCAR converter |
+| `pos2exyz` | POSCAR to extxyz | convert a single structure |
+| `cif2pos` | CIF to POSCAR | prepare VASP input from CIF |
+| `cif2exyz` | CIF to extxyz | prepare GPUMDkit input from CIF |
+| `xdat2exyz` | XDATCAR to extxyz | convert VASP MD trajectory |
+| `pos2lmp` | POSCAR to LAMMPS data | prepare LAMMPS input |
+| `lmp2exyz` | LAMMPS dump to extxyz | convert LAMMPS trajectory |
+| `traj2exyz` | ASE traj to extxyz | convert ASE trajectory |
+
+## Quick Command Reference
+
+| Source | Target | Command |
+|--------|--------|---------|
+| OUTCAR directory | extxyz | `gpumdkit.sh -out2xyz <dir>` |
+| OUTCAR directory | extxyz | `gpumdkit.sh -out2exyz <dir>` |
+| POSCAR | extxyz | `gpumdkit.sh -pos2exyz <POSCAR> <output.xyz>` |
+| extxyz | POSCAR files | `gpumdkit.sh -exyz2pos <input.xyz>` |
+| XDATCAR | extxyz | `gpumdkit.sh -xdat2exyz XDATCAR dump.xyz` |
+| POSCAR | LAMMPS data | `gpumdkit.sh -pos2lmp POSCAR lammps.data` |
+| LAMMPS dump | extxyz | `gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl` |
+| CIF | POSCAR | `gpumdkit.sh -cif2pos input.cif POSCAR.vasp` |
+| CIF | extxyz | `gpumdkit.sh -cif2exyz input.cif model.xyz` |
+| ASE traj | extxyz | `gpumdkit.sh -traj2exyz input.traj output.xyz` |
+| extxyz | clean extxyz | `gpumdkit.sh -clean_xyz input.xyz clean.xyz` |
+
+## Common Examples
+
+### Convert VASP calculations to extxyz
+
+If each calculation directory contains an `OUTCAR`, run:
+
+```bash
+gpumdkit.sh -out2xyz ./vasp_results/
+```
+
+The shell version searches the target directory and converts VASP results into an extxyz file suitable for later analysis. If you prefer the Python implementation:
+
+```bash
+gpumdkit.sh -out2exyz ./vasp_results/
+```
+
+From interactive mode, choose `101`. You will see:
+
+```text
+>-------------------------------------------------<
+| Calling the script in Scripts/format_conversion |
+| Script: out2xyz.sh                              |
+| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |
+>-------------------------------------------------<
+Input the directory containing OUTCARs
+Example: ./
+------------>>
+```
+
+### Add group labels
+
+Some GPUMD-related workflows use group labels for atom grouping, for example in species-specific MSD or diffusion calculations.
+
+```bash
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+```
+
+This command reads the input structure and writes an extxyz file with group information.
+
+From interactive mode, choose `106`. You will see:
+
+```text
+>-------------------------------------------------<
+| Calling the script in Scripts/format_conversion |
+| Script: add_groups.py                           |
+| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
+>-------------------------------------------------<
+Input <POSCAR> <element1> <element2> ...
+Example: POSCAR Li Y Cl
+------------>>
+```
+
+## Script Details
+
+### POSCAR to extxyz
+
+```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+```
+
+Use this when you have a single VASP structure and want an extxyz output.
+
+Interactive keyword: `pos2exyz`
+
+```text
+Input <POSCAR> <output.xyz>
+Example: POSCAR model.xyz
+------------>>
+```
+
+### extxyz to POSCAR
+
+```bash
+gpumdkit.sh -exyz2pos structures.xyz
+```
+
+This converts all frames in an extxyz file into `POSCAR_*.vasp` files. Frame indices are 0-based in most GPUMDkit scripts, but output filenames are meant for direct inspection and batch calculations.
+
+Interactive entry: `105`
+
+```text
+Input the name of extxyz
+Example: ./train.xyz
+------------>>
+```
+
+### LAMMPS dump to extxyz
+
+```bash
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
+```
+
+The element symbols must match the LAMMPS atom type IDs. For example, if type `1` is Li, type `2` is Y, and type `3` is Cl, the order should be `Li Y Cl`.
+
+Interactive keyword: `lmp2exyz`
+
+```text
+Input <dump_file> <element1> <element2> ...
+Example: dump.lammpstrj Li O
+------------>>
+```
+
+### CIF conversion
+
+```bash
+gpumdkit.sh -cif2pos input.cif POSCAR.vasp
+gpumdkit.sh -cif2exyz input.cif model.xyz
+```
+
+Use `-cif2pos` if you want a VASP-style structure, and `-cif2exyz` if the next step is GPUMDkit analysis.
+
+### Add weights
+
+```bash
+gpumdkit.sh -addweight train.xyz train_weighted.xyz 5
+```
+
+This is useful when you want some structures to have a different training weight in a NEP dataset.
+
+### Replicate structures
+
+```bash
+gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2
+gpumdkit.sh -replicate POSCAR supercell.vasp 256
+```
+
+The first form uses explicit replication factors. The second form tries to build a supercell close to a target atom count.
+
+### Extract one frame
+
+```bash
+gpumdkit.sh -get_frame dump.xyz 1000
+```
+
+This extracts frame index `1000` from an extxyz trajectory.
+
+## Common Mistakes
+
+| Problem | What to Check |
+|---------|---------------|
+| LAMMPS elements are wrong | Check the element order passed after the dump file |
+| A trajectory has strange metadata | Try `-clean_xyz input.xyz clean.xyz` |
+| A converted structure looks shifted | Inspect PBC/cell information in the source file |
+| Frame extraction gives the wrong structure | Remember that frame indices are 0-based |
+
+## Notes
+
+If a Python package required by a specific converter is missing, Python will report it when that converter is used.
diff --git a/docs/tutorials2/en/README.md b/docs/tutorials/en/index.md
similarity index 59%
rename from docs/tutorials2/en/README.md
rename to docs/tutorials/en/index.md
index bf09b0c..a6333ce 100644
--- a/docs/tutorials2/en/README.md
+++ b/docs/tutorials/en/index.md
@@ -1,12 +1,8 @@
 <div align="center">
-  <h1>GPUMDkit Tutorials</h1>
-  <p>
-    <strong>English</strong> | <a href="../zh/README.md">简体中文</a>
-  </p>
+  <h1>📚 GPUMDkit Tutorials</h1>
+  <p style="text-align: justify;">Welcome to <strong>GPUMDkit</strong>, a command-line toolkit for GPUMD and NEP.</p>
 </div>
 
-Welcome to **GPUMDkit** - a command-line toolkit for GPUMD and NEP.
-
 ## What is GPUMDkit?
 
 GPUMDkit streamlines common tasks in computational materials science:
@@ -33,7 +29,7 @@ source ./install.sh
 ```bash
 conda create -n gpumdkit python=3.12
 conda activate gpumdkit
-pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
+pip install neptrain dpdata calorine
 ```
 
 ### Usage
@@ -53,29 +49,30 @@ gpumdkit.sh -h
 
 | Tutorial | Description |
 |----------|-------------|
-| [Quick Start](quickstart.md) | Installation and first steps |
+| [Quick Start](quick_start.md) | Installation and first steps |
+| [Command Reference](command_reference.md) | One-page CLI and menu reference |
 | [Format Conversion](format_conversion.md) | Convert between file formats |
-| [Calculators](calculators.md) | Compute material properties |
-| [Analyzers](analyzers.md) | Structure analysis and validation |
-| [Visualization](visualization.md) | Plotting and visualization |
-| [Workflows](workflows.md) | Batch processing and automation |
-| [Structure Sampling](sampling.md) | Structure selection methods |
-| [NEP Training](nep_training.md) | Complete NEP training workflow |
-
-## Example: NEP Training Pipeline
+| [Calculator Scripts](calculator_scripts.md) | Compute material properties |
+| [Analyzer Scripts](analyzer_scripts.md) | Structure analysis and validation |
+| [Plot Scripts](plot_scripts.md) | Plotting and visualization |
+| [Workflow Scripts](workflow_scripts.md) | Batch processing and automation |
+| [Structure Sampling](structure_sampling.md) | Structure selection methods |
+| [Custom Commands](custom_commands.md) | User-defined GPUMDkit shortcuts |
+| [Active Learning Workflow](active_learning_workflow.md) | Batch active-learning workflow notes |
+| [Polar Material Analysis](polar_material_analysis.md) | Ferroelectric and polarization tools |
+| [Contributing to GPUMDkit](contributing_to_gpumdkit.md) | Development notes |
+
+## Example: Convert VASP OUTCARs
 
 ```bash
-# Convert DFT data
 gpumdkit.sh -out2xyz ./vasp_results/
+```
 
-# Add group labels
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-
-# Sample structures
-gpumdkit.sh  # Select: 2) Sample Structures -> 203
+## Example: Plot NEP Results
 
-# Validate training
+```bash
 gpumdkit.sh -plt train
+gpumdkit.sh -plt prediction
 ```
 
 ## Example: Ionic Conductivity
@@ -91,7 +88,7 @@ gpumdkit.sh -plt msd
 | Module | Menu | CLI | Description |
 |--------|------|-----|-------------|
 | Format Conversion | 1 | `-out2xyz`, `-pos2exyz` | File conversion |
-| Sample Structures | 2 | `-pynep` | Structure sampling |
+| Sample Structures | 2 | `-neptrain`, interactive menu | Structure sampling |
 | Workflow | 3 | - | Batch processing |
 | Calculators | 4 | `-calc <type>` | Property calculations |
 | Analyzer | 5 | `-range`, `-min_dist` | Structure analysis |
diff --git a/docs/tutorials/en/plot_scripts.md b/docs/tutorials/en/plot_scripts.md
new file mode 100644
index 0000000..bc4a9fa
--- /dev/null
+++ b/docs/tutorials/en/plot_scripts.md
@@ -0,0 +1,397 @@
+<div align="center">
+  <h1>📊 Plot Scripts</h1>
+  <p style="text-align: justify;">The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators.</p>
+</div>
+
+**Script Location:** `Scripts/plt_scripts/`
+
+## Quick Access
+
+```bash
+gpumdkit.sh -plt          # show all plotting options
+gpumdkit.sh -plt <type>   # generate a plot
+gpumdkit.sh -plt <type> save
+gpumdkit.sh -plt <type> -h
+```
+
+## NEP Training and Prediction
+
+### Training Results
+
+`plt_train.py` visualizes NEP training progress, including loss curves and parity plots for energy, force, and virial/stress.
+
+**Input files:**
+
+- `loss.out`
+- `energy_train.out`
+- `force_train.out`
+- `virial_train.out`
+
+**Usage:**
+
+```bash
+gpumdkit.sh -plt train
+```
+
+<div align="center">
+  <img src="../../Gallery/train.png" alt="NEP training results" width="75%" />
+</div>
+
+### Prediction Results
+
+`plt_prediction.py` visualizes prediction/test-set results.
+
+**Input files:**
+
+- `energy_test.out`
+- `force_test.out`
+- `virial_test.out`
+
+**Usage:**
+
+```bash
+gpumdkit.sh -plt prediction
+gpumdkit.sh -plt test
+```
+
+<div align="center">
+  <img src="../../Gallery/prediction.png" alt="NEP prediction results" width="75%" />
+</div>
+
+### Train/Test Comparison
+
+```bash
+gpumdkit.sh -plt train_test
+```
+
+<div align="center">
+  <img src="../../Gallery/train_test.png" alt="NEP train and test comparison" width="75%" />
+</div>
+
+### Density Parity Plot
+
+For large datasets, density-based parity plots are often easier to read than raw scatter plots.
+
+```bash
+gpumdkit.sh -plt parity_density
+```
+
+<div align="center">
+  <img src="../../Gallery/parity_plot_density.png" alt="Parity density plot" width="70%" />
+</div>
+
+### Force Error Analysis
+
+`plt_force_errors.py` plots force magnitude and angular errors following the analysis style proposed by [Liu et al.](https://doi.org/10.1038/s41524-023-01123-3).
+
+```bash
+gpumdkit.sh -plt force_errors
+```
+
+<div align="center">
+  <img src="../../Gallery/force_errors.png" alt="Force error analysis" width="70%" />
+</div>
+
+### Restart Parameters
+
+```bash
+gpumdkit.sh -plt restart
+```
+
+<div align="center">
+  <img src="../../Gallery/nep_restart.png" alt="NEP restart parameters" width="60%" />
+</div>
+
+### Charge and Born Effective Charge
+
+For qNEP charge output:
+
+```bash
+gpumdkit.sh -plt charge
+```
+
+<div align="center">
+  <img src="../../Gallery/charge.png" alt="Charge distribution" width="45%" />
+</div>
+
+For Born effective charge prediction:
+
+```bash
+gpumdkit.sh -plt born_charge
+gpumdkit.sh -plt bec
+```
+
+<div align="center">
+  <img src="../../Gallery/born_charge.png" alt="Born effective charge parity plot" width="45%" />
+</div>
+
+## Molecular Dynamics and Thermodynamics
+
+### Thermodynamic Properties
+
+`plt_thermo.py` reads `thermo.out` and plots temperature, potential energy, pressure, and other thermodynamic quantities.
+
+```bash
+gpumdkit.sh -plt thermo
+gpumdkit.sh -plt thermo2
+gpumdkit.sh -plt thermo3
+```
+
+<div align="center">
+  <img src="../../Gallery/thermo.png" alt="Thermo plot" width="75%" />
+</div>
+
+### Radial Distribution Function
+
+```bash
+gpumdkit.sh -plt rdf
+gpumdkit.sh -plt rdf <column>
+```
+
+Full RDF output:
+
+<div align="center">
+  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
+</div>
+
+Single pair RDF:
+
+<div align="center">
+  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
+</div>
+
+### Velocity Autocorrelation and PDOS
+
+```bash
+gpumdkit.sh -plt pdos
+gpumdkit.sh -plt pdos save
+```
+
+**Input files:** `model.xyz`, `run.in`, `dos.out`, `mvac.out`
+
+<div align="center">
+  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
+</div>
+
+Heat capacity output:
+
+<div align="center">
+  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
+</div>
+
+## Diffusion and Ionic Transport
+
+### Mean Square Displacement
+
+```bash
+gpumdkit.sh -plt msd
+```
+
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="Mean square displacement" width="48%" />
+</div>
+
+### MSD for All Species
+
+Use this when `compute_msd` in `run.in` was configured with `all_groups`.
+
+```bash
+gpumdkit.sh -plt msd_all msd.out Li P S
+```
+
+<div align="center">
+  <img src="../../Gallery/msd_all.png" alt="MSD for all species" width="48%" />
+</div>
+
+### MSD Convergence Check
+
+```bash
+gpumdkit.sh -plt msd_conv
+```
+
+<div align="center">
+  <img src="../../Gallery/msd_convergence.png" alt="MSD convergence" width="48%" />
+</div>
+
+### Self-Diffusion Coefficient
+
+```bash
+gpumdkit.sh -plt sdc
+```
+
+<div align="center">
+  <img src="../../Gallery/sdc.png" alt="Self-diffusion coefficient" width="48%" />
+</div>
+
+### Arrhenius Diffusivity
+
+```bash
+gpumdkit.sh -plt arrhenius_d
+gpumdkit.sh -plt D
+```
+
+<div align="center">
+  <img src="../../Gallery/Arrhenius_D.png" alt="Arrhenius diffusivity" width="58%" />
+</div>
+
+Example output:
+
+```text
+T: 300K, D_total: 1.001e-07 cm2/s
+T: 350K, D_total: 4.184e-07 cm2/s
+T: 400K, D_total: 1.027e-06 cm2/s
+Ea: 0.230 eV
+```
+
+### Arrhenius Ionic Conductivity
+
+```bash
+gpumdkit.sh -plt arrhenius_sigma
+gpumdkit.sh -plt sigma
+```
+
+<div align="center">
+  <img src="../../Gallery/Arrhenius_sigma.png" alt="Arrhenius ionic conductivity" width="58%" />
+</div>
+
+## Heat Transport
+
+### EMD
+
+```bash
+gpumdkit.sh -plt emd x
+```
+
+<div align="center">
+  <img src="../../Gallery/emd.png" alt="EMD thermal conductivity" width="72%" />
+</div>
+
+### NEMD
+
+```bash
+gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]
+```
+
+Parameter notes:
+
+| Parameter | Meaning |
+|-----------|---------|
+| `real_length` | real length of heat-transfer zone in nm; use `Auto` for automatic calculation |
+| `scale_eff_size` | scale factor for effective cross-sectional area |
+| `cutoff_freq` | cutoff frequency for SHC calculation in THz |
+| `save` | optional flag to save the figure |
+
+<div align="center">
+  <img src="../../Gallery/nemd.png" alt="NEMD results" width="72%" />
+</div>
+
+### HNEMD
+
+```bash
+gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]
+```
+
+<div align="center">
+  <img src="../../Gallery/hnemd.png" alt="HNEMD results" width="72%" />
+</div>
+
+## Descriptor, Dimer, and Extra Analysis
+
+### Descriptor Visualization
+
+First calculate descriptors:
+
+```bash
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+```
+
+Then visualize:
+
+```bash
+gpumdkit.sh -plt des pca
+gpumdkit.sh -plt des umap
+```
+
+<div align="center">
+  <img src="../../Gallery/des_umap.png" alt="UMAP descriptor visualization" width="52%" />
+</div>
+
+### Dimer Curve
+
+`plt_dimer.py` places two atoms in a large cubic box and calculates energy/force as a function of dimer distance using a NEP model.
+
+```bash
+gpumdkit.sh -plt dimer Li Li nep.txt
+```
+
+<div align="center">
+  <img src="../../Gallery/dimer_nep.png" alt="Dimer NEP curve" width="45%" />
+  <img src="../../Gallery/dimer.png" alt="Dimer comparison" width="45%" />
+</div>
+
+**Reference:** [J. Chem. Inf. Model. 2026, 66, 3, 1406-1413](https://doi.org/10.1021/acs.jcim.5c02335)
+
+### Density of Atomistic States
+
+`plt_doas.py` plots the density of atomistic states proposed by [Wang et al.](https://doi.org/10.1002/anie.202215544).
+
+```bash
+gpumdkit.sh -plt doas doas.out Li
+```
+
+<div align="center">
+  <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
+</div>
+
+### Net Force Distribution
+
+```bash
+gpumdkit.sh -plt net_force train.xyz
+```
+
+**Reference:** [arXiv:2510.19774](https://arxiv.org/abs/2510.19774)
+
+<div align="center">
+  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
+</div>
+
+## Plane-Grid Plot for Polar Materials
+
+This workflow maps displacement or polarization data onto a grid and plots selected plane profiles.
+
+Typical upstream steps:
+
+```bash
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat
+gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz
+```
+
+Plot:
+
+```bash
+gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr
+gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1
+```
+
+This function requires `ferrodispcalc`.
+
+## Quick Reference Table
+
+| Command | Input File(s) | Purpose |
+|---------|---------------|---------|
+| `train` | `loss.out`, `*_train.out` | NEP training plots |
+| `prediction` | `*_test.out` | NEP prediction plots |
+| `train_test` | train/test outputs | combined parity plots |
+| `thermo` | `thermo.out` | thermodynamic properties |
+| `msd` | `msd.out` | mean square displacement |
+| `sdc` | `msd.out` | self-diffusion coefficient |
+| `rdf` | `rdf.out` | radial distribution function |
+| `pdos` | `dos.out`, `mvac.out` | VAC and PDOS |
+| `emd` | EMD outputs | EMD thermal conductivity |
+| `nemd` | NEMD outputs | NEMD thermal transport |
+| `hnemd` | HNEMD outputs | HNEMD thermal transport |
+| `des` | `descriptors.npy` | descriptor PCA/UMAP |
+| `dimer` | `nep.txt` | dimer energy/force curve |
+| `doas` | `doas.out` | density of atomistic states |
+| `net_force` | `train.xyz` | net force distribution |
diff --git a/docs/tutorials/polar_material_analysis.md b/docs/tutorials/en/polar_material_analysis.md
similarity index 100%
rename from docs/tutorials/polar_material_analysis.md
rename to docs/tutorials/en/polar_material_analysis.md
diff --git a/docs/tutorials/en/quick_start.md b/docs/tutorials/en/quick_start.md
new file mode 100644
index 0000000..17189db
--- /dev/null
+++ b/docs/tutorials/en/quick_start.md
@@ -0,0 +1,231 @@
+<div align="center">
+  <h1>🚀 Quick Start</h1>
+  <p style="text-align: justify;">This page introduces the basic installation and several common commands. GPUMDkit can be used through the interactive menu or by direct command-line options.</p>
+</div>
+
+## 1. Prepare a Python Environment
+
+You can use a clean conda environment:
+
+```bash
+conda create -n gpumdkit python=3.12
+conda activate gpumdkit
+```
+
+Some optional functions use additional packages:
+
+```bash
+pip install neptrain dpdata calorine
+```
+
+Other Python dependencies are loaded by the corresponding scripts. If a package is missing, Python will report it when that function is used.
+
+## 2. Install GPUMDkit
+
+Clone the repository:
+
+```bash
+git clone https://github.com/zhyan0603/GPUMDkit.git
+cd GPUMDkit
+```
+
+Run the installer:
+
+```bash
+source ./install.sh
+```
+
+The installer writes `GPUMDkit_path` and `PATH` settings to your shell configuration and loads them for the current shell. It writes to `~/.bashrc` by default; if the current shell is zsh, it writes to `~/.zshrc`. If an existing GPUMDkit path is found, the installer prints the old path and asks whether to replace it. Before changing the rc file, it creates a backup.
+
+Typical installation output:
+
+```text
+======================================================
+  GPUMDkit Installation
+======================================================
+ [1/4] Detecting GPUMDkit directory...
+       /path/to/GPUMDkit
+ [2/4] Detecting shell configuration...
+       Target: /Users/you/.bashrc
+       Adding environment variables to /Users/you/.bashrc
+       Success: Environment variables added.
+ [3/4] Setting executable permissions...
+       Added executable permission to gpumdkit.sh
+ [4/4] Loading environment...
+
+======================================================
+  Installation Complete!  GPUMDkit is ready to use.
+======================================================
+```
+
+If GPUMDkit was installed before, you may see:
+
+```text
+Existing GPUMDkit configuration found.
+Existing path(s):
+  - /old/path/to/GPUMDkit
+New path:
+  - /new/path/to/GPUMDkit
+
+Replace the existing GPUMDkit configuration with the new path? [y/N]:
+```
+
+Check the command:
+
+```bash
+gpumdkit.sh -h
+```
+
+The help table:
+
+```text
++-------------------------------------------------------------------------------------------------------+
+|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
++-------------------------------------------------------------------------------------------------------+
+|                                          MAIN FUNCTIONS                                               |
++-------------------------------------------------------------------------------------------------------+
+| -h            Show this help table            | -plt <type>        Plot and visualization tools       |
+| -calc <type>  Calculator tools                | -time <gpumd|nep>  Time-consuming analyzer            |
+| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
++-------------------------------------------------------------------------------------------------------+
+|                                         FORMAT CONVERSION                                             |
++-------------------------------------------------------------------------------------------------------+
+| -out2xyz      OUTCAR -> extxyz (shell)        | -out2exyz          OUTCAR -> extxyz (python)          |
+| -cp2k2xyz     CP2K log -> xyz                 | -xdat2exyz         XDATCAR -> extxyz                  |
+| -cif2pos      cif -> POSCAR                   | -cif2exyz          cif -> extxyz                      |
+| -pos2exyz     POSCAR -> extxyz                | -exyz2pos          extxyz -> POSCAR                   |
+| -pos2lmp      POSCAR -> LAMMPS data           | -lmp2exyz          LAMMPS dump -> extxyz              |
+| -traj2exyz    ASE traj -> extxyz              | -replicate         Replicate structure                |
+| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
+| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
+| -frame_range  Extract frames by range         |                                                       |
++-------------------------------------------------------------------------------------------------------+
+|                                            ANALYSIS                                                   |
++-------------------------------------------------------------------------------------------------------+
+| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
+| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
+| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
+| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
+| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
+| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
++-------------------------------------------------------------------------------------------------------+
+| Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
++-------------------------------------------------------------------------------------------------------+
+```
+
+## 3. Usage Modes
+
+### Interactive Mode
+
+```bash
+gpumdkit.sh
+```
+
+Main menu:
+
+```text
+           ____ ____  _   _ __  __ ____  _    _ _
+          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
+         | |  _| |_) | | | | |\/| | | | | |/ / | __|
+         | |_| |  __/| |_| | |  | | |_| |   <| | |_
+          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
+
+          GPUMDkit Version 1.5.6 (dev) (2026-06-17)
+    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+ Main Contributors: Denan LI, Xin WU, Zhoulin LIU & Chen HUA
+
+ ---------------------- GPUMD ------------------------
+ 1) Format Conversion          2) Sample Structures
+ 3) Workflow                   4) Calculators
+ 5) Analyzer                   6) Visualization
+ 7) Utilities                  8) Developing...
+ 0) Exit
+ ------------>>
+ Input the function number:
+```
+
+### Command-Line Mode
+
+Direct commands use fixed positional arguments:
+
+```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+gpumdkit.sh -plt train
+gpumdkit.sh -plt thermo
+```
+
+For example:
+
+```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+```
+
+means reading `POSCAR` and writing `model.xyz`.
+
+## 4. Practical Examples
+
+### Convert POSCAR to extxyz
+
+```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+```
+
+### Add GPUMD Group Labels
+
+```bash
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+```
+
+Group labels are used by some GPUMD-related workflows and analyses that need atom grouping, such as species-specific MSD or diffusion calculations.
+
+### Plot NEP Training Results
+
+```bash
+gpumdkit.sh -plt train
+```
+
+<div align="center">
+  <img src="../../Gallery/train.png" alt="NEP training results" width="72%" />
+</div>
+
+### Plot NEP Test Results
+
+```bash
+gpumdkit.sh -plt test
+```
+
+<div align="center">
+  <img src="../../Gallery/prediction.png" alt="NEP test results" width="72%" />
+</div>
+
+### Plot Thermodynamic Data
+
+```bash
+gpumdkit.sh -plt thermo
+```
+
+<div align="center">
+  <img src="../../Gallery/thermo.png" alt="Thermo plot" width="72%" />
+</div>
+
+### Plot MSD and Self-Diffusion Coefficient
+
+```bash
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+```
+
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
+  <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
+</div>
+
+## 5. Help
+
+```bash
+gpumdkit.sh -h
+gpumdkit.sh -plt -h
+gpumdkit.sh -calc -h
+gpumdkit.sh -plt train -h
+gpumdkit.sh -calc msd -h
+```
diff --git a/docs/tutorials/en/structure_sampling.md b/docs/tutorials/en/structure_sampling.md
new file mode 100644
index 0000000..e12dd24
--- /dev/null
+++ b/docs/tutorials/en/structure_sampling.md
@@ -0,0 +1,257 @@
+<div align="center">
+  <h1>📦 Structure Sampling</h1>
+  <p style="text-align: justify;">Structure sampling is used to select, generate, or filter candidate configurations for NEP training and molecular dynamics workflows.</p>
+</div>
+
+**Script Location:** `Scripts/sample_structures/`
+
+## Interactive Mode
+
+Sampling tasks are usually easier to run from the interactive menu:
+
+```bash
+gpumdkit.sh
+```
+
+Choose:
+
+```text
+2) Sample Structures
+```
+
+The menu is:
+
+```text
++------------------------------------------------------+
+|                 SAMPLE STRUCTURE TOOLS               |
++------------------------------------------------------+
+| 201) Sample structures from extxyz                   |
+| 202) PyNEP sampling [deprecated]                    |
+| 203) FPS sampling by NepTrain [preferred]            |
+| 204) Perturb structure                               |
+| 205) Select max force deviation structs              |
++------------------------------------------------------+
+| 000) Return to the main menu                         |
++------------------------------------------------------+
+Input the function number:
+```
+
+Available entries:
+
+| Menu | Method | Use Case |
+|------|--------|----------|
+| 201 | Uniform/random sampling | quick frame selection from a trajectory |
+| 202 | PyNEP notice | prints a notice; use `gpumdkit.sh -pynep` to run PyNEP |
+| 203 | NepTrain FPS | descriptor-based FPS with NepTrain |
+| 204 | Perturb structure | generate perturbed structures from POSCAR/CONTCAR |
+| 205 | Force-deviation selection | select structures with high model deviation |
+
+## Uniform and Random Sampling
+
+From interactive mode, choose `201`. You will see:
+
+```text
+Input <extxyz_file> <sampling_method> <num_samples> [skip_num]
+[skip_num]: number of initial frames to skip, default value is 0
+Sampling_method: 'uniform' or 'random'
+Example: train.xyz uniform 50
+------------>>
+```
+
+Example input:
+
+```text
+dump.xyz uniform 50
+```
+
+or:
+
+```text
+dump.xyz random 100 500
+```
+
+Arguments:
+
+| Argument | Meaning |
+|----------|---------|
+| `dump.xyz` | input trajectory |
+| `uniform` / `random` | sampling method |
+| `50` / `100` | number of selected structures |
+| `500` | optional number of initial frames to skip |
+
+Output:
+
+- `sampled_structures.xyz`
+
+## Farthest Point Sampling with NepTrain
+
+This entry uses NepTrain descriptors for FPS.
+
+```bash
+python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
+```
+
+From interactive mode, choose `203`. You will see:
+
+```text
+Input <sample.xyz> <train.xyz> <nep_model>
+Example: dump.xyz train.xyz nep.txt
+------------>>
+```
+
+Inputs:
+
+| File | Meaning |
+|------|---------|
+| `dump.xyz` | candidate structures |
+| `train.xyz` | existing training set |
+| `nep.txt` | current NEP model used to compute descriptors |
+
+Outputs:
+
+- `selected.xyz`
+- `select.png`
+- `pca_sample.txt`
+- `pca_train.txt`
+- `pca_selected.txt`
+
+During execution, choose one of two selection modes:
+
+1. select until the descriptor distance is below a threshold;
+2. select a specified number of structures.
+
+The script then prints a selection prompt:
+
+```text
+Choose selection method:
+1) Select structures based on minimum distance
+2) Select structures based on number of structures
+------------>>
+```
+
+This function requires the `NepTrain` package. If you use this function, we recommend citing the NepTrain paper printed by the script.
+
+## Deprecated PyNEP FPS
+
+PyNEP FPS is kept for compatibility, but it is only exposed through the direct `-pynep` entry:
+
+If you choose `202` from the interactive menu, it prints:
+
+```text
++-------------------------------------------------+
+| Function 202 is no longer supported here.       |
+| PyNEP package is no longer actively maintained. |
+| Please use 203) NepTrain sampling instead.      |
+| If you still need PyNEP compatibility, run:     |
+|                 gpumdkit.sh -pynep              |
++-------------------------------------------------+
+```
+
+```bash
+gpumdkit.sh -pynep
+```
+
+Then input:
+
+```text
+dump.xyz train.xyz nep.txt 8
+```
+
+This entry requires `pynep` and is kept for compatibility.
+
+## Structure Perturbation
+
+Use perturbation when you want to generate initial structures around a known configuration.
+
+```bash
+python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
+```
+
+From interactive mode, choose `204`. You will see:
+
+```text
+Input <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>
+The default parameters for perturb are 20 0.03 0.2 uniform
+Example: POSCAR 20 0.03 0.2 uniform
+------------>>
+```
+
+Arguments:
+
+| Argument | Meaning |
+|----------|---------|
+| `POSCAR` | input VASP structure |
+| `20` | number of perturbed structures |
+| `0.03` | cell perturbation fraction |
+| `0.2` | atom perturbation distance in Angstrom |
+| `uniform` | perturbation style: `normal`, `uniform`, or `const` |
+
+Output:
+
+- `POSCAR_01.vasp`, `POSCAR_02.vasp`, ...
+
+This function requires `dpdata`.
+
+## Force-Deviation Selection
+
+Use this together with the GPUMD `active` command. The `active` command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. `select_max_modev.py` selects structures with large force deviations from `active.out` and `active.xyz`, then writes them to `selected.xyz`.
+
+```bash
+python Scripts/sample_structures/select_max_modev.py 200 0.15
+```
+
+From interactive mode, choose `205`. You will see:
+
+```text
++----------------------------------------------------+
+| Select max force deviation structs from active.xyz |
+|     generated by the active command in gpumd.      |
++----------------------------------------------------+
+Input <structs_num> <threshold> (eg. 200 0.15)
+------------>>
+```
+
+Arguments:
+
+| Argument | Meaning |
+|----------|---------|
+| `200` | maximum number of structures to keep |
+| `0.15` | minimum force deviation threshold |
+
+Required files:
+
+- `active.out`
+- `active.xyz`
+
+Output:
+
+- `selected.xyz`
+
+## Frame Range Extraction
+
+Use this to extract a fraction of a trajectory:
+
+```bash
+python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
+```
+
+This writes frames from 0% to 80% of the trajectory.
+
+## Example Commands
+
+An example sequence using several sampling-related tools:
+
+```bash
+gpumdkit.sh -min_dist_pbc dump.xyz
+gpumdkit.sh -filter_box dump.xyz 13
+python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
+```
+
+## Common Mistakes
+
+| Problem | Recommendation |
+|---------|----------------|
+| FPS selects too many similar structures | increase the distance threshold or select fewer structures |
+| Perturbed structures are unphysical | reduce `cell_pert` and `atom_pert`, then check minimum distances |
+| `active.out` and `active.xyz` do not match | regenerate both from the same GPUMD active run |
+| PCA plot looks strange | check whether `nep.txt` matches the chemical species in both datasets |
diff --git a/docs/tutorials/en/workflow_scripts.md b/docs/tutorials/en/workflow_scripts.md
new file mode 100644
index 0000000..17f750c
--- /dev/null
+++ b/docs/tutorials/en/workflow_scripts.md
@@ -0,0 +1,223 @@
+<div align="center">
+  <h1>🔧 Workflow Scripts</h1>
+  <p style="text-align: justify;">Workflow scripts automate repetitive preparation steps for DFT, MD, and NEP development.</p>
+</div>
+
+**Script Location:** `Scripts/workflow/`
+
+## Interactive Entry
+
+```bash
+gpumdkit.sh
+```
+
+Choose:
+
+```text
+3) Workflow
+```
+
+Typical workflow menu:
+
+| Menu | Workflow | Purpose |
+|------|----------|---------|
+| 301 | SCF batch pretreatment | prepare single-point DFT calculations |
+| 302 | MD sample batch pretreatment (GPUMD) | prepare GPUMD sampling calculations |
+| 303 | MD sample batch pretreatment (LAMMPS) | prepare LAMMPS sampling calculations |
+
+## SCF Batch Pretreatment
+
+Use this when you have many structures and want to prepare single-point DFT calculations.
+
+### VASP
+
+Interactive mode:
+
+```bash
+gpumdkit.sh
+# choose 3 -> 301 -> VASP
+```
+
+Before running, put structure files in the current directory. The script checks files in this order:
+
+1. if one or more `.vasp` files exist, it processes `.vasp` files;
+2. if both `.vasp` and `.xyz` files exist, it prints a notice and only processes `.vasp` files;
+3. if no `.vasp` file exists and one `.xyz` file exists, it converts that extxyz file to POSCAR files;
+4. if no `.vasp` file exists and multiple `.xyz` files exist, it asks you to choose one.
+
+Typical input directory before running:
+
+```text
+current directory/
+├── POSCAR_1.vasp
+├── POSCAR_2.vasp
+└── POSCAR_3.vasp
+```
+
+or:
+
+```text
+current directory/
+└── sampled.xyz
+```
+
+After running, the script creates:
+
+```text
+current directory/
+├── struct_fp/
+│   ├── POSCAR_1.vasp
+│   ├── POSCAR_2.vasp
+│   └── ...
+├── fp/
+├── <prefix>_1/
+├── <prefix>_2/
+└── presub.sh
+```
+
+You must place `INCAR`, `POTCAR`, and `KPOINTS` in the generated `fp/` directory after the script creates it. The calculation folders link to files in `fp/`.
+
+The `prefix` you input during the workflow becomes the calculation folder prefix. When `out2xyz` is later used to extract results, the folder name is stored as `config_type` in the extxyz file, which makes it easier to trace where each structure came from.
+
+### CP2K
+
+CP2K SCF batch pretreatment is available from the workflow menu and can also be called directly:
+
+```bash
+gpumdkit.sh
+# choose 3 -> 301 -> CP2K
+```
+
+```bash
+python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc
+```
+
+The interactive wrapper asks for:
+
+```text
+<extxyz_file> <template.inp> <prefix_name>
+```
+
+Example:
+
+```text
+dump.xyz template.inp H2O
+```
+
+The template should be configured to read coordinates from `pos.xyz`. A reference template is available at:
+
+```text
+Scripts/workflow/cp2k_template.inp
+```
+
+The script creates `<prefix>_<index>/` directories, writes `input.inp`, and writes `pos.xyz` for each structure.
+
+## MD Sampling Pretreatment
+
+### GPUMD
+
+Interactive mode:
+
+```bash
+gpumdkit.sh
+# choose 3 -> 302
+```
+
+Typical preparation:
+Before running, put `.vasp` files or one extxyz file in the current directory. The detection order is the same as the VASP SCF workflow: `.vasp` files are preferred; if multiple `.xyz` files are found without `.vasp`, the script asks you to choose one.
+
+Typical input directory:
+
+```text
+current directory/
+├── POSCAR_1.vasp
+└── POSCAR_2.vasp
+```
+
+or:
+
+```text
+current directory/
+└── dump.xyz
+```
+
+After running, the script creates:
+
+```text
+current directory/
+├── struct_md/
+│   ├── model_1.xyz
+│   ├── model_2.xyz
+│   └── ...
+├── md/
+├── sample_1/
+├── sample_2/
+└── presub.sh
+```
+
+You must place `nep.txt` and `run_*.in` files in the generated `md/` directory. The script links `run_1.in` to `sample_1/run.in`, `run_2.in` to `sample_2/run.in`, and so on.
+
+### LAMMPS
+
+Interactive mode:
+
+```bash
+gpumdkit.sh
+# choose 3 -> 303
+```
+
+Typical preparation:
+Before running, put `.vasp` files or one extxyz file in the current directory. `.vasp` files are preferred when both formats exist.
+
+After running, the script creates LAMMPS data files in `struct_md/`, sample folders, and an `md/` directory:
+
+```text
+current directory/
+├── struct_md/
+│   ├── lammps_1.data
+│   ├── lammps_2.data
+│   └── ...
+├── md/
+├── sample_1/
+├── sample_2/
+└── presub.sh
+```
+
+You must place `lmprun.in` and `nep.txt` in the generated `md/` directory.
+
+## Active-Learning Style Workflow
+
+A common NEP improvement loop is:
+
+1. run MD with the current `nep.txt`;
+2. collect `dump.xyz` or `active.xyz`;
+3. remove unphysical structures;
+4. select diverse or uncertain structures;
+5. run DFT single-point calculations;
+6. convert DFT results to extxyz;
+7. append new structures to `train.xyz`;
+8. retrain the NEP model.
+
+For the development active-learning script, see [Active Learning](active_learning_workflow.md).
+
+## Template-Based Temperature Series
+
+For a simple temperature series, a shell loop is often enough:
+
+```bash
+for temp in 300 500 700 900; do
+    mkdir -p "${temp}K"
+    cp model.xyz "${temp}K/"
+    cp nep.txt "${temp}K/"
+    sed "s/TEMPERATURE/$temp/g" run_template.in > "${temp}K/run.in"
+done
+```
+
+Then submit the generated folders according to your local cluster system.
+
+## Practical Notes
+
+- Workflow scripts are cluster- and template-dependent. Always test with a small number of structures first.
+- Keep template files (`INCAR`, `KPOINTS`, `POTCAR`, `run.in`, CP2K inputs) under version control if possible.
+- Check generated folders before submitting a large batch.
+- Use analyzers and sampling scripts before expensive DFT calculations.
diff --git a/docs/tutorials/format_conversion.md b/docs/tutorials/format_conversion.md
deleted file mode 100644
index 5795a79..0000000
--- a/docs/tutorials/format_conversion.md
+++ /dev/null
@@ -1,375 +0,0 @@
-<div align="center">
-  <h1>🔄 Format Conversion</h1>
-    <p style="text-align: justify;">This directory (Scripts/format_conversion/) contains utilities for converting between different file formats commonly used in computational materials science.</p>
-</div>
-
-**Script Location:** `Scripts/format_conversion/`
-
-This section covers the format conversion tools in GPUMDkit (Interactive Mode - Option 1).
-
-## Interactive Mode
-
-```bash
-gpumdkit.sh
-# Select: 1) Format Conversion
-```
-
-You'll see the following menu:
-
-```
- +-------------------------------------------------------------+
- |                   FORMAT CONVERSION TOOLS                   |
- +-------------------------------------------------------------+
- | 101) VASP to extxyz            106) Add group labels        |
- | 102) MTP to extxyz             107) Add weight to extxyz    |
- | 103) CP2K to extxyz            108) Extract frame extxyz    |
- | 104) ABACUS to extxyz          109) Clean XYZ info          |
- | 105) extxyz to POSCAR          110) Replicate structure     |
- +-------------------------------------------------------------+
- | out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |
- | pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |
- | cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |
- | cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|
- +-------------------------------------------------------------+
- | 000) Return to main menu                                    |
- +-------------------------------------------------------------+
- Input the function number or converter keyword:
-```
-
-for `101`:
-
-```
- >-------------------------------------------------<
- | Calling the script in Scripts/format_conversion |
- | Script: out2xyz.sh                              |
- | Developer: Yanzhou WANG (yanzhowang@gmail.com)  |
- >-------------------------------------------------<
- Choose the type of conversion:
- 1) OUTCAR to extxyz
- 2) vasprun.xml to extxyz
- ------------>>
-```
-
-for `102`:
-
-```
- >-------------------------------------------------<
- | Calling the script in Scripts/format_conversion |
- | Script: mtp2xyz.py                              |
- | Developer: Ke XU (kickhsu@gmail.com)            |
- >-------------------------------------------------<
- Input <filename.cfg> <Symbol1 Symbol2 Symbol3 ...>
- Examp: train.cfg Pd Ag
- ------------>>
-```
-
-for `103`:
-
-```
- >-------------------------------------------------<
- | Calling the script in Scripts/format_conversion |
- | Script: cp2k2xyz.py                             |
- | Developer: Ke XU (kickhsu@gmail.com)            |
- >-------------------------------------------------<
- Input [pos.xyz] [frc.xyz] [cell.cell] [-shifted yes/no]
- ------------>>
-```
-
-for `104`:
-
-```
- >-------------------------------------------------<
- | Calling the script in Scripts/format_conversion |
- | Script: abacus2xyz-scf.sh/abacus2xyz-md.sh      |
- | Developer: Benrui TANG (tang070205@proton.me)   |
- >-------------------------------------------------<
- Choose the type of ABACUS calculation:
- 1) SCF calculation
- 2) MD calculation
- ------------>>
-```
-
-for `105`:
-
-```
- >-------------------------------------------------<
- | Calling the script in Scripts/format_conversion |
- | Script: exyz2pos.py                             |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input the name of extxyz
- Examp: ./train.xyz
- ------------>>
-```
-
-Follow the prompts to complete the function.
-
----
-
-## Command-line Mode
-
-| Source Format | Target Format | Command |
-|---------------|---------------|---------|
-| OUTCAR | extxyz | `gpumdkit.sh -out2xyz <dir>` |
-| vasprun.xml | extxyz | `gpumdkit.sh -xml2xyz <dir>` |
-| POSCAR | extxyz | `gpumdkit.sh -pos2exyz <poscar> <xyz>` |
-| extxyz | POSCAR | `gpumdkit.sh -exyz2pos <xyz>` |
-| POSCAR | LAMMPS | `gpumdkit.sh -pos2lmp <poscar> <lmp> <elem...>` |
-| LAMMPS dump | extxyz | `gpumdkit.sh -lmp2exyz <dump> <elem...>` |
-| CIF | extxyz | `gpumdkit.sh -cif2exyz <cif>` |
-| CIF | POSCAR | `gpumdkit.sh -cif2pos <cif>` |
-| Add groups | - | `gpumdkit.sh -addgroup <poscar> <elem...>` |
-| Add weight | - | `gpumdkit.sh -addweight <in> <out> <weight>` |
-| Replicate1 | - | `gpumdkit.sh -replicate input.vasp output.vasp 2 2 2` |
-| Replicate2 | - | `gpumdkit.sh -replicate input.vasp output.vasp <target_num>` |
-| Get frame | - | `gpumdkit.sh -ge_frame <extxyz> <index>` |
-
----
-
-## Scripts
-
-### add_groups.py
-
----
-
-This script adds group labels to structures based on specified elements.
-
-#### Usage
-
-```
-python add_groups.py <filename> <Symbols1> <Symbols2> ...
-```
-
-- `<filename>`: The path to the input file (e.g., POSCAR).
-- `<Symbols>`: Space-separated list of element symbols to group (e.g., Li Y Cl).
-
-#### Example
-
-```sh
-python add_groups.py POSCAR Li Y Cl
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-```
-
-This command will read the `POSCAR` file and add group labels for the elements `Li`, `Y`, and `Cl`. The output will be saved to a file named `model.xyz`.
-
-
-
-### add_weight.py
-
----
-
-This script adds weight labels to structures.
-
-#### Usage
-
-```
-python add_weight.py <input_file> <output_file> <new_weight>
-```
-
-- `<inputfile>`: The path to the input file (e.g., train.xyz).
-- `<outputfile>`: The path to the input file (e.g., train_weighted.xyz).
-- `<new_weight>`: The `weight` you need to change.
-
-#### Example
-
-```sh
-python add_weight.py train.xyz train_weighted.xyz 5
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -addweight train.xyz train_weighted.xyz 5
-```
-
-This command will read the `train.xyz` file and add `Weight=5` labels for all structures. The output will be saved to a file named `train_weighted.xyz`.
-
-
-
-### exyz2pos.py
-
----
-
-This script converts all frames in an `extxyz` file to `POSCAR` format.
-
-#### Usage
-
-```sh
-python exyz2pos.py <extxyz_file>
-```
-
-#### Example
-
-```sh
-python exyz2pos.py structs.xyz
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -exyz2pos structs.xyz
-```
-
-This command will convert all frames in `structs.xyz` to `POSCAR_*.vasp` files.
-
-
-
-### pos2exyz.py
-
----
-
-This script converts a `POSCAR` file to `extxyz` format.
-
-#### Usage
-
-```
-python pos2exyz.py <POSCAR_file> <extxyz_file>
-```
-
-- `<POSCAR_file>`: The path to the input `POSCAR` file.
-- `<extxyz_file>`: The desired name for the output `extxyz` file.
-
-#### Example
-
-```
-python pos2exyz.py POSCAR model.xyz
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -pos2exyz POSCAR model.xyz
-```
-
-This command will read the `POSCAR` file and convert it to `model.xyz` in `extxyz` format.
-
-
-
-### pos2lmp.py
-
----
-
-This script converts a `POSCAR` file to `lammps-data` format.
-
-#### Usage
-
-```
-python pos2lmp.py <poscar_file> <lammps_data_file>
-```
-
-- `<poscar_file>`: The path to the input `POSCAR` file.
-- `<lammps_data_file>`: The desired name for the output `lammps-data` file.
-
-#### Example
-
-```
-python pos2lmp.py POSCAR lammps.data
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -pos2lmp POSCAR lammps.data
-```
-
-This command will read the `POSCAR` file and convert it to `lammps.data` in `lammps-data` format.
-
-
-
-### split_single_xyz.py
-
----
-
-This script splits an `extxyz` file into individual frames, each written to a separate file.
-
-#### Usage
-
-```
-python split_single_xyz.py <extxyz_file>
-```
-
-This command will split all frames in `extxyz_file` into separate files named `model_*.xyz`.
-
-
-
-### lmp2exyz.py
-
----
-
-This script will convert the `lammps-dump` to `extxyz` format.
-
-#### Usage
-
-```
-python lmp2exyz.py <dump_file> <element1> <element2> ...
-```
-
-- `<dump_file>`: The path to the input `lammps-dump` file.
-- `<element>`: The order of the specified elements.
-
-#### Example
-
-```sh
-python lmp2exyz.py dump.data Li Y Cl
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -lmp2exyz dump.data Li Y Cl
-```
-
-It will convert the `dump.data` to `dump.xyz` file
-
-
-
-### get_frame.py
-
----
-
-This script will read the `extxyz` file and return the specified frame by index..
-
-#### Usage
-
-```
-python get_frame.py <extxyz_file> <frame_index>
-```
-
-- `<extxyz_file>`: The path to the input `extxyz` file.
-- `<frame_index>`: The index of the specified frame.
-
-#### Example
-
-```sh
-python get_frame.py dump.xyz 1000
-```
-
-#### Command-Line Mode Example
-
-```
-gpumdkit.sh -get_frame dump.xyz 1000
-```
-
-You will get the `frame_1000.xyz` file after perform the script.
-
-
-
-## Contributing
-
-To add new format converters:
-
-1. **Follow naming**: `<source>2<target>.py`
-2. **Handle errors**: Validate input format before processing
-3. **Document**: Add usage to this README
-6. **Update gpumdkit.sh**: Add command-line flag if appropriate
-
-See [CONTRIBUTING.md](contributing.md) for detailed guidelines.
-
----
-
-Thank you for using GPUMDkit! If you have questions about format conversion, please open an issue on our [GitHub repository](https://github.com/zhyan0603/GPUMDkit/issues) or contact Zihan YAN (yanzihan@westlake.edu.cn).
diff --git a/docs/tutorials/index.md b/docs/tutorials/index.md
new file mode 100644
index 0000000..2091f0d
--- /dev/null
+++ b/docs/tutorials/index.md
@@ -0,0 +1,39 @@
+<div align="center">
+  <h1>📚 GPUMDkit Documentation</h1>
+  <p style="text-align: justify;">A practical bilingual tutorial for GPUMDkit, covering installation, command-line tools, interactive workflows, plotting, and analysis utilities.</p>
+</div>
+
+## Language
+
+| Language | Start Here | Command Reference |
+|----------|------------|-------------------|
+| English | [GPUMDkit Tutorials](en/index.md) | [Command Reference](en/command_reference.md) |
+| 简体中文 | [GPUMDkit 教程](zh/index.md) | [命令参考](zh/命令参考.md) |
+
+## What You Can Learn Here
+
+This documentation is organized as a practical tutorial rather than only a command list. New users are encouraged to start from the overview and quick start pages, then move to the topic that matches their task.
+
+| Topic | What it Covers |
+|-------|----------------|
+| Quick Start | Installation, environment setup, interactive mode, direct command mode |
+| Format Conversion | VASP, LAMMPS, CP2K, ABACUS, CIF, extxyz, group labels, weights |
+| Sampling | Uniform/random sampling, NepTrain FPS, perturbation, force-deviation selection |
+| Calculators | MSD, ionic conductivity, NEP prediction, descriptors, DOAS, NEB, polarization tools |
+| Analyzers | Composition checks, distance checks, filters, property range analysis |
+| Visualization | NEP training plots, MD plots, transport plots, thermal transport plots, example figures |
+| Workflows | Batch DFT/MD processing and active-learning style workflows |
+
+For complex operations, use the interactive menu:
+
+```bash
+gpumdkit.sh
+```
+
+For common operations with fixed arguments, use direct command-line mode:
+
+```bash
+gpumdkit.sh -h
+gpumdkit.sh -plt -h
+gpumdkit.sh -calc -h
+```
diff --git a/docs/tutorials/plot_scripts.md b/docs/tutorials/plot_scripts.md
deleted file mode 100644
index 50d8228..0000000
--- a/docs/tutorials/plot_scripts.md
+++ /dev/null
@@ -1,685 +0,0 @@
-<div align="center">
-  <h1>📊 Plot Scripts</h1>
-    <p style="text-align: justify;">This directory (Scripts/plt_scripts/) contains Python scripts for comprehensive visualization of data generated by <strong>GPUMD</strong> and <strong>NEP</strong>. These plotting tools help analyze molecular dynamics simulations, NEP training results, and various material properties.</p>
-</div>
-
-**Script Location:** `Scripts/plt_scripts/`
-
-GPUMDkit provides comprehensive visualization tools for GPUMD and NEP data.
-
-## Command-Line Mode
-
-```bash
-gpumdkit.sh -plt <plot_type> [options]
-```
-
-For a complete list:
-```bash
- +-----------------------------------------------------------------------------------------------+
- |                     GPUMDkit 1.5.5 (dev) (2026-05-10) PLOT & VISUALIZATION TOOLS              |
- +-----------------------------------------------------------------------------------------------+
- |  Usage: gpumdkit.sh -plt <type>                        Help: gpumdkit.sh -plt <type> -h       |
- +-----------------------------------------------------------------------------------------------+
- |                                    NEP Training & Evaluation                                  |
- +-----------------------------------------------------------------------------------------------+
- |  train          - NEP training results           prediction     - NEP prediction results      |
- |  train_test     - NEP train and test results     parity_density - Parity density plot         |
- |  train_density  - Training results density plot  restart        - Parameters in nep.restart   |
- |  charge         - Charge distribution            born_charge    - Born effective charges      |
- |  dimer          - Dimer energy/force curve       force_errors   - Force errors                |
- |  des            - Descriptors                    lr             - Learning rate for gnep      |
- +-----------------------------------------------------------------------------------------------+
- |                                     Diffusion & Transport                                     |
- +-----------------------------------------------------------------------------------------------+
- |  msd            - Mean square displacement       msd_conv       - MSD convergence             |
- |  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |
- |  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|
- |  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |
- |  D_xyz          - Directional Arrhenius D                                                     |
- +-----------------------------------------------------------------------------------------------+
- |                                    MD & Structural Analysis                                   |
- +-----------------------------------------------------------------------------------------------+
- |  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |
- |  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
- |  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
- |  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
- |  doas           - Density of atomistic states                                                 |
- +-----------------------------------------------------------------------------------------------+
- |                                        Heat Transport                                         |
- +-----------------------------------------------------------------------------------------------+
- |  emd            - EMD results                    nemd           - NEMD results                |
- |  hnemd          - HNEMD results                  viscosity      - Viscosity                   |
- +-----------------------------------------------------------------------------------------------+
- |                                          Phonons                                              |
- +-----------------------------------------------------------------------------------------------+
- |  pdos           - VAC and PDOS                                                                |
- +-----------------------------------------------------------------------------------------------+
-```
-
----
-
-## Script Categories
-
-### 🔬 NEP Training & Prediction
-
-Scripts for monitoring and analyzing NEP model training and predictions.
-
-#### plt_train.py
-
-Visualizes NEP training progress including loss curves, RMSE evolution, and parity plots comparing DFT vs NEP predictions for energy, forces, and stresses.
-
-**Input File:** `loss.out`, `energy_train.out`, `force_train.out`, `virial_train.out`
-
-**Usage:**
-```bash
-gpumdkit.sh -plt train
-```
-
-<div align="center">
-    <img src="../Gallery/train.png" alt="NEP training results" width="75%" />
-</div>
-
-
----
-
-#### plt_prediction.py
-
-Visualizes NEP prediction results.
-
-**Input Files:** `energy_test.out`, `force_test.out`, `virial_test.out`
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt prediction
-gpumdkit.sh -plt test             # Alternative command
-```
-
-![](../Gallery/prediction.png)
-
----
-
-#### plt_train_test.py
-
-Creates combined parity plots for both training and testing datasets.
-
-**Input Files:** `*_train.out`, `*_test.out`
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt train_test  
-```
-
-![](../Gallery/train_test.png)
-
----
-
-#### plt_parity_density.py
-
-Generates density-based parity plots for energies, forces, and stresses, useful for large datasets.
-
-**Input Files:** `energy_train.out`, `force_train.out`, `virial_train.out`
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt parity_density
-```
-
-![](../../docs/Gallery/parity_plot_density.png)
-
----
-
-#### plt_force_errors.py
-
-Plots force error evaluation metrics as proposed in [Liu et al.](https://doi.org/10.1038/s41524-023-01123-3).
-
-**Input File:** `force_train.out`
-
-**Usage:**
-```bash
-gpumdkit.sh -plt force_errors
-```
-
-**Metrics Displayed:**
-- Force magnitude errors (delta_F)
-- Force angle errors  (delta_theta)
-- Distribution of errors
-
-![](../Gallery/force_errors.png)
-
----
-
-#### plt_learning_rate.py
-
-Visualizes learning rate during `gnep` training.
-
-**Input File:** `loss.out` 
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt lr 
-```
-
-**Use Case:** Monitor learning rate decay. 
-
-**Note:** this is only for the `gnep` training process.
-
----
-
-#### plt_nep_restart.py
-
-Visualizes parameters stored in `nep.restart` file.
-
-**Input File:** `nep.restart`
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt restart    
-```
-
-<div align="center">
-    <img src="../Gallery/nep_restart.png" alt="NEP restart parameters" width="60%" />
-</div>
-
-
----
-
-### 🌡️ Thermodynamic Properties
-
-Scripts for visualizing thermo info from GPUMD simulations.
-
-#### plt_thermo.py
-
-Primary script for comprehensive thermodynamic property visualization.
-
-**Input File:** `thermo.out`
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt thermo  
-```
-
-![](../Gallery/thermo.png)
-
----
-
-#### plt_thermo2.py & plt_thermo3.py
-
-Alternative thermodynamic visualization (different styles).
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt thermo2 
-gpumdkit.sh -plt thermo3
-```
-
----
-
-### 🔄 Transport Properties
-
-Scripts for analyzing diffusion, ionic conductivity, and thermal transport, etc.
-
-#### plt_msd.py
-
-Plots mean square displacement (MSD) for all directions.
-
-**Input File:** `msd.out`
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt msd
-```
-
-<div align="center">
-    <img src="../Gallery/msd.png" alt="Mean square displacement" width="45%" />
-</div>
-
-
----
-
-#### plt_msd_all.py
-
-Plots MSD for all atomic species separately when using `all_groups` in GPUMD.
-
-**Input File:** `msd.out` (computed with `all_groups` option)
-
-**Usage:**
-```bash
-gpumdkit.sh -plt msd_all <species1> <species2> ...
-gpumdkit.sh -plt msd_all Li P S
-```
-
-**Requirements:** Must use `all_groups` in the `compute_msd` command in `run.in`.
-
-<div align="center">
-    <img src="../Gallery/msd_all.png" alt="MSD for all species" width="45%" />
-</div>
-
-
----
-
-#### plt_msd_convergence_check.py
-
-Checks convergence of MSD calculations across different time windows.
-
-**Input File:** `msd.out` (computed with `save_every` option)
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt msd_conv
-```
-
-**Requirements:** Use `save_every` in the `compute_msd` command.
-
-**Purpose:** Verify MSD has converged sufficiently for accurate diffusion coefficient calculation.
-
-<div align="center">
-    <img src="../Gallery/msd_convergence.png" alt="MSD convergence" width="45%" />
-</div>
-
-
----
-
-#### plt_sdc.py
-
-Plots self-diffusion coefficient (SDC) vs time.
-
-**Input File:** `msd.out`
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt sdc
-```
-
-<div align="center">
-    <img src="../Gallery/sdc.png" alt="Self-diffusion coefficient" width="45%" />
-</div>
-
-
----
-
-#### plt_arrhenius_d.py
-
-Creates Arrhenius plot for diffusivity (log10 D vs 1000/T).
-
-**Input Files:** `*K/msd.out` files
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt arrhenius_d
-gpumdkit.sh -plt D  # Alternative command
-```
-
-<div align="center">
-    <img src="../Gallery/Arrhenius_D.png" alt="Arrhenius D" width="55%" />
-</div>
-
-
-**Output:**
-
-```
-T: 300K, D_total: 1.001e-07 cm2/s
-T: 350K, D_total: 4.184e-07 cm2/s
-T: 400K, D_total: 1.027e-06 cm2/s
-T: 450K, D_total: 2.069e-06 cm2/s
-T: 500K, D_total: 3.563e-06 cm2/s
-Ea: 0.230 eV
-```
-
----
-
-#### plt_arrhenius_sigma.py
-
-Creates Arrhenius plot for ionic conductivity (ln(σ·T) vs 1000/T).
-
-**Input Files:** `*K/{model.xyz, run.in, thermo.out, msd.out}`
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt arrhenius_sigma
-gpumdkit.sh -plt sigma         # Alternative command
-```
-
-<div align="center">
-    <img src="../Gallery/Arrhenius_sigma.png" alt="Arrhenius sigma" width="55%" />
-</div>
-
-
-**Output:**
-
-```
-[Note] No run.in file found, assuming no replication
-
-Conductivity Data:
-T (K)  Sigma (S/cm)    Sigma·T (K·S/cm)
-------------------------------------
-300    1.141e-02       3.422e+00
-350    4.377e-02       1.532e+01
-400    9.470e-02       3.788e+01
-450    1.688e-01       7.595e+01
-500    2.625e-01       1.312e+02
-------------------------------------
-
-msd, Ea: 0.234 eV
-at 300K, LGPS: Sigma = 1.250e-02 S/cm
-```
-
----
-
-#### plt_emd.py
-
-Analyzes and plots thermal conductivity from equilibrium molecular dynamics (EMD).
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt emd <direction>
-gpumdkit.sh -plt emd x # for x direction
-```
-
-<div align="center">
-    <img src="../Gallery/emd.png" alt="EMD thermal conductivity" width="70%" />
-</div>
-
-
-
----
-
-#### plt_nemd.py
-
-Visualizes non-equilibrium molecular dynamics (NEMD) thermal transport properties.
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]
-```
-
-**Params:**
-
-```
-real_length   : Real length of heat tranfer zone in nm (set to 'Auto', with auto-calculation)
-scale_eff_size: Optional, Scale factor for effective cross-sectional area (default: 1)
-               • For 3D bulk systems: use 1
-               • For low-dimensional systems with vacuum layer: S_box / S_eff
-                 - S_box: box area perpendicular to heat transfer direction
-                 - S_eff: real or effective area of the system
-cutoff_freq   : Optional, Cutoff frequency for SHC calculation in THz (default: 60)
-save          : Optional, save the plot as 'nemd.png'
-!!! Note !!!  : If no SHC data, set [scale_eff_size] and [cutoff_freq] to any number as placeholders when using 'save'.
-```
-
-<div align="center">
-    <img src="../Gallery/nemd.png" alt="NEMD results" width="70%" />
-</div>
-
-
-
----
-
-#### plt_hnemd.py
-
-Plots homogeneous non-equilibrium molecular dynamics (HNEMD) results.
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]
-```
-
-**Params:**
-
-```
-scale_eff_size: Optional, Scale factor for effective cross-sectional area (default: 1)
-               • For 3D bulk systems: use 1
-               • For low-dimensional systems with vacuum layer: S_box / S_eff
-                 - S_box: box area perpendicular to heat transfer direction
-                 - S_eff: real or effective area of the system
-cutoff_freq   : Optional, Cutoff frequency for SHC calculation in THz (default: 60)
-save          : Optional, save the plot as 'hnemd.png'
-!!! Note !!!  : If no SHC data, set [scale_eff_size] and [cutoff_freq] to any number as placeholders when using 'save'.
-```
-
-
-
-<div align="center">
-    <img src="../Gallery/hnemd.png" alt="HNEMD results" width="70%" />
-</div>
-
-
-
----
-
-#### plt_pdos.py
-
-Calculates and Plots normalized VAC, PDOS, and Heat Capacity (Cv).
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt pdos [save]
-```
-
-**Input Files:** `model.xyz, run.in, dos.out, mvac.out`
-
-<div align="center">
-    <img src="../Gallery/vac_pdos.png" alt="VAS PDOS" width="70%" />
-</div>
-
-
-
-and heat capacity:
-
-<div align="center">
-    <img src="../Gallery/heat_capacity.png" alt="Heat Capacity" width="50%" />
-</div>
-
-
-
-
----
-
-### 📐 Structural Analysis
-
-Scripts for analyzing atomic structure and distributions.
-
-#### plt_rdf.py
-
-Plots radial distribution function (RDF) showing pair correlations.
-
-**Input File:** `rdf.out`
-
-**Usage:**
-
-```bash
-# Plot all RDF pairs
-gpumdkit.sh -plt rdf               # Display all
-
-# Plot specific column
-gpumdkit.sh -plt rdf <column>      # Display specific pair
-```
-
-**Full RDF output:**
-<img src="../Gallery/rdf1.png" alt="Complete RDF" width="100%" />
-
-**Single pair RDF:**
-<div align="center">
-    <img src="../Gallery/rdf2.png" alt="Single RDF" width="50%" />
-</div>
-
-
----
-
-#### plt_charge.py
-
-Plots charge distribution in `charge_train.out` from `qNEP` model.
-
-**Input File:** `charge_train.out`
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt charge
-```
-
-**Important:** Ensure consistency between training set and charge output atom ordering. Use full batch training or run prediction step first.
-
-<div align="center">
-    <img src="../Gallery/charge.png" alt="Charge distribution" width="45%" />
-</div>
-
-
----
-
-### 🧬 Extra Analysis
-
-Specialized scripts for some analysis.
-
-#### plt_descriptors.py
-
-Visualizes high-dimensional descriptors using dimensionality reduction (PCA/UMAP).
-
-**Input Files:** `descriptors.npy` (generated by `calc_descriptors.py`)
-
-**Usage:**
-
-```bash
-# First generate descriptors
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-
-# Then plot
-gpumdkit.sh -plt des <method>
-```
-
-**Methods:**
-- `pca` - Principal Component Analysis
-- `umap` - Uniform Manifold Approximation and Projection
-
-You need some additional modifications to get the following plot, see the [code]([SourceFiles/NEP-ZBL/PCA_UMAP at main · zhyan0603/SourceFiles](https://github.com/zhyan0603/SourceFiles/tree/main/NEP-ZBL/PCA_UMAP)) here.
-
-<div align="center">
-    <img src="../Gallery/des_umap.png" alt="UMAP descriptor visualization" width="50%" />
-</div>
-
-
----
-
-#### plt_descriptors_compare.py
-
-Compares descriptors from multiple training sets or models.
-
----
-
-#### plt_dimer.py
-
-Plots dimer interaction curves. Two atoms are placed in a cubic box with the length of 30 angstrom. And then, the potential energy and the force will be calculated as a function of dimer distance.
-
-**Usage:**
-```bash
-gpumdkit.sh -plt dimer <element1> <element2> <nepmodel>
-```
-
-**Example:**
-```bash
-gpumdkit.sh -plt dimer Li Li nep.txt
-```
-
-<div align="center">
-    <img src="../Gallery/dimer_nep.png" alt="Dimer NEP" width="45%" />
-    <img src="../Gallery/dimer.png" alt="Dimer comparison" width="45%" />
-</div>
-
-
-**Reference:** [*J. Chem. Inf. Model.* 2026, 66, 3, 1406–1413](https://doi.org/10.1021/acs.jcim.5c02335)
-
----
-
-#### plt_doas.py
-
-Plots density of atomistic states (DOAS) proposed by [Wang et al.](https://doi.org/10.1002/anie.202215544).
-
-**Input Files:** `doas.out` file calculated by `gpumdkit.sh -calc doas`
-
-**Usage:**
-
-```bash
-gpumdkit.sh -plt doas <doas.out> <species>
-gpumdkit.sh -plt doas doas.out Li
-```
-
-<div align="center">
-    <img src="../Gallery/doas.png" alt="Density of atomistic states" width="50%" />
-</div>
-
-
----
-
-#### plt_net_force.py
-
-Plots distribution of net forces on structures, useful for identifying problematic configurations.
-
-**Usage:**
-```bash
-gpumdkit.sh -plt net_force <extxyzfile>
-gpumdkit.sh -plt net_force train.xyz
-```
-
-**Reference:** [arXiv:2510.19774](https://arxiv.org/abs/2510.19774)
-
-<div align="center">
-    <img src="../Gallery/net_force_distribution.png" alt="Net force distribution" width="55%" />
-</div>
-
-
----
-
-### Quick Reference Table
-
-| Command | Input File(s) | Description |
-|---------|---------------|-------------|
-| `thermo` | `thermo.out` | Thermodynamic properties evolution |
-| `train` | `loss.out`, `*_train.out` | NEP training plot |
-| `prediction` | `*_test.out` | NEP prediction plot |
-| `train_test` | `*_train.out`, `*_test.out` | parity plots of train&test |
-| `msd` | `msd.out` | Mean square displacement |
-| `sdc` | `msd.out` | Self-diffusion coefficient |
-| `rdf` | `rdf.out` | Radial distribution function |
-| `vac` | `vac.out` | Velocity autocorrelation |
-| `charge` | `charge_train.out` | Charge distribution |
-| `doas` | DOAS files | Density of atomistic states |
-| `des` | `descriptors.npy` | Descriptor visualization |
-| `dimer` | Needs nep model | Dimer interaction curve |
-| `force_errors` | `force_train.out` | Force error metrics |
-| `lr` | `loss.out` from `gnep` | Learning rate |
-| `restart` | `nep.restart` from `nep` | Restart file parameters |
-| `net_force` | train.xyz | Net force distribution |
-| `emd` | EMD outputs | EMD thermal conductivity |
-| `nemd` | NEMD outputs | NEMD thermal transport |
-| `hnemd` | HNEMD outputs | HNEMD thermal transport |
-| `arrhenius_d` | Multiple MSD | Arrhenius diffusivity |
-| `arrhenius_sigma` | Conductivity data | Arrhenius conductivity |
-
-## Contributing
-
-To add new plotting scripts:
-
-1. **Create script** following naming conventions
-2. **Add documentation** to this README
-5. **Update gpumdkit.sh** to integrate new plot type
-
-See [CONTRIBUTING.md](contributing.md) for detailed guidelines.
-
----
-
-Thank you for using GPUMDkit! If you have any questions, need further assistance, or want to contribute new plotting scripts, feel free to open an issue on our [GitHub repository](https://github.com/zhyan0603/GPUMDkit/issues) or contact Zihan YAN (yanzihan@westlake.edu.cn).
diff --git a/docs/tutorials/sample_structures.md b/docs/tutorials/sample_structures.md
deleted file mode 100644
index 3778c41..0000000
--- a/docs/tutorials/sample_structures.md
+++ /dev/null
@@ -1,216 +0,0 @@
-<div align="center">
-  <h1>📦 Structure Sampling</h1>
-    <p style="text-align: justify;">This directory (Scripts/sample_structures/) contains tools for sampling, selecting, and generating atomic structures for NEP training and molecular dynamics simulations.</p>
-</div>
-
-**Script Location:** `Scripts/sample_structures/`
-
-This section covers the structure sampling tools in GPUMDkit (Interactive Mode - Option 2).
-
-Structure sampling is crucial for creating diverse configurations. These scripts provide:
-
-- **Uniform and random sampling**: Basic sampling methods
-- **FPS (Farthest Point Sampling)**: Maximizing structural diversity using PyNEP or NEPtrain
-- **Structure perturbation**: Generating variations for training set augmentation
-- **maximum force deviations selection**: Identifying structures with maximum force deviations
-- **Frame extraction**: Selecting specific range from trajectories
-
-## Interactive Mode
-
-```bash
-gpumdkit.sh
-# Select: 2) Sample Structures
-```
-
-You'll see the following menu:
-
-```
- +------------------------------------------------------+
- |                 SAMPLE STRUCTURE TOOLS               |
- +------------------------------------------------------+
- | 201) Sample structures from extxyz                   |
- | 202) FPS sampling by PyNEP [deprecated]              |
- | 203) FPS sampling by NepTrain [preferred]            |
- | 204) Perturb structure                               |
- | 205) Select max force deviation structs              |
- +------------------------------------------------------+
- | 000) Return to the main menu                         |
- +------------------------------------------------------+
- Input the function number:
-```
-
-### Option 201: Sample Structures from extxyz
-
-This option allows you to sample structures from an `extxyz` file using a specified method.
-
-Select option `201` from the menu:
-
-```
-201
-```
-
-You will see the following prompt:
-
-```
- >-------------------------------------------------<
- | Calling the script in Scripts/sample_structures |
- | Script: sample_structures.py                    |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- Input <extxyz_file> <sampling_method> <num_samples> [skip_num]
- [skip_num]: number of initial frames to skip, default value is 0
- Sampling_method: 'uniform' or 'random'
- Examp: train.xyz uniform 50
- ------------>>
-```
-
-Enter the `extxyz` file name, sampling method, and number of samples:
-
-```
-train.xyz uniform 50
-```
-
-The script `sample_structures.py` in the `Scripts/sample_strcutures` will be called to perform the sampling.
-
-### Option 202: FPS sampling by PyNEP
-
-This function calls the `pynep_select_structs.py` in the `Scripts/sample_structures` to sampling the structures by `pynep`.
-
-Select option `202` from the menu:
-
-```
-202
-```
-
-You will see the following prompt:
-
-```
- +-------------------------------------------------+
- |  Function 202 (pynep sampling) is deprecated.   |
- |  PyNEP package is no longer actively maintained.|
- |  Please use 203) neptrain sampling instead.     |
- |  If you still insist on pynep, run directly:    |
- |                 gpumdkit.sh -pynep              |
- +-------------------------------------------------+
-```
-
-**Note:** pynep package is no longer actively maintained, this function will be removed soon.
-
-### Option 203: FPS sampling by NepTrain
-
-This function calls the `neptrain_select_structs.py` script in the `Scripts/sample_structures` to sampling the structures by `neptrain`
-
-Select option `203` from the menu:
-
-```
-203
-```
-
-You will see the following prompt:
-
-```
- >-------------------------------------------------<
- | Calling the script in Scripts/sample_structures |
- | Script: neptrain_select_structs.py              |
- | Developer: Benrui TANG (tang070205@proton.me)   |
- >-------------------------------------------------<
- Input <sample.xyz> <train.xyz> <nep_model>
- Examp: dump.xyz train.xyz nep.txt
- ------------>>
-```
-
-`<samle.xyz>`: extxyz file
-
-`<train.xyz>`: train.xyz
-
-`<nep_model>`: nep.txt
-
-Enter the following parameters:
-
-```
-dump.xyz train.xyz nep.txt
-```
-
-### Option 204: Perturb structure
-
-This function calls the `perturb_structure.py` script  in the `Scripts/sample_structures`  to generate the perturbed structures.
-
-Select option `204` from the menu:
-
-```
-204
-```
-
-You will see the following prompt:
-
-```
->-------------------------------------------------<
-| This function calls the script in Scripts       |
-| Script: perturb_structure.py                    |
-| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
->-------------------------------------------------<
-Input <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>
-The default paramters for perturb are 20 0.03 0.2 uniform
-Examp: POSCAR 20 0.03 0.2 normal
------------->>
-```
-
-`<input.vasp>`: filename.vasp
-
-`<pert_num>`: number of perturbed structures
-
-`<cell_pert_fraction>`: A fraction determines how much (relatively) will cell deform
-
-`<atom_pert_distance>`: A distance determines how far atoms will move (in angstrom).
-
-`<atom_pert_style>`: `<uniform>`, `<normal>`, `<const>`
-
-Enter your parameters like:
-
-```
-POSCAR 20 0.03 0.2 uniform
-```
-
-The script `perturb_structure.py` in the `Scripts/sample_strcutures` will be called to perform the perturbation.
-
-### Option 205: Select max force deviation structs
-
-This option allows you to select max force deviation structures from `active.xyz` generated by the command `active` in `gpumd`.
-
-Select option `205` from the menu:
-
-```
-205
-```
-
-You will see the following prompt:
-
-```
- >-------------------------------------------------<
- | Calling the script in Scripts/sample_structures |
- | Script: select_max_modev.py                     |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
- +----------------------------------------------------+
- | Select max force deviation structs from active.xyz |
- |     generated by the active command in gpumd.      |
- +----------------------------------------------------+
- Input <structs_num> <threshold> (eg. 200 0.15)
- ------------>>
-```
-
-Enter the number of structures and the `threshold` used in your `run.in`:
-
-```
-200 0.15
-```
-
-The script `select_max_modev.py` in the `Scripts/sample_strcutures` will be called to perform the sampling.
-
-## Contributing
-
-See [CONTRIBUTING.md](contributing.md) for detailed guidelines.
-
----
-
-Thank you for using GPUMDkit! If you have questions about structure sampling, please open an issue on our [GitHub repository](https://github.com/zhyan0603/GPUMDkit/issues) or contact Zihan YAN (yanzihan@westlake.edu.cn).
diff --git a/docs/tutorials/tutorials.md b/docs/tutorials/tutorials.md
deleted file mode 100644
index 9a07ad3..0000000
--- a/docs/tutorials/tutorials.md
+++ /dev/null
@@ -1,369 +0,0 @@
-# GPUMDkit Tutorials
-
-Welcome to **GPUMDkit**!
-
-## What is GPUMDkit?
-
-GPUMDkit is a powerful command-line toolkit that streamlines your tasks for GPUMD and NEP. It provides:
-
-- **🎯 Two Usage Modes**: Interactive mode and command-line mode
-- **🔄 Format Conversion**: Convert between VASP, LAMMPS, CP2K, CASTEP, ABACUS, and extxyz formats.
-- **📊 Visualization**: Comprehensive plotting tools for NEP training, MD simulations, and analysis.
-- **🧮 Calculators**: Compute ionic conductivity, descriptors, etc.
-- **🔍 Analysis Tools**: Structure validation, filtering, composition analysis, and quality checks, etc.
-- **⚙️ Workflow Automation**: Batch processing for DFT calculations and MD simulations.
-- **🤖 Active Learning**: Semi-Automated NEP model training workflow.
-
-## Quick Start
-
-### Installation
-
-```bash
-# 1. Clone the repository
-git clone https://github.com/zhyan0603/GPUMDkit.git
-
-# 2. Add to your ~/.bashrc
-export GPUMDkit_path=/path/to/GPUMDkit
-export PATH=${GPUMDkit_path}:${PATH}
-source ${GPUMDkit_path}/Scripts/utils/completion.sh
-
-# 3. Reload your shell
-source ~/.bashrc
-
-# 4. Make executable
-cd ${GPUMDkit_path}
-chmod +x gpumdkit.sh
-```
-
-## Two Ways to Use GPUMDkit
-
-### 🖱️ Interactive Mode (Beginner-Friendly)
-
-Launch the interactive menu:
-```bash
-gpumdkit.sh
-```
-
-You'll see:
-```
-           ____ ____  _   _ __  __ ____  _    _ _
-          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
-         | |  _| |_) | | | | |\/| | | | | |/ / | __|
-         | |_| |  __/| |_| | |  | | |_| |   <| | |_
-          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
-
-          GPUMDkit Version 1.5.5 (dev) (2026-05-10)
-    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
- Main Contributors: Denan LI, Xin WU, Zhoulin LIU & Chen HUA
-
- ---------------------- GPUMD ------------------------
- 1) Format Conversion          2) Sample Structures
- 3) Workflow                   4) Calculators
- 5) Analyzer                   6) Visualization
- 7) Utilities                  8) Developing...
- 0) Exit
- ------------>>
- Input the function number:
-```
-
-**Best for:**
-
-- Learning GPUMDkit features
-- Complex multi-step tasks
-- When you need guided prompts
-
-### ⚡ Command-Line Mode
-
-Direct command execution:
-```bash
-gpumdkit.sh -h
-```
-
-You will see:
-
-```
-+-------------------------------------------------------------------------------------------------------+
-|                          GPUMDkit 1.5.5 (dev) (2026-05-10) Command Help                               |
-+-------------------------------------------------------------------------------------------------------+
-|                                          MAIN FUNCTIONS                                               |
-+-------------------------------------------------------------------------------------------------------+
-| -h            Show this help table            | -plt <type>        Plot and visualization tools       |
-| -calc <type>  Calculator tools                | -time <gpumd|nep>  Time-consuming analyzer            |
-| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
-+-------------------------------------------------------------------------------------------------------+
-|                                         FORMAT CONVERSION                                             |
-+-------------------------------------------------------------------------------------------------------+
-| -out2xyz      OUTCAR -> extxyz (shell)        | -out2exyz          OUTCAR -> extxyz (python)          |
-| -cp2k2xyz     CP2K log -> xyz                 | -xdat2exyz         XDATCAR -> extxyz                  |
-| -cif2pos      cif -> POSCAR                   | -cif2exyz          cif -> extxyz                      |
-| -pos2exyz     POSCAR -> extxyz                | -exyz2pos          extxyz -> POSCAR                   |
-| -pos2lmp      POSCAR -> LAMMPS data           | -lmp2exyz          LAMMPS dump -> extxyz              |
-| -traj2exyz    ASE traj -> extxyz              | -replicate         Replicate structure                |
-| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
-| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
-| -frame_range  Extract frames by range         |                                                       |
-+-------------------------------------------------------------------------------------------------------+
-|                                            ANALYSIS                                                   |
-+-------------------------------------------------------------------------------------------------------+
-| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
-| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
-| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
-| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-| -pynep        FPS sampling by PyNEP           |                                                       |
-+-------------------------------------------------------------------------------------------------------+
-| Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
-+-------------------------------------------------------------------------------------------------------+
-```
-
-**Best for:**
-
-- Quick one-off operations
-- Scripting and automation
-- Batch processing
-
-## Some Functionalities
-
-### 1. Format Conversion
-
-Convert structure files between different formats:
-
-#### Interactive mode (option 1)
-
-```shell
- +-------------------------------------------------------------+
- |                   FORMAT CONVERSION TOOLS                   |
- +-------------------------------------------------------------+
- | 101) VASP to extxyz            106) Add group labels        |
- | 102) MTP to extxyz             107) Add weight to extxyz    |
- | 103) CP2K to extxyz            108) Extract frame extxyz    |
- | 104) ABACUS to extxyz          109) Clean XYZ info          |
- | 105) extxyz to POSCAR          110) Replicate structure     |
- +-------------------------------------------------------------+
- | out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |
- | pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |
- | cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |
- | cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|
- +-------------------------------------------------------------+
- | 000) Return to main menu                                    |
- +-------------------------------------------------------------+
- Input the function number or converter keyword:
-```
-
-#### Command-line mode
-
-```shell
-# VASP → extxyz
-gpumdkit.sh -out2xyz <dir>
-
-# POSCAR → extxyz
-gpumdkit.sh -pos2exyz POSCAR model.xyz
-
-# CIF → extxyz
-gpumdkit.sh -cif2exyz input.cif model.xyz
-
-# LAMMPS → extxyz
-gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
-
-# Add group labels
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-
-# Add weights to structures
-gpumdkit.sh -addweight train.xyz weighted.xyz 2.0
-```
-
-**📖 Learn more:** [Format Conversion Guide](format_conversion.md)
-
-### 2. Structure Sampling
-
-Select diverse structures for training:
-
-#### Interactive mode (option 2)
-
-```shell
- +------------------------------------------------------+
- |                 SAMPLE STRUCTURE TOOLS               |
- +------------------------------------------------------+
- | 201) Sample structures from extxyz                   |
- | 202) FPS sampling by PyNEP [deprecated]              |
- | 203) FPS sampling by NepTrain [preferred]            |
- | 204) Perturb structure                               |
- | 205) Select max force deviation structs              |
- +------------------------------------------------------+
- | 000) Return to the main menu                         |
- +------------------------------------------------------+
- Input the function number:
-```
-
-**📖 Learn more:** [Structure Sampling Guide](sample_structures.md)
-
-### 3. Workflow
-
-Batch processing for high-throughput calculations:
-
-#### Interactive mode (option 3)
-
-```
- +---------------------------------------------------------+
- |                      WORKFLOW TOOLS                     |
- +---------------------------------------------------------+
- | 301) SCF batch pretreatment                             |
- | 302) MD sample batch pretreatment (gpumd)               |
- | 303) MD sample batch pretreatment (lmp)                 |
- +---------------------------------------------------------+
- | 000) Return to the main menu                            |
- +---------------------------------------------------------+
- Input the function number:
-```
-
-**📖 Learn more:** [Workflow Guide](workflow.md) | [Active Learning](workflow_active_learning.md)
-
-### 4. Calculators
-
-Compute material properties:
-
-#### Interactive mode (option 4)
-
-```shell
- +----------------------------------------------------------+
- |                     CALCULATOR TOOLS                     |
- +----------------------------------------------------------+
- | 401) Calc ionic conductivity                             |
- | 402) Calc properties by nep                              |
- | 403) Calc descriptors of specific elements               |
- | 404) Calc density of atomistic states (DOAS)             |
- | 405) Calc nudged elastic band (NEB) by nep               |
- | 406) Build neighbor list                                 |
- | 407) Calc displacement from trajectory                   |
- | 408) Calc averaged structure                             |
- | 409) Calc octahedral tilt                                |
- | 410) Calc polarization for ABO3                          |
- | 411) Minimize structure by nep                           |
- | 412) Calc mean square displacement (MSD) from trajectory |
- +----------------------------------------------------------+
- | 000) Return to the main menu                             |
- +----------------------------------------------------------+
- Input the function number:
-```
-
-#### Command-line mode
-
-```bash
-# Ionic conductivity from MSD
-gpumdkit.sh -calc ionic-cond Li 1
-
-# Calculate descriptors
-gpumdkit.sh -calc des train.xyz desc.npy nep.txt Li
-
-# Density of atomistic states
-gpumdkit.sh -calc doas structures.xyz nep.txt doas.txt
-```
-
-**📖 Learn more:** [Calculators Guide](calculators.md)
-
-### 5. Structure Analysis
-
-Validate and filter structure files:
-
-#### Interactive mode (option 5)
-
-```
- +------------------------------------------------------+
- |                    ANALYZER TOOLS                    |
- +------------------------------------------------------+
- | 501) Analyze composition of extxyz                   |
- | 502) Find outliers of extxyz                         |
- | 503) Analyze chemical species of extxyz              |
- | 504) Check charge balance of extxyz                  |
- | 505) Analyze energy/force/virial range               |
- | 506) Filter structures by minimum distance           |
- | 507) Get minimum interatomic distance                |
- | 508) Probability density analysis                    |
- +------------------------------------------------------+
- | 000) Return to the main menu                         |
- +------------------------------------------------------+
- Input the function number:
-```
-
-#### Command-line mode
-
-```bash
-# Check data quality
-gpumdkit.sh -range train.xyz force
-gpumdkit.sh -min_dist_pbc dump.xyz
-gpumdkit.sh -analyze_comp train.xyz
-```
-
-**📖 Learn more:** [Analyzer Guide](analyzer.md)
-
-### 6. Visualization & Plotting
-
-Visualize simulation results and training data:
-
-```bash
-# NEP Training
-gpumdkit.sh -plt train           # Training plot
-gpumdkit.sh -plt prediction      # Prediction plot
-gpumdkit.sh -plt force_errors    # Force error analysis
-
-# MD Simulations
-gpumdkit.sh -plt thermo          # Thermo info
-gpumdkit.sh -plt msd             # Mean square displacement
-gpumdkit.sh -plt rdf             # Radial distribution function
-
-# Transport Properties
-gpumdkit.sh -plt sdc             # Self-diffusion coefficient
-gpumdkit.sh -plt emd             # Thermal conductivity
-```
-
-**📖 Learn more:** [Plot Scripts Guide](plot_scripts.md)
-
-## Detailed Topic Guides
-
-For in-depth information on specific topics:
-
-- 📄 [Format Conversion](format_conversion.md) - Converting between file formats
-- 📊 [Plot Scripts](plot_scripts.md) - Visualization and plotting
-- 🧮 [Calculators](calculators.md) - Property calculations
-- 🔍 [Analyzer](analyzer.md) - Data analysis and quality control
-- 📦 [Structure Sampling](sample_structures.md) - Sampling methods and strategies
-- ⚙️ [Workflow Automation](workflow.md) - Batch processing
-- 🤖 [Active Learning](workflow_active_learning.md) - NEP model improvement
-- 🔧 [Custom Commands](custom_commands.md) - Extending GPUMDkit
-
-## Advanced Features
-
-### Custom Commands
-
-Extend GPUMDkit with your own shortcuts by editing `~/.gpumdkit.in`:
-
-```bash
-custom_quick_analyze() {
-    gpumdkit.sh -range "$1" force
-}
-```
-
-Then use: `gpumdkit.sh -quick_analyze train.xyz`
-
-**Learn more:** [Custom Commands Guide](custom_commands.md)
-
-### Scripting with GPUMDkit
-
-GPUMDkit commands work great in shell scripts:
-
-```bash
-#!/bin/bash
-for temp in 600 900 1200; do
-    cd temp_${temp}/
-    gpumdkit.sh -plt thermo save
-    gpumdkit.sh -plt msd save
-    (echo 201; echo "dump.xyz random 50") | gpumdkit.sh > /dev/null
-    cd ..
-done
-```
-
----
-
-**🎉 Ready to get started?** Try the interactive mode: `gpumdkit.sh`
-
-Thank you for using GPUMDkit! For questions or feedback, please contact Zihan YAN (yanzihan@westlake.edu.cn) or open an issue on GitHub.
diff --git a/docs/tutorials/workflow.md b/docs/tutorials/workflow.md
deleted file mode 100644
index 314ab4b..0000000
--- a/docs/tutorials/workflow.md
+++ /dev/null
@@ -1,188 +0,0 @@
-<div align="center">
-  <h1>🔧 Workflow</h1>
-    <p style="text-align: justify;">This directory (Scripts/workflow/) contains automation scripts for high-throughput computational workflows, particularly for NEP model development and active learning cycles.</p>
-</div>
-
-**Script Location:** `Scripts/workflow/`
-
-This section covers the workflow automation tools in GPUMDkit (Interactive Mode - Function 3).
-
-Workflow scripts automate repetitive tasks in computational materials research:
-
-- **SCF Batch preprocessin**: Set up VASP/CP2K single-point energy calculations
-- **MD sampling**: Prepare molecular dynamics simulations with GPUMD/LAMMPS
-
-## Interactive Mode
-
-```bash
-gpumdkit.sh
-# Select: 3) Workflow
-```
-
-You'll see the following menu:
-
-```
- +---------------------------------------------------------+
- |                      WORKFLOW TOOLS                     |
- +---------------------------------------------------------+
- | 301) SCF batch pretreatment                             |
- | 302) MD sample batch pretreatment (gpumd)               |
- | 303) MD sample batch pretreatment (lmp)                 |
- +---------------------------------------------------------+
- | 000) Return to the main menu                            |
- +---------------------------------------------------------+
- Input the function number:
-```
-
----
-
-### Option 301: SCF batch pretreatment
-
-This script automates the preprocessing of `POSCAR` or `extxyz` files for *self-consistent field* (`SCF`) calculations. The script includes the following steps:
-
-1. Converts a `.xyz` file to `POSCAR` format using `GPUMDkit` if no `.vasp` files are found in the current directory.
-2. Renames and organizes `.vasp` files into a `struct_fp` directory.
-3. Creates individual directories for each `POSCAR` file, setting up symbolic links to the necessary `VASP` input files.
-4. Generates a `presub.sh` script to automate running `VASP` `SCF` calculations.
-
-#### Usage
-
-Ensure all `.vasp` files or a single `.xyz` file are in the current directory.
-
-Select option `301` from the menu:
-
-```
-301
-```
-
-You will see the following prompt:
-
-```
- ------------>>
- Input the function number:
- 301
- ------------>>
- 1) VASP scf batch pretreatment
- 2) CP2K scf batch pretreatment
- ------------>>
- Input the function number:
-```
-
-choose `1`or `2`:
-
-```
- Starting SCF batch pretreatment...
- Found 8 .vasp files.
- >-------------------------------------------------<
- | This function calls the script in Scripts       |
- | Script: scf_batch_pretreatment.sh               |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
-
- We recommend using the prefix to locate the structure.
- The folder name will be added to the second line of XYZ.
- config_type=<prefix>_<ID>
- ------------>>
- Please enter the prefix of directory (e.g. FAPBI3_iter01)
-```
-
-Enter the `prefix` of the folder name:
-
-```
-Li7La3Zr2O12_iter01
-```
-
-The script `scf_batch_pretreatment.sh` in the `Scripts` will be called to perform the pretreatment.
-
-You will see the following prompts:
-
-```
- >-----------------------------------------------------<
- ATTENTION: Place POTCAR, KPOINTS and INCAR in 'fp' Dir.
- ATTENTION: Place POTCAR, KPOINTS and INCAR in 'fp' Dir.
- ATTENTION: Place POTCAR, KPOINTS and INCAR in 'fp' Dir.
- >-----------------------------------------------------<
-```
-
-You need to prepare the `POTCAR`, `KPOINTS`, and `INCAR` files and place them in a directory named `fp`.
-
-### Option 302: MD sample batch pretreatment (gpumd)
-
-This script automates the preprocessing of `POSCAR` or `extxyz` files for MD sampling using `GPUMD`.
-
-1. If `.vasp` files are found in the current directory, it will convert them to `extxyz` format to prepare the `model.xyz` file for `GPUMD`. If `.vasp` files are not found, the `.xyz` file will be read and all frames in it will be split into a individual sample.
-2. Renames and organizes `.xyz` files into a `struct_md` directory.
-3. Creates individual directories for each `model.xyz` file, setting up symbolic links to the necessary `GPUMD` input files.
-4. Generates a `presub.sh` script to automate running MD simulations.
-
-#### Usage
-
-Ensure all `.vasp` files or a single `.xyz` file are in the current directory.
-
-Select option `302` from the menu:
-
-```
-302
-```
-
-You will see the following prompt:
-
-```
- Starting MD sample batch pretreatment...
- No .vasp files found, but found one XYZ file.
- Converting it to model.xyz using GPUMDkit...
- All frames from "NEP-dataset.xyz" have been split into individual model files.
- 20 model.xyz files were generated.
- >-------------------------------------------------<
- | This function calls the script in Scripts       |
- | Script: md_sample_batch_pretreatment.sh         |
- | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
- >-------------------------------------------------<
-```
-
-You will see the following prompts:
-
-```
- >----------------------------------------------------<
- | ATTENTION: Place run_*.in and nep.txt in 'md' Dir. |
- >----------------------------------------------------<
- | You need to provide MD control parameter files in  |
- | the format run_*.in (e.g., run_1.in, run_2.in),    |
- | each corresponding to a sample (e.g., sample_1,    |
- | sample_2) for molecular dynamics simulations.      |
- >----------------------------------------------------<
- Thank you for using GPUMDkit. Have a great day!
-```
-
-You need to prepare the `run.in` and`nep.txt` files and place them in a directory named `md`.
-
-### Option 303: MD sample batch pretreatment (lmp)
-
-The same with option `302`.
-
-## workflow_active_learning_dev.sh
-
-Implements automated active learning cycles for iterative NEP model improvement.
-
-**Purpose:** Automates the active learning pipeline:
-
-1. Generate candidate structures (MD sampling)
-2. Evaluate with current NEP model
-3. Select uncertain structures
-4. Run DFT calculations
-5. Add to training set
-6. Retrain NEP model
-
-**Status:** Development version - **under active development**
-
-**Documentation:** See detailed tutorial in [docs/tutorials/](tutorials.md)
-
----
-
-## Contributing
-
-To add new workflow capabilities, see [CONTRIBUTING.md](contributing.md) for detailed guidelines.
-
----
-
-Thank you for using GPUMDkit! For questions about workflows or to share your workflow adaptations, please open an issue on our [GitHub repository](https://github.com/zhyan0603/GPUMDkit/issues) or contact Zihan YAN (yanzihan@westlake.edu.cn).
diff --git a/docs/tutorials2/zh/README.md b/docs/tutorials/zh/index.md
similarity index 58%
rename from docs/tutorials2/zh/README.md
rename to docs/tutorials/zh/index.md
index eb31e0e..9027e2b 100644
--- a/docs/tutorials2/zh/README.md
+++ b/docs/tutorials/zh/index.md
@@ -1,12 +1,8 @@
 <div align="center">
-  <h1>GPUMDkit 教程</h1>
-  <p>
-    <strong>简体中文</strong> | <a href="../en/README.md">English</a>
-  </p>
+  <h1>📚 GPUMDkit 教程</h1>
+  <p style="text-align: justify;">欢迎使用 <strong>GPUMDkit</strong>，这是一个面向 GPUMD 和 NEP 的命令行工具包。</p>
 </div>
 
-欢迎使用 **GPUMDkit** - GPUMD 和 NEP 的命令行工具包。
-
 ## 什么是 GPUMDkit？
 
 GPUMDkit 简化了计算材料科学中的常见任务：
@@ -33,7 +29,7 @@ source ./install.sh
 ```bash
 conda create -n gpumdkit python=3.12
 conda activate gpumdkit
-pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
+pip install neptrain dpdata calorine
 ```
 
 ### 使用方法
@@ -53,29 +49,30 @@ gpumdkit.sh -h
 
 | 教程 | 描述 |
 |------|------|
-| [快速入门](quickstart.md) | 安装和第一步 |
-| [格式转换](format_conversion.md) | 在文件格式之间转换 |
-| [计算器](calculators.md) | 计算材料属性 |
-| [分析工具](analyzers.md) | 结构分析和验证 |
-| [可视化](visualization.md) | 绘图和可视化 |
-| [工作流](workflows.md) | 批处理和自动化 |
-| [结构采样](sampling.md) | 结构选择方法 |
-| [NEP 训练](nep_training.md) | 完整的 NEP 训练工作流 |
-
-## 示例：NEP 训练流程
+| [快速入门](快速入门.md) | 安装和第一步 |
+| [命令参考](命令参考.md) | 常用 CLI 和菜单入口速查 |
+| [格式转换](格式转换.md) | 在文件格式之间转换 |
+| [计算器脚本](计算器脚本.md) | 计算材料属性 |
+| [分析工具](分析工具.md) | 结构分析和验证 |
+| [绘图脚本](绘图脚本.md) | 绘图和可视化 |
+| [工作流脚本](工作流脚本.md) | 批处理和自动化 |
+| [结构采样](结构采样.md) | 结构选择方法 |
+| [自定义命令](自定义命令.md) | 用户自定义 GPUMDkit 快捷命令 |
+| [主动学习工作流](主动学习工作流.md) | 批量主动学习流程说明 |
+| [极性材料分析](极性材料分析.md) | 铁电和极化相关工具 |
+| [贡献指南](贡献指南.md) | 开发和贡献说明 |
+
+## 示例：转换 VASP OUTCAR
 
 ```bash
-# 转换 DFT 数据
 gpumdkit.sh -out2xyz ./vasp_results/
+```
 
-# 添加组标签
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-
-# 采样结构
-gpumdkit.sh  # 选择: 2) Sample Structures -> 203
+## 示例：绘制 NEP 结果
 
-# 验证训练
+```bash
 gpumdkit.sh -plt train
+gpumdkit.sh -plt prediction
 ```
 
 ## 示例：离子电导率
@@ -91,7 +88,7 @@ gpumdkit.sh -plt msd
 | 模块 | 菜单 | CLI | 描述 |
 |------|------|-----|------|
 | 格式转换 | 1 | `-out2xyz`, `-pos2exyz` | 文件转换 |
-| 结构采样 | 2 | `-pynep` | 结构采样 |
+| 结构采样 | 2 | `-neptrain`、交互菜单 | 结构采样 |
 | 工作流 | 3 | - | 批处理 |
 | 计算器 | 4 | `-calc <类型>` | 属性计算 |
 | 分析工具 | 5 | `-range`, `-min_dist` | 结构分析 |
diff --git "a/docs/tutorials/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.md" "b/docs/tutorials/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.md"
new file mode 100644
index 0000000..258ce9f
--- /dev/null
+++ "b/docs/tutorials/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.md"
@@ -0,0 +1,152 @@
+<div align="center">
+  <h1>🔁 主动学习工作流</h1>
+  <p style="text-align: justify;"><code>workflow_active_learning_dev.sh</code> 用于组织一轮 NEP 主动学习流程：运行 GPUMD 分子动力学、筛选结构、抽样、提交第一性原理计算，并进行 NEP 预测检查。</p>
+</div>
+
+### 概览
+
+该脚本用于处理 NEP 主动学习中常见的一轮流程：运行分子动力学、筛选结构、抽样、提交 SCF 计算，并整理后续 prediction 检查。
+
+## 1. SLURM 设置
+
+脚本开头包含集群提交参数，例如：
+
+```bash
+#!/bin/bash -l
+#SBATCH -p intel-sc3,intel-sc3-32c
+#SBATCH -q huge
+#SBATCH -N 1
+#SBATCH -J workflow
+#SBATCH -o workflow.log
+#SBATCH --ntasks-per-node=1
+```
+
+这些参数需要根据自己的集群环境修改。如果没有 SLURM 环境，也可以直接后台运行：
+
+```bash
+nohup bash workflow_active_learning_dev.sh > workflow.log 2>&1 &
+```
+
+## 2. 基本设置
+
+脚本会进入提交目录，并加载提交模板：
+
+```bash
+cd $SLURM_SUBMIT_DIR
+source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh
+python_pynep=python
+```
+
+- `GPUMDkit_path` 是安装脚本写入的 GPUMDkit 路径。
+- `python_pynep` 仅用于旧的 PyNEP 兼容分支。
+
+## 3. 主要变量
+
+这个工作流适合已经有初始 `nep.txt`、`nep.in`、`train.xyz` 和 GPUMD/DFT 输入文件，并希望在集群上自动扩展训练集的情况。
+
+脚本开头通常需要根据体系修改：
+
+```bash
+work_dir=${PWD}
+prefix_name=LiF_iter01
+min_dist=1.4
+box_limit=13
+max_fp_num=50
+sample_method=pynep
+pynep_sample_dist=0.01
+```
+
+- `prefix_name` 用于命名本轮计算。
+- `min_dist` 和 `box_limit` 用于过滤明显不合理的结构。
+- `max_fp_num` 控制最多提交多少个单点计算。
+- `sample_method` 可选 `uniform`、`random` 或 `pynep`。
+
+## 4. 检查输入文件
+
+常见输入包括：
+
+- `nep.txt`
+- `nep.in`
+- `train.xyz`
+- `run.in`
+- `INCAR`
+- `POTCAR`
+- `KPOINTS`
+- 初始采样结构文件，例如 `sample_struct.xyz`
+
+脚本会把公共输入移动到 `common/`，并创建 `00.modev/`、`01.select/` 等工作目录。
+
+## 5. 文件组织
+
+脚本会创建公共输入目录和 MD 目录：
+
+```bash
+mkdir 00.modev common
+mv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common
+cp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev
+```
+
+- `00.modev`：用于运行 GPUMD MD 采样。
+- `common`：保存 `nep.txt`、`run.in`、结构文件和 DFT 输入文件等公共资源。
+
+## 6. 提交 MD 任务
+
+```bash
+submit_gpumd_array modev ${sample_struct_num}
+sbatch submit.slurm
+```
+
+脚本会通过提交模板创建数组任务。不同集群上的提交命令和模板可能需要自己修改。
+
+## 7. 检查任务完成
+
+脚本会持续检查 `00.modev/` 下各个 `sample_*/log` 文件，确认是否出现：
+
+```bash
+Finished running GPUMD.
+```
+
+如果发现 `Error`，脚本会停止。
+
+## 8. 分析和过滤结构
+
+MD 完成后，脚本会进入 `01.select`，对 `dump.xyz` 中的结构进行筛选。常见检查包括：
+
+- 最小原子距离；
+- 模拟盒子边长；
+- 结构数量是否超过 `max_fp_num`。
+
+这些步骤会调用 analyzer 和 sample_structures 中的脚本。
+
+## 9. 抽样方法
+
+脚本根据 `sample_method` 选择抽样方式：
+
+```bash
+case $sample_method in
+    "uniform")
+    "random")
+    "pynep")
+```
+
+- `uniform`：均匀抽帧；
+- `random`：随机抽帧；
+- `pynep`：旧的 PyNEP 兼容分支。
+
+## 10. 提交 SCF 计算
+
+抽样完成后，脚本会提交 VASP 单点计算：
+
+```bash
+submit_vasp_array scf ${selected_struct_num} ${prefix_name}
+```
+
+这里的 `prefix_name` 会用于计算目录命名，也方便后续追踪结构来源。
+
+## 11. Prediction 步骤
+
+最后脚本会提交 NEP prediction，用于检查当前模型在新增结构上的误差。
+
+---
+
+这个脚本和计算环境强相关，正式使用前建议先用小体系或少量结构测试一轮，并检查提交模板、路径和输入文件是否符合自己的集群环境。
diff --git "a/docs/tutorials/zh/\345\210\206\346\236\220\345\267\245\345\205\267.md" "b/docs/tutorials/zh/\345\210\206\346\236\220\345\267\245\345\205\267.md"
new file mode 100644
index 0000000..8e4b3b3
--- /dev/null
+++ "b/docs/tutorials/zh/\345\210\206\346\236\220\345\267\245\345\205\267.md"
@@ -0,0 +1,128 @@
+<div align="center">
+  <h1>🔍 分析工具</h1>
+  <p style="text-align: justify;">分析工具用于对 extxyz 数据集进行结构统计、距离检查、过滤和组分分析。</p>
+</div>
+
+**脚本位置：** `Scripts/analyzer/`
+
+## 功能概览
+
+| 任务 | 命令 | 用途 |
+|------|------|------|
+| 组分分析 | `gpumdkit.sh -analyze_comp train.xyz` | 按化学组分统计结构 |
+| 元素列表 | `gpumdkit.sh -chem_species train.xyz` | 查看文件中有哪些元素 |
+| 性质范围 | `gpumdkit.sh -range train.xyz force` | 检查能量/力/virial 范围 |
+| 最小距离 | `gpumdkit.sh -min_dist dump.xyz` | 快速检查，不考虑 PBC |
+| PBC 最小距离 | `gpumdkit.sh -min_dist_pbc dump.xyz` | 考虑 PBC 的距离检查 |
+| 电荷平衡 | `gpumdkit.sh -cbc train.xyz` | 检查常见氧化态是否平衡 |
+| 距离过滤 | `gpumdkit.sh -filter_dist_pbc dump.xyz 1.0` | 删除短距离结构 |
+| 盒子过滤 | `gpumdkit.sh -filter_box dump.xyz 13` | 删除盒子边长过大的结构 |
+| 数值过滤 | `gpumdkit.sh -filter_value train.xyz force 20` | 按性质阈值过滤 |
+| 元素对距离 | `gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0` | 按元素对距离范围提取 |
+
+## 组分分析
+
+```bash
+gpumdkit.sh -analyze_comp train.xyz
+```
+
+示例输出：
+
+```text
+Index    Compositions           N atoms      Count
+---------------------------------------------------
+1        Li56O96Zr16La24        192          51
+---------------------------------------------------
+Enter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:
+```
+
+如果一个 `train.xyz` 中混合了多个体系或不同超胞，这个功能很有用。
+
+## 能量/力/virial 范围
+
+```bash
+gpumdkit.sh -range train.xyz force
+gpumdkit.sh -range train.xyz energy
+gpumdkit.sh -range train.xyz virial
+gpumdkit.sh -range train.xyz force hist
+```
+
+使用 `hist` 可以画出所选性质的直方图。
+
+<div align="center">
+  <img src="../../Gallery/range_force.png" alt="Force range histogram" width="52%" />
+</div>
+
+## 最小距离检查
+
+快速版本：
+
+```bash
+gpumdkit.sh -min_dist dump.xyz
+```
+
+考虑 PBC 的版本：
+
+```bash
+gpumdkit.sh -min_dist_pbc dump.xyz
+```
+
+PBC 版本会考虑周期性边界条件。
+
+## 结构过滤
+
+按最小距离过滤：
+
+```bash
+gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
+```
+
+按盒子大小过滤：
+
+```bash
+gpumdkit.sh -filter_box dump.xyz 13
+```
+
+按性质值过滤：
+
+```bash
+gpumdkit.sh -filter_value train.xyz force 20
+```
+
+按元素对距离范围提取：
+
+```bash
+gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0
+```
+
+## 电荷平衡检查
+
+```bash
+gpumdkit.sh -cbc train.xyz
+```
+
+可能输出：
+
+- `balanced.xyz`
+- `unbalanced.xyz`
+- `indices.txt`
+
+这个功能适合常见氧化态有意义的离子材料。
+
+## 示例命令
+
+性质和距离检查：
+
+```bash
+gpumdkit.sh -analyze_comp train.xyz
+gpumdkit.sh -range train.xyz force hist
+gpumdkit.sh -range train.xyz energy hist
+gpumdkit.sh -min_dist_pbc train.xyz
+```
+
+过滤示例：
+
+```bash
+gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
+gpumdkit.sh -filter_box filtered_dist.xyz 13
+```
diff --git "a/docs/tutorials/zh/\345\221\275\344\273\244\345\217\202\350\200\203.md" "b/docs/tutorials/zh/\345\221\275\344\273\244\345\217\202\350\200\203.md"
new file mode 100644
index 0000000..2a7a845
--- /dev/null
+++ "b/docs/tutorials/zh/\345\221\275\344\273\244\345\217\202\350\200\203.md"
@@ -0,0 +1,127 @@
+<div align="center">
+  <h1>📋 命令参考</h1>
+  <p style="text-align: justify;">本页列出 GPUMDkit 稳定的命令行快捷入口。对于参数较多、需要选择的任务，也可以使用交互模式。</p>
+</div>
+
+源表维护在 `docs/command_reference.tsv`。
+
+## `gpumdkit.sh -h` 输出
+
+```text
++-------------------------------------------------------------------------------------------------------+
+|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
++-------------------------------------------------------------------------------------------------------+
+|                                          MAIN FUNCTIONS                                               |
++-------------------------------------------------------------------------------------------------------+
+| -h            Show this help table            | -plt <type>        Plot and visualization tools       |
+| -calc <type>  Calculator tools                | -time <gpumd|nep>  Time-consuming analyzer            |
+| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
++-------------------------------------------------------------------------------------------------------+
+|                                         FORMAT CONVERSION                                             |
++-------------------------------------------------------------------------------------------------------+
+| -out2xyz      OUTCAR -> extxyz (shell)        | -out2exyz          OUTCAR -> extxyz (python)          |
+| -cp2k2xyz     CP2K log -> xyz                 | -xdat2exyz         XDATCAR -> extxyz                  |
+| -cif2pos      cif -> POSCAR                   | -cif2exyz          cif -> extxyz                      |
+| -pos2exyz     POSCAR -> extxyz                | -exyz2pos          extxyz -> POSCAR                   |
+| -pos2lmp      POSCAR -> LAMMPS data           | -lmp2exyz          LAMMPS dump -> extxyz              |
+| -traj2exyz    ASE traj -> extxyz              | -replicate         Replicate structure                |
+| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
+| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
+| -frame_range  Extract frames by range         |                                                       |
++-------------------------------------------------------------------------------------------------------+
+|                                            ANALYSIS                                                   |
++-------------------------------------------------------------------------------------------------------+
+| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
+| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
+| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
+| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
+| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
+| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
++-------------------------------------------------------------------------------------------------------+
+| Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
++-------------------------------------------------------------------------------------------------------+
+```
+
+## 主命令
+
+| 命令 | 语法 | 说明 |
+|---|---|---|
+| `-h` | `gpumdkit.sh -h` | 显示通用帮助 |
+| `-update` | `gpumdkit.sh -update` | 更新 GPUMDkit |
+| `-clean` | `gpumdkit.sh -clean` | 清理当前目录中的冗余文件 |
+
+## 格式转换
+
+| 命令 | 语法 | 说明 |
+|---|---|---|
+| `-out2xyz` | `gpumdkit.sh -out2xyz <dir>` | OUTCAR 转 extxyz，shell 版本 |
+| `-out2exyz` | `gpumdkit.sh -out2exyz <dir>` | OUTCAR 转 extxyz，Python 版本 |
+| `-cp2k2xyz` | `gpumdkit.sh -cp2k2xyz` | CP2K 输出转 xyz/extxyz |
+| `-xdat2exyz` | `gpumdkit.sh -xdat2exyz <XDATCAR> <output.xyz>` | XDATCAR 转 extxyz |
+| `-cif2pos` | `gpumdkit.sh -cif2pos <input.cif> <output.vasp>` | CIF 转 POSCAR/VASP |
+| `-cif2exyz` | `gpumdkit.sh -cif2exyz <input.cif> <output.xyz>` | CIF 转 extxyz |
+| `-pos2exyz` | `gpumdkit.sh -pos2exyz <POSCAR> <output.xyz>` | POSCAR 转 extxyz |
+| `-exyz2pos` | `gpumdkit.sh -exyz2pos <input.xyz>` | extxyz 多帧转 POSCAR 文件 |
+| `-pos2lmp` | `gpumdkit.sh -pos2lmp <POSCAR> <output.data>` | POSCAR 转 LAMMPS data |
+| `-lmp2exyz` | `gpumdkit.sh -lmp2exyz <dump> <element...>` | LAMMPS dump 转 extxyz |
+| `-traj2exyz` | `gpumdkit.sh -traj2exyz <input.traj> <output.xyz>` | ASE trajectory 转 extxyz |
+| `-replicate` | `gpumdkit.sh -replicate <input> <output> a b c` | 按晶胞倍数扩胞 |
+| `-replicate` | `gpumdkit.sh -replicate <input> <output> <target_num>` | 按目标原子数扩胞 |
+| `-addgroup` | `gpumdkit.sh -addgroup <POSCAR> <element...>` | 添加 GPUMD group 标签 |
+| `-addweight` | `gpumdkit.sh -addweight <input.xyz> <output.xyz> <weight>` | 添加结构权重 |
+| `-get_frame` | `gpumdkit.sh -get_frame <input.xyz> <frame_index>` | 提取单帧 |
+| `-clean_xyz` | `gpumdkit.sh -clean_xyz <input.xyz> <output.xyz>` | 清理 extxyz 冗余属性 |
+| `-frame_range` | `gpumdkit.sh -frame_range <input.xyz> <start_frac> <end_frac>` | 按比例范围提取帧 |
+
+## 计算器
+
+| 命令 | 语法 | 说明 |
+|---|---|---|
+| `-calc ionic-cond` | `gpumdkit.sh -calc ionic-cond <element> <charge>` | 离子电导率 |
+| `-calc nep` | `gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>` | NEP 性质预测 |
+| `-calc des` | `gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>` | NEP 描述符 |
+| `-calc doas` | `gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>` | 原子态密度 |
+| `-calc neb` | `gpumdkit.sh -calc neb <initial.xyz> <final.xyz> <n_images> <nep.txt>` | 基于 NEP 的 NEB |
+| `-calc minimize` | `gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]` | 结构优化 |
+| `-calc msd` | `gpumdkit.sh -calc msd <trajectory.xyz> <element> <dt_fs> [max_corr_steps]` | 从轨迹计算 MSD |
+| `-calc nlist` | `gpumdkit.sh -calc nlist [args...]` | 邻居列表 |
+| `-calc disp` | `gpumdkit.sh -calc disp [args...]` | 位移 |
+| `-calc avg-struct` | `gpumdkit.sh -calc avg-struct [args...]` | 平均结构 |
+| `-calc oct-tilt` | `gpumdkit.sh -calc oct-tilt [args...]` | 八面体倾斜 |
+| `-calc pol-abo3` | `gpumdkit.sh -calc pol-abo3 [args...]` | ABO3 局域极化 |
+
+## 分析工具
+
+| 命令 | 语法 | 说明 |
+|---|---|---|
+| `-range` | `gpumdkit.sh -range <input.xyz> <energy\|force\|virial> [hist]` | 性质范围分析 |
+| `-analyze_comp` | `gpumdkit.sh -analyze_comp <input.xyz>` | 成分分析 |
+| `-chem_species` | `gpumdkit.sh -chem_species <input.xyz>` | 元素列表 |
+| `-cbc` | `gpumdkit.sh -cbc <input.xyz>` | 电荷平衡检查 |
+| `-min_dist` | `gpumdkit.sh -min_dist <input.xyz>` | 无 PBC 最小距离 |
+| `-min_dist_pbc` | `gpumdkit.sh -min_dist_pbc <input.xyz>` | 带 PBC 最小距离 |
+| `-filter_dist` | `gpumdkit.sh -filter_dist <input.xyz> <min_dist>` | 距离过滤 |
+| `-filter_dist_pbc` | `gpumdkit.sh -filter_dist_pbc <input.xyz> <min_dist>` | 带 PBC 距离过滤 |
+| `-filter_box` | `gpumdkit.sh -filter_box <input.xyz> <edge_limit>` | 盒子边长过滤 |
+| `-filter_value` | `gpumdkit.sh -filter_value <input.xyz> <property> <threshold>` | 性质阈值过滤 |
+| `-filter_range` | `gpumdkit.sh -filter_range <input.xyz> <element1> <element2> <min_dist> <max_dist>` | 元素对距离范围过滤 |
+| `-pda` | `gpumdkit.sh -pda <ref_struct> <trajectory.xyz> <species> <interval>` | 概率密度分析 |
+
+## 可视化
+
+使用：
+
+```bash
+gpumdkit.sh -plt <type> [options]
+gpumdkit.sh -plt -h
+```
+
+常用类型包括 `train`、`prediction`、`thermo`、`msd`、`sdc`、`rdf`、`emd`、`nemd`、`hnemd`、`pdos` 和 `plane-grid`。
+
+## 工具
+
+| 命令 | 语法 | 说明 |
+|---|---|---|
+| `-time` | `gpumdkit.sh -time <gpumd\|nep>` | 监控 GPUMD 或 NEP 进度 |
+| `-nep_modifier` | `gpumdkit.sh -nep_modifier` | 交互式修改 NEP 模型 |
+| `-pynep` | `gpumdkit.sh -pynep` | 已弃用的 PyNEP FPS 采样 |
diff --git "a/docs/tutorials/zh/\345\267\245\344\275\234\346\265\201\350\204\232\346\234\254.md" "b/docs/tutorials/zh/\345\267\245\344\275\234\346\265\201\350\204\232\346\234\254.md"
new file mode 100644
index 0000000..75a35e9
--- /dev/null
+++ "b/docs/tutorials/zh/\345\267\245\344\275\234\346\265\201\350\204\232\346\234\254.md"
@@ -0,0 +1,199 @@
+<div align="center">
+  <h1>🔧 工作流脚本</h1>
+  <p style="text-align: justify;">工作流脚本用于自动化重复性的 DFT、MD 和 NEP 数据准备步骤。</p>
+</div>
+
+**脚本位置：** `Scripts/workflow/`
+
+## 交互入口
+
+```bash
+gpumdkit.sh
+```
+
+选择：
+
+```text
+3) Workflow
+```
+
+常见菜单：
+
+| 菜单 | 工作流 | 用途 |
+|------|--------|------|
+| 301 | SCF batch pretreatment | 准备 DFT 单点计算 |
+| 302 | MD sample batch pretreatment (GPUMD) | 准备 GPUMD 采样计算 |
+| 303 | MD sample batch pretreatment (LAMMPS) | 准备 LAMMPS 采样计算 |
+
+## SCF 批处理预处理
+
+适用于已有多个结构，需要准备第一性原理单点计算的情况。
+
+### VASP
+
+```bash
+gpumdkit.sh
+# 选择 3 -> 301 -> VASP
+```
+
+运行前，把结构文件放在当前目录。脚本按以下顺序检测：
+
+1. 如果存在一个或多个 `.vasp` 文件，优先处理 `.vasp`；
+2. 如果 `.vasp` 和 `.xyz` 同时存在，会打印提示，并只处理 `.vasp`；
+3. 如果没有 `.vasp` 且只有一个 `.xyz`，会把这个 extxyz 转为 POSCAR 文件；
+4. 如果没有 `.vasp` 且存在多个 `.xyz`，会让用户选择一个。
+
+运行前的典型目录：
+
+```text
+current directory/
+├── POSCAR_1.vasp
+├── POSCAR_2.vasp
+└── POSCAR_3.vasp
+```
+
+或：
+
+```text
+current directory/
+└── sampled.xyz
+```
+
+运行后脚本会创建：
+
+```text
+current directory/
+├── struct_fp/
+│   ├── POSCAR_1.vasp
+│   ├── POSCAR_2.vasp
+│   └── ...
+├── fp/
+├── <prefix>_1/
+├── <prefix>_2/
+└── presub.sh
+```
+
+`fp/` 是脚本自动创建的。脚本结束后，需要用户把 `INCAR`、`POTCAR`、`KPOINTS` 放到 `fp/` 中，计算目录会链接这里的文件。
+
+运行过程中输入的 `prefix` 会作为计算文件夹名前缀。后续使用 `out2xyz` 提取结果时，文件夹名会作为 `config_type` 写入 extxyz，便于之后检查结构来源。
+
+### CP2K
+
+CP2K 可以从交互菜单进入，也可以直接命令行调用：
+
+```bash
+gpumdkit.sh
+# 选择 3 -> 301 -> CP2K
+```
+
+```bash
+python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc
+```
+
+交互模式会要求输入：
+
+```text
+<extxyz_file> <template.inp> <prefix_name>
+```
+
+示例：
+
+```text
+dump.xyz template.inp H2O
+```
+
+CP2K 模板应设置为从 `pos.xyz` 读取坐标。参考模板在：
+
+```text
+Scripts/workflow/cp2k_template.inp
+```
+
+脚本会为每个结构生成 `<prefix>_<index>/` 目录，并写入 `input.inp` 和 `pos.xyz`。
+
+## MD 采样预处理
+
+### GPUMD
+
+```bash
+gpumdkit.sh
+# 选择 3 -> 302
+```
+
+运行前，把 `.vasp` 文件或一个 extxyz 文件放在当前目录。检测顺序与 VASP SCF 预处理一致：优先处理 `.vasp`；如果没有 `.vasp` 且存在多个 `.xyz`，会让用户选择一个。
+
+运行前典型目录：
+
+```text
+current directory/
+├── POSCAR_1.vasp
+└── POSCAR_2.vasp
+```
+
+或：
+
+```text
+current directory/
+└── dump.xyz
+```
+
+运行后脚本会创建：
+
+```text
+current directory/
+├── struct_md/
+│   ├── model_1.xyz
+│   ├── model_2.xyz
+│   └── ...
+├── md/
+├── sample_1/
+├── sample_2/
+└── presub.sh
+```
+
+`md/` 是脚本自动创建的。脚本结束后，需要把 `nep.txt` 和 `run_*.in` 放入 `md/`。例如 `run_1.in` 会链接到 `sample_1/run.in`，`run_2.in` 会链接到 `sample_2/run.in`。
+
+### LAMMPS
+
+```bash
+gpumdkit.sh
+# 选择 3 -> 303
+```
+
+运行前，把 `.vasp` 文件或一个 extxyz 文件放在当前目录；两种格式同时存在时优先处理 `.vasp`。
+
+运行后脚本会创建：
+
+```text
+current directory/
+├── struct_md/
+│   ├── lammps_1.data
+│   ├── lammps_2.data
+│   └── ...
+├── md/
+├── sample_1/
+├── sample_2/
+└── presub.sh
+```
+
+脚本结束后，需要把 `lmprun.in` 和 `nep.txt` 放到 `md/` 中。
+
+## 主动学习式流程
+
+常见 NEP 数据迭代流程：
+
+1. 使用当前 `nep.txt` 运行 MD；
+2. 收集 `dump.xyz` 或 `active.xyz`；
+3. 删除明显不合理结构；
+4. 选择多样性高或偏差大的结构；
+5. 运行 DFT 单点；
+6. 将 DFT 结果转换为 extxyz；
+7. 追加到 `train.xyz`；
+8. 重新训练 NEP。
+
+更完整的开发版主动学习脚本说明见 [主动学习](主动学习工作流.md)。
+
+## 使用建议
+
+- 工作流脚本和集群环境强相关，正式批量提交前先用少量结构测试。
+- 模板文件如 `INCAR`、`KPOINTS`、`POTCAR`、`run.in` 应仔细检查。
+- 批量 DFT 前先用分析和采样脚本清理候选结构。
diff --git "a/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md" "b/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md"
new file mode 100644
index 0000000..fdb62cf
--- /dev/null
+++ "b/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md"
@@ -0,0 +1,231 @@
+<div align="center">
+  <h1>🚀 快速入门</h1>
+  <p style="text-align: justify;">本页介绍 GPUMDkit 的基本安装方式和几个常用命令。GPUMDkit 既可以通过交互菜单使用，也可以直接通过命令行选项调用。</p>
+</div>
+
+## 1. 准备 Python 环境
+
+可以使用干净的 conda 环境：
+
+```bash
+conda create -n gpumdkit python=3.12
+conda activate gpumdkit
+```
+
+部分可选功能需要额外依赖：
+
+```bash
+pip install neptrain dpdata calorine
+```
+
+其他 Python 依赖由对应脚本在运行时导入。如果缺少某个包，使用对应功能时 Python 会给出提示。
+
+## 2. 安装 GPUMDkit
+
+克隆仓库：
+
+```bash
+git clone https://github.com/zhyan0603/GPUMDkit.git
+cd GPUMDkit
+```
+
+运行安装脚本：
+
+```bash
+source ./install.sh
+```
+
+安装脚本会写入 `GPUMDkit_path` 和 `PATH` 设置，并在当前 shell 中加载。默认写入 `~/.bashrc`；如果当前 shell 是 zsh，则写入 `~/.zshrc`。如果检测到已有 GPUMDkit 路径，安装脚本会打印旧路径并询问是否替换；修改 rc 文件前会先创建备份。
+
+典型安装输出：
+
+```text
+======================================================
+  GPUMDkit Installation
+======================================================
+ [1/4] Detecting GPUMDkit directory...
+       /path/to/GPUMDkit
+ [2/4] Detecting shell configuration...
+       Target: /Users/you/.bashrc
+       Adding environment variables to /Users/you/.bashrc
+       Success: Environment variables added.
+ [3/4] Setting executable permissions...
+       Added executable permission to gpumdkit.sh
+ [4/4] Loading environment...
+
+======================================================
+  Installation Complete!  GPUMDkit is ready to use.
+======================================================
+```
+
+如果之前已经安装过 GPUMDkit，可能会看到：
+
+```text
+Existing GPUMDkit configuration found.
+Existing path(s):
+  - /old/path/to/GPUMDkit
+New path:
+  - /new/path/to/GPUMDkit
+
+Replace the existing GPUMDkit configuration with the new path? [y/N]:
+```
+
+检查命令：
+
+```bash
+gpumdkit.sh -h
+```
+
+帮助表：
+
+```text
++-------------------------------------------------------------------------------------------------------+
+|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
++-------------------------------------------------------------------------------------------------------+
+|                                          MAIN FUNCTIONS                                               |
++-------------------------------------------------------------------------------------------------------+
+| -h            Show this help table            | -plt <type>        Plot and visualization tools       |
+| -calc <type>  Calculator tools                | -time <gpumd|nep>  Time-consuming analyzer            |
+| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
++-------------------------------------------------------------------------------------------------------+
+|                                         FORMAT CONVERSION                                             |
++-------------------------------------------------------------------------------------------------------+
+| -out2xyz      OUTCAR -> extxyz (shell)        | -out2exyz          OUTCAR -> extxyz (python)          |
+| -cp2k2xyz     CP2K log -> xyz                 | -xdat2exyz         XDATCAR -> extxyz                  |
+| -cif2pos      cif -> POSCAR                   | -cif2exyz          cif -> extxyz                      |
+| -pos2exyz     POSCAR -> extxyz                | -exyz2pos          extxyz -> POSCAR                   |
+| -pos2lmp      POSCAR -> LAMMPS data           | -lmp2exyz          LAMMPS dump -> extxyz              |
+| -traj2exyz    ASE traj -> extxyz              | -replicate         Replicate structure                |
+| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
+| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
+| -frame_range  Extract frames by range         |                                                       |
++-------------------------------------------------------------------------------------------------------+
+|                                            ANALYSIS                                                   |
++-------------------------------------------------------------------------------------------------------+
+| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
+| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
+| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
+| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
+| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
+| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
++-------------------------------------------------------------------------------------------------------+
+| Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
++-------------------------------------------------------------------------------------------------------+
+```
+
+## 3. 使用方式
+
+### 交互模式
+
+```bash
+gpumdkit.sh
+```
+
+主菜单：
+
+```text
+           ____ ____  _   _ __  __ ____  _    _ _
+          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
+         | |  _| |_) | | | | |\/| | | | | |/ / | __|
+         | |_| |  __/| |_| | |  | | |_| |   <| | |_
+          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
+
+          GPUMDkit Version 1.5.6 (dev) (2026-06-17)
+    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+ Main Contributors: Denan LI, Xin WU, Zhoulin LIU & Chen HUA
+
+ ---------------------- GPUMD ------------------------
+ 1) Format Conversion          2) Sample Structures
+ 3) Workflow                   4) Calculators
+ 5) Analyzer                   6) Visualization
+ 7) Utilities                  8) Developing...
+ 0) Exit
+ ------------>>
+ Input the function number:
+```
+
+### 命令行模式
+
+直接命令使用固定的位置参数：
+
+```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+gpumdkit.sh -plt train
+gpumdkit.sh -plt thermo
+```
+
+例如：
+
+```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+```
+
+表示读取 `POSCAR`，写出 `model.xyz`。
+
+## 4. 实际例子
+
+### POSCAR 转 extxyz
+
+```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+```
+
+### 添加 GPUMD group 标签
+
+```bash
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+```
+
+group 标签用于一些需要原子分组的 GPUMD 相关流程和分析，例如特定元素的 MSD 或扩散性质计算。
+
+### 绘制 NEP 训练结果
+
+```bash
+gpumdkit.sh -plt train
+```
+
+<div align="center">
+  <img src="../../Gallery/train.png" alt="NEP training results" width="72%" />
+</div>
+
+### 绘制 NEP 测试集结果
+
+```bash
+gpumdkit.sh -plt test
+```
+
+<div align="center">
+  <img src="../../Gallery/prediction.png" alt="NEP test results" width="72%" />
+</div>
+
+### 绘制热力学量
+
+```bash
+gpumdkit.sh -plt thermo
+```
+
+<div align="center">
+  <img src="../../Gallery/thermo.png" alt="Thermo plot" width="72%" />
+</div>
+
+### 绘制 MSD 和自扩散系数
+
+```bash
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+```
+
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
+  <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
+</div>
+
+## 5. 获取帮助
+
+```bash
+gpumdkit.sh -h
+gpumdkit.sh -plt -h
+gpumdkit.sh -calc -h
+gpumdkit.sh -plt train -h
+gpumdkit.sh -calc msd -h
+```
diff --git "a/docs/tutorials/zh/\346\236\201\346\200\247\346\235\220\346\226\231\345\210\206\346\236\220.md" "b/docs/tutorials/zh/\346\236\201\346\200\247\346\235\220\346\226\231\345\210\206\346\236\220.md"
new file mode 100644
index 0000000..e5d0f40
--- /dev/null
+++ "b/docs/tutorials/zh/\346\236\201\346\200\247\346\235\220\346\226\231\345\210\206\346\236\220.md"
@@ -0,0 +1,431 @@
+<div align="center">
+  <h1>🧲 极性材料分析</h1>
+  <p style="text-align: justify;">本教程介绍 GPUMDkit 中计算器选项 <code>406-410</code>，以及 <code>plane-grid</code> 绘图流程。</p>
+</div>
+
+**脚本位置：** `Scripts/calculators/` 和 `Scripts/plt_scripts/`
+
+本教程包含通用工具和体系相关工具：
+
+- `nlist`、`disp` 和 `avg-struct` 可广泛用于结构和轨迹分析。
+- `oct-tilt` 用于八面体环境分析，需要每个中心原子周围有 6 个近邻。
+- `pol-abo3` 专用于 `ABO3` 体系的极化分析。
+
+## 依赖
+
+这些脚本需要 `ferrodispcalc`：
+
+```bash
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
+```
+
+## 交互模式入口
+
+选项 `406-410` 是本教程中的核心功能。下面各节会说明每个功能的用途和运行方式。
+
+完整参数说明可以通过以下命令查看：
+
+```bash
+gpumdkit.sh -calc nlist -h
+gpumdkit.sh -calc disp -h
+gpumdkit.sh -calc avg-struct -h
+gpumdkit.sh -calc oct-tilt -h
+gpumdkit.sh -calc pol-abo3 -h
+gpumdkit.sh -plt plane-grid -h
+```
+
+## 406) 构建近邻列表 (`calc_neighbor_list.py`)
+
+为指定中心元素和近邻元素构建近邻列表。
+
+使用场景：
+这通常是运行 `disp`、`oct-tilt` 和 `pol-abo3` 之前的第一步，因为这些脚本会读取 `nl-*.dat` 近邻文件。
+
+### 用法
+
+```bash
+# 示例 1：为八面体分析构建 Ti-O 最近 6 个近邻
+gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat
+
+# 示例 2：为 A 位中心分析构建 Pb/Sr-O 最近 12 个近邻
+gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O
+```
+
+### 参数（完整）
+
+- `-i, --input`：
+  输入结构文件。默认值：`model.xyz`。
+- `-x, --index`：
+  从输入文件中读取的帧编号。默认值：`0`。
+- `-c, --cutoff`（必需）：
+  近邻搜索截断距离，单位为 Angstrom。
+- `-n, --neighbor-num`（必需）：
+  每个中心原子的近邻数量。
+- `-d, --defect`：
+  缺陷模式。启用后，如果近邻数量不足，缺失位置会用中心原子编号填充。
+- `-C, --center-elements`（必需）：
+  中心元素列表。
+- `-E, --neighbor-elements`（必需）：
+  近邻元素列表。
+- `-o, --output`：
+  输出文件路径。默认值：`nl-<center>-<neighbor>.dat`。
+
+### 输出文件
+
+- 主要输出：近邻列表文本文件，例如 `nl-Ti-O.dat`。
+- 文件是一个二维整数数组，形状为 `(n_center, neighbor_num + 1)`。每一行对应一个中心原子：第一列是中心原子编号，后续列是近邻原子编号，所有编号均为 1-based。
+
+## 407) 从轨迹计算位移 (`calc_displacement.py`)
+
+根据轨迹或模型结构以及近邻列表，计算局域位移矢量。
+
+### 用法
+
+```bash
+# 示例 1：从 model.xyz 计算单帧位移
+gpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat
+
+# 示例 2：使用 movie.xyz 的最后 20% 帧
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat
+```
+
+### 参数（完整）
+
+- `-i, --input`：
+  输入 xyz 文件。默认值：`model.xyz`。
+- `-n, --neighbor-list`（必需）：
+  由 `nlist` 生成的近邻列表文件。
+- `-o, --output`：
+  输出文件。默认值：`displacements.dat`。
+- `-s, --start`：
+  切片起始帧。默认值：`0`。
+- `-t, --stop`：
+  切片终止帧。默认值：到末尾。
+- `-p, --step`：
+  切片步长。默认值：`1`。
+- `-l, --last`：
+  选择末尾部分帧。
+  整数表示最后 `N` 帧；
+  `0 < value < 1` 表示最后一部分比例的帧。
+- `--last` 与 `-s/-t/-p` 互斥。
+
+### 输出文件
+
+- 主要输出：`displacements.dat`，或你指定的输出文件名。
+- 保存的文本文件是二维数组：对于单帧输入，形状为 `(n_center, 3)`；对于多帧输入，形状为 `(n_selected_frame * n_center, 3)`，按帧优先顺序排列。三列分别为 `dx`、`dy` 和 `dz` 位移分量，单位为 Angstrom。
+
+## 408) 计算平均结构 (`calc_averaged_structure.py`)
+
+从选定轨迹帧生成一个平均结构。
+通常可在体系平衡后使用：对于接近平衡的固体，可以对目标温度下的一段轨迹取平均，并分析该代表性结构，而不是逐帧处理每个 snapshot。
+
+### 用法
+
+```bash
+# 示例 1：平均所有帧
+gpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz
+
+# 示例 2：平均选定帧范围 (100:500:2)
+gpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz
+```
+
+### 参数（完整）
+
+- `-i, --input`：
+  输入轨迹文件。默认值：`movie.xyz`。
+- `-o, --output`：
+  输出结构文件。默认值：`averaged_structure.xyz`。
+- `-s, --start`：
+  切片起始帧。默认值：`0`。
+- `-t, --stop`：
+  切片终止帧。默认值：到末尾。
+- `-p, --step`：
+  切片步长。默认值：`1`。
+- `-l, --last`：
+  选择末尾帧，可以是最后 `N` 帧或最后一部分比例的帧。
+- `--last` 与 `-s/-t/-p` 互斥。
+
+### 输出文件
+
+- 主要输出：单帧平均结构 extxyz 文件。
+- 位置平均会相对于所选第一帧进行 MIC/PBC 修正。
+
+## 409) 计算八面体倾转 (`calc_oct_tilt.py`)
+
+根据 B-O 近邻列表计算八面体倾转角。
+该功能常用于分析 `ABO3` 体系中的八面体转动模式，例如 `SrTiO3` 和 `PbZrO3`。
+
+### 用法
+
+```bash
+# 示例 1：从单帧结构计算 TiO6 八面体倾转
+gpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat
+
+# 示例 2：从轨迹最后 20% 帧计算 TiO6 八面体倾转
+gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat
+```
+
+### 参数（完整）
+
+- `-i, --input`：
+  输入 xyz 文件。默认值：`model.xyz`。
+- `-n, --neighbor-list`（必需）：
+  B-O 近邻列表文件。
+- `-o, --output`：
+  输出文件。默认值：`octahedral_tilt.dat`。
+- `-s, --start`：
+  切片起始帧。默认值：`0`。
+- `-t, --stop`：
+  切片终止帧。默认值：到末尾。
+- `-p, --step`：
+  切片步长。默认值：`1`。
+- `-l, --last`：
+  选择末尾帧，可以是最后 `N` 帧或最后一部分比例的帧。
+- `--last` 与 `-s/-t/-p` 互斥。
+
+### 输出文件
+
+- 主要输出：`octahedral_tilt.dat`，或自定义输出文件名。
+- 保存的文本文件是三列二维数组，分别为 `theta_x`、`theta_y`、`theta_z`，单位为 degree。对于单帧输入，形状为 `(n_center, 3)`；对于多帧输入，形状为 `(n_selected_frame * n_center, 3)`。
+
+## 410) 计算 ABO3 体系极化 (`calc_polarization_abo3.py`)
+
+计算 `ABO3` 体系的局域极化矢量。
+
+### 用法
+
+```bash
+# 示例 1：单帧 ABO3 极化
+gpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \
+  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat
+
+# 示例 2：选定轨迹帧范围上的极化
+gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \
+  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat
+```
+
+### 参数（完整）
+
+- `-i, --input`：
+  输入 xyz 文件。默认值：`model.xyz`。
+- `--nl-ba`（必需）：
+  B-A 近邻列表。
+- `--nl-bo`（必需）：
+  B-O 近邻列表。
+- `-o, --output`：
+  输出文件。默认值：`polarization.dat`。
+- `--bec`（必需）：
+  Born 有效电荷项，格式为 `Element=value`。
+  示例：`Pb=2.5 Ti=4.0 O=-2.0`。
+- `-s, --start`：
+  切片起始帧。默认值：`0`。
+- `-t, --stop`：
+  切片终止帧。默认值：到末尾。
+- `-p, --step`：
+  切片步长。默认值：`1`。
+- `-l, --last`：
+  选择末尾帧，可以是最后 `N` 帧或最后一部分比例的帧。
+- `--last` 与 `-s/-t/-p` 互斥。
+
+重要检查：
+
+- `--bec` 必须包含输入结构中的所有元素种类。
+- `--nl-ba` 和 `--nl-bo` 中的中心原子编号必须匹配。
+
+### 输出文件
+
+- 主要输出：`polarization.dat`，或自定义输出文件名。
+- 保存的文本文件是三列二维数组，分别为 `Px`、`Py`、`Pz`，单位为 `C/m^2`。对于单帧输入，形状为 `(n_center, 3)`；对于多帧输入，形状为 `(n_selected_frame * n_center, 3)`，按帧优先顺序排列。如果总 Born 电荷不平衡，脚本会打印 warning。
+
+### Plane-grid 可视化 (`plt_plane_grid.py`)
+
+你可以可视化 `displacements.dat` 或 `polarization.dat`：
+
+```bash
+# 示例 1：Ti 位点上的位移图，选择第一个 XY 层
+gpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0
+
+# 示例 2：Pb 位点上的极化图，选择 XZ 和 YZ 层
+gpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4
+```
+
+参数（完整）：
+
+- `-i, --input`：
+  用于原子布局和分层的输入 xyz 文件。默认值：`model.xyz`。
+- `-d, --disp`：
+  矢量场数据文件。默认值：`displacements.dat`。
+- `-e, --elements`（必需）：
+  用于将矢量映射到晶格层上的中心元素符号。
+- `-m, --tol`：
+  网格映射的层容差。默认值：`1.0`。
+- `-g, --target-size`：
+  期望网格大小，格式为 `nx ny nz`。
+- `-o, --save-dir`：
+  图片输出目录。默认值：`plot`。
+- `-f, --frame`：
+  当矢量数据包含多帧时，要可视化的帧编号。默认值：`0`。
+- `--select-xy`：
+  选定的 XY 层编号。
+- `--select-xz`：
+  选定的 XZ 层编号。
+- `--select-yz`：
+  选定的 YZ 层编号。
+
+输出：
+
+- 如果需要，会创建输出目录。
+- 图片保存为 `XY_*.png`、`XZ_*.png`、`YZ_*.png`。
+
+<div align="center">
+    <img src="../Gallery/PTO_STO_superlattice.png" alt="PTO_STO" width="65%" />
+</div>
+
+## 输出文件一览
+
+| 脚本 | 主要输出 | 保存内容 |
+|---|---|---|
+| `calc_neighbor_list.py` | `nl-*.dat` | 1-based 中心原子编号和近邻原子编号 |
+| `calc_displacement.py` | `*.dat` | 局域位移矢量（`dx dy dz`，Angstrom） |
+| `calc_averaged_structure.py` | `*.xyz` | 一个平均结构 |
+| `calc_oct_tilt.py` | `*.dat` | 八面体倾转角（`theta_x theta_y theta_z`，degree） |
+| `calc_polarization_abo3.py` | `*.dat` | 局域极化矢量（`Px Py Pz`，`C/m^2`） |
+| `plt_plane_grid.py` | `plot/*.png` | 根据矢量场数据绘制的 XY/XZ/YZ 平面图 |
+
+## 真实案例
+
+### PbTiO3 的温度驱动铁电-顺电相变
+
+假设所有文件都位于当前目录 `./`：
+
+```text
+./
+├── model.xyz
+├── 300K.xyz
+├── 350K.xyz
+├── 400K.xyz
+├── ...
+└── 800K.xyz
+```
+
+`model.xyz` 是用于进行 MD 模拟的初始结构。每个 `TEMP K.xyz` 是对应温度下的轨迹。
+
+#### 第 1 步：从每条轨迹的后半段得到平均结构
+
+```bash
+for f in *K.xyz; do
+  tag="${f%.xyz}"
+  gpumdkit.sh -calc avg-struct -i "$f" -l 0.5 -o "${tag}-avg.xyz"
+done
+```
+
+这会写出 `300K-avg.xyz`、`350K-avg.xyz`、...、`800K-avg.xyz`。
+
+#### 第 2 步：基于 `model.xyz` 构建近邻列表
+
+```bash
+# B-O list: for each Ti, find the nearest 6 O atoms
+gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat
+
+# A-O list: for each Pb, find the nearest 12 O atoms
+gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat
+
+# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms
+gpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat
+```
+
+#### 第 3 步：为每个温度计算位移和极化
+
+这里使用 Born 有效电荷（BEC），不是名义离子电荷。对于本例中的 PbTiO3：
+
+```python
+PTO = {
+    'Pb': 3.44,
+    'Ti': 5.18,
+    'O': -(3.44 + 5.18) / 3
+}
+```
+
+你可以从自己的 DFPT 计算或文献中获得 BEC。因此，可以使用以下命令计算局域位移和极化：
+
+```bash
+for f in *K.xyz; do
+  tag="${f%.xyz}"
+  gpumdkit.sh -calc disp -i "$f" -n nl-Ti-O.dat -l 0.5 -o "${tag}-disp.dat"
+  gpumdkit.sh -calc pol-abo3 -i "$f" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \
+    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o "${tag}-pol.dat"
+done
+```
+
+#### 第 4 步：绘制实空间位移和极化图
+
+```bash
+for f in *K.xyz; do
+  tag="${f%.xyz}"
+  gpumdkit.sh -plt plane-grid -i "${tag}-avg.xyz" -d "${tag}-disp.dat" -e Ti --select-xz 1 -o "plot-${tag}-disp"
+  gpumdkit.sh -plt plane-grid -i "${tag}-avg.xyz" -d "${tag}-pol.dat" -e Ti --select-xz 1 -o "plot-${tag}-pol"
+done
+```
+
+#### 第 5 步：构建温度-序参量曲线
+
+结合每个温度平均结构的晶格信息和极化文件（`XX-pol.dat`）进行分析，可以得到如下图：
+
+<div align="center">
+    <img src="../Gallery/PTO-temp.png" alt="PTO-temp" width="65%" />
+</div>
+
+该趋势显示在约 `600 K` 附近发生明显相变，此时极化消失。
+
+### PbTiO3/SrTiO3 超晶格中的拓扑结构
+
+假设 `movie.xyz` 是当前目录下 PbTiO3/SrTiO3 超晶格的轨迹。
+
+#### 第 1 步：使用最后 25% 帧构建平均结构
+
+```bash
+gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz
+```
+
+#### 第 2 步：构建 Ti 近邻列表
+
+```bash
+gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat
+```
+
+#### 第 3 步：绘制 plane-grid 图
+
+```bash
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat
+gpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology
+```
+
+<div align="center">
+    <img src="../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
+</div>
+
+这会得到与前面展示相似的图。在 PTO 区域可以看到类似涡旋的极化图样，而 STO 区域的极化接近于零。通过分析涡旋核附近极化的变化，可以估计局域介电响应，但这超出了本教程范围。
+
+注意：该图使用的 colormap 与 GPUMDkit 默认绘图风格不同。默认输出不会与图中完全一致，但可以通过少量修改绘图脚本获得这种风格。
+
+### 其他体系
+
+#### 有机-无机杂化铁电体
+
+在许多有机-无机铁电体中，极化与各向异性的分子单元密切相关。跟踪分子取向的一种实用方法是使用键矢量。
+
+对于 TMCM-CdCl3，可以使用 TMCM 分子中的 C-Cl 键方向作为取向代理，并据此估计极化态：
+
+```bash
+# Find the nearest Cl around each C (tune cutoff if needed)
+gpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat
+
+# Compute C-Cl bond vectors from the trajectory
+gpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat
+```
+
+随后可以把 `ccl_vectors.dat` 作为取向序参量进行分析。更多细节可参考：Phys. Rev. Lett. 136, 016801。
+
+#### 其他铁电材料家族
+
+除 `ABO3` 外，`ferrodispcalc` 也可以适配许多铁电体系，包括氮化物、氧化铪基化合物、有机-无机杂化体系以及部分二维铁电材料。
diff --git "a/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md" "b/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
new file mode 100644
index 0000000..12967a7
--- /dev/null
+++ "b/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
@@ -0,0 +1,230 @@
+<div align="center">
+  <h1>🔄 格式转换</h1>
+  <p style="text-align: justify;">格式转换模块用于在常见原子模拟文件格式之间转换，同时提供 group 标签、权重、帧提取等元数据处理功能。</p>
+</div>
+
+**脚本位置：** `Scripts/format_conversion/`
+
+## 支持的格式
+
+- **VASP**：`POSCAR`、`CONTCAR`、`OUTCAR`、`XDATCAR`
+- **LAMMPS**：data 文件和 dump 轨迹
+- **CP2K**：输出 log、坐标、力和晶胞文件
+- **ABACUS**：SCF/MD 输出
+- **CIF**：晶体结构文件
+- **ASE trajectory**：`.traj`
+- **extxyz**：GPUMD 和 NEP 常用的结构格式
+
+## 交互模式
+
+打开 GPUMDkit：
+
+```bash
+gpumdkit.sh
+```
+
+选择：
+
+```text
+1) Format Conversion
+```
+
+菜单如下：
+
+```text
++-------------------------------------------------------------+
+|                   FORMAT CONVERSION TOOLS                   |
++-------------------------------------------------------------+
+| 101) VASP to extxyz            106) Add group labels        |
+| 102) MTP to extxyz             107) Add weight to extxyz    |
+| 103) CP2K to extxyz            108) Extract frame extxyz    |
+| 104) ABACUS to extxyz          109) Clean XYZ info          |
+| 105) extxyz to POSCAR          110) Replicate structure     |
++-------------------------------------------------------------+
+| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |
+| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |
+| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |
+| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|
++-------------------------------------------------------------+
+| 000) Return to main menu                                    |
++-------------------------------------------------------------+
+Input the function number or converter keyword:
+```
+
+### 每个入口的作用
+
+| 入口 | 功能 | 适用场景 |
+|------|------|----------|
+| `101` | VASP OUTCAR 转 extxyz，shell 版本 | 批量转换 VASP 计算目录 |
+| `102` | MTP cfg 转 extxyz | 转换 MTP 数据 |
+| `103` | CP2K 转 extxyz | 可选择 log/inp 路线或 pos/frc/cell 路线 |
+| `104` | ABACUS 转 extxyz | 转换 ABACUS SCF 或 MD 输出 |
+| `105` | extxyz 转 POSCAR | 将 extxyz 每一帧写成 POSCAR |
+| `106` | 添加 group 标签 | 为 GPUMD 相关流程添加原子分组标签 |
+| `107` | 添加权重 | 修改训练集结构权重 |
+| `108` | 提取单帧 | 从 extxyz 轨迹导出某一帧 |
+| `109` | 清理 XYZ 信息 | 删除多余 extxyz 属性 |
+| `110` | 扩胞 | 按倍数或目标原子数扩胞 |
+| `out2exyz` | OUTCAR 转 extxyz，Python 版本 | VASP OUTCAR 转换的另一个入口 |
+| `pos2exyz` | POSCAR 转 extxyz | 转换单个结构 |
+| `cif2pos` | CIF 转 POSCAR | 从 CIF 准备 VASP 输入 |
+| `cif2exyz` | CIF 转 extxyz | 从 CIF 准备 GPUMDkit 输入 |
+| `xdat2exyz` | XDATCAR 转 extxyz | 转换 VASP MD 轨迹 |
+| `pos2lmp` | POSCAR 转 LAMMPS data | 准备 LAMMPS 输入 |
+| `lmp2exyz` | LAMMPS dump 转 extxyz | 转换 LAMMPS 轨迹 |
+| `traj2exyz` | ASE traj 转 extxyz | 转换 ASE 轨迹 |
+
+## 快速命令表
+
+| 来源 | 目标 | 命令 |
+|------|------|------|
+| OUTCAR 目录 | extxyz | `gpumdkit.sh -out2xyz <dir>` |
+| OUTCAR 目录 | extxyz | `gpumdkit.sh -out2exyz <dir>` |
+| POSCAR | extxyz | `gpumdkit.sh -pos2exyz POSCAR model.xyz` |
+| extxyz | POSCAR 文件 | `gpumdkit.sh -exyz2pos train.xyz` |
+| XDATCAR | extxyz | `gpumdkit.sh -xdat2exyz XDATCAR dump.xyz` |
+| POSCAR | LAMMPS data | `gpumdkit.sh -pos2lmp POSCAR lammps.data` |
+| LAMMPS dump | extxyz | `gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl` |
+| CIF | POSCAR | `gpumdkit.sh -cif2pos input.cif POSCAR.vasp` |
+| CIF | extxyz | `gpumdkit.sh -cif2exyz input.cif model.xyz` |
+| ASE traj | extxyz | `gpumdkit.sh -traj2exyz input.traj output.xyz` |
+
+## 常见例子
+
+### 转换 VASP 结果
+
+如果每个计算目录下都有 `OUTCAR`：
+
+```bash
+gpumdkit.sh -out2xyz ./vasp_results/
+```
+
+也可以使用 Python 版本：
+
+```bash
+gpumdkit.sh -out2exyz ./vasp_results/
+```
+
+在交互模式中选择 `101`，会看到：
+
+```text
+>-------------------------------------------------<
+| Calling the script in Scripts/format_conversion |
+| Script: out2xyz.sh                              |
+| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |
+>-------------------------------------------------<
+Input the directory containing OUTCARs
+Example: ./
+------------>>
+```
+
+### 添加 group 标签
+
+一些 GPUMD 相关流程会使用 group 标签进行原子分组，例如特定元素的 MSD 或扩散性质计算。
+
+```bash
+gpumdkit.sh -addgroup POSCAR Li Y Cl
+```
+
+该命令读取输入结构，并写出带 group 信息的 extxyz 文件。
+
+在交互模式中选择 `106`，会看到：
+
+```text
+>-------------------------------------------------<
+| Calling the script in Scripts/format_conversion |
+| Script: add_groups.py                           |
+| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
+>-------------------------------------------------<
+Input <POSCAR> <element1> <element2> ...
+Example: POSCAR Li Y Cl
+------------>>
+```
+
+## 常用脚本说明
+
+### POSCAR 转 extxyz
+
+```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+```
+
+适合把单个 VASP 结构转成 extxyz 文件。
+
+交互模式关键词：`pos2exyz`
+
+```text
+Input <POSCAR> <output.xyz>
+Example: POSCAR model.xyz
+------------>>
+```
+
+### extxyz 转 POSCAR
+
+```bash
+gpumdkit.sh -exyz2pos structures.xyz
+```
+
+会将 extxyz 中所有帧转换成 `POSCAR_*.vasp` 文件。
+
+交互模式入口：`105`
+
+```text
+Input the name of extxyz
+Example: ./train.xyz
+------------>>
+```
+
+### LAMMPS dump 转 extxyz
+
+```bash
+gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl
+```
+
+元素顺序必须对应 LAMMPS 中的 atom type ID。例如 type 1 是 Li、type 2 是 Y、type 3 是 Cl，则输入 `Li Y Cl`。
+
+交互模式关键词：`lmp2exyz`
+
+```text
+Input <dump_file> <element1> <element2> ...
+Example: dump.lammpstrj Li O
+------------>>
+```
+
+### CIF 转换
+
+```bash
+gpumdkit.sh -cif2pos input.cif POSCAR.vasp
+gpumdkit.sh -cif2exyz input.cif model.xyz
+```
+
+如果后续需要 VASP 计算，使用 `-cif2pos`；如果后续要进入 GPUMDkit 分析，使用 `-cif2exyz`。
+
+### 添加权重
+
+```bash
+gpumdkit.sh -addweight train.xyz train_weighted.xyz 5
+```
+
+用于给训练集结构添加或修改权重。
+
+### 扩胞
+
+```bash
+gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2
+gpumdkit.sh -replicate POSCAR supercell.vasp 256
+```
+
+第一种按晶胞倍数扩胞，第二种按目标原子数自动选择扩胞方式。
+
+## 常见问题
+
+| 问题 | 建议 |
+|------|------|
+| LAMMPS 转换后元素不对 | 检查 dump 文件后的元素顺序 |
+| extxyz 元数据太多 | 使用 `-clean_xyz input.xyz clean.xyz` |
+| 提取帧不对 | 注意帧索引通常从 0 开始 |
+
+## 说明
+
+如果某个转换脚本缺少所需 Python 包，运行该功能时 Python 会给出相应提示。
diff --git "a/docs/tutorials/zh/\347\273\223\346\236\204\351\207\207\346\240\267.md" "b/docs/tutorials/zh/\347\273\223\346\236\204\351\207\207\346\240\267.md"
new file mode 100644
index 0000000..1263e57
--- /dev/null
+++ "b/docs/tutorials/zh/\347\273\223\346\236\204\351\207\207\346\240\267.md"
@@ -0,0 +1,229 @@
+<div align="center">
+  <h1>📦 结构采样</h1>
+  <p style="text-align: justify;">结构采样用于从轨迹中选择候选结构、生成扰动结构，或根据模型偏差挑选值得进一步计算的结构。</p>
+</div>
+
+**脚本位置：** `Scripts/sample_structures/`
+
+## 交互模式入口
+
+```bash
+gpumdkit.sh
+```
+
+选择：
+
+```text
+2) Sample Structures
+```
+
+菜单如下：
+
+```text
++------------------------------------------------------+
+|                 SAMPLE STRUCTURE TOOLS               |
++------------------------------------------------------+
+| 201) Sample structures from extxyz                   |
+| 202) PyNEP sampling [deprecated]                    |
+| 203) FPS sampling by NepTrain [preferred]            |
+| 204) Perturb structure                               |
+| 205) Select max force deviation structs              |
++------------------------------------------------------+
+| 000) Return to the main menu                         |
++------------------------------------------------------+
+Input the function number:
+```
+
+常用功能：
+
+| 菜单 | 方法 | 用途 |
+|------|------|------|
+| 201 | uniform/random | 从轨迹中均匀或随机抽帧 |
+| 202 | PyNEP notice | 只打印提示；真正运行 PyNEP 请用 `gpumdkit.sh -pynep` |
+| 203 | NepTrain FPS | 使用 NepTrain 描述符的 FPS 采样 |
+| 204 | perturb | 从 POSCAR/CONTCAR 生成扰动结构 |
+| 205 | force deviation | 从 active learning 输出中选择高偏差结构 |
+
+## 均匀/随机采样
+
+交互模式选择 `201`，会看到：
+
+```text
+Input <extxyz_file> <sampling_method> <num_samples> [skip_num]
+[skip_num]: number of initial frames to skip, default value is 0
+Sampling_method: 'uniform' or 'random'
+Example: train.xyz uniform 50
+------------>>
+```
+
+例如输入：
+
+```text
+dump.xyz uniform 50
+```
+
+或：
+
+```text
+dump.xyz random 100 500
+```
+
+参数含义：
+
+| 参数 | 含义 |
+|------|------|
+| `dump.xyz` | 输入轨迹 |
+| `uniform` / `random` | 采样方法 |
+| `50` / `100` | 采样结构数 |
+| `500` | 可选，跳过前 500 帧 |
+
+输出：
+
+- `sampled_structures.xyz`
+
+## NepTrain FPS
+
+NepTrain 版本的 FPS：
+
+```bash
+python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
+```
+
+交互模式选择 `203`，会看到：
+
+```text
+Input <sample.xyz> <train.xyz> <nep_model>
+Example: dump.xyz train.xyz nep.txt
+------------>>
+```
+
+输入：
+
+| 文件 | 含义 |
+|------|------|
+| `dump.xyz` | 候选结构 |
+| `train.xyz` | 当前训练集 |
+| `nep.txt` | 用于计算描述符的 NEP 模型 |
+
+输出：
+
+- `selected.xyz`
+- `select.png`
+- `pca_sample.txt`
+- `pca_train.txt`
+- `pca_selected.txt`
+
+运行时可以选择按最小距离阈值采样，或指定采样结构数。脚本随后会打印：
+
+```text
+Choose selection method:
+1) Select structures based on minimum distance
+2) Select structures based on number of structures
+------------>>
+```
+
+该功能需要 `NepTrain`，运行时会提示相关引用。
+
+## PyNEP 旧入口
+
+PyNEP FPS 仍然保留兼容，但只通过 `-pynep` 入口调用：
+
+如果在交互菜单中选择 `202`，会看到：
+
+```text
++-------------------------------------------------+
+| Function 202 is no longer supported here.       |
+| PyNEP package is no longer actively maintained. |
+| Please use 203) NepTrain sampling instead.      |
+| If you still need PyNEP compatibility, run:     |
+|                 gpumdkit.sh -pynep              |
++-------------------------------------------------+
+```
+
+```bash
+gpumdkit.sh -pynep
+```
+
+随后输入：
+
+```text
+dump.xyz train.xyz nep.txt 8
+```
+
+这个入口需要 `pynep`。
+
+## 结构扰动
+
+```bash
+python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
+```
+
+交互模式选择 `204`，会看到：
+
+```text
+Input <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>
+The default parameters for perturb are 20 0.03 0.2 uniform
+Example: POSCAR 20 0.03 0.2 uniform
+------------>>
+```
+
+参数含义：
+
+| 参数 | 含义 |
+|------|------|
+| `POSCAR` | 输入结构 |
+| `20` | 生成结构数 |
+| `0.03` | 晶胞扰动比例 |
+| `0.2` | 原子扰动距离，单位 Angstrom |
+| `uniform` | 扰动方式，可选 `normal`、`uniform`、`const` |
+
+输出：
+
+- `POSCAR_01.vasp`、`POSCAR_02.vasp` 等
+
+该功能需要 `dpdata`。
+
+## 最大力偏差结构选择
+
+该功能需要配合 GPUMD 的 `active` 命令使用。`active` 通过委员会评审机制，让多条势函数对同一结构进行预测，并记录每个结构的最大力偏差。`select_max_modev.py` 会从 `active.out` 和 `active.xyz` 中选择力偏差较大的结构，写入 `selected.xyz`。
+
+```bash
+python Scripts/sample_structures/select_max_modev.py 200 0.15
+```
+
+交互模式选择 `205`，会看到：
+
+```text
++----------------------------------------------------+
+| Select max force deviation structs from active.xyz |
+|     generated by the active command in gpumd.      |
++----------------------------------------------------+
+Input <structs_num> <threshold> (eg. 200 0.15)
+------------>>
+```
+
+需要当前目录下有：
+
+- `active.out`
+- `active.xyz`
+
+输出：
+
+- `selected.xyz`
+
+## 示例命令
+
+```bash
+gpumdkit.sh -min_dist_pbc dump.xyz
+gpumdkit.sh -filter_box dump.xyz 13
+python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
+```
+
+## 常见问题
+
+| 问题 | 建议 |
+|------|------|
+| FPS 选出太多相似结构 | 调大距离阈值或限制最大选择数 |
+| 扰动结构不合理 | 减小 `cell_pert` 和 `atom_pert` |
+| `active.out` 和 `active.xyz` 不匹配 | 确保来自同一次 GPUMD active 运行 |
+| PCA 图异常 | 检查 `nep.txt` 是否和两个数据集元素一致 |
diff --git "a/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md" "b/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md"
new file mode 100644
index 0000000..dffd4fc
--- /dev/null
+++ "b/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md"
@@ -0,0 +1,228 @@
+<div align="center">
+  <h1>📊 绘图脚本</h1>
+  <p style="text-align: justify;">绘图模块用于可视化 GPUMD、NEP 和 GPUMDkit 计算器产生的数据。</p>
+</div>
+
+**脚本位置：** `Scripts/plt_scripts/`
+
+## 快速入口
+
+```bash
+gpumdkit.sh -plt
+gpumdkit.sh -plt <type>
+gpumdkit.sh -plt <type> save
+gpumdkit.sh -plt <type> -h
+```
+
+## NEP 训练与预测
+
+### 训练结果
+
+读取 `loss.out`、`energy_train.out`、`force_train.out`、`virial_train.out`，绘制 loss 和能量/力/virial 的 parity plot。
+
+```bash
+gpumdkit.sh -plt train
+```
+
+<div align="center">
+  <img src="../../Gallery/train.png" alt="NEP training results" width="75%" />
+</div>
+
+### 预测结果
+
+```bash
+gpumdkit.sh -plt prediction
+gpumdkit.sh -plt test
+```
+
+<div align="center">
+  <img src="../../Gallery/prediction.png" alt="NEP prediction results" width="75%" />
+</div>
+
+### 训练/测试集对比
+
+```bash
+gpumdkit.sh -plt train_test
+```
+
+<div align="center">
+  <img src="../../Gallery/train_test.png" alt="NEP train and test comparison" width="75%" />
+</div>
+
+### 密度 parity plot
+
+大数据集散点太密时，密度图更容易观察误差分布：
+
+```bash
+gpumdkit.sh -plt parity_density
+```
+
+<div align="center">
+  <img src="../../Gallery/parity_plot_density.png" alt="Parity density plot" width="70%" />
+</div>
+
+### 力误差分析
+
+`plt_force_errors.py` 参考 [Liu et al.](https://doi.org/10.1038/s41524-023-01123-3) 的方式分析力大小误差和角度误差。
+
+```bash
+gpumdkit.sh -plt force_errors
+```
+
+<div align="center">
+  <img src="../../Gallery/force_errors.png" alt="Force error analysis" width="70%" />
+</div>
+
+### 电荷和 Born 有效电荷
+
+```bash
+gpumdkit.sh -plt charge
+gpumdkit.sh -plt born_charge
+gpumdkit.sh -plt bec
+```
+
+<div align="center">
+  <img src="../../Gallery/charge.png" alt="Charge distribution" width="45%" />
+  <img src="../../Gallery/born_charge.png" alt="Born effective charge parity plot" width="45%" />
+</div>
+
+## MD 和结构分析绘图
+
+### 热力学量
+
+```bash
+gpumdkit.sh -plt thermo
+gpumdkit.sh -plt thermo2
+gpumdkit.sh -plt thermo3
+```
+
+<div align="center">
+  <img src="../../Gallery/thermo.png" alt="Thermo plot" width="75%" />
+</div>
+
+### RDF
+
+```bash
+gpumdkit.sh -plt rdf
+gpumdkit.sh -plt rdf <column>
+```
+
+<div align="center">
+  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
+  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
+</div>
+
+### VAC 和 PDOS
+
+```bash
+gpumdkit.sh -plt pdos
+gpumdkit.sh -plt pdos save
+```
+
+输入文件通常包括 `model.xyz`、`run.in`、`dos.out`、`mvac.out`。
+
+<div align="center">
+  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
+  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
+</div>
+
+## 扩散和离子输运
+
+```bash
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+gpumdkit.sh -plt msd_conv
+gpumdkit.sh -plt arrhenius_d
+gpumdkit.sh -plt arrhenius_sigma
+```
+
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="Mean square displacement" width="45%" />
+  <img src="../../Gallery/sdc.png" alt="Self-diffusion coefficient" width="45%" />
+</div>
+
+Arrhenius 图：
+
+<div align="center">
+  <img src="../../Gallery/Arrhenius_D.png" alt="Arrhenius diffusivity" width="55%" />
+  <img src="../../Gallery/Arrhenius_sigma.png" alt="Arrhenius ionic conductivity" width="55%" />
+</div>
+
+## 热输运
+
+```bash
+gpumdkit.sh -plt emd x
+gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]
+gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]
+```
+
+<div align="center">
+  <img src="../../Gallery/emd.png" alt="EMD thermal conductivity" width="70%" />
+  <img src="../../Gallery/nemd.png" alt="NEMD results" width="70%" />
+  <img src="../../Gallery/hnemd.png" alt="HNEMD results" width="70%" />
+</div>
+
+## 描述符、Dimer 和其他分析
+
+### 描述符可视化
+
+```bash
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+gpumdkit.sh -plt des pca
+gpumdkit.sh -plt des umap
+```
+
+<div align="center">
+  <img src="../../Gallery/des_umap.png" alt="UMAP descriptor visualization" width="52%" />
+</div>
+
+### Dimer 曲线
+
+```bash
+gpumdkit.sh -plt dimer Li Li nep.txt
+```
+
+<div align="center">
+  <img src="../../Gallery/dimer_nep.png" alt="Dimer NEP curve" width="45%" />
+  <img src="../../Gallery/dimer.png" alt="Dimer comparison" width="45%" />
+</div>
+
+**Reference:** [J. Chem. Inf. Model. 2026, 66, 3, 1406-1413](https://doi.org/10.1021/acs.jcim.5c02335)
+
+### DOAS
+
+```bash
+gpumdkit.sh -plt doas doas.out Li
+```
+
+<div align="center">
+  <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
+</div>
+
+### Net force
+
+```bash
+gpumdkit.sh -plt net_force train.xyz
+```
+
+**Reference:** [arXiv:2510.19774](https://arxiv.org/abs/2510.19774)
+
+<div align="center">
+  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
+</div>
+
+## 快速表
+
+| 命令 | 输入文件 | 用途 |
+|------|----------|------|
+| `train` | `loss.out`, `*_train.out` | NEP 训练结果 |
+| `prediction` | `*_test.out` | NEP 预测结果 |
+| `thermo` | `thermo.out` | 热力学量 |
+| `msd` | `msd.out` | 均方位移 |
+| `sdc` | `msd.out` | 自扩散系数 |
+| `rdf` | `rdf.out` | 径向分布函数 |
+| `pdos` | `dos.out`, `mvac.out` | VAC 和 PDOS |
+| `emd`/`nemd`/`hnemd` | 热输运输出 | 热导率分析 |
+| `des` | `descriptors.npy` | 描述符降维 |
+| `dimer` | `nep.txt` | 二聚体能量/力曲线 |
+| `doas` | `doas.out` | 原子态密度 |
diff --git "a/docs/tutorials/zh/\350\207\252\345\256\232\344\271\211\345\221\275\344\273\244.md" "b/docs/tutorials/zh/\350\207\252\345\256\232\344\271\211\345\221\275\344\273\244.md"
new file mode 100644
index 0000000..832b6a0
--- /dev/null
+++ "b/docs/tutorials/zh/\350\207\252\345\256\232\344\271\211\345\221\275\344\273\244.md"
@@ -0,0 +1,152 @@
+<div align="center">
+  <h1>🔧 自定义命令</h1>
+  <p style="text-align: justify;">GPUMDkit 支持从 <strong>~/.gpumdkit.in</strong> 加载自定义命令。你可以把常用脚本或工作流封装成 <code>custom_</code> 开头的 Bash 函数，然后通过 <code>gpumdkit.sh -命令名</code> 调用。</p>
+</div>
+
+## 设置
+
+编辑配置文件：
+
+```bash
+vi ~/.gpumdkit.in
+```
+
+自定义函数需要使用 `custom_` 前缀。
+
+## 示例
+
+### 简单问候
+
+在 `~/.gpumdkit.in` 中写入：
+
+```bash
+custom_hello() {
+    echo "Hello, GPUMDkit user! This is a custom command."
+    echo "Current GPUMDkit path: ${GPUMDkit_path}"
+}
+```
+
+然后运行：
+
+```bash
+gpumdkit.sh -hello
+```
+
+你会看到类似输出：
+
+```text
+Hello, GPUMDkit user! This is a custom command.
+Current GPUMDkit path: /home/yanzihan/software/GPUMDkit
+```
+
+### 带必需参数的命令
+
+```bash
+custom_greet() {
+    name=$1
+    echo "Hello, ${name}!"
+}
+```
+
+运行：
+
+```bash
+gpumdkit.sh -greet Zihan
+```
+
+输出：
+
+```text
+Hello, Zihan!
+```
+
+传递参数时，可以用 `"$@"` 安全地转发所有参数；如果需要从第一个参数开始引用，也可以使用 `${@:1}`。
+
+### 调用外部脚本
+
+如果希望像调用 GPUMDkit 内置命令一样调用自己的脚本：
+
+```bash
+custom_nepanalyse() {
+    python ~/my_gpumd_tools/analyse_nep.py
+}
+```
+
+运行：
+
+```bash
+gpumdkit.sh -nepanalyse
+```
+
+## 进阶示例
+
+### 批处理绘图
+
+对多个目录批量绘图：
+
+```bash
+custom_batch_plot() {
+    for dir in "$@"; do
+        cd "$dir"
+        gpumdkit.sh -plt thermo save
+        gpumdkit.sh -plt msd save
+        cd ..
+    done
+}
+```
+
+用法：
+
+```bash
+gpumdkit.sh -batch_plot dir1 dir2 dir3
+```
+
+### 训练集分析流程
+
+把多个分析命令组合成一个入口：
+
+```bash
+custom_analyze_training() {
+    xyz_file=$1
+    echo "Analyzing $xyz_file..."
+
+    gpumdkit.sh -range "$xyz_file" force
+    gpumdkit.sh -min_dist_pbc "$xyz_file"
+    gpumdkit.sh -analyze_comp "$xyz_file"
+
+    echo "Analysis complete!"
+}
+```
+
+用法：
+
+```bash
+gpumdkit.sh -analyze_training train.xyz
+```
+
+### 自定义数据准备流程
+
+```bash
+custom_prep_training() {
+    echo "Preparing training data..."
+
+    gpumdkit.sh -out2xyz ./
+    gpumdkit.sh -filter_value train.xyz force 30
+    gpumdkit.sh -range filtered_force.xyz energy
+
+    echo "Training data ready!"
+}
+```
+
+用法：
+
+```bash
+gpumdkit.sh -prep_training
+```
+
+## 使用建议
+
+- 命令名尽量清楚，例如 `custom_analyze_training` 比 `custom_at` 更容易维护。
+- 对需要参数的命令，建议在参数为空时打印用法提示。
+- 调用外部脚本时，尽量用 `"$@"` 保留参数中的空格和特殊字符。
+- 批处理目录时，注意使用 `cd "$dir"`，避免路径中有空格时出错。
diff --git "a/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md" "b/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md"
new file mode 100644
index 0000000..a316052
--- /dev/null
+++ "b/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md"
@@ -0,0 +1,271 @@
+<div align="center">
+  <h1>🧮 计算器脚本</h1>
+  <p style="text-align: justify;">计算器模块用于从 MD 轨迹、NEP 模型和结构文件中计算材料性质。</p>
+</div>
+
+**脚本位置：** `Scripts/calculators/`
+
+## 功能概览
+
+| 任务 | 命令 | 主要输入 |
+|------|------|----------|
+| 离子电导率 | `gpumdkit.sh -calc ionic-cond <element> <charge>` | `msd.out`、`thermo.out`、`model.xyz` |
+| MSD | `gpumdkit.sh -calc msd <trajectory.xyz> <element> <dt_fs>` | extxyz 轨迹 |
+| NEP 预测 | `gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>` | extxyz + NEP 模型 |
+| NEP 描述符 | `gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>` | extxyz + NEP 模型 |
+| DOAS | `gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>` | extxyz + NEP 模型 |
+| NEB | `gpumdkit.sh -calc neb <initial.xyz> <final.xyz> <n_images> <nep.txt>` | 初末态结构 |
+| 结构优化 | `gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]` | 结构 + NEP 模型 |
+| 邻居列表 | `gpumdkit.sh -calc nlist [args...]` | 结构 |
+| 位移 | `gpumdkit.sh -calc disp [args...]` | 轨迹 + 邻居列表 |
+| 平均结构 | `gpumdkit.sh -calc avg-struct [args...]` | 轨迹 |
+| 八面体倾转 | `gpumdkit.sh -calc oct-tilt [args...]` | 轨迹 + B-O 邻居列表 |
+| ABO3 极化 | `gpumdkit.sh -calc pol-abo3 [args...]` | 轨迹 + 邻居列表 |
+
+查看完整帮助：
+
+```bash
+gpumdkit.sh -calc -h
+```
+
+命令行帮助表类似：
+
+```text
++-------------------------------------------------------------------------------------------------------+
+|                                      CALCULATOR TOOLS                                                 |
++-------------------------------------------------------------------------------------------------------+
+| Usage: gpumdkit.sh -calc <type> [args...]                                                             |
++-------------------------------------------------------------------------------------------------------+
+| ionic-cond <element> <charge>                 Calculate ionic conductivity from MSD data              |
+| nep <input.xyz> <output.xyz> <nep_model>      Calculate energy/force/virial with a NEP model          |
+| des <input.xyz> <output.npy> <nep_model> <el> Calculate NEP descriptors for one element               |
+| doas <input.xyz> <nep_model> <output.txt>     Calculate density of atomistic states                   |
+| neb <initial.xyz> <final.xyz> <n_images> <nep> Run NEB calculation with a NEP model                   |
+| minimize <structure> <nep_model> [fmax] [n]   Minimize a structure with a NEP model                   |
+| msd <trajectory.xyz> <element> <dt_fs> [n]    Calculate MSD from an extxyz trajectory                 |
+| nlist [script args...]                        Build neighbor lists                                    |
+| disp [script args...]                         Calculate displacement from trajectory                  |
+| avg-struct [script args...]                   Calculate averaged structure                            |
+| oct-tilt [script args...]                     Calculate octahedral tilt                               |
+| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |
++-------------------------------------------------------------------------------------------------------+
+```
+
+交互模式中选择 `4) Calculators`，菜单如下：
+
+```text
++----------------------------------------------------------+
+|                     CALCULATOR TOOLS                     |
++----------------------------------------------------------+
+| 401) Calc ionic conductivity                             |
+| 402) Calc properties by nep                              |
+| 403) Calc descriptors of specific elements               |
+| 404) Calc density of atomistic states (DOAS)             |
+| 405) Calc nudged elastic band (NEB) by nep               |
+| 406) Build neighbor list                                 |
+| 407) Calc displacement from trajectory                   |
+| 408) Calc averaged structure                             |
+| 409) Calc octahedral tilt                                |
+| 410) Calc polarization for ABO3                          |
+| 411) Minimize structure by nep                           |
+| 412) Calc mean square displacement (MSD) from trajectory |
++----------------------------------------------------------+
+| 000) Return to the main menu                             |
++----------------------------------------------------------+
+Input the function number:
+```
+
+## 离子电导率
+
+```bash
+gpumdkit.sh -calc ionic-cond Li 1
+```
+
+交互模式选择 `401`，会看到：
+
+```text
+>-------------------------------------------------<
+| This function calls the script in calculators   |
+| Script: calc_ion_conductivity.py                |
+| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
+>-------------------------------------------------<
+Input <element> <charge> (eg. Li 1)
+------------>>
+```
+
+常用输入文件：
+
+| 文件 | 作用 |
+|------|------|
+| `msd.out` | 必需，MSD 数据 |
+| `thermo.out` | 可选，自动读取温度 |
+| `model.xyz` | 可选，自动读取体积和离子数 |
+| `run.in` | 可选，识别扩胞信息 |
+
+如果缺少自动识别所需文件，脚本会交互式询问温度、体积和离子数。
+
+手动模式的提示类似：
+
+```text
+Files 'thermo.out' and 'model.xyz' are not found.
+Please provide the following values:
+--------------------------->
+Enter average temperature (in K):
+Enter system volume (in A^3):
+Enter number of ions:
+```
+
+## 从轨迹计算 MSD
+
+```bash
+gpumdkit.sh -calc msd dump.xyz Li 10
+gpumdkit.sh -calc msd dump.xyz Li 10 5000
+```
+
+交互模式选择 `412`，会看到：
+
+```text
+Input <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]
+  Optional argument: max_corr_steps (default: frame number)
+Example: dump.xyz Li 10
+------------>>
+```
+
+参数含义：
+
+| 参数 | 含义 |
+|------|------|
+| `dump.xyz` | 输入轨迹 |
+| `Li` | 目标扩散元素 |
+| `10` | 帧间隔，单位 fs |
+| `5000` | 可选，最大相关步数 |
+
+输出：
+
+- `msd.out`
+
+随后可绘图：
+
+```bash
+gpumdkit.sh -plt msd
+gpumdkit.sh -plt sdc
+```
+
+<div align="center">
+  <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
+  <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
+</div>
+
+## NEP 预测性质
+
+```bash
+gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
+```
+
+该功能使用训练好的 NEP 模型计算能量、力和应力。只有当你确认模型质量可靠，并明确希望使用 NEP 作为替代计算器时，才建议使用它。
+
+## NEP 描述符
+
+```bash
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+```
+
+用途包括：
+
+- 用 PCA/UMAP 可视化局域环境；
+- 比较训练集和候选结构；
+- 判断新数据是否扩展了描述符空间。
+
+绘图：
+
+```bash
+gpumdkit.sh -plt des pca
+gpumdkit.sh -plt des umap
+```
+
+<div align="center">
+  <img src="../../Gallery/des_umap.png" alt="Descriptor UMAP" width="52%" />
+</div>
+
+## DOAS
+
+`calc_doas.py` 用于计算 [Wang et al.](https://doi.org/10.1002/anie.202215544) 提出的 density of atomistic states。
+
+```bash
+gpumdkit.sh -calc doas structures.xyz nep.txt doas.out
+gpumdkit.sh -plt doas doas.out Li
+```
+
+脚本会：
+
+1. 读取所有结构；
+2. 使用 NEP 进行结构优化；
+3. 提取每个原子的能量；
+4. 按元素分组输出；
+5. 用绘图脚本可视化分布。
+
+<div align="center">
+  <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
+</div>
+
+## NEB 和结构优化
+
+NEB：
+
+```bash
+gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt
+```
+
+结构优化：
+
+```bash
+gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
+```
+
+输出包括：
+
+- `minimize.xyz`
+- `minimize.log`
+
+## 铁电和极性材料工具
+
+这些工具需要 `ferrodispcalc`：
+
+```bash
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
+```
+
+`ferrodispcalc` 目前没有需要额外引用的论文。
+
+### 邻居列表
+
+```bash
+gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat
+```
+
+### 位移
+
+```bash
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat
+```
+
+### 平均结构
+
+```bash
+gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz
+```
+
+### 八面体倾转
+
+```bash
+gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat
+```
+
+### ABO3 局域极化
+
+```bash
+gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \
+  --bec Pb=2 Ti=4.0 O=-2.0 -o polarization.dat
+```
+
+`--bec` 应根据你的体系或参考数据设置。
diff --git "a/docs/tutorials/zh/\350\264\241\347\214\256\346\214\207\345\215\227.md" "b/docs/tutorials/zh/\350\264\241\347\214\256\346\214\207\345\215\227.md"
new file mode 100644
index 0000000..281b11d
--- /dev/null
+++ "b/docs/tutorials/zh/\350\264\241\347\214\256\346\214\207\345\215\227.md"
@@ -0,0 +1,413 @@
+<div align="center">
+  <h1>🤝 贡献指南</h1>
+  <p style="text-align: justify;">感谢你有兴趣为 <strong>GPUMDkit</strong> 做贡献。我们非常感谢你愿意花时间和精力帮助改进这个工具包。</p>
+</div>
+
+`GPUMDkit` 是一个开源软件包。无论是修复 bug、添加新功能、改进文档，还是提出使用建议，我们都欢迎社区贡献。
+
+---
+
+## 目录
+
+- 开发限制和指南
+- 报告 Bug
+- 提出功能建议
+- 贡献代码
+- Fork 并克隆仓库
+- 创建功能分支
+- 进行修改
+- 交互模式贡献
+- 命令行模式贡献
+- 更新 Tab 补全
+- 代码风格和最佳实践
+- 测试你的修改
+- 提交信息
+- 推送并打开 Pull Request
+
+---
+
+## 开发限制和指南
+
+为了保持项目代码质量和一致性，请遵守以下指南。
+
+### 语言要求
+
+- **所有代码应使用英文编写**：包括变量名、函数名、注释、docstring、提交信息和文档。
+- 我们理解贡献者可能来自不同背景，但使用英文可以让代码库对更广泛的用户保持可读和可维护。
+
+### 模块化和可复用性
+
+- **编写模块化、可复用的代码**：函数和脚本应尽量具有灵活性。
+- **优先通过参数传递信息，避免硬编码**：使用函数参数、命令行参数或配置文件，而不是把数值直接写死。不过，某些文件名是 GPUMD 和 NEP 程序固定要求的，例如 `train.xyz`、`thermo.out`，这类情况可以按需要保留固定文件名。
+- **示例**：
+
+  ```bash
+  # Good: accepts parameters
+  function convert_file() {
+      local input_file=$1
+      local output_file=$2
+      # processing logic
+  }
+
+  # Avoid: hardcoded values (unless required by GPUMD/NEP)
+  function convert_file() {
+      local input_file="hardcoded_input.xyz"
+      # processing logic
+  }
+  ```
+
+### 代码风格
+
+- 编写清晰、易于他人维护和修改的代码。
+- 使用有意义的变量名和函数名。
+- 在必要时添加注释，解释复杂逻辑。
+
+### 文档
+
+- 确保帮助信息（例如 `-h` 参数）清晰、准确。
+- `docs/` 目录中的文档通常由维护者更新，因此一般不需要贡献者直接修改。
+
+---
+
+## 报告 Bug
+
+如果你遇到 bug，请通过 GitHub Issues 帮助我们定位和修复：
+
+1. **先搜索已有 issue**，确认这个 bug 是否已经被报告过。
+2. **如果还没有报告，请创建新 issue**：[Create an Issue](https://github.com/zhyan0603/GPUMDkit/issues/new)
+3. **详细描述问题**，如果可以，请提供测试文件。
+
+你也可以通过以下方式联系我们：
+
+- **QQ 群**：825696376
+- **Email**：yanzihan@westlake.edu.cn
+- **脚本开发者**：联系脚本文件头部列出的开发者
+
+---
+
+## 提出功能建议
+
+我们欢迎新的功能建议。提出新功能时，可以按以下方式进行：
+
+1. **先搜索已有 issue**，确认是否已经有人提出过类似建议。
+2. **创建新的功能请求**：[Create a Feature Request](https://github.com/zhyan0603/GPUMDkit/issues/new)，并提及 @zhyan0603。
+3. **清楚描述你的需求**，并说明它为什么有用。
+
+---
+
+## 贡献代码
+
+### Fork 并克隆仓库
+
+1. 在 GitHub 的 [GPUMDkit 仓库页面](https://github.com/zhyan0603/GPUMDkit)右上角点击 "Fork"，将仓库 fork 到自己的账号下。
+
+2. 将你的 fork 克隆到本地：
+
+   ```bash
+   git clone https://github.com/YOUR_USERNAME/GPUMDkit.git
+   cd GPUMDkit
+   ```
+
+3. 设置 upstream remote，方便和主仓库保持同步：
+
+   ```bash
+   git remote add upstream https://github.com/zhyan0603/GPUMDkit.git
+   ```
+
+### 创建功能分支
+
+为你的修改创建一个新分支：
+
+```bash
+# Create and checkout a new branch from main
+git checkout -b your-branch-name
+```
+
+分支名可以按你的习惯命名。
+
+### 进行修改
+
+`GPUMDkit` 的结构包括：
+
+- **`gpumdkit.sh`**：主入口 Bash 脚本，负责交互菜单模式和命令行模式。
+- **`Scripts/`**：按功能分类组织的 Python 工具脚本。
+  - `plt_scripts/`：绘图脚本
+  - `calculators/`：计算工具
+  - `format_conversion/`：格式转换工具
+  - `workflow/`：工作流自动化
+  - `sample_structures/`：结构采样工具
+  - `analyzer/`：分析工具
+  - `utils/`：实用函数，包括用于 Tab 补全的 `completion.sh`
+- **`src/`**：包含交互模式菜单函数的 Shell 脚本。
+  - `f1_format_conversions.sh`
+  - `f2_sample_structures.sh`
+  - `f3_workflows.sh`
+  - `f4_calculators.sh`
+  - `f5_analyzers.sh`
+  - `f6_plots.sh`
+  - `f7_utilities.sh`
+- **`docs/`**：文档文件。
+
+#### 交互模式贡献
+
+如果要添加一个可通过交互菜单访问的新功能：
+
+1. **在合适的 `Scripts/` 子目录中创建实现脚本**：
+
+   ```bash
+   # Example: Add a new format conversion script
+   touch Scripts/format_conversion/new_converter.py
+   ```
+
+2. **实现你的功能**，并遵循模块化指南：接受参数，避免不必要的硬编码。
+
+3. **在对应的 `src/` 文件中添加包装函数**：
+
+   ```bash
+   # Example: Edit src/f1_format_conversions.sh
+   vim src/f1_format_conversions.sh
+   ```
+
+   添加一个新函数：
+
+   ```bash
+   function f106_new_converter(){
+   echo " >-------------------------------------------------<"
+   echo " | Calling the script in Scripts/format_conversion |"
+   echo " | Script: new_converter.py                        |"
+   echo " | Developer: Your Name (your@email.com)           |"
+   echo " >-------------------------------------------------<"
+   echo " Input the required parameters:"
+   echo " Example: input.xyz output.lmp"
+   echo " ------------>>"
+   read -p " " converter_params
+   echo " ---------------------------------------------------"
+   python ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py ${converter_params}
+   echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py"
+   echo " ---------------------------------------------------"
+   }
+   ```
+
+4. **更新 `gpumdkit.sh` 中的菜单显示**：
+
+   ```bash
+   # Find the menu() function and update it if needed
+   # Find the array_choice array and add your new choice number
+   array_choice=(
+       "0" "1" "101" "102" "103" "104" "105" "106"  # Added "106"
+       # ... rest of choices
+   )
+   ```
+
+5. **在 `gpumdkit.sh` 中添加 case 分支**：
+
+   ```bash
+   # In the main() function, find the appropriate case statement
+   case "${choice:0:1}" in
+       # ...
+       "1")
+           source ${GPUMDkit_path}/src/f1_format_conversions.sh
+           case $choice in
+               "1") f1_format_conversion ;;
+               "101") f101_out2xyz ;;
+               # ... existing cases ...
+               "106") f106_new_converter ;;  # Add your case
+           esac ;;
+       # ...
+   esac
+   ```
+
+#### 命令行模式贡献
+
+如果要添加新的命令行 flag 或子命令：
+
+1. **在合适的 `Scripts/` 子目录中创建实现脚本**：
+
+   ```bash
+   # Example: Add a new analyzer script
+   touch Scripts/analyzer/analyze_bonds.py
+   ```
+
+2. **实现功能，并明确参数要求**：
+
+   ```python
+   # Example: Scripts/analyzer/analyze_bonds.py
+   import sys
+
+   def main():
+       if len(sys.argv) != 3:
+           print("Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>")
+           print("Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0")
+           sys.exit(1)
+
+       input_file = sys.argv[1]
+       cutoff = float(sys.argv[2])
+
+       # Your implementation here
+
+   if __name__ == "__main__":
+       main()
+   ```
+
+3. **在 `gpumdkit.sh` 中添加命令行 flag 处理逻辑**：
+
+   ```bash
+   # Find the command-line parsing section (after line ~167)
+   # Add your new flag in the appropriate location
+
+   case $1 in
+       # ... existing cases ...
+       -analyze_bonds)
+           if [ ! -z "$2" ] && [ ! -z "$3" ]; then
+               python ${analyzer_path}/analyze_bonds.py "$2" "$3"
+           else
+               echo " Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>"
+               echo " Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0"
+               echo " Code path: ${analyzer_path}/analyze_bonds.py"
+               exit 1
+           fi ;;
+       # ... rest of cases ...
+   esac
+   ```
+
+4. **更新 `gpumdkit.sh` 中的帮助信息**：
+
+   ```bash
+   # Find the help_info_table() function and add your command
+   function help_info_table(){
+       echo "+====================================== Analysis ===============================================+"
+       echo "| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |"
+       # ... rest of help table ...
+   }
+   ```
+
+#### 更新 Tab 补全
+
+添加新的命令行 flag 时，请更新 Tab 补全脚本：
+
+```bash
+# Edit Scripts/utils/completion.sh
+vim Scripts/utils/completion.sh
+```
+
+将新的 flag 加入 `opts` 变量：
+
+```bash
+# Find the line with local opts=...
+local opts="-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ..."
+#                                                      ^^^^^^^^^^^^^^ Add your flag here
+```
+
+如果这个 flag 接受二级选项，例如 `-plt` 或 `-calc`，也需要为它添加对应的 `case` 分支：
+
+```bash
+case "$prev" in
+    # ... existing cases ...
+    -analyze_bonds)
+        COMPREPLY=($(compgen -f -- "$cur"))  # Complete with filenames
+        ;;
+    # ... rest of cases ...
+esac
+```
+
+### 代码风格和最佳实践
+
+- **Shell 脚本**：
+  - 使用 `${variable}` 进行变量展开。
+  - 编写清晰、易维护的代码。
+
+- **Python 脚本**：
+  - 编写清晰、可维护的代码。
+  - 使用有意义的变量名。
+
+### 测试你的修改
+
+提交贡献前，请进行测试：
+
+1. **测试交互模式**（如果适用）：
+
+   ```bash
+   gpumdkit.sh
+   # Navigate to your new feature and test it thoroughly
+   ```
+
+2. **测试命令行模式**（如果适用）：
+
+   ```bash
+   gpumdkit.sh -your_new_flag [arguments]
+   gpumdkit.sh -your_new_flag -h  # Test help message
+   ```
+
+3. **测试 Tab 补全**（如果修改了 `completion.sh`）：
+
+   ```bash
+   source Scripts/utils/completion.sh
+   gpumdkit.sh -<TAB>  # Should show your new flag
+   ```
+
+4. **使用不同输入测试**：
+
+   - 测试常规输入。
+   - 测试边界情况，例如空文件、大文件等。
+   - 测试错误处理，例如缺少文件、参数无效等。
+
+5. **确认没有回归问题**：确保已有功能仍然可以正常工作。
+
+### 提交信息
+
+提交信息应清楚、具体，说明你修改了什么。不要求严格格式，但需要让他人能够理解。
+
+### 推送并打开 Pull Request
+
+1. **提交你的修改**：
+
+   ```bash
+   git add .
+   git commit -m "your descriptive message"
+   ```
+
+2. **让你的分支与 upstream `main` 分支保持同步**：
+
+   ```bash
+   git fetch upstream
+   git rebase upstream/main
+   ```
+
+3. **将分支推送到你的 fork**：
+
+   ```bash
+   git push origin your-branch-name
+   ```
+
+4. **打开 Pull Request**：
+
+   - 进入 [GPUMDkit repository](https://github.com/zhyan0603/GPUMDkit)。
+   - 点击 "Pull Requests" -> "New Pull Request"。
+   - 将 base branch 设置为 `dev`，用于代码审查。
+   - 将 compare branch 设置为你的功能分支。
+   - 填写 PR 描述，包括：
+     - **Title**：简要描述修改内容。
+     - **Description**：详细说明修改了什么以及为什么修改。
+     - **Testing**：说明你如何测试这些修改。
+
+5. **回应审查意见**：
+
+   - 接受建议和建设性意见。
+   - 及时完成要求的修改。
+   - 将额外提交推送到你的分支，它们会自动显示在 PR 中。
+
+6. **审查通过后**：维护者会合并你的 PR。
+
+---
+
+## 有问题或需要帮助？
+
+如果你对贡献流程有疑问，或需要帮助：
+
+- **打开讨论**：一般问题可以使用 [GitHub Discussions](https://github.com/zhyan0603/GPUMDkit/discussions)。
+- **在 issue 中提问**：与具体问题相关的内容可以在对应 issue 下评论。
+- **联系维护者**：联系 README 中列出的核心开发者。
+
+---
+
+再次感谢你为 `GPUMDkit` 做贡献。你的工作会帮助整个 GPUMD 和 NEP 社区更好地使用这个工具包。
diff --git a/docs/tutorials2/en/analyzers.md b/docs/tutorials2/en/analyzers.md
deleted file mode 100644
index 0b47abe..0000000
--- a/docs/tutorials2/en/analyzers.md
+++ /dev/null
@@ -1,92 +0,0 @@
-<div align="center">
-  <h1>Analyzers</h1>
-  <p>
-    <strong>English</strong> | <a href="../zh/analyzers.md">简体中文</a>
-  </p>
-</div>
-
-Structure analysis, validation, and filtering tools.
-
-## Available Tools
-
-| Tool | Command | Description |
-|------|---------|-------------|
-| Composition Analysis | `-analyze_comp` | Group structures by composition |
-| Property Range | `-range` | Energy/force/virial statistics |
-| Minimum Distance | `-min_dist` | Calculate min distances (no PBC) |
-| Minimum Distance (PBC) | `-min_dist_pbc` | Calculate min distances (with PBC) |
-| Charge Balance | `-cbc` | Check oxidation-state balance |
-| Distance Filter | `-filter_dist_pbc` | Filter by minimum distance |
-| Box Filter | `-filter_box` | Filter by box size |
-| Value Filter | `-filter_value` | Filter by property value |
-| Distance Range | `-filter_range` | Filter by element-pair distance |
-| Time Monitor | `-time` | Monitor GPUMD/NEP progress |
-
-## Command Reference
-
-### Composition Analysis
-
-```bash
-gpumdkit.sh -analyze_comp train.xyz
-```
-
-### Property Range
-
-```bash
-gpumdkit.sh -range <file> <property> [hist]
-
-# Examples
-gpumdkit.sh -range train.xyz force
-gpumdkit.sh -range train.xyz energy
-gpumdkit.sh -range train.xyz force hist
-```
-
-### Minimum Distance
-
-```bash
-# Fast (no PBC)
-gpumdkit.sh -min_dist dump.xyz
-
-# Accurate (with PBC)
-gpumdkit.sh -min_dist_pbc dump.xyz
-```
-
-### Charge Balance
-
-```bash
-gpumdkit.sh -cbc train.xyz
-```
-
-Output: `balanced.xyz`, `unbalanced.xyz`
-
-### Filtering
-
-```bash
-# By minimum distance
-gpumdkit.sh -filter_dist_pbc train.xyz 1.0
-
-# By box size
-gpumdkit.sh -filter_box dump.xyz 20
-
-# By property value
-gpumdkit.sh -filter_value train.xyz force 20
-
-# By element-pair distance range
-gpumdkit.sh -filter_range dump.xyz Li Li 1.9 2.0
-```
-
-### Time Monitoring
-
-```bash
-gpumdkit.sh -time gpumd
-gpumdkit.sh -time nep
-```
-
-## Dependencies
-
-| Tool | Packages |
-|------|----------|
-| All | ase, numpy |
-| Distance | scipy |
-| Charge balance | pymatgen, tqdm |
-| Property range | matplotlib |
diff --git a/docs/tutorials2/en/calculators.md b/docs/tutorials2/en/calculators.md
deleted file mode 100644
index 2fbfc4f..0000000
--- a/docs/tutorials2/en/calculators.md
+++ /dev/null
@@ -1,153 +0,0 @@
-<div align="center">
-  <h1>Calculators</h1>
-  <p>
-    <strong>English</strong> | <a href="../zh/calculators.md">简体中文</a>
-  </p>
-</div>
-
-Compute material properties from molecular dynamics data.
-
-## Available Calculators
-
-| Calculator | Command | Description |
-|------------|---------|-------------|
-| Ionic Conductivity | `-calc ionic-cond` | Calculate ionic conductivity from MSD |
-| NEP Properties | `-calc nep` | Compute energy/force/stress with NEP |
-| Descriptors | `-calc des` | Calculate NEP descriptors for analysis |
-| DOAS | `-calc doas` | Density of atomistic states |
-| MSD | `-calc msd` | Mean square displacement from trajectory |
-| Neighbor List | `-calc nlist` | Build neighbor lists for analysis |
-| Displacement | `-calc disp` | Calculate atomic displacements |
-| Averaged Structure | `-calc avg-struct` | Time-averaged structure from trajectory |
-| Octahedral Tilt | `-calc oct-tilt` | Perovskite octahedral tilt angles |
-| Polarization | `-calc pol-abo3` | ABO3 local polarization |
-| Minimization | `-calc minimize` | Structure relaxation with NEP |
-| NEB | Direct Python | Nudged elastic band calculation |
-
-## Command Reference
-
-### Ionic Conductivity
-
-```bash
-gpumdkit.sh -calc ionic-cond <element> <charge>
-
-# Examples
-gpumdkit.sh -calc ionic-cond Li 1    # Li+
-gpumdkit.sh -calc ionic-cond O -2    # O2-
-```
-
-Required files: `msd.out`, `thermo.out`, `model.xyz`, `run.in`
-
-### NEP Properties
-
-```bash
-gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>
-
-# Example
-gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
-```
-
-### Descriptors
-
-```bash
-gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <element>
-
-# Example
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-```
-
-Visualize with: `gpumdkit.sh -plt des pca` or `gpumdkit.sh -plt des umap`
-
-### DOAS
-
-```bash
-gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>
-
-# Example
-gpumdkit.sh -calc doas structures.xyz nep.txt doas.out
-```
-
-### MSD
-
-```bash
-gpumdkit.sh -calc msd <trajectory.xyz> <element> <dt_fs> [max_corr_steps]
-
-# Example
-gpumdkit.sh -calc msd dump.xyz Li 10
-```
-
-Output: `msd.out` (Time/ps, MSD_x, MSD_y, MSD_z)
-
-### Neighbor List
-
-```bash
-gpumdkit.sh -calc nlist -i <input> -c <cutoff> -n <num> -C <center> -E <neighbor>
-
-# Example
-gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
-```
-
-### Displacement
-
-```bash
-gpumdkit.sh -calc disp -i <trajectory.xyz> -n <neighbor_list> -o <output>
-
-# Example
-gpumdkit.sh -calc disp -i movie.xyz -n nl-Pb-O.dat -o displacements.dat
-```
-
-### Averaged Structure
-
-```bash
-gpumdkit.sh -calc avg-struct -i <trajectory.xyz> -l <fraction> -o <output>
-
-# Example: Average last 20% of frames
-gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged.xyz
-```
-
-### Octahedral Tilt
-
-```bash
-gpumdkit.sh -calc oct-tilt -i <input.xyz> -n <B-O list> -o <output>
-
-# Example
-gpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o tilt.dat
-```
-
-### Polarization (ABO3)
-
-```bash
-gpumdkit.sh -calc pol-abo3 -i <input.xyz> --nl-ba <B-A list> --nl-bo <B-O list> --bec <Element=charge ...>
-
-# Example
-gpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat --bec Pb=2.5 Ti=4.0 O=-2.0
-```
-
-### Minimization
-
-```bash
-gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]
-
-# Example
-gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
-```
-
-Output: `minimize.xyz`
-
-### NEB
-
-```bash
-python Scripts/calculators/neb_calculation.py <initial.xyz> <final.xyz> <n_images> <nep.txt>
-
-# Example
-python Scripts/calculators/neb_calculation.py init.xyz fin.xyz 9 nep.txt
-```
-
-## Dependencies
-
-| Calculator | Packages |
-|------------|----------|
-| All | numpy, ase |
-| ionic-cond | scipy |
-| nep, des, doas, minimize | calorine |
-| nlist, disp, oct-tilt, pol-abo3 | ferrodispcalc |
diff --git a/docs/tutorials2/en/format_conversion.md b/docs/tutorials2/en/format_conversion.md
deleted file mode 100644
index 0aca344..0000000
--- a/docs/tutorials2/en/format_conversion.md
+++ /dev/null
@@ -1,100 +0,0 @@
-<div align="center">
-  <h1>Format Conversion</h1>
-  <p>
-    <strong>English</strong> | <a href="../zh/format_conversion.md">简体中文</a>
-  </p>
-</div>
-
-Convert between computational materials science file formats.
-
-## Supported Formats
-
-| Format | Extensions | Software |
-|--------|-----------|----------|
-| VASP | POSCAR, OUTCAR, XDATCAR, vasprun.xml | VASP |
-| LAMMPS | .data, dump.* | LAMMPS |
-| CP2K | .log, pos.xyz, frc.xyz, cell.cell | CP2K |
-| ABACUS | running_scf.log, running_md.log | ABACUS |
-| CIF | .cif | Various |
-| MTP | .cfg | MTP |
-| ASE | .traj | ASE |
-| extxyz | .xyz | Various (primary format) |
-
-## Quick Reference
-
-```bash
-# VASP
-gpumdkit.sh -out2xyz <dir>              # OUTCAR -> extxyz
-gpumdkit.sh -pos2exyz POSCAR model.xyz  # POSCAR -> extxyz
-gpumdkit.sh -exyz2pos structures.xyz    # extxyz -> POSCAR
-
-# LAMMPS
-gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl  # LAMMPS -> extxyz
-gpumdkit.sh -pos2lmp POSCAR lammps.data        # POSCAR -> LAMMPS
-
-# CIF
-gpumdkit.sh -cif2pos input.cif POSCAR.vasp     # CIF -> POSCAR
-gpumdkit.sh -cif2exyz input.cif model.xyz      # CIF -> extxyz
-
-# Other
-gpumdkit.sh -xdat2exyz XDATCAR output.xyz      # XDATCAR -> extxyz
-gpumdkit.sh -traj2exyz input.traj output.xyz   # ASE traj -> extxyz
-```
-
-## Structure Manipulation
-
-```bash
-# Add group labels (required for NEP)
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-
-# Add weights
-gpumdkit.sh -addweight input.xyz output.xyz 2.0
-
-# Replicate structure
-gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2
-gpumdkit.sh -replicate POSCAR supercell.vasp 256  # by atom count
-
-# Extract frame (0-based)
-gpumdkit.sh -get_frame trajectory.xyz 1000
-
-# Clean metadata
-gpumdkit.sh -clean_xyz input.xyz clean.xyz
-```
-
-## Examples
-
-### Convert VASP Output
-
-```bash
-gpumdkit.sh -out2xyz .
-gpumdkit.sh -addgroup POSCAR Pb Ti O
-```
-
-### Prepare LAMMPS Simulation
-
-```bash
-gpumdkit.sh -pos2lmp POSCAR system.data
-# After simulation
-gpumdkit.sh -lmp2exyz dump.lammpstrj Li P S
-```
-
-### Batch Conversion
-
-```bash
-for dir in run_*; do
-    gpumdkit.sh -out2xyz "$dir"
-done
-```
-
-## Notes
-
-- extxyz is the primary format for GPUMDkit
-- Group labels are required for GPUMD/NEP
-- Frame indexing is 0-based
-- LAMMPS element order must match atom type IDs
-
-## Dependencies
-
-```bash
-pip install ase numpy
-```
diff --git a/docs/tutorials2/en/nep_training.md b/docs/tutorials2/en/nep_training.md
deleted file mode 100644
index f41ce49..0000000
--- a/docs/tutorials2/en/nep_training.md
+++ /dev/null
@@ -1,113 +0,0 @@
-<div align="center">
-  <h1>NEP Training Guide</h1>
-  <p>
-    <strong>English</strong> | <a href="../zh/nep_training.md">简体中文</a>
-  </p>
-</div>
-
-Complete workflow for training NEP (Neuroevolution Potential) models.
-
-## Overview
-
-1. **Data Preparation** - Convert and organize training data
-2. **Quality Check** - Validate and filter structures
-3. **Sampling** - Select diverse structures
-4. **Training** - Train the NEP model (external)
-5. **Validation** - Check training quality
-6. **Active Learning** - Iteratively improve the model
-
-## Step 1: Data Preparation
-
-```bash
-# Convert DFT data
-gpumdkit.sh -out2xyz ./vasp_results/
-
-# Add group labels
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-
-# Combine training data
-cat */model.xyz > train.xyz
-```
-
-## Step 2: Quality Check
-
-```bash
-# Check composition
-gpumdkit.sh -analyze_comp train.xyz
-
-# Check distances
-gpumdkit.sh -min_dist_pbc train.xyz
-
-# Check force range
-gpumdkit.sh -range train.xyz force
-
-# Filter structures
-gpumdkit.sh -filter_dist_pbc train.xyz 1.0
-```
-
-## Step 3: Sampling
-
-```bash
-# FPS sampling (recommended)
-gpumdkit.sh  # Select: 2) Sample Structures -> 203
-
-# Or uniform sampling
-python Scripts/sample_structures/sample_structures.py train.xyz uniform 100
-```
-
-## Step 4: Training
-
-Create `nep.in`:
-
-```
-type 3 Li Y Cl
-cutoff 6 4
-n_max 4
-l_max 4
-neuron 100
-batch 1000
-generation 100000
-```
-
-Run training:
-
-```bash
-gpumd
-```
-
-## Step 5: Validation
-
-```bash
-# Plot training results
-gpumdkit.sh -plt train
-gpumdkit.sh -plt prediction
-gpumdkit.sh -plt force_errors
-
-# Analyze descriptors
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-gpumdkit.sh -plt des pca
-```
-
-## Step 6: Active Learning
-
-```bash
-# Run MD with current NEP
-gpumdkit.sh  # Select: 3) Workflow -> 302
-
-# Filter and sample
-gpumdkit.sh -min_dist_pbc dump.xyz
-gpumdkit.sh -filter_box dump.xyz 13
-
-# Prepare DFT calculations
-gpumdkit.sh  # Select: 3) Workflow -> 301
-
-# Retrain with new data
-cat new_structures.xyz >> train.xyz
-```
-
-## Tips
-
-- Include diverse structures, temperatures, and compositions
-- At least 1000-5000 structures for good accuracy
-- Keep 10-20% of data for testing
-- Check for outliers before training
diff --git a/docs/tutorials2/en/quickstart.md b/docs/tutorials2/en/quickstart.md
deleted file mode 100644
index 63040e1..0000000
--- a/docs/tutorials2/en/quickstart.md
+++ /dev/null
@@ -1,137 +0,0 @@
-<div align="center">
-  <h1>Quick Start</h1>
-  <p>
-    <strong>English</strong> | <a href="../zh/quickstart.md">简体中文</a>
-  </p>
-</div>
-
-Get up and running with GPUMDkit in 5 minutes.
-
-## Prerequisites
-
-- Linux or macOS (Windows via WSL)
-- Python 3.8+ (3.12 recommended)
-- Git
-
-## Installation
-
-### Step 1: Clone
-
-```bash
-git clone https://github.com/zhyan0603/GPUMDkit.git
-cd GPUMDkit
-```
-
-### Step 2: Install
-
-```bash
-source ./install.sh
-```
-
-### Step 3: Reload Shell
-
-```bash
-source ~/.bashrc  # or source ~/.zshrc
-```
-
-### Step 4: Verify
-
-```bash
-gpumdkit.sh -h
-```
-
-## Python Dependencies
-
-```bash
-conda create -n gpumdkit python=3.12
-conda activate gpumdkit
-pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
-```
-
-> Make sure the `gpumdkit` environment is activated before using GPUMDkit.
-
-## Usage Modes
-
-### Interactive Mode
-
-```bash
-gpumdkit.sh
-```
-
-```
-           ____ ____  _   _ __  __ ____  _    _ _
-          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
-         | |  _| |_) | | | | |\/| | | | | |/ / | __|
-         | |_| |  __/| |_| | |  | | |_| |   <| | |_
-          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
-
-          GPUMDkit Version 1.5.5 (dev) (2026-05-10)
-
- ---------------------- GPUMD ------------------------
-  1) Format Conversion          2) Sample Structures
-  3) Workflow                   4) Calculators
-  5) Analyzer                   6) Visualization
-  7) Utilities                  0) Exit
- ------------>>
-```
-
-### Command-Line Mode
-
-```bash
-gpumdkit.sh -h                    # Show help
-gpumdkit.sh -pos2exyz POSCAR model.xyz  # Direct command
-```
-
-## First Examples
-
-### Convert Structure
-
-```bash
-gpumdkit.sh -pos2exyz POSCAR model.xyz
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-```
-
-### Analyze Data
-
-```bash
-gpumdkit.sh -range train.xyz force
-gpumdkit.sh -min_dist_pbc train.xyz
-gpumdkit.sh -analyze_comp train.xyz
-```
-
-### Plot Results
-
-```bash
-gpumdkit.sh -plt train
-gpumdkit.sh -plt msd
-gpumdkit.sh -plt rdf
-```
-
-## Getting Help
-
-```bash
-gpumdkit.sh -h              # General help
-gpumdkit.sh -plt -h         # Plot help
-gpumdkit.sh -calc -h        # Calculator help
-gpumdkit.sh -pos2exyz -h    # Specific command help
-```
-
-## Troubleshooting
-
-**Command not found**
-```bash
-export GPUMDkit_path=/path/to/GPUMDkit
-export PATH=${GPUMDkit_path}:${PATH}
-```
-
-**Missing packages**
-```bash
-conda activate gpumdkit
-```
-
-## Next Steps
-
-- [Format Conversion](format_conversion.md)
-- [Calculators](calculators.md)
-- [Visualization](visualization.md)
-- [NEP Training](nep_training.md)
diff --git a/docs/tutorials2/en/sampling.md b/docs/tutorials2/en/sampling.md
deleted file mode 100644
index d94c27d..0000000
--- a/docs/tutorials2/en/sampling.md
+++ /dev/null
@@ -1,88 +0,0 @@
-<div align="center">
-  <h1>Structure Sampling</h1>
-  <p>
-    <strong>English</strong> | <a href="../zh/sampling.md">简体中文</a>
-  </p>
-</div>
-
-Structure selection and sampling tools.
-
-## Available Methods
-
-| Method | Menu | Description |
-|--------|------|-------------|
-| Uniform/Random | 201 | Select evenly spaced or random frames |
-| FPS by NepTrain | 203 | Farthest point sampling (preferred) |
-| Perturbation | 204 | Generate perturbed structures |
-| Force Deviation | 205 | Select high-force-deviation structures |
-
-## Uniform/Random Sampling
-
-```bash
-python Scripts/sample_structures/sample_structures.py <input.xyz> <method> <num> [skip]
-
-# Examples
-python Scripts/sample_structures/sample_structures.py dump.xyz uniform 50
-python Scripts/sample_structures/sample_structures.py dump.xyz random 100 500
-```
-
-Output: `sampled_structures.xyz`
-
-## Farthest Point Sampling (FPS)
-
-```bash
-python Scripts/sample_structures/neptrain_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
-
-# Example
-python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
-```
-
-Output: `selected.xyz`, `select.png`
-
-## Structure Perturbation
-
-```bash
-python Scripts/sample_structures/perturb_structure.py <input.vasp> <num> <cell_pert> <atom_pert> <style>
-
-# Example
-python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
-```
-
-Parameters:
-- `num`: Number of perturbed structures
-- `cell_pert`: Cell perturbation fraction (e.g., 0.03 = 3%)
-- `atom_pert`: Atom perturbation distance (Angstrom)
-- `style`: `normal`, `uniform`, or `const`
-
-Output: `POSCAR_01.vasp`, `POSCAR_02.vasp`, ...
-
-## Force Deviation Selection
-
-```bash
-python Scripts/sample_structures/select_max_modev.py <top_n> <min_deviation>
-
-# Example
-python Scripts/sample_structures/select_max_modev.py 200 0.15
-```
-
-Required files: `active.out`, `active.xyz`
-
-Output: `selected.xyz`
-
-## Frame Range Extraction
-
-```bash
-python Scripts/sample_structures/frame_range.py <input.xyz> <start> <end>
-
-# Example: First 80% of frames
-python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
-```
-
-## Dependencies
-
-| Method | Packages |
-|--------|----------|
-| Uniform/Random | numpy, ase |
-| FPS | numpy, ase, matplotlib, scikit-learn, scipy, NepTrain |
-| Perturbation | dpdata |
-| Force Deviation | numpy, ase |
diff --git a/docs/tutorials2/en/visualization.md b/docs/tutorials2/en/visualization.md
deleted file mode 100644
index b698673..0000000
--- a/docs/tutorials2/en/visualization.md
+++ /dev/null
@@ -1,106 +0,0 @@
-<div align="center">
-  <h1>Visualization</h1>
-  <p>
-    <strong>English</strong> | <a href="../zh/visualization.md">简体中文</a>
-  </p>
-</div>
-
-Plotting and visualization tools for simulation results.
-
-## Quick Reference
-
-```bash
-gpumdkit.sh -plt <type>              # Display plot
-gpumdkit.sh -plt <type> save         # Save as PNG
-gpumdkit.sh -plt <type> -h           # Get help
-```
-
-## NEP Training Plots
-
-| Command | Description |
-|---------|-------------|
-| `train` | Training loss curves and parity plots |
-| `prediction` / `test` | Test set parity plots |
-| `train_test` | Combined train/test parity plots |
-| `force_errors` | Force error analysis |
-| `des` | Descriptor PCA/UMAP visualization |
-| `dimer` | Dimer interaction curves |
-| `charge` | Charge distribution (qNEP) |
-| `born_charge` / `bec` | Born effective charges |
-
-```bash
-gpumdkit.sh -plt train
-gpumdkit.sh -plt prediction
-gpumdkit.sh -plt force_errors
-gpumdkit.sh -plt des pca
-gpumdkit.sh -plt dimer Li Li nep.txt
-```
-
-## Transport Plots
-
-| Command | Description |
-|---------|-------------|
-| `msd` | Mean square displacement |
-| `sdc` | Self-diffusion coefficient |
-| `msd_sdc` | MSD and SDC combined |
-| `arrhenius_sigma` | Arrhenius ionic conductivity |
-| `arrhenius_d` | Arrhenius diffusivity |
-
-```bash
-gpumdkit.sh -plt msd
-gpumdkit.sh -plt sdc
-gpumdkit.sh -plt arrhenius_sigma
-gpumdkit.sh -plt arrhenius_d
-```
-
-## Structural Plots
-
-| Command | Description |
-|---------|-------------|
-| `thermo` | Thermodynamic properties |
-| `rdf` | Radial distribution function |
-| `rdf_pmf` | RDF + potential of mean force |
-| `vac` | Velocity autocorrelation |
-| `doas` | Density of atomistic states |
-| `net_force` | Net force distribution |
-
-```bash
-gpumdkit.sh -plt thermo
-gpumdkit.sh -plt rdf
-gpumdkit.sh -plt doas doas.out Li
-gpumdkit.sh -plt net_force train.xyz
-```
-
-## Heat Transport Plots
-
-| Command | Description |
-|---------|-------------|
-| `emd` | EMD thermal conductivity |
-| `nemd` | NEMD thermal transport |
-| `hnemd` | HNEMD thermal transport |
-| `viscosity` | Viscosity components |
-
-```bash
-gpumdkit.sh -plt emd x
-gpumdkit.sh -plt nemd <real_length> <scale_eff_size> <cutoff_freq> save
-gpumdkit.sh -plt hnemd <scale_eff_size> <cutoff_freq> save
-```
-
-## Output Files
-
-| Plot | PNG Filename |
-|------|--------------|
-| `train` | `train.png` |
-| `prediction` | `prediction.png` |
-| `msd` | `msd.png` |
-| `sdc` | `sdc.png` |
-| `thermo` | `thermo.png` |
-| `rdf` | `rdf.png` |
-| `arrhenius_sigma` | `Arrhenius_sigma.png` |
-| `arrhenius_d` | `Arrhenius_D.png` |
-
-## Dependencies
-
-```bash
-pip install matplotlib numpy
-```
diff --git a/docs/tutorials2/en/workflows.md b/docs/tutorials2/en/workflows.md
deleted file mode 100644
index f1d9d20..0000000
--- a/docs/tutorials2/en/workflows.md
+++ /dev/null
@@ -1,106 +0,0 @@
-<div align="center">
-  <h1>Workflows</h1>
-  <p>
-    <strong>English</strong> | <a href="../zh/workflows.md">简体中文</a>
-  </p>
-</div>
-
-Batch processing and workflow automation tools.
-
-## Available Workflows
-
-| Workflow | Menu | Description |
-|----------|------|-------------|
-| SCF Batch (VASP) | 301.1 | VASP single-point batch setup |
-| SCF Batch (CP2K) | 301.2 | CP2K single-point batch setup |
-| MD Batch (GPUMD) | 302 | GPUMD MD sampling batch setup |
-| MD Batch (LAMMPS) | 303 | LAMMPS MD sampling batch setup |
-
-## SCF Batch Pretreatment
-
-### VASP
-
-```bash
-gpumdkit.sh  # Select: 3) Workflow -> 301 -> VASP
-```
-
-Prerequisites:
-1. POSCAR files in current directory
-2. `fp/` directory with INCAR, POTCAR, KPOINTS
-
-Output: `<prefix>_1/`, `<prefix>_2/`, ..., `presub.sh`
-
-### CP2K
-
-```bash
-python Scripts/workflow/scf_batch_pretreatment_cp2k.py <extxyz> <template.inp> <prefix>
-```
-
-## MD Batch Pretreatment
-
-### GPUMD
-
-```bash
-gpumdkit.sh  # Select: 3) Workflow -> 302
-```
-
-Prerequisites:
-1. POSCAR files in current directory
-2. `md/` directory with `nep.txt`, `run_*.in`
-
-Output: `sample_1/`, `sample_2/`, ..., `presub.sh`
-
-### LAMMPS
-
-```bash
-gpumdkit.sh  # Select: 3) Workflow -> 303
-```
-
-Prerequisites:
-1. POSCAR files in current directory
-2. `md/` directory with `nep.txt`, `lmprun.in`
-
-## Active Learning
-
-Iterative NEP model improvement:
-
-```bash
-# 1. MD sampling
-gpumdkit.sh  # Select: 3) Workflow -> 302
-
-# 2. Filter and sample
-gpumdkit.sh -min_dist_pbc dump.xyz
-gpumdkit.sh -filter_box dump.xyz 13
-
-# 3. Prepare SCF
-gpumdkit.sh  # Select: 3) Workflow -> 301
-
-# 4. Run DFT (external)
-
-# 5. Retrain NEP
-```
-
-## Examples
-
-### Temperature-Dependent MD
-
-```bash
-for temp in 300 500 700 900; do
-    mkdir -p "${temp}K"
-    cp model.xyz "${temp}K/"
-    cp nep.txt "${temp}K/"
-    sed "s/TEMPERATURE/$temp/g" run_template.in > "${temp}K/run.in"
-done
-```
-
-### Batch Structure Preparation
-
-```bash
-for struct in structures/*.vasp; do
-    name=$(basename "$struct" .vasp)
-    mkdir -p "calc_$name"
-    cp "$struct" "calc_$name/POSCAR"
-    ln -s ../POTCAR "calc_$name/"
-    ln -s ../INCAR "calc_$name/"
-done
-```
diff --git a/docs/tutorials2/zh/analyzers.md b/docs/tutorials2/zh/analyzers.md
deleted file mode 100644
index b157391..0000000
--- a/docs/tutorials2/zh/analyzers.md
+++ /dev/null
@@ -1,92 +0,0 @@
-<div align="center">
-  <h1>分析工具</h1>
-  <p>
-    <strong>简体中文</strong> | <a href="../en/analyzers.md">English</a>
-  </p>
-</div>
-
-结构分析、验证和过滤工具。
-
-## 可用工具
-
-| 工具 | 命令 | 描述 |
-|------|------|------|
-| 成分分析 | `-analyze_comp` | 按成分分组结构 |
-| 属性范围 | `-range` | 能量/力/应力统计 |
-| 最小距离 | `-min_dist` | 计算最小距离（无 PBC） |
-| 最小距离 (PBC) | `-min_dist_pbc` | 计算最小距离（带 PBC） |
-| 电荷平衡 | `-cbc` | 检查氧化态平衡 |
-| 距离过滤 | `-filter_dist_pbc` | 按最小距离过滤 |
-| 盒子过滤 | `-filter_box` | 按盒子大小过滤 |
-| 值过滤 | `-filter_value` | 按属性值过滤 |
-| 距离范围 | `-filter_range` | 按元素对距离过滤 |
-| 时间监控 | `-time` | 监控 GPUMD/NEP 进度 |
-
-## 命令参考
-
-### 成分分析
-
-```bash
-gpumdkit.sh -analyze_comp train.xyz
-```
-
-### 属性范围
-
-```bash
-gpumdkit.sh -range <文件> <属性> [hist]
-
-# 示例
-gpumdkit.sh -range train.xyz force
-gpumdkit.sh -range train.xyz energy
-gpumdkit.sh -range train.xyz force hist
-```
-
-### 最小距离
-
-```bash
-# 快速（无 PBC）
-gpumdkit.sh -min_dist dump.xyz
-
-# 精确（带 PBC）
-gpumdkit.sh -min_dist_pbc dump.xyz
-```
-
-### 电荷平衡
-
-```bash
-gpumdkit.sh -cbc train.xyz
-```
-
-输出：`balanced.xyz`, `unbalanced.xyz`
-
-### 过滤
-
-```bash
-# 按最小距离
-gpumdkit.sh -filter_dist_pbc train.xyz 1.0
-
-# 按盒子大小
-gpumdkit.sh -filter_box dump.xyz 20
-
-# 按属性值
-gpumdkit.sh -filter_value train.xyz force 20
-
-# 按元素对距离范围
-gpumdkit.sh -filter_range dump.xyz Li Li 1.9 2.0
-```
-
-### 时间监控
-
-```bash
-gpumdkit.sh -time gpumd
-gpumdkit.sh -time nep
-```
-
-## 依赖
-
-| 工具 | 包 |
-|------|-----|
-| 所有 | ase, numpy |
-| 距离 | scipy |
-| 电荷平衡 | pymatgen, tqdm |
-| 属性范围 | matplotlib |
diff --git a/docs/tutorials2/zh/calculators.md b/docs/tutorials2/zh/calculators.md
deleted file mode 100644
index 3f696bd..0000000
--- a/docs/tutorials2/zh/calculators.md
+++ /dev/null
@@ -1,153 +0,0 @@
-<div align="center">
-  <h1>计算器</h1>
-  <p>
-    <strong>简体中文</strong> | <a href="../en/calculators.md">English</a>
-  </p>
-</div>
-
-从分子动力学数据计算材料属性。
-
-## 可用计算器
-
-| 计算器 | 命令 | 描述 |
-|--------|------|------|
-| 离子电导率 | `-calc ionic-cond` | 从 MSD 计算离子电导率 |
-| NEP 属性 | `-calc nep` | 使用 NEP 计算能量/力/应力 |
-| 描述符 | `-calc des` | 计算 NEP 描述符用于分析 |
-| DOAS | `-calc doas` | 原子态密度 |
-| MSD | `-calc msd` | 从轨迹计算均方位移 |
-| 邻居列表 | `-calc nlist` | 构建用于分析的邻居列表 |
-| 位移 | `-calc disp` | 计算原子位移 |
-| 平均结构 | `-calc avg-struct` | 从轨迹计算时间平均结构 |
-| 八面体倾斜 | `-calc oct-tilt` | 钙钛矿八面体倾斜角 |
-| 极化 | `-calc pol-abo3` | ABO3 局部极化 |
-| 最小化 | `-calc minimize` | 使用 NEP 进行结构弛豫 |
-| NEB | 直接 Python | 推移弹性带计算 |
-
-## 命令参考
-
-### 离子电导率
-
-```bash
-gpumdkit.sh -calc ionic-cond <元素> <电荷>
-
-# 示例
-gpumdkit.sh -calc ionic-cond Li 1    # Li+
-gpumdkit.sh -calc ionic-cond O -2    # O2-
-```
-
-需要文件：`msd.out`, `thermo.out`, `model.xyz`, `run.in`
-
-### NEP 属性
-
-```bash
-gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep.txt>
-
-# 示例
-gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
-```
-
-### 描述符
-
-```bash
-gpumdkit.sh -calc des <input.xyz> <output.npy> <nep.txt> <元素>
-
-# 示例
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-```
-
-可视化：`gpumdkit.sh -plt des pca` 或 `gpumdkit.sh -plt des umap`
-
-### DOAS
-
-```bash
-gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>
-
-# 示例
-gpumdkit.sh -calc doas structures.xyz nep.txt doas.out
-```
-
-### MSD
-
-```bash
-gpumdkit.sh -calc msd <trajectory.xyz> <元素> <dt_fs> [max_corr_steps]
-
-# 示例
-gpumdkit.sh -calc msd dump.xyz Li 10
-```
-
-输出：`msd.out`（时间/ps, MSD_x, MSD_y, MSD_z）
-
-### 邻居列表
-
-```bash
-gpumdkit.sh -calc nlist -i <input> -c <cutoff> -n <num> -C <中心元素> -E <邻居元素>
-
-# 示例
-gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O
-```
-
-### 位移
-
-```bash
-gpumdkit.sh -calc disp -i <trajectory.xyz> -n <邻居列表> -o <输出>
-
-# 示例
-gpumdkit.sh -calc disp -i movie.xyz -n nl-Pb-O.dat -o displacements.dat
-```
-
-### 平均结构
-
-```bash
-gpumdkit.sh -calc avg-struct -i <trajectory.xyz> -l <比例> -o <输出>
-
-# 示例：平均最后 20% 的帧
-gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged.xyz
-```
-
-### 八面体倾斜
-
-```bash
-gpumdkit.sh -calc oct-tilt -i <input.xyz> -n <B-O 列表> -o <输出>
-
-# 示例
-gpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o tilt.dat
-```
-
-### 极化 (ABO3)
-
-```bash
-gpumdkit.sh -calc pol-abo3 -i <input.xyz> --nl-ba <B-A 列表> --nl-bo <B-O 列表> --bec <元素=电荷 ...>
-
-# 示例
-gpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat --bec Pb=2.5 Ti=4.0 O=-2.0
-```
-
-### 最小化
-
-```bash
-gpumdkit.sh -calc minimize <结构> <nep.txt> [fmax] [max_steps]
-
-# 示例
-gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
-```
-
-输出：`minimize.xyz`
-
-### NEB
-
-```bash
-python Scripts/calculators/neb_calculation.py <initial.xyz> <final.xyz> <n_images> <nep.txt>
-
-# 示例
-python Scripts/calculators/neb_calculation.py init.xyz fin.xyz 9 nep.txt
-```
-
-## 依赖
-
-| 计算器 | 包 |
-|--------|-----|
-| 所有 | numpy, ase |
-| ionic-cond | scipy |
-| nep, des, doas, minimize | calorine |
-| nlist, disp, oct-tilt, pol-abo3 | ferrodispcalc |
diff --git a/docs/tutorials2/zh/format_conversion.md b/docs/tutorials2/zh/format_conversion.md
deleted file mode 100644
index 277c22b..0000000
--- a/docs/tutorials2/zh/format_conversion.md
+++ /dev/null
@@ -1,100 +0,0 @@
-<div align="center">
-  <h1>格式转换</h1>
-  <p>
-    <strong>简体中文</strong> | <a href="../en/format_conversion.md">English</a>
-  </p>
-</div>
-
-在计算材料科学文件格式之间转换。
-
-## 支持的格式
-
-| 格式 | 扩展名 | 软件 |
-|------|--------|------|
-| VASP | POSCAR, OUTCAR, XDATCAR, vasprun.xml | VASP |
-| LAMMPS | .data, dump.* | LAMMPS |
-| CP2K | .log, pos.xyz, frc.xyz, cell.cell | CP2K |
-| ABACUS | running_scf.log, running_md.log | ABACUS |
-| CIF | .cif | 各种软件 |
-| MTP | .cfg | MTP |
-| ASE | .traj | ASE |
-| extxyz | .xyz | 各种软件（主要格式） |
-
-## 快速参考
-
-```bash
-# VASP
-gpumdkit.sh -out2xyz <目录>              # OUTCAR -> extxyz
-gpumdkit.sh -pos2exyz POSCAR model.xyz   # POSCAR -> extxyz
-gpumdkit.sh -exyz2pos structures.xyz     # extxyz -> POSCAR
-
-# LAMMPS
-gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl  # LAMMPS -> extxyz
-gpumdkit.sh -pos2lmp POSCAR lammps.data        # POSCAR -> LAMMPS
-
-# CIF
-gpumdkit.sh -cif2pos input.cif POSCAR.vasp     # CIF -> POSCAR
-gpumdkit.sh -cif2exyz input.cif model.xyz      # CIF -> extxyz
-
-# 其他
-gpumdkit.sh -xdat2exyz XDATCAR output.xyz      # XDATCAR -> extxyz
-gpumdkit.sh -traj2exyz input.traj output.xyz   # ASE 轨迹 -> extxyz
-```
-
-## 结构操作
-
-```bash
-# 添加组标签（NEP 必需）
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-
-# 添加权重
-gpumdkit.sh -addweight input.xyz output.xyz 2.0
-
-# 复制结构
-gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2
-gpumdkit.sh -replicate POSCAR supercell.vasp 256  # 按原子数
-
-# 提取帧（从 0 开始）
-gpumdkit.sh -get_frame trajectory.xyz 1000
-
-# 清理元数据
-gpumdkit.sh -clean_xyz input.xyz clean.xyz
-```
-
-## 示例
-
-### 转换 VASP 输出
-
-```bash
-gpumdkit.sh -out2xyz .
-gpumdkit.sh -addgroup POSCAR Pb Ti O
-```
-
-### 准备 LAMMPS 模拟
-
-```bash
-gpumdkit.sh -pos2lmp POSCAR system.data
-# 模拟后
-gpumdkit.sh -lmp2exyz dump.lammpstrj Li P S
-```
-
-### 批量转换
-
-```bash
-for dir in run_*; do
-    gpumdkit.sh -out2xyz "$dir"
-done
-```
-
-## 注意事项
-
-- extxyz 是 GPUMDkit 的主要格式
-- GPUMD/NEP 需要组标签
-- 帧索引从 0 开始
-- LAMMPS 元素顺序必须与原子类型 ID 匹配
-
-## 依赖
-
-```bash
-pip install ase numpy
-```
diff --git a/docs/tutorials2/zh/nep_training.md b/docs/tutorials2/zh/nep_training.md
deleted file mode 100644
index 449897d..0000000
--- a/docs/tutorials2/zh/nep_training.md
+++ /dev/null
@@ -1,113 +0,0 @@
-<div align="center">
-  <h1>NEP 训练指南</h1>
-  <p>
-    <strong>简体中文</strong> | <a href="../en/nep_training.md">English</a>
-  </p>
-</div>
-
-训练 NEP（神经演化势）模型的完整工作流。
-
-## 概述
-
-1. **数据准备** - 转换和组织训练数据
-2. **质量检查** - 验证和过滤结构
-3. **采样** - 选择多样化结构
-4. **训练** - 训练 NEP 模型（外部）
-5. **验证** - 检查训练质量
-6. **主动学习** - 迭代改进模型
-
-## 步骤 1：数据准备
-
-```bash
-# 转换 DFT 数据
-gpumdkit.sh -out2xyz ./vasp_results/
-
-# 添加组标签
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-
-# 合并训练数据
-cat */model.xyz > train.xyz
-```
-
-## 步骤 2：质量检查
-
-```bash
-# 检查成分
-gpumdkit.sh -analyze_comp train.xyz
-
-# 检查距离
-gpumdkit.sh -min_dist_pbc train.xyz
-
-# 检查力范围
-gpumdkit.sh -range train.xyz force
-
-# 过滤结构
-gpumdkit.sh -filter_dist_pbc train.xyz 1.0
-```
-
-## 步骤 3：采样
-
-```bash
-# FPS 采样（推荐）
-gpumdkit.sh  # 选择: 2) Sample Structures -> 203
-
-# 或均匀采样
-python Scripts/sample_structures/sample_structures.py train.xyz uniform 100
-```
-
-## 步骤 4：训练
-
-创建 `nep.in`：
-
-```
-type 3 Li Y Cl
-cutoff 6 4
-n_max 4
-l_max 4
-neuron 100
-batch 1000
-generation 100000
-```
-
-运行训练：
-
-```bash
-gpumd
-```
-
-## 步骤 5：验证
-
-```bash
-# 绘制训练结果
-gpumdkit.sh -plt train
-gpumdkit.sh -plt prediction
-gpumdkit.sh -plt force_errors
-
-# 分析描述符
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
-gpumdkit.sh -plt des pca
-```
-
-## 步骤 6：主动学习
-
-```bash
-# 使用当前 NEP 运行 MD
-gpumdkit.sh  # 选择: 3) Workflow -> 302
-
-# 过滤和采样
-gpumdkit.sh -min_dist_pbc dump.xyz
-gpumdkit.sh -filter_box dump.xyz 13
-
-# 准备 DFT 计算
-gpumdkit.sh  # 选择: 3) Workflow -> 301
-
-# 用新数据重新训练
-cat new_structures.xyz >> train.xyz
-```
-
-## 建议
-
-- 包含多样化的结构、温度和成分
-- 至少 1000-5000 个结构以获得良好精度
-- 保留 10-20% 的数据用于测试
-- 训练前检查异常值
diff --git a/docs/tutorials2/zh/quickstart.md b/docs/tutorials2/zh/quickstart.md
deleted file mode 100644
index b8c30f6..0000000
--- a/docs/tutorials2/zh/quickstart.md
+++ /dev/null
@@ -1,137 +0,0 @@
-<div align="center">
-  <h1>快速入门</h1>
-  <p>
-    <strong>简体中文</strong> | <a href="../en/quickstart.md">English</a>
-  </p>
-</div>
-
-5 分钟内开始使用 GPUMDkit。
-
-## 前提条件
-
-- Linux 或 macOS（Windows 通过 WSL）
-- Python 3.8+（推荐 3.12）
-- Git
-
-## 安装
-
-### 步骤 1：克隆
-
-```bash
-git clone https://github.com/zhyan0603/GPUMDkit.git
-cd GPUMDkit
-```
-
-### 步骤 2：安装
-
-```bash
-source ./install.sh
-```
-
-### 步骤 3：重新加载 Shell
-
-```bash
-source ~/.bashrc  # 或 source ~/.zshrc
-```
-
-### 步骤 4：验证
-
-```bash
-gpumdkit.sh -h
-```
-
-## Python 依赖
-
-```bash
-conda create -n gpumdkit python=3.12
-conda activate gpumdkit
-pip install neptrain ase pymatgen dpdata numpy scipy matplotlib
-```
-
-> 使用 GPUMDkit 前请确保已激活 `gpumdkit` 环境。
-
-## 使用模式
-
-### 交互模式
-
-```bash
-gpumdkit.sh
-```
-
-```
-           ____ ____  _   _ __  __ ____  _    _ _
-          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
-         | |  _| |_) | | | | |\/| | | | | |/ / | __|
-         | |_| |  __/| |_| | |  | | |_| |   <| | |_
-          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
-
-          GPUMDkit Version 1.5.5 (dev) (2026-05-10)
-
- ---------------------- GPUMD ------------------------
-  1) Format Conversion          2) Sample Structures
-  3) Workflow                   4) Calculators
-  5) Analyzer                   6) Visualization
-  7) Utilities                  0) Exit
- ------------>>
-```
-
-### 命令行模式
-
-```bash
-gpumdkit.sh -h                    # 显示帮助
-gpumdkit.sh -pos2exyz POSCAR model.xyz  # 直接命令
-```
-
-## 第一个例子
-
-### 转换结构
-
-```bash
-gpumdkit.sh -pos2exyz POSCAR model.xyz
-gpumdkit.sh -addgroup POSCAR Li Y Cl
-```
-
-### 分析数据
-
-```bash
-gpumdkit.sh -range train.xyz force
-gpumdkit.sh -min_dist_pbc train.xyz
-gpumdkit.sh -analyze_comp train.xyz
-```
-
-### 绘制结果
-
-```bash
-gpumdkit.sh -plt train
-gpumdkit.sh -plt msd
-gpumdkit.sh -plt rdf
-```
-
-## 获取帮助
-
-```bash
-gpumdkit.sh -h              # 通用帮助
-gpumdkit.sh -plt -h         # 绘图帮助
-gpumdkit.sh -calc -h        # 计算器帮助
-gpumdkit.sh -pos2exyz -h    # 特定命令帮助
-```
-
-## 故障排除
-
-**命令未找到**
-```bash
-export GPUMDkit_path=/path/to/GPUMDkit
-export PATH=${GPUMDkit_path}:${PATH}
-```
-
-**缺少包**
-```bash
-conda activate gpumdkit
-```
-
-## 下一步
-
-- [格式转换](format_conversion.md)
-- [计算器](calculators.md)
-- [可视化](visualization.md)
-- [NEP 训练](nep_training.md)
diff --git a/docs/tutorials2/zh/sampling.md b/docs/tutorials2/zh/sampling.md
deleted file mode 100644
index 056da8a..0000000
--- a/docs/tutorials2/zh/sampling.md
+++ /dev/null
@@ -1,88 +0,0 @@
-<div align="center">
-  <h1>结构采样</h1>
-  <p>
-    <strong>简体中文</strong> | <a href="../en/sampling.md">English</a>
-  </p>
-</div>
-
-结构选择和采样工具。
-
-## 可用方法
-
-| 方法 | 菜单 | 描述 |
-|------|------|------|
-| 均匀/随机 | 201 | 选择均匀间隔或随机帧 |
-| FPS by NepTrain | 203 | 最远点采样（推荐） |
-| 扰动 | 204 | 生成扰动结构 |
-| 力偏差 | 205 | 选择高力偏差结构 |
-
-## 均匀/随机采样
-
-```bash
-python Scripts/sample_structures/sample_structures.py <input.xyz> <method> <num> [skip]
-
-# 示例
-python Scripts/sample_structures/sample_structures.py dump.xyz uniform 50
-python Scripts/sample_structures/sample_structures.py dump.xyz random 100 500
-```
-
-输出：`sampled_structures.xyz`
-
-## 最远点采样 (FPS)
-
-```bash
-python Scripts/sample_structures/neptrain_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
-
-# 示例
-python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
-```
-
-输出：`selected.xyz`, `select.png`
-
-## 结构扰动
-
-```bash
-python Scripts/sample_structures/perturb_structure.py <input.vasp> <num> <cell_pert> <atom_pert> <style>
-
-# 示例
-python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
-```
-
-参数：
-- `num`：扰动结构数量
-- `cell_pert`：晶胞扰动比例（如 0.03 = 3%）
-- `atom_pert`：原子扰动距离（埃）
-- `style`：`normal`, `uniform` 或 `const`
-
-输出：`POSCAR_01.vasp`, `POSCAR_02.vasp`, ...
-
-## 力偏差选择
-
-```bash
-python Scripts/sample_structures/select_max_modev.py <top_n> <min_deviation>
-
-# 示例
-python Scripts/sample_structures/select_max_modev.py 200 0.15
-```
-
-需要文件：`active.out`, `active.xyz`
-
-输出：`selected.xyz`
-
-## 帧范围提取
-
-```bash
-python Scripts/sample_structures/frame_range.py <input.xyz> <start> <end>
-
-# 示例：前 80% 的帧
-python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
-```
-
-## 依赖
-
-| 方法 | 包 |
-|------|-----|
-| 均匀/随机 | numpy, ase |
-| FPS | numpy, ase, matplotlib, scikit-learn, scipy, NepTrain |
-| 扰动 | dpdata |
-| 力偏差 | numpy, ase |
diff --git a/docs/tutorials2/zh/visualization.md b/docs/tutorials2/zh/visualization.md
deleted file mode 100644
index cd58dbe..0000000
--- a/docs/tutorials2/zh/visualization.md
+++ /dev/null
@@ -1,106 +0,0 @@
-<div align="center">
-  <h1>可视化</h1>
-  <p>
-    <strong>简体中文</strong> | <a href="../en/visualization.md">English</a>
-  </p>
-</div>
-
-模拟结果的绘图和可视化工具。
-
-## 快速参考
-
-```bash
-gpumdkit.sh -plt <类型>              # 显示图表
-gpumdkit.sh -plt <类型> save         # 保存为 PNG
-gpumdkit.sh -plt <类型> -h           # 获取帮助
-```
-
-## NEP 训练图表
-
-| 命令 | 描述 |
-|------|------|
-| `train` | 训练损失曲线和对比图 |
-| `prediction` / `test` | 测试集对比图 |
-| `train_test` | 组合训练/测试对比图 |
-| `force_errors` | 力误差分析 |
-| `des` | 描述符 PCA/UMAP 可视化 |
-| `dimer` | 二聚体相互作用曲线 |
-| `charge` | 电荷分布 (qNEP) |
-| `born_charge` / `bec` | Born 有效电荷 |
-
-```bash
-gpumdkit.sh -plt train
-gpumdkit.sh -plt prediction
-gpumdkit.sh -plt force_errors
-gpumdkit.sh -plt des pca
-gpumdkit.sh -plt dimer Li Li nep.txt
-```
-
-## 传输属性图表
-
-| 命令 | 描述 |
-|------|------|
-| `msd` | 均方位移 |
-| `sdc` | 自扩散系数 |
-| `msd_sdc` | MSD 和 SDC 组合 |
-| `arrhenius_sigma` | Arrhenius 离子电导率 |
-| `arrhenius_d` | Arrhenius 扩散率 |
-
-```bash
-gpumdkit.sh -plt msd
-gpumdkit.sh -plt sdc
-gpumdkit.sh -plt arrhenius_sigma
-gpumdkit.sh -plt arrhenius_d
-```
-
-## 结构图表
-
-| 命令 | 描述 |
-|------|------|
-| `thermo` | 热力学属性 |
-| `rdf` | 径向分布函数 |
-| `rdf_pmf` | RDF + 平均力势 |
-| `vac` | 速度自相关 |
-| `doas` | 原子态密度 |
-| `net_force` | 净力分布 |
-
-```bash
-gpumdkit.sh -plt thermo
-gpumdkit.sh -plt rdf
-gpumdkit.sh -plt doas doas.out Li
-gpumdkit.sh -plt net_force train.xyz
-```
-
-## 热传输图表
-
-| 命令 | 描述 |
-|------|------|
-| `emd` | EMD 热导率 |
-| `nemd` | NEMD 热传输 |
-| `hnemd` | HNEMD 热传输 |
-| `viscosity` | 粘度分量 |
-
-```bash
-gpumdkit.sh -plt emd x
-gpumdkit.sh -plt nemd <real_length> <scale_eff_size> <cutoff_freq> save
-gpumdkit.sh -plt hnemd <scale_eff_size> <cutoff_freq> save
-```
-
-## 输出文件
-
-| 图表 | PNG 文件名 |
-|------|-----------|
-| `train` | `train.png` |
-| `prediction` | `prediction.png` |
-| `msd` | `msd.png` |
-| `sdc` | `sdc.png` |
-| `thermo` | `thermo.png` |
-| `rdf` | `rdf.png` |
-| `arrhenius_sigma` | `Arrhenius_sigma.png` |
-| `arrhenius_d` | `Arrhenius_D.png` |
-
-## 依赖
-
-```bash
-pip install matplotlib numpy
-```
diff --git a/docs/tutorials2/zh/workflows.md b/docs/tutorials2/zh/workflows.md
deleted file mode 100644
index 14b6e51..0000000
--- a/docs/tutorials2/zh/workflows.md
+++ /dev/null
@@ -1,106 +0,0 @@
-<div align="center">
-  <h1>工作流</h1>
-  <p>
-    <strong>简体中文</strong> | <a href="../en/workflows.md">English</a>
-  </p>
-</div>
-
-批处理和工作流自动化工具。
-
-## 可用工作流
-
-| 工作流 | 菜单 | 描述 |
-|--------|------|------|
-| SCF 批处理 (VASP) | 301.1 | VASP 单点批处理设置 |
-| SCF 批处理 (CP2K) | 301.2 | CP2K 单点批处理设置 |
-| MD 批处理 (GPUMD) | 302 | GPUMD MD 采样批处理设置 |
-| MD 批处理 (LAMMPS) | 303 | LAMMPS MD 采样批处理设置 |
-
-## SCF 批处理
-
-### VASP
-
-```bash
-gpumdkit.sh  # 选择: 3) Workflow -> 301 -> VASP
-```
-
-前提条件：
-1. POSCAR 文件在当前目录
-2. `fp/` 目录包含 INCAR, POTCAR, KPOINTS
-
-输出：`<prefix>_1/`, `<prefix>_2/`, ..., `presub.sh`
-
-### CP2K
-
-```bash
-python Scripts/workflow/scf_batch_pretreatment_cp2k.py <extxyz> <template.inp> <prefix>
-```
-
-## MD 批处理
-
-### GPUMD
-
-```bash
-gpumdkit.sh  # 选择: 3) Workflow -> 302
-```
-
-前提条件：
-1. POSCAR 文件在当前目录
-2. `md/` 目录包含 `nep.txt`, `run_*.in`
-
-输出：`sample_1/`, `sample_2/`, ..., `presub.sh`
-
-### LAMMPS
-
-```bash
-gpumdkit.sh  # 选择: 3) Workflow -> 303
-```
-
-前提条件：
-1. POSCAR 文件在当前目录
-2. `md/` 目录包含 `nep.txt`, `lmprun.in`
-
-## 主动学习
-
-迭代改进 NEP 模型：
-
-```bash
-# 1. MD 采样
-gpumdkit.sh  # 选择: 3) Workflow -> 302
-
-# 2. 过滤和采样
-gpumdkit.sh -min_dist_pbc dump.xyz
-gpumdkit.sh -filter_box dump.xyz 13
-
-# 3. 准备 SCF
-gpumdkit.sh  # 选择: 3) Workflow -> 301
-
-# 4. 运行 DFT（外部）
-
-# 5. 重新训练 NEP
-```
-
-## 示例
-
-### 温度依赖的 MD
-
-```bash
-for temp in 300 500 700 900; do
-    mkdir -p "${temp}K"
-    cp model.xyz "${temp}K/"
-    cp nep.txt "${temp}K/"
-    sed "s/TEMPERATURE/$temp/g" run_template.in > "${temp}K/run.in"
-done
-```
-
-### 批量结构准备
-
-```bash
-for struct in structures/*.vasp; do
-    name=$(basename "$struct" .vasp)
-    mkdir -p "calc_$name"
-    cp "$struct" "calc_$name/POSCAR"
-    ln -s ../POTCAR "calc_$name/"
-    ln -s ../INCAR "calc_$name/"
-done
-```
diff --git a/gpumdkit.sh b/gpumdkit.sh
index 1100830..0e355c1 100755
--- a/gpumdkit.sh
+++ b/gpumdkit.sh
@@ -188,13 +188,38 @@ function help_info_table(){
     echo "| -chem_species Analyze chemical species        | -cbc               Charge balance check               |"
     echo "| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |"
     echo "| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |"
-    echo "| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |"
-    echo "| -pynep        FPS sampling by PyNEP           | -filter_box        Filter by box-edge length          |"
+    echo "| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |"
+    echo "| -pynep        Deprecated PyNEP sampling       |                                                       |"
     echo "+-------------------------------------------------------------------------------------------------------+"
     echo "| Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |"
     echo "+-------------------------------------------------------------------------------------------------------+"
 }
 
+function calculator_help_table(){
+    echo "+-------------------------------------------------------------------------------------------------------+"
+    echo "|                                      CALCULATOR TOOLS                                                 |"
+    echo "+-------------------------------------------------------------------------------------------------------+"
+    echo "| Usage: gpumdkit.sh -calc <type> [args...]                                                             |"
+    echo "+-------------------------------------------------------------------------------------------------------+"
+    echo "| ionic-cond <element> <charge>                 Calculate ionic conductivity from MSD data              |"
+    echo "| nep <input.xyz> <output.xyz> <nep_model>      Calculate energy/force/virial with a NEP model          |"
+    echo "| des <input.xyz> <output.npy> <nep_model> <el> Calculate NEP descriptors for one element               |"
+    echo "| doas <input.xyz> <nep_model> <output.txt>     Calculate density of atomistic states                   |"
+    echo "| neb <initial.xyz> <final.xyz> <n_images> <nep> Run NEB calculation with a NEP model                   |"
+    echo "| minimize <structure> <nep_model> [fmax] [n]   Minimize a structure with a NEP model                   |"
+    echo "| msd <trajectory.xyz> <element> <dt_fs> [n]    Calculate MSD from an extxyz trajectory                 |"
+    echo "| nlist [script args...]                        Build neighbor lists                                    |"
+    echo "| disp [script args...]                         Calculate displacement from trajectory                  |"
+    echo "| avg-struct [script args...]                   Calculate averaged structure                            |"
+    echo "| oct-tilt [script args...]                     Calculate octahedral tilt                               |"
+    echo "| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |"
+    echo "+-------------------------------------------------------------------------------------------------------+"
+    echo "| Examples: gpumdkit.sh -calc ionic-cond Li 1                                                           |"
+    echo "|           gpumdkit.sh -calc msd dump.xyz Li 10                                                        |"
+    echo "|           gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O                                  |"
+    echo "+-------------------------------------------------------------------------------------------------------+"
+}
+
 # function citation(){
 # echo "+-----------------------------------------------------------------------+"
 # echo "|                     THANK YOU FOR USING GPUMDKIT                      |"
@@ -308,12 +333,24 @@ if [ ! -z "$1" ]; then
                             echo " Code path: ${calc_path}/calc_ion_conductivity.py"
                             python ${calc_path}/calc_ion_conductivity.py $3 $4
                         else
-                            echo " Usage: -calc ion-cond <element> <charge>"
-                            echo " Examp: gpumdkit.sh -calc ion-cond Li 1"
+                            echo " Usage: -calc ionic-cond <element> <charge>"
+                            echo " Example: gpumdkit.sh -calc ionic-cond Li 1"
                             echo " See the codes in calculators folder for more details"
                             echo " Code path: ${calc_path}/calc_ion_conductivity.py"
                             exit 1
                         fi ;;
+                    neb)
+                        if [ ! -z "$3" ] && [ ! -z "$4" ] && [ ! -z "$5" ] && [ ! -z "$6" ]; then
+                            echo " Calling script by Zhoulin LIU. "
+                            echo " Code path: ${calc_path}/neb_calculation.py"
+                            python ${calc_path}/neb_calculation.py ${@:3}
+                        else
+                            echo " Usage: -calc neb <initial_structure> <final_structure> <n_images> <nep_model>"
+                            echo " Example: gpumdkit.sh -calc neb init.xyz final.xyz 9 nep.txt"
+                            echo " See the codes in calculators folder for more details"
+                            echo " Code path: ${calc_path}/neb_calculation.py"
+                            exit 1
+                        fi ;;
                     nep)
                         if [ ! -z "$3" ] && [ ! -z "$4" ] && [ ! -z "$5" ]; then
                             echo " Calling script by Zihan YAN. "
@@ -321,7 +358,7 @@ if [ ! -z "$1" ]; then
                             python ${calc_path}/calc_properties_with_nep.py $3 $4 $5
                         else
                             echo " Usage: -calc nep <input.xyz> <output.xyz> <nep_model>"
-                            echo " Examp: gpumdkit.sh -calc nep input.xyz output.xyz nep.txt"
+                            echo " Example: gpumdkit.sh -calc nep input.xyz output.xyz nep.txt"
                             echo " See the codes in calculators folder for more details"
                             echo " Code path: ${calc_path}/calc_properties_with_nep.py"
                             exit 1
@@ -333,7 +370,7 @@ if [ ! -z "$1" ]; then
                             python ${calc_path}/calc_descriptors.py $3 $4 $5 $6
                         else
                             echo " Usage: -calc des <input.xyz> <output.npy> <nep_model> <element>"
-                            echo " Examp: gpumdkit.sh -calc des train.xyz des_Li.npy nep.txt Li"
+                            echo " Example: gpumdkit.sh -calc des train.xyz des_Li.npy nep.txt Li"
                             echo " See the codes in calculators folder for more details"
                             echo " Code path: ${calc_path}/calc_descriptors.py"
                             exit 1
@@ -345,7 +382,7 @@ if [ ! -z "$1" ]; then
                             python ${calc_path}/calc_doas.py $3 $4 $5
                         else
                             echo " Usage: -calc doas <input.xyz> <nep_model> <output_file>"
-                            echo " Examp: gpumdkit.sh -calc doas dump.xyz nep.txt doas.out"
+                            echo " Example: gpumdkit.sh -calc doas dump.xyz nep.txt doas.out"
                             echo " See the codes in calculators folder for more details"
                             echo " Code path: ${calc_path}/calc_doas.py"
                             exit 1
@@ -383,8 +420,7 @@ if [ ! -z "$1" ]; then
                         echo " Code path: ${calc_path}"; exit 1 ;;
                 esac
             else
-                echo " See the codes in calculators folder for more details"
-                echo " Code path: ${calc_path}"
+                calculator_help_table
             fi ;;
 
         -range)
@@ -598,7 +634,7 @@ if [ ! -z "$1" ]; then
                 echo " Code path: ${analyzer_path}/filter_structures_by_distance.py"
                 python ${analyzer_path}/filter_structures_by_distance.py $2 $3
             else
-                echo " Usage: -filter_xyz <exyzfile> <min_dist>"
+                echo " Usage: -filter_dist <exyzfile> <min_dist>"
                 echo " See the source code of filter_structures_by_distance.py for more details"
                 echo " Code path: ${analyzer_path}/filter_structures_by_distance.py"
             fi ;;
@@ -609,7 +645,7 @@ if [ ! -z "$1" ]; then
                 echo " Code path: ${analyzer_path}/filter_structures_by_distance_pbc.py"
                 python ${analyzer_path}/filter_structures_by_distance_pbc.py $2 $3
             else
-                echo " Usage: -filter_xyz_pbc <exyzfile> <min_dist>"
+                echo " Usage: -filter_dist_pbc <exyzfile> <min_dist>"
                 echo " See the source code of filter_structures_by_distance_pbc.py for more details"
                 echo " Code path: ${analyzer_path}/filter_structures_by_distance_pbc.py"
             fi ;;
@@ -679,7 +715,7 @@ if [ ! -z "$1" ]; then
                 python ${sample_path}/frame_range.py $2 $3 $4
             else
                 echo " Usage: -frame_range <exyzfile> <start_frac> <end_frac>"
-                echo " Examp: gpumdkit.sh -frame_range dump.xyz 0.2 0.5"
+                echo " Example: gpumdkit.sh -frame_range dump.xyz 0.2 0.5"
                 echo " See the source code of frame_range.py for more details"
                 echo " Code path: ${sample_path}/frame_range.py"
             fi ;;
@@ -705,7 +741,7 @@ if [ ! -z "$1" ]; then
                 python ${analyzer_path}/probability_density_analysis.py $2 $3 $4 $5
             else
                 echo " Usage: -pda <ref_struct> <trajectory_file> <species> <interval>"
-                echo " Examp: gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25"
+                echo " Example: gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25"
                 echo " See the source code of probability_density_analysis.py for more details"
                 echo " Code path: ${analyzer_path}/probability_density_analysis.py"
             fi ;;
diff --git a/install.sh b/install.sh
index 3e94417..5fb1035 100644
--- a/install.sh
+++ b/install.sh
@@ -12,22 +12,37 @@ echo "       ${INSTALL_DIR}"
 # 2. Determine the Shell configuration file
 RC_FILE="$HOME/.bashrc"
 if [[ "$SHELL" == *"zsh"* ]]; then
-    if [ -f "$HOME/.zshrc" ]; then
-        RC_FILE="$HOME/.zshrc"
-    fi
+    RC_FILE="$HOME/.zshrc"
 fi
+touch "$RC_FILE"
 echo " [2/4] Detecting shell configuration..."
 echo "       Target: ${RC_FILE}"
 
-# 3. Write environment variables
-# Check if the configuration already exists to prevent duplicate entries
-if grep -q "export GPUMDkit_path=" "$RC_FILE"; then
-    echo "       Warning: GPUMDkit configuration already exists."
-    echo "       Skipping environment variable setup to avoid duplicates."
-else
-    echo "       Adding environment variables to ${RC_FILE}"
+backup_rc_file() {
+    local backup_file="${RC_FILE}.gpumdkit.bak.$(date +%Y%m%d_%H%M%S)"
+    cp "$RC_FILE" "$backup_file"
+    echo "       Backup created: ${backup_file}"
+}
+
+remove_old_gpumdkit_config() {
+    local tmp_file
+    tmp_file=$(mktemp)
+
+    # Remove the managed GPUMDkit block first.
+    awk '
+        /^########### GPUMDkit Configuration ###########$/ { in_block=1; next }
+        /^##############################################$/ && in_block { in_block=0; next }
+        !in_block { print }
+    ' "$RC_FILE" > "$tmp_file"
+
+    # Remove older single-line GPUMDkit entries if they were not inside the block.
+    grep -v -E '(^export GPUMDkit_path=|^export PATH=\$\{GPUMDkit_path\}:\$\{PATH\}$|^source \$\{GPUMDkit_path\}/Scripts/utils/completion\.sh$)' "$tmp_file" > "${tmp_file}.clean"
+    mv "${tmp_file}.clean" "$RC_FILE"
+    rm -f "$tmp_file"
+}
 
-    # Append the configuration block
+write_gpumdkit_config() {
+    echo "       Adding environment variables to ${RC_FILE}"
     {
         echo ""
         echo "########### GPUMDkit Configuration ###########"
@@ -42,6 +57,29 @@ else
     } >> "$RC_FILE"
 
     echo "       Success: Environment variables added."
+}
+
+# 3. Write environment variables
+if grep -q "export GPUMDkit_path=" "$RC_FILE"; then
+    current_paths=$(grep "export GPUMDkit_path=" "$RC_FILE" | sed 's/^[[:space:]]*export GPUMDkit_path=//')
+    echo "       Existing GPUMDkit configuration found."
+    echo "       Existing path(s):"
+    echo "$current_paths" | sed 's/^/         - /'
+    echo "       New path:"
+    echo "         - ${INSTALL_DIR}"
+    echo ""
+    read -r -p "       Replace the existing GPUMDkit configuration with the new path? [y/N]: " replace_config
+
+    if [[ "$replace_config" == [yY]* ]]; then
+        backup_rc_file
+        remove_old_gpumdkit_config
+        write_gpumdkit_config
+    else
+        echo "       Keeping existing GPUMDkit configuration."
+    fi
+else
+    backup_rc_file
+    write_gpumdkit_config
 fi
 
 # 4. Set executable permissions
diff --git a/skills/README.md b/skills/README.md
index dcebae2..342d42c 100644
--- a/skills/README.md
+++ b/skills/README.md
@@ -14,6 +14,7 @@ to effectively use GPUMDkit functionality.
 | [gpumdkit-visualization](gpumdkit-visualization/SKILL.md) | Plotting and visualization |
 | [gpumdkit-workflows](gpumdkit-workflows/SKILL.md) | Batch processing and automation |
 | [gpumdkit-sampling](gpumdkit-sampling/SKILL.md) | Structure sampling and selection |
+| [gpumdkit-contributing](gpumdkit-contributing/SKILL.md) | Code conventions and adding new features |
 
 ## Usage with Different Agent Tools
 
@@ -42,6 +43,7 @@ ln -s ../../skills/gpumdkit-analyzers .
 ln -s ../../skills/gpumdkit-visualization .
 ln -s ../../skills/gpumdkit-workflows .
 ln -s ../../skills/gpumdkit-sampling .
+ln -s ../../skills/gpumdkit-contributing .
 cd ../..
 ```
 
@@ -60,6 +62,7 @@ ln -s ../../skills/gpumdkit-analyzers .
 ln -s ../../skills/gpumdkit-visualization .
 ln -s ../../skills/gpumdkit-workflows .
 ln -s ../../skills/gpumdkit-sampling .
+ln -s ../../skills/gpumdkit-contributing .
 cd ../..
 ```
 
diff --git a/skills/gpumdkit-analyzers/SKILL.md b/skills/gpumdkit-analyzers/SKILL.md
index 3eb946e..fa6d3d1 100644
--- a/skills/gpumdkit-analyzers/SKILL.md
+++ b/skills/gpumdkit-analyzers/SKILL.md
@@ -20,11 +20,11 @@ allowed-tools: Bash(gpumdkit *) Bash(python3 *)
 | Chemical Species | Menu 503 | List unique elements |
 | Charge Balance | `-cbc` | Check oxidation-state balance |
 | Property Range | `-range` | Energy/force/virial statistics |
-| Distance Filter | Menu 506 | Filter by minimum distance (no PBC) |
-| Distance Filter (PBC) | Menu 506b | Filter by minimum distance (with PBC) |
+| Distance Filter | `-filter_dist` or Menu 506 | Filter by minimum distance (no PBC) |
+| Distance Filter (PBC) | `-filter_dist_pbc` | Filter by minimum distance with PBC |
 | Minimum Distance | `-min_dist` | Calculate min distances (no PBC) |
 | Minimum Distance (PBC) | `-min_dist_pbc` | Calculate min distances (with PBC) |
-| Probability Density | Menu 508 | 3D diffusion channel analysis |
+| Probability Density | `-pda` or Menu 508 | 3D diffusion channel analysis |
 
 ## Command Reference
 
@@ -86,14 +86,13 @@ gpumdkit.sh  # Select: 5) Analyzer -> 503
 
 #### By Minimum Distance (No PBC)
 ```bash
-gpumdkit.sh  # Select: 5) Analyzer -> 506
-# Input: extxyz file, distance threshold
+gpumdkit.sh -filter_dist dump.xyz 1.5
 # Output: filtered_<file>.xyz, filtered_out_<file>.xyz
 ```
 
 #### By Minimum Distance (With PBC)
 ```bash
-gpumdkit.sh  # Select: 5) Analyzer -> 506b
+gpumdkit.sh -filter_dist_pbc dump.xyz 1.5
 # More accurate for periodic systems
 ```
 
@@ -138,9 +137,9 @@ gpumdkit.sh  # Select: 5) Analyzer -> 502
 ### Probability Density Analysis
 ```bash
 # Calculate 3D probability density of mobile ions
-gpumdkit.sh  # Select: 5) Analyzer -> 508
+gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25
 
-# Parameters (interactive):
+# Parameters:
 # - Reference structure (POSCAR)
 # - Trajectory file (extxyz)
 # - Mobile species (e.g., Li)
@@ -170,7 +169,7 @@ gpumdkit.sh  # Select: 5) Analyzer -> 502
 ### Structure Filtering Pipeline
 ```bash
 # 1. Filter by distance
-gpumdkit.sh  # Select: 5) Analyzer -> 506
+gpumdkit.sh -filter_dist_pbc dump.xyz 1.5
 
 # 2. Filter by box size
 gpumdkit.sh -filter_box filtered.xyz 20
@@ -182,7 +181,7 @@ gpumdkit.sh -filter_value filtered_by_box.xyz force 15
 ### Diffusion Channel Analysis
 ```bash
 # 1. Calculate probability density
-gpumdkit.sh  # Select: 5) Analyzer -> 508
+gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25
 
 # 2. Visualize with VESTA or similar
 # Open probability_density_0.25.vasp
@@ -215,6 +214,8 @@ python Scripts/analyzer/get_volume.py
 | `-min_dist` | Min distance (no PBC) | `gpumdkit.sh -min_dist <file>` |
 | `-min_dist_pbc` | Min distance (PBC) | `gpumdkit.sh -min_dist_pbc <file>` |
 | `-cbc` | Charge balance | `gpumdkit.sh -cbc <file>` |
+| `-filter_dist` | Filter by minimum distance | `gpumdkit.sh -filter_dist <file> <min_dist>` |
+| `-filter_dist_pbc` | Filter by minimum distance with PBC | `gpumdkit.sh -filter_dist_pbc <file> <min_dist>` |
 | `-filter_range` | Filter by distance range | `gpumdkit.sh -filter_range <file> <e1> <e2> <min> <max>` |
 | `-filter_box` | Filter by box size | `gpumdkit.sh -filter_box <file> <limit>` |
 | `-filter_value` | Filter by property | `gpumdkit.sh -filter_value <file> <prop> <thresh>` |
@@ -232,4 +233,4 @@ python Scripts/analyzer/get_volume.py
 
 ## Detailed Documentation
 
-See [analyzer.md](../../docs/tutorials/analyzer.md) for comprehensive guide.
+See [analyzer_scripts.md](../../docs/tutorials/en/analyzer_scripts.md) for comprehensive guide.
diff --git a/skills/gpumdkit-calculators/SKILL.md b/skills/gpumdkit-calculators/SKILL.md
index a1f71ef..4038d9a 100644
--- a/skills/gpumdkit-calculators/SKILL.md
+++ b/skills/gpumdkit-calculators/SKILL.md
@@ -238,4 +238,4 @@ pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
 
 ## Detailed Documentation
 
-See [calculators.md](../../docs/tutorials/calculators.md) for comprehensive guide.
+See [calculator_scripts.md](../../docs/tutorials/en/calculator_scripts.md) for comprehensive guide.
diff --git a/skills/gpumdkit-contributing/SKILL.md b/skills/gpumdkit-contributing/SKILL.md
new file mode 100644
index 0000000..c104e7d
--- /dev/null
+++ b/skills/gpumdkit-contributing/SKILL.md
@@ -0,0 +1,289 @@
+---
+name: gpumdkit-contributing
+description: >
+  Use when adding new features, commands, or scripts to GPUMDkit.
+  Provides coding conventions, file structure patterns, and step-by-step guides
+  for implementing new interactive menu items, CLI flags, calculators, analyzers,
+  format converters, plotting scripts, and workflow tools.
+  Use when user asks about: adding a new command, creating a new script,
+  contributing to GPUMDkit, code conventions, or how to extend the toolkit.
+allowed-tools: Bash(gpumdkit *) Bash(python3 *) Bash(python *) Bash(ls *) Bash(mkdir *)
+---
+
+# GPUMDkit Contributing Guide
+
+## Project Structure
+
+```
+GPUMDkit/
+├── gpumdkit.sh              # Main entry: CLI routing + interactive menu
+├── install.sh               # Installation script
+├── src/                     # Shell menu modules (interactive mode wrappers)
+│   ├── f1_format_conversions.sh
+│   ├── f2_sample_structures.sh
+│   ├── f3_workflows.sh
+│   ├── f4_calculators.sh
+│   ├── f5_analyzers.sh
+│   ├── f6_plots.sh
+│   └── f7_utilities.sh
+├── Scripts/                 # Implementation scripts (Python + Bash)
+│   ├── format_conversion/
+│   ├── sample_structures/
+│   ├── workflow/
+│   ├── calculators/
+│   ├── analyzer/
+│   ├── plt_scripts/
+│   └── utils/
+├── skills/                  # AI agent skill definitions
+├── docs/                    # Documentation
+│   ├── tutorials/en/        # English tutorials
+│   ├── tutorials/zh/        # Chinese tutorials
+│   ├── mkdocs.yml           # MkDocs config
+│   └── htmls/               # Generated HTML
+```
+
+## How Routing Works
+
+`gpumdkit.sh` has two modes:
+
+1. **Interactive mode**: `gpumdkit.sh` (no arguments) → shows numbered menu
+   - User selects a category (1-7) → sources the corresponding `src/fN_*.sh`
+   - User selects a function (e.g., 403) → calls the function (e.g., `f403_calc_descriptors`)
+   - The function prompts for input, calls a Python/Bash script from `Scripts/`, prints the code path
+
+2. **CLI mode**: `gpumdkit.sh -flag [args]` → routes via `case $1 in`
+   - Each flag maps to a script in `Scripts/`
+   - Help messages go in `help_info_table()` and `calculator_help_table()`
+
+## Adding a New Interactive Mode Feature
+
+### Step 1: Create the implementation script
+
+Place it in the appropriate `Scripts/` subdirectory:
+
+```bash
+# Python script example: Scripts/calculators/calc_new_feature.py
+```
+
+### Step 2: Add a wrapper function in `src/fN_*.sh`
+
+Follow this exact pattern:
+
+```bash
+function f413_new_feature(){
+echo " >-------------------------------------------------<"
+echo " | Calling the script in Scripts/calculators       |"
+echo " | Script: calc_new_feature.py                     |"
+echo " | Developer: Your Name (your@email.com)           |"
+echo " >-------------------------------------------------<"
+echo " Input <param1> <param2> [optional_param3]"
+echo " Example: input.xyz nep.txt"
+echo " ------------>>"
+read -r -a feature_args
+echo " ---------------------------------------------------"
+python ${GPUMDkit_path}/Scripts/calculators/calc_new_feature.py "${feature_args[@]}"
+echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_new_feature.py"
+echo " ---------------------------------------------------"
+}
+```
+
+Key conventions:
+- Banner uses `>-----<` and `| ... |` format
+- `echo " Input <...>"` describes parameters
+- `echo " Example: ..."` shows a concrete example (not "Examp:")
+- `read -r -a varname` reads into an array
+- `"${varname[@]}"` passes all arguments properly quoted
+- Function name format: `f<Category><Number>_<descriptive_name>`
+
+### Step 3: Register in `gpumdkit.sh`
+
+1. Add the choice number to `array_choice` (line ~57)
+2. Add the case in the `main()` function's nested case statement:
+   ```bash
+   "413") f413_new_feature ;;
+   ```
+
+### Step 4: Update the menu display in `src/f6_plots.sh` or the relevant `fN_*.sh`
+
+If it's a calculator, update the calculator menu display in `f4_calculators.sh`.
+
+## Adding a New CLI Flag
+
+### Step 1: Create the implementation script
+
+Same as above — place in `Scripts/`.
+
+### Step 2: Add the CLI handler in `gpumdkit.sh`
+
+Add a new case in the main `case $1 in` block:
+
+```bash
+-new_flag)
+    if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ]; then
+        python ${analyzer_path}/new_script.py $2 $3
+    else
+        echo " Usage: -new_flag <param1> <param2>"
+        echo " Example: gpumdkit.sh -new_flag input.xyz 3.0"
+        echo " Code path: ${analyzer_path}/new_script.py"
+    fi ;;
+```
+
+Key conventions:
+- Check `$2 != "-h"` to handle help requests
+- No quotes around `$2`, `$3` in the python call (paths with spaces not supported)
+- No `exit 1` in the else branch (just print usage and fall through)
+- Place alphabetically among existing flags for readability
+
+### Step 3: Add to help table
+
+Update `help_info_table()` or `calculator_help_table()` in `gpumdkit.sh`:
+
+```bash
+echo "| -new_flag  Description of new flag           | -existing_flag    Description                   |"
+```
+
+### Step 4: Update tab completion
+
+Edit `Scripts/utils/completion.sh`:
+
+1. Add `-new_flag` to the `opts` string (line 16)
+2. If it needs file completion, add it to the `|`-separated case (line 33):
+   ```bash
+   -out2xyz|-...|-new_flag)
+       COMPREPLY=($(compgen -f -- "$cur")) ;;
+   ```
+3. If it needs secondary options, add a new case block
+
+## Python Script Conventions
+
+### File header
+
+```python
+"""
+Script:     new_script.py
+Category:   Calculator Scripts
+Purpose:    Brief description of what this script does.
+Usage:      python new_script.py <param1> <param2>
+Arguments:
+  param1    Description of param1
+  param2    Description of param2
+Author:     Your Name (your@email.com)
+"""
+```
+
+### Argument parsing
+
+Use `sys.argv` for simple scripts (most common pattern):
+
+```python
+import sys
+
+if len(sys.argv) != 3:
+    print("Usage: python new_script.py <param1> <param2>")
+    print("Example: python new_script.py input.xyz nep.txt")
+    sys.exit(1)
+
+param1 = sys.argv[1]
+param2 = sys.argv[2]
+```
+
+Use `argparse` only if the script has many optional flags with complex defaults.
+
+### Main guard (optional)
+
+GPUMDkit scripts run directly — a `main()` function with `if __name__ == "__main__":` guard is optional. Most existing scripts execute at module level. Use whichever style you prefer, but do not wrap the entire script in a `main()` function just for the sake of it.
+
+### Dependency notices
+
+If your script requires a heavy/special package (`NepTrain`, `calorine`, `dpdata`), add a notice:
+
+```python
+def print_dependency_notice():
+    print("This function requires the 'calorine' package.")
+    print("If you use this function, please cite:")
+    print("  Bochkov et al., npj Comput Mater 6, 170 (2020)")
+
+# Call it early in the script
+print_dependency_notice()
+```
+
+Do NOT add notices for common packages like `ase`, `numpy`, `pymatgen`.
+
+### Error messages
+
+```python
+# Good
+print("Error: File 'input.xyz' not found.")
+sys.exit(1)
+
+# Avoid
+raise FileNotFoundError("input.xyz")
+```
+
+## Shell Script Conventions
+
+### File header (in `src/`)
+
+```bash
+# ============================================================
+# GPUMDkit <module name> module
+# Repository: https://github.com/zhyan0603/GPUMDkit
+# Author: Your Name (your@email.com)
+# ============================================================
+```
+
+### Variable checks
+
+```bash
+# Non-empty check (project convention)
+if [ ! -z "$var" ]; then
+    ...
+fi
+
+# Not the -h flag check
+if [ ! -z "$2" ] && [ "$2" != "-h" ]; then
+    ...
+fi
+```
+
+### Interactive menu pattern
+
+```bash
+function f413_new_feature(){
+echo " >-------------------------------------------------<"
+echo " | Calling the script in Scripts/calculators       |"
+echo " | Script: calc_new_feature.py                     |"
+echo " | Developer: Your Name (your@email.com)           |"
+echo " >-------------------------------------------------<"
+echo " Input <param1> <param2>"
+echo " Example: input.xyz nep.txt"
+echo " ------------>>"
+read -r -a feature_args
+echo " ---------------------------------------------------"
+python ${GPUMDkit_path}/Scripts/calculators/calc_new_feature.py "${feature_args[@]}"
+echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_new_feature.py"
+echo " ---------------------------------------------------"
+}
+```
+
+## Validation Checklist
+
+Before committing, run these checks:
+
+```bash
+# Shell syntax
+bash -n gpumdkit.sh
+find src Scripts -name '*.sh' -exec bash -n {} +
+
+# Python syntax
+python3 -m py_compile Scripts/path/to/your_script.py
+
+# Clean up __pycache__ after py_compile
+find . -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null
+
+# MkDocs build (if docs changed)
+mkdocs build -f docs/mkdocs.yml
+
+# Whitespace check
+git diff --check
+```
diff --git a/skills/gpumdkit-format-conversion/SKILL.md b/skills/gpumdkit-format-conversion/SKILL.md
index 630501e..6e3397e 100644
--- a/skills/gpumdkit-format-conversion/SKILL.md
+++ b/skills/gpumdkit-format-conversion/SKILL.md
@@ -14,7 +14,7 @@ allowed-tools: Bash(gpumdkit *) Bash(python3 *)
 
 | Format | Extensions | Description |
 |--------|-----------|-------------|
-| VASP | POSCAR, OUTCAR, XDATCAR, vasprun.xml | Vienna Ab initio Simulation Package |
+| VASP | POSCAR, OUTCAR, XDATCAR | Vienna Ab initio Simulation Package |
 | LAMMPS | .data, dump.* | Large-scale Atomic/Molecular Massively Parallel Simulator |
 | CP2K | .log, pos.xyz, frc.xyz, cell.cell | Quantum chemistry and solid state physics |
 | ABACUS | running_scf.log, running_md.log | Atomic-orbital Based Ab-initio Computation at UStc |
@@ -170,4 +170,4 @@ Most Python scripts require:
 
 ## Detailed Documentation
 
-See [format_conversion.md](../../docs/tutorials/format_conversion.md) for comprehensive guide.
+See [format_conversion.md](../../docs/tutorials/en/format_conversion.md) for comprehensive guide.
diff --git a/skills/gpumdkit-main/SKILL.md b/skills/gpumdkit-main/SKILL.md
index 4015515..1392c31 100644
--- a/skills/gpumdkit-main/SKILL.md
+++ b/skills/gpumdkit-main/SKILL.md
@@ -145,9 +145,9 @@ gpumdkit.sh -range train.xyz energy
 
 ## Detailed Documentation
 
-- [Format Conversion Guide](../../docs/tutorials/format_conversion.md)
-- [Calculators Guide](../../docs/tutorials/calculators.md)
-- [Analyzer Guide](../../docs/tutorials/analyzer.md)
-- [Visualization Guide](../../docs/tutorials/plot_scripts.md)
-- [Workflow Guide](../../docs/tutorials/workflow.md)
-- [Sampling Guide](../../docs/tutorials/sample_structures.md)
+- [Format Conversion Guide](../../docs/tutorials/en/format_conversion.md)
+- [Calculators Guide](../../docs/tutorials/en/calculator_scripts.md)
+- [Analyzer Guide](../../docs/tutorials/en/analyzer_scripts.md)
+- [Visualization Guide](../../docs/tutorials/en/plot_scripts.md)
+- [Workflow Guide](../../docs/tutorials/en/workflow_scripts.md)
+- [Sampling Guide](../../docs/tutorials/en/structure_sampling.md)
diff --git a/skills/gpumdkit-sampling/SKILL.md b/skills/gpumdkit-sampling/SKILL.md
index fe04dd8..68ee56e 100644
--- a/skills/gpumdkit-sampling/SKILL.md
+++ b/skills/gpumdkit-sampling/SKILL.md
@@ -16,7 +16,8 @@ allowed-tools: Bash(gpumdkit *) Bash(python3 *)
 | Method | Menu | Description |
 |--------|------|-------------|
 | Uniform/Random | 201 | Select evenly spaced or random frames |
-| FPS by PyNEP | 202 | Farthest point sampling (deprecated) |
+| PyNEP notice | 202 | Prints a notice only; run PyNEP through `gpumdkit.sh -pynep` |
+| FPS by PyNEP | `-pynep` | Farthest point sampling (deprecated compatibility entry) |
 | FPS by NepTrain | 203 | Farthest point sampling (preferred) |
 | Perturbation | 204 | Generate perturbed structures |
 | Force Deviation | 205 | Select high-force-deviation structures |
@@ -77,8 +78,8 @@ python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz n
 #### Using PyNEP (Deprecated)
 
 ```bash
-# Direct execution
-python Scripts/sample_structures/pynep_select_structs.py <sample.xyz> <train.xyz> <nep.txt>
+# GPUMDkit entry
+gpumdkit.sh -pynep
 
 # Note: PyNEP package is no longer actively maintained
 # Use NepTrain (method 203) instead
@@ -189,14 +190,14 @@ python Scripts/sample_structures/perturb_structure.py POSCAR 50 0.05 0.3 uniform
 # 4. Add to training set
 ```
 
-### Parallel FPS Sampling (Advanced)
+### PyNEP Compatibility Path
 
 ```bash
-# Parallel version for large datasets
-python Scripts/sample_structures/parallel_pynep_select_structs.py <sample.xyz> <train.xyz> <nep.txt> [threads]
+# gpumdkit.sh -pynep calls the parallel PyNEP compatibility script.
+gpumdkit.sh -pynep
 
-# Example with 8 threads
-python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8
+# Example input after launching:
+dump.xyz train.xyz nep.txt 8
 ```
 
 ## Dependencies
@@ -225,4 +226,4 @@ pip install neptrain  # For FPS by NepTrain
 
 ## Detailed Documentation
 
-See [sample_structures.md](../../docs/tutorials/sample_structures.md) for comprehensive guide.
+See [structure_sampling.md](../../docs/tutorials/en/structure_sampling.md) for comprehensive guide.
diff --git a/skills/gpumdkit-visualization/SKILL.md b/skills/gpumdkit-visualization/SKILL.md
index 74147ba..60bb237 100644
--- a/skills/gpumdkit-visualization/SKILL.md
+++ b/skills/gpumdkit-visualization/SKILL.md
@@ -213,4 +213,4 @@ All plotting scripts require:
 
 ## Detailed Documentation
 
-See [plot_scripts.md](../../docs/tutorials/plot_scripts.md) for comprehensive guide.
+See [plot_scripts.md](../../docs/tutorials/en/plot_scripts.md) for comprehensive guide.
diff --git a/skills/gpumdkit-workflows/SKILL.md b/skills/gpumdkit-workflows/SKILL.md
index c0a52b8..c7fa63a 100644
--- a/skills/gpumdkit-workflows/SKILL.md
+++ b/skills/gpumdkit-workflows/SKILL.md
@@ -220,5 +220,5 @@ gpumdkit.sh  # Select: 3) Workflow -> 301
 
 ## Detailed Documentation
 
-- [Workflow Guide](../../docs/tutorials/workflow.md)
-- [Active Learning Guide](../../docs/tutorials/workflow_active_learning.md)
+- [Workflow Guide](../../docs/tutorials/en/workflow_scripts.md)
+- [Active Learning Guide](../../docs/tutorials/en/active_learning_workflow.md)
diff --git a/src/README.md b/src/README.md
index 4bef1b9..3c2cce6 100644
--- a/src/README.md
+++ b/src/README.md
@@ -9,7 +9,7 @@ Contains functions for format conversion operations (Interactive mode `option 1`
 
 **Functions:**
 
-- `f101_out2xyz` - Convert VASP OUTCAR or vasprun.xml to extxyz
+- `f101_out2xyz` - Convert VASP OUTCAR to extxyz
 - `f102_mtp2xyz` - Convert MTP .cfg format to extxyz
 - `cp2k2xyz_chenhua` - Convert CP2K to extxyz (method by Chen HUA)
 - `cp2k2xyz_kexu` - Convert CP2K to extxyz (method by Ke XU)
@@ -35,8 +35,7 @@ Contains functions for structure sampling (Interactive mode `option 2`).
 
 **Functions:**
 - `f201_sample_structures` - Sample structures using uniform or random methods
-- `f202_pynep_sample_structures` - Sample structures using farthest point sampling (powered by PyNEP)
-- `parallel_pynep_sample_structures` - Parallel version of pynep sampling with multi-processing
+- `parallel_pynep_sample_structures` - Compatibility PyNEP sampling path used by `gpumdkit.sh -pynep`
 - `f203_neptrain_sample_structures` - Sample structures using farthest point sampling (powered by NepTrain)
 - `f204_perturb_structure` - Generate perturbed structures
 - `f205_select_max_force_deviation_structs` - Select structures with high force deviations
@@ -116,15 +115,15 @@ then you will see:
        | |_| |  __/| |_| | |  | | |_| |   <| | |_
         \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
 
-        GPUMDkit Version 1.5.5 (dev) (2026-05-16)
+        GPUMDkit Version 1.5.6 (dev) (2026-06-17)
   Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
 
  ----------------------- GPUMD -----------------------
   1) Format Conversion          2) Sample Structures
   3) Workflow                   4) Calculators
-  5) Analyzer                   6) Plots
-  7) Utilities
-  0) Quit!
+  5) Analyzer                   6) Visualization
+  7) Utilities                  8) Developing...
+  0) Exit
  ------------>>
  Input the function number:
 ```
diff --git a/src/f1_format_conversions.sh b/src/f1_format_conversions.sh
index a373b15..ee2d3b3 100644
--- a/src/f1_format_conversions.sh
+++ b/src/f1_format_conversions.sh
@@ -6,40 +6,21 @@
 # Author: Zihan YAN (yanzihan@westlake.edu.cn)
 # ============================================================
 
-# Convert VASP to extxyz
+# Convert VASP OUTCAR to extxyz
 function f101_out2xyz(){
 echo " >-------------------------------------------------<"
 echo " | Calling the script in Scripts/format_conversion |"
 echo " | Script: out2xyz.sh                              |"
 echo " | Developer: Yanzhou WANG (yanzhowang@gmail.com)  |"
 echo " >-------------------------------------------------<"
-echo " Choose the type of conversion:"
-echo " 1) OUTCAR to extxyz"
-echo " 2) vasprun.xml to extxyz"
+echo " Input the directory containing OUTCARs"
+echo " Example: ./ "
 echo " ------------>>"
-read -p " " outcar_type
-if [ "$outcar_type" == "1" ]; then
-    echo " Input the directory containing OUTCARs"
-    echo " Examp: ./ "
-    echo " ------------>>"
-    read -p " " dir_outcars
-    echo " ---------------------------------------------------"
-    bash ${GPUMDkit_path}/Scripts/format_conversion/out2xyz.sh ${dir_outcars}
-    echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/out2xyz.sh"
-    echo " ---------------------------------------------------"
-elif [ "$outcar_type" == "2" ]; then
-    echo " Input the directory containing vasprun.xml files"
-    echo " Examp: ./ "
-    echo " ------------>>"
-    read -p " " dir_vasprun
-    echo " ---------------------------------------------------"
-    python ${GPUMDkit_path}/Scripts/format_conversion/xml2xyz.py ${dir_vasprun}
-    echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/xml2xyz.py"
-    echo " ---------------------------------------------------"
-else
-    echo " Your input is illegal, please try again"
-    return
-fi
+read -p " " dir_outcars
+echo " ---------------------------------------------------"
+bash ${GPUMDkit_path}/Scripts/format_conversion/out2xyz.sh ${dir_outcars}
+echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/out2xyz.sh"
+echo " ---------------------------------------------------"
 }
 
 # Convert mtp to extxyz
@@ -50,7 +31,7 @@ echo " | Script: mtp2xyz.py                              |"
 echo " | Developer: Ke XU (kickhsu@gmail.com)            |"
 echo " >-------------------------------------------------<"
 echo " Input <filename.cfg> <Symbol1 Symbol2 Symbol3 ...>"
-echo " Examp: train.cfg Pd Ag"
+echo " Example: train.cfg Pd Ag"
 echo " ------------>>"
 read -p " " mtp_variables
 echo " ---------------------------------------------------"
@@ -127,7 +108,7 @@ echo " ------------>>"
 read -p " " abacus_type
 if [ "$abacus_type" == "1" ]; then
     echo " Input the directory containing running_scf.log"
-    echo " Examp: ./ "
+    echo " Example: ./ "
     echo " ------------>>"
     read -p " " dir_abacus_scf
     echo " ---------------------------------------------------"
@@ -156,7 +137,7 @@ echo " | Script: exyz2pos.py                             |"
 echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
 echo " >-------------------------------------------------<"
 echo " Input the name of extxyz"
-echo " Examp: ./train.xyz "
+echo " Example: ./train.xyz "
 echo " ------------>>"
 read -p " " filename
 echo " ---------------------------------------------------"
diff --git a/src/f2_sample_structures.sh b/src/f2_sample_structures.sh
index 936ad4d..9f6e4c7 100644
--- a/src/f2_sample_structures.sh
+++ b/src/f2_sample_structures.sh
@@ -16,7 +16,7 @@ echo " >-------------------------------------------------<"
 echo " Input <extxyz_file> <sampling_method> <num_samples> [skip_num]"
 echo " [skip_num]: number of initial frames to skip, default value is 0"
 echo " Sampling_method: 'uniform' or 'random'"
-echo " Examp: train.xyz uniform 50 "
+echo " Example: train.xyz uniform 50 "
 echo " ------------>>"
 read -p " " sample_choice
 echo " ---------------------------------------------------"
@@ -25,16 +25,15 @@ echo " Code path: ${GPUMDkit_path}/Scripts/sample_structures/sample_structures.p
 echo " ---------------------------------------------------"
 }
 
-# Sample structures by pynep
+# PyNEP sampling is kept only as a direct command-line compatibility entry.
 function f202_pynep_sample_structures(){
 echo " +-------------------------------------------------+"
-echo " |  Function 202 (pynep sampling) is deprecated.   |"
-echo " |  PyNEP package is no longer actively maintained.|"
-echo " |  Please use 203) neptrain sampling instead.     |"
-echo " |  If you still insist on pynep, run directly:    |"
+echo " | Function 202 is no longer supported here.       |"
+echo " | PyNEP package is no longer actively maintained. |"
+echo " | Please use 203) NepTrain sampling instead.      |"
+echo " | If you still need PyNEP compatibility, run:     |"
 echo " |                 gpumdkit.sh -pynep              |"
 echo " +-------------------------------------------------+"
-exit 0
 }
 
 # Parallel sample structures by pynep
@@ -52,9 +51,9 @@ echo " | Calling the script in Scripts/sample_structures |"
 echo " | Script: parallel_pynep_select_structs.py        |"
 echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
 echo " >-------------------------------------------------<"
-echo " Input <sample.xyz> <train.xyz> <nep_model>"
-echo " Examp: dump.xyz train.xyz nep.txt [threads]"
-echo " [threads]: number of CPU threads to use, default value is cpu_count"
+echo " Input <sample.xyz> <train.xyz> <nep_model> <threads>"
+echo " Example: dump.xyz train.xyz nep.txt 8"
+echo " <threads>: number of CPU threads to use"
 echo " ------------>>"
 read -p " " sample_choice
 echo " ---------------------------------------------------"
@@ -71,7 +70,7 @@ echo " | Script: neptrain_select_structs.py              |"
 echo " | Developer: Benrui TANG (tang070205@proton.me)   |"
 echo " >-------------------------------------------------<"
 echo " Input <sample.xyz> <train.xyz> <nep_model>"
-echo " Examp: dump.xyz train.xyz nep.txt "
+echo " Example: dump.xyz train.xyz nep.txt "
 echo " ------------>>"
 read -p " " sample_choice
 echo " ---------------------------------------------------"
@@ -95,8 +94,8 @@ echo " | Script: perturb_structure.py                    |"
 echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
 echo " >-------------------------------------------------<"
 echo " Input <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>"
-echo " The default paramters for perturb are 20 0.03 0.2 uniform"
-echo " Examp: POSCAR 20 0.03 0.2 uniform"
+echo " The default parameters for perturb are 20 0.03 0.2 uniform"
+echo " Example: POSCAR 20 0.03 0.2 uniform"
 echo " ------------>>"
 read -p " " perturb_choice
 echo " ---------------------------------------------------"
@@ -131,7 +130,7 @@ echo " +------------------------------------------------------+"
 echo " |                 SAMPLE STRUCTURE TOOLS               |"
 echo " +------------------------------------------------------+"
 echo " | 201) Sample structures from extxyz                   |"
-echo " | 202) FPS sampling by PyNEP [deprecated]              |"
+echo " | 202) PyNEP sampling [deprecated]                    |"
 echo " | 203) FPS sampling by NepTrain [preferred]            |"
 echo " | 204) Perturb structure                               |"
 echo " | 205) Select max force deviation structs              |"
diff --git a/src/f3_workflows.sh b/src/f3_workflows.sh
index 5794c27..53fb8ba 100644
--- a/src/f3_workflows.sh
+++ b/src/f3_workflows.sh
@@ -27,7 +27,7 @@ fi
 
 echo " ---------------------------------------------------"
 echo " Input <extxyz_file> <template.inp> <prefix_name>"
-echo " Examp: dump.xyz template.inp H2O"
+echo " Example: dump.xyz template.inp H2O"
 echo " ------------>>"
 read -p " " input_results
 echo " ---------------------------------------------------"
diff --git a/src/f4_calculators.sh b/src/f4_calculators.sh
index cbb1cbf..dc9923d 100644
--- a/src/f4_calculators.sh
+++ b/src/f4_calculators.sh
@@ -30,7 +30,7 @@ echo " | Script: calc_properties_with_nep.py             |"
 echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
 echo " >-------------------------------------------------<"
 echo " Input <input.xyz> <output.xyz> <nep_model> "
-echo " Examp: input.xyz output.xyz nep.txt"
+echo " Example: input.xyz output.xyz nep.txt"
 echo " ------------>>"
 read -p " " input_calc_properties
 echo " ---------------------------------------------------"
@@ -47,7 +47,7 @@ echo " | Script: calc_descriptors.py                     |"
 echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
 echo " >-------------------------------------------------<"
 echo " Input <input.xyz> <output.npy> <nep_model> <element>"
-echo " Examp: train.xyz des_Li.npy nep.txt Li"
+echo " Example: train.xyz des_Li.npy nep.txt Li"
 echo " ------------>>"
 read -p " " input_calc_descriptors
 echo " ---------------------------------------------------"
@@ -64,7 +64,7 @@ echo " | Script: calc_doas.py                            |"
 echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
 echo " >-------------------------------------------------<"
 echo " Input <input.xyz> <nep_model> <output_file>"
-echo " Examp: dump.xyz nep.txt doas.out"
+echo " Example: dump.xyz nep.txt doas.out"
 echo " ------------>>"
 read -p " " input_calc_doas
 echo " ---------------------------------------------------"
@@ -81,7 +81,7 @@ echo " | Script: neb_calculation.py                      |"
 echo " | Developer: Zhoulin LIU (1776627910@qq.com)      |"
 echo " >-------------------------------------------------<"
 echo " Input <initial_struct> <final_struct> <n_image> <nep_model>"
-echo " Examp: IS.xyz FS.xyz 5 nep.txt"
+echo " Example: IS.xyz FS.xyz 5 nep.txt"
 echo " ------------>>"
 read -p " " input_calc_neb
 echo " ---------------------------------------------------"
diff --git a/src/f5_analyzers.sh b/src/f5_analyzers.sh
index 8bc0c24..a25d69d 100644
--- a/src/f5_analyzers.sh
+++ b/src/f5_analyzers.sh
@@ -62,7 +62,7 @@ echo " | Script: charge_balance_check.py                 |"
 echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
 echo " >-------------------------------------------------<"
 echo " Input <input.xyz> you want to analyze"
-echo " Examp: train.xyz"
+echo " Example: train.xyz"
 echo " ------------>>"
 read -p " " input_extxyz
 echo " ---------------------------------------------------"

From 29f60f14374a52abc50a2e3a980ddf19608345a3 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Tue, 30 Jun 2026 16:49:55 +0800
Subject: [PATCH 12/24] update

---
 README.md                                     |   2 +-
 Scripts/README.md                             |   1 -
 Scripts/analyzer/analyze_chem_species.py      |  14 +-
 Scripts/analyzer/analyze_composition.py       |   8 +-
 Scripts/analyzer/charge_balance_check.py      |   8 +-
 .../analyzer/energy_force_virial_analyzer.py  |  16 +-
 Scripts/analyzer/filter_dist_range.py         |   8 +-
 Scripts/analyzer/filter_exyz_by_box.py        |   8 +-
 Scripts/analyzer/filter_exyz_by_value.py      |   8 +-
 .../analyzer/filter_structures_by_distance.py |  12 +-
 .../filter_structures_by_distance_pbc.py      |  12 +-
 Scripts/analyzer/find_outliers.py             |   2 +-
 Scripts/analyzer/get_min_dist.py              |  12 +-
 Scripts/analyzer/get_min_dist_pbc.py          |  12 +-
 Scripts/analyzer/get_volume.py                |   2 +-
 .../analyzer/probability_density_analysis.py  |  17 +-
 Scripts/analyzer/time_consuming_gpumd.sh      |   2 +-
 Scripts/analyzer/time_consuming_nep.sh        |   2 +-
 .../calculators/calc_averaged_structure.py    |  34 +-
 Scripts/calculators/calc_descriptors.py       |  28 +-
 Scripts/calculators/calc_displacement.py      |   3 +-
 Scripts/calculators/calc_doas.py              |  20 +-
 Scripts/calculators/calc_ion_conductivity.py  |  32 +-
 Scripts/calculators/calc_minimize.py          |  30 +-
 Scripts/calculators/calc_msd.py               |  24 +-
 Scripts/calculators/calc_neighbor_list.py     |   3 +-
 Scripts/calculators/calc_oct_tilt.py          |   3 +-
 Scripts/calculators/calc_polarization_abo3.py |   3 +-
 .../calculators/calc_properties_with_nep.py   |  20 +-
 Scripts/calculators/neb_calculation.py        |  41 +-
 .../calculators/neb_calculation_neptrain.py   |  11 +-
 Scripts/calculators/rdf_calculator_ovito.py   |   8 +-
 Scripts/format_conversion/abacus2xyz_md.sh    |   2 +-
 Scripts/format_conversion/abacus2xyz_scf.py   |   8 +-
 Scripts/format_conversion/abacus2xyz_scf.sh   |   2 +-
 Scripts/format_conversion/add_groups.py       |   9 +-
 Scripts/format_conversion/add_weight.py       |   9 +-
 Scripts/format_conversion/cif2exyz.py         |   9 +-
 Scripts/format_conversion/cif2pos.py          |   9 +-
 Scripts/format_conversion/clean_xyz.py        |   9 +-
 Scripts/format_conversion/cp2k2xyz.py         |   2 +-
 Scripts/format_conversion/cp2k_log2xyz.py     |   2 +-
 Scripts/format_conversion/exyz2lmp.py         |   4 +-
 Scripts/format_conversion/exyz2pos.py         |  13 +-
 Scripts/format_conversion/get_frame.py        |   9 +-
 Scripts/format_conversion/lmp2exyz.py         |  11 +-
 Scripts/format_conversion/mtp2xyz.py          |  11 +-
 Scripts/format_conversion/out2exyz.py         |  15 +-
 Scripts/format_conversion/out2xyz.sh          |   2 +-
 Scripts/format_conversion/pos2exyz.py         |   9 +-
 Scripts/format_conversion/pos2lmp.py          |   9 +-
 Scripts/format_conversion/replicate.py        |  12 +-
 Scripts/format_conversion/split_single_xyz.py |   4 +-
 Scripts/format_conversion/traj2exyz.py        |   9 +-
 Scripts/format_conversion/xdatcar2exyz.py     |   9 +-
 Scripts/plt_scripts/README.md                 |   2 +-
 Scripts/plt_scripts/plt_arrhenius_d.py        |   2 +-
 Scripts/plt_scripts/plt_arrhenius_d_xyz.py    |   2 +-
 Scripts/plt_scripts/plt_arrhenius_sigma.py    |   2 +-
 .../plt_scripts/plt_arrhenius_sigma_xyz.py    |   2 +-
 Scripts/plt_scripts/plt_born_charge.py        |   2 +-
 Scripts/plt_scripts/plt_charge.py             |   7 +-
 Scripts/plt_scripts/plt_cohesive.py           |   2 +-
 Scripts/plt_scripts/plt_descriptors.py        |   9 +-
 .../plt_scripts/plt_descriptors_compare.py    |   2 +-
 Scripts/plt_scripts/plt_dimer.py              |   9 +-
 Scripts/plt_scripts/plt_doas.py               |   2 +-
 Scripts/plt_scripts/plt_emd.py                |   2 +-
 Scripts/plt_scripts/plt_force_errors.py       |   2 +-
 Scripts/plt_scripts/plt_hnemd.py              |   2 +-
 Scripts/plt_scripts/plt_learning_rate.py      |   2 +-
 Scripts/plt_scripts/plt_msd.py                |   2 +-
 Scripts/plt_scripts/plt_msd_all.py            |   2 +-
 .../plt_scripts/plt_msd_convergence_check.py  |   2 +-
 Scripts/plt_scripts/plt_msd_sdc.py            |   2 +-
 Scripts/plt_scripts/plt_nemd.py               |   2 +-
 Scripts/plt_scripts/plt_nep_restart.py        |   2 +-
 Scripts/plt_scripts/plt_net_force.py          |   7 +-
 Scripts/plt_scripts/plt_parity_density.py     |   2 +-
 Scripts/plt_scripts/plt_pdos.py               |   5 +-
 Scripts/plt_scripts/plt_plane_grid.py         |   2 +-
 Scripts/plt_scripts/plt_prediction.py         |   2 +-
 Scripts/plt_scripts/plt_prediction2.py        |   2 +-
 Scripts/plt_scripts/plt_rdf.py                |   9 +-
 Scripts/plt_scripts/plt_rdf_pmf.py            |   2 +-
 Scripts/plt_scripts/plt_sdc.py                |   2 +-
 Scripts/plt_scripts/plt_thermo.py             |   2 +-
 Scripts/plt_scripts/plt_thermo2.py            |   2 +-
 Scripts/plt_scripts/plt_thermo3.py            |   2 +-
 Scripts/plt_scripts/plt_train.py              |   2 +-
 Scripts/plt_scripts/plt_train_density.py      |   2 +-
 Scripts/plt_scripts/plt_train_test.py         |   2 +-
 Scripts/plt_scripts/plt_vac.py                |   2 +-
 Scripts/plt_scripts/plt_viscosity.py          |   2 +-
 Scripts/sample_structures/frame_range.py      |  11 +-
 .../neptrain_select_structs.py                |   2 +-
 .../parallel_pynep_select_structs.py          |   2 +-
 .../sample_structures/perturb_structure.py    |   2 +-
 .../sample_structures/pynep_select_structs.py |   2 +-
 .../sample_structures/sample_structures.py    |   2 +-
 Scripts/sample_structures/select_max_modev.py |   2 +-
 Scripts/utils/README.md                       |  73 +++
 Scripts/utils/completion.sh                   |  19 +-
 Scripts/utils/nep_modifier/README.md          |   2 +-
 Scripts/utils/nep_modifier/README_zh-CN.md    |   2 +-
 Scripts/utils/nep_modifier/nep_modifier.py    |   2 +-
 Scripts/utils/renumber_atoms.py               |   6 +-
 .../md_sample_batch_pretreatment_gpumd.sh     |   2 +-
 .../md_sample_batch_pretreatment_lmp.sh       |   2 +-
 .../workflow/scf_batch_pretreatment_cp2k.py   |   2 +-
 .../workflow/scf_batch_pretreatment_vasp.sh   |   2 +-
 docs/README_zh-CN.md                          |   2 +-
 docs/index.html                               |   2 +-
 docs/tutorials/en/active_learning_workflow.md |  46 +-
 docs/tutorials/en/analyzer_scripts.md         | 303 +++++++++-
 docs/tutorials/en/calculator_scripts.md       |  54 ++
 docs/tutorials/en/contributing_to_gpumdkit.md | 137 +++--
 docs/tutorials/en/custom_commands.md          |   2 +-
 docs/tutorials/en/format_conversion.md        |  39 ++
 docs/tutorials/en/plot_scripts.md             | 533 ++++++++++++-----
 docs/tutorials/en/polar_material_analysis.md  |  55 +-
 docs/tutorials/en/quick_start.md              |   4 +-
 docs/tutorials/en/structure_sampling.md       |  20 +-
 docs/tutorials/en/workflow_scripts.md         |  23 +-
 ...40\345\267\245\344\275\234\346\265\201.md" |  22 +-
 ...06\346\236\220\345\267\245\345\205\267.md" | 330 +++++++++--
 ...34\346\265\201\350\204\232\346\234\254.md" |  32 +-
 ...53\351\200\237\345\205\245\351\227\250.md" |   4 +-
 ...20\346\226\231\345\210\206\346\236\220.md" |  54 +-
 ...74\345\274\217\350\275\254\346\215\242.md" |  48 ++
 ...23\346\236\204\351\207\207\346\240\267.md" |  30 +-
 ...30\345\233\276\350\204\232\346\234\254.md" | 558 ++++++++++++++++--
 ...27\345\231\250\350\204\232\346\234\254.md" |  56 +-
 ...41\347\214\256\346\214\207\345\215\227.md" | 399 +++++++------
 gpumdkit.sh                                   | 390 ++----------
 skills/gpumdkit-calculators/SKILL.md          |   9 +-
 skills/gpumdkit-contributing/SKILL.md         |   2 +-
 skills/gpumdkit-workflows/SKILL.md            |   4 +-
 src/f1_format_conversions.sh                  |   2 +-
 src/f2_sample_structures.sh                   |   4 +-
 src/f3_workflows.sh                           |   2 +-
 src/f4_calculators.sh                         |   2 +-
 src/f5_analyzers.sh                           |   2 +-
 src/f6_plots.sh                               |   2 +-
 src/f7_utilities.sh                           |   2 +-
 145 files changed, 2859 insertions(+), 1146 deletions(-)
 create mode 100644 Scripts/utils/README.md

diff --git a/README.md b/README.md
index e6bf2b4..65074f1 100644
--- a/README.md
+++ b/README.md
@@ -297,4 +297,4 @@ Also, welcome to join our QQ group ([825696376](https://qun.qq.com/universal-sha
 
 **GPUMDkit** is an open-source tool freely available for everyone. If you find it helpful in your research or workflow, please ⭐ [star us on GitHub](https://github.com/zhyan0603/GPUMDkit). Additionally, if GPUMDkit contributes to your published work, please cite our paper:
 
-> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, e70074](https://doi.org/10.1002/mgea.70074).
+> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, 4, e70074](https://doi.org/10.1002/mgea.70074).
diff --git a/Scripts/README.md b/Scripts/README.md
index 5b5a8df..32b50b1 100644
--- a/Scripts/README.md
+++ b/Scripts/README.md
@@ -35,7 +35,6 @@ Computational tools for property calculations:
 
 **Quick Start:**
 ```bash
-for example
 gpumdkit.sh -calc ionic-cond Li 1              # Calculate ionic conductivity
 gpumdkit.sh -calc nep input.xyz output.xyz nep.txt  # Calculate with NEP
 ```
diff --git a/Scripts/analyzer/analyze_chem_species.py b/Scripts/analyzer/analyze_chem_species.py
index 4a3877a..1c1591b 100644
--- a/Scripts/analyzer/analyze_chem_species.py
+++ b/Scripts/analyzer/analyze_chem_species.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     analyze_chem_species.py
 Category:   Analyzer Scripts
 Purpose:    Identify all unique chemical elements present in an extxyz
             trajectory.
-Usage:      python analyze_chem_species.py <input.xyz>
+Usage:      gpumdkit.sh -chem_species <input.xyz>
+            python analyze_chem_species.py <input.xyz>
 Arguments:
   input.xyz  Input extxyz file
 Output:
@@ -24,12 +25,13 @@
 from ase.data import chemical_symbols, atomic_numbers
 
 # Load all frames from the provided extxyz file
-try:
-    atoms_list = read(sys.argv[1], index=':')
-except IndexError:
-    print("Usage: python analyze_chem_species.py <input.xyz>")
+if len(sys.argv) < 2:
+    print(" Usage: gpumdkit.sh -chem_species <exyzfile>")
+    print("    or: python analyze_chem_species.py <input.xyz>")
     sys.exit(1)
 
+atoms_list = read(sys.argv[1], index=':')
+
 # Identify all unique elements present across all frames
 element_set = set()
 for atoms in atoms_list:
diff --git a/Scripts/analyzer/analyze_composition.py b/Scripts/analyzer/analyze_composition.py
index c2aaeac..a7a3f46 100644
--- a/Scripts/analyzer/analyze_composition.py
+++ b/Scripts/analyzer/analyze_composition.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     analyze_composition.py
 Category:   Analyzer Scripts
 Purpose:    Analyze and group structures by chemical composition from an
             extxyz file, and selectively export structures by composition.
-Usage:      python analyze_composition.py <input.xyz>
+Usage:      gpumdkit.sh -analyze_comp <input.xyz>
+            python analyze_composition.py <input.xyz>
 Arguments:
   input.xyz  Input extxyz file
 Output:
@@ -113,7 +114,8 @@ def analyze_xyz_compositions(filename):
 # Run the analysis
 if __name__ == "__main__":
     if len(sys.argv) != 2:
-        print(" Usage: python analyze_composition.py <input.xyz>")
+        print(" Usage: gpumdkit.sh -analyze_comp <exyzfile>")
+        print("    or: python analyze_composition.py <input.xyz>")
         sys.exit(1)
     filename = sys.argv[1]  # your extxyz file
     analyze_xyz_compositions(filename)
diff --git a/Scripts/analyzer/charge_balance_check.py b/Scripts/analyzer/charge_balance_check.py
index cbbf2ab..346c268 100644
--- a/Scripts/analyzer/charge_balance_check.py
+++ b/Scripts/analyzer/charge_balance_check.py
@@ -3,14 +3,15 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     charge_balance_check.py
 Category:   Analyzer Scripts
 Purpose:    Check oxidation-state balance for all structures in an extxyz
             file. Outputs separate files for balanced and unbalanced
             structures.
-Usage:      python charge_balance_check.py <input.xyz>
+Usage:      gpumdkit.sh -cbc <exyzfile>
+            python charge_balance_check.py <input.extxyz>
 Arguments:
   input.xyz  Input extxyz file
 Output:
@@ -77,7 +78,8 @@ def process_structure(idx_atoms):
 def main():
     # Check if input file is provided
     if len(sys.argv) != 2:
-        print("Usage: python charge_balance_check.py <input.extxyz>", file=sys.stderr)
+        print(" Usage: gpumdkit.sh -cbc <exyzfile>")
+        print("    or: python charge_balance_check.py <input.extxyz>")
         sys.exit(1)
     
     input_file = sys.argv[1]
diff --git a/Scripts/analyzer/energy_force_virial_analyzer.py b/Scripts/analyzer/energy_force_virial_analyzer.py
index 5e275a1..689ba8c 100644
--- a/Scripts/analyzer/energy_force_virial_analyzer.py
+++ b/Scripts/analyzer/energy_force_virial_analyzer.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     energy_force_virial_analyzer.py
 Category:   Analyzer Scripts
 Purpose:    Compute the range (min, max) of energy, force, or virial in an
             extxyz file. Optionally plot a histogram.
-Usage:      python energy_force_virial_analyzer.py <filename> <property> [hist]
+Usage:      gpumdkit.sh -range <filename> <property> [hist]
+            python energy_force_virial_analyzer.py <filename> <property> [hist]
 Arguments:
   filename   Input extxyz file
   property   Property to analyze: energy, force, or virial
@@ -22,6 +23,12 @@
 """
 
 import sys
+
+if len(sys.argv) < 3:
+    print(" Usage: gpumdkit.sh -range <exyzfile> <property> [hist]")
+    print("    or: python energy_force_virial_analyzer.py <filename> <property> [hist]")
+    sys.exit(1)
+
 import numpy as np
 from ase.io import read
 import matplotlib.pyplot as plt
@@ -63,11 +70,6 @@ def plot_histogram(values, property_name):
     #plt.savefig(f'range_{property_name.capitalize()}.png')
 
 if __name__ == "__main__":
-    # Check if the required arguments are provided
-    if len(sys.argv) < 3:
-        print("Usage: python energy_force_virial_analyzer.py <filename> <property> [hist]")
-        sys.exit(1)
-    
     filename = sys.argv[1]
     property_name = sys.argv[2]
     plot_hist = len(sys.argv) > 3 and sys.argv[3] == 'hist'
diff --git a/Scripts/analyzer/filter_dist_range.py b/Scripts/analyzer/filter_dist_range.py
index 7d5790a..319f502 100644
--- a/Scripts/analyzer/filter_dist_range.py
+++ b/Scripts/analyzer/filter_dist_range.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     filter_dist_range.py
 Category:   Analyzer Scripts
 Purpose:    Filter structures by minimum interatomic distance between two
             elements falling within a specified range.
-Usage:      python filter_dist_range.py <input.xyz> <element1> <element2> <min_dist> <max_dist>
+Usage:      gpumdkit.sh -filter_range <input.xyz> <element1> <element2> <min_dist> <max_dist>
+            python filter_dist_range.py <input.xyz> <element1> <element2> <min_dist> <max_dist>
 Arguments:
   input.xyz  Input extxyz file
   element1   First element symbol (e.g., Li)
@@ -54,7 +55,8 @@ def get_min_distance(atoms, symbol1, symbol2):
 def main():
     # Parse command line arguments
     if len(sys.argv) != 6:
-        print(" Usage: python filter_dist_range.py <input.xyz> <element1> <element2> <min_dist> <max_dist>")
+        print(" Usage: gpumdkit.sh -filter_range <exyzfile> <element1> <element2> <min_dist> <max_dist>")
+        print("    or: python filter_dist_range.py <input.xyz> <element1> <element2> <min_dist> <max_dist>")
         sys.exit(1)
     
     input_file = sys.argv[1]
diff --git a/Scripts/analyzer/filter_exyz_by_box.py b/Scripts/analyzer/filter_exyz_by_box.py
index 9eafab8..19242b7 100644
--- a/Scripts/analyzer/filter_exyz_by_box.py
+++ b/Scripts/analyzer/filter_exyz_by_box.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     filter_exyz_by_box.py
 Category:   Analyzer Scripts
 Purpose:    Filter structures by a maximum box-edge length. Structures with
             any box edge exceeding the limit are discarded.
-Usage:      python filter_exyz_by_box.py <input_file> <edge_limit>
+Usage:      gpumdkit.sh -filter_box <input_file> <edge_limit>
+            python filter_exyz_by_box.py <input_file> <edge_limit>
 Arguments:
   input_file   Input extxyz file
   edge_limit   Maximum allowed box-edge length (Angstrom)
@@ -49,7 +50,8 @@ def filter_frames(input_file, output_file, edge_limit):
 
 if __name__ == "__main__":
     if len(sys.argv) != 3:
-        print("Usage: python filter_exyz_by_box.py <input_file> <edge_limit>")
+        print(" Usage: gpumdkit.sh -filter_box <exyzfile> <edge_limit>")
+        print("    or: python filter_exyz_by_box.py <input_file> <edge_limit>")
         sys.exit(1)
 
     input_file = sys.argv[1]
diff --git a/Scripts/analyzer/filter_exyz_by_value.py b/Scripts/analyzer/filter_exyz_by_value.py
index 59f8f1b..d01d7c2 100644
--- a/Scripts/analyzer/filter_exyz_by_value.py
+++ b/Scripts/analyzer/filter_exyz_by_value.py
@@ -3,12 +3,13 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     filter_exyz_by_value.py
 Category:   Analyzer Scripts
 Purpose:    Filter structures based on energy, force, or virial thresholds.
-Usage:      python filter_exyz_by_value.py <input_file> <property> <threshold>
+Usage:      gpumdkit.sh -filter_value <input_file> <property> <threshold>
+            python filter_exyz_by_value.py <input_file> <property> <threshold>
 Arguments:
   input_file  Input extxyz file
   property    Filtering property: energy, force, or virial
@@ -57,6 +58,7 @@ def main():
 
 if __name__ == "__main__":
     if len(sys.argv) != 4:
-        print("Usage: python filter_exyz_by_value.py <input_file> <property> <threshold>")
+        print(" Usage: gpumdkit.sh -filter_value <input_file> <property> <threshold>")
+        print("    or: python filter_exyz_by_value.py <input_file> <property> <threshold>")
         sys.exit(1)
     main()
diff --git a/Scripts/analyzer/filter_structures_by_distance.py b/Scripts/analyzer/filter_structures_by_distance.py
index c716faa..8a007c4 100644
--- a/Scripts/analyzer/filter_structures_by_distance.py
+++ b/Scripts/analyzer/filter_structures_by_distance.py
@@ -3,14 +3,16 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     filter_structures_by_distance.py
 Category:   Analyzer Scripts
 Purpose:    Filter structures by minimum interatomic distance without
             periodic boundary conditions (no PBC). Faster than the PBC
             version for large systems.
-Usage:      python filter_structures_by_distance.py <file_name> [distance_threshold]
+Usage:      gpumdkit.sh -filter_dist <file_name> [distance_threshold]
+            python filter_structures_by_distance.py <file_name> [distance_threshold]
+Example:    gpumdkit.sh -filter_dist train.xyz 1.5
 Arguments:
   file_name          Input extxyz file
   distance_threshold (optional) Minimum allowed interatomic distance
@@ -36,6 +38,12 @@ def print_progress_bar(iteration, total, length=50):
     if iteration == total:
         print()
 
+# Check command-line arguments
+if len(sys.argv) < 2:
+    print(" Usage: gpumdkit.sh -filter_dist <file_name> [distance_threshold]")
+    print("    or: python filter_structures_by_distance.py <file_name> [distance_threshold]")
+    sys.exit(1)
+
 # Read the file name from command line arguments
 file_name = sys.argv[1]
 
diff --git a/Scripts/analyzer/filter_structures_by_distance_pbc.py b/Scripts/analyzer/filter_structures_by_distance_pbc.py
index 85bce0a..cd487d3 100644
--- a/Scripts/analyzer/filter_structures_by_distance_pbc.py
+++ b/Scripts/analyzer/filter_structures_by_distance_pbc.py
@@ -3,13 +3,15 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     filter_structures_by_distance_pbc.py
 Category:   Analyzer Scripts
 Purpose:    Filter structures by minimum interatomic distance with periodic
             boundary conditions. Based on NepTrainKit distance function.
-Usage:      python filter_structures_by_distance_pbc.py <file_name> [distance_threshold]
+Usage:      gpumdkit.sh -filter_dist_pbc <file_name> [distance_threshold]
+            python filter_structures_by_distance_pbc.py <file_name> [distance_threshold]
+Example:    gpumdkit.sh -filter_dist_pbc train.xyz 1.5
 Arguments:
   file_name          Input extxyz file
   distance_threshold (optional) Minimum allowed interatomic distance
@@ -60,6 +62,12 @@ def calculate_pairwise_distances(lattice_params, atom_coords, fractional=True):
     np.fill_diagonal(distances, 0)
     return distances
 
+# Check command-line arguments
+if len(sys.argv) < 2:
+    print(" Usage: gpumdkit.sh -filter_dist_pbc <file_name> [distance_threshold]")
+    print("    or: python filter_structures_by_distance_pbc.py <file_name> [distance_threshold]")
+    sys.exit(1)
+
 # Read the file name from command line arguments
 file_name = sys.argv[1]
 
diff --git a/Scripts/analyzer/find_outliers.py b/Scripts/analyzer/find_outliers.py
index 5e87669..0dcc9e9 100644
--- a/Scripts/analyzer/find_outliers.py
+++ b/Scripts/analyzer/find_outliers.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     find_outliers.py
 Category:   Analyzer Scripts
diff --git a/Scripts/analyzer/get_min_dist.py b/Scripts/analyzer/get_min_dist.py
index b3638e4..72abbe2 100644
--- a/Scripts/analyzer/get_min_dist.py
+++ b/Scripts/analyzer/get_min_dist.py
@@ -3,14 +3,16 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     get_min_dist.py
 Category:   Analyzer Scripts
 Purpose:    Compute the minimum interatomic distance for each element pair
             across all frames in an extxyz file (no PBC, faster for large
             systems).
-Usage:      python get_min_dist.py <file_name>
+Usage:      gpumdkit.sh -min_dist <file_name>
+            python get_min_dist.py <file_name>
+Example:    gpumdkit.sh -min_dist train.xyz
 Arguments:
   file_name  Input extxyz file
 Output:
@@ -25,6 +27,12 @@
 from ase.io import read
 from scipy.spatial.distance import pdist, squareform
 
+# Check command-line arguments
+if len(sys.argv) != 2:
+    print(" Usage: gpumdkit.sh -min_dist <file_name>")
+    print("    or: python get_min_dist.py <file_name>")
+    sys.exit(1)
+
 # Read the file name from command line arguments
 file_name = sys.argv[1]
 
diff --git a/Scripts/analyzer/get_min_dist_pbc.py b/Scripts/analyzer/get_min_dist_pbc.py
index 78e718f..a6bca8c 100644
--- a/Scripts/analyzer/get_min_dist_pbc.py
+++ b/Scripts/analyzer/get_min_dist_pbc.py
@@ -3,14 +3,16 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     get_min_dist_pbc.py
 Category:   Analyzer Scripts
 Purpose:    Compute the minimum interatomic distance for each element pair
             across all frames in an extxyz file, accounting for periodic
             boundary conditions.
-Usage:      python get_min_dist_pbc.py <file_name>
+Usage:      gpumdkit.sh -min_dist_pbc <file_name>
+            python get_min_dist_pbc.py <file_name>
+Example:    gpumdkit.sh -min_dist_pbc train.xyz
 Arguments:
   file_name  Input extxyz file
 Output:
@@ -50,6 +52,12 @@ def calculate_pairwise_distances(lattice_params, atom_coords, fractional=True):
     np.fill_diagonal(distances, 0)
     return distances
 
+# Check command-line arguments
+if len(sys.argv) != 2:
+    print(" Usage: gpumdkit.sh -min_dist_pbc <file_name>")
+    print("    or: python get_min_dist_pbc.py <file_name>")
+    sys.exit(1)
+
 # Read the file name from command line arguments
 file_name = sys.argv[1]
 
diff --git a/Scripts/analyzer/get_volume.py b/Scripts/analyzer/get_volume.py
index 5db1c4c..39483cd 100644
--- a/Scripts/analyzer/get_volume.py
+++ b/Scripts/analyzer/get_volume.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     get_volume.py
 Category:   Analyzer Scripts
diff --git a/Scripts/analyzer/probability_density_analysis.py b/Scripts/analyzer/probability_density_analysis.py
index c707e66..2809dfe 100644
--- a/Scripts/analyzer/probability_density_analysis.py
+++ b/Scripts/analyzer/probability_density_analysis.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     probability_density_analysis.py
 Category:   Analyzer Scripts
 Purpose:    Compute the 3D probability density of mobile ions from an AIMD
             trajectory using pymatgen, and save the result as a CHGCAR file.
-Usage:      python probability_density_analysis.py <ref_struct> <trajectory_file> <species> <interval>
+Usage:      gpumdkit.sh -pda <ref_struct> <trajectory_file> <species> <interval>
+            python probability_density_analysis.py <ref_struct> <trajectory_file> <species> <interval>
 Arguments:
   ref_struct       Reference structure file (e.g., POSCAR)
   trajectory_file  AIMD trajectory in extxyz format
@@ -23,16 +24,18 @@
 """
 
 import sys
+
+# Check if required arguments are provided before heavy imports
+if len(sys.argv) != 5:
+    print(" Usage: gpumdkit.sh -pda <ref_struct> <trajectory_file> <species> <interval>")
+    print("    or: python probability_density_analysis.py <ref_struct> <trajectory_file> <species> <interval>")
+    sys.exit(1)
+
 import numpy as np
 from pymatgen.analysis.diffusion.aimd.pathway import ProbabilityDensityAnalysis
 from pymatgen.core import Structure
 from ase.io import read
 
-# Check if required arguments are provided
-if len(sys.argv) != 5:
-    print("Usage: python probability_density_analysis.py <ref_struct> <trajectory_file> <species> <interval>")
-    sys.exit(1)
-
 # Parse command-line arguments
 structure_file = sys.argv[1]
 trajectory_file = sys.argv[2]
diff --git a/Scripts/analyzer/time_consuming_gpumd.sh b/Scripts/analyzer/time_consuming_gpumd.sh
index d42c550..07657f7 100644
--- a/Scripts/analyzer/time_consuming_gpumd.sh
+++ b/Scripts/analyzer/time_consuming_gpumd.sh
@@ -3,7 +3,7 @@
 # GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-#           MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+#           MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 # =============================================================================
 # Script:     time_consuming_gpumd.sh
 # Category:   Analyzer Scripts
diff --git a/Scripts/analyzer/time_consuming_nep.sh b/Scripts/analyzer/time_consuming_nep.sh
index 8f59826..dcfc1da 100644
--- a/Scripts/analyzer/time_consuming_nep.sh
+++ b/Scripts/analyzer/time_consuming_nep.sh
@@ -3,7 +3,7 @@
 # GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-#           MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+#           MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 # =============================================================================
 # Script:     time_consuming_nep.sh
 # Category:   Analyzer Scripts
diff --git a/Scripts/calculators/calc_averaged_structure.py b/Scripts/calculators/calc_averaged_structure.py
index 81fdcdd..37c0b18 100644
--- a/Scripts/calculators/calc_averaged_structure.py
+++ b/Scripts/calculators/calc_averaged_structure.py
@@ -3,20 +3,22 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     calc_averaged_structure.py
 Category:   Calculator Scripts
 Purpose:    Calculate and save the averaged structure from trajectory frames
-            using the ferrodispcalc package.
-Usage:      python calc_averaged_structure.py -i <movie.xyz> -o <output.xyz> [options]
+            using ASE and NumPy.
+Usage:      gpumdkit.sh -calc avg-struct [options]
+            python calc_averaged_structure.py -i <movie.xyz> -o <output.xyz> [options]
+Example:    gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz
 Arguments:
   -i, --input   Input trajectory file (default: movie.xyz)
   -s            Start index
   -t            End index
   -p            Step (process every p-th frame)
   -l            Fraction or number of last frames to average
-  -o, --output  Output averaged structure file (required)
+  -o, --output  Output averaged structure file (default: averaged_structure.xyz)
 Output:
   Averaged structure in extxyz format
 Author:     Denan LI (lidenan@westlake.edu.cn)
@@ -24,10 +26,29 @@
 =============================================================================
 """
 
+import sys
+
+if __name__ == "__main__" and (
+    len(sys.argv) == 1 or (len(sys.argv) > 1 and sys.argv[1] in ("-h", "--help"))
+):
+    print(" Usage: gpumdkit.sh -calc avg-struct -i <movie.xyz> -o <output.xyz> [options]")
+    print("    or: python calc_averaged_structure.py -i <movie.xyz> -o <output.xyz> [options]")
+    print("")
+    print(" Arguments:")
+    print("   -i, --input   Input trajectory file")
+    print("   -o, --output  Output averaged structure file")
+    print("   -s, --start   Slice start index")
+    print("   -t, --stop    Slice stop index")
+    print("   -p, --step    Slice step")
+    print("   -l, --last    Use the last frames; integer N or 0 < ratio < 1")
+    print("")
+    print(" Example: gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz")
+    print("")
+    sys.exit(0 if len(sys.argv) > 1 and sys.argv[1] in ("-h", "--help") else 1)
+
 from ase.io import read, write
 import argparse
 import math
-import sys
 from ase import Atoms
 import numpy as np
 
@@ -109,6 +130,7 @@ def parse_args():
         epilog=(
             "Examples :\n"
             "1. Use all frames:\n"
+            ">>  gpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n"
             ">>  python calc_averaged_structure.py -i movie.xyz -o averaged_structure.xyz\n"
             "2. Average every 2 frames from index 100 to 500:\n"
             ">>  python calc_averaged_structure.py -i movie.xyz -s 100 -t 500 -p 2 -o avg.xyz\n"
@@ -175,4 +197,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()
diff --git a/Scripts/calculators/calc_descriptors.py b/Scripts/calculators/calc_descriptors.py
index b9ea329..5fb98d5 100644
--- a/Scripts/calculators/calc_descriptors.py
+++ b/Scripts/calculators/calc_descriptors.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     calc_descriptors.py
 Category:   Calculator Scripts
 Purpose:    Compute and save NEP descriptors for a target element from a
             multi-frame extxyz file.
-Usage:      python calc_descriptors.py <input.xyz> <output.npy> <nep.txt> <element>
+Usage:      gpumdkit.sh -calc des <input.xyz> <output.npy> <nep_model> <element>
+            python calc_descriptors.py <input.xyz> <output.npy> <nep.txt> <element>
 Arguments:
   input.xyz   Input extxyz file
   output.npy  Output .npy file for descriptors
@@ -22,10 +23,26 @@
 =============================================================================
 """
 
+import sys
+
+# Check command-line arguments before importing optional heavy dependencies.
+if __name__ == "__main__" and (len(sys.argv) != 5 or sys.argv[1] in ("-h", "--help")):
+    print(" Usage: gpumdkit.sh -calc des <input.xyz> <output.npy> <nep_model> <element>")
+    print("    or: python calc_descriptors.py <input.xyz> <output.npy> <nep.txt> <element>")
+    print("")
+    print(" Arguments:")
+    print("   input.xyz   Input extxyz file")
+    print("   output.npy  Output .npy file for descriptors")
+    print("   nep.txt     Path to the NEP model file")
+    print("   element     Target element symbol (e.g., Li)")
+    print("")
+    print(" Example: gpumdkit.sh -calc des input.xyz descriptors.npy nep.txt Li")
+    print("")
+    sys.exit(0 if len(sys.argv) > 1 and sys.argv[1] in ("-h", "--help") else 1)
+
 import numpy as np
 from ase.io import read
 from calorine.nep import get_descriptors
-import sys
 import os
 
 
@@ -44,11 +61,6 @@ def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, lengt
     if iteration == total:
         print()
 
-# Check command-line arguments
-if len(sys.argv) != 5:
-    print(" Usage: python calc_descriptors.py input.xyz output.npy nep.txt element")
-    sys.exit(1)
-
 input_file, output_file, model_file, target_element = sys.argv[1:5]
 
 print_dependency_notice()
diff --git a/Scripts/calculators/calc_displacement.py b/Scripts/calculators/calc_displacement.py
index 0e049ae..582deb2 100644
--- a/Scripts/calculators/calc_displacement.py
+++ b/Scripts/calculators/calc_displacement.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     calc_displacement.py
 Category:   Calculator Scripts
@@ -56,6 +56,7 @@ def parse_args():
         epilog=(
             "Examples :\n"
             "1. Single-frame model.xyz:\n"
+            ">>  gpumdkit.sh -calc disp -i model.xyz -n nl-Pb-O.dat -o displacements.dat\n"
             ">>  python calc_displacement.py -i model.xyz -n nl-Pb-O.dat -o displacements.dat\n"
             "2. Multi-frame movie.xyz with slice:\n"
             ">>  python calc_displacement.py -i movie.xyz -n nl-Pb-O.dat -s 100 -t 500 -p 2 -o disp_slice.dat\n"
diff --git a/Scripts/calculators/calc_doas.py b/Scripts/calculators/calc_doas.py
index 15cdb48..1ffc088 100644
--- a/Scripts/calculators/calc_doas.py
+++ b/Scripts/calculators/calc_doas.py
@@ -3,14 +3,15 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     calc_doas.py
 Category:   Calculator Scripts
 Purpose:    Calculate the density of atomistic states (DOAS) proposed by
             Wang et al. by reading and optimizing structures with NEP_CPU
             and computing per-atom energies.
-Usage:      python calc_doas.py <input.xyz> <nep.txt> <output.txt>
+Usage:      gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>
+            python calc_doas.py <input.xyz> <nep.txt> <output.txt>
 Arguments:
   input.xyz   Input extxyz file
   nep.txt     Path to the NEP model file
@@ -22,6 +23,21 @@
 =============================================================================
 """
 import sys
+
+# Check command-line arguments before importing optional heavy dependencies.
+if __name__ == "__main__" and (len(sys.argv) < 4 or sys.argv[1] in ("-h", "--help")):
+    print(" Usage: gpumdkit.sh -calc doas <input.xyz> <nep_model> <output_file>")
+    print("    or: python calc_doas.py <input.xyz> <nep.txt> <output.txt>")
+    print("")
+    print(" Arguments:")
+    print("   input.xyz    Input extxyz file")
+    print("   nep_model    Path to the NEP model file")
+    print("   output_file  Output text file for grouped atomic energies")
+    print("")
+    print(" Example: gpumdkit.sh -calc doas input.xyz nep.txt energies.txt")
+    print("")
+    sys.exit(0 if len(sys.argv) > 1 and sys.argv[1] in ("-h", "--help") else 1)
+
 from tqdm import tqdm
 import numpy as np
 from ase import Atoms
diff --git a/Scripts/calculators/calc_ion_conductivity.py b/Scripts/calculators/calc_ion_conductivity.py
index a7c4759..09bbb69 100644
--- a/Scripts/calculators/calc_ion_conductivity.py
+++ b/Scripts/calculators/calc_ion_conductivity.py
@@ -3,16 +3,26 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     calc_ion_conductivity.py
 Category:   Calculator Scripts
 Purpose:    Calculate diffusivity and ionic conductivity from MSD data
-            (msd.out) via the Nernst-Einstein equation.
-Usage:      python calc_ion_conductivity.py <element> <charge>
+            (msd.out) via the Nernst-Einstein equation. Automatically reads
+            temperature and volume from thermo.out, ion count from model.xyz,
+            and replication from run.in when available; falls back to
+            interactive prompts if files are missing.
+Usage:      gpumdkit.sh -calc ionic-cond <element> <charge>
+            python calc_ion_conductivity.py <element> <charge>
+Example:    gpumdkit.sh -calc ionic-cond Li 1
 Arguments:
   element  Chemical species (e.g., Li)
   charge   Ion charge (e.g., 1 for Li+)
+Input files (auto-detected):
+  thermo.out   Thermodynamic data (temperature, box dimensions)
+  model.xyz    Structure file (ion count)
+  run.in       GPUMD input (replication factor)
+  msd.out      Mean square displacement data
 Output:
   Calculated diffusivity and ionic conductivity (printed to terminal)
 Author:     Zihan YAN (yanzihan@westlake.edu.cn), Shengjie Tang (tangshengjie@westlake.edu.cn)
@@ -200,10 +210,22 @@ def count_ions(atom_type="Li"):
 
 # Main function to orchestrate the process
 def main():
+    if len(sys.argv) < 3 or (len(sys.argv) > 1 and sys.argv[1] in ("-h", "--help")):
+        print(" Usage: gpumdkit.sh -calc ionic-cond <element> <charge>")
+        print("    or: python calc_ion_conductivity.py <element> <charge>")
+        print("")
+        print(" Arguments:")
+        print("   element    Chemical species (e.g., Li, Na)")
+        print("   charge     Ion charge (e.g., 1 for Li+)")
+        print("")
+        print(" Example: gpumdkit.sh -calc ionic-cond Li 1")
+        print("")
+        sys.exit(0 if len(sys.argv) > 1 and sys.argv[1] in ("-h", "--help") else 1)
+
     # Check if thermo.out and model.xyz exist to extract or prompt for values
     if os.path.exists("./thermo.out") and os.path.exists("model.xyz"):
         avg_temperature, avg_volume = extract_thermo_data()
-        atom_type = sys.argv[1] if len(sys.argv) > 1 else "Li"  # Default to Li if not passed as argument
+        atom_type = sys.argv[1]
         num_ions = count_ions(atom_type)
     else:
         # If files don't exist, prompt the user to enter values manually
@@ -262,5 +284,3 @@ def main():
 # Run the main function
 if __name__ == "__main__":
     main()
-
-
diff --git a/Scripts/calculators/calc_minimize.py b/Scripts/calculators/calc_minimize.py
index c8405eb..1cb1045 100644
--- a/Scripts/calculators/calc_minimize.py
+++ b/Scripts/calculators/calc_minimize.py
@@ -3,14 +3,15 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     calc_minimize.py
 Category:   Calculator Scripts
 Purpose:    Perform structure relaxation using calorine (CPUNEP) from a
             POSCAR or extxyz file with configurable force convergence and
             max optimization steps.
-Usage:      python calc_minimize.py <structure_file> <nep.txt> [fmax=0.01] [max_steps=1000]
+Usage:      gpumdkit.sh -calc minimize <structure_file> <nep.txt> [fmax] [max_steps]
+            python calc_minimize.py <structure_file> <nep.txt> [fmax=0.01] [max_steps=1000]
 Arguments:
   structure_file  Input structure file (POSCAR or .xyz)
   nep.txt         Path to the NEP model file
@@ -24,6 +25,22 @@
 """
 
 import sys
+
+# Check command-line arguments before importing optional heavy dependencies.
+if __name__ == "__main__" and (len(sys.argv) < 3 or sys.argv[1] in ("-h", "--help")):
+    print(" Usage: gpumdkit.sh -calc minimize <structure_file> <nep.txt> [fmax] [max_steps]")
+    print("    or: python calc_minimize.py <structure_file> <nep.txt> [fmax] [max_steps]")
+    print("")
+    print(" Arguments:")
+    print("   structure_file  Input structure file (POSCAR or .xyz)")
+    print("   nep.txt         Path to the NEP model file")
+    print("   fmax            Force convergence threshold (eV/A, default: 0.01)")
+    print("   max_steps       Max optimization steps (default: 1000)")
+    print("")
+    print(" Example: gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000")
+    print("")
+    sys.exit(0 if len(sys.argv) > 1 and sys.argv[1] in ("-h", "--help") else 1)
+
 from tqdm import tqdm
 import numpy as np
 from ase import Atoms
@@ -50,15 +67,6 @@ def __call__(self):
         self.trajectory.append(self.atoms.copy())
 
 def main():
-    # Parse command line arguments
-    if len(sys.argv) < 3:
-        print(" Usage: python calc_minimize.py <structure_file> <nep.txt> [fmax=0.01] [max_steps=1000]")
-        print(" Supported structure formats: POSCAR, .xyz")
-        print(" Optional arguments: ")
-        print("  fmax: Force convergence threshold in eV/Ang (default: 0.01)")
-        print("  max_steps: Maximum number of optimization steps (default: 1000)")
-        sys.exit(1)
-
     print_dependency_notice()
 
     structure_file = sys.argv[1]  # Structure file (POSCAR or extxyz)
diff --git a/Scripts/calculators/calc_msd.py b/Scripts/calculators/calc_msd.py
index e3edfb0..42f1a52 100644
--- a/Scripts/calculators/calc_msd.py
+++ b/Scripts/calculators/calc_msd.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     calc_msd.py
 Category:   Calculator Scripts
 Purpose:    Compute directional MSD (x, y, z) from an extxyz trajectory via
             the Wiener-Khinchin FFT algorithm for a target element.
-Usage:      python calc_msd.py <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]
+Usage:      gpumdkit.sh -calc msd <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]
+            python calc_msd.py <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]
 Arguments:
   extxyz_file       Path to the input extxyz trajectory file
   element_symbol    Chemical symbol (e.g., Li, O, Na)
@@ -46,12 +47,23 @@ def parse_args():
     args = sys.argv[1:]
 
     if len(args) == 0 or args[0] in ("-h", "--help"):
-        print(__doc__)
-        sys.exit(0)
+        print(" Usage: gpumdkit.sh -calc msd <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]")
+        print("    or: python calc_msd.py <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]")
+        print("")
+        print(" Arguments:")
+        print("   extxyz_file       Path to the input extxyz trajectory file")
+        print("   element_symbol    Chemical symbol (e.g., Li, O, Na)")
+        print("   dt_fs             Time step between consecutive frames (fs)")
+        print("   max_corr_steps    Max correlation lag steps (optional)")
+        print("")
+        print(" Example: gpumdkit.sh -calc msd dump.xyz Li 1.0 500")
+        print("")
+        sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
 
     if len(args) not in (3, 4):
         print(" Error: Expected 3 or 4 positional arguments, got %d." % len(args))
-        print("        Run with -h for usage information.")
+        print(" Usage: gpumdkit.sh -calc msd <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]")
+        print("    or: python calc_msd.py <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]")
         sys.exit(1)
 
     extxyz_file    = args[0]
@@ -396,4 +408,4 @@ def calculate_msd_from_extxyz(extxyz_file, element_symbol, dt_fs, max_corr_steps
     calculate_msd_from_extxyz(extxyz_file, element_symbol, dt_fs, max_corr_steps)
 
     print(" Total elapsed time: %.2f s" % (time.perf_counter() - t0))
-    print(" "+ "=" * 60)
\ No newline at end of file
+    print(" "+ "=" * 60)
diff --git a/Scripts/calculators/calc_neighbor_list.py b/Scripts/calculators/calc_neighbor_list.py
index bf53d80..d3555a4 100644
--- a/Scripts/calculators/calc_neighbor_list.py
+++ b/Scripts/calculators/calc_neighbor_list.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     calc_neighbor_list.py
 Category:   Calculator Scripts
@@ -55,6 +55,7 @@ def parse_args():
         epilog=(
             "Examples :\n"
             "1. Find the Pb and Sr's nearest 12 oxygen atoms: \n"
+            ">>  gpumdkit.sh -calc nlist -c 4 -n 12 -C Pb Sr -E O\n"
             ">>  python calc_neighbor_list.py -c 4 -n 12 -C Pb Sr -E O\n"
         ),
     )
diff --git a/Scripts/calculators/calc_oct_tilt.py b/Scripts/calculators/calc_oct_tilt.py
index 833869d..bc9cdde 100644
--- a/Scripts/calculators/calc_oct_tilt.py
+++ b/Scripts/calculators/calc_oct_tilt.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     calc_oct_tilt.py
 Category:   Calculator Scripts
@@ -56,6 +56,7 @@ def parse_args():
         epilog=(
             "Examples :\n"
             "1. Single-frame model.xyz:\n"
+            ">>  gpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt.dat\n"
             ">>  python calc_oct_tilt.py -i model.xyz -n nl-Ti-O.dat -o oct_tilt.dat\n"
             "2. Multi-frame movie.xyz with slice:\n"
             ">>  python calc_oct_tilt.py -i movie.xyz -n nl-Ti-O.dat -s 100 -t 500 -p 2 -o oct_tilt_slice.dat\n"
diff --git a/Scripts/calculators/calc_polarization_abo3.py b/Scripts/calculators/calc_polarization_abo3.py
index 5bf6901..aabac9f 100644
--- a/Scripts/calculators/calc_polarization_abo3.py
+++ b/Scripts/calculators/calc_polarization_abo3.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     calc_polarization_abo3.py
 Category:   Calculator Scripts
@@ -59,6 +59,7 @@ def parse_args():
         epilog=(
             "Examples :\n"
             "1. Single-frame model.xyz:\n"
+            ">>  gpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-A.dat --nl-bo nl-Ti-O.dat --bec Pb=2.5 Sr=2.0 Ti=4.0 O=-2.0\n"
             ">>  python calc_polarization_abo3.py -i model.xyz --nl-ba nl-Ti-A.dat --nl-bo nl-Ti-O.dat\n"
             "2. Multi-frame movie.xyz with slice:\n"
             ">>  python calc_polarization_abo3.py -i movie.xyz --nl-ba nl-Ti-A.dat --nl-bo nl-Ti-O.dat -s 100 -t 500 -p 2 -o pol_slice.dat\n"
diff --git a/Scripts/calculators/calc_properties_with_nep.py b/Scripts/calculators/calc_properties_with_nep.py
index 546b0ce..ca39d44 100644
--- a/Scripts/calculators/calc_properties_with_nep.py
+++ b/Scripts/calculators/calc_properties_with_nep.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     calc_properties_with_nep.py
 Category:   Calculator Scripts
 Purpose:    Calculate energy, forces, and stress for structures using a NEP
             model via calorine, and write results to an output extxyz file.
-Usage:      python calc_properties_with_nep.py <input.xyz> <output.xyz> <nep.txt>
+Usage:      gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep_model>
+            python calc_properties_with_nep.py <input.xyz> <output.xyz> <nep.txt>
 Arguments:
   input.xyz   Input extxyz file
   output.xyz  Output extxyz file with computed properties
@@ -22,6 +23,21 @@
 """
 
 import sys
+
+# Check command-line arguments before importing optional heavy dependencies.
+if __name__ == "__main__" and (len(sys.argv) < 4 or sys.argv[1] in ("-h", "--help")):
+    print(" Usage: gpumdkit.sh -calc nep <input.xyz> <output.xyz> <nep_model>")
+    print("    or: python calc_properties_with_nep.py <input.xyz> <output.xyz> <nep.txt>")
+    print("")
+    print(" Arguments:")
+    print("   input.xyz   Input extxyz file")
+    print("   output.xyz  Output extxyz file with computed properties")
+    print("   nep.txt     Path to the NEP model file")
+    print("")
+    print(" Example: gpumdkit.sh -calc nep input.xyz output.xyz nep.txt")
+    print("")
+    sys.exit(0 if len(sys.argv) > 1 and sys.argv[1] in ("-h", "--help") else 1)
+
 import numpy as np
 from ase import Atoms
 from ase.io import read, write
diff --git a/Scripts/calculators/neb_calculation.py b/Scripts/calculators/neb_calculation.py
index 8519166..5c9ce9a 100644
--- a/Scripts/calculators/neb_calculation.py
+++ b/Scripts/calculators/neb_calculation.py
@@ -3,26 +3,52 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     neb_calculation.py
 Category:   Calculator Scripts
 Purpose:    Perform NEB calculations with a NEP model using calorine.
-Usage:      python neb_calculation.py <initial_structure> <final_structure>
-            <n_image> <nep_model>
+Usage:      gpumdkit.sh -calc neb <initial_structure> <final_structure>
+            <n_images> <nep_model>
+            python neb_calculation.py <initial_structure> <final_structure>
+            <n_images> <nep_model>
+Example:    gpumdkit.sh -calc neb init.xyz final.xyz 9 nep.txt
 Arguments:
   initial_structure  Path to the initial structure XYZ file
   final_structure    Path to the final structure XYZ file
-  n_image            Number of intermediate images
+  n_images           Number of intermediate images
   nep_model          Path to the NEP model file
 Output:
-  NEB barrier profile (printed and plotted)
+  neb.traj               ASE Trajectory file with NEB optimization steps
+  neb.xyz                Final NEB path in extxyz format
+  images/                Directory containing individual image structures
+  images/transition_state.xyz  Transition state structure
+  images/image_*.xyz     All NEB image structures
+  images/fixed_atoms.txt Summary of fixed atom constraints
+  nep_barrier.png        Energy profile plot
+  (Note: interactive prompts for atom fixing method selection)
 Author:     Zhoulin LIU (1776627910@qq.com), Zihan YAN (yanzihan@westlake.edu.cn)
 Last-modified: 2026-05-16
 =============================================================================
 """
 import os
 import sys
+
+# Check command-line arguments before importing optional heavy dependencies.
+if __name__ == "__main__" and (len(sys.argv) != 5 or sys.argv[1] in ("-h", "--help")):
+    print(" Usage: gpumdkit.sh -calc neb <initial_structure> <final_structure> <n_images> <nep_model>")
+    print("    or: python neb_calculation.py <initial_structure> <final_structure> <n_images> <nep_model>")
+    print("")
+    print(" Arguments:")
+    print("   initial_structure  Path to the initial structure XYZ file")
+    print("   final_structure    Path to the final structure XYZ file")
+    print("   n_images           Number of intermediate images (e.g., 9)")
+    print("   nep_model          Path to the NEP model file")
+    print("")
+    print(" Example: gpumdkit.sh -calc neb init.xyz final.xyz 9 nep.txt")
+    print("")
+    sys.exit(0 if len(sys.argv) > 1 and sys.argv[1] in ("-h", "--help") else 1)
+
 import numpy as np
 from ase.io import read
 from ase.mep import NEB
@@ -40,11 +66,6 @@ def print_dependency_notice():
     print(" https://doi.org/10.21105/joss.06264")
 
 
-# Check command-line arguments
-if len(sys.argv) != 5:
-    print("python neb_calculation.py <initial_structure> <final_structure> <n_image> <nep_model>")
-    sys.exit(1)
-
 print_dependency_notice()
 
 initial_file = sys.argv[1]
diff --git a/Scripts/calculators/neb_calculation_neptrain.py b/Scripts/calculators/neb_calculation_neptrain.py
index a4e3958..ec644f4 100644
--- a/Scripts/calculators/neb_calculation_neptrain.py
+++ b/Scripts/calculators/neb_calculation_neptrain.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     neb_calculation_neptrain.py
 Category:   Calculator Scripts
@@ -16,7 +16,14 @@
   n_image            Number of intermediate images
   nep_model          Path to the NEP model file
 Output:
-  NEB barrier profile plot
+  neb.traj               ASE Trajectory file with NEB optimization steps
+  neb.xyz                Final NEB path in extxyz format
+  images/                Directory containing individual image structures
+  images/transition_state.xyz  Transition state structure
+  images/image_*.xyz     All NEB image structures
+  images/fixed_atoms.txt Summary of fixed atom constraints
+  nep_barrier.png        Energy profile plot
+  (Note: interactive prompts for atom fixing method selection)
 Author:     Zhoulin LIU (1776627910@qq.com)
 Last-modified: 2026-05-16
 =============================================================================
diff --git a/Scripts/calculators/rdf_calculator_ovito.py b/Scripts/calculators/rdf_calculator_ovito.py
index 8dda5c6..cfcbcb1 100644
--- a/Scripts/calculators/rdf_calculator_ovito.py
+++ b/Scripts/calculators/rdf_calculator_ovito.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     rdf_calculator_ovito.py
 Category:   Calculator Scripts
@@ -32,11 +32,11 @@
     sys.exit(1)
 
 exyzfile = sys.argv[1]
-cutoff = sys.argv[2]
-bins = sys.argv[3]
+cutoff = float(sys.argv[2])
+bins = int(sys.argv[3])
 
 pipeline = import_file(exyzfile)
-modifier = CoordinationAnalysisModifier(cutoff=cutoff,number_of_bins=bins,partial=True)
+modifier = CoordinationAnalysisModifier(cutoff=cutoff, number_of_bins=bins, partial=True)
 pipeline.modifiers.append(modifier)
 pipeline.modifiers.append(TimeAveragingModifier(operate_on='table:coordination-rdf'))
 export_file(pipeline,"rdf.txt","txt/table",key="coordination-rdf[average]")
diff --git a/Scripts/format_conversion/abacus2xyz_md.sh b/Scripts/format_conversion/abacus2xyz_md.sh
index 4032903..50c1823 100644
--- a/Scripts/format_conversion/abacus2xyz_md.sh
+++ b/Scripts/format_conversion/abacus2xyz_md.sh
@@ -3,7 +3,7 @@
 # GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-#           MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+#           MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 # =============================================================================
 # Script:     abacus2xyz_md.sh
 # Category:   Format Conversion Scripts
diff --git a/Scripts/format_conversion/abacus2xyz_scf.py b/Scripts/format_conversion/abacus2xyz_scf.py
index 906c495..28431a3 100644
--- a/Scripts/format_conversion/abacus2xyz_scf.py
+++ b/Scripts/format_conversion/abacus2xyz_scf.py
@@ -3,12 +3,13 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     abacus2xyz_scf.py
 Category:   Format Conversion Scripts
 Purpose:    Convert ABACUS SCF output files to extended XYZ format.
 Usage:      python abacus2xyz_scf.py <dir> <extxyz>
+            (invoked interactively via gpumdkit.sh menu 104)
 Arguments:
   dir      Directory containing ABACUS SCF outputs
   extxyz   Output extxyz file
@@ -25,8 +26,8 @@
 
 def main():
     if len(sys.argv) != 3:
-        print("Usage: python abacus2xyz_scf.py <dir> <extxyz>")
-        print("   or: gpumdkit.sh -abacus2xyz <dir> <extxyz>")
+        print(" Usage: python abacus2xyz_scf.py <dir> <extxyz>")
+        print("  (invoked interactively via gpumdkit.sh menu 104)")
         sys.exit(1)
 if __name__ == "__main__":
     main()
@@ -111,4 +112,3 @@ def get_scf_info(root):
         for i in range(natoms):
             f.write(f"{symbols[i]:<20}{positions[i][0]:20.10f}{positions[i][1]:20.10f}{positions[i][2]:20.10f}{forces[i][0]:20.10f}{forces[i][1]:20.10f}{forces[i][2]:20.10f} \n")  
     print(f" Successfully converted structure in {root} to extxyz format")
-
diff --git a/Scripts/format_conversion/abacus2xyz_scf.sh b/Scripts/format_conversion/abacus2xyz_scf.sh
index 3428e3a..5b6614f 100644
--- a/Scripts/format_conversion/abacus2xyz_scf.sh
+++ b/Scripts/format_conversion/abacus2xyz_scf.sh
@@ -3,7 +3,7 @@
 # GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-#           MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+#           MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 # =============================================================================
 # Script:     abacus2xyz_scf.sh
 # Category:   Format Conversion Scripts
diff --git a/Scripts/format_conversion/add_groups.py b/Scripts/format_conversion/add_groups.py
index 6dba5f9..2bf4d55 100644
--- a/Scripts/format_conversion/add_groups.py
+++ b/Scripts/format_conversion/add_groups.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     add_groups.py
 Category:   Format Conversion Scripts
 Purpose:    Add group information to atoms in a structure file based on
             element types, outputting the result to model.xyz.
-Usage:      python add_groups.py <input.xyz> <element1> <element2> ...
+Usage:      gpumdkit.sh -addgroup <input.xyz> <element1> <element2> ...
+            python add_groups.py <input.xyz> <element1> <element2> ...
 Arguments:
   input.xyz   Input structure file
   elementX    Element symbols to assign group indices
@@ -26,8 +27,8 @@
 
 # Check arguments
 if len(sys.argv) < 3:
-    print("Usage: python add_groups.py <input.xyz> <element1> <element2> ...")
-    print("   or: gpumdkit.sh -addgroup <input.xyz> <element1> <element2> ...")
+    print(" Usage: gpumdkit.sh -addgroup <input.xyz> <element1> <element2> ...")
+    print("    or: python add_groups.py <input.xyz> <element1> <element2> ...")
     sys.exit(1)
 
 # Read the file name from command line arguments
diff --git a/Scripts/format_conversion/add_weight.py b/Scripts/format_conversion/add_weight.py
index 4011e0f..4924463 100644
--- a/Scripts/format_conversion/add_weight.py
+++ b/Scripts/format_conversion/add_weight.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     add_weight.py
 Category:   Format Conversion Scripts
 Purpose:    Add a weight value to the 'Weight' attribute of each structure
             in an input file and save the modified structures.
-Usage:      python add_weight.py <input_file> <output_file> <new_weight>
+Usage:      gpumdkit.sh -addweight <input_file> <output_file> <new_weight>
+            python add_weight.py <input_file> <output_file> <new_weight>
 Arguments:
   input_file   Input structure file
   output_file  Output structure file with added weight
@@ -28,8 +29,8 @@
 def main():
     # Check if the correct number of arguments are provided
     if len(sys.argv) != 4:
-        print("Usage: python add_weight.py <input.xyz> <output.xyz> <weight>")
-        print("   or: gpumdkit.sh -addweight <input.xyz> <output.xyz> <weight>")
+        print(" Usage: gpumdkit.sh -addweight <input.xyz> <output.xyz> <weight>")
+        print("    or: python add_weight.py <input.xyz> <output.xyz> <weight>")
         sys.exit(1)
 
     # Parse command line arguments
diff --git a/Scripts/format_conversion/cif2exyz.py b/Scripts/format_conversion/cif2exyz.py
index 0f56b72..13c89ea 100644
--- a/Scripts/format_conversion/cif2exyz.py
+++ b/Scripts/format_conversion/cif2exyz.py
@@ -3,12 +3,13 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     cif2exyz.py
 Category:   Format Conversion Scripts
 Purpose:    Convert CIF file to extended XYZ format using ASE.
-Usage:      python cif2exyz.py <input.cif> <output.xyz>
+Usage:      gpumdkit.sh -cif2exyz <input.cif> <output.xyz>
+            python cif2exyz.py <input.cif> <output.xyz>
 Arguments:
   input.cif   Input CIF file
   output.xyz  Output extxyz file
@@ -24,8 +25,8 @@
 
 # Check command line arguments
 if len(sys.argv) != 3:
-    print("Usage: python cif2exyz.py <input.cif> <output.xyz>")
-    print("   or: gpumdkit.sh -cif2exyz <input.cif> <output.xyz>")
+    print(" Usage: gpumdkit.sh -cif2exyz <input.cif> <output.xyz>")
+    print("    or: python cif2exyz.py <input.cif> <output.xyz>")
     sys.exit(1)
 
 # Read input and output file paths
diff --git a/Scripts/format_conversion/cif2pos.py b/Scripts/format_conversion/cif2pos.py
index 8624acc..e3a24bd 100644
--- a/Scripts/format_conversion/cif2pos.py
+++ b/Scripts/format_conversion/cif2pos.py
@@ -3,12 +3,13 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     cif2pos.py
 Category:   Format Conversion Scripts
 Purpose:    Convert CIF file to VASP POSCAR format using ASE.
-Usage:      python cif2pos.py <input.cif> <output.vasp>
+Usage:      gpumdkit.sh -cif2pos <input.cif> <output.vasp>
+            python cif2pos.py <input.cif> <output.vasp>
 Arguments:
   input.cif    Input CIF file
   output.vasp  Output VASP POSCAR file
@@ -24,8 +25,8 @@
 
 # Check command line arguments
 if len(sys.argv) != 3:
-    print("Usage: python cif2pos.py <input.cif> <output.vasp>")
-    print("   or: gpumdkit.sh -cif2pos <input.cif> <output.vasp>")
+    print(" Usage: gpumdkit.sh -cif2pos <input.cif> <output.vasp>")
+    print("    or: python cif2pos.py <input.cif> <output.vasp>")
     sys.exit(1)
 
 # Read input and output file paths
diff --git a/Scripts/format_conversion/clean_xyz.py b/Scripts/format_conversion/clean_xyz.py
index 62faf75..20918d2 100644
--- a/Scripts/format_conversion/clean_xyz.py
+++ b/Scripts/format_conversion/clean_xyz.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     clean_xyz.py
 Category:   Format Conversion Scripts
 Purpose:    Remove stress, virial, and force information from an extxyz
             training file, keeping only structural information.
-Usage:      python clean_xyz.py <input.xyz> <output.xyz>
+Usage:      gpumdkit.sh -clean_xyz <input.xyz> <output.xyz>
+            python clean_xyz.py <input.xyz> <output.xyz>
 Arguments:
   input.xyz    Input extxyz training file
   output.xyz   Output cleaned extxyz file
@@ -25,8 +26,8 @@
 
 # Check arguments
 if len(sys.argv) < 3:
-    print("Usage: python clean_xyz.py <input.xyz> <output.xyz>")
-    print("   or: gpumdkit.sh -clean_xyz <input.xyz> <output.xyz>")
+    print(" Usage: gpumdkit.sh -clean_xyz <input.xyz> <output.xyz>")
+    print("    or: python clean_xyz.py <input.xyz> <output.xyz>")
     sys.exit(1)
 
 # Read all frames from the input train.xyz file
diff --git a/Scripts/format_conversion/cp2k2xyz.py b/Scripts/format_conversion/cp2k2xyz.py
index ca10567..01238fd 100644
--- a/Scripts/format_conversion/cp2k2xyz.py
+++ b/Scripts/format_conversion/cp2k2xyz.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     cp2k2xyz.py
 Category:   Format Conversion Scripts
diff --git a/Scripts/format_conversion/cp2k_log2xyz.py b/Scripts/format_conversion/cp2k_log2xyz.py
index e88ed24..c4655f0 100644
--- a/Scripts/format_conversion/cp2k_log2xyz.py
+++ b/Scripts/format_conversion/cp2k_log2xyz.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     cp2k_log2xyz.py
 Category:   Format Conversion Scripts
diff --git a/Scripts/format_conversion/exyz2lmp.py b/Scripts/format_conversion/exyz2lmp.py
index f9e6d2b..630fc5f 100644
--- a/Scripts/format_conversion/exyz2lmp.py
+++ b/Scripts/format_conversion/exyz2lmp.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     exyz2lmp.py
 Category:   Format Conversion Scripts
@@ -70,7 +70,7 @@ def convert_extxyz_to_lammps_data(extxyz_file, lammps_data_file):
 
 if __name__ == '__main__':
     if len(sys.argv) != 3:
-        print("Usage: python exyz2lmp.py <extxyz_file> <lammps_data_file>")
+        print(" Usage: python exyz2lmp.py <extxyz_file> <lammps_data_file>")
         sys.exit(1)
     
     extxyz_file = sys.argv[1]
diff --git a/Scripts/format_conversion/exyz2pos.py b/Scripts/format_conversion/exyz2pos.py
index bf00692..148d446 100644
--- a/Scripts/format_conversion/exyz2pos.py
+++ b/Scripts/format_conversion/exyz2pos.py
@@ -3,16 +3,17 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     exyz2pos.py
 Category:   Format Conversion Scripts
 Purpose:    Convert extended XYZ file(s) to VASP POSCAR format(s).
-Usage:      python exyz2pos.py <input.xyz>
+Usage:      gpumdkit.sh -exyz2pos <input.xyz>
+            python exyz2pos.py <input.xyz>
 Arguments:
-  extxyz_file Input extxyz file (default: train.xyz)
+  input.xyz  Input extxyz file
 Output:
-  POSCAR file(s) in VASP format
+  POSCAR_*.vasp   POSCAR file(s) in VASP format (one per frame)
 Author:     Zihan YAN (yanzihan@westlake.edu.cn)
 Last-modified: 2026-05-16
 =============================================================================
@@ -32,8 +33,8 @@ def print_progress_bar(iteration, total, length=50):
 
 # Check arguments
 if len(sys.argv) < 2:
-    print("Usage: python exyz2pos.py <input.xyz>")
-    print("   or: gpumdkit.sh -exyz2pos <input.xyz>")
+    print(" Usage: gpumdkit.sh -exyz2pos <input.xyz>")
+    print("    or: python exyz2pos.py <input.xyz>")
     sys.exit(1)
 
 input_file = sys.argv[1]
diff --git a/Scripts/format_conversion/get_frame.py b/Scripts/format_conversion/get_frame.py
index 10ead91..bd3a918 100644
--- a/Scripts/format_conversion/get_frame.py
+++ b/Scripts/format_conversion/get_frame.py
@@ -3,12 +3,13 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     get_frame.py
 Category:   Format Conversion Scripts
 Purpose:    Extract a single frame from an extxyz trajectory by frame number.
-Usage:      python get_frame.py <input.xyz> <frame_number>
+Usage:      gpumdkit.sh -get_frame <input.xyz> <frame_number>
+            python get_frame.py <input.xyz> <frame_number>
 Arguments:
   input.xyz      Input extxyz trajectory file
   frame_number   Frame number to extract (1-indexed)
@@ -24,8 +25,8 @@
 
 # Check arguments
 if len(sys.argv) < 3:
-    print("Usage: python get_frame.py <input.xyz> <frame_number>")
-    print("   or: gpumdkit.sh -get_frame <input.xyz> <frame_number>")
+    print(" Usage: gpumdkit.sh -get_frame <input.xyz> <frame_number>")
+    print("    or: python get_frame.py <input.xyz> <frame_number>")
     sys.exit(1)
 
 def get_frame():
diff --git a/Scripts/format_conversion/lmp2exyz.py b/Scripts/format_conversion/lmp2exyz.py
index 08f9ad4..9ff11ce 100644
--- a/Scripts/format_conversion/lmp2exyz.py
+++ b/Scripts/format_conversion/lmp2exyz.py
@@ -3,18 +3,19 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     lmp2exyz.py
 Category:   Format Conversion Scripts
 Purpose:    Convert LAMMPS dump file to extended XYZ format with proper
             element type mapping.
-Usage:      python lmp2exyz.py <dump_file> <element1> <element2> ...
+Usage:      gpumdkit.sh -lmp2exyz <dump_file> <element1> <element2> ...
+            python lmp2exyz.py <dump_file> <element1> <element2> ...
 Arguments:
   dump_file  Input LAMMPS dump file
   elementX   Chemical element symbols in order of atomic types
 Output:
-  Converted structures in extxyz format
+  dump.xyz   Converted structures in extxyz format
 Author:     Zihan YAN (yanzihan@westlake.edu.cn)
 Last-modified: 2026-05-16
 =============================================================================
@@ -48,8 +49,8 @@ def lmp2exyz(dump_file, elements):
 
 if __name__ == '__main__':
     if len(sys.argv) < 3:
-        print("Usage: python lmp2exyz.py <dump_file> <element1> <element2> ...")
-        print("   or: gpumdkit.sh -lmp2exyz <dump_file> <element1> <element2> ...")
+        print(" Usage: gpumdkit.sh -lmp2exyz <dump_file> <element1> <element2> ...")
+        print("    or: python lmp2exyz.py <dump_file> <element1> <element2> ...")
         sys.exit(1)
     
     dump_file = sys.argv[1]
diff --git a/Scripts/format_conversion/mtp2xyz.py b/Scripts/format_conversion/mtp2xyz.py
index aca1e12..fd226e0 100644
--- a/Scripts/format_conversion/mtp2xyz.py
+++ b/Scripts/format_conversion/mtp2xyz.py
@@ -3,18 +3,19 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     mtp2xyz.py
 Category:   Format Conversion Scripts
 Purpose:    Convert MTP (Machine Learning Interatomic Potential) input file
-            format to extended XYZ using dpdata.
-Usage:      python mtp2xyz.py <train.cfg> <Symbol1> <Symbol2> ...
+            format to extended XYZ using a custom cfg parser and ASE.
+Usage:      Interactive: gpumdkit.sh -> 1 -> 102
+            python mtp2xyz.py <train.cfg> <Symbol1> <Symbol2> ...
 Arguments:
   train.cfg   MTP training data file
   SymbolX     Chemical element symbols in order
 Output:
-  Converted structure in extxyz format (printed to terminal or saved)
+  XYZ/mtp2xyz.xyz   Converted structures in extxyz format
 Author:     Ke XU (kickhsu@gmail.com)
 Last-modified: 2026-05-16
 =============================================================================
@@ -134,7 +135,7 @@ def dump_xyz(frames):
 if __name__ == "__main__":
     # Check arguments
     if len(sys.argv) < 3:
-        print("Usage: python mtp2xyz.py <train.cfg> <Symbol1> <Symbol2> ...")
+        print(" Usage: python mtp2xyz.py <train.cfg> <Symbol1> <Symbol2> ...")
         sys.exit(1)
     
     type_to_symbol = {i: s for i, s in enumerate(sys.argv[2:])}
diff --git a/Scripts/format_conversion/out2exyz.py b/Scripts/format_conversion/out2exyz.py
index 72a4c7e..9d4786b 100644
--- a/Scripts/format_conversion/out2exyz.py
+++ b/Scripts/format_conversion/out2exyz.py
@@ -3,15 +3,18 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     out2exyz.py
 Category:   Format Conversion Scripts
 Purpose:    Convert VASP OUTCAR files to extended XYZ format with energy,
-            forces, stress, and virial information.
-Usage:      python out2exyz.py <directory>
+            forces, and virial information.
+Usage:      gpumdkit.sh -out2exyz <directory>
+            python out2exyz.py <directory>
+Arguments:
+  directory  Root directory to search for OUTCAR files
 Output:
-  Converted structures in extxyz format
+  train.xyz  Converted structures in extxyz format
 Author:     Zihan YAN (yanzihan@westlake.edu.cn)
 Last-modified: 2026-05-16
 =============================================================================
@@ -25,8 +28,8 @@
 
 # Check arguments
 if len(sys.argv) < 2:
-    print("Usage: python out2exyz.py <directory>")
-    print("   or: gpumdkit.sh -out2exyz <directory>")
+    print(" Usage: gpumdkit.sh -out2exyz <directory>")
+    print("    or: python out2exyz.py <directory>")
     sys.exit(1)
 
 def Convert_atoms(atom):
diff --git a/Scripts/format_conversion/out2xyz.sh b/Scripts/format_conversion/out2xyz.sh
index 8c46b64..b612524 100644
--- a/Scripts/format_conversion/out2xyz.sh
+++ b/Scripts/format_conversion/out2xyz.sh
@@ -3,7 +3,7 @@
 # GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-#           MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+#           MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 # =============================================================================
 # Script:     out2xyz.sh
 # Category:   Format Conversion Scripts
diff --git a/Scripts/format_conversion/pos2exyz.py b/Scripts/format_conversion/pos2exyz.py
index 211d450..d778f69 100644
--- a/Scripts/format_conversion/pos2exyz.py
+++ b/Scripts/format_conversion/pos2exyz.py
@@ -3,12 +3,13 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     pos2exyz.py
 Category:   Format Conversion Scripts
 Purpose:    Convert one or more VASP POSCAR files to extended XYZ format.
-Usage:      python pos2exyz.py <POSCAR> <output.xyz>
+Usage:      gpumdkit.sh -pos2exyz <POSCAR> <output.xyz>
+            python pos2exyz.py <POSCAR> <output.xyz>
 Arguments:
   POSCAR       One or more VASP POSCAR files
   output.xyz   Output extxyz file
@@ -44,8 +45,8 @@ def convert_poscar_to_extxyz(poscar_filenames, extxyz_filename):
 if __name__ == '__main__':
     # Check if the number of arguments is correct
     if len(sys.argv) < 3:
-        print("Usage: python pos2exyz.py <POSCAR> <output.xyz>")
-        print("   or: gpumdkit.sh -pos2exyz <POSCAR> <output.xyz>")
+        print(" Usage: gpumdkit.sh -pos2exyz <POSCAR> <output.xyz>")
+        print("    or: python pos2exyz.py <POSCAR> <output.xyz>")
         sys.exit(1)
 
     poscar_filename_pattern = sys.argv[1]
diff --git a/Scripts/format_conversion/pos2lmp.py b/Scripts/format_conversion/pos2lmp.py
index 83122ae..b266b40 100644
--- a/Scripts/format_conversion/pos2lmp.py
+++ b/Scripts/format_conversion/pos2lmp.py
@@ -3,12 +3,13 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     pos2lmp.py
 Category:   Format Conversion Scripts
 Purpose:    Convert VASP POSCAR file to LAMMPS data format using OVITO.
-Usage:      python pos2lmp.py <poscar_file> <lammps_data_file>
+Usage:      gpumdkit.sh -pos2lmp <poscar_file> <lammps_data_file>
+            python pos2lmp.py <poscar_file> <lammps_data_file>
 Arguments:
   poscar_file      Input VASP POSCAR file
   lammps_data_file Output LAMMPS data file
@@ -29,8 +30,8 @@ def convert_poscar_to_lammps(poscar_path, lammps_data_path):
 
 if __name__ == "__main__":
     if len(sys.argv) != 3:
-        print("Usage: python pos2lmp.py <poscar_file> <lammps_data_file>")
-        print("   or: gpumdkit.sh -pos2lmp <poscar_file> <lammps_data_file>")
+        print(" Usage: gpumdkit.sh -pos2lmp <poscar_file> <lammps_data_file>")
+        print("    or: python pos2lmp.py <poscar_file> <lammps_data_file>")
         sys.exit(1)
     
     poscar_file = sys.argv[1]
diff --git a/Scripts/format_conversion/replicate.py b/Scripts/format_conversion/replicate.py
index cb574ad..34bd484 100644
--- a/Scripts/format_conversion/replicate.py
+++ b/Scripts/format_conversion/replicate.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     replicate.py
 Category:   Format Conversion Scripts
@@ -106,10 +106,10 @@ def reorder_atoms_by_input_species_order(atoms, original_atoms):
 
 def main():
     if len(sys.argv) < 4:
-        print("Usage 1: python replicate.py input.vasp output.vasp a b c")
-        print("Usage 2: python replicate.py input.vasp output.vasp target_num")
-        print("   or: gpumdkit.sh -replicate input.vasp output.vasp a b c")
-        print("   or: gpumdkit.sh -replicate input.vasp output.vasp target_num")
+        print(" Usage 1: gpumdkit.sh -replicate input.vasp output.vasp a b c")
+        print(" Usage 2: gpumdkit.sh -replicate input.vasp output.vasp target_num")
+        print("    or: python replicate.py input.vasp output.vasp a b c")
+        print("    or: python replicate.py input.vasp output.vasp target_num")
         sys.exit(1)
 
     infile = sys.argv[1]
@@ -173,4 +173,4 @@ def main():
         sys.exit(1)
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()
diff --git a/Scripts/format_conversion/split_single_xyz.py b/Scripts/format_conversion/split_single_xyz.py
index b862765..3728c41 100644
--- a/Scripts/format_conversion/split_single_xyz.py
+++ b/Scripts/format_conversion/split_single_xyz.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     split_single_xyz.py
 Category:   Format Conversion Scripts
@@ -45,7 +45,7 @@ def split_xyz_to_individual_models(input_xyz_filename):
 if __name__ == '__main__':
     # Check if the number of arguments is correct
     if len(sys.argv) < 2:
-        print("Usage: python split_single_xyz.py <input.xyz>")
+        print(" Usage: python split_single_xyz.py <input.xyz>")
         sys.exit(1)
 
     # Get input XYZ filename from command line argument
diff --git a/Scripts/format_conversion/traj2exyz.py b/Scripts/format_conversion/traj2exyz.py
index 7466b7d..30bdddb 100644
--- a/Scripts/format_conversion/traj2exyz.py
+++ b/Scripts/format_conversion/traj2exyz.py
@@ -3,12 +3,13 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     traj2exyz.py
 Category:   Format Conversion Scripts
 Purpose:    Convert an ASE .traj trajectory file to extended XYZ format.
-Usage:      python traj2exyz.py <input.traj> <output.xyz>
+Usage:      gpumdkit.sh -traj2exyz <input.traj> <output.xyz>
+            python traj2exyz.py <input.traj> <output.xyz>
 Arguments:
   input.traj   Input ASE trajectory file
   output.xyz   Output extxyz file
@@ -47,8 +48,8 @@ def convert_traj_to_extxyz(input_file, output_file):
 if __name__ == "__main__":
     # Check if correct number of arguments are provided
     if len(sys.argv) != 3:
-        print("Usage: python traj2exyz.py <input.traj> <output.xyz>")
-        print("   or: gpumdkit.sh -traj2exyz <input.traj> <output.xyz>")
+        print(" Usage: gpumdkit.sh -traj2exyz <input.traj> <output.xyz>")
+        print("    or: python traj2exyz.py <input.traj> <output.xyz>")
         sys.exit(1)
     
     input_path = sys.argv[1]
diff --git a/Scripts/format_conversion/xdatcar2exyz.py b/Scripts/format_conversion/xdatcar2exyz.py
index e910238..8d3ca60 100644
--- a/Scripts/format_conversion/xdatcar2exyz.py
+++ b/Scripts/format_conversion/xdatcar2exyz.py
@@ -3,12 +3,13 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     xdatcar2exyz.py
 Category:   Format Conversion Scripts
 Purpose:    Convert VASP XDATCAR file to extended XYZ format using ASE.
-Usage:      python xdatcar2exyz.py <XDATCAR> <output.xyz>
+Usage:      gpumdkit.sh -xdat2exyz <XDATCAR> <output.xyz>
+            python xdatcar2exyz.py <XDATCAR> <output.xyz>
 Arguments:
   input       Path to the input XDATCAR file
   output      Path to the output .xyz file
@@ -24,8 +25,8 @@
 
 # Check arguments
 if len(sys.argv) < 3:
-    print("Usage: python xdatcar2exyz.py <XDATCAR> <output.xyz>")
-    print("   or: gpumdkit.sh -xdat2exyz <XDATCAR> <output.xyz>")
+    print(" Usage: gpumdkit.sh -xdat2exyz <XDATCAR> <output.xyz>")
+    print("    or: python xdatcar2exyz.py <XDATCAR> <output.xyz>")
     sys.exit(1)
 
 input_file = sys.argv[1]
diff --git a/Scripts/plt_scripts/README.md b/Scripts/plt_scripts/README.md
index 6b31e32..b217b1d 100644
--- a/Scripts/plt_scripts/README.md
+++ b/Scripts/plt_scripts/README.md
@@ -598,7 +598,7 @@ gpumdkit.sh -plt dimer Li Li nep.txt
     <img src="../../docs/Gallery/dimer.png" alt="Dimer comparison" width="45%" />
 </div>
 
-**Reference:** [arXiv:2504.15925](https://doi.org/10.48550/arXiv.2504.15925)
+**Reference:** [J. Chem. Inf. Model. 2026, 66, 3, 1406-1413](https://doi.org/10.1021/acs.jcim.5c02335)
 
 ---
 
diff --git a/Scripts/plt_scripts/plt_arrhenius_d.py b/Scripts/plt_scripts/plt_arrhenius_d.py
index 88e84a1..da3e70a 100644
--- a/Scripts/plt_scripts/plt_arrhenius_d.py
+++ b/Scripts/plt_scripts/plt_arrhenius_d.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_arrhenius_d.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_arrhenius_d_xyz.py b/Scripts/plt_scripts/plt_arrhenius_d_xyz.py
index 0888897..c94b4ee 100644
--- a/Scripts/plt_scripts/plt_arrhenius_d_xyz.py
+++ b/Scripts/plt_scripts/plt_arrhenius_d_xyz.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_arrhenius_d_xyz.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_arrhenius_sigma.py b/Scripts/plt_scripts/plt_arrhenius_sigma.py
index 4102f80..6611d63 100644
--- a/Scripts/plt_scripts/plt_arrhenius_sigma.py
+++ b/Scripts/plt_scripts/plt_arrhenius_sigma.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_arrhenius_sigma.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_arrhenius_sigma_xyz.py b/Scripts/plt_scripts/plt_arrhenius_sigma_xyz.py
index 333b0fc..169a05e 100644
--- a/Scripts/plt_scripts/plt_arrhenius_sigma_xyz.py
+++ b/Scripts/plt_scripts/plt_arrhenius_sigma_xyz.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_arrhenius_sigma_xyz.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_born_charge.py b/Scripts/plt_scripts/plt_born_charge.py
index 8614abf..f7f1a2b 100644
--- a/Scripts/plt_scripts/plt_born_charge.py
+++ b/Scripts/plt_scripts/plt_born_charge.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_born_charge.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_charge.py b/Scripts/plt_scripts/plt_charge.py
index cf534aa..abe8179 100644
--- a/Scripts/plt_scripts/plt_charge.py
+++ b/Scripts/plt_scripts/plt_charge.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_charge.py
 Category:   Plot Scripts
@@ -13,8 +13,11 @@
             python plt_charge.py [save]
 Arguments:
   save      Save the plot as 'charge.png' instead of displaying it
+Input files (required in working directory):
+  train.xyz         Training structures in extxyz format
+  charge_train.out  Charge data from qNEP model
 Output:
-  Display of charge distribution plot
+  charge.png   Charge distribution plot (saved or displayed)
 Author:     Zihan YAN (yanzihan@westlake.edu.cn)
 Last-modified: 2026-05-16
 =============================================================================
diff --git a/Scripts/plt_scripts/plt_cohesive.py b/Scripts/plt_scripts/plt_cohesive.py
index d22fdd1..09ebd92 100644
--- a/Scripts/plt_scripts/plt_cohesive.py
+++ b/Scripts/plt_scripts/plt_cohesive.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_cohesive.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_descriptors.py b/Scripts/plt_scripts/plt_descriptors.py
index fc73f15..6441dcb 100644
--- a/Scripts/plt_scripts/plt_descriptors.py
+++ b/Scripts/plt_scripts/plt_descriptors.py
@@ -3,14 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_descriptors.py
 Category:   Plot Scripts
 Purpose:    Visualize high-dimensional NEP descriptors using dimensionality
             reduction (PCA or UMAP) with configurable file paths and labels.
-Usage:      gpumdkit.sh -plt des <method>
-            python plt_descriptors.py <method> <file1> <file2> ...
+Usage:      gpumdkit.sh -plt des <method> <file1.npy> <file2.npy> ...
+            python plt_descriptors.py <method> <file1.npy> <file2.npy> ...
 Arguments:
   method    Dimensionality reduction method: 'pca' or 'umap'
   file1...  Paths to .npy files containing descriptors
@@ -110,7 +110,8 @@ def plot_reduced_data(reduced_splits, labels, method):
 def main():
     # Check command-line arguments
     if len(sys.argv) < 3:
-        print("Usage: python plt_descriptors.py <method> <file1.npy> <file2.npy> ...")
+        print("Usage: gpumdkit.sh -plt des <method> <file1.npy> <file2.npy> ...")
+        print("   or: python plt_descriptors.py <method> <file1.npy> <file2.npy> ...")
         print("Method: 'pca' or 'umap'")
         sys.exit(1)
     
diff --git a/Scripts/plt_scripts/plt_descriptors_compare.py b/Scripts/plt_scripts/plt_descriptors_compare.py
index c33f80c..b57b663 100644
--- a/Scripts/plt_scripts/plt_descriptors_compare.py
+++ b/Scripts/plt_scripts/plt_descriptors_compare.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_descriptors_compare.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_dimer.py b/Scripts/plt_scripts/plt_dimer.py
index 38a31c2..b6fde58 100644
--- a/Scripts/plt_scripts/plt_dimer.py
+++ b/Scripts/plt_scripts/plt_dimer.py
@@ -3,14 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_dimer.py
 Category:   Plot Scripts
 Purpose:    Plot dimer interaction curves (energy and force vs distance)
             for a pair of atoms using a NEP model.
-Usage:      gpumdkit.sh -plt dimer <element1> <element2> <nep_dir>
-            python plt_dimer.py <element1> <element2> <nep_dir>
+Usage:      gpumdkit.sh -plt dimer <element1> <element2> <nep_dir> [save]
+            python plt_dimer.py <element1> <element2> <nep_dir> [save]
 Arguments:
   element1, element2  Atom symbols (e.g., Li Li)
   nep_dir             Path to the NEP potential file (e.g., ./nep.txt)
@@ -42,7 +42,8 @@ def print_dependency_notice():
 
 # Check the number of command-line arguments
 if len(sys.argv) < 4:
-    print("Usage: python plt_dimer.py <atom_symbol1> <atom_symbol2> <nep_dir>")
+    print("Usage: gpumdkit.sh -plt dimer <element1> <element2> <nep_dir> [save]")
+    print("   or: python plt_dimer.py <atom_symbol1> <atom_symbol2> <nep_dir>")
     print("Example: python plt_dimer.py Li Li ./nep.txt")
     sys.exit(1)
 
diff --git a/Scripts/plt_scripts/plt_doas.py b/Scripts/plt_scripts/plt_doas.py
index 9faceda..2fff1da 100644
--- a/Scripts/plt_scripts/plt_doas.py
+++ b/Scripts/plt_scripts/plt_doas.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_doas.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_emd.py b/Scripts/plt_scripts/plt_emd.py
index d093095..585cff7 100644
--- a/Scripts/plt_scripts/plt_emd.py
+++ b/Scripts/plt_scripts/plt_emd.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_emd.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_force_errors.py b/Scripts/plt_scripts/plt_force_errors.py
index 49c2ec5..e051bba 100644
--- a/Scripts/plt_scripts/plt_force_errors.py
+++ b/Scripts/plt_scripts/plt_force_errors.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_force_errors.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_hnemd.py b/Scripts/plt_scripts/plt_hnemd.py
index 73e54fd..6c81b01 100644
--- a/Scripts/plt_scripts/plt_hnemd.py
+++ b/Scripts/plt_scripts/plt_hnemd.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_hnemd.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_learning_rate.py b/Scripts/plt_scripts/plt_learning_rate.py
index ed580c3..0b0a1f9 100644
--- a/Scripts/plt_scripts/plt_learning_rate.py
+++ b/Scripts/plt_scripts/plt_learning_rate.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_learning_rate.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_msd.py b/Scripts/plt_scripts/plt_msd.py
index 58f6a07..7524a7c 100644
--- a/Scripts/plt_scripts/plt_msd.py
+++ b/Scripts/plt_scripts/plt_msd.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_msd.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_msd_all.py b/Scripts/plt_scripts/plt_msd_all.py
index a1709d0..2fad542 100644
--- a/Scripts/plt_scripts/plt_msd_all.py
+++ b/Scripts/plt_scripts/plt_msd_all.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_msd_all.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_msd_convergence_check.py b/Scripts/plt_scripts/plt_msd_convergence_check.py
index d971bac..a32ac83 100644
--- a/Scripts/plt_scripts/plt_msd_convergence_check.py
+++ b/Scripts/plt_scripts/plt_msd_convergence_check.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_msd_convergence_check.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_msd_sdc.py b/Scripts/plt_scripts/plt_msd_sdc.py
index 05bcbd4..d6f6272 100644
--- a/Scripts/plt_scripts/plt_msd_sdc.py
+++ b/Scripts/plt_scripts/plt_msd_sdc.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_msd_sdc.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_nemd.py b/Scripts/plt_scripts/plt_nemd.py
index 2bee6db..6494dfc 100644
--- a/Scripts/plt_scripts/plt_nemd.py
+++ b/Scripts/plt_scripts/plt_nemd.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_nemd.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_nep_restart.py b/Scripts/plt_scripts/plt_nep_restart.py
index a389a2f..1940648 100644
--- a/Scripts/plt_scripts/plt_nep_restart.py
+++ b/Scripts/plt_scripts/plt_nep_restart.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_nep_restart.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_net_force.py b/Scripts/plt_scripts/plt_net_force.py
index a8a88ab..75d90e2 100644
--- a/Scripts/plt_scripts/plt_net_force.py
+++ b/Scripts/plt_scripts/plt_net_force.py
@@ -3,13 +3,13 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_net_force.py
 Category:   Plot Scripts
 Purpose:    Plot distribution of net forces on structures to identify
             problematic configurations in training datasets.
-Usage:      gpumdkit.sh -plt net_force <extxyzfile>
+Usage:      gpumdkit.sh -plt net_force <extxyzfile> [save]
             python plt_net_force.py <extxyzfile> [save]
 Arguments:
   extxyzfile  Path to the extended XYZ file (e.g., train.xyz)
@@ -217,7 +217,8 @@ def check_convergence(xyz_file, threshold=0.001, save_flag=False):
 # Main function
 def main():
     if len(sys.argv) < 2:
-        print(" Usage: python plt_net_force.py train.xyz [save]")
+        print(" Usage: gpumdkit.sh -plt net_force <extxyzfile> [save]")
+        print("    or: python plt_net_force.py <extxyzfile> [save]")
         sys.exit(1)
     
     xyz_file = sys.argv[1]
diff --git a/Scripts/plt_scripts/plt_parity_density.py b/Scripts/plt_scripts/plt_parity_density.py
index d944554..3862e74 100644
--- a/Scripts/plt_scripts/plt_parity_density.py
+++ b/Scripts/plt_scripts/plt_parity_density.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_parity_density.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_pdos.py b/Scripts/plt_scripts/plt_pdos.py
index 5006c5e..f1c28fa 100644
--- a/Scripts/plt_scripts/plt_pdos.py
+++ b/Scripts/plt_scripts/plt_pdos.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_pdos.py
 Category:   Plot Scripts
@@ -45,7 +45,8 @@ def set_fig_properties(ax_list, tl=4, tw=1.2, tlm=4):
 trap = np.trapezoid if hasattr(np, "trapezoid") else np.trapz
 
 def print_usage():
-    print("Usage: python plt_pdos.py [save]")
+    print("Usage: gpumdkit.sh -plt pdos [save]")
+    print("   or: python plt_pdos.py [save]")
     print("  save : Optional. If provided, saves figures (.png) and data (.xlsx).")
 
 class VAC_DOS_Processor:
diff --git a/Scripts/plt_scripts/plt_plane_grid.py b/Scripts/plt_scripts/plt_plane_grid.py
index b7596ed..b782ca6 100644
--- a/Scripts/plt_scripts/plt_plane_grid.py
+++ b/Scripts/plt_scripts/plt_plane_grid.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_plane_grid.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_prediction.py b/Scripts/plt_scripts/plt_prediction.py
index ba36883..c5ea16f 100644
--- a/Scripts/plt_scripts/plt_prediction.py
+++ b/Scripts/plt_scripts/plt_prediction.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_prediction.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_prediction2.py b/Scripts/plt_scripts/plt_prediction2.py
index ad555a3..7fb5ec7 100644
--- a/Scripts/plt_scripts/plt_prediction2.py
+++ b/Scripts/plt_scripts/plt_prediction2.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_prediction2.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_rdf.py b/Scripts/plt_scripts/plt_rdf.py
index 133cc86..2f009dc 100644
--- a/Scripts/plt_scripts/plt_rdf.py
+++ b/Scripts/plt_scripts/plt_rdf.py
@@ -3,19 +3,18 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_rdf.py
 Category:   Plot Scripts
 Purpose:    Plot radial distribution function (RDF) from rdf.out showing
             pair correlations for all atom pairs.
-Usage:      gpumdkit.sh -plt rdf [column] [save]
+Usage:      gpumdkit.sh -plt rdf [save]
             python plt_rdf.py [save]
 Arguments:
-  column   Optional column index to plot a specific RDF pair
-  save     Save the plot as PNG instead of displaying it
+  save     Save the plot as 'rdf.png' instead of displaying it
 Output:
-  RDF plot(s) displayed or saved
+  rdf.png  RDF plot (saved or displayed)
 Author:     Zihan YAN (yanzihan@westlake.edu.cn)
 Last-modified: 2026-05-16
 =============================================================================
diff --git a/Scripts/plt_scripts/plt_rdf_pmf.py b/Scripts/plt_scripts/plt_rdf_pmf.py
index 49a93fe..c522b9f 100644
--- a/Scripts/plt_scripts/plt_rdf_pmf.py
+++ b/Scripts/plt_scripts/plt_rdf_pmf.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_rdf_pmf.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_sdc.py b/Scripts/plt_scripts/plt_sdc.py
index 3d6c948..8c4b726 100644
--- a/Scripts/plt_scripts/plt_sdc.py
+++ b/Scripts/plt_scripts/plt_sdc.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_sdc.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_thermo.py b/Scripts/plt_scripts/plt_thermo.py
index a89ef10..1cfe764 100644
--- a/Scripts/plt_scripts/plt_thermo.py
+++ b/Scripts/plt_scripts/plt_thermo.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_thermo.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_thermo2.py b/Scripts/plt_scripts/plt_thermo2.py
index 9fa8818..07d3063 100644
--- a/Scripts/plt_scripts/plt_thermo2.py
+++ b/Scripts/plt_scripts/plt_thermo2.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_thermo2.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_thermo3.py b/Scripts/plt_scripts/plt_thermo3.py
index a13d9de..321dc80 100644
--- a/Scripts/plt_scripts/plt_thermo3.py
+++ b/Scripts/plt_scripts/plt_thermo3.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_thermo3.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_train.py b/Scripts/plt_scripts/plt_train.py
index 8a5f4eb..e3c9869 100644
--- a/Scripts/plt_scripts/plt_train.py
+++ b/Scripts/plt_scripts/plt_train.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_train.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_train_density.py b/Scripts/plt_scripts/plt_train_density.py
index 6b8baf4..97bbaae 100644
--- a/Scripts/plt_scripts/plt_train_density.py
+++ b/Scripts/plt_scripts/plt_train_density.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_train_density.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_train_test.py b/Scripts/plt_scripts/plt_train_test.py
index 06eb442..01a9b1f 100644
--- a/Scripts/plt_scripts/plt_train_test.py
+++ b/Scripts/plt_scripts/plt_train_test.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_train_test.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_vac.py b/Scripts/plt_scripts/plt_vac.py
index d5fe943..5af1fd4 100644
--- a/Scripts/plt_scripts/plt_vac.py
+++ b/Scripts/plt_scripts/plt_vac.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_vac.py
 Category:   Plot Scripts
diff --git a/Scripts/plt_scripts/plt_viscosity.py b/Scripts/plt_scripts/plt_viscosity.py
index a782bb0..957c22f 100644
--- a/Scripts/plt_scripts/plt_viscosity.py
+++ b/Scripts/plt_scripts/plt_viscosity.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     plt_viscosity.py
 Category:   Plot Scripts
diff --git a/Scripts/sample_structures/frame_range.py b/Scripts/sample_structures/frame_range.py
index b59d4fd..231648a 100644
--- a/Scripts/sample_structures/frame_range.py
+++ b/Scripts/sample_structures/frame_range.py
@@ -3,13 +3,14 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     frame_range.py
 Category:   Sample Structure Scripts
 Purpose:    Extract a range of frames from an extxyz trajectory by start
             and end fractions (e.g., first 80% or last 50%).
-Usage:      python frame_range.py <input.xyz> <start_fraction> <end_fraction>
+Usage:      gpumdkit.sh -frame_range <input.xyz> <start_fraction> <end_fraction>
+            python frame_range.py <input.xyz> <start_fraction> <end_fraction>
 Arguments:
   input.xyz       Input extxyz trajectory file
   start_fraction  Start fraction (0.0 to 1.0, e.g., 0 for beginning)
@@ -26,9 +27,9 @@
 
 # Check command line arguments
 if len(sys.argv) != 4:
-    print(" Usage: python frame_range.py input.xyz start_fraction end_fraction")
-    print(" Example: python frame_range.py dump.xyz 0 0.8")
-    print(" Example: python frame_range.py dump.xyz 0.5 1")
+    print(" Usage: gpumdkit.sh -frame_range <exyzfile> <start_fraction> <end_fraction>")
+    print("    or: python frame_range.py input.xyz start_fraction end_fraction")
+    print(" Example: gpumdkit.sh -frame_range dump.xyz 0.2 0.5")
     sys.exit(1)
 
 input_file = sys.argv[1]
diff --git a/Scripts/sample_structures/neptrain_select_structs.py b/Scripts/sample_structures/neptrain_select_structs.py
index 5125d57..4926aa3 100644
--- a/Scripts/sample_structures/neptrain_select_structs.py
+++ b/Scripts/sample_structures/neptrain_select_structs.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     neptrain_select_structs.py
 Category:   Sample Structure Scripts
diff --git a/Scripts/sample_structures/parallel_pynep_select_structs.py b/Scripts/sample_structures/parallel_pynep_select_structs.py
index 03e68b1..4ada447 100644
--- a/Scripts/sample_structures/parallel_pynep_select_structs.py
+++ b/Scripts/sample_structures/parallel_pynep_select_structs.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     parallel_pynep_select_structs.py
 Category:   Sample Structure Scripts
diff --git a/Scripts/sample_structures/perturb_structure.py b/Scripts/sample_structures/perturb_structure.py
index 53c6a8e..e4a0d46 100644
--- a/Scripts/sample_structures/perturb_structure.py
+++ b/Scripts/sample_structures/perturb_structure.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     perturb_structure.py
 Category:   Sample Structure Scripts
diff --git a/Scripts/sample_structures/pynep_select_structs.py b/Scripts/sample_structures/pynep_select_structs.py
index 00dd7df..9da9456 100644
--- a/Scripts/sample_structures/pynep_select_structs.py
+++ b/Scripts/sample_structures/pynep_select_structs.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     pynep_select_structs.py
 Category:   Sample Structure Scripts
diff --git a/Scripts/sample_structures/sample_structures.py b/Scripts/sample_structures/sample_structures.py
index 7ec9d80..a208794 100644
--- a/Scripts/sample_structures/sample_structures.py
+++ b/Scripts/sample_structures/sample_structures.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     sample_structures.py
 Category:   Sample Structure Scripts
diff --git a/Scripts/sample_structures/select_max_modev.py b/Scripts/sample_structures/select_max_modev.py
index 91930d7..9892286 100644
--- a/Scripts/sample_structures/select_max_modev.py
+++ b/Scripts/sample_structures/select_max_modev.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     select_max_modev.py
 Category:   Sample Structure Scripts
diff --git a/Scripts/utils/README.md b/Scripts/utils/README.md
new file mode 100644
index 0000000..2b920e7
--- /dev/null
+++ b/Scripts/utils/README.md
@@ -0,0 +1,73 @@
+<div align="center">
+  <h1>🛠️ Utility Scripts</h1>
+  <p style="text-align: justify;">Utility scripts provide maintenance helpers for GPUMDkit itself and small data-cleanup tools used by command-line workflows.</p>
+</div>
+
+## Overview
+
+| Tool | Entry | Purpose |
+|------|-------|---------|
+| `clean_extra_files.sh` | `gpumdkit.sh -clean` | Interactively remove temporary files in the current directory |
+| `update_gpumdkit.sh` | `gpumdkit.sh -update` or `gpumdkit.sh -U` | Pull the latest GPUMDkit code from the current Git branch |
+| `completion.sh` | sourced by the installer | Bash completion for `gpumdkit.sh` commands |
+| `renumber_atoms.py` | `gpumdkit.sh -re_atoms <input> <output>` | Renumber atom IDs in LAMMPS dump files |
+| `nep_modifier/` | `gpumdkit.sh -nep_modifier` | Interactive NEP model editing utilities |
+
+---
+
+## Clean Extra Files
+
+```bash
+gpumdkit.sh -clean
+```
+
+This helper scans the current directory and proposes files to remove. It keeps common GPUMDkit input files such as `run.in`, `nep.in`, `model.xyz`, `nep.txt`, `train.xyz`, and `test.xyz`, plus shell/slurm submission files.
+
+Before deleting anything, it prints the candidate file list and asks for confirmation:
+
+```text
+Do you want to delete all these files?
+y/yes to delete, n/no to cancel, or input files to keep (separated by spaces):
+```
+
+Use this command only after checking that the current directory is the calculation folder you intend to clean.
+
+---
+
+## Update GPUMDkit
+
+```bash
+gpumdkit.sh -update
+gpumdkit.sh -U
+```
+
+The updater checks the current Git branch against the remote GPUMDkit repository and runs `git pull` when updates are available. If the command is launched outside a Git repository, it tries to use the configured `GPUMDkit_path`.
+
+---
+
+## Shell Completion
+
+`completion.sh` provides Bash completion for common GPUMDkit options, plot types, and calculator types. It is normally configured by the installer, so users do not need to run it manually.
+
+---
+
+## Renumber LAMMPS Atom IDs
+
+```bash
+gpumdkit.sh -re_atoms dump.lammpstrj renumbered.lammpstrj
+```
+
+This command rewrites atom IDs in each `ITEM: ATOMS` section of a LAMMPS dump file so that IDs start from 1 in every frame.
+
+---
+
+## NEP Modifier
+
+```bash
+gpumdkit.sh -nep_modifier
+```
+
+The NEP modifier is an interactive utility for editing NEP model files. See:
+
+- `Scripts/utils/nep_modifier/README.md`
+- `Scripts/utils/nep_modifier/README_zh-CN.md`
diff --git a/Scripts/utils/completion.sh b/Scripts/utils/completion.sh
index 81d77aa..2e0f2ef 100644
--- a/Scripts/utils/completion.sh
+++ b/Scripts/utils/completion.sh
@@ -13,7 +13,16 @@ _gpumdkit_completions() {
     prev="${COMP_WORDS[COMP_CWORD-1]}" # Previous word
 
     # List of primary options (extracted from gpumdkit.sh)
-    local opts="-h -help -update -U -clean -time -plt -calc -cbc -range -out2xyz -out2exyz -cp2k2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -xdat2exyz -pos2lmp -lmp2exyz -traj2exyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -filter_range -get_frame -clean_xyz -get_volume -analyze_comp -chem_species -replicate -hbond -pda -pynep -frame_range -re_atoms -nep_modifier"
+    local opts="-h -help -update -U -clean -time -plt -calc -cbc -range -out2xyz -out2exyz -cp2k2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -xdat2exyz -pos2lmp -lmp2exyz -traj2exyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -filter_range -get_frame -clean_xyz -get_volume -analyze_comp -chem_species -replicate -pda -pynep -frame_range -re_atoms -nep_modifier"
+
+    # Calculator subcommands
+    local calc_subcmds="ionic-cond nep des doas neb minimize msd nlist disp avg-struct oct-tilt pol-abo3"
+
+    # If we are completing a subcommand right after -calc
+    if [[ "$prev" == "-calc" ]]; then
+        COMPREPLY=($(compgen -W "$calc_subcmds" -- "$cur"))
+        return
+    fi
 
     # Provide secondary completion based on the previous word
     case "$prev" in
@@ -25,10 +34,6 @@ _gpumdkit_completions() {
         -plt)
             COMPREPLY=($(compgen -W "thermo thermo2 thermo3 train train_density prediction test train_test parity_density born_charge bec msd msd_all msd_conv msd_sdc sdc rdf rdf_pmf vac restart dimer force_errors des doas charge lr arrhenius_d arrhenius_sigma sigma D sigma_xyz D_xyz net_force emd nemd hnemd pdos plane-grid cohesive viscosity" -- "$cur")) ;;
 
-        # Secondary options for -calc
-        -calc)
-            COMPREPLY=($(compgen -W "ionic-cond nep des doas neb minimize msd nlist disp avg-struct oct-tilt pol-abo3" -- "$cur")) ;;
-            
         # Options requiring files or directories, complete with filenames
         -out2xyz|-out2exyz|-cp2k2xyz|-exyz2pos|-min_dist|-min_dist_pbc|-filter_dist|-filter_dist_pbc|-filter_box|-filter_value|-filter_range|-get_frame|-clean_xyz|-pos2exyz|-cif2exyz|-cif2pos|-pos2lmp|-lmp2exyz|-traj2exyz|-addgroup|-addlabel|-addweight|-analyze_comp|-replicate|-pda|-cbc|-frame_range|-chem_species|-xdat2exyz|-re_atoms)
             COMPREPLY=($(compgen -f -- "$cur")) ;;
@@ -39,5 +44,7 @@ _gpumdkit_completions() {
     esac
 }
 
-# Register the completion function
+# Register the completion function for gpumdkit.sh and common invocations
 complete -F _gpumdkit_completions gpumdkit.sh
+complete -F _gpumdkit_completions ./gpumdkit.sh
+complete -F _gpumdkit_completions gpumdkit
diff --git a/Scripts/utils/nep_modifier/README.md b/Scripts/utils/nep_modifier/README.md
index c3bcca7..b31c7de 100644
--- a/Scripts/utils/nep_modifier/README.md
+++ b/Scripts/utils/nep_modifier/README.md
@@ -291,7 +291,7 @@ If you use this tool in your research, please cite both calorine and GPUMDkit:
 
 **GPUMDkit:**
 
-> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, e70074](https://doi.org/10.1002/mgea.70074).
+> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, 4, e70074](https://doi.org/10.1002/mgea.70074).
 
 ## Join Us
 
diff --git a/Scripts/utils/nep_modifier/README_zh-CN.md b/Scripts/utils/nep_modifier/README_zh-CN.md
index 317fda3..68af01c 100644
--- a/Scripts/utils/nep_modifier/README_zh-CN.md
+++ b/Scripts/utils/nep_modifier/README_zh-CN.md
@@ -291,7 +291,7 @@ gpumdkit.sh -nep_modifier
 
 **GPUMDkit:**
 
-> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, e70074](https://doi.org/10.1002/mgea.70074).
+> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, 4, e70074](https://doi.org/10.1002/mgea.70074).
 
 ## 加入我们
 
diff --git a/Scripts/utils/nep_modifier/nep_modifier.py b/Scripts/utils/nep_modifier/nep_modifier.py
index ed59ccc..a4a15b7 100644
--- a/Scripts/utils/nep_modifier/nep_modifier.py
+++ b/Scripts/utils/nep_modifier/nep_modifier.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     nep_modifier.py
 Category:   Model Modification Scripts
diff --git a/Scripts/utils/renumber_atoms.py b/Scripts/utils/renumber_atoms.py
index 004897d..f7adcff 100644
--- a/Scripts/utils/renumber_atoms.py
+++ b/Scripts/utils/renumber_atoms.py
@@ -2,10 +2,11 @@
 Renumber atom IDs in a LAMMPS dump file.
 
 Usage:
+    gpumdkit.sh -re_atoms <input_file> <output_file>
     python renumber_atoms.py <input_file> <output_file>
 
 Author:
-    Dian HUANG <huangdian@stu.xjtu.edu.cn>
+    Dian HUANG (huangdian@stu.xjtu.edu.cn)
 """
 
 import sys
@@ -13,7 +14,8 @@
 
 # Check command-line arguments
 if len(sys.argv) != 3:
-    print("Usage: python renumber_atoms.py <input_file> <output_file>")
+    print(" Usage: gpumdkit.sh -re_atoms <input_file> <output_file>")
+    print("    or: python renumber_atoms.py <input_file> <output_file>")
     sys.exit(1)
 
 input_file = sys.argv[1]
diff --git a/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh b/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
index 053e323..7d057f0 100644
--- a/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
+++ b/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
@@ -3,7 +3,7 @@
 # GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-#           MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+#           MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 # =============================================================================
 # Script:     md_sample_batch_pretreatment_gpumd.sh
 # Category:   Workflow Scripts
diff --git a/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh b/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
index f77fc4a..735cab1 100644
--- a/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
+++ b/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
@@ -3,7 +3,7 @@
 # GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-#           MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+#           MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 # =============================================================================
 # Script:     md_sample_batch_pretreatment_lmp.sh
 # Category:   Workflow Scripts
diff --git a/Scripts/workflow/scf_batch_pretreatment_cp2k.py b/Scripts/workflow/scf_batch_pretreatment_cp2k.py
index 13ea9c3..96d82aa 100644
--- a/Scripts/workflow/scf_batch_pretreatment_cp2k.py
+++ b/Scripts/workflow/scf_batch_pretreatment_cp2k.py
@@ -3,7 +3,7 @@
 GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 Repository: https://github.com/zhyan0603/GPUMDkit
 Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-          MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 =============================================================================
 Script:     scf_batch_pretreatment_cp2k.py
 Category:   Workflow Scripts
diff --git a/Scripts/workflow/scf_batch_pretreatment_vasp.sh b/Scripts/workflow/scf_batch_pretreatment_vasp.sh
index c75f57d..f67329d 100644
--- a/Scripts/workflow/scf_batch_pretreatment_vasp.sh
+++ b/Scripts/workflow/scf_batch_pretreatment_vasp.sh
@@ -3,7 +3,7 @@
 # GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
-#           MGE Advances, 2026, e70074 (https://doi.org/10.1002/mgea.70074)
+#           MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
 # =============================================================================
 # Script:     scf_batch_pretreatment_vasp.sh
 # Category:   Workflow Scripts
diff --git a/docs/README_zh-CN.md b/docs/README_zh-CN.md
index 724f605..daad7f7 100644
--- a/docs/README_zh-CN.md
+++ b/docs/README_zh-CN.md
@@ -296,4 +296,4 @@ gpumdkit.sh -plt thermo save
 
 **GPUMDkit** 是一款面向所有人的开源工具。如果在你的研究或工作中它有所帮助，欢迎 ⭐ [在 GitHub 上给我们点亮 Star](https://github.com/zhyan0603/GPUMDkit)。此外，如果 GPUMDkit 对你的发表工作有贡献，请引用我们的论文：
 
-> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, e70074](https://doi.org/10.1002/mgea.70074).
+> Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, 4, e70074](https://doi.org/10.1002/mgea.70074).
diff --git a/docs/index.html b/docs/index.html
index c8d114c..07e8e14 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -321,7 +321,7 @@ <h3>Citation</h3>
                             <div class="citation-body-modern">
                                 <h4 class="paper-title-modern">GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP</h4>
                                 <div class="paper-meta-modern">
-                                    <span class="meta-text">MGE Advances, 2026, e70074</span>
+                                    <span class="meta-text">MGE Advances, 2026, 4, e70074</span>
                                 </div>
                                 <div class="paper-authors-modern">
                                     Zihan Yan, Denan Li, Xin Wu, Zhoulin Liu, Chen Hua, Boyi Situ, Hao Yang, Shengjie Tang, Benrui Tang, Ziyang Wang, Shangzhao Yi, Huan Wang, Dian Huang, Ke Li, Qilin Guo, Zherui Chen, Ke Xu, Yanzhou Wang, Ziliang Wang, Gang Tang, Shi Liu, Zheyong Fan, Yizhou Zhu
diff --git a/docs/tutorials/en/active_learning_workflow.md b/docs/tutorials/en/active_learning_workflow.md
index c1e7056..724ce96 100644
--- a/docs/tutorials/en/active_learning_workflow.md
+++ b/docs/tutorials/en/active_learning_workflow.md
@@ -3,11 +3,29 @@
   <p style="text-align: justify;">This tutorial explains the steps and considerations involved in the <code>workflow_active_learning_dev.sh</code> script. The workflow is used to generate, select, and analyze molecular structures, followed by simulations and data collection.</p>
 </div>
 
-### Overview
+**Script Location:** `Scripts/workflow/`
 
-This script is designed to handle molecular dynamics simulations, sampling, and SCF (self-consistent field) calculations for NEP. Below is a step-by-step guide explaining how the script works and what each part does.
+## Overview
 
-### 1. **SLURM Directives**
+This script automates one iteration of NEP active learning. The typical workflow includes:
+
+| Step | Action | Purpose |
+|------|--------|---------|
+| 1 | Run MD simulations | Generate candidate structures with current NEP model |
+| 2 | Filter structures | Remove unphysical configurations (short distances, large boxes) |
+| 3 | Sample structures | Select diverse or uncertain structures for DFT |
+| 4 | Run SCF calculations | Compute DFT reference energies/forces |
+| 5 | NEP prediction | Check model accuracy on new structures |
+
+Unlike menu-driven modules, this workflow is a shell script that you customize and run directly:
+
+```bash
+bash Scripts/workflow/workflow_active_learning_dev.sh
+```
+
+The sections below explain the main blocks in the script and what each part does.
+
+## 1. **SLURM Directives**
 
 ```
 #!/bin/bash -l
@@ -34,7 +52,7 @@ The SLURM directives are used to define how the job will be submitted to the clu
 nohup bash workflow_active_learning_dev.sh &>workflow.log &
 ```
 
-### 2. **Basic Setup**
+## 2. **Basic Setup**
 
 ```
 cd $SLURM_SUBMIT_DIR 
@@ -52,7 +70,7 @@ python_pynep=python  # Python executable for the deprecated pynep branch if need
 
 ------
 
-### 3. **Variable Definitions**
+## 3. **Variable Definitions**
 
 ```
 work_dir=${PWD}  # Set the working directory
@@ -73,7 +91,7 @@ You can customize:
 
 ------
 
-### 4. **Check Required Files**
+## 4. **Check Required Files**
 
 ```
 if [ -f nep.txt ] && [ -f nep.in ] && [ -f train.xyz ] && [ -f run.in ] && [ -f INCAR ] && [ -f POTCAR ] ; then
@@ -88,7 +106,7 @@ Make sure the necessary files (`nep.txt`, `nep.in`, `train.xyz`, `run.in`, `INCA
 
 ------
 
-### 5. **File Organization**
+## 5. **File Organization**
 
 ```
 mkdir 00.modev common
@@ -103,7 +121,7 @@ The script organizes the working files into two folders:
 
 ------
 
-### 6. **Molecular Dynamics Simulation Submission**
+## 6. **Molecular Dynamics Simulation Submission**
 
 ```
 submit_gpumd_array modev ${sample_struct_num}
@@ -114,7 +132,7 @@ After preparing the input files, the script submits an array of molecular dynami
 
 ------
 
-### 7. **Monitoring Task Completion**
+## 7. **Monitoring Task Completion**
 
 ```
 while true; do
@@ -137,7 +155,7 @@ The script continuously checks whether all MD tasks have finished by searching f
 
 ------
 
-### 8. **Analysis and Filtering**
+## 8. **Analysis and Filtering**
 
 ```
 mkdir ${work_dir}/01.select
@@ -148,7 +166,7 @@ In the `01.select` folder, all structures in the trajectory file `dump.xyz` duri
 
 ------
 
-### 9. **Sampling Methods**
+## 9. **Sampling Methods**
 
 ```
 case $sample_method in
@@ -161,7 +179,7 @@ The script supports three sampling methods: `uniform`, `random`, and `pynep`. It
 
 ------
 
-### 10. **SCF Calculations**
+## 10. **SCF Calculations**
 
 ```
 submit_vasp_array scf ${selected_struct_num} ${prefix_name}
@@ -171,13 +189,13 @@ After sampling, SCF calculations are submitted using `submit_vasp_array`. The pr
 
 ------
 
-### 11. **Prediction Step**
+## 11. **Prediction Step**
 
 ```
 submit_nep_prediction
 ```
 
-The final step involves submitting the NEP prediction task to check  the accuracy of the NEP model. 
+The final step involves submitting the NEP prediction task to check the accuracy of the NEP model. 
 
 
 
diff --git a/docs/tutorials/en/analyzer_scripts.md b/docs/tutorials/en/analyzer_scripts.md
index 3a9f3aa..d358b1f 100644
--- a/docs/tutorials/en/analyzer_scripts.md
+++ b/docs/tutorials/en/analyzer_scripts.md
@@ -1,6 +1,6 @@
 <div align="center">
   <h1>🔍 Analyzer Scripts</h1>
-  <p style="text-align: justify;">Analyzer scripts provide structure statistics, distance checks, filters, and composition analysis for extxyz datasets.</p>
+  <p style="text-align: justify;">Analyzer scripts provide structure statistics, distance checks, filters, composition analysis, outlier detection, and time estimation for extxyz datasets.</p>
 </div>
 
 **Script Location:** `Scripts/analyzer/`
@@ -9,24 +9,65 @@
 
 | Task | Command | Purpose |
 |------|---------|---------|
-| Composition | `gpumdkit.sh -analyze_comp train.xyz` | group structures by chemical composition |
-| Chemical species | `gpumdkit.sh -chem_species train.xyz` | list species in a file |
-| Property range | `gpumdkit.sh -range train.xyz force` | inspect energy/force/virial range |
-| Minimum distance | `gpumdkit.sh -min_dist dump.xyz` | fast distance check without PBC |
-| Minimum distance with PBC | `gpumdkit.sh -min_dist_pbc dump.xyz` | accurate distance check with PBC |
-| Charge balance | `gpumdkit.sh -cbc train.xyz` | oxidation-state balance check |
-| Distance filter | `gpumdkit.sh -filter_dist_pbc dump.xyz 1.0` | remove structures with short contacts |
-| Box filter | `gpumdkit.sh -filter_box dump.xyz 13` | remove structures with too-large box edges |
-| Property filter | `gpumdkit.sh -filter_value train.xyz force 20` | filter by energy/force/virial threshold |
-| Pair-distance range | `gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0` | extract structures by pair distance |
+| Composition | `gpumdkit.sh -analyze_comp train.xyz` | Group structures by chemical composition |
+| Chemical species | `gpumdkit.sh -chem_species train.xyz` | List species in a file |
+| Property range | `gpumdkit.sh -range train.xyz force` | Inspect energy/force/virial range |
+| Minimum distance | `gpumdkit.sh -min_dist dump.xyz` | Fast distance check without PBC |
+| Minimum distance with PBC | `gpumdkit.sh -min_dist_pbc dump.xyz` | Accurate distance check with PBC |
+| Charge balance | `gpumdkit.sh -cbc train.xyz` | Oxidation-state balance check |
+| Distance filter | `gpumdkit.sh -filter_dist_pbc dump.xyz 1.0` | Remove structures with short contacts |
+| Box filter | `gpumdkit.sh -filter_box dump.xyz 13` | Remove structures with too-large box edges |
+| Property filter | `gpumdkit.sh -filter_value train.xyz force 20` | Filter by energy/force/virial threshold |
+| Pair-distance range | `gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0` | Extract structures by pair distance |
+| Outlier detection | Menu 502 | Find high-RMSE structures in training set |
+| GPUMD time | `gpumdkit.sh -time gpumd` | Estimate remaining GPUMD run time |
+| NEP time | `gpumdkit.sh -time nep` | Estimate remaining NEP training time |
+
+---
+
+## Interactive Mode
+
+Open GPUMDkit and choose `5) Analyzer`:
+
+```bash
+gpumdkit.sh
+```
+
+The analyzer menu is:
+
+```text
++------------------------------------------------------+
+|                    ANALYZER TOOLS                    |
++------------------------------------------------------+
+| 501) Analyze composition of extxyz                   |
+| 502) Find outliers of extxyz                         |
+| 503) Analyze chemical species of extxyz              |
+| 504) Check charge balance of extxyz                  |
+| 505) Analyze energy/force/virial range               |
+| 506) Filter structures by minimum distance           |
+| 507) Get minimum interatomic distance                |
+| 508) Probability density analysis                    |
++------------------------------------------------------+
+| 000) Return to the main menu                         |
++------------------------------------------------------+
+Input the function number:
+```
+
+Most analyzer functions also have direct CLI shortcuts, which are listed in the overview table and in the sections below.
+
+---
 
 ## Composition Analysis
 
+`analyze_composition.py` analyzes the composition of your extxyz file and lets you export subsets.
+
+**Input file:** `train.xyz` (extxyz format)
+
 ```bash
 gpumdkit.sh -analyze_comp train.xyz
 ```
 
-Example output:
+**Output example:**
 
 ```text
 Index    Compositions           N atoms      Count
@@ -38,112 +79,310 @@ Enter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:
 
 This is useful when `train.xyz` contains structures from different systems or different cell sizes. You can export a subset by composition from the interactive prompt.
 
+---
+
+## Chemical Species
+
+`analyze_chem_species.py` lists all unique chemical species in an extxyz file.
+
+**Input file:** `train.xyz` (extxyz format)
+
+```bash
+gpumdkit.sh -chem_species train.xyz
+```
+
+---
+
 ## Property Range Analysis
 
+`energy_force_virial_analyzer.py` calculates and visualizes the range of properties from an extxyz file.
+
+**Input file:** `train.xyz` (extxyz format)
+
+**Supported properties:** `energy`, `force`, `virial`
+
 ```bash
 gpumdkit.sh -range train.xyz force
 gpumdkit.sh -range train.xyz energy
 gpumdkit.sh -range train.xyz virial
-gpumdkit.sh -range train.xyz force hist
+gpumdkit.sh -range train.xyz force hist    # Show histogram
 ```
 
-Use `hist` to show a histogram of the selected property.
+**Output example:**
+
+```text
+Force range: 0.03210566767721861 to 9.230115912468435
+```
+
+With `hist` option:
 
 <div align="center">
   <img src="../../Gallery/range_force.png" alt="Force range histogram" width="52%" />
 </div>
 
+---
+
 ## Minimum Distance Checks
 
-Fast check without PBC:
+### Without PBC (Fast)
+
+`get_min_dist.py` calculates minimum interatomic distances without considering periodic boundary conditions. Fast but may be inaccurate for periodic systems.
+
+**Input file:** `dump.xyz` (extxyz format)
 
 ```bash
 gpumdkit.sh -min_dist dump.xyz
 ```
 
-Accurate check with PBC:
+**Output example:**
+
+```text
++---------------------------+
+|   PBC ignored for speed   |
+| use -min_dist_pbc for PBC |
++---------------------------+
+Minimum interatomic distances:
++---------------------------+
+| Atom Pair |  Distance (Å) |
++---------------------------+
+|   Li-Li   |     1.696     |
+|   Li-O    |     1.587     |
+|   O-O     |     2.480     |
++---------------------------+
+Overall min_distance: 1.587 Å
+```
+
+### With PBC (Accurate)
+
+`get_min_dist_pbc.py` calculates minimum interatomic distances considering periodic boundary conditions.
+
+**Input file:** `dump.xyz` (extxyz format)
 
 ```bash
 gpumdkit.sh -min_dist_pbc dump.xyz
 ```
 
-Typical output:
+**Output example:**
 
 ```text
 Minimum interatomic distances (with PBC):
 +---------------------------+
-| Atom Pair |  Distance (A) |
+| Atom Pair |  Distance (Å) |
 +---------------------------+
 |   Li-Li   |     1.696     |
 |   Li-O    |     1.587     |
 |   O-O     |     2.355     |
 +---------------------------+
-Overall min_distance: 1.587 A
+Overall min_distance: 1.587 Å
 ```
 
-The PBC version considers periodic boundary conditions.
+---
 
 ## Filtering Structures
 
 ### Filter by Minimum Distance
 
+`filter_structures_by_distance_pbc.py` removes structures with any interatomic distance below a threshold.
+
+**Input file:** `dump.xyz` (extxyz format)
+
 ```bash
 gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
 ```
 
-This removes structures with any interatomic distance below `1.0 A`.
+This removes structures with any interatomic distance below `1.0 Å`.
 
 ### Filter by Box Size
 
+`filter_exyz_by_box.py` filters structures by box-edge length.
+
+**Input file:** `dump.xyz` (extxyz format)
+
 ```bash
 gpumdkit.sh -filter_box dump.xyz 13
 ```
 
-This filters structures by box-edge length.
+This keeps structures where all box edges are below `13 Å`.
 
 ### Filter by Property Value
 
+`filter_exyz_by_value.py` filters structures by energy, force, or virial threshold.
+
+**Input file:** `train.xyz` (extxyz format)
+
+**Supported properties:** `energy`, `force`, `virial`
+
 ```bash
 gpumdkit.sh -filter_value train.xyz force 20
 gpumdkit.sh -filter_value train.xyz energy 5
 ```
 
+This filters out structures with force components exceeding `20 eV/Å` (or energy exceeding `5 eV/atom`).
+
 ### Filter by Pair-Distance Range
 
+`filter_dist_range.py` extracts structures where a specific element-pair distance falls within a given range.
+
+**Input file:** `dump.xyz` (extxyz format)
+
 ```bash
 gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0
 ```
 
-This extracts structures where the Li-Li minimum distance is between `1.8 A` and `2.0 A`.
+This extracts structures where the Li-Li minimum distance is between `1.8 Å` and `2.0 Å`. Output: `filtered_Li_Li_1.8_2.0.xyz`.
+
+---
 
 ## Charge Balance Check
 
+`charge_balance_check.py` checks the oxidation-state balance of structures.
+
+**Input file:** `train.xyz` (extxyz format)
+
 ```bash
 gpumdkit.sh -cbc train.xyz
 ```
 
-Outputs may include:
+**Output files:**
 
-- `balanced.xyz`
-- `unbalanced.xyz`
-- `indices.txt`
+- `balanced.xyz` — structures with balanced charges
+- `unbalanced.xyz` — structures with unbalanced charges
+- `indices.txt` — indices of balanced structures
 
 This is intended for systems where common oxidation states are meaningful.
 
-## Example Commands
+---
 
-Property and distance checks:
+## Outlier Detection
+
+`find_outliers.py` finds outlier structures in NEP training data based on RMSE thresholds for energy, force, and stress.
+
+**Input files:** `energy_train.out`, `force_train.out`, `stress_train.out`, `train.xyz`
+
+These files are generated during NEP training. The script compares DFT vs NEP predictions and identifies structures with large errors.
+
+```bash
+# Interactive mode
+gpumdkit.sh    # Select: 5) Analyzer → 502) Find outliers of extxyz
+```
+
+**Interactive prompts:**
+
+```text
+Enter energy RMSE threshold (meV/atom): 1
+Enter force RMSE threshold (meV/Å): 60
+Enter stress RMSE threshold (GPa): 0.03
+```
+
+**Output files:**
+
+- `selected.xyz` — structures exceeding the RMSE thresholds (outliers)
+- `remained.xyz` — structures within the thresholds
+- `selected_remained.png` — comparison plot
+
+**Use case:** After NEP training, use this to identify problematic structures that contribute most to the error. Remove or improve these structures to enhance the training set.
+
+---
+
+## Time Estimation
+
+### GPUMD Remaining Time
+
+`time_consuming_gpumd.sh` estimates the remaining time for a GPUMD simulation.
+
+**Input files:** `run.in`, `thermo.out` (in the current GPUMD working directory)
+
+```bash
+gpumdkit.sh -time gpumd
+```
+
+**Output example:**
+
+```text
+----------------- System Information ----------------
+total frames: 1050000
+-----------------------------------------------------
+Current Frame  Speed (steps/s)   Total Time       Time Left       Estimated End
+-------------   -------------   -------------   -------------   -----------------
+    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04
+    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56
+```
+
+### NEP Remaining Time
+
+`time_consuming_nep.sh` estimates the remaining time for NEP training.
+
+**Input files:** `loss.out` (in the current NEP working directory)
 
 ```bash
+gpumdkit.sh -time nep
+```
+
+**Output example:**
+
+```text
++-----------------+-----------+-----------------+---------------------+
+|       Step      | Time Diff |    Time Left    |    Finish Time      |
++-----------------+-----------+-----------------+---------------------+
+| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |
+| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |
+| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |
++-----------------+-----------+-----------------+---------------------+
+```
+
+---
+
+## Probability Density Analysis
+
+`probability_density_analysis.py` calculates 3D probability density of mobile ions for diffusion channel analysis.
+
+**Input files:** Reference structure (POSCAR), trajectory file (extxyz)
+
+```bash
+gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25
+```
+
+**Output:** `probability_density_0.25.vasp` — probability density grid for visualization with VESTA or similar tools.
+
+---
+
+## Example Workflows
+
+### Structure Quality Check
+
+```bash
+# 1. Check composition
 gpumdkit.sh -analyze_comp train.xyz
+
+# 2. Check energy/force range
 gpumdkit.sh -range train.xyz force hist
-gpumdkit.sh -range train.xyz energy hist
+
+# 3. Check minimum distances
 gpumdkit.sh -min_dist_pbc train.xyz
+
+# 4. Find outliers (after NEP training)
+# Interactive: 5) Analyzer → 502
 ```
 
-Filtering examples:
+### Structure Filtering Pipeline
 
 ```bash
+# 1. Filter by minimum distance
 gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
-gpumdkit.sh -filter_box filtered_dist.xyz 13
+
+# 2. Filter by box size
+gpumdkit.sh -filter_box filtered_dist_pbc.xyz 13
+
+# 3. Filter by force threshold
+gpumdkit.sh -filter_value filtered_box.xyz force 20
+```
+
+### Diffusion Channel Analysis
+
+```bash
+# 1. Calculate probability density
+gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25
+
+# 2. Visualize with VESTA
+# Open probability_density_0.25.vasp
 ```
diff --git a/docs/tutorials/en/calculator_scripts.md b/docs/tutorials/en/calculator_scripts.md
index e4cd732..1a261f6 100644
--- a/docs/tutorials/en/calculator_scripts.md
+++ b/docs/tutorials/en/calculator_scripts.md
@@ -184,12 +184,24 @@ gpumdkit.sh -plt sdc
 
 `calc_properties_with_nep.py` calculates energy, force, and stress for structures using a NEP model.
 
+**Dependency:** `calorine`
+
+```bash
+pip install calorine
+```
+
 ```bash
 gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
 ```
 
 This function is useful when you intentionally want to use a trained NEP model as a surrogate calculator. It should not be treated as a replacement for DFT unless the model quality has been carefully validated.
 
+**Tip:** Before prediction, you may want to clean the extxyz metadata:
+
+```bash
+gpumdkit.sh -clean_xyz train.xyz clean_train.xyz
+```
+
 ## NEP Descriptors
 
 `calc_descriptors.py` extracts NEP descriptors for a selected element.
@@ -253,6 +265,14 @@ This runs a NEB calculation with `9` intermediate images. During execution, the
 
 ## Structure Minimization
 
+`calc_minimize.py` minimizes a structure using a NEP model through `calorine`.
+
+**Dependency:** `calorine`
+
+```bash
+pip install calorine
+```
+
 ```bash
 gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
 ```
@@ -271,6 +291,40 @@ Output:
 - `minimize.xyz`
 - `minimize.log`
 
+## RDF Calculation with OVITO
+
+`rdf_calculator_ovito.py` calculates radial distribution function using OVITO's analysis tools.
+
+**Dependency:** OVITO
+
+```bash
+pip install ovito
+```
+
+**Input file:** Structure file (single frame or trajectory)
+
+```bash
+python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400
+```
+
+**Parameters:**
+
+| Argument | Meaning |
+|----------|---------|
+| `trajectory.xyz` | Input structure file |
+| `6.0` | Maximum distance for RDF calculation (Å) |
+| `400` | Number of histogram bins |
+
+**Visualization:**
+
+```bash
+gpumdkit.sh -plt rdf
+```
+
+**Note:** It is recommended to use the `compute_rdf` command directly in GPUMD when possible.
+
+---
+
 ## Ferroelectric and Polar Material Tools
 
 The following tools are useful for perovskite and polar-material analysis. They require `ferrodispcalc`:
diff --git a/docs/tutorials/en/contributing_to_gpumdkit.md b/docs/tutorials/en/contributing_to_gpumdkit.md
index e279a2d..ced6035 100644
--- a/docs/tutorials/en/contributing_to_gpumdkit.md
+++ b/docs/tutorials/en/contributing_to_gpumdkit.md
@@ -3,8 +3,16 @@
   <p style="text-align: justify;">Thank you for your interest in contributing to <strong>GPUMDkit</strong>! We appreciate your time and effort in helping improve this toolkit.</p>
 </div>
 
+<p align="center">
+  <strong>English</strong>
+  &nbsp;·&nbsp;
+  <a href="../zh/贡献指南.md">简体中文</a>
+</p>
+
 `GPUMDkit` is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.
 
+> **Note**: The authoritative version of this document is [`CONTRIBUTING.md`](https://github.com/zhyan0603/GPUMDkit/blob/main/CONTRIBUTING.md) in the repository root. This tutorial page mirrors its content.
+
 ---
 
 ## Table of Contents
@@ -64,7 +72,9 @@ To maintain code quality and consistency across the project, please adhere to th
 ### Documentation
 
 - Ensure that help messages (e.g., `-h` flags) are clear and accurate.
-- Documentation files in the `docs/` directory will be updated by the maintainers, so you generally don't need to modify them.
+- Tutorial documentation lives in `docs/tutorials/en/` (English) and `docs/tutorials/zh/` (Chinese).
+  If you add a new feature, consider updating the relevant tutorial page.
+- After editing tutorial markdown files, rebuild the HTML with `mkdocs build -f docs/mkdocs.yml`.
 
 ---
 
@@ -126,7 +136,8 @@ Name your branch as you prefer.
 
 The structure of `GPUMDkit` consists of:
 - **`gpumdkit.sh`**: Main entry point (Bash script) handling both interactive menu mode and command-line mode
-- **`Scripts/`**: Python utility scripts organized by functionality
+- **`install.sh`**: Installation script that sets up environment variables and shell configuration
+- **`Scripts/`**: Python and Bash implementation scripts organized by functionality
   - `plt_scripts/`: Plotting scripts
   - `calculators/`: Calculation utilities
   - `format_conversion/`: Format conversion tools
@@ -142,7 +153,12 @@ The structure of `GPUMDkit` consists of:
   - `f5_analyzers.sh`
   - `f6_plots.sh`
   - `f7_utilities.sh`
+- **`skills/`**: AI agent skill definitions (SKILL.md files for opencode/Claude Code integration)
 - **`docs/`**: Documentation files
+  - `tutorials/en/` and `tutorials/zh/`: Bilingual tutorial pages
+  - `mkdocs.yml`: MkDocs configuration for building tutorial HTML
+  - `command_reference.tsv`: Machine-readable command reference
+  - `htmls/`: Generated HTML output from MkDocs
 
 #### Interactive Mode Contributions
 
@@ -165,18 +181,18 @@ To add a new feature accessible through the interactive menu:
    
    Add a new function:
    ```bash
-   function f106_new_converter(){
+   function f111_new_converter(){
    echo " >-------------------------------------------------<"
    echo " | Calling the script in Scripts/format_conversion |"
    echo " | Script: new_converter.py                        |"
    echo " | Developer: Your Name (your@email.com)           |"
    echo " >-------------------------------------------------<"
-   echo " Input the required parameters:"
+   echo " Input <required_param1> <required_param2>"
    echo " Example: input.xyz output.lmp"
    echo " ------------>>"
-   read -p " " converter_params
+   read -r -a converter_args
    echo " ---------------------------------------------------"
-   python ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py ${converter_params}
+   python ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py "${converter_args[@]}"
    echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py"
    echo " ---------------------------------------------------"
    }
@@ -187,7 +203,7 @@ To add a new feature accessible through the interactive menu:
    # Find the menu() function and update it if needed
    # Find the array_choice array and add your new choice number
    array_choice=(
-       "0" "1" "101" "102" "103" "104" "105" "106"  # Added "106"
+       "0" "1" "101" "102" "103" "104" "105" "106" "107" "108" "109" "110" "111"  # Added "111"
        # ... rest of choices
    )
    ```
@@ -201,9 +217,9 @@ To add a new feature accessible through the interactive menu:
            source ${GPUMDkit_path}/src/f1_format_conversions.sh
            case $choice in
                "1") f1_format_conversion ;;
-               "101") f101_out2xyz ;;
-               # ... existing cases ...
-               "106") f106_new_converter ;;  # Add your case
+                "101") f101_out2xyz ;;
+                # ... existing cases ...
+                "111") f111_new_converter ;;  # Add your case
            esac ;;
        # ...
    esac
@@ -224,36 +240,35 @@ To add a new command-line flag or subcommand:
    # Example: Scripts/analyzer/analyze_bonds.py
    import sys
    
-   def main():
-       if len(sys.argv) != 3:
-           print("Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>")
-           print("Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0")
-           sys.exit(1)
-       
-       input_file = sys.argv[1]
-       cutoff = float(sys.argv[2])
-       
-       # Your implementation here
-       
-   if __name__ == "__main__":
-       main()
+   if len(sys.argv) != 3:
+       print("Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>")
+       print("Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0")
+       sys.exit(1)
+   
+   input_file = sys.argv[1]
+   cutoff = float(sys.argv[2])
+   
+   # Your implementation here
    ```
+   
+   > **Note**: GPUMDkit Python scripts are designed to run directly (not imported as modules).
+   > You may use a `main()` function with `if __name__ == "__main__":` guard if you prefer,
+   > but it is not required. Most existing scripts execute at module level.
 
 3. **Add the command-line flag handler** in `gpumdkit.sh`:
    ```bash
-   # Find the command-line parsing section (after line ~167)
+   # Find the command-line parsing section (the large "case $1 in" block)
    # Add your new flag in the appropriate location
    
    case $1 in
        # ... existing cases ...
        -analyze_bonds)
-           if [ ! -z "$2" ] && [ ! -z "$3" ]; then
-               python ${analyzer_path}/analyze_bonds.py "$2" "$3"
+           if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ]; then
+               python ${analyzer_path}/analyze_bonds.py $2 $3
            else
                echo " Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>"
                echo " Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0"
                echo " Code path: ${analyzer_path}/analyze_bonds.py"
-               exit 1
            fi ;;
        # ... rest of cases ...
    esac
@@ -281,17 +296,23 @@ vim Scripts/utils/completion.sh
 Add your new flag to the `opts` variable:
 ```bash
 # Find the line with local opts=...
-local opts="-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ..."
-#                                                      ^^^^^^^^^^^^^^ Add your flag here
+local opts="-h -help -update -U -clean -time -plt -calc ... -your_new_flag ..."
+#                                                        Add your flag here
+```
+
+If your flag requires file arguments, add it to the existing file-completion case:
+```bash
+# Find the case for file-requiring flags and add yours with |
+-out2xyz|-out2exyz|-...|-your_new_flag)
+    COMPREPLY=($(compgen -f -- "$cur")) ;;
 ```
 
-If your flag accepts secondary options (like `-plt` or `-calc`), add a case for it:
+If your flag accepts secondary options (like `-plt` or `-calc`), add a new case:
 ```bash
 case "$prev" in
     # ... existing cases ...
-    -analyze_bonds)
-        COMPREPLY=($(compgen -f -- "$cur"))  # Complete with filenames
-        ;;
+    -your_new_flag)
+        COMPREPLY=($(compgen -W "option1 option2 option3" -- "$cur")) ;;
     # ... rest of cases ...
 esac
 ```
@@ -300,15 +321,53 @@ esac
 
 - **Shell Scripts**:
   - Use `${variable}` for variable expansion
-  - Write code that is clear and easy to maintain
+  - Use `[ ! -z "$var" ]` for non-empty checks (project convention)
+  - Interactive functions should follow the banner format:
+    ```bash
+    echo " >-------------------------------------------------<"
+    echo " | Calling the script in Scripts/<category>        |"
+    echo " | Script: <script_name>.py                        |"
+    echo " | Developer: <Name> (<email>)                     |"
+    echo " >-------------------------------------------------<"
+    ```
+  - Use `read -r -a varname` for multi-word input, then pass with `"${varname[@]}"`
+  - Shell scripts in `src/` should start with a file header block:
+    ```bash
+    # ============================================================
+    # GPUMDkit <module name> module
+    # Repository: https://github.com/zhyan0603/GPUMDkit
+    # Author: <Name> (<email>)
+    # ============================================================
+    ```
 
 - **Python Scripts**:
   - Write clear, maintainable code
   - Use meaningful variable names
+  - Use `sys.argv` for argument parsing (consistent with most existing scripts)
+  - Provide clear usage messages with `print("Usage: ...")` and `print("Example: ...")`
+  - If your script uses heavy/special packages (`NepTrain`, `calorine`, `dpdata`), add a
+    `print_dependency_notice()` function to inform users about citation recommendations
 
 ### Testing Your Changes
 
-Before submitting your contribution:
+Before submitting your contribution, run the relevant validation commands:
+
+```bash
+# Shell syntax checks (always run these)
+bash -n gpumdkit.sh
+find src Scripts -name '*.sh' -exec bash -n {} +
+
+# Python syntax checks (for modified Python files)
+python3 -m py_compile path/to/modified_script.py
+
+# MkDocs build (if you modified documentation)
+mkdocs build -f docs/mkdocs.yml
+
+# Check for trailing whitespace issues
+git diff --check
+```
+
+Then test functionality:
 
 1. **Test interactive mode** (if applicable):
    ```bash
@@ -347,10 +406,10 @@ Write clear, descriptive commit messages that explain what you changed. There ar
    git commit -m "your descriptive message"
    ```
 
-2. **Keep your branch updated** with the upstream `main` branch:
+2. **Keep your branch updated** with the latest `dev` branch:
    ```bash
-   git fetch upstream
-   git rebase upstream/main
+   git fetch origin
+   git rebase origin/dev
    ```
 
 3. **Push your branch** to your fork:
@@ -387,4 +446,4 @@ If you have questions about contributing or need help with your contribution:
 
 ---
 
-Thank you again for contributing to `GPUMDkit`! Your efforts help make this toolkit better for the entire GPUMD and NEP community. 🚀
+Thank you again for contributing to `GPUMDkit`! Your efforts help make this toolkit better for the entire GPUMD and NEP community.
diff --git a/docs/tutorials/en/custom_commands.md b/docs/tutorials/en/custom_commands.md
index 7192bda..9be5bd6 100644
--- a/docs/tutorials/en/custom_commands.md
+++ b/docs/tutorials/en/custom_commands.md
@@ -43,7 +43,7 @@ custom_greet() {
 }
 ```
 
-and you can add a argument, for example: `gpumdkit.sh -greet Zihan`, then you will see:
+and you can add an argument, for example: `gpumdkit.sh -greet Zihan`, then you will see:
 
 ```
 Hello, Zihan!
diff --git a/docs/tutorials/en/format_conversion.md b/docs/tutorials/en/format_conversion.md
index 08fa3a2..9995b98 100644
--- a/docs/tutorials/en/format_conversion.md
+++ b/docs/tutorials/en/format_conversion.md
@@ -228,6 +228,45 @@ gpumdkit.sh -get_frame dump.xyz 1000
 
 This extracts frame index `1000` from an extxyz trajectory.
 
+### Split multi-frame extxyz
+
+`split_single_xyz.py` splits an extxyz file into individual frames, each written to a separate file.
+
+```bash
+python Scripts/format_conversion/split_single_xyz.py dump.xyz
+```
+
+This creates `model_0.xyz`, `model_1.xyz`, ... for each frame in the trajectory.
+
+### MTP conversion
+
+Convert MTP `.cfg` format to extxyz:
+
+```bash
+gpumdkit.sh    # Select: 1) Format Conversion → 102
+```
+
+Interactive prompt:
+
+```text
+Input <filename.cfg> <Symbol1 Symbol2 Symbol3 ...>
+Example: train.cfg Pd Ag
+------------>>
+```
+
+### ABACUS conversion
+
+Convert ABACUS output to extxyz:
+
+```bash
+gpumdkit.sh    # Select: 1) Format Conversion → 104
+```
+
+The menu offers two options:
+
+1. SCF output (`running_scf.log`)
+2. MD output (`running_md.log`)
+
 ## Common Mistakes
 
 | Problem | What to Check |
diff --git a/docs/tutorials/en/plot_scripts.md b/docs/tutorials/en/plot_scripts.md
index bc4a9fa..9315480 100644
--- a/docs/tutorials/en/plot_scripts.md
+++ b/docs/tutorials/en/plot_scripts.md
@@ -1,6 +1,6 @@
 <div align="center">
   <h1>📊 Plot Scripts</h1>
-  <p style="text-align: justify;">The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators.</p>
+  <p style="text-align: justify;">The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators. All plots can be displayed interactively or saved as high-resolution PNG files.</p>
 </div>
 
 **Script Location:** `Scripts/plt_scripts/`
@@ -8,26 +8,61 @@
 ## Quick Access
 
 ```bash
-gpumdkit.sh -plt          # show all plotting options
-gpumdkit.sh -plt <type>   # generate a plot
-gpumdkit.sh -plt <type> save
-gpumdkit.sh -plt <type> -h
+gpumdkit.sh -plt              # Show all plotting options
+gpumdkit.sh -plt <type>       # Generate a plot
+gpumdkit.sh -plt <type> save  # Save plot as PNG
+gpumdkit.sh -plt <type> -h    # Show help for a specific plot type
 ```
 
-## NEP Training and Prediction
+Running `gpumdkit.sh -plt` prints the plotting command menu:
 
-### Training Results
+```text
++-----------------------------------------------------------------------------------------------+
+|                     GPUMDkit <version> PLOT & VISUALIZATION TOOLS              |
++-----------------------------------------------------------------------------------------------+
+|  Usage: gpumdkit.sh -plt <type>                        Help: gpumdkit.sh -plt <type> -h       |
++-----------------------------------------------------------------------------------------------+
+|                                    NEP Training & Evaluation                                  |
++-----------------------------------------------------------------------------------------------+
+|  train          - NEP training results           prediction     - NEP prediction results      |
+|  train_test     - NEP train and test results     parity_density - Parity density plot         |
+|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |
+|  charge         - Charge distribution            born_charge    - Born effective charges      |
+|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |
+|  des            - Descriptors                    lr             - Learning rate for gnep      |
++-----------------------------------------------------------------------------------------------+
+|                                     Diffusion & Transport                                     |
++-----------------------------------------------------------------------------------------------+
+|  msd            - Mean square displacement       msd_conv       - MSD convergence             |
+|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |
+|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|
+|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |
+|  D_xyz          - Directional Arrhenius D                                                     |
++-----------------------------------------------------------------------------------------------+
+|                                    MD & Structural Analysis                                   |
++-----------------------------------------------------------------------------------------------+
+|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |
+|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
+|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
+|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
+|  doas           - Density of atomistic states                                                 |
++-----------------------------------------------------------------------------------------------+
+|                                        Heat Transport                                         |
++-----------------------------------------------------------------------------------------------+
+|  emd            - EMD results                    nemd           - NEMD results                |
+|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |
++-----------------------------------------------------------------------------------------------+
+```
 
-`plt_train.py` visualizes NEP training progress, including loss curves and parity plots for energy, force, and virial/stress.
+---
 
-**Input files:**
+## NEP Training and Prediction
 
-- `loss.out`
-- `energy_train.out`
-- `force_train.out`
-- `virial_train.out`
+### plt_train.py
 
-**Usage:**
+Visualizes NEP training progress including loss curves, RMSE evolution, and parity plots comparing DFT vs NEP predictions for energy, forces, and stresses.
+
+**Input Files:** `loss.out`, `energy_train.out`, `force_train.out`, `virial_train.out`
 
 ```bash
 gpumdkit.sh -plt train
@@ -37,28 +72,30 @@ gpumdkit.sh -plt train
   <img src="../../Gallery/train.png" alt="NEP training results" width="75%" />
 </div>
 
-### Prediction Results
+---
 
-`plt_prediction.py` visualizes prediction/test-set results.
+### plt_prediction.py
 
-**Input files:**
+Visualizes NEP prediction results on the test set.
 
-- `energy_test.out`
-- `force_test.out`
-- `virial_test.out`
-
-**Usage:**
+**Input Files:** `energy_test.out`, `force_test.out`, `virial_test.out`
 
 ```bash
 gpumdkit.sh -plt prediction
-gpumdkit.sh -plt test
+gpumdkit.sh -plt test         # Alternative command
 ```
 
 <div align="center">
   <img src="../../Gallery/prediction.png" alt="NEP prediction results" width="75%" />
 </div>
 
-### Train/Test Comparison
+---
+
+### plt_train_test.py
+
+Creates combined parity plots for both training and testing datasets.
+
+**Input Files:** `energy_train.out`, `force_train.out`, `virial_train.out`, `energy_test.out`, `force_test.out`, `virial_test.out`
 
 ```bash
 gpumdkit.sh -plt train_test
@@ -68,9 +105,13 @@ gpumdkit.sh -plt train_test
   <img src="../../Gallery/train_test.png" alt="NEP train and test comparison" width="75%" />
 </div>
 
-### Density Parity Plot
+---
+
+### plt_parity_density.py
+
+Generates density-based parity plots for energies, forces, and stresses. Useful for large datasets where scatter plots become unreadable.
 
-For large datasets, density-based parity plots are often easier to read than raw scatter plots.
+**Input Files:** `energy_train.out`, `force_train.out`, `virial_train.out`
 
 ```bash
 gpumdkit.sh -plt parity_density
@@ -80,9 +121,18 @@ gpumdkit.sh -plt parity_density
   <img src="../../Gallery/parity_plot_density.png" alt="Parity density plot" width="70%" />
 </div>
 
-### Force Error Analysis
+---
 
-`plt_force_errors.py` plots force magnitude and angular errors following the analysis style proposed by [Liu et al.](https://doi.org/10.1038/s41524-023-01123-3).
+### plt_force_errors.py
+
+Plots force error evaluation metrics as proposed by [Liu et al.](https://doi.org/10.1038/s41524-023-01123-3).
+
+**Input File:** `force_train.out`
+
+**Metrics Displayed:**
+- Force magnitude errors (delta_F)
+- Force angle errors (delta_theta)
+- Distribution of errors
 
 ```bash
 gpumdkit.sh -plt force_errors
@@ -92,7 +142,27 @@ gpumdkit.sh -plt force_errors
   <img src="../../Gallery/force_errors.png" alt="Force error analysis" width="70%" />
 </div>
 
-### Restart Parameters
+---
+
+### plt_learning_rate.py
+
+Visualizes learning rate during `gnep` training.
+
+**Input File:** `loss.out`
+
+**Note:** Only for the `gnep` training process.
+
+```bash
+gpumdkit.sh -plt lr
+```
+
+---
+
+### plt_nep_restart.py
+
+Visualizes parameters stored in the `nep.restart` file.
+
+**Input File:** `nep.restart`
 
 ```bash
 gpumdkit.sh -plt restart
@@ -102,9 +172,15 @@ gpumdkit.sh -plt restart
   <img src="../../Gallery/nep_restart.png" alt="NEP restart parameters" width="60%" />
 </div>
 
-### Charge and Born Effective Charge
+---
+
+### plt_charge.py
+
+Plots charge distribution from `qNEP` model.
+
+**Input File:** `charge_train.out`
 
-For qNEP charge output:
+**Important:** Ensure consistency between training set and charge output atom ordering. Use full batch training or run prediction step first.
 
 ```bash
 gpumdkit.sh -plt charge
@@ -114,74 +190,63 @@ gpumdkit.sh -plt charge
   <img src="../../Gallery/charge.png" alt="Charge distribution" width="45%" />
 </div>
 
-For Born effective charge prediction:
+---
+
+### plt_born_charge.py
+
+Creates parity plots for Born effective charges (BEC) on training and testing datasets. Structures with all-zero reference BEC are filtered out.
+
+**Input Files:** `bec_train.out`, `bec_test.out`
 
 ```bash
 gpumdkit.sh -plt born_charge
-gpumdkit.sh -plt bec
+gpumdkit.sh -plt bec          # Alternative command
 ```
 
 <div align="center">
   <img src="../../Gallery/born_charge.png" alt="Born effective charge parity plot" width="45%" />
 </div>
 
-## Molecular Dynamics and Thermodynamics
+---
 
-### Thermodynamic Properties
+## Thermodynamic Properties
 
-`plt_thermo.py` reads `thermo.out` and plots temperature, potential energy, pressure, and other thermodynamic quantities.
+### plt_thermo.py
+
+Primary script for comprehensive thermodynamic property visualization.
+
+**Input File:** `thermo.out`
 
 ```bash
 gpumdkit.sh -plt thermo
-gpumdkit.sh -plt thermo2
-gpumdkit.sh -plt thermo3
 ```
 
 <div align="center">
   <img src="../../Gallery/thermo.png" alt="Thermo plot" width="75%" />
 </div>
 
-### Radial Distribution Function
+---
 
-```bash
-gpumdkit.sh -plt rdf
-gpumdkit.sh -plt rdf <column>
-```
+### plt_thermo2.py & plt_thermo3.py
 
-Full RDF output:
+Alternative thermodynamic visualization with different styles.
 
-<div align="center">
-  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
-</div>
-
-Single pair RDF:
-
-<div align="center">
-  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
-</div>
-
-### Velocity Autocorrelation and PDOS
+**Input File:** `thermo.out`
 
 ```bash
-gpumdkit.sh -plt pdos
-gpumdkit.sh -plt pdos save
+gpumdkit.sh -plt thermo2
+gpumdkit.sh -plt thermo3
 ```
 
-**Input files:** `model.xyz`, `run.in`, `dos.out`, `mvac.out`
+---
 
-<div align="center">
-  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
-</div>
+## Diffusion and Ionic Transport
 
-Heat capacity output:
+### plt_msd.py
 
-<div align="center">
-  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
-</div>
-
-## Diffusion and Ionic Transport
+Plots mean square displacement (MSD) for all directions.
 
-### Mean Square Displacement
+**Input File:** `msd.out`
 
 ```bash
 gpumdkit.sh -plt msd
@@ -191,9 +256,15 @@ gpumdkit.sh -plt msd
   <img src="../../Gallery/msd.png" alt="Mean square displacement" width="48%" />
 </div>
 
-### MSD for All Species
+---
+
+### plt_msd_all.py
+
+Plots MSD for all atomic species separately when using `all_groups` in GPUMD.
 
-Use this when `compute_msd` in `run.in` was configured with `all_groups`.
+**Input File:** `msd.out` (computed with `all_groups` option)
+
+**Requirements:** Must use `all_groups` in the `compute_msd` command in `run.in`.
 
 ```bash
 gpumdkit.sh -plt msd_all msd.out Li P S
@@ -203,7 +274,17 @@ gpumdkit.sh -plt msd_all msd.out Li P S
   <img src="../../Gallery/msd_all.png" alt="MSD for all species" width="48%" />
 </div>
 
-### MSD Convergence Check
+---
+
+### plt_msd_convergence_check.py
+
+Checks convergence of MSD calculations across different time windows.
+
+**Input File:** `msd_step*.out` (computed with `save_every` option)
+
+**Requirements:** Use `save_every` in the `compute_msd` command.
+
+**Purpose:** Verify MSD has converged sufficiently for accurate diffusion coefficient calculation.
 
 ```bash
 gpumdkit.sh -plt msd_conv
@@ -213,7 +294,13 @@ gpumdkit.sh -plt msd_conv
   <img src="../../Gallery/msd_convergence.png" alt="MSD convergence" width="48%" />
 </div>
 
-### Self-Diffusion Coefficient
+---
+
+### plt_sdc.py
+
+Plots self-diffusion coefficient (SDC) vs time.
+
+**Input File:** `msd.out`
 
 ```bash
 gpumdkit.sh -plt sdc
@@ -223,18 +310,20 @@ gpumdkit.sh -plt sdc
   <img src="../../Gallery/sdc.png" alt="Self-diffusion coefficient" width="48%" />
 </div>
 
-### Arrhenius Diffusivity
+---
+
+### plt_arrhenius_d.py
+
+Creates Arrhenius plot for diffusivity (log10 D vs 1000/T).
+
+**Input Files:** `*K/msd.out` files (each temperature subdirectory should contain an `msd.out`)
 
 ```bash
 gpumdkit.sh -plt arrhenius_d
-gpumdkit.sh -plt D
+gpumdkit.sh -plt D             # Alternative command
 ```
 
-<div align="center">
-  <img src="../../Gallery/Arrhenius_D.png" alt="Arrhenius diffusivity" width="58%" />
-</div>
-
-Example output:
+**Output example:**
 
 ```text
 T: 300K, D_total: 1.001e-07 cm2/s
@@ -243,71 +332,221 @@ T: 400K, D_total: 1.027e-06 cm2/s
 Ea: 0.230 eV
 ```
 
-### Arrhenius Ionic Conductivity
+<div align="center">
+  <img src="../../Gallery/Arrhenius_D.png" alt="Arrhenius diffusivity" width="58%" />
+</div>
+
+---
+
+### plt_arrhenius_sigma.py
+
+Creates Arrhenius plot for ionic conductivity (ln(σ·T) vs 1000/T).
+
+**Input Files:** `*K/{model.xyz, run.in, thermo.out, msd.out}` (each temperature subdirectory)
 
 ```bash
 gpumdkit.sh -plt arrhenius_sigma
-gpumdkit.sh -plt sigma
+gpumdkit.sh -plt sigma         # Alternative command
 ```
 
 <div align="center">
   <img src="../../Gallery/Arrhenius_sigma.png" alt="Arrhenius ionic conductivity" width="58%" />
 </div>
 
+---
+
 ## Heat Transport
 
-### EMD
+### plt_emd.py
+
+Analyzes and plots thermal conductivity from equilibrium molecular dynamics (EMD).
+
+**Input Files:** EMD output files from GPUMD
 
 ```bash
-gpumdkit.sh -plt emd x
+gpumdkit.sh -plt emd x        # for x direction
 ```
 
 <div align="center">
-  <img src="../../Gallery/emd.png" alt="EMD thermal conductivity" width="72%" />
+  <img src="../../Gallery/emd.png" alt="EMD thermal conductivity" width="70%" />
 </div>
 
-### NEMD
+---
+
+### plt_nemd.py
+
+Visualizes non-equilibrium molecular dynamics (NEMD) thermal transport properties.
+
+**Input Files:** NEMD output files from GPUMD
+
+**Parameters:**
+
+| Parameter | Description |
+|-----------|-------------|
+| `real_length` | Real length of heat transfer zone in nm (set to `Auto` for auto-calculation) |
+| `scale_eff_size` | Scale factor for effective cross-sectional area (default: 1). For 3D bulk: use 1. For low-dimensional systems with vacuum: S_box / S_eff |
+| `cutoff_freq` | Cutoff frequency for SHC calculation in THz (default: 60) |
+| `save` | Optional, save the plot as `nemd.png` |
+
+**Note:** If no SHC data, set `scale_eff_size` and `cutoff_freq` to any number as placeholders when using `save`.
 
 ```bash
 gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]
 ```
 
-Parameter notes:
+<div align="center">
+  <img src="../../Gallery/nemd.png" alt="NEMD results" width="70%" />
+</div>
+
+---
+
+### plt_hnemd.py
+
+Plots homogeneous non-equilibrium molecular dynamics (HNEMD) results.
+
+**Input Files:** HNEMD output files from GPUMD
 
-| Parameter | Meaning |
-|-----------|---------|
-| `real_length` | real length of heat-transfer zone in nm; use `Auto` for automatic calculation |
-| `scale_eff_size` | scale factor for effective cross-sectional area |
-| `cutoff_freq` | cutoff frequency for SHC calculation in THz |
-| `save` | optional flag to save the figure |
+**Parameters:**
+
+| Parameter | Description |
+|-----------|-------------|
+| `scale_eff_size` | Scale factor for effective cross-sectional area (default: 1) |
+| `cutoff_freq` | Cutoff frequency for SHC calculation in THz (default: 60) |
+| `save` | Optional, save the plot as `hnemd.png` |
+
+**Note:** If no SHC data, set `scale_eff_size` and `cutoff_freq` to any number as placeholders when using `save`.
+
+```bash
+gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]
+```
 
 <div align="center">
-  <img src="../../Gallery/nemd.png" alt="NEMD results" width="72%" />
+  <img src="../../Gallery/hnemd.png" alt="HNEMD results" width="70%" />
 </div>
 
-### HNEMD
+---
+
+## Structural Analysis
+
+### plt_rdf.py
+
+Plots radial distribution function (RDF) showing pair correlations.
+
+**Input File:** `rdf.out`
 
 ```bash
-gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]
+gpumdkit.sh -plt rdf               # Plot all RDF pairs
+gpumdkit.sh -plt rdf <column>      # Plot specific pair
 ```
 
+**Full RDF output:**
+
+<div align="center">
+  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
+</div>
+
+**Single pair RDF:**
+
 <div align="center">
-  <img src="../../Gallery/hnemd.png" alt="HNEMD results" width="72%" />
+  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
 </div>
 
-## Descriptor, Dimer, and Extra Analysis
+---
+
+### plt_rdf_pmf.py
 
-### Descriptor Visualization
+Plots RDF combined with potential of mean force (PMF).
 
-First calculate descriptors:
+**Input File:** `rdf.out`
 
 ```bash
-gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+gpumdkit.sh -plt rdf_pmf
 ```
 
-Then visualize:
+---
+
+### plt_vac.py
+
+Plots velocity autocorrelation function.
+
+**Input File:** `vac.out`
 
 ```bash
+gpumdkit.sh -plt vac
+```
+
+---
+
+### plt_cohesive.py
+
+Plots cohesive energy curve.
+
+```bash
+gpumdkit.sh -plt cohesive
+```
+
+---
+
+### plt_net_force.py
+
+Plots distribution of net forces on structures, useful for identifying problematic configurations.
+
+**Input File:** `train.xyz` (extxyz format)
+
+```bash
+gpumdkit.sh -plt net_force train.xyz
+```
+
+**Reference:** [arXiv:2510.19774](https://arxiv.org/abs/2510.19774)
+
+<div align="center">
+  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
+</div>
+
+---
+
+## Phonons
+
+### plt_pdos.py
+
+Calculates and plots normalized VAC, PDOS, and Heat Capacity (Cv).
+
+**Input Files:** `model.xyz`, `run.in`, `dos.out`, `mvac.out`
+
+```bash
+gpumdkit.sh -plt pdos
+gpumdkit.sh -plt pdos save
+```
+
+<div align="center">
+  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
+</div>
+
+Heat capacity output:
+
+<div align="center">
+  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
+</div>
+
+---
+
+## Descriptor, Dimer, and Extra Analysis
+
+### plt_descriptors.py
+
+Visualizes high-dimensional NEP descriptors using dimensionality reduction (PCA or UMAP).
+
+**Input File:** `descriptors.npy` (generated by `gpumdkit.sh -calc des`)
+
+**Methods:**
+- `pca` — Principal Component Analysis
+- `umap` — Uniform Manifold Approximation and Projection
+
+```bash
+# First generate descriptors
+gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+
+# Then visualize
 gpumdkit.sh -plt des pca
 gpumdkit.sh -plt des umap
 ```
@@ -316,11 +555,26 @@ gpumdkit.sh -plt des umap
   <img src="../../Gallery/des_umap.png" alt="UMAP descriptor visualization" width="52%" />
 </div>
 
-### Dimer Curve
+---
 
-`plt_dimer.py` places two atoms in a large cubic box and calculates energy/force as a function of dimer distance using a NEP model.
+### plt_descriptors_compare.py
+
+Compares descriptors from multiple training sets or models.
 
 ```bash
+gpumdkit.sh -plt des_compare
+```
+
+---
+
+### plt_dimer.py
+
+Plots dimer interaction curves. Two atoms are placed in a cubic box (30 Å) and the potential energy and force are calculated as a function of dimer distance using a NEP model.
+
+**Input File:** `nep.txt`
+
+```bash
+gpumdkit.sh -plt dimer <element1> <element2> <nep_model>
 gpumdkit.sh -plt dimer Li Li nep.txt
 ```
 
@@ -331,11 +585,16 @@ gpumdkit.sh -plt dimer Li Li nep.txt
 
 **Reference:** [J. Chem. Inf. Model. 2026, 66, 3, 1406-1413](https://doi.org/10.1021/acs.jcim.5c02335)
 
-### Density of Atomistic States
+---
+
+### plt_doas.py
+
+Plots density of atomistic states (DOAS) proposed by [Wang et al.](https://doi.org/10.1002/anie.202215544).
 
-`plt_doas.py` plots the density of atomistic states proposed by [Wang et al.](https://doi.org/10.1002/anie.202215544).
+**Input File:** `doas.out` (calculated by `gpumdkit.sh -calc doas`)
 
 ```bash
+gpumdkit.sh -plt doas <doas.out> <species>
 gpumdkit.sh -plt doas doas.out Li
 ```
 
@@ -343,23 +602,19 @@ gpumdkit.sh -plt doas doas.out Li
   <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
 </div>
 
-### Net Force Distribution
-
-```bash
-gpumdkit.sh -plt net_force train.xyz
-```
-
-**Reference:** [arXiv:2510.19774](https://arxiv.org/abs/2510.19774)
-
-<div align="center">
-  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
-</div>
+---
 
 ## Plane-Grid Plot for Polar Materials
 
 This workflow maps displacement or polarization data onto a grid and plots selected plane profiles.
 
-Typical upstream steps:
+**Dependency:**
+
+```bash
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
+```
+
+**Typical upstream steps:**
 
 ```bash
 gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O
@@ -367,31 +622,45 @@ gpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat
 gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz
 ```
 
-Plot:
+**Usage:**
 
 ```bash
 gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr
 gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1
 ```
 
-This function requires `ferrodispcalc`.
+---
 
 ## Quick Reference Table
 
-| Command | Input File(s) | Purpose |
-|---------|---------------|---------|
+| Command | Input File(s) | Description |
+|---------|---------------|-------------|
 | `train` | `loss.out`, `*_train.out` | NEP training plots |
-| `prediction` | `*_test.out` | NEP prediction plots |
-| `train_test` | train/test outputs | combined parity plots |
-| `thermo` | `thermo.out` | thermodynamic properties |
-| `msd` | `msd.out` | mean square displacement |
-| `sdc` | `msd.out` | self-diffusion coefficient |
-| `rdf` | `rdf.out` | radial distribution function |
-| `pdos` | `dos.out`, `mvac.out` | VAC and PDOS |
+| `prediction` / `test` | `*_test.out` | NEP prediction plots |
+| `train_test` | `*_train.out`, `*_test.out` | Combined parity plots |
+| `parity_density` | `*_train.out` | Density-based parity plots |
+| `force_errors` | `force_train.out` | Force error metrics |
+| `lr` | `loss.out` (gnep) | Learning rate |
+| `restart` | `nep.restart` | Restart file parameters |
+| `charge` | `charge_train.out` | Charge distribution |
+| `born_charge` / `bec` | `bec_train.out`, `bec_test.out` | Born effective charges |
+| `thermo` | `thermo.out` | Thermodynamic properties |
+| `msd` | `msd.out` | Mean square displacement |
+| `msd_all` | `msd.out` (all_groups) | MSD for all species |
+| `msd_conv` | `msd_step*.out` | MSD convergence check |
+| `sdc` | `msd.out` | Self-diffusion coefficient |
+| `arrhenius_d` / `D` | `*K/msd.out` | Arrhenius diffusivity |
+| `arrhenius_sigma` / `sigma` | `*K/{model.xyz, run.in, thermo.out, msd.out}` | Arrhenius ionic conductivity |
+| `rdf` | `rdf.out` | Radial distribution function |
+| `rdf_pmf` | `rdf.out` | RDF + potential of mean force |
+| `vac` | `vac.out` | Velocity autocorrelation |
+| `cohesive` | — | Cohesive energy curve |
+| `net_force` | `train.xyz` | Net force distribution |
+| `doas` | `doas.out` | Density of atomistic states |
+| `des` | `descriptors.npy` | Descriptor PCA/UMAP |
+| `dimer` | `nep.txt` | Dimer energy/force curve |
+| `pdos` | `model.xyz`, `run.in`, `dos.out`, `mvac.out` | VAC and PDOS |
 | `emd` | EMD outputs | EMD thermal conductivity |
 | `nemd` | NEMD outputs | NEMD thermal transport |
 | `hnemd` | HNEMD outputs | HNEMD thermal transport |
-| `des` | `descriptors.npy` | descriptor PCA/UMAP |
-| `dimer` | `nep.txt` | dimer energy/force curve |
-| `doas` | `doas.out` | density of atomistic states |
-| `net_force` | `train.xyz` | net force distribution |
+| `viscosity` | Viscosity outputs | Viscosity |
diff --git a/docs/tutorials/en/polar_material_analysis.md b/docs/tutorials/en/polar_material_analysis.md
index af7e4c8..207c60e 100644
--- a/docs/tutorials/en/polar_material_analysis.md
+++ b/docs/tutorials/en/polar_material_analysis.md
@@ -11,6 +11,17 @@ This tutorial includes both general and system-specific tools:
 - `oct-tilt` is for octahedral environments (requires 6 neighbors around each center).
 - `pol-abo3` is specific to `ABO3` polarization analysis.
 
+## Overview
+
+| Step | CLI Command | Main Input | Output |
+|------|-------------|------------|--------|
+| Build neighbor list | `gpumdkit.sh -calc nlist ...` | `model.xyz` | `nl-*.dat` |
+| Calculate displacement | `gpumdkit.sh -calc disp ...` | trajectory + `nl-*.dat` | `displacements.dat` |
+| Average trajectory | `gpumdkit.sh -calc avg-struct ...` | trajectory | averaged extxyz |
+| Octahedral tilt | `gpumdkit.sh -calc oct-tilt ...` | trajectory + B-O neighbor list | tilt-angle table |
+| ABO3 polarization | `gpumdkit.sh -calc pol-abo3 ...` | trajectory + neighbor lists | polarization table |
+| Plane-grid plot | `gpumdkit.sh -plt plane-grid ...` | structure + displacement data | plane profile plot |
+
 ## Dependency
 
 These scripts require `ferrodispcalc`:
@@ -23,6 +34,35 @@ pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
 
 Options `406-410` are the core functions for this tutorial. The sections below explain when to use each one and how to run it.
 
+```bash
+gpumdkit.sh
+# choose 4) Calculators
+```
+
+The calculator menu is:
+
+```text
++----------------------------------------------------------+
+|                     CALCULATOR TOOLS                     |
++----------------------------------------------------------+
+| 401) Calc ionic conductivity                             |
+| 402) Calc properties by nep                              |
+| 403) Calc descriptors of specific elements               |
+| 404) Calc density of atomistic states (DOAS)             |
+| 405) Calc nudged elastic band (NEB) by nep               |
+| 406) Build neighbor list                                 |
+| 407) Calc displacement from trajectory                   |
+| 408) Calc averaged structure                             |
+| 409) Calc octahedral tilt                                |
+| 410) Calc polarization for ABO3                          |
+| 411) Minimize structure by nep                           |
+| 412) Calc mean square displacement (MSD) from trajectory |
++----------------------------------------------------------+
+| 000) Return to the main menu                             |
++----------------------------------------------------------+
+Input the function number:
+```
+
 For full argument details, use:
 
 ```bash
@@ -107,7 +147,7 @@ gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat
   Select trailing frames.
   Integer: last `N` frames.
   `0 < value < 1`: last ratio of frames.
-- `--last` is mutually exclusive with `-s/-t/-p`.
+- `-l/--last` is mutually exclusive with `-s/-t/-p`.
 
 ### Output file
 
@@ -143,7 +183,7 @@ gpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz
   Slice step. Default: `1`.
 - `-l, --last`:
   Select trailing frames (`last N` or `last ratio`).
-- `--last` is mutually exclusive with `-s/-t/-p`.
+- `-l/--last` is mutually exclusive with `-s/-t/-p`.
 
 ### Output file
 
@@ -181,7 +221,7 @@ gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt
   Slice step. Default: `1`.
 - `-l, --last`:
   Select trailing frames (`last N` or `last ratio`).
-- `--last` is mutually exclusive with `-s/-t/-p`.
+- `-l/--last` is mutually exclusive with `-s/-t/-p`.
 
 ### Output file
 
@@ -225,7 +265,7 @@ gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat
   Slice step. Default: `1`.
 - `-l, --last`:
   Select trailing frames (`last N` or `last ratio`).
-- `--last` is mutually exclusive with `-s/-t/-p`.
+- `-l/--last` is mutually exclusive with `-s/-t/-p`.
 
 Important checks:
 
@@ -278,7 +318,7 @@ Output:
 - Saves figures as `XY_*.png`, `XZ_*.png`, `YZ_*.png`.
 
 <div align="center">
-    <img src="../Gallery/PTO_STO_superlattice.png" alt="PTO_STO" width="65%" />
+    <img src="../../Gallery/PTO_STO_superlattice.png" alt="PTO_STO" width="65%" />
 </div>
 
 ## Output files at a glance
@@ -372,7 +412,7 @@ done
 By analyzing the lattice of each temperature-averaged structure together with its polarization (`XX-pol.dat`), we can obtain the following figure:
 
 <div align="center">
-    <img src="../Gallery/PTO-temp.png" alt="PTO-temp" width="65%" />
+    <img src="../../Gallery/PTO-temp.png" alt="PTO-temp" width="65%" />
 </div>
 
 The trend shows a clear phase transition around `600 K`, where the polarization vanishes.
@@ -401,7 +441,7 @@ gpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-x
 ```
 
 <div align="center">
-    <img src="../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
+    <img src="../../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
 </div>
 
 This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero. By analyzing how polarization varies around the vortex core, you can estimate the local dielectric response, but that is beyond the scope of this tutorial.
@@ -429,4 +469,3 @@ gpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat
 #### Other ferroelectric families
 
 Beyond `ABO3`, `ferrodispcalc` can be adapted to many ferroelectric systems, including nitrides, hafnia-based compounds, organic-inorganic hybrids, and some 2D ferroelectrics.
-
diff --git a/docs/tutorials/en/quick_start.md b/docs/tutorials/en/quick_start.md
index 17189db..ad1dd16 100644
--- a/docs/tutorials/en/quick_start.md
+++ b/docs/tutorials/en/quick_start.md
@@ -106,8 +106,8 @@ The help table:
 | -chem_species Analyze chemical species        | -cbc               Charge balance check               |
 | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
+| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
+| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
 +-------------------------------------------------------------------------------------------------------+
 | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
 +-------------------------------------------------------------------------------------------------------+
diff --git a/docs/tutorials/en/structure_sampling.md b/docs/tutorials/en/structure_sampling.md
index e12dd24..c1a7627 100644
--- a/docs/tutorials/en/structure_sampling.md
+++ b/docs/tutorials/en/structure_sampling.md
@@ -133,7 +133,7 @@ This function requires the `NepTrain` package. If you use this function, we reco
 
 ## Deprecated PyNEP FPS
 
-PyNEP FPS is kept for compatibility, but it is only exposed through the direct `-pynep` entry:
+PyNEP FPS is kept for compatibility, but it is only exposed through the direct `-pynep` entry.
 
 If you choose `202` from the interactive menu, it prints:
 
@@ -147,6 +147,22 @@ If you choose `202` from the interactive menu, it prints:
 +-------------------------------------------------+
 ```
 
+### Serial PyNEP
+
+```bash
+python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt
+```
+
+### Parallel PyNEP
+
+```bash
+python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8
+```
+
+The last argument is the number of CPU threads.
+
+### GPUMDkit Entry
+
 ```bash
 gpumdkit.sh -pynep
 ```
@@ -190,7 +206,7 @@ Output:
 
 - `POSCAR_01.vasp`, `POSCAR_02.vasp`, ...
 
-This function requires `dpdata`.
+This function requires `dpdata`. If you use this function, we recommend citing the dpdata package.
 
 ## Force-Deviation Selection
 
diff --git a/docs/tutorials/en/workflow_scripts.md b/docs/tutorials/en/workflow_scripts.md
index 17f750c..77ed4ca 100644
--- a/docs/tutorials/en/workflow_scripts.md
+++ b/docs/tutorials/en/workflow_scripts.md
@@ -17,13 +17,28 @@ Choose:
 3) Workflow
 ```
 
-Typical workflow menu:
+The workflow menu looks like:
+
+```text
++---------------------------------------------------------+
+|                      WORKFLOW TOOLS                     |
++---------------------------------------------------------+
+| 301) SCF batch pretreatment                             |
+| 302) MD sample batch pretreatment (gpumd)               |
+| 303) MD sample batch pretreatment (lmp)                 |
++---------------------------------------------------------+
+| 000) Return to the main menu                            |
++---------------------------------------------------------+
+Input the function number:
+```
+
+Available entries:
 
 | Menu | Workflow | Purpose |
 |------|----------|---------|
-| 301 | SCF batch pretreatment | prepare single-point DFT calculations |
-| 302 | MD sample batch pretreatment (GPUMD) | prepare GPUMD sampling calculations |
-| 303 | MD sample batch pretreatment (LAMMPS) | prepare LAMMPS sampling calculations |
+| 301 | SCF batch pretreatment | Prepare single-point DFT calculations |
+| 302 | MD sample batch pretreatment (GPUMD) | Prepare GPUMD sampling calculations |
+| 303 | MD sample batch pretreatment (LAMMPS) | Prepare LAMMPS sampling calculations |
 
 ## SCF Batch Pretreatment
 
diff --git "a/docs/tutorials/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.md" "b/docs/tutorials/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.md"
index 258ce9f..a6d5574 100644
--- "a/docs/tutorials/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.md"
+++ "b/docs/tutorials/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.md"
@@ -3,9 +3,27 @@
   <p style="text-align: justify;"><code>workflow_active_learning_dev.sh</code> 用于组织一轮 NEP 主动学习流程：运行 GPUMD 分子动力学、筛选结构、抽样、提交第一性原理计算，并进行 NEP 预测检查。</p>
 </div>
 
-### 概览
+**脚本位置：** `Scripts/workflow/`
 
-该脚本用于处理 NEP 主动学习中常见的一轮流程：运行分子动力学、筛选结构、抽样、提交 SCF 计算，并整理后续 prediction 检查。
+## 概览
+
+该脚本自动化了 NEP 主动学习的一轮迭代。典型流程包括：
+
+| 步骤 | 操作 | 目的 |
+|------|------|------|
+| 1 | 运行 MD 模拟 | 使用当前 NEP 模型生成候选结构 |
+| 2 | 过滤结构 | 移除不合理的构型（短距离、大盒子） |
+| 3 | 采样结构 | 选择多样性高或偏差大的结构进行 DFT 计算 |
+| 4 | 运行 SCF 计算 | 计算 DFT 参考能量/力 |
+| 5 | NEP 预测 | 检查模型在新结构上的精度 |
+
+与菜单驱动的模块不同，这个工作流是一个需要按体系修改后直接运行的 shell 脚本：
+
+```bash
+bash Scripts/workflow/workflow_active_learning_dev.sh
+```
+
+下面按脚本中的主要代码块说明每一步的作用。
 
 ## 1. SLURM 设置
 
diff --git "a/docs/tutorials/zh/\345\210\206\346\236\220\345\267\245\345\205\267.md" "b/docs/tutorials/zh/\345\210\206\346\236\220\345\267\245\345\205\267.md"
index 8e4b3b3..dbaf464 100644
--- "a/docs/tutorials/zh/\345\210\206\346\236\220\345\267\245\345\205\267.md"
+++ "b/docs/tutorials/zh/\345\210\206\346\236\220\345\267\245\345\205\267.md"
@@ -1,32 +1,73 @@
 <div align="center">
   <h1>🔍 分析工具</h1>
-  <p style="text-align: justify;">分析工具用于对 extxyz 数据集进行结构统计、距离检查、过滤和组分分析。</p>
+  <p style="text-align: justify;">分析脚本为 extxyz 数据集提供结构统计、距离检查、过滤、成分分析、异常检测和时间估算功能。</p>
 </div>
 
 **脚本位置：** `Scripts/analyzer/`
 
-## 功能概览
+## 概览
 
 | 任务 | 命令 | 用途 |
 |------|------|------|
-| 组分分析 | `gpumdkit.sh -analyze_comp train.xyz` | 按化学组分统计结构 |
-| 元素列表 | `gpumdkit.sh -chem_species train.xyz` | 查看文件中有哪些元素 |
+| 成分分析 | `gpumdkit.sh -analyze_comp train.xyz` | 按化学成分分组 |
+| 化学物种 | `gpumdkit.sh -chem_species train.xyz` | 列出文件中的元素 |
 | 性质范围 | `gpumdkit.sh -range train.xyz force` | 检查能量/力/virial 范围 |
-| 最小距离 | `gpumdkit.sh -min_dist dump.xyz` | 快速检查，不考虑 PBC |
-| PBC 最小距离 | `gpumdkit.sh -min_dist_pbc dump.xyz` | 考虑 PBC 的距离检查 |
-| 电荷平衡 | `gpumdkit.sh -cbc train.xyz` | 检查常见氧化态是否平衡 |
-| 距离过滤 | `gpumdkit.sh -filter_dist_pbc dump.xyz 1.0` | 删除短距离结构 |
-| 盒子过滤 | `gpumdkit.sh -filter_box dump.xyz 13` | 删除盒子边长过大的结构 |
-| 数值过滤 | `gpumdkit.sh -filter_value train.xyz force 20` | 按性质阈值过滤 |
-| 元素对距离 | `gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0` | 按元素对距离范围提取 |
+| 最短距离 | `gpumdkit.sh -min_dist dump.xyz` | 快速距离检查（无 PBC） |
+| 最短距离（PBC） | `gpumdkit.sh -min_dist_pbc dump.xyz` | 准确距离检查（含 PBC） |
+| 电荷平衡 | `gpumdkit.sh -cbc train.xyz` | 氧化态平衡检查 |
+| 距离过滤 | `gpumdkit.sh -filter_dist_pbc dump.xyz 1.0` | 移除短距离接触的结构 |
+| 盒子过滤 | `gpumdkit.sh -filter_box dump.xyz 13` | 移除盒子过大的结构 |
+| 性质过滤 | `gpumdkit.sh -filter_value train.xyz force 20` | 按能量/力/virial 阈值过滤 |
+| 对距离范围 | `gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0` | 按对距离提取结构 |
+| 异常检测 | 菜单 502 | 查找训练集中高 RMSE 的结构 |
+| GPUMD 时间 | `gpumdkit.sh -time gpumd` | 估算 GPUMD 剩余运行时间 |
+| NEP 时间 | `gpumdkit.sh -time nep` | 估算 NEP 剩余训练时间 |
 
-## 组分分析
+---
+
+## 交互模式
+
+打开 GPUMDkit 并选择 `5) Analyzer`：
+
+```bash
+gpumdkit.sh
+```
+
+分析工具菜单如下：
+
+```text
++------------------------------------------------------+
+|                    ANALYZER TOOLS                    |
++------------------------------------------------------+
+| 501) Analyze composition of extxyz                   |
+| 502) Find outliers of extxyz                         |
+| 503) Analyze chemical species of extxyz              |
+| 504) Check charge balance of extxyz                  |
+| 505) Analyze energy/force/virial range               |
+| 506) Filter structures by minimum distance           |
+| 507) Get minimum interatomic distance                |
+| 508) Probability density analysis                    |
++------------------------------------------------------+
+| 000) Return to the main menu                         |
++------------------------------------------------------+
+Input the function number:
+```
+
+大多数分析功能也提供直接 CLI 调用方式，概览表和后续小节中列出了常用命令。
+
+---
+
+## 成分分析
+
+`analyze_composition.py` 分析 extxyz 文件的成分，并允许导出子集。
+
+**输入文件：** `train.xyz`（extxyz 格式）
 
 ```bash
 gpumdkit.sh -analyze_comp train.xyz
 ```
 
-示例输出：
+**输出示例：**
 
 ```text
 Index    Compositions           N atoms      Count
@@ -36,93 +77,312 @@ Index    Compositions           N atoms      Count
 Enter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:
 ```
 
-如果一个 `train.xyz` 中混合了多个体系或不同超胞，这个功能很有用。
+当 `train.xyz` 包含不同体系或不同尺寸的结构时很有用。可以从交互提示中按成分导出子集。
+
+---
 
-## 能量/力/virial 范围
+## 化学物种
+
+`analyze_chem_species.py` 列出 extxyz 文件中所有唯一的化学物种。
+
+**输入文件：** `train.xyz`（extxyz 格式）
+
+```bash
+gpumdkit.sh -chem_species train.xyz
+```
+
+---
+
+## 性质范围分析
+
+`energy_force_virial_analyzer.py` 计算并可视化 extxyz 文件中性质的范围。
+
+**输入文件：** `train.xyz`（extxyz 格式）
+
+**支持的性质：** `energy`、`force`、`virial`
 
 ```bash
 gpumdkit.sh -range train.xyz force
 gpumdkit.sh -range train.xyz energy
 gpumdkit.sh -range train.xyz virial
-gpumdkit.sh -range train.xyz force hist
+gpumdkit.sh -range train.xyz force hist    # 显示直方图
+```
+
+**输出示例：**
+
+```text
+Force range: 0.03210566767721861 to 9.230115912468435
 ```
 
-使用 `hist` 可以画出所选性质的直方图。
+使用 `hist` 选项：
 
 <div align="center">
   <img src="../../Gallery/range_force.png" alt="Force range histogram" width="52%" />
 </div>
 
-## 最小距离检查
+---
+
+## 最短距离检查
+
+### 无 PBC（快速）
+
+`get_min_dist.py` 计算不考虑周期性边界条件的最短原子间距。速度快，但对周期性体系可能不准确。
 
-快速版本：
+**输入文件：** `dump.xyz`（extxyz 格式）
 
 ```bash
 gpumdkit.sh -min_dist dump.xyz
 ```
 
-考虑 PBC 的版本：
+**输出示例：**
+
+```text
++---------------------------+
+|   PBC ignored for speed   |
+| use -min_dist_pbc for PBC |
++---------------------------+
+Minimum interatomic distances:
++---------------------------+
+| Atom Pair |  Distance (Å) |
++---------------------------+
+|   Li-Li   |     1.696     |
+|   Li-O    |     1.587     |
+|   O-O     |     2.480     |
++---------------------------+
+Overall min_distance: 1.587 Å
+```
+
+### 含 PBC（准确）
+
+`get_min_dist_pbc.py` 计算考虑周期性边界条件的最短原子间距。
+
+**输入文件：** `dump.xyz`（extxyz 格式）
 
 ```bash
 gpumdkit.sh -min_dist_pbc dump.xyz
 ```
 
-PBC 版本会考虑周期性边界条件。
+**输出示例：**
+
+```text
+Minimum interatomic distances (with PBC):
++---------------------------+
+| Atom Pair |  Distance (Å) |
++---------------------------+
+|   Li-Li   |     1.696     |
+|   Li-O    |     1.587     |
+|   O-O     |     2.355     |
++---------------------------+
+Overall min_distance: 1.587 Å
+```
+
+---
 
 ## 结构过滤
 
-按最小距离过滤：
+### 按最短距离过滤
+
+`filter_structures_by_distance_pbc.py` 移除任何原子间距低于阈值的结构。
+
+**输入文件：** `dump.xyz`（extxyz 格式）
 
 ```bash
 gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
 ```
 
-按盒子大小过滤：
+移除任何原子间距低于 `1.0 Å` 的结构。
+
+### 按盒子大小过滤
+
+`filter_exyz_by_box.py` 按盒子边长过滤结构。
+
+**输入文件：** `dump.xyz`（extxyz 格式）
 
 ```bash
 gpumdkit.sh -filter_box dump.xyz 13
 ```
 
-按性质值过滤：
+保留所有盒子边长低于 `13 Å` 的结构。
+
+### 按性质值过滤
+
+`filter_exyz_by_value.py` 按能量、力或 virial 阈值过滤结构。
+
+**输入文件：** `train.xyz`（extxyz 格式）
+
+**支持的性质：** `energy`、`force`、`virial`
 
 ```bash
 gpumdkit.sh -filter_value train.xyz force 20
+gpumdkit.sh -filter_value train.xyz energy 5
 ```
 
-按元素对距离范围提取：
+过滤掉力分量超过 `20 eV/Å`（或能量超过 `5 eV/atom`）的结构。
+
+### 按对距离范围过滤
+
+`filter_dist_range.py` 提取特定元素对距离在给定范围内的结构。
+
+**输入文件：** `dump.xyz`（extxyz 格式）
 
 ```bash
 gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0
 ```
 
+提取 Li-Li 最短距离在 `1.8 Å` 到 `2.0 Å` 之间的结构。输出：`filtered_Li_Li_1.8_2.0.xyz`。
+
+---
+
 ## 电荷平衡检查
 
+`charge_balance_check.py` 检查结构的氧化态平衡。
+
+**输入文件：** `train.xyz`（extxyz 格式）
+
 ```bash
 gpumdkit.sh -cbc train.xyz
 ```
 
-可能输出：
+**输出文件：**
+
+- `balanced.xyz` — 电荷平衡的结构
+- `unbalanced.xyz` — 电荷不平衡的结构
+- `indices.txt` — 平衡结构的索引
+
+适用于具有明确氧化态的体系。
+
+---
+
+## 异常检测
+
+`find_outliers.py` 基于能量、力和应力的 RMSE 阈值查找 NEP 训练数据中的异常结构。
+
+**输入文件：** `energy_train.out`、`force_train.out`、`stress_train.out`、`train.xyz`
+
+这些文件在 NEP 训练过程中生成。脚本比较 DFT 与 NEP 的预测，识别误差较大的结构。
+
+```bash
+# 交互模式
+gpumdkit.sh    # 选择：5) 分析工具 → 502) 查找异常结构
+```
+
+**交互提示：**
+
+```text
+Enter energy RMSE threshold (meV/atom): 1
+Enter force RMSE threshold (meV/Å): 60
+Enter stress RMSE threshold (GPa): 0.03
+```
 
-- `balanced.xyz`
-- `unbalanced.xyz`
-- `indices.txt`
+**输出文件：**
+
+- `selected.xyz` — 超过 RMSE 阈值的结构（异常值）
+- `remained.xyz` — 在阈值内的结构
+- `selected_remained.png` — 对比图
+
+**用途：** NEP 训练后，用此工具识别对误差贡献最大的问题结构。移除或改进这些结构以提升训练集质量。
+
+---
+
+## 时间估算
+
+### GPUMD 剩余时间
+
+`time_consuming_gpumd.sh` 估算 GPUMD 模拟的剩余时间。
+
+**输入文件：** `run.in`、`thermo.out`（在当前 GPUMD 工作目录中）
+
+```bash
+gpumdkit.sh -time gpumd
+```
+
+**输出示例：**
+
+```text
+----------------- System Information ----------------
+total frames: 1050000
+-----------------------------------------------------
+Current Frame  Speed (steps/s)   Total Time       Time Left       Estimated End
+-------------   -------------   -------------   -------------   -----------------
+    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04
+    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56
+```
 
-这个功能适合常见氧化态有意义的离子材料。
+### NEP 剩余时间
 
-## 示例命令
+`time_consuming_nep.sh` 估算 NEP 训练的剩余时间。
 
-性质和距离检查：
+**输入文件：** `loss.out`（在当前 NEP 工作目录中）
 
 ```bash
+gpumdkit.sh -time nep
+```
+
+**输出示例：**
+
+```text
++-----------------+-----------+-----------------+---------------------+
+|       Step      | Time Diff |    Time Left    |    Finish Time      |
++-----------------+-----------+-----------------+---------------------+
+| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |
+| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |
+| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |
++-----------------+-----------+-----------------+---------------------+
+```
+
+---
+
+## 概率密度分析
+
+`probability_density_analysis.py` 计算移动离子的 3D 概率密度，用于扩散通道分析。
+
+**输入文件：** 参考结构（POSCAR）、轨迹文件（extxyz）
+
+```bash
+gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25
+```
+
+**输出：** `probability_density_0.25.vasp` — 概率密度网格，可用 VESTA 等工具可视化。
+
+---
+
+## 示例工作流
+
+### 结构质量检查
+
+```bash
+# 1. 检查成分
 gpumdkit.sh -analyze_comp train.xyz
+
+# 2. 检查能量/力范围
 gpumdkit.sh -range train.xyz force hist
-gpumdkit.sh -range train.xyz energy hist
+
+# 3. 检查最短距离
 gpumdkit.sh -min_dist_pbc train.xyz
+
+# 4. 查找异常值（NEP 训练后）
+# 交互：5) 分析工具 → 502
 ```
 
-过滤示例：
+### 结构过滤流水线
 
 ```bash
+# 1. 按最短距离过滤
 gpumdkit.sh -filter_dist_pbc dump.xyz 1.0
-gpumdkit.sh -filter_box filtered_dist.xyz 13
+
+# 2. 按盒子大小过滤
+gpumdkit.sh -filter_box filtered_dist_pbc.xyz 13
+
+# 3. 按力阈值过滤
+gpumdkit.sh -filter_value filtered_box.xyz force 20
+```
+
+### 扩散通道分析
+
+```bash
+# 1. 计算概率密度
+gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25
+
+# 2. 用 VESTA 可视化
+# 打开 probability_density_0.25.vasp
 ```
diff --git "a/docs/tutorials/zh/\345\267\245\344\275\234\346\265\201\350\204\232\346\234\254.md" "b/docs/tutorials/zh/\345\267\245\344\275\234\346\265\201\350\204\232\346\234\254.md"
index 75a35e9..0921e90 100644
--- "a/docs/tutorials/zh/\345\267\245\344\275\234\346\265\201\350\204\232\346\234\254.md"
+++ "b/docs/tutorials/zh/\345\267\245\344\275\234\346\265\201\350\204\232\346\234\254.md"
@@ -17,7 +17,22 @@ gpumdkit.sh
 3) Workflow
 ```
 
-常见菜单：
+菜单如下：
+
+```text
++---------------------------------------------------------+
+|                      WORKFLOW TOOLS                     |
++---------------------------------------------------------+
+| 301) SCF batch pretreatment                             |
+| 302) MD sample batch pretreatment (gpumd)               |
+| 303) MD sample batch pretreatment (lmp)                 |
++---------------------------------------------------------+
+| 000) Return to the main menu                            |
++---------------------------------------------------------+
+Input the function number:
+```
+
+常用功能：
 
 | 菜单 | 工作流 | 用途 |
 |------|--------|------|
@@ -192,6 +207,21 @@ current directory/
 
 更完整的开发版主动学习脚本说明见 [主动学习](主动学习工作流.md)。
 
+## 基于模板的温度系列
+
+对于简单的温度系列模拟，使用 shell 循环即可：
+
+```bash
+for temp in 300 500 700 900; do
+    mkdir -p "${temp}K"
+    cp model.xyz "${temp}K/"
+    cp nep.txt "${temp}K/"
+    sed "s/TEMPERATURE/$temp/g" run_template.in > "${temp}K/run.in"
+done
+```
+
+然后根据你的集群系统提交生成的文件夹。
+
 ## 使用建议
 
 - 工作流脚本和集群环境强相关，正式批量提交前先用少量结构测试。
diff --git "a/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md" "b/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md"
index fdb62cf..d326281 100644
--- "a/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md"
+++ "b/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md"
@@ -106,8 +106,8 @@ gpumdkit.sh -h
 | -chem_species Analyze chemical species        | -cbc               Charge balance check               |
 | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
+| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
+| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
 +-------------------------------------------------------------------------------------------------------+
 | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
 +-------------------------------------------------------------------------------------------------------+
diff --git "a/docs/tutorials/zh/\346\236\201\346\200\247\346\235\220\346\226\231\345\210\206\346\236\220.md" "b/docs/tutorials/zh/\346\236\201\346\200\247\346\235\220\346\226\231\345\210\206\346\236\220.md"
index e5d0f40..619892d 100644
--- "a/docs/tutorials/zh/\346\236\201\346\200\247\346\235\220\346\226\231\345\210\206\346\236\220.md"
+++ "b/docs/tutorials/zh/\346\236\201\346\200\247\346\235\220\346\226\231\345\210\206\346\236\220.md"
@@ -11,6 +11,17 @@
 - `oct-tilt` 用于八面体环境分析，需要每个中心原子周围有 6 个近邻。
 - `pol-abo3` 专用于 `ABO3` 体系的极化分析。
 
+## 概览
+
+| 步骤 | CLI 命令 | 主要输入 | 输出 |
+|------|----------|----------|------|
+| 构建近邻列表 | `gpumdkit.sh -calc nlist ...` | `model.xyz` | `nl-*.dat` |
+| 计算位移 | `gpumdkit.sh -calc disp ...` | 轨迹 + `nl-*.dat` | `displacements.dat` |
+| 平均轨迹结构 | `gpumdkit.sh -calc avg-struct ...` | 轨迹 | 平均结构 extxyz |
+| 八面体倾斜 | `gpumdkit.sh -calc oct-tilt ...` | 轨迹 + B-O 近邻列表 | 倾斜角数据表 |
+| ABO3 极化 | `gpumdkit.sh -calc pol-abo3 ...` | 轨迹 + 近邻列表 | 极化数据表 |
+| plane-grid 绘图 | `gpumdkit.sh -plt plane-grid ...` | 结构 + 位移数据 | 平面剖面图 |
+
 ## 依赖
 
 这些脚本需要 `ferrodispcalc`：
@@ -23,6 +34,35 @@ pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
 
 选项 `406-410` 是本教程中的核心功能。下面各节会说明每个功能的用途和运行方式。
 
+```bash
+gpumdkit.sh
+# 选择 4) Calculators
+```
+
+计算器菜单如下：
+
+```text
++----------------------------------------------------------+
+|                     CALCULATOR TOOLS                     |
++----------------------------------------------------------+
+| 401) Calc ionic conductivity                             |
+| 402) Calc properties by nep                              |
+| 403) Calc descriptors of specific elements               |
+| 404) Calc density of atomistic states (DOAS)             |
+| 405) Calc nudged elastic band (NEB) by nep               |
+| 406) Build neighbor list                                 |
+| 407) Calc displacement from trajectory                   |
+| 408) Calc averaged structure                             |
+| 409) Calc octahedral tilt                                |
+| 410) Calc polarization for ABO3                          |
+| 411) Minimize structure by nep                           |
+| 412) Calc mean square displacement (MSD) from trajectory |
++----------------------------------------------------------+
+| 000) Return to the main menu                             |
++----------------------------------------------------------+
+Input the function number:
+```
+
 完整参数说明可以通过以下命令查看：
 
 ```bash
@@ -107,7 +147,7 @@ gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat
   选择末尾部分帧。
   整数表示最后 `N` 帧；
   `0 < value < 1` 表示最后一部分比例的帧。
-- `--last` 与 `-s/-t/-p` 互斥。
+- `-l/--last` 与 `-s/-t/-p` 互斥。
 
 ### 输出文件
 
@@ -143,7 +183,7 @@ gpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz
   切片步长。默认值：`1`。
 - `-l, --last`：
   选择末尾帧，可以是最后 `N` 帧或最后一部分比例的帧。
-- `--last` 与 `-s/-t/-p` 互斥。
+- `-l/--last` 与 `-s/-t/-p` 互斥。
 
 ### 输出文件
 
@@ -181,7 +221,7 @@ gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt
   切片步长。默认值：`1`。
 - `-l, --last`：
   选择末尾帧，可以是最后 `N` 帧或最后一部分比例的帧。
-- `--last` 与 `-s/-t/-p` 互斥。
+- `-l/--last` 与 `-s/-t/-p` 互斥。
 
 ### 输出文件
 
@@ -225,7 +265,7 @@ gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat
   切片步长。默认值：`1`。
 - `-l, --last`：
   选择末尾帧，可以是最后 `N` 帧或最后一部分比例的帧。
-- `--last` 与 `-s/-t/-p` 互斥。
+- `-l/--last` 与 `-s/-t/-p` 互斥。
 
 重要检查：
 
@@ -278,7 +318,7 @@ gpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0
 - 图片保存为 `XY_*.png`、`XZ_*.png`、`YZ_*.png`。
 
 <div align="center">
-    <img src="../Gallery/PTO_STO_superlattice.png" alt="PTO_STO" width="65%" />
+    <img src="../../Gallery/PTO_STO_superlattice.png" alt="PTO_STO" width="65%" />
 </div>
 
 ## 输出文件一览
@@ -372,7 +412,7 @@ done
 结合每个温度平均结构的晶格信息和极化文件（`XX-pol.dat`）进行分析，可以得到如下图：
 
 <div align="center">
-    <img src="../Gallery/PTO-temp.png" alt="PTO-temp" width="65%" />
+    <img src="../../Gallery/PTO-temp.png" alt="PTO-temp" width="65%" />
 </div>
 
 该趋势显示在约 `600 K` 附近发生明显相变，此时极化消失。
@@ -401,7 +441,7 @@ gpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-x
 ```
 
 <div align="center">
-    <img src="../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
+    <img src="../../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
 </div>
 
 这会得到与前面展示相似的图。在 PTO 区域可以看到类似涡旋的极化图样，而 STO 区域的极化接近于零。通过分析涡旋核附近极化的变化，可以估计局域介电响应，但这超出了本教程范围。
diff --git "a/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md" "b/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
index 12967a7..29b61b8 100644
--- "a/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
+++ "b/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
@@ -88,6 +88,7 @@ Input the function number or converter keyword:
 | CIF | POSCAR | `gpumdkit.sh -cif2pos input.cif POSCAR.vasp` |
 | CIF | extxyz | `gpumdkit.sh -cif2exyz input.cif model.xyz` |
 | ASE traj | extxyz | `gpumdkit.sh -traj2exyz input.traj output.xyz` |
+| extxyz | clean extxyz | `gpumdkit.sh -clean_xyz input.xyz clean.xyz` |
 
 ## 常见例子
 
@@ -217,6 +218,53 @@ gpumdkit.sh -replicate POSCAR supercell.vasp 256
 
 第一种按晶胞倍数扩胞，第二种按目标原子数自动选择扩胞方式。
 
+### 提取单帧
+
+```bash
+gpumdkit.sh -get_frame dump.xyz 1000
+```
+
+从 extxyz 轨迹中提取第 `1000` 帧（索引从 0 开始）。
+
+### 拆分多帧 extxyz
+
+`split_single_xyz.py` 将多帧 extxyz 文件拆分为单帧文件。
+
+```bash
+python Scripts/format_conversion/split_single_xyz.py dump.xyz
+```
+
+生成 `model_0.xyz`、`model_1.xyz`、... 等单帧文件。
+
+### MTP 转换
+
+将 MTP `.cfg` 格式转换为 extxyz：
+
+```bash
+gpumdkit.sh    # 选择：1) 格式转换 → 102
+```
+
+交互提示：
+
+```text
+Input <filename.cfg> <Symbol1 Symbol2 Symbol3 ...>
+Example: train.cfg Pd Ag
+------------>>
+```
+
+### ABACUS 转换
+
+将 ABACUS 输出转换为 extxyz：
+
+```bash
+gpumdkit.sh    # 选择：1) 格式转换 → 104
+```
+
+菜单提供两个选项：
+
+1. SCF 输出（`running_scf.log`）
+2. MD 输出（`running_md.log`）
+
 ## 常见问题
 
 | 问题 | 建议 |
diff --git "a/docs/tutorials/zh/\347\273\223\346\236\204\351\207\207\346\240\267.md" "b/docs/tutorials/zh/\347\273\223\346\236\204\351\207\207\346\240\267.md"
index 1263e57..57dc0da 100644
--- "a/docs/tutorials/zh/\347\273\223\346\236\204\351\207\207\346\240\267.md"
+++ "b/docs/tutorials/zh/\347\273\223\346\236\204\351\207\207\346\240\267.md"
@@ -126,7 +126,7 @@ Choose selection method:
 
 ## PyNEP 旧入口
 
-PyNEP FPS 仍然保留兼容，但只通过 `-pynep` 入口调用：
+PyNEP FPS 仍然保留兼容，但只通过 `-pynep` 入口调用。
 
 如果在交互菜单中选择 `202`，会看到：
 
@@ -140,6 +140,22 @@ PyNEP FPS 仍然保留兼容，但只通过 `-pynep` 入口调用：
 +-------------------------------------------------+
 ```
 
+### 串行 PyNEP
+
+```bash
+python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt
+```
+
+### 并行 PyNEP
+
+```bash
+python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8
+```
+
+最后一个参数是 CPU 线程数。
+
+### GPUMDkit 入口
+
 ```bash
 gpumdkit.sh -pynep
 ```
@@ -181,7 +197,7 @@ Example: POSCAR 20 0.03 0.2 uniform
 
 - `POSCAR_01.vasp`、`POSCAR_02.vasp` 等
 
-该功能需要 `dpdata`。
+该功能需要 `dpdata`。使用此功能时建议引用 dpdata 包。
 
 ## 最大力偏差结构选择
 
@@ -211,6 +227,16 @@ Input <structs_num> <threshold> (eg. 200 0.15)
 
 - `selected.xyz`
 
+## 帧范围提取
+
+提取轨迹的一部分帧：
+
+```bash
+python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
+```
+
+这会写入轨迹 0% 到 80% 的帧。
+
 ## 示例命令
 
 ```bash
diff --git "a/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md" "b/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md"
index dffd4fc..6bcca6f 100644
--- "a/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md"
+++ "b/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md"
@@ -1,6 +1,6 @@
 <div align="center">
   <h1>📊 绘图脚本</h1>
-  <p style="text-align: justify;">绘图模块用于可视化 GPUMD、NEP 和 GPUMDkit 计算器产生的数据。</p>
+  <p style="text-align: justify;">绘图模块包含一系列 Python 脚本，用于可视化 GPUMD、NEP 和 GPUMDkit 计算器产生的数据。所有图表均可交互显示或保存为高分辨率 PNG 文件。</p>
 </div>
 
 **脚本位置：** `Scripts/plt_scripts/`
@@ -8,17 +8,61 @@
 ## 快速入口
 
 ```bash
-gpumdkit.sh -plt
-gpumdkit.sh -plt <type>
-gpumdkit.sh -plt <type> save
-gpumdkit.sh -plt <type> -h
+gpumdkit.sh -plt              # 显示所有绘图选项
+gpumdkit.sh -plt <type>       # 生成指定图表
+gpumdkit.sh -plt <type> save  # 保存为 PNG
+gpumdkit.sh -plt <type> -h    # 显示特定图表的帮助
 ```
 
+运行 `gpumdkit.sh -plt` 会显示绘图命令菜单：
+
+```text
++-----------------------------------------------------------------------------------------------+
+|                     GPUMDkit <version> PLOT & VISUALIZATION TOOLS              |
++-----------------------------------------------------------------------------------------------+
+|  Usage: gpumdkit.sh -plt <type>                        Help: gpumdkit.sh -plt <type> -h       |
++-----------------------------------------------------------------------------------------------+
+|                                    NEP Training & Evaluation                                  |
++-----------------------------------------------------------------------------------------------+
+|  train          - NEP training results           prediction     - NEP prediction results      |
+|  train_test     - NEP train and test results     parity_density - Parity density plot         |
+|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |
+|  charge         - Charge distribution            born_charge    - Born effective charges      |
+|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |
+|  des            - Descriptors                    lr             - Learning rate for gnep      |
++-----------------------------------------------------------------------------------------------+
+|                                     Diffusion & Transport                                     |
++-----------------------------------------------------------------------------------------------+
+|  msd            - Mean square displacement       msd_conv       - MSD convergence             |
+|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |
+|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|
+|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |
+|  D_xyz          - Directional Arrhenius D                                                     |
++-----------------------------------------------------------------------------------------------+
+|                                    MD & Structural Analysis                                   |
++-----------------------------------------------------------------------------------------------+
+|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |
+|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
+|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
+|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
+|  doas           - Density of atomistic states                                                 |
++-----------------------------------------------------------------------------------------------+
+|                                        Heat Transport                                         |
++-----------------------------------------------------------------------------------------------+
+|  emd            - EMD results                    nemd           - NEMD results                |
+|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |
++-----------------------------------------------------------------------------------------------+
+```
+
+---
+
 ## NEP 训练与预测
 
-### 训练结果
+### plt_train.py
+
+可视化 NEP 训练过程，包括 loss 曲线、RMSE 演化，以及能量/力/virial 的 DFT vs NEP parity plot。
 
-读取 `loss.out`、`energy_train.out`、`force_train.out`、`virial_train.out`，绘制 loss 和能量/力/virial 的 parity plot。
+**输入文件：** `loss.out`、`energy_train.out`、`force_train.out`、`virial_train.out`
 
 ```bash
 gpumdkit.sh -plt train
@@ -28,18 +72,30 @@ gpumdkit.sh -plt train
   <img src="../../Gallery/train.png" alt="NEP training results" width="75%" />
 </div>
 
-### 预测结果
+---
+
+### plt_prediction.py
+
+可视化测试集上的 NEP 预测结果。
+
+**输入文件：** `energy_test.out`、`force_test.out`、`virial_test.out`
 
 ```bash
 gpumdkit.sh -plt prediction
-gpumdkit.sh -plt test
+gpumdkit.sh -plt test         # 替代命令
 ```
 
 <div align="center">
   <img src="../../Gallery/prediction.png" alt="NEP prediction results" width="75%" />
 </div>
 
-### 训练/测试集对比
+---
+
+### plt_train_test.py
+
+将训练集和测试集的 parity plot 合并显示。
+
+**输入文件：** `energy_train.out`、`force_train.out`、`virial_train.out`、`energy_test.out`、`force_test.out`、`virial_test.out`
 
 ```bash
 gpumdkit.sh -plt train_test
@@ -49,9 +105,13 @@ gpumdkit.sh -plt train_test
   <img src="../../Gallery/train_test.png" alt="NEP train and test comparison" width="75%" />
 </div>
 
-### 密度 parity plot
+---
+
+### plt_parity_density.py
+
+生成基于密度的 parity plot，适用于大数据集（散点图过于密集时更易阅读）。
 
-大数据集散点太密时，密度图更容易观察误差分布：
+**输入文件：** `energy_train.out`、`force_train.out`、`virial_train.out`
 
 ```bash
 gpumdkit.sh -plt parity_density
@@ -61,9 +121,18 @@ gpumdkit.sh -plt parity_density
   <img src="../../Gallery/parity_plot_density.png" alt="Parity density plot" width="70%" />
 </div>
 
-### 力误差分析
+---
 
-`plt_force_errors.py` 参考 [Liu et al.](https://doi.org/10.1038/s41524-023-01123-3) 的方式分析力大小误差和角度误差。
+### plt_force_errors.py
+
+参考 [Liu et al.](https://doi.org/10.1038/s41524-023-01123-3) 的方法绘制力误差评估指标。
+
+**输入文件：** `force_train.out`
+
+**显示指标：**
+- 力大小误差 (delta_F)
+- 力角度误差 (delta_theta)
+- 误差分布
 
 ```bash
 gpumdkit.sh -plt force_errors
@@ -73,101 +142,411 @@ gpumdkit.sh -plt force_errors
   <img src="../../Gallery/force_errors.png" alt="Force error analysis" width="70%" />
 </div>
 
-### 电荷和 Born 有效电荷
+---
+
+### plt_learning_rate.py
+
+可视化 `gnep` 训练过程中的学习率变化。
+
+**输入文件：** `loss.out`
+
+**注意：** 仅适用于 `gnep` 训练过程。
+
+```bash
+gpumdkit.sh -plt lr
+```
+
+---
+
+### plt_nep_restart.py
+
+可视化 `nep.restart` 文件中存储的参数。
+
+**输入文件：** `nep.restart`
+
+```bash
+gpumdkit.sh -plt restart
+```
+
+<div align="center">
+  <img src="../../Gallery/nep_restart.png" alt="NEP restart parameters" width="60%" />
+</div>
+
+---
+
+### plt_charge.py
+
+绘制 `qNEP` 模型的电荷分布。
+
+**输入文件：** `charge_train.out`
+
+**重要提示：** 确保训练集和电荷输出的原子排序一致。建议使用全 batch 训练或先运行预测步骤。
 
 ```bash
 gpumdkit.sh -plt charge
-gpumdkit.sh -plt born_charge
-gpumdkit.sh -plt bec
 ```
 
 <div align="center">
   <img src="../../Gallery/charge.png" alt="Charge distribution" width="45%" />
+</div>
+
+---
+
+### plt_born_charge.py
+
+为训练集和测试集创建 Born 有效电荷 (BEC) 的 parity plot。全零参考 BEC 的结构会被过滤。
+
+**输入文件：** `bec_train.out`、`bec_test.out`
+
+```bash
+gpumdkit.sh -plt born_charge
+gpumdkit.sh -plt bec          # 替代命令
+```
+
+<div align="center">
   <img src="../../Gallery/born_charge.png" alt="Born effective charge parity plot" width="45%" />
 </div>
 
-## MD 和结构分析绘图
+---
+
+## 热力学量
+
+### plt_thermo.py
+
+综合可视化热力学性质的主脚本。
 
-### 热力学量
+**输入文件：** `thermo.out`
 
 ```bash
 gpumdkit.sh -plt thermo
-gpumdkit.sh -plt thermo2
-gpumdkit.sh -plt thermo3
 ```
 
 <div align="center">
   <img src="../../Gallery/thermo.png" alt="Thermo plot" width="75%" />
 </div>
 
-### RDF
+---
+
+### plt_thermo2.py & plt_thermo3.py
+
+不同风格的热力学量可视化。
+
+**输入文件：** `thermo.out`
+
+```bash
+gpumdkit.sh -plt thermo2
+gpumdkit.sh -plt thermo3
+```
+
+---
+
+## 扩散和离子输运
+
+### plt_msd.py
+
+绘制各方向的均方位移 (MSD)。
+
+**输入文件：** `msd.out`
 
 ```bash
-gpumdkit.sh -plt rdf
-gpumdkit.sh -plt rdf <column>
+gpumdkit.sh -plt msd
 ```
 
 <div align="center">
-  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
-  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
+  <img src="../../Gallery/msd.png" alt="Mean square displacement" width="48%" />
 </div>
 
-### VAC 和 PDOS
+---
+
+### plt_msd_all.py
+
+当 GPUMD 中使用 `all_groups` 时，分别绘制每种原子的 MSD。
+
+**输入文件：** `msd.out`（需要使用 `all_groups` 选项计算）
+
+**要求：** `run.in` 中的 `compute_msd` 命令必须使用 `all_groups`。
 
 ```bash
-gpumdkit.sh -plt pdos
-gpumdkit.sh -plt pdos save
+gpumdkit.sh -plt msd_all msd.out Li P S
 ```
 
-输入文件通常包括 `model.xyz`、`run.in`、`dos.out`、`mvac.out`。
+<div align="center">
+  <img src="../../Gallery/msd_all.png" alt="MSD for all species" width="48%" />
+</div>
+
+---
+
+### plt_msd_convergence_check.py
+
+检查不同时间窗口下 MSD 计算的收敛性。
+
+**输入文件：** `msd_step*.out`（需要在 `compute_msd` 中使用 `save_every` 选项）
+
+**要求：** 在 `compute_msd` 命令中使用 `save_every`。
+
+**用途：** 验证 MSD 是否已充分收敛以准确计算扩散系数。
+
+```bash
+gpumdkit.sh -plt msd_conv
+```
 
 <div align="center">
-  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
-  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
+  <img src="../../Gallery/msd_convergence.png" alt="MSD convergence" width="48%" />
 </div>
 
-## 扩散和离子输运
+---
+
+### plt_sdc.py
+
+绘制自扩散系数 (SDC) 随时间的变化。
+
+**输入文件：** `msd.out`
 
 ```bash
-gpumdkit.sh -plt msd
 gpumdkit.sh -plt sdc
-gpumdkit.sh -plt msd_conv
+```
+
+<div align="center">
+  <img src="../../Gallery/sdc.png" alt="Self-diffusion coefficient" width="48%" />
+</div>
+
+---
+
+### plt_arrhenius_d.py
+
+创建 Arrhenius 扩散系数图（log10 D vs 1000/T）。
+
+**输入文件：** `*K/msd.out`（每个温度子目录下的 `msd.out`）
+
+```bash
 gpumdkit.sh -plt arrhenius_d
-gpumdkit.sh -plt arrhenius_sigma
+gpumdkit.sh -plt D             # 替代命令
+```
+
+**输出示例：**
+
+```text
+T: 300K, D_total: 1.001e-07 cm2/s
+T: 350K, D_total: 4.184e-07 cm2/s
+T: 400K, D_total: 1.027e-06 cm2/s
+Ea: 0.230 eV
 ```
 
 <div align="center">
-  <img src="../../Gallery/msd.png" alt="Mean square displacement" width="45%" />
-  <img src="../../Gallery/sdc.png" alt="Self-diffusion coefficient" width="45%" />
+  <img src="../../Gallery/Arrhenius_D.png" alt="Arrhenius diffusivity" width="58%" />
 </div>
 
-Arrhenius 图：
+---
+
+### plt_arrhenius_sigma.py
+
+创建 Arrhenius 离子电导率图（ln(σ·T) vs 1000/T）。
+
+**输入文件：** `*K/{model.xyz, run.in, thermo.out, msd.out}`（每个温度子目录）
+
+```bash
+gpumdkit.sh -plt arrhenius_sigma
+gpumdkit.sh -plt sigma         # 替代命令
+```
 
 <div align="center">
-  <img src="../../Gallery/Arrhenius_D.png" alt="Arrhenius diffusivity" width="55%" />
-  <img src="../../Gallery/Arrhenius_sigma.png" alt="Arrhenius ionic conductivity" width="55%" />
+  <img src="../../Gallery/Arrhenius_sigma.png" alt="Arrhenius ionic conductivity" width="58%" />
 </div>
 
+---
+
 ## 热输运
 
+### plt_emd.py
+
+分析并绘制平衡分子动力学 (EMD) 热导率。
+
+**输入文件：** GPUMD 的 EMD 输出文件
+
 ```bash
-gpumdkit.sh -plt emd x
-gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]
-gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]
+gpumdkit.sh -plt emd x        # x 方向
 ```
 
 <div align="center">
   <img src="../../Gallery/emd.png" alt="EMD thermal conductivity" width="70%" />
+</div>
+
+---
+
+### plt_nemd.py
+
+可视化非平衡分子动力学 (NEMD) 热输运性质。
+
+**输入文件：** GPUMD 的 NEMD 输出文件
+
+**参数说明：**
+
+| 参数 | 说明 |
+|------|------|
+| `real_length` | 传热区实际长度（nm），设为 `Auto` 可自动计算 |
+| `scale_eff_size` | 有效截面积缩放因子（默认：1）。三维体相用 1；含真空层的低维体系用 S_box / S_eff |
+| `cutoff_freq` | SHC 计算的截止频率（THz，默认：60） |
+| `save` | 可选，保存图片为 `nemd.png` |
+
+**注意：** 如果没有 SHC 数据，使用 `save` 时请将 `scale_eff_size` 和 `cutoff_freq` 设为任意占位数字。
+
+```bash
+gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]
+```
+
+<div align="center">
   <img src="../../Gallery/nemd.png" alt="NEMD results" width="70%" />
+</div>
+
+---
+
+### plt_hnemd.py
+
+绘制非均匀非平衡分子动力学 (HNEMD) 结果。
+
+**输入文件：** GPUMD 的 HNEMD 输出文件
+
+**参数说明：**
+
+| 参数 | 说明 |
+|------|------|
+| `scale_eff_size` | 有效截面积缩放因子（默认：1） |
+| `cutoff_freq` | SHC 计算的截止频率（THz，默认：60） |
+| `save` | 可选，保存图片为 `hnemd.png` |
+
+**注意：** 如果没有 SHC 数据，使用 `save` 时请将 `scale_eff_size` 和 `cutoff_freq` 设为任意占位数字。
+
+```bash
+gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]
+```
+
+<div align="center">
   <img src="../../Gallery/hnemd.png" alt="HNEMD results" width="70%" />
 </div>
 
+---
+
+## 结构分析
+
+### plt_rdf.py
+
+绘制径向分布函数 (RDF)，展示原子对关联。
+
+**输入文件：** `rdf.out`
+
+```bash
+gpumdkit.sh -plt rdf               # 显示所有 RDF 对
+gpumdkit.sh -plt rdf <column>      # 显示特定对
+```
+
+**完整 RDF 输出：**
+
+<div align="center">
+  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
+</div>
+
+**单对 RDF：**
+
+<div align="center">
+  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
+</div>
+
+---
+
+### plt_rdf_pmf.py
+
+绘制 RDF 与平均力势 (PMF) 的组合图。
+
+**输入文件：** `rdf.out`
+
+```bash
+gpumdkit.sh -plt rdf_pmf
+```
+
+---
+
+### plt_vac.py
+
+绘制速度自相关函数。
+
+**输入文件：** `vac.out`
+
+```bash
+gpumdkit.sh -plt vac
+```
+
+---
+
+### plt_cohesive.py
+
+绘制内聚能曲线。
+
+```bash
+gpumdkit.sh -plt cohesive
+```
+
+---
+
+### plt_net_force.py
+
+绘制结构上的净力分布，可用于识别问题构型。
+
+**输入文件：** `train.xyz`（extxyz 格式）
+
+```bash
+gpumdkit.sh -plt net_force train.xyz
+```
+
+**参考文献：** [arXiv:2510.19774](https://arxiv.org/abs/2510.19774)
+
+<div align="center">
+  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
+</div>
+
+---
+
+## 声子
+
+### plt_pdos.py
+
+计算并绘制归一化的速度自相关函数 (VAC)、声子态密度 (PDOS) 和热容 (Cv)。
+
+**输入文件：** `model.xyz`、`run.in`、`dos.out`、`mvac.out`
+
+```bash
+gpumdkit.sh -plt pdos
+gpumdkit.sh -plt pdos save
+```
+
+<div align="center">
+  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
+</div>
+
+热容输出：
+
+<div align="center">
+  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
+</div>
+
+---
+
 ## 描述符、Dimer 和其他分析
 
-### 描述符可视化
+### plt_descriptors.py
+
+使用降维方法（PCA 或 UMAP）可视化高维 NEP 描述符。
+
+**输入文件：** `descriptors.npy`（由 `gpumdkit.sh -calc des` 生成）
+
+**方法：**
+- `pca` — 主成分分析
+- `umap` — 统一流形逼近与投影
 
 ```bash
+# 先计算描述符
 gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li
+
+# 再可视化
 gpumdkit.sh -plt des pca
 gpumdkit.sh -plt des umap
 ```
@@ -176,9 +555,26 @@ gpumdkit.sh -plt des umap
   <img src="../../Gallery/des_umap.png" alt="UMAP descriptor visualization" width="52%" />
 </div>
 
-### Dimer 曲线
+---
+
+### plt_descriptors_compare.py
+
+比较多个训练集或模型的描述符。
+
+```bash
+gpumdkit.sh -plt des_compare
+```
+
+---
+
+### plt_dimer.py
+
+绘制二聚体相互作用曲线。将两个原子放入立方盒子（30 Å），使用 NEP 模型计算势能和力随距离的变化。
+
+**输入文件：** `nep.txt`
 
 ```bash
+gpumdkit.sh -plt dimer <element1> <element2> <nep_model>
 gpumdkit.sh -plt dimer Li Li nep.txt
 ```
 
@@ -187,11 +583,18 @@ gpumdkit.sh -plt dimer Li Li nep.txt
   <img src="../../Gallery/dimer.png" alt="Dimer comparison" width="45%" />
 </div>
 
-**Reference:** [J. Chem. Inf. Model. 2026, 66, 3, 1406-1413](https://doi.org/10.1021/acs.jcim.5c02335)
+**参考文献：** [J. Chem. Inf. Model. 2026, 66, 3, 1406-1413](https://doi.org/10.1021/acs.jcim.5c02335)
 
-### DOAS
+---
+
+### plt_doas.py
+
+绘制 [Wang et al.](https://doi.org/10.1002/anie.202215544) 提出的原子态密度 (DOAS)。
+
+**输入文件：** `doas.out`（由 `gpumdkit.sh -calc doas` 计算）
 
 ```bash
+gpumdkit.sh -plt doas <doas.out> <species>
 gpumdkit.sh -plt doas doas.out Li
 ```
 
@@ -199,30 +602,65 @@ gpumdkit.sh -plt doas doas.out Li
   <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
 </div>
 
-### Net force
+---
+
+## 极性材料的 Plane-Grid 绘图
+
+此工作流将位移或极化数据映射到网格上，并绘制选定平面的轮廓。
+
+**依赖：**
 
 ```bash
-gpumdkit.sh -plt net_force train.xyz
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
 ```
 
-**Reference:** [arXiv:2510.19774](https://arxiv.org/abs/2510.19774)
+**典型前置步骤：**
 
-<div align="center">
-  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
-</div>
+```bash
+gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O
+gpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat
+gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz
+```
 
-## 快速表
+**使用方法：**
+
+```bash
+gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr
+gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1
+```
+
+---
+
+## 快速参考表
 
 | 命令 | 输入文件 | 用途 |
 |------|----------|------|
 | `train` | `loss.out`, `*_train.out` | NEP 训练结果 |
-| `prediction` | `*_test.out` | NEP 预测结果 |
+| `prediction` / `test` | `*_test.out` | NEP 预测结果 |
+| `train_test` | `*_train.out`, `*_test.out` | 合并 parity plot |
+| `parity_density` | `*_train.out` | 密度 parity plot |
+| `force_errors` | `force_train.out` | 力误差指标 |
+| `lr` | `loss.out` (gnep) | 学习率 |
+| `restart` | `nep.restart` | 重启文件参数 |
+| `charge` | `charge_train.out` | 电荷分布 |
+| `born_charge` / `bec` | `bec_train.out`, `bec_test.out` | Born 有效电荷 |
 | `thermo` | `thermo.out` | 热力学量 |
 | `msd` | `msd.out` | 均方位移 |
+| `msd_all` | `msd.out` (all_groups) | 全组分 MSD |
+| `msd_conv` | `msd_step*.out` | MSD 收敛性检查 |
 | `sdc` | `msd.out` | 自扩散系数 |
+| `arrhenius_d` / `D` | `*K/msd.out` | Arrhenius 扩散系数 |
+| `arrhenius_sigma` / `sigma` | `*K/{model.xyz, run.in, thermo.out, msd.out}` | Arrhenius 离子电导率 |
 | `rdf` | `rdf.out` | 径向分布函数 |
-| `pdos` | `dos.out`, `mvac.out` | VAC 和 PDOS |
-| `emd`/`nemd`/`hnemd` | 热输运输出 | 热导率分析 |
-| `des` | `descriptors.npy` | 描述符降维 |
-| `dimer` | `nep.txt` | 二聚体能量/力曲线 |
+| `rdf_pmf` | `rdf.out` | RDF + 平均力势 |
+| `vac` | `vac.out` | 速度自相关 |
+| `cohesive` | — | 内聚能曲线 |
+| `net_force` | `train.xyz` | 净力分布 |
 | `doas` | `doas.out` | 原子态密度 |
+| `des` | `descriptors.npy` | 描述符 PCA/UMAP |
+| `dimer` | `nep.txt` | 二聚体能量/力曲线 |
+| `pdos` | `model.xyz`, `run.in`, `dos.out`, `mvac.out` | VAC 和 PDOS |
+| `emd` | EMD 输出 | EMD 热导率 |
+| `nemd` | NEMD 输出 | NEMD 热输运 |
+| `hnemd` | HNEMD 输出 | HNEMD 热输运 |
+| `viscosity` | 粘度输出 | 粘度 |
diff --git "a/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md" "b/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md"
index a316052..ec58b1a 100644
--- "a/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md"
+++ "b/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md"
@@ -158,11 +158,25 @@ gpumdkit.sh -plt sdc
 
 ## NEP 预测性质
 
+`calc_properties_with_nep.py` 使用训练好的 NEP 模型计算能量、力和应力。
+
+**依赖：** `calorine`
+
+```bash
+pip install calorine
+```
+
 ```bash
 gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
 ```
 
-该功能使用训练好的 NEP 模型计算能量、力和应力。只有当你确认模型质量可靠，并明确希望使用 NEP 作为替代计算器时，才建议使用它。
+只有当你确认模型质量可靠，并明确希望使用 NEP 作为替代计算器时，才建议使用它。
+
+**提示：** 预测前可以清理 extxyz 元数据：
+
+```bash
+gpumdkit.sh -clean_xyz train.xyz clean_train.xyz
+```
 
 ## NEP 描述符
 
@@ -216,7 +230,13 @@ NEB：
 gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt
 ```
 
-结构优化：
+结构优化（通过 `calorine`）：
+
+**依赖：** `calorine`
+
+```bash
+pip install calorine
+```
 
 ```bash
 gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
@@ -227,6 +247,38 @@ gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
 - `minimize.xyz`
 - `minimize.log`
 
+## 使用 OVITO 计算 RDF
+
+`rdf_calculator_ovito.py` 使用 OVITO 的分析工具计算径向分布函数。
+
+**依赖：** OVITO
+
+```bash
+pip install ovito
+```
+
+**输入文件：** 结构文件（单帧或轨迹）
+
+```bash
+python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400
+```
+
+**参数：**
+
+| 参数 | 含义 |
+|------|------|
+| `trajectory.xyz` | 输入结构文件 |
+| `6.0` | RDF 计算的最大距离（Å） |
+| `400` | 直方图的分箱数 |
+
+**可视化：**
+
+```bash
+gpumdkit.sh -plt rdf
+```
+
+**注意：** 建议优先使用 GPUMD 中的 `compute_rdf` 命令。
+
 ## 铁电和极性材料工具
 
 这些工具需要 `ferrodispcalc`：
diff --git "a/docs/tutorials/zh/\350\264\241\347\214\256\346\214\207\345\215\227.md" "b/docs/tutorials/zh/\350\264\241\347\214\256\346\214\207\345\215\227.md"
index 281b11d..043f6ff 100644
--- "a/docs/tutorials/zh/\350\264\241\347\214\256\346\214\207\345\215\227.md"
+++ "b/docs/tutorials/zh/\350\264\241\347\214\256\346\214\207\345\215\227.md"
@@ -1,97 +1,104 @@
 <div align="center">
-  <h1>🤝 贡献指南</h1>
-  <p style="text-align: justify;">感谢你有兴趣为 <strong>GPUMDkit</strong> 做贡献。我们非常感谢你愿意花时间和精力帮助改进这个工具包。</p>
+  <h1>🤝 为 GPUMDkit 贡献代码</h1>
+  <p style="text-align: justify;">感谢你有兴趣为 <strong>GPUMDkit</strong> 做出贡献！我们感谢你为改善这个工具包所付出的时间和努力。</p>
 </div>
 
-`GPUMDkit` 是一个开源软件包。无论是修复 bug、添加新功能、改进文档，还是提出使用建议，我们都欢迎社区贡献。
+<p align="center">
+  <a href="../en/contributing_to_gpumdkit.md">English</a>
+  &nbsp;·&nbsp;
+  <strong>简体中文</strong>
+</p>
+
+`GPUMDkit` 是一个开源项目，我们欢迎社区的各种贡献，无论是修复 bug、添加新功能、改进文档还是提出建议。
+
+> **注意**：本文档的权威版本位于仓库根目录的 [`CONTRIBUTING.md`](https://github.com/zhyan0603/GPUMDkit/blob/main/CONTRIBUTING.md)。本教程页面同步其内容。中文版请参见 [`docs/CONTRIBUTING_zh-CN.md`](https://github.com/zhyan0603/GPUMDkit/blob/main/docs/CONTRIBUTING_zh-CN.md)。
 
 ---
 
 ## 目录
 
-- 开发限制和指南
-- 报告 Bug
-- 提出功能建议
-- 贡献代码
-- Fork 并克隆仓库
-- 创建功能分支
-- 进行修改
-- 交互模式贡献
-- 命令行模式贡献
-- 更新 Tab 补全
-- 代码风格和最佳实践
-- 测试你的修改
-- 提交信息
-- 推送并打开 Pull Request
+- [开发规范与准则](#开发规范与准则)
+- [报告问题](#报告问题)
+- [功能建议](#功能建议)
+- [贡献代码](#贡献代码)
+  - [Fork 并克隆仓库](#fork-并克隆仓库)
+  - [创建功能分支](#创建功能分支)
+  - [进行修改](#进行修改)
+    - [交互模式贡献](#交互模式贡献)
+    - [命令行模式贡献](#命令行模式贡献)
+    - [更新 Tab 补全](#更新-tab-补全)
+  - [代码风格与最佳实践](#代码风格与最佳实践)
+  - [测试你的修改](#测试你的修改)
+  - [提交信息](#提交信息)
+  - [推送并创建 Pull Request](#推送并创建-pull-request)
 
 ---
 
-## 开发限制和指南
+## 开发规范与准则
 
-为了保持项目代码质量和一致性，请遵守以下指南。
+为保持代码质量和项目一致性，请遵循以下准则：
 
 ### 语言要求
 
-- **所有代码应使用英文编写**：包括变量名、函数名、注释、docstring、提交信息和文档。
-- 我们理解贡献者可能来自不同背景，但使用英文可以让代码库对更广泛的用户保持可读和可维护。
+- **所有代码应使用英文编写**：包括变量名、函数名、注释、文档字符串、提交信息和文档。
+- 虽然我们理解贡献者来自不同背景，但使用英文能确保代码库对最广泛的用户群体可访问。
 
-### 模块化和可复用性
+### 模块化与可复用性
 
-- **编写模块化、可复用的代码**：函数和脚本应尽量具有灵活性。
-- **优先通过参数传递信息，避免硬编码**：使用函数参数、命令行参数或配置文件，而不是把数值直接写死。不过，某些文件名是 GPUMD 和 NEP 程序固定要求的，例如 `train.xyz`、`thermo.out`，这类情况可以按需要保留固定文件名。
+- **编写模块化和可复用的代码**：函数和脚本的设计应具有灵活性。
+- **优先传递参数而非硬编码值**：使用函数参数、命令行参数或配置文件来替代硬编码值。但某些文件名由 GPUMD 和 NEP 程序固定要求（如 `train.xyz`、`thermo.out`），这些可以按需硬编码。
 - **示例**：
-
   ```bash
-  # Good: accepts parameters
+  # 好的做法：接受参数
   function convert_file() {
       local input_file=$1
       local output_file=$2
-      # processing logic
+      # 处理逻辑
   }
-
-  # Avoid: hardcoded values (unless required by GPUMD/NEP)
+  
+  # 避免：硬编码值（除非 GPUMD/NEP 要求）
   function convert_file() {
       local input_file="hardcoded_input.xyz"
-      # processing logic
+      # 处理逻辑
   }
   ```
 
 ### 代码风格
 
 - 编写清晰、易于他人维护和修改的代码。
-- 使用有意义的变量名和函数名。
-- 在必要时添加注释，解释复杂逻辑。
+- 使用有意义的变量和函数名。
+- 在必要处添加注释以解释复杂逻辑。
 
 ### 文档
 
-- 确保帮助信息（例如 `-h` 参数）清晰、准确。
-- `docs/` 目录中的文档通常由维护者更新，因此一般不需要贡献者直接修改。
+- 确保帮助信息（如 `-h` 标志）清晰准确。
+- 教程文档位于 `docs/tutorials/en/`（英文）和 `docs/tutorials/zh/`（中文）。如果你添加了新功能，请考虑更新相关教程页面。
+- 编辑教程 Markdown 文件后，使用 `mkdocs build -f docs/mkdocs.yml` 重新构建 HTML。
 
 ---
 
-## 报告 Bug
+## 报告问题
 
-如果你遇到 bug，请通过 GitHub Issues 帮助我们定位和修复：
+如果你遇到 bug，请通过 GitHub Issues 帮助我们修复：
 
-1. **先搜索已有 issue**，确认这个 bug 是否已经被报告过。
-2. **如果还没有报告，请创建新 issue**：[Create an Issue](https://github.com/zhyan0603/GPUMDkit/issues/new)
-3. **详细描述问题**，如果可以，请提供测试文件。
+1. **搜索现有 issues** 查看该 bug 是否已被报告。
+2. **创建新 issue**（如果尚未被报告）：[创建 Issue](https://github.com/zhyan0603/GPUMDkit/issues/new)
+3. **详细描述问题**，如果可能请提供测试文件。
 
 你也可以通过以下方式联系我们：
-
 - **QQ 群**：825696376
-- **Email**：yanzihan@westlake.edu.cn
-- **脚本开发者**：联系脚本文件头部列出的开发者
+- **邮箱**：yanzihan@westlake.edu.cn
+- **脚本开发者**：联系脚本头部列出的开发者
 
 ---
 
-## 提出功能建议
+## 功能建议
 
-我们欢迎新的功能建议。提出新功能时，可以按以下方式进行：
+我们欢迎功能建议！提出新功能：
 
-1. **先搜索已有 issue**，确认是否已经有人提出过类似建议。
-2. **创建新的功能请求**：[Create a Feature Request](https://github.com/zhyan0603/GPUMDkit/issues/new)，并提及 @zhyan0603。
-3. **清楚描述你的需求**，并说明它为什么有用。
+1. **搜索现有 issues** 查看是否已有人提出。
+2. **创建新功能请求**：[创建功能请求](https://github.com/zhyan0603/GPUMDkit/issues/new) 并 mention @zhyan0603
+3. **清楚描述你的需求** 并解释其用途。
 
 ---
 
@@ -99,46 +106,45 @@
 
 ### Fork 并克隆仓库
 
-1. 在 GitHub 的 [GPUMDkit 仓库页面](https://github.com/zhyan0603/GPUMDkit)右上角点击 "Fork"，将仓库 fork 到自己的账号下。
+1. 在 GitHub 上 **Fork 仓库**，点击 [仓库页面](https://github.com/zhyan0603/GPUMDkit) 右上角的 "Fork" 按钮。
 
-2. 将你的 fork 克隆到本地：
+2. **克隆你的 fork** 到本地：
 
    ```bash
    git clone https://github.com/YOUR_USERNAME/GPUMDkit.git
    cd GPUMDkit
    ```
 
-3. 设置 upstream remote，方便和主仓库保持同步：
-
+3. **设置 upstream remote** 以保持 fork 同步：
    ```bash
    git remote add upstream https://github.com/zhyan0603/GPUMDkit.git
    ```
 
 ### 创建功能分支
 
-为你的修改创建一个新分支：
+为你的修改创建新分支：
 
 ```bash
-# Create and checkout a new branch from main
+# 从 main 创建并切换到新分支
 git checkout -b your-branch-name
 ```
 
-分支名可以按你的习惯命名。
+分支名称随意。
 
 ### 进行修改
 
 `GPUMDkit` 的结构包括：
-
-- **`gpumdkit.sh`**：主入口 Bash 脚本，负责交互菜单模式和命令行模式。
-- **`Scripts/`**：按功能分类组织的 Python 工具脚本。
+- **`gpumdkit.sh`**：主入口（Bash 脚本），处理交互菜单模式和命令行模式
+- **`install.sh`**：安装脚本，设置环境变量和 shell 配置
+- **`Scripts/`**：按功能组织的 Python 和 Bash 实现脚本
   - `plt_scripts/`：绘图脚本
   - `calculators/`：计算工具
   - `format_conversion/`：格式转换工具
   - `workflow/`：工作流自动化
   - `sample_structures/`：结构采样工具
   - `analyzer/`：分析工具
-  - `utils/`：实用函数，包括用于 Tab 补全的 `completion.sh`
-- **`src/`**：包含交互模式菜单函数的 Shell 脚本。
+  - `utils/`：实用函数（包括 `completion.sh` Tab 补全）
+- **`src/`**：交互模式菜单函数的 Shell 脚本
   - `f1_format_conversions.sh`
   - `f2_sample_structures.sh`
   - `f3_workflows.sh`
@@ -146,63 +152,64 @@ git checkout -b your-branch-name
   - `f5_analyzers.sh`
   - `f6_plots.sh`
   - `f7_utilities.sh`
-- **`docs/`**：文档文件。
+- **`skills/`**：AI agent 技能定义（用于 opencode/Claude Code 集成的 SKILL.md 文件）
+- **`docs/`**：文档文件
+  - `tutorials/en/` 和 `tutorials/zh/`：双语教程页面
+  - `mkdocs.yml`：构建教程 HTML 的 MkDocs 配置
+  - `command_reference.tsv`：机器可读的命令参考
+  - `htmls/`：MkDocs 生成的 HTML 输出
 
 #### 交互模式贡献
 
-如果要添加一个可通过交互菜单访问的新功能：
+要添加通过交互菜单访问的新功能：
 
-1. **在合适的 `Scripts/` 子目录中创建实现脚本**：
+1. **在相应的 `Scripts/` 子目录中创建实现脚本**：
 
    ```bash
-   # Example: Add a new format conversion script
+   # 示例：添加新的格式转换脚本
    touch Scripts/format_conversion/new_converter.py
    ```
 
-2. **实现你的功能**，并遵循模块化指南：接受参数，避免不必要的硬编码。
-
-3. **在对应的 `src/` 文件中添加包装函数**：
+2. **实现你的功能**，遵循模块化准则（接受参数，避免硬编码）。
 
+3. **在相应的 `src/` 文件中添加包装函数**：
    ```bash
-   # Example: Edit src/f1_format_conversions.sh
+   # 示例：编辑 src/f1_format_conversions.sh
    vim src/f1_format_conversions.sh
    ```
 
-   添加一个新函数：
-
+   添加新函数：
    ```bash
-   function f106_new_converter(){
+   function f111_new_converter(){
    echo " >-------------------------------------------------<"
    echo " | Calling the script in Scripts/format_conversion |"
    echo " | Script: new_converter.py                        |"
    echo " | Developer: Your Name (your@email.com)           |"
    echo " >-------------------------------------------------<"
-   echo " Input the required parameters:"
+   echo " Input <required_param1> <required_param2>"
    echo " Example: input.xyz output.lmp"
    echo " ------------>>"
-   read -p " " converter_params
+   read -r -a converter_args
    echo " ---------------------------------------------------"
-   python ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py ${converter_params}
+   python ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py "${converter_args[@]}"
    echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py"
    echo " ---------------------------------------------------"
    }
    ```
 
-4. **更新 `gpumdkit.sh` 中的菜单显示**：
-
+4. **在 `gpumdkit.sh` 中更新菜单显示**：
    ```bash
-   # Find the menu() function and update it if needed
-   # Find the array_choice array and add your new choice number
+   # 找到 menu() 函数并按需更新
+   # 找到 array_choice 数组并添加你的新选择编号
    array_choice=(
-       "0" "1" "101" "102" "103" "104" "105" "106"  # Added "106"
-       # ... rest of choices
+       "0" "1" "101" "102" "103" "104" "105" "106" "107" "108" "109" "110" "111"  # 添加 "111"
+       # ... 其余选择
    )
    ```
 
-5. **在 `gpumdkit.sh` 中添加 case 分支**：
-
+5. **在 `gpumdkit.sh` 中添加 case 语句**：
    ```bash
-   # In the main() function, find the appropriate case statement
+   # 在 main() 函数中找到相应的 case 语句
    case "${choice:0:1}" in
        # ...
        "1")
@@ -210,8 +217,8 @@ git checkout -b your-branch-name
            case $choice in
                "1") f1_format_conversion ;;
                "101") f101_out2xyz ;;
-               # ... existing cases ...
-               "106") f106_new_converter ;;  # Add your case
+               # ... 现有 case ...
+               "111") f111_new_converter ;;  # 添加你的 case
            esac ;;
        # ...
    esac
@@ -219,195 +226,223 @@ git checkout -b your-branch-name
 
 #### 命令行模式贡献
 
-如果要添加新的命令行 flag 或子命令：
-
-1. **在合适的 `Scripts/` 子目录中创建实现脚本**：
+要添加新的命令行标志或子命令：
 
+1. **在相应的 `Scripts/` 子目录中创建实现脚本**：
    ```bash
-   # Example: Add a new analyzer script
+   # 示例：添加新的分析器脚本
    touch Scripts/analyzer/analyze_bonds.py
    ```
 
-2. **实现功能，并明确参数要求**：
-
+2. **实现你的功能**，明确参数要求：
    ```python
-   # Example: Scripts/analyzer/analyze_bonds.py
+   # 示例：Scripts/analyzer/analyze_bonds.py
    import sys
-
-   def main():
-       if len(sys.argv) != 3:
-           print("Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>")
-           print("Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0")
-           sys.exit(1)
-
-       input_file = sys.argv[1]
-       cutoff = float(sys.argv[2])
-
-       # Your implementation here
-
-   if __name__ == "__main__":
-       main()
+   
+   if len(sys.argv) != 3:
+       print("Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>")
+       print("Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0")
+       sys.exit(1)
+   
+   input_file = sys.argv[1]
+   cutoff = float(sys.argv[2])
+   
+   # 你的实现
    ```
 
-3. **在 `gpumdkit.sh` 中添加命令行 flag 处理逻辑**：
+   > **注意**：GPUMDkit Python 脚本设计为直接运行（不作为模块导入）。
+   > 如果你愿意，可以使用 `main()` 函数配合 `if __name__ == "__main__":` 保护，
+   > 但这不是必需的。大多数现有脚本在模块级别执行。
 
+3. **在 `gpumdkit.sh` 中添加命令行标志处理**：
    ```bash
-   # Find the command-line parsing section (after line ~167)
-   # Add your new flag in the appropriate location
-
+   # 找到命令行解析部分（大的 "case $1 in" 块）
+   # 在适当位置添加你的新标志
+   
    case $1 in
-       # ... existing cases ...
+       # ... 现有 case ...
        -analyze_bonds)
-           if [ ! -z "$2" ] && [ ! -z "$3" ]; then
-               python ${analyzer_path}/analyze_bonds.py "$2" "$3"
+           if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ]; then
+               python ${analyzer_path}/analyze_bonds.py $2 $3
            else
                echo " Usage: gpumdkit.sh -analyze_bonds <input.xyz> <cutoff_distance>"
                echo " Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0"
                echo " Code path: ${analyzer_path}/analyze_bonds.py"
-               exit 1
            fi ;;
-       # ... rest of cases ...
+       # ... 其余 case ...
    esac
    ```
 
-4. **更新 `gpumdkit.sh` 中的帮助信息**：
-
+4. **在 `gpumdkit.sh` 中更新帮助信息**：
    ```bash
-   # Find the help_info_table() function and add your command
+   # 找到 help_info_table() 函数并添加你的命令
    function help_info_table(){
        echo "+====================================== Analysis ===============================================+"
        echo "| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |"
-       # ... rest of help table ...
+       # ... 其余帮助表 ...
    }
    ```
 
 #### 更新 Tab 补全
 
-添加新的命令行 flag 时，请更新 Tab 补全脚本：
+添加新的命令行标志时，更新 Tab 补全脚本：
 
 ```bash
-# Edit Scripts/utils/completion.sh
+# 编辑 Scripts/utils/completion.sh
 vim Scripts/utils/completion.sh
 ```
 
-将新的 flag 加入 `opts` 变量：
-
+将你的新标志添加到 `opts` 变量：
 ```bash
-# Find the line with local opts=...
-local opts="-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ..."
-#                                                      ^^^^^^^^^^^^^^ Add your flag here
+# 找到 local opts=... 行
+local opts="-h -help -update -U -clean -time -plt -calc ... -your_new_flag ..."
+#                                                        在此添加你的标志
 ```
 
-如果这个 flag 接受二级选项，例如 `-plt` 或 `-calc`，也需要为它添加对应的 `case` 分支：
+如果你的标志需要文件参数，将其添加到现有的文件补全 case 中：
+```bash
+# 找到需要文件参数的 case 并用 | 添加你的标志
+-out2xyz|-out2exyz|-...|-your_new_flag)
+    COMPREPLY=($(compgen -f -- "$cur")) ;;
+```
 
+如果你的标志接受二级选项（如 `-plt` 或 `-calc`），添加新 case：
 ```bash
 case "$prev" in
-    # ... existing cases ...
-    -analyze_bonds)
-        COMPREPLY=($(compgen -f -- "$cur"))  # Complete with filenames
-        ;;
-    # ... rest of cases ...
+    # ... 现有 case ...
+    -your_new_flag)
+        COMPREPLY=($(compgen -W "option1 option2 option3" -- "$cur")) ;;
+    # ... 其余 case ...
 esac
 ```
 
-### 代码风格和最佳实践
+### 代码风格与最佳实践
 
 - **Shell 脚本**：
-  - 使用 `${variable}` 进行变量展开。
-  - 编写清晰、易维护的代码。
+  - 使用 `${variable}` 进行变量展开
+  - 使用 `[ ! -z "$var" ]` 进行非空检查（项目约定）
+  - 交互函数应遵循 banner 格式：
+    ```bash
+    echo " >-------------------------------------------------<"
+    echo " | Calling the script in Scripts/<category>        |"
+    echo " | Script: <script_name>.py                        |"
+    echo " | Developer: <Name> (<email>)                     |"
+    echo " >-------------------------------------------------<"
+    ```
+  - 使用 `read -r -a varname` 读取多词输入，然后用 `"${varname[@]}"` 传递
+  - `src/` 中的 Shell 脚本应以文件头注释块开始：
+    ```bash
+    # ============================================================
+    # GPUMDkit <module name> module
+    # Repository: https://github.com/zhyan0603/GPUMDkit
+    # Author: <Name> (<email>)
+    # ============================================================
+    ```
 
 - **Python 脚本**：
-  - 编写清晰、可维护的代码。
-  - 使用有意义的变量名。
+  - 编写清晰、可维护的代码
+  - 使用有意义的变量名
+  - 使用 `sys.argv` 进行参数解析（与大多数现有脚本一致）
+  - 提供清晰的使用信息：`print("Usage: ...")` 和 `print("Example: ...")`
+  - 如果你的脚本使用重型/特殊包（`NepTrain`、`calorine`、`dpdata`），请添加
+    `print_dependency_notice()` 函数以通知用户引用建议
 
 ### 测试你的修改
 
-提交贡献前，请进行测试：
+提交贡献前，运行相关验证命令：
+
+```bash
+# Shell 语法检查（始终运行）
+bash -n gpumdkit.sh
+find src Scripts -name '*.sh' -exec bash -n {} +
+
+# Python 语法检查（针对修改的 Python 文件）
+python3 -m py_compile path/to/modified_script.py
+
+# MkDocs 构建（如果修改了文档）
+mkdocs build -f docs/mkdocs.yml
+
+# 检查尾随空格问题
+git diff --check
+```
 
-1. **测试交互模式**（如果适用）：
+然后测试功能：
 
+1. **测试交互模式**（如适用）：
    ```bash
    gpumdkit.sh
-   # Navigate to your new feature and test it thoroughly
+   # 导航到你的新功能并充分测试
    ```
 
-2. **测试命令行模式**（如果适用）：
-
+2. **测试命令行模式**（如适用）：
    ```bash
    gpumdkit.sh -your_new_flag [arguments]
-   gpumdkit.sh -your_new_flag -h  # Test help message
+   gpumdkit.sh -your_new_flag -h  # 测试帮助信息
    ```
 
-3. **测试 Tab 补全**（如果修改了 `completion.sh`）：
-
+3. **测试 Tab 补全**（如果你修改了 `completion.sh`）：
    ```bash
    source Scripts/utils/completion.sh
-   gpumdkit.sh -<TAB>  # Should show your new flag
+   gpumdkit.sh -<TAB>  # 应显示你的新标志
    ```
 
-4. **使用不同输入测试**：
+4. **用各种输入测试**：
+   - 用典型输入测试
+   - 用边缘情况测试（空文件、大文件等）
+   - 测试错误处理（缺少文件、无效参数）
 
-   - 测试常规输入。
-   - 测试边界情况，例如空文件、大文件等。
-   - 测试错误处理，例如缺少文件、参数无效等。
-
-5. **确认没有回归问题**：确保已有功能仍然可以正常工作。
+5. **验证无回归**：确保现有功能仍然正常工作。
 
 ### 提交信息
 
-提交信息应清楚、具体，说明你修改了什么。不要求严格格式，但需要让他人能够理解。
+编写清晰、描述性的提交信息来解释你做了什么更改。没有严格的格式要求——只要确保你的信息是可理解的。
 
-### 推送并打开 Pull Request
+### 推送并创建 Pull Request
 
 1. **提交你的修改**：
-
    ```bash
    git add .
-   git commit -m "your descriptive message"
+   git commit -m "你的描述性信息"
    ```
 
-2. **让你的分支与 upstream `main` 分支保持同步**：
-
+2. **保持你的分支与最新的 `dev` 分支同步**：
    ```bash
-   git fetch upstream
-   git rebase upstream/main
+   git fetch origin
+   git rebase origin/dev
    ```
 
-3. **将分支推送到你的 fork**：
-
+3. **推送你的分支**到你的 fork：
    ```bash
    git push origin your-branch-name
    ```
 
-4. **打开 Pull Request**：
-
-   - 进入 [GPUMDkit repository](https://github.com/zhyan0603/GPUMDkit)。
-   - 点击 "Pull Requests" -> "New Pull Request"。
-   - 将 base branch 设置为 `dev`，用于代码审查。
-   - 将 compare branch 设置为你的功能分支。
-   - 填写 PR 描述，包括：
-     - **Title**：简要描述修改内容。
-     - **Description**：详细说明修改了什么以及为什么修改。
-     - **Testing**：说明你如何测试这些修改。
-
-5. **回应审查意见**：
+4. **创建 Pull Request**：
+   - 前往 [GPUMDkit 仓库](https://github.com/zhyan0603/GPUMDkit)
+   - 点击 "Pull Requests" → "New Pull Request"
+   - 设置目标分支为 `dev` 进行代码审查
+   - 设置比较分支为你的功能分支
+   - 填写 PR 描述：
+     - **标题**：简要描述更改
+     - **描述**：详细解释更改内容和原因
+     - **测试**：描述你如何测试这些更改
 
-   - 接受建议和建设性意见。
-   - 及时完成要求的修改。
-   - 将额外提交推送到你的分支，它们会自动显示在 PR 中。
+5. **回应审查反馈**：
+   - 对建议和建设性批评保持开放
+   - 及时进行请求的修改
+   - 推送额外提交到你的分支（它们会自动出现在 PR 中）
 
-6. **审查通过后**：维护者会合并你的 PR。
+6. **批准后**：维护者将合并你的 PR。
 
 ---
 
 ## 有问题或需要帮助？
 
-如果你对贡献流程有疑问，或需要帮助：
+如果你对贡献有疑问或需要帮助：
 
-- **打开讨论**：一般问题可以使用 [GitHub Discussions](https://github.com/zhyan0603/GPUMDkit/discussions)。
-- **在 issue 中提问**：与具体问题相关的内容可以在对应 issue 下评论。
-- **联系维护者**：联系 README 中列出的核心开发者。
+- **发起讨论**：使用 [GitHub Discussions](https://github.com/zhyan0603/GPUMDkit/discussions) 提出一般性问题
+- **在 issue 中提问**：在相关 issue 中评论以获取具体问题的帮助
+- **联系维护者**：联系 README 中列出的核心开发者
 
 ---
 
-再次感谢你为 `GPUMDkit` 做贡献。你的工作会帮助整个 GPUMD 和 NEP 社区更好地使用这个工具包。
+再次感谢你为 `GPUMDkit` 做出贡献！你的努力帮助这个工具包为整个 GPUMD 和 NEP 社区变得更好。
diff --git a/gpumdkit.sh b/gpumdkit.sh
index 0e355c1..62ffa96 100755
--- a/gpumdkit.sh
+++ b/gpumdkit.sh
@@ -52,6 +52,7 @@ function main(){
         "5" "501" "502" "503" "504" "505" "506" "507" "508"
         "6"
         "7" "701"
+        "8"
     ) 
     read -p " " choice
     while ! echo "${array_choice[@]}" | grep -wq "$choice" 
@@ -148,6 +149,10 @@ function main(){
                 "7") f7_utilities ;;
                 "701") f701_time_consuming_analyzer ;;
             esac ;;
+        "8")
+            echo " ------------>>"
+            echo " This module is under development. Coming soon."
+            ;;
         *)
             echo " Incorrect Options"
             ;;
@@ -189,7 +194,7 @@ function help_info_table(){
     echo "| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |"
     echo "| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |"
     echo "| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |"
-    echo "| -pynep        Deprecated PyNEP sampling       |                                                       |"
+    echo "| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |"
     echo "+-------------------------------------------------------------------------------------------------------+"
     echo "| Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |"
     echo "+-------------------------------------------------------------------------------------------------------+"
@@ -220,21 +225,6 @@ function calculator_help_table(){
     echo "+-------------------------------------------------------------------------------------------------------+"
 }
 
-# function citation(){
-# echo "+-----------------------------------------------------------------------+"
-# echo "|                     THANK YOU FOR USING GPUMDKIT                      |"
-# echo "+-----------------------------------------------------------------------+"
-# echo "│ If you find it useful, please star us on GitHub and cite our paper:   │"
-# echo "│                                                                       │"
-# echo "│ Z. Yan, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang,      │"
-# echo "│ B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen,   │"
-# echo "│ K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, Y. Zhu.             │"
-# echo "│ GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP. arXiv:2603.17367 │"
-# echo "│                                                                       │"
-# echo "| Welcome to join our QQ group (825696376) for support and discussions! │"
-# echo "+-----------------------------------------------------------------------+"
-# }
-
 function citation(){
 echo " +------------------------------------------------------+"
 echo " |           THANK YOU FOR USING GPUMDKIT               |"
@@ -250,6 +240,17 @@ echo " +------------------------------------------------------+"
 }
 
 #--------------------- command line ----------------------
+# Helper: run a Python calculator script with author/path banner
+# Usage: run_python_script "Author Name" /path/to/script.py [args...]
+run_python_script() {
+    local author="$1"; shift
+    local script="$1"; shift
+    echo " Calling script by ${author}. "
+    echo " Code path: ${script}"
+    echo " ------------------------------------------------------------"
+    python "${script}" "$@"
+}
+
 if [ ! -z "$1" ]; then
     case $1 in
         -h|-help) help_info_table ;;
@@ -328,93 +329,29 @@ if [ ! -z "$1" ]; then
             if [ ! -z "$2" ] && [ "$2" != "-h" ]; then
                 case $2 in
                     ionic-cond)
-                        if [ ! -z "$3" ] && [ ! -z "$4" ] ; then
-                            echo " Calling script by Zihan YAN. "
-                            echo " Code path: ${calc_path}/calc_ion_conductivity.py"
-                            python ${calc_path}/calc_ion_conductivity.py $3 $4
-                        else
-                            echo " Usage: -calc ionic-cond <element> <charge>"
-                            echo " Example: gpumdkit.sh -calc ionic-cond Li 1"
-                            echo " See the codes in calculators folder for more details"
-                            echo " Code path: ${calc_path}/calc_ion_conductivity.py"
-                            exit 1
-                        fi ;;
+                        run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${calc_path}/calc_ion_conductivity.py" "${@:3}" ;;
                     neb)
-                        if [ ! -z "$3" ] && [ ! -z "$4" ] && [ ! -z "$5" ] && [ ! -z "$6" ]; then
-                            echo " Calling script by Zhoulin LIU. "
-                            echo " Code path: ${calc_path}/neb_calculation.py"
-                            python ${calc_path}/neb_calculation.py ${@:3}
-                        else
-                            echo " Usage: -calc neb <initial_structure> <final_structure> <n_images> <nep_model>"
-                            echo " Example: gpumdkit.sh -calc neb init.xyz final.xyz 9 nep.txt"
-                            echo " See the codes in calculators folder for more details"
-                            echo " Code path: ${calc_path}/neb_calculation.py"
-                            exit 1
-                        fi ;;
+                        run_python_script "Zhoulin LIU (1776627910@qq.com)" "${calc_path}/neb_calculation.py" "${@:3}" ;;
                     nep)
-                        if [ ! -z "$3" ] && [ ! -z "$4" ] && [ ! -z "$5" ]; then
-                            echo " Calling script by Zihan YAN. "
-                            echo " Code path: ${calc_path}/calc_properties_with_nep.py"
-                            python ${calc_path}/calc_properties_with_nep.py $3 $4 $5
-                        else
-                            echo " Usage: -calc nep <input.xyz> <output.xyz> <nep_model>"
-                            echo " Example: gpumdkit.sh -calc nep input.xyz output.xyz nep.txt"
-                            echo " See the codes in calculators folder for more details"
-                            echo " Code path: ${calc_path}/calc_properties_with_nep.py"
-                            exit 1
-                        fi ;;
+                        run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${calc_path}/calc_properties_with_nep.py" "${@:3}" ;;
                     des)
-                        if [ ! -z "$3" ] && [ ! -z "$4" ] && [ ! -z "$5" ] && [ ! -z "$6" ]; then
-                            echo " Calling script by Zihan YAN. "
-                            echo " Code path: ${calc_path}/calc_descriptors.py"
-                            python ${calc_path}/calc_descriptors.py $3 $4 $5 $6
-                        else
-                            echo " Usage: -calc des <input.xyz> <output.npy> <nep_model> <element>"
-                            echo " Example: gpumdkit.sh -calc des train.xyz des_Li.npy nep.txt Li"
-                            echo " See the codes in calculators folder for more details"
-                            echo " Code path: ${calc_path}/calc_descriptors.py"
-                            exit 1
-                        fi ;; 
+                        run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${calc_path}/calc_descriptors.py" "${@:3}" ;;
                     doas)
-                        if [ ! -z "$3" ] && [ ! -z "$4" ] && [ ! -z "$5" ]; then
-                            echo " Calling script by Zihan YAN. "
-                            echo " Code path: ${calc_path}/calc_doas.py"
-                            python ${calc_path}/calc_doas.py $3 $4 $5
-                        else
-                            echo " Usage: -calc doas <input.xyz> <nep_model> <output_file>"
-                            echo " Example: gpumdkit.sh -calc doas dump.xyz nep.txt doas.out"
-                            echo " See the codes in calculators folder for more details"
-                            echo " Code path: ${calc_path}/calc_doas.py"
-                            exit 1
-                        fi ;;
+                        run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${calc_path}/calc_doas.py" "${@:3}" ;;
                     minimize)
-                        echo " Calling script by Zihan YAN. "
-                        echo " Code path: ${calc_path}/calc_minimize.py"
-                        python ${calc_path}/calc_minimize.py ${@:3} ;;                     
+                        run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${calc_path}/calc_minimize.py" "${@:3}" ;;
                     msd)
-                        echo " Calling script by Zihan YAN. "
-                        echo " Code path: ${calc_path}/calc_msd.py"
-                        python ${calc_path}/calc_msd.py ${@:3} ;;                        
+                        run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${calc_path}/calc_msd.py" "${@:3}" ;;
                     nlist)
-                        echo " Calling script by Denan LI. "
-                        echo " Code path: ${calc_path}/calc_neighbor_list.py"
-                        python ${calc_path}/calc_neighbor_list.py ${@:3} ;;
+                        run_python_script "Denan LI (lidenan@westlake.edu.cn)" "${calc_path}/calc_neighbor_list.py" "${@:3}" ;;
                     disp)
-                        echo " Calling script by Denan LI. "
-                        echo " Code path: ${calc_path}/calc_displacement.py"
-                        python ${calc_path}/calc_displacement.py ${@:3} ;;
+                        run_python_script "Denan LI (lidenan@westlake.edu.cn)" "${calc_path}/calc_displacement.py" "${@:3}" ;;
                     avg-struct)
-                        echo " Calling script by Denan LI. "
-                        echo " Code path: ${calc_path}/calc_averaged_structure.py"
-                        python ${calc_path}/calc_averaged_structure.py ${@:3} ;;
+                        run_python_script "Denan LI (lidenan@westlake.edu.cn)" "${calc_path}/calc_averaged_structure.py" "${@:3}" ;;
                     oct-tilt)
-                        echo " Calling script by Denan LI. "
-                        echo " Code path: ${calc_path}/calc_oct_tilt.py"
-                        python ${calc_path}/calc_oct_tilt.py ${@:3} ;;
+                        run_python_script "Denan LI (lidenan@westlake.edu.cn)" "${calc_path}/calc_oct_tilt.py" "${@:3}" ;;
                     pol-abo3)
-                        echo " Calling script by Denan LI. "
-                        echo " Code path: ${calc_path}/calc_polarization_abo3.py"
-                        python ${calc_path}/calc_polarization_abo3.py ${@:3} ;;
+                        run_python_script "Denan LI (lidenan@westlake.edu.cn)" "${calc_path}/calc_polarization_abo3.py" "${@:3}" ;;
                     *)
                         echo " See the codes in calculators folder for more details"
                         echo " Code path: ${calc_path}"; exit 1 ;;
@@ -424,28 +361,10 @@ if [ ! -z "$1" ]; then
             fi ;;
 
         -range)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ]  ; then
-                echo " Calling script by Zihan YAN. "
-                echo " Code path: ${analyzer_path}/energy_force_virial_analyzer.py"
-                python ${analyzer_path}/energy_force_virial_analyzer.py $2 $3 ${@:4}
-            else
-                echo " Usage: -range <exyzfile> <property> [hist] (eg. gpumdkit.sh -range train.xyz energy hist)" 
-                echo " See the source code of energy_force_virial_analyzer.py for more details"
-                echo " Code path: ${analyzer_path}/energy_force_virial_analyzer.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/energy_force_virial_analyzer.py" "${@:2}" ;;
 
         -replicate)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Boyi SITU. "
-                echo " Code path: ${format_conv_path}/replicate.py"
-                python ${format_conv_path}/replicate.py $2 $3 ${@:4}
-            else
-                echo " Please give the file name suffix (e.g. input.xyz or output.vasp)"
-                echo " Usage 1: -replicate <inputfile> <outputfile> a b c" 
-                echo " Usage 2: -replicate <inputfile> <outputfile> target_num"
-                echo " See the source code of replicate.py for more details"
-                echo " Code path: ${format_conv_path}/replicate.py"
-            fi ;;
+            run_python_script "Boyi SITU (situboyi@westlake.edu.cn)" "${format_conv_path}/replicate.py" "${@:2}" ;;
 
         -out2xyz)
             if [ ! -z "$2" ] && [ "$2" != "-h" ]; then
@@ -459,15 +378,7 @@ if [ ! -z "$1" ]; then
             fi ;;
 
         -out2exyz)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ]; then
-                echo " Calling script by Zihan YAN et al. "
-                python ${format_conv_path}/out2exyz.py $2
-                echo " Code path: ${format_conv_path}/out2exyz.py"
-            else
-                echo " Usage: -out2exyz dir_name (eg. gpumdkit.sh -out2exyz .)"
-                echo " See the source code of out2exyz.py for more details"
-                echo " Code path: ${format_conv_path}/out2exyz.py"               
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/out2exyz.py" "${@:2}" ;;
 
         -cp2k2xyz)
             echo " Calling script by Chen HUA "
@@ -475,231 +386,70 @@ if [ ! -z "$1" ]; then
             echo " Code path: ${format_conv_path}/cp2k_log2xyz.py" ;;
 
         -pos2exyz)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${format_conv_path}/pos2exyz.py"
-                python ${format_conv_path}/pos2exyz.py $2 $3
-            else
-                echo " Usage: -pos2exyz POSCAR model.xyz"
-                echo " See the source code of pos2exyz.py for more details"
-                echo " Code path: ${format_conv_path}/pos2exyz.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/pos2exyz.py" "${@:2}" ;;
 
         -cif2pos)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Boyi SITU "
-                echo " Code path: ${format_conv_path}/cif2pos.py"
-                python ${format_conv_path}/cif2pos.py $2 $3
-            else
-                echo " Usage: -cif2pos input.cif POSCAR.vasp"
-                echo " See the source code of cif2pos.py for more details"
-                echo " Code path: ${format_conv_path}/cif2pos.py"
-            fi ;;
+            run_python_script "Boyi SITU (situboyi@westlake.edu.cn)" "${format_conv_path}/cif2pos.py" "${@:2}" ;;
 
         -cif2exyz)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Boyi SITU "
-                echo " Code path: ${format_conv_path}/cif2exyz.py"
-                python ${format_conv_path}/cif2exyz.py $2 $3
-            else
-                echo " Usage: -cif2exyz input.cif model.xyz"
-                echo " See the source code of cif2exyz.py for more details"
-                echo " Code path: ${format_conv_path}/cif2exyz.py"
-            fi ;;
+            run_python_script "Boyi SITU (situboyi@westlake.edu.cn)" "${format_conv_path}/cif2exyz.py" "${@:2}" ;;
 
         -exyz2pos)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${format_conv_path}/exyz2pos.py"
-                python ${format_conv_path}/exyz2pos.py $2
-            else
-                echo " Usage: -exyz2pos model.xyz"
-                echo " See the source code of exyz2pos.py for more details"
-                echo " Code path: ${format_conv_path}/exyz2pos.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/exyz2pos.py" "${@:2}" ;;
 
         -xdat2exyz)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${format_conv_path}/xdatcar2exyz.py"
-                python ${format_conv_path}/xdatcar2exyz.py $2 $3
-            else
-                echo " Usage: -xdat2exyz XDATCAR dump.xyz"
-                echo " See the source code of xdatcar2exyz.py for more details"
-                echo " Code path: ${format_conv_path}/xdatcar2exyz.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/xdatcar2exyz.py" "${@:2}" ;;
 
         -pos2lmp)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${format_conv_path}/pos2lmp.py"
-                python ${format_conv_path}/pos2lmp.py $2 $3
-            else
-                echo " Usage: -pos2lmp POSCAR lammps.data"
-                echo " See the source code of pos2lmp.py for more details"
-                echo " Code path: ${format_conv_path}/pos2lmp.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/pos2lmp.py" "${@:2}" ;;
 
         -lmp2exyz)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${format_conv_path}/lmp2exyz.py"
-                python ${format_conv_path}/lmp2exyz.py $2 ${@:3}
-            else
-                echo " Usage: -lmp2exyz <dump_file> <element1> <element2> ..."
-                echo " See the source code of lmp2exyz.py for more details"
-                echo " Code path: ${format_conv_path}/lmp2exyz.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/lmp2exyz.py" "${@:2}" ;;
 
         -traj2exyz)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${format_conv_path}/traj2exyz.py"
-                python ${format_conv_path}/traj2exyz.py $2 $3
-            else
-                echo " Usage: -traj2exyz <input.traj> <output.xyz>"
-                echo " See the source code of traj2exyz.py for more details"
-                echo " Code path: ${format_conv_path}/traj2exyz.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/traj2exyz.py" "${@:2}" ;;
 
         -addgroup|-addlabel)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${format_conv_path}/add_groups.py"
-                python ${format_conv_path}/add_groups.py $2 ${@:3}
-            else
-                echo " Usage: -addgroup <POSCAR> <element1> <element2> ..."
-                echo " See the source code of add_groups.py for more details"
-                echo " Code path: ${format_conv_path}/add_groups.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/add_groups.py" "${@:2}" ;;
 
         -addweight)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] && [ ! -z "$4" ]; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${format_conv_path}/add_weight.py"
-                python ${format_conv_path}/add_weight.py $2 $3 $4
-            else
-                echo " Usage: -addweight <input.xyz> <output.xyz> <weight> "
-                echo " See the source code of add_groups.py for more details"
-                echo " Code path: ${format_conv_path}/add_weight.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/add_weight.py" "${@:2}" ;;
 
         -get_frame)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${format_conv_path}/get_frame.py"
-                python ${format_conv_path}/get_frame.py $2 $3
-            else
-                echo " Usage: -get_frame <exyzfile> <frame_index>"
-                echo " See the source code of get_frame.py for more details"
-                echo " Code path: ${format_conv_path}/get_frame.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/get_frame.py" "${@:2}" ;;
 
         -clean_xyz)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${format_conv_path}/clean_xyz.py"
-                python ${format_conv_path}/clean_xyz.py $2 $3
-            else
-                echo " Usage: -clean_xyz <input.xyz> <output.xyz>"
-                echo " See the source code of clean_xyz.py for more details"
-                echo " Code path: ${format_conv_path}/clean_xyz.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/clean_xyz.py" "${@:2}" ;;
 
         -min_dist)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ]; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${analyzer_path}/get_min_dist.py"
-                python ${analyzer_path}/get_min_dist.py $2
-            else
-                echo " Usage: -min_dist <exyzfile>"
-                echo " See the source code of get_min_dist.py for more details"
-                echo " Code path: ${analyzer_path}/get_min_dist.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/get_min_dist.py" "${@:2}" ;;
 
         -min_dist_pbc)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ]; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${analyzer_path}/get_min_dist_pbc.py"
-                python ${analyzer_path}/get_min_dist_pbc.py $2
-            else
-                echo " Usage: -min_dist_pbc <exyzfile>"
-                echo " See the source code of get_min_dist_pbc.py for more details"
-                echo " Code path: ${analyzer_path}/get_min_dist_pbc.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/get_min_dist_pbc.py" "${@:2}" ;;
 
         -filter_dist)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ]; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${analyzer_path}/filter_structures_by_distance.py"
-                python ${analyzer_path}/filter_structures_by_distance.py $2 $3
-            else
-                echo " Usage: -filter_dist <exyzfile> <min_dist>"
-                echo " See the source code of filter_structures_by_distance.py for more details"
-                echo " Code path: ${analyzer_path}/filter_structures_by_distance.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/filter_structures_by_distance.py" "${@:2}" ;;
 
         -filter_dist_pbc)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ]; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${analyzer_path}/filter_structures_by_distance_pbc.py"
-                python ${analyzer_path}/filter_structures_by_distance_pbc.py $2 $3
-            else
-                echo " Usage: -filter_dist_pbc <exyzfile> <min_dist>"
-                echo " See the source code of filter_structures_by_distance_pbc.py for more details"
-                echo " Code path: ${analyzer_path}/filter_structures_by_distance_pbc.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/filter_structures_by_distance_pbc.py" "${@:2}" ;;
 
         -filter_box)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${analyzer_path}/filter_exyz_by_box.py"
-                python ${analyzer_path}/filter_exyz_by_box.py $2 $3
-            else
-                echo " Usage: -filter_box <exyzfile> <lattice limit>"
-                echo " See the source code of filter_exyz_by_box.py for more details"
-                echo " Code path: ${analyzer_path}/filter_exyz_by_box.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/filter_exyz_by_box.py" "${@:2}" ;;
 
         -filter_value)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${analyzer_path}/filter_exyz_by_value.py"
-                python ${analyzer_path}/filter_exyz_by_value.py $2 $3 $4
-            else
-                echo " Usage: -filter_value <exyzfile> <property> <value>"
-                echo " See the source code of filter_exyz_by_value.py for more details"
-                echo " Code path: ${analyzer_path}/filter_exyz_by_value.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/filter_exyz_by_value.py" "${@:2}" ;;
 
         -filter_range)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${analyzer_path}/filter_dist_range.py"
-                python ${analyzer_path}/filter_dist_range.py $2 $3 $4 $5 $6
-            else
-                echo " Usage: -filter_range <exyzfile> <element1> <element2> <min_dist> <max_dist>"
-                echo " See the source code of filter_dist_range.py for more details"
-                echo " Code path: ${analyzer_path}/filter_dist_range.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/filter_dist_range.py" "${@:2}" ;;
 
         -analyze_comp)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ]; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${analyzer_path}/analyze_composition.py"
-                python ${analyzer_path}/analyze_composition.py $2
-            else
-                echo " Usage: -analyze_composition <exyzfile>"
-                echo " See the source code of analyze_composition.py for more details"
-                echo " Code path: ${analyzer_path}/analyze_composition.py"
-                exit 1
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/analyze_composition.py" "${@:2}" ;;
 
         -get_volume)
             python ${analyzer_path}/get_volume.py ;;
 
         -chem_species)
-            python ${analyzer_path}/analyze_chem_species.py $2 ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/analyze_chem_species.py" "${@:2}" ;;
 
         -pynep)
             source ${GPUMDkit_path}/src/f2_sample_structures.sh
@@ -709,42 +459,16 @@ if [ ! -z "$1" ]; then
             python ${GPUMDkit_path}/Scripts/utils/nep_modifier/nep_modifier.py ;;
 
         -frame_range)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] && [ ! -z "$4" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${sample_path}/frame_range.py"
-                python ${sample_path}/frame_range.py $2 $3 $4
-            else
-                echo " Usage: -frame_range <exyzfile> <start_frac> <end_frac>"
-                echo " Example: gpumdkit.sh -frame_range dump.xyz 0.2 0.5"
-                echo " See the source code of frame_range.py for more details"
-                echo " Code path: ${sample_path}/frame_range.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${sample_path}/frame_range.py" "${@:2}" ;;
 
         -re_atoms)
-            echo " Calling script by Dian HUANG et al. "
-            python ${utils_path}/renumber_atoms.py $2 $3 ;;
+            run_python_script "Dian HUANG (huangdian@stu.xjtu.edu.cn)" "${utils_path}/renumber_atoms.py" "${@:2}" ;;
 
         -cbc)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] ; then
-                echo " Calling script by Zihan YAN "
-                python ${analyzer_path}/charge_balance_check.py $2
-            else
-                echo " Usage: -cbc <exyzfile>"
-                echo " See the source code of charge_balance_check.py for more details"
-                echo " Code path: ${analyzer_path}/charge_balance_check.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/charge_balance_check.py" "${@:2}" ;;
 
         -pda)
-            if [ ! -z "$2" ] && [ "$2" != "-h" ] && [ ! -z "$3" ] && [ ! -z "$4" ] && [ ! -z "$5" ] ; then
-                echo " Calling script by Zihan YAN "
-                echo " Code path: ${analyzer_path}/probability_density_analysis.py"
-                python ${analyzer_path}/probability_density_analysis.py $2 $3 $4 $5
-            else
-                echo " Usage: -pda <ref_struct> <trajectory_file> <species> <interval>"
-                echo " Example: gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25"
-                echo " See the source code of probability_density_analysis.py for more details"
-                echo " Code path: ${analyzer_path}/probability_density_analysis.py"
-            fi ;;
+            run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/probability_density_analysis.py" "${@:2}" ;;
 
         -hbond)
             echo " Calling script by Zherui CHEN "
diff --git a/skills/gpumdkit-calculators/SKILL.md b/skills/gpumdkit-calculators/SKILL.md
index 4038d9a..6eeaf5b 100644
--- a/skills/gpumdkit-calculators/SKILL.md
+++ b/skills/gpumdkit-calculators/SKILL.md
@@ -19,7 +19,7 @@ allowed-tools: Bash(gpumdkit *) Bash(python3 *)
 | NEP Properties | `-calc nep` | Compute energy/force/stress with NEP |
 | Descriptors | `-calc des` | Calculate NEP descriptors for analysis |
 | DOAS | `-calc doas` | Density of atomistic states |
-| NEB | Direct Python | Nudged elastic band calculation |
+| NEB | `-calc neb` | Nudged elastic band calculation |
 | Neighbor List | `-calc nlist` | Build neighbor lists for analysis |
 | Displacement | `-calc disp` | Calculate atomic displacements |
 | Averaged Structure | `-calc avg-struct` | Time-averaged structure from trajectory |
@@ -165,10 +165,13 @@ gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000
 
 ### NEB Calculation
 ```bash
-# Direct Python execution (no CLI shortcut)
-python Scripts/calculators/neb_calculation.py <initial.xyz> <final.xyz> <n_images> <nep.txt>
+# CLI shortcut
+gpumdkit.sh -calc neb <initial.xyz> <final.xyz> <n_images> <nep.txt>
 
 # Example
+gpumdkit.sh -calc neb init.xyz fin.xyz 9 nep.txt
+
+# Direct Python execution (also works)
 python Scripts/calculators/neb_calculation.py init.xyz fin.xyz 9 nep.txt
 
 # Alternative with NepTrainKit:
diff --git a/skills/gpumdkit-contributing/SKILL.md b/skills/gpumdkit-contributing/SKILL.md
index c104e7d..bf07508 100644
--- a/skills/gpumdkit-contributing/SKILL.md
+++ b/skills/gpumdkit-contributing/SKILL.md
@@ -97,7 +97,7 @@ Key conventions:
 
 ### Step 3: Register in `gpumdkit.sh`
 
-1. Add the choice number to `array_choice` (line ~57)
+1. Add the choice number to `array_choice` (line ~47)
 2. Add the case in the `main()` function's nested case statement:
    ```bash
    "413") f413_new_feature ;;
diff --git a/skills/gpumdkit-workflows/SKILL.md b/skills/gpumdkit-workflows/SKILL.md
index c7fa63a..1b8effe 100644
--- a/skills/gpumdkit-workflows/SKILL.md
+++ b/skills/gpumdkit-workflows/SKILL.md
@@ -15,8 +15,8 @@ allowed-tools: Bash(gpumdkit *) Bash(python3 *)
 
 | Workflow | Menu | Description |
 |----------|------|-------------|
-| SCF Batch (VASP) | 301.1 | VASP single-point batch setup |
-| SCF Batch (CP2K) | 301.2 | CP2K single-point batch setup |
+| SCF Batch (VASP) | 301 → 1 | VASP single-point batch setup |
+| SCF Batch (CP2K) | 301 → 2 | CP2K single-point batch setup |
 | MD Batch (GPUMD) | 302 | GPUMD MD sampling batch setup |
 | MD Batch (LAMMPS) | 303 | LAMMPS MD sampling batch setup |
 
diff --git a/src/f1_format_conversions.sh b/src/f1_format_conversions.sh
index ee2d3b3..3d25608 100644
--- a/src/f1_format_conversions.sh
+++ b/src/f1_format_conversions.sh
@@ -2,7 +2,7 @@
 # GPUMDkit format conversion module
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit
-#           for GPUMD and NEP, MGE Advances, 2026, e70074
+#           for GPUMD and NEP, MGE Advances, 2026, 4, e70074
 # Author: Zihan YAN (yanzihan@westlake.edu.cn)
 # ============================================================
 
diff --git a/src/f2_sample_structures.sh b/src/f2_sample_structures.sh
index 9f6e4c7..f340144 100644
--- a/src/f2_sample_structures.sh
+++ b/src/f2_sample_structures.sh
@@ -2,7 +2,7 @@
 # GPUMDkit sample structures module
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit
-#           for GPUMD and NEP, MGE Advances, 2026, e70074
+#           for GPUMD and NEP, MGE Advances, 2026, 4, e70074
 # Author: Zihan YAN (yanzihan@westlake.edu.cn)
 # ============================================================
 
@@ -130,7 +130,7 @@ echo " +------------------------------------------------------+"
 echo " |                 SAMPLE STRUCTURE TOOLS               |"
 echo " +------------------------------------------------------+"
 echo " | 201) Sample structures from extxyz                   |"
-echo " | 202) PyNEP sampling [deprecated]                    |"
+echo " | 202) PyNEP sampling [deprecated]                     |"
 echo " | 203) FPS sampling by NepTrain [preferred]            |"
 echo " | 204) Perturb structure                               |"
 echo " | 205) Select max force deviation structs              |"
diff --git a/src/f3_workflows.sh b/src/f3_workflows.sh
index 53fb8ba..ae8fcec 100644
--- a/src/f3_workflows.sh
+++ b/src/f3_workflows.sh
@@ -2,7 +2,7 @@
 # GPUMDkit workflow module
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit
-#           for GPUMD and NEP, MGE Advances, 2026, e70074
+#           for GPUMD and NEP, MGE Advances, 2026, 4, e70074
 # Author: Zihan YAN (yanzihan@westlake.edu.cn)
 # ============================================================
 
diff --git a/src/f4_calculators.sh b/src/f4_calculators.sh
index dc9923d..52cd239 100644
--- a/src/f4_calculators.sh
+++ b/src/f4_calculators.sh
@@ -2,7 +2,7 @@
 # GPUMDkit calculators module
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit
-#           for GPUMD and NEP, MGE Advances, 2026, e70074
+#           for GPUMD and NEP, MGE Advances, 2026, 4, e70074
 # Author: Zihan YAN (yanzihan@westlake.edu.cn)
 # ============================================================
 
diff --git a/src/f5_analyzers.sh b/src/f5_analyzers.sh
index a25d69d..29982cc 100644
--- a/src/f5_analyzers.sh
+++ b/src/f5_analyzers.sh
@@ -2,7 +2,7 @@
 # GPUMDkit analyzer module
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit
-#           for GPUMD and NEP, MGE Advances, 2026, e70074
+#           for GPUMD and NEP, MGE Advances, 2026, 4, e70074
 # Author: Zihan YAN (yanzihan@westlake.edu.cn)
 # ============================================================
 
diff --git a/src/f6_plots.sh b/src/f6_plots.sh
index 32010dc..87cb7e4 100644
--- a/src/f6_plots.sh
+++ b/src/f6_plots.sh
@@ -2,7 +2,7 @@
 # GPUMDkit plots module
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit
-#           for GPUMD and NEP, MGE Advances, 2026, e70074
+#           for GPUMD and NEP, MGE Advances, 2026, 4, e70074
 # Author: Zihan YAN (yanzihan@westlake.edu.cn)
 # ============================================================
 
diff --git a/src/f7_utilities.sh b/src/f7_utilities.sh
index 119cdd1..f826e28 100644
--- a/src/f7_utilities.sh
+++ b/src/f7_utilities.sh
@@ -2,7 +2,7 @@
 # GPUMDkit utilities module
 # Repository: https://github.com/zhyan0603/GPUMDkit
 # Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit
-#           for GPUMD and NEP, MGE Advances, 2026, e70074
+#           for GPUMD and NEP, MGE Advances, 2026, 4, e70074
 # Author: Zihan YAN (yanzihan@westlake.edu.cn)
 # ============================================================
 

From 4b9209e156c1ef5dfed97abc244dee3111b7afda Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Wed, 1 Jul 2026 00:16:07 +0800
Subject: [PATCH 13/24] update

---
 Scripts/analyzer/analyze_chem_species.py      |   17 +-
 Scripts/analyzer/analyze_composition.py       |   21 +-
 Scripts/analyzer/charge_balance_check.py      |   24 +-
 .../analyzer/energy_force_virial_analyzer.py  |   13 +-
 Scripts/analyzer/filter_dist_range.py         |   26 +-
 Scripts/analyzer/filter_exyz_by_box.py        |   22 +-
 Scripts/analyzer/filter_exyz_by_value.py      |   22 +-
 .../analyzer/filter_structures_by_distance.py |   24 +-
 .../filter_structures_by_distance_pbc.py      |   24 +-
 Scripts/analyzer/get_min_dist.py              |   22 +-
 Scripts/analyzer/get_min_dist_pbc.py          |   22 +-
 .../analyzer/probability_density_analysis.py  |   17 +-
 Scripts/format_conversion/add_groups.py       |   23 +-
 Scripts/format_conversion/add_weight.py       |   21 +-
 Scripts/format_conversion/cif2exyz.py         |   16 +-
 Scripts/format_conversion/cif2pos.py          |   16 +-
 Scripts/format_conversion/clean_xyz.py        |   21 +-
 Scripts/format_conversion/exyz2pos.py         |   22 +-
 Scripts/format_conversion/get_frame.py        |   19 +-
 Scripts/format_conversion/lmp2exyz.py         |   24 +-
 Scripts/format_conversion/out2exyz.py         |   22 +-
 Scripts/format_conversion/pos2exyz.py         |   20 +-
 Scripts/format_conversion/pos2lmp.py          |   21 +-
 Scripts/format_conversion/replicate.py        |   50 +-
 Scripts/format_conversion/traj2exyz.py        |   20 +-
 Scripts/format_conversion/xdatcar2exyz.py     |   16 +-
 Scripts/sample_structures/frame_range.py      |   21 +-
 Scripts/utils/completion.sh                   |    4 +-
 Scripts/utils/renumber_atoms.py               |   23 +-
 docs/htmls/en/active_learning_workflow.html   |  171 ++-
 docs/htmls/en/analyzer_scripts.html           |  692 +++++++++-
 docs/htmls/en/calculator_scripts.html         |  230 ++--
 docs/htmls/en/command_reference.html          |    4 +-
 docs/htmls/en/contributing_to_gpumdkit.html   |  168 ++-
 docs/htmls/en/custom_commands.html            |    2 +-
 docs/htmls/en/format_conversion.html          |  165 ++-
 docs/htmls/en/index.html                      |  278 ++--
 docs/htmls/en/plot_scripts.html               | 1013 ++++++++++----
 docs/htmls/en/polar_material_analysis.html    |  279 ++--
 docs/htmls/en/quick_start.html                |  358 ++---
 docs/htmls/en/structure_sampling.html         |  126 +-
 docs/htmls/en/workflow_scripts.html           |  132 +-
 docs/htmls/search/search_index.json           |    2 +-
 docs/htmls/sitemap.xml                        |   54 +-
 docs/htmls/sitemap.xml.gz                     |  Bin 615 -> 615 bytes
 docs/htmls/zh/index.html                      |  286 ++--
 ...\345\267\245\344\275\234\346\265\201.html" |  103 +-
 ...\346\236\220\345\267\245\345\205\267.html" |  841 ++++++++++--
 ...\344\273\244\345\217\202\350\200\203.html" |    4 +-
 ...\346\265\201\350\204\232\346\234\254.html" |  148 +-
 ...\351\200\237\345\205\245\351\227\250.html" |  320 ++---
 ...\346\226\231\345\210\206\346\236\220.html" |  399 ++++--
 ...\345\274\217\350\275\254\346\215\242.html" |  236 +++-
 ...\346\236\204\351\207\207\346\240\267.html" |  159 ++-
 ...\345\233\276\350\204\232\346\234\254.html" | 1221 ++++++++++++++---
 ...\345\231\250\350\204\232\346\234\254.html" |  225 ++-
 ...\347\214\256\346\214\207\345\215\227.html" |  605 ++++----
 docs/script.js                                |    4 +-
 docs/tutorials/en/analyzer_scripts.md         |   51 +-
 docs/tutorials/en/calculator_scripts.md       |   61 +-
 docs/tutorials/en/command_reference.md        |    4 +-
 docs/tutorials/en/format_conversion.md        |   30 +-
 docs/tutorials/en/index.md                    |   85 +-
 docs/tutorials/en/plot_scripts.md             |   18 +-
 docs/tutorials/en/polar_material_analysis.md  |    4 +-
 docs/tutorials/en/quick_start.md              |  108 +-
 docs/tutorials/zh/index.md                    |   85 +-
 ...06\346\236\220\345\267\245\345\205\267.md" |   49 +-
 ...75\344\273\244\345\217\202\350\200\203.md" |    4 +-
 ...53\351\200\237\345\205\245\351\227\250.md" |   92 +-
 ...20\346\226\231\345\210\206\346\236\220.md" |    4 +-
 ...74\345\274\217\350\275\254\346\215\242.md" |   24 +-
 ...30\345\233\276\350\204\232\346\234\254.md" |   18 +-
 ...27\345\231\250\350\204\232\346\234\254.md" |   51 +-
 gpumdkit.sh                                   |    5 -
 src/f1_format_conversions.sh                  |    2 +-
 src/f4_calculators.sh                         |    2 +-
 77 files changed, 6602 insertions(+), 2933 deletions(-)

diff --git a/Scripts/analyzer/analyze_chem_species.py b/Scripts/analyzer/analyze_chem_species.py
index 1c1591b..454fcdb 100644
--- a/Scripts/analyzer/analyze_chem_species.py
+++ b/Scripts/analyzer/analyze_chem_species.py
@@ -21,14 +21,21 @@
 """
 
 import sys
-from ase.io import read
-from ase.data import chemical_symbols, atomic_numbers
 
-# Load all frames from the provided extxyz file
-if len(sys.argv) < 2:
+args = sys.argv[1:]
+if len(args) < 1 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -chem_species <exyzfile>")
     print("    or: python analyze_chem_species.py <input.xyz>")
-    sys.exit(1)
+    print("")
+    print(" Arguments:")
+    print("   exyzfile    Input extxyz trajectory file")
+    print("")
+    print(" Example: gpumdkit.sh -chem_species train.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+from ase.io import read
+from ase.data import chemical_symbols, atomic_numbers
 
 atoms_list = read(sys.argv[1], index=':')
 
diff --git a/Scripts/analyzer/analyze_composition.py b/Scripts/analyzer/analyze_composition.py
index a7a3f46..8e6682c 100644
--- a/Scripts/analyzer/analyze_composition.py
+++ b/Scripts/analyzer/analyze_composition.py
@@ -21,8 +21,21 @@
 =============================================================================
 """
 
-import re
 import sys
+
+args = sys.argv[1:]
+if len(args) < 1 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -analyze_comp <exyzfile>")
+    print("    or: python analyze_composition.py <input.xyz>")
+    print("")
+    print(" Arguments:")
+    print("   exyzfile    Input extxyz trajectory file")
+    print("")
+    print(" Example: gpumdkit.sh -analyze_comp train.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+import re
 from ase.io import read, write
 from ase.data import atomic_numbers
 from collections import Counter
@@ -113,9 +126,5 @@ def analyze_xyz_compositions(filename):
 
 # Run the analysis
 if __name__ == "__main__":
-    if len(sys.argv) != 2:
-        print(" Usage: gpumdkit.sh -analyze_comp <exyzfile>")
-        print("    or: python analyze_composition.py <input.xyz>")
-        sys.exit(1)
-    filename = sys.argv[1]  # your extxyz file
+    filename = sys.argv[1]
     analyze_xyz_compositions(filename)
diff --git a/Scripts/analyzer/charge_balance_check.py b/Scripts/analyzer/charge_balance_check.py
index 346c268..78dc779 100644
--- a/Scripts/analyzer/charge_balance_check.py
+++ b/Scripts/analyzer/charge_balance_check.py
@@ -24,6 +24,24 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 1 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -cbc <exyzfile>")
+    print("    or: python charge_balance_check.py <input.extxyz>")
+    print("")
+    print(" Arguments:")
+    print("   exyzfile    Input extxyz trajectory file")
+    print("")
+    print(" Output:")
+    print("   balanced.xyz     Structures with balanced oxidation states")
+    print("   unbalanced.xyz   Structures with unbalanced oxidation states")
+    print("   indices.txt      Summary of indices and output files")
+    print("")
+    print(" Example: gpumdkit.sh -cbc train.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 from ase.io import read, write
 from ase.data import atomic_numbers
 from collections import Counter
@@ -76,12 +94,6 @@ def process_structure(idx_atoms):
     return atoms
 
 def main():
-    # Check if input file is provided
-    if len(sys.argv) != 2:
-        print(" Usage: gpumdkit.sh -cbc <exyzfile>")
-        print("    or: python charge_balance_check.py <input.extxyz>")
-        sys.exit(1)
-    
     input_file = sys.argv[1]
     balanced_file = "balanced.xyz"
     unbalanced_file = "unbalanced.xyz"
diff --git a/Scripts/analyzer/energy_force_virial_analyzer.py b/Scripts/analyzer/energy_force_virial_analyzer.py
index 689ba8c..2cc712b 100644
--- a/Scripts/analyzer/energy_force_virial_analyzer.py
+++ b/Scripts/analyzer/energy_force_virial_analyzer.py
@@ -24,10 +24,19 @@
 
 import sys
 
-if len(sys.argv) < 3:
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -range <exyzfile> <property> [hist]")
     print("    or: python energy_force_virial_analyzer.py <filename> <property> [hist]")
-    sys.exit(1)
+    print("")
+    print(" Arguments:")
+    print("   exyzfile    Input extxyz trajectory file")
+    print("   property    Property to analyze: energy, force, or virial")
+    print("   hist        (optional) If 'hist', plot a histogram")
+    print("")
+    print(" Example: gpumdkit.sh -range train.xyz force hist")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
 
 import numpy as np
 from ase.io import read
diff --git a/Scripts/analyzer/filter_dist_range.py b/Scripts/analyzer/filter_dist_range.py
index 319f502..f4f6760 100644
--- a/Scripts/analyzer/filter_dist_range.py
+++ b/Scripts/analyzer/filter_dist_range.py
@@ -25,6 +25,26 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 5 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -filter_range <exyzfile> <element1> <element2> <min_dist> <max_dist>")
+    print("    or: python filter_dist_range.py <input.xyz> <element1> <element2> <min_dist> <max_dist>")
+    print("")
+    print(" Arguments:")
+    print("   exyzfile    Input extxyz trajectory file")
+    print("   element1    First element symbol (e.g., Li)")
+    print("   element2    Second element symbol (e.g., Cl)")
+    print("   min_dist    Minimum distance (Angstrom)")
+    print("   max_dist    Maximum distance (Angstrom)")
+    print("")
+    print(" Output:")
+    print("   filtered_<element1>_<element2>_<min_dist>_<max_dist>.xyz")
+    print("")
+    print(" Example: gpumdkit.sh -filter_range train.xyz Li Cl 1.5 3.0")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 import numpy as np
 from ase.io import read, write
 
@@ -53,12 +73,6 @@ def get_min_distance(atoms, symbol1, symbol2):
     return np.min(distances)
 
 def main():
-    # Parse command line arguments
-    if len(sys.argv) != 6:
-        print(" Usage: gpumdkit.sh -filter_range <exyzfile> <element1> <element2> <min_dist> <max_dist>")
-        print("    or: python filter_dist_range.py <input.xyz> <element1> <element2> <min_dist> <max_dist>")
-        sys.exit(1)
-    
     input_file = sys.argv[1]
     atom1 = sys.argv[2]
     atom2 = sys.argv[3]
diff --git a/Scripts/analyzer/filter_exyz_by_box.py b/Scripts/analyzer/filter_exyz_by_box.py
index 19242b7..09bb44d 100644
--- a/Scripts/analyzer/filter_exyz_by_box.py
+++ b/Scripts/analyzer/filter_exyz_by_box.py
@@ -22,6 +22,23 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -filter_box <exyzfile> <edge_limit>")
+    print("    or: python filter_exyz_by_box.py <input_file> <edge_limit>")
+    print("")
+    print(" Arguments:")
+    print("   exyzfile    Input extxyz trajectory file")
+    print("   edge_limit  Maximum allowed box-edge length (Angstrom)")
+    print("")
+    print(" Output:")
+    print("   filtered_by_box.xyz  Structures that pass the filter")
+    print("")
+    print(" Example: gpumdkit.sh -filter_box train.xyz 20.0")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 from ase.io import read, write
 import numpy as np
 
@@ -49,11 +66,6 @@ def filter_frames(input_file, output_file, edge_limit):
     print(f"Number of structures discarded: {discarded_count}")
 
 if __name__ == "__main__":
-    if len(sys.argv) != 3:
-        print(" Usage: gpumdkit.sh -filter_box <exyzfile> <edge_limit>")
-        print("    or: python filter_exyz_by_box.py <input_file> <edge_limit>")
-        sys.exit(1)
-
     input_file = sys.argv[1]
     output_file = "filtered_by_box.xyz"
     edge_limit = float(sys.argv[2])
diff --git a/Scripts/analyzer/filter_exyz_by_value.py b/Scripts/analyzer/filter_exyz_by_value.py
index d01d7c2..32b1543 100644
--- a/Scripts/analyzer/filter_exyz_by_value.py
+++ b/Scripts/analyzer/filter_exyz_by_value.py
@@ -22,6 +22,24 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 3 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -filter_value <input_file> <property> <threshold>")
+    print("    or: python filter_exyz_by_value.py <input_file> <property> <threshold>")
+    print("")
+    print(" Arguments:")
+    print("   input_file   Input extxyz trajectory file")
+    print("   property     Filtering property: energy, force, or virial")
+    print("   threshold    Maximum allowed value for the specified property")
+    print("")
+    print(" Output:")
+    print("   filtered.xyz  Structures that pass the filter")
+    print("")
+    print(" Example: gpumdkit.sh -filter_value train.xyz energy -3.5")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 from ase.io import read, write
 
 def main():
@@ -57,8 +75,4 @@ def main():
     write(output_filename, filtered_images)
 
 if __name__ == "__main__":
-    if len(sys.argv) != 4:
-        print(" Usage: gpumdkit.sh -filter_value <input_file> <property> <threshold>")
-        print("    or: python filter_exyz_by_value.py <input_file> <property> <threshold>")
-        sys.exit(1)
     main()
diff --git a/Scripts/analyzer/filter_structures_by_distance.py b/Scripts/analyzer/filter_structures_by_distance.py
index 8a007c4..b7a57f2 100644
--- a/Scripts/analyzer/filter_structures_by_distance.py
+++ b/Scripts/analyzer/filter_structures_by_distance.py
@@ -25,6 +25,24 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 1 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -filter_dist <file_name> [distance_threshold]")
+    print("    or: python filter_structures_by_distance.py <file_name> [distance_threshold]")
+    print("")
+    print(" Arguments:")
+    print("   file_name           Input extxyz trajectory file")
+    print("   distance_threshold  (optional) Minimum allowed interatomic distance (Angstrom)")
+    print("")
+    print(" Output:")
+    print("   filtered_<file_name>       Structures that pass the filter")
+    print("   filtered_out_<file_name>   Structures that fail the filter")
+    print("")
+    print(" Example: gpumdkit.sh -filter_dist train.xyz 1.5")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 import numpy as np
 from ase.io import read, write
 from scipy.spatial.distance import pdist
@@ -38,12 +56,6 @@ def print_progress_bar(iteration, total, length=50):
     if iteration == total:
         print()
 
-# Check command-line arguments
-if len(sys.argv) < 2:
-    print(" Usage: gpumdkit.sh -filter_dist <file_name> [distance_threshold]")
-    print("    or: python filter_structures_by_distance.py <file_name> [distance_threshold]")
-    sys.exit(1)
-
 # Read the file name from command line arguments
 file_name = sys.argv[1]
 
diff --git a/Scripts/analyzer/filter_structures_by_distance_pbc.py b/Scripts/analyzer/filter_structures_by_distance_pbc.py
index cd487d3..d60308b 100644
--- a/Scripts/analyzer/filter_structures_by_distance_pbc.py
+++ b/Scripts/analyzer/filter_structures_by_distance_pbc.py
@@ -24,6 +24,24 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 1 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -filter_dist_pbc <file_name> [distance_threshold]")
+    print("    or: python filter_structures_by_distance_pbc.py <file_name> [distance_threshold]")
+    print("")
+    print(" Arguments:")
+    print("   file_name           Input extxyz trajectory file")
+    print("   distance_threshold  (optional) Minimum allowed interatomic distance (Angstrom)")
+    print("")
+    print(" Output:")
+    print("   filtered_<file_name>       Structures that pass the filter")
+    print("   filtered_out_<file_name>   Structures that fail the filter")
+    print("")
+    print(" Example: gpumdkit.sh -filter_dist_pbc train.xyz 1.5")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 import numpy as np
 from ase.io import read, write
 from scipy.spatial.distance import pdist
@@ -62,12 +80,6 @@ def calculate_pairwise_distances(lattice_params, atom_coords, fractional=True):
     np.fill_diagonal(distances, 0)
     return distances
 
-# Check command-line arguments
-if len(sys.argv) < 2:
-    print(" Usage: gpumdkit.sh -filter_dist_pbc <file_name> [distance_threshold]")
-    print("    or: python filter_structures_by_distance_pbc.py <file_name> [distance_threshold]")
-    sys.exit(1)
-
 # Read the file name from command line arguments
 file_name = sys.argv[1]
 
diff --git a/Scripts/analyzer/get_min_dist.py b/Scripts/analyzer/get_min_dist.py
index 72abbe2..b368d0e 100644
--- a/Scripts/analyzer/get_min_dist.py
+++ b/Scripts/analyzer/get_min_dist.py
@@ -23,15 +23,25 @@
 """
 
 import sys
-import numpy as np
-from ase.io import read
-from scipy.spatial.distance import pdist, squareform
 
-# Check command-line arguments
-if len(sys.argv) != 2:
+args = sys.argv[1:]
+if len(args) < 1 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -min_dist <file_name>")
     print("    or: python get_min_dist.py <file_name>")
-    sys.exit(1)
+    print("")
+    print(" Arguments:")
+    print("   file_name   Input extxyz trajectory file")
+    print("")
+    print(" Output:")
+    print("   Table of minimum distances for each element pair and overall minimum")
+    print("")
+    print(" Example: gpumdkit.sh -min_dist train.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+import numpy as np
+from ase.io import read
+from scipy.spatial.distance import pdist, squareform
 
 # Read the file name from command line arguments
 file_name = sys.argv[1]
diff --git a/Scripts/analyzer/get_min_dist_pbc.py b/Scripts/analyzer/get_min_dist_pbc.py
index a6bca8c..34b94bd 100644
--- a/Scripts/analyzer/get_min_dist_pbc.py
+++ b/Scripts/analyzer/get_min_dist_pbc.py
@@ -23,6 +23,22 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 1 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -min_dist_pbc <file_name>")
+    print("    or: python get_min_dist_pbc.py <file_name>")
+    print("")
+    print(" Arguments:")
+    print("   file_name   Input extxyz trajectory file")
+    print("")
+    print(" Output:")
+    print("   Table of minimum distances (with PBC) for each element pair")
+    print("")
+    print(" Example: gpumdkit.sh -min_dist_pbc train.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 import numpy as np
 from ase.io import read
 
@@ -52,12 +68,6 @@ def calculate_pairwise_distances(lattice_params, atom_coords, fractional=True):
     np.fill_diagonal(distances, 0)
     return distances
 
-# Check command-line arguments
-if len(sys.argv) != 2:
-    print(" Usage: gpumdkit.sh -min_dist_pbc <file_name>")
-    print("    or: python get_min_dist_pbc.py <file_name>")
-    sys.exit(1)
-
 # Read the file name from command line arguments
 file_name = sys.argv[1]
 
diff --git a/Scripts/analyzer/probability_density_analysis.py b/Scripts/analyzer/probability_density_analysis.py
index 2809dfe..8f02f02 100644
--- a/Scripts/analyzer/probability_density_analysis.py
+++ b/Scripts/analyzer/probability_density_analysis.py
@@ -26,10 +26,23 @@
 import sys
 
 # Check if required arguments are provided before heavy imports
-if len(sys.argv) != 5:
+args = sys.argv[1:]
+if len(args) < 4 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -pda <ref_struct> <trajectory_file> <species> <interval>")
     print("    or: python probability_density_analysis.py <ref_struct> <trajectory_file> <species> <interval>")
-    sys.exit(1)
+    print("")
+    print(" Arguments:")
+    print("   ref_struct       Reference structure file (e.g., POSCAR)")
+    print("   trajectory_file  AIMD trajectory in extxyz format")
+    print("   species          Mobile species symbol (e.g., Li)")
+    print("   interval         Grid interval for probability density (Angstrom)")
+    print("")
+    print(" Output:")
+    print("   probability_density_<interval>.vasp (CHGCAR-like file)")
+    print("")
+    print(" Example: gpumdkit.sh -pda POSCAR dump.xyz Li 0.1")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
 
 import numpy as np
 from pymatgen.analysis.diffusion.aimd.pathway import ProbabilityDensityAnalysis
diff --git a/Scripts/format_conversion/add_groups.py b/Scripts/format_conversion/add_groups.py
index 2bf4d55..221ff9a 100644
--- a/Scripts/format_conversion/add_groups.py
+++ b/Scripts/format_conversion/add_groups.py
@@ -10,6 +10,7 @@
 Purpose:    Add group information to atoms in a structure file based on
             element types, outputting the result to model.xyz.
 Usage:      gpumdkit.sh -addgroup <input.xyz> <element1> <element2> ...
+            gpumdkit.sh -addlabel <input.xyz> <element1> <element2> ...
             python add_groups.py <input.xyz> <element1> <element2> ...
 Arguments:
   input.xyz   Input structure file
@@ -22,14 +23,26 @@
 """
 
 import sys
-from ase.io import read, write
-import numpy as np
 
-# Check arguments
-if len(sys.argv) < 3:
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -addgroup <input.xyz> <element1> <element2> ...")
+    print("        gpumdkit.sh -addlabel <input.xyz> <element1> <element2> ...")
     print("    or: python add_groups.py <input.xyz> <element1> <element2> ...")
-    sys.exit(1)
+    print("")
+    print(" Arguments:")
+    print("   input.xyz   Input structure file")
+    print("   elementX    Element symbols to assign group indices (in order)")
+    print("")
+    print(" Output:")
+    print("   model.xyz   Structure with group information")
+    print("")
+    print(" Example: gpumdkit.sh -addgroup POSCAR Li Ti O")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+from ase.io import read, write
+import numpy as np
 
 # Read the file name from command line arguments
 file_name = sys.argv[1]
diff --git a/Scripts/format_conversion/add_weight.py b/Scripts/format_conversion/add_weight.py
index 4924463..7b7492b 100644
--- a/Scripts/format_conversion/add_weight.py
+++ b/Scripts/format_conversion/add_weight.py
@@ -24,15 +24,24 @@
 
 import os
 import sys
+
+args = sys.argv[1:]
+if len(args) < 3 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -addweight <input.xyz> <output.xyz> <weight>")
+    print("    or: python add_weight.py <input.xyz> <output.xyz> <weight>")
+    print("")
+    print(" Arguments:")
+    print("   input.xyz   Input extxyz file")
+    print("   output.xyz  Output extxyz file with added weight")
+    print("   weight      Weight value to assign (e.g., 1.0)")
+    print("")
+    print(" Example: gpumdkit.sh -addweight train.xyz weighted.xyz 2.0")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 from ase.io import read, write
 
 def main():
-    # Check if the correct number of arguments are provided
-    if len(sys.argv) != 4:
-        print(" Usage: gpumdkit.sh -addweight <input.xyz> <output.xyz> <weight>")
-        print("    or: python add_weight.py <input.xyz> <output.xyz> <weight>")
-        sys.exit(1)
-
     # Parse command line arguments
     input_file = sys.argv[1]
     output_file = sys.argv[2]
diff --git a/Scripts/format_conversion/cif2exyz.py b/Scripts/format_conversion/cif2exyz.py
index 13c89ea..687959d 100644
--- a/Scripts/format_conversion/cif2exyz.py
+++ b/Scripts/format_conversion/cif2exyz.py
@@ -21,13 +21,21 @@
 """
 
 import sys
-from ase.io import read, write
 
-# Check command line arguments
-if len(sys.argv) != 3:
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -cif2exyz <input.cif> <output.xyz>")
     print("    or: python cif2exyz.py <input.cif> <output.xyz>")
-    sys.exit(1)
+    print("")
+    print(" Arguments:")
+    print("   input.cif   Input CIF file")
+    print("   output.xyz  Output extxyz file")
+    print("")
+    print(" Example: gpumdkit.sh -cif2exyz structure.cif output.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+from ase.io import read, write
 
 # Read input and output file paths
 cif_file = sys.argv[1]
diff --git a/Scripts/format_conversion/cif2pos.py b/Scripts/format_conversion/cif2pos.py
index e3a24bd..238e999 100644
--- a/Scripts/format_conversion/cif2pos.py
+++ b/Scripts/format_conversion/cif2pos.py
@@ -21,13 +21,21 @@
 """
 
 import sys
-from ase.io import read, write
 
-# Check command line arguments
-if len(sys.argv) != 3:
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -cif2pos <input.cif> <output.vasp>")
     print("    or: python cif2pos.py <input.cif> <output.vasp>")
-    sys.exit(1)
+    print("")
+    print(" Arguments:")
+    print("   input.cif    Input CIF file")
+    print("   output.vasp  Output VASP POSCAR file")
+    print("")
+    print(" Example: gpumdkit.sh -cif2pos structure.cif POSCAR")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+from ase.io import read, write
 
 # Read input and output file paths
 cif_file = sys.argv[1]
diff --git a/Scripts/format_conversion/clean_xyz.py b/Scripts/format_conversion/clean_xyz.py
index 20918d2..3060116 100644
--- a/Scripts/format_conversion/clean_xyz.py
+++ b/Scripts/format_conversion/clean_xyz.py
@@ -21,14 +21,26 @@
 =============================================================================
 """
 
-from ase.io import read, write
 import sys
 
-# Check arguments
-if len(sys.argv) < 3:
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -clean_xyz <input.xyz> <output.xyz>")
     print("    or: python clean_xyz.py <input.xyz> <output.xyz>")
-    sys.exit(1)
+    print("")
+    print(" Arguments:")
+    print("   input.xyz    Input extxyz training file")
+    print("   output.xyz   Output cleaned extxyz file")
+    print("")
+    print(" Output:")
+    print("   Cleaned extxyz file with only structural information")
+    print("   (stress, virial, and force data are removed)")
+    print("")
+    print(" Example: gpumdkit.sh -clean_xyz train.xyz cleaned.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+from ase.io import read, write
 
 # Read all frames from the input train.xyz file
 frames = read(sys.argv[1], index=':')
@@ -57,3 +69,4 @@
 
 # Export the cleaned frames to a new extxyz file, containing only lattice and atomic information
 write(sys.argv[2], frames, format='extxyz')
+print(f" Cleaned {len(frames)} frames, saved to {sys.argv[2]}")
diff --git a/Scripts/format_conversion/exyz2pos.py b/Scripts/format_conversion/exyz2pos.py
index 148d446..edb037c 100644
--- a/Scripts/format_conversion/exyz2pos.py
+++ b/Scripts/format_conversion/exyz2pos.py
@@ -20,6 +20,22 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 1 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -exyz2pos <input.xyz>")
+    print("    or: python exyz2pos.py <input.xyz>")
+    print("")
+    print(" Arguments:")
+    print("   input.xyz   Input extxyz trajectory file")
+    print("")
+    print(" Output:")
+    print("   POSCAR_*.vasp   POSCAR file(s) in VASP format (one per frame)")
+    print("")
+    print(" Example: gpumdkit.sh -exyz2pos train.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 from ase.io import read, write
 
 def print_progress_bar(iteration, total, length=50):
@@ -31,12 +47,6 @@ def print_progress_bar(iteration, total, length=50):
     if iteration == total:
         print()
 
-# Check arguments
-if len(sys.argv) < 2:
-    print(" Usage: gpumdkit.sh -exyz2pos <input.xyz>")
-    print("    or: python exyz2pos.py <input.xyz>")
-    sys.exit(1)
-
 input_file = sys.argv[1]
 
 # Read all frames
diff --git a/Scripts/format_conversion/get_frame.py b/Scripts/format_conversion/get_frame.py
index bd3a918..5dbb08e 100644
--- a/Scripts/format_conversion/get_frame.py
+++ b/Scripts/format_conversion/get_frame.py
@@ -21,13 +21,24 @@
 """
 
 import sys
-from ase.io import read, write
 
-# Check arguments
-if len(sys.argv) < 3:
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -get_frame <input.xyz> <frame_number>")
     print("    or: python get_frame.py <input.xyz> <frame_number>")
-    sys.exit(1)
+    print("")
+    print(" Arguments:")
+    print("   input.xyz      Input extxyz trajectory file")
+    print("   frame_number   Frame number to extract (1-indexed)")
+    print("")
+    print(" Output:")
+    print("   frame_<N>.xyz  Extracted single frame")
+    print("")
+    print(" Example: gpumdkit.sh -get_frame train.xyz 10")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+from ase.io import read, write
 
 def get_frame():
     input_file = sys.argv[1]
diff --git a/Scripts/format_conversion/lmp2exyz.py b/Scripts/format_conversion/lmp2exyz.py
index 9ff11ce..6d78ce4 100644
--- a/Scripts/format_conversion/lmp2exyz.py
+++ b/Scripts/format_conversion/lmp2exyz.py
@@ -22,6 +22,23 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -lmp2exyz <dump_file> <element1> <element2> ...")
+    print("    or: python lmp2exyz.py <dump_file> <element1> <element2> ...")
+    print("")
+    print(" Arguments:")
+    print("   dump_file   Input LAMMPS dump file")
+    print("   elementX    Chemical element symbols in order of atomic types")
+    print("")
+    print(" Output:")
+    print("   dump.xyz    Converted structures in extxyz format")
+    print("")
+    print(" Example: gpumdkit.sh -lmp2exyz dump.lammps Si O")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 from ase.io import read, write
 
 def lmp2exyz(dump_file, elements):
@@ -48,12 +65,7 @@ def lmp2exyz(dump_file, elements):
 #   print(f" Converted {dump_file} to {extxyz_file}")
 
 if __name__ == '__main__':
-    if len(sys.argv) < 3:
-        print(" Usage: gpumdkit.sh -lmp2exyz <dump_file> <element1> <element2> ...")
-        print("    or: python lmp2exyz.py <dump_file> <element1> <element2> ...")
-        sys.exit(1)
-    
     dump_file = sys.argv[1]
     elements = sys.argv[2:]
-    
+
     lmp2exyz(dump_file, elements)
diff --git a/Scripts/format_conversion/out2exyz.py b/Scripts/format_conversion/out2exyz.py
index 9d4786b..bf7d84e 100644
--- a/Scripts/format_conversion/out2exyz.py
+++ b/Scripts/format_conversion/out2exyz.py
@@ -21,17 +21,27 @@
 """
 
 import os, sys
+
+args = sys.argv[1:]
+if len(args) < 1 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -out2exyz <directory>")
+    print("    or: python out2exyz.py <directory>")
+    print("")
+    print(" Arguments:")
+    print("   directory   Root directory to search for OUTCAR files")
+    print("")
+    print(" Output:")
+    print("   train.xyz   Converted structures in extxyz format")
+    print("")
+    print(" Example: gpumdkit.sh -out2exyz .")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 import numpy as np
 from ase.io import read, write
 from ase import Atoms, Atom
 from tqdm import tqdm
 
-# Check arguments
-if len(sys.argv) < 2:
-    print(" Usage: gpumdkit.sh -out2exyz <directory>")
-    print("    or: python out2exyz.py <directory>")
-    sys.exit(1)
-
 def Convert_atoms(atom):
     xx,yy,zz,yz,xz,xy = -atom.calc.results['stress']*atom.get_volume() 
     atom.info['virial'] = np.array([(xx, xy, xz), (xy, yy, yz), (xz, yz, zz)])
diff --git a/Scripts/format_conversion/pos2exyz.py b/Scripts/format_conversion/pos2exyz.py
index d778f69..7936fc7 100644
--- a/Scripts/format_conversion/pos2exyz.py
+++ b/Scripts/format_conversion/pos2exyz.py
@@ -21,6 +21,20 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -pos2exyz <POSCAR> <output.xyz>")
+    print("    or: python pos2exyz.py <POSCAR> <output.xyz>")
+    print("")
+    print(" Arguments:")
+    print("   POSCAR       One or more VASP POSCAR files (supports wildcards)")
+    print("   output.xyz   Output extxyz file")
+    print("")
+    print(" Example: gpumdkit.sh -pos2exyz POSCAR output.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 import glob
 from ase.io import read, write
 
@@ -43,12 +57,6 @@ def convert_poscar_to_extxyz(poscar_filenames, extxyz_filename):
     write(extxyz_filename, all_frames, format='extxyz', append=False)
 
 if __name__ == '__main__':
-    # Check if the number of arguments is correct
-    if len(sys.argv) < 3:
-        print(" Usage: gpumdkit.sh -pos2exyz <POSCAR> <output.xyz>")
-        print("    or: python pos2exyz.py <POSCAR> <output.xyz>")
-        sys.exit(1)
-
     poscar_filename_pattern = sys.argv[1]
     extxyz_filename = sys.argv[2]
 
diff --git a/Scripts/format_conversion/pos2lmp.py b/Scripts/format_conversion/pos2lmp.py
index b266b40..02b85f2 100644
--- a/Scripts/format_conversion/pos2lmp.py
+++ b/Scripts/format_conversion/pos2lmp.py
@@ -21,6 +21,20 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -pos2lmp <poscar_file> <lammps_data_file>")
+    print("    or: python pos2lmp.py <poscar_file> <lammps_data_file>")
+    print("")
+    print(" Arguments:")
+    print("   poscar_file       Input VASP POSCAR file")
+    print("   lammps_data_file  Output LAMMPS data file")
+    print("")
+    print(" Example: gpumdkit.sh -pos2lmp POSCAR data.lammps")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 from ovito.io import import_file, export_file
 
 def convert_poscar_to_lammps(poscar_path, lammps_data_path):
@@ -29,13 +43,8 @@ def convert_poscar_to_lammps(poscar_path, lammps_data_path):
     export_file(pipeline, lammps_data_path, "lammps/data", multiple_frames=False)
 
 if __name__ == "__main__":
-    if len(sys.argv) != 3:
-        print(" Usage: gpumdkit.sh -pos2lmp <poscar_file> <lammps_data_file>")
-        print("    or: python pos2lmp.py <poscar_file> <lammps_data_file>")
-        sys.exit(1)
-    
     poscar_file = sys.argv[1]
     lammps_data_file = sys.argv[2]
-    
+
     convert_poscar_to_lammps(poscar_file, lammps_data_file)
     print(f" Converted {poscar_file} to {lammps_data_file} successfully.")
diff --git a/Scripts/format_conversion/replicate.py b/Scripts/format_conversion/replicate.py
index 34bd484..c7a6fba 100644
--- a/Scripts/format_conversion/replicate.py
+++ b/Scripts/format_conversion/replicate.py
@@ -9,11 +9,14 @@
 Category:   Format Conversion Scripts
 Purpose:    Replicate a unit cell to generate a supercell with a target
             number of atoms, finding the nearest compatible supercell size.
-Usage:      python replicate.py input.vasp output.vasp a b c
+Usage:      gpumdkit.sh -replicate input.vasp output.vasp a b c
+            gpumdkit.sh -replicate input.vasp output.vasp target_num
+            python replicate.py input.vasp output.vasp a b c
             python replicate.py input.vasp output.vasp target_num
 Arguments:
   input.vasp       Input structure file
   output.vasp      Output supercell file
+  a b c            Replication factors along x, y, z axes
   target_n_atoms   Target number of atoms in the supercell
 Output:
   <output.vasp>  (replicated supercell structure)
@@ -25,6 +28,25 @@
 import sys
 import os
 import math
+
+args = sys.argv[1:]
+if len(args) not in (3, 5) or args[0] in ("-h", "--help"):
+    print(" Usage 1: gpumdkit.sh -replicate input.vasp output.vasp a b c")
+    print(" Usage 2: gpumdkit.sh -replicate input.vasp output.vasp target_num")
+    print("    or: python replicate.py input.vasp output.vasp a b c")
+    print("    or: python replicate.py input.vasp output.vasp target_num")
+    print("")
+    print(" Arguments:")
+    print("   input.vasp    Input structure file (any ASE-supported format)")
+    print("   output.vasp   Output supercell file")
+    print("   a b c         Replication factors along x, y, z axes")
+    print("   target_num    Target number of atoms (auto-finds best a,b,c)")
+    print("")
+    print(" Example: gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2")
+    print("          gpumdkit.sh -replicate POSCAR supercell.vasp 256")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 import numpy as np
 from ase.io import read, write
 from ase.build import make_supercell
@@ -105,22 +127,16 @@ def reorder_atoms_by_input_species_order(atoms, original_atoms):
     return reordered_atoms
 
 def main():
-    if len(sys.argv) < 4:
-        print(" Usage 1: gpumdkit.sh -replicate input.vasp output.vasp a b c")
-        print(" Usage 2: gpumdkit.sh -replicate input.vasp output.vasp target_num")
-        print("    or: python replicate.py input.vasp output.vasp a b c")
-        print("    or: python replicate.py input.vasp output.vasp target_num")
-        sys.exit(1)
-
     infile = sys.argv[1]
     outfile = sys.argv[2]
-    args = sys.argv[3:]
+    args_inner = sys.argv[3:]
 
-    # Infer input/output format
+    # Infer input/output format from file extension
+    # When there is no extension (e.g. POSCAR), let ASE auto-detect
     in_ext = os.path.splitext(infile)[1][1:].lower()
     out_ext = os.path.splitext(outfile)[1][1:].lower()
-    in_format = "extxyz" if in_ext == "xyz" else in_ext or "extxyz"
-    out_format = "extxyz" if out_ext == "xyz" else out_ext or "extxyz"
+    in_format = "extxyz" if in_ext == "xyz" else (in_ext if in_ext else None)
+    out_format = "extxyz" if out_ext == "xyz" else (out_ext if out_ext else "vasp")
     
     try:
         atoms = read(infile, format=in_format)
@@ -129,19 +145,19 @@ def main():
         sys.exit(1)
     
     n_atoms = len(atoms)
-    
-    if len(args) == 1:  # Target atom number
+
+    if len(args_inner) == 1:  # Target atom number
         try:
-            target_num = int(args[0])
+            target_num = int(args_inner[0])
         except ValueError:
             print(" Error: num must be an integer")
             sys.exit(1)
         a, b, c = find_nearest_supercell(atoms, target_num)
         total_atoms = n_atoms * a * b * c
         print(f"Original atoms: {n_atoms}, Target: {target_num}, Selected: {a}x{b}x{c} (total {total_atoms} atoms)")
-    elif len(args) == 3:  # a b c
+    elif len(args_inner) == 3:  # a b c
         try:
-            a, b, c = map(int, args)
+            a, b, c = map(int, args_inner)
         except ValueError:
             print(" Error: a, b, c must be integers")
             sys.exit(1)
diff --git a/Scripts/format_conversion/traj2exyz.py b/Scripts/format_conversion/traj2exyz.py
index 30bdddb..0c5beb0 100644
--- a/Scripts/format_conversion/traj2exyz.py
+++ b/Scripts/format_conversion/traj2exyz.py
@@ -21,6 +21,20 @@
 """
 
 import sys
+
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -traj2exyz <input.traj> <output.xyz>")
+    print("    or: python traj2exyz.py <input.traj> <output.xyz>")
+    print("")
+    print(" Arguments:")
+    print("   input.traj   Input ASE trajectory file")
+    print("   output.xyz   Output extxyz file")
+    print("")
+    print(" Example: gpumdkit.sh -traj2exyz md.traj output.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
 import os
 from ase.io import read, write
 
@@ -46,12 +60,6 @@ def convert_traj_to_extxyz(input_file, output_file):
         print(f" An unexpected error occurred: {e}")
 
 if __name__ == "__main__":
-    # Check if correct number of arguments are provided
-    if len(sys.argv) != 3:
-        print(" Usage: gpumdkit.sh -traj2exyz <input.traj> <output.xyz>")
-        print("    or: python traj2exyz.py <input.traj> <output.xyz>")
-        sys.exit(1)
-    
     input_path = sys.argv[1]
     output_path = sys.argv[2]
     convert_traj_to_extxyz(input_path, output_path)
\ No newline at end of file
diff --git a/Scripts/format_conversion/xdatcar2exyz.py b/Scripts/format_conversion/xdatcar2exyz.py
index 8d3ca60..d0bd6f9 100644
--- a/Scripts/format_conversion/xdatcar2exyz.py
+++ b/Scripts/format_conversion/xdatcar2exyz.py
@@ -21,13 +21,21 @@
 """
 
 import sys
-from ase.io import read, write
 
-# Check arguments
-if len(sys.argv) < 3:
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -xdat2exyz <XDATCAR> <output.xyz>")
     print("    or: python xdatcar2exyz.py <XDATCAR> <output.xyz>")
-    sys.exit(1)
+    print("")
+    print(" Arguments:")
+    print("   XDATCAR     Path to the input XDATCAR file")
+    print("   output.xyz  Path to the output extxyz file")
+    print("")
+    print(" Example: gpumdkit.sh -xdat2exyz XDATCAR output.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+from ase.io import read, write
 
 input_file = sys.argv[1]
 output_file = sys.argv[2]
diff --git a/Scripts/sample_structures/frame_range.py b/Scripts/sample_structures/frame_range.py
index 231648a..d0fab35 100644
--- a/Scripts/sample_structures/frame_range.py
+++ b/Scripts/sample_structures/frame_range.py
@@ -23,14 +23,25 @@
 """
 
 import sys
-from ase.io import read, write
 
-# Check command line arguments
-if len(sys.argv) != 4:
+args = sys.argv[1:]
+if len(args) < 3 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -frame_range <exyzfile> <start_fraction> <end_fraction>")
-    print("    or: python frame_range.py input.xyz start_fraction end_fraction")
+    print("    or: python frame_range.py <input.xyz> <start_fraction> <end_fraction>")
+    print("")
+    print(" Arguments:")
+    print("   exyzfile         Input extxyz trajectory file")
+    print("   start_fraction   Start fraction (0.0 to 1.0, e.g., 0 for beginning)")
+    print("   end_fraction     End fraction (0.0 to 1.0, e.g., 0.8 for first 80%)")
+    print("")
+    print(" Output:")
+    print("   <input>_<start>_<end>.xyz  Extracted frame range")
+    print("")
     print(" Example: gpumdkit.sh -frame_range dump.xyz 0.2 0.5")
-    sys.exit(1)
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+from ase.io import read, write
 
 input_file = sys.argv[1]
 start_fraction = float(sys.argv[2])
diff --git a/Scripts/utils/completion.sh b/Scripts/utils/completion.sh
index 2e0f2ef..5a2a440 100644
--- a/Scripts/utils/completion.sh
+++ b/Scripts/utils/completion.sh
@@ -13,7 +13,7 @@ _gpumdkit_completions() {
     prev="${COMP_WORDS[COMP_CWORD-1]}" # Previous word
 
     # List of primary options (extracted from gpumdkit.sh)
-    local opts="-h -help -update -U -clean -time -plt -calc -cbc -range -out2xyz -out2exyz -cp2k2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -xdat2exyz -pos2lmp -lmp2exyz -traj2exyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -filter_range -get_frame -clean_xyz -get_volume -analyze_comp -chem_species -replicate -pda -pynep -frame_range -re_atoms -nep_modifier"
+    local opts="-h -help -update -U -clean -time -plt -calc -cbc -range -out2xyz -out2exyz -cp2k2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -xdat2exyz -pos2lmp -lmp2exyz -traj2exyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -filter_range -get_frame -clean_xyz -analyze_comp -chem_species -replicate -pda -pynep -frame_range -nep_modifier"
 
     # Calculator subcommands
     local calc_subcmds="ionic-cond nep des doas neb minimize msd nlist disp avg-struct oct-tilt pol-abo3"
@@ -35,7 +35,7 @@ _gpumdkit_completions() {
             COMPREPLY=($(compgen -W "thermo thermo2 thermo3 train train_density prediction test train_test parity_density born_charge bec msd msd_all msd_conv msd_sdc sdc rdf rdf_pmf vac restart dimer force_errors des doas charge lr arrhenius_d arrhenius_sigma sigma D sigma_xyz D_xyz net_force emd nemd hnemd pdos plane-grid cohesive viscosity" -- "$cur")) ;;
 
         # Options requiring files or directories, complete with filenames
-        -out2xyz|-out2exyz|-cp2k2xyz|-exyz2pos|-min_dist|-min_dist_pbc|-filter_dist|-filter_dist_pbc|-filter_box|-filter_value|-filter_range|-get_frame|-clean_xyz|-pos2exyz|-cif2exyz|-cif2pos|-pos2lmp|-lmp2exyz|-traj2exyz|-addgroup|-addlabel|-addweight|-analyze_comp|-replicate|-pda|-cbc|-frame_range|-chem_species|-xdat2exyz|-re_atoms)
+        -out2xyz|-out2exyz|-cp2k2xyz|-exyz2pos|-min_dist|-min_dist_pbc|-filter_dist|-filter_dist_pbc|-filter_box|-filter_value|-filter_range|-get_frame|-clean_xyz|-pos2exyz|-cif2exyz|-cif2pos|-pos2lmp|-lmp2exyz|-traj2exyz|-addgroup|-addlabel|-addweight|-analyze_comp|-replicate|-pda|-cbc|-frame_range|-chem_species|-xdat2exyz)
             COMPREPLY=($(compgen -f -- "$cur")) ;;
 
         # Default case: complete primary options
diff --git a/Scripts/utils/renumber_atoms.py b/Scripts/utils/renumber_atoms.py
index f7adcff..b42f040 100644
--- a/Scripts/utils/renumber_atoms.py
+++ b/Scripts/utils/renumber_atoms.py
@@ -5,18 +5,33 @@
     gpumdkit.sh -re_atoms <input_file> <output_file>
     python renumber_atoms.py <input_file> <output_file>
 
+Arguments:
+    input_file   Input LAMMPS dump file
+    output_file  Output LAMMPS dump file with renumbered atom IDs
+
+Example:
+    gpumdkit.sh -re_atoms dump.lammps dump_renumbered.lammps
+
 Author:
     Dian HUANG (huangdian@stu.xjtu.edu.cn)
 """
 
 import sys
-from tqdm import tqdm
 
-# Check command-line arguments
-if len(sys.argv) != 3:
+args = sys.argv[1:]
+if len(args) < 2 or args[0] in ("-h", "--help"):
     print(" Usage: gpumdkit.sh -re_atoms <input_file> <output_file>")
     print("    or: python renumber_atoms.py <input_file> <output_file>")
-    sys.exit(1)
+    print("")
+    print(" Arguments:")
+    print("   input_file   Input LAMMPS dump file")
+    print("   output_file  Output LAMMPS dump file with renumbered atom IDs")
+    print("")
+    print(" Example: gpumdkit.sh -re_atoms dump.lammps dump_renumbered.lammps")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+from tqdm import tqdm
 
 input_file = sys.argv[1]
 output_file = sys.argv[2]
diff --git a/docs/htmls/en/active_learning_workflow.html b/docs/htmls/en/active_learning_workflow.html
index 069dfe6..fe2ad79 100644
--- a/docs/htmls/en/active_learning_workflow.html
+++ b/docs/htmls/en/active_learning_workflow.html
@@ -1515,16 +1515,57 @@ <h1>🔁 Active Learning Workflow</h1>
   <p style="text-align: justify;">This tutorial explains the steps and considerations involved in the <code>workflow_active_learning_dev.sh</code> script. The workflow is used to generate, select, and analyze molecular structures, followed by simulations and data collection.</p>
 </div>
 
-<h3 id="overview">Overview</h3>
-<p>This script is designed to handle molecular dynamics simulations, sampling, and SCF (self-consistent field) calculations for NEP. Below is a step-by-step guide explaining how the script works and what each part does.</p>
-<h3 id="1-slurm-directives">1. <strong>SLURM Directives</strong></h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>#!/bin/bash -l
-<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>#SBATCH -p intel-sc3,intel-sc3-32c
-<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>#SBATCH -q huge
-<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>#SBATCH -N 1
-<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a>#SBATCH -J workflow
-<a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a>#SBATCH -o workflow.log
-<a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a>#SBATCH --ntasks-per-node=1
+<p><strong>Script Location:</strong> <code>Scripts/workflow/</code></p>
+<h2 id="overview">Overview</h2>
+<p>This script automates one iteration of NEP active learning. The typical workflow includes:</p>
+<table>
+<thead>
+<tr>
+<th>Step</th>
+<th>Action</th>
+<th>Purpose</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>1</td>
+<td>Run MD simulations</td>
+<td>Generate candidate structures with current NEP model</td>
+</tr>
+<tr>
+<td>2</td>
+<td>Filter structures</td>
+<td>Remove unphysical configurations (short distances, large boxes)</td>
+</tr>
+<tr>
+<td>3</td>
+<td>Sample structures</td>
+<td>Select diverse or uncertain structures for DFT</td>
+</tr>
+<tr>
+<td>4</td>
+<td>Run SCF calculations</td>
+<td>Compute DFT reference energies/forces</td>
+</tr>
+<tr>
+<td>5</td>
+<td>NEP prediction</td>
+<td>Check model accuracy on new structures</td>
+</tr>
+</tbody>
+</table>
+<p>Unlike menu-driven modules, this workflow is a shell script that you customize and run directly:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>bash<span class="w"> </span>Scripts/workflow/workflow_active_learning_dev.sh
+</code></pre></div>
+<p>The sections below explain the main blocks in the script and what each part does.</p>
+<h2 id="1-slurm-directives">1. <strong>SLURM Directives</strong></h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>#!/bin/bash -l
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>#SBATCH -p intel-sc3,intel-sc3-32c
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>#SBATCH -q huge
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>#SBATCH -N 1
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>#SBATCH -J workflow
+<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>#SBATCH -o workflow.log
+<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a>#SBATCH --ntasks-per-node=1
 </code></pre></div>
 <p>The SLURM directives are used to define how the job will be submitted to the cluster:</p>
 <ul>
@@ -1536,28 +1577,28 @@ <h3 id="1-slurm-directives">1. <strong>SLURM Directives</strong></h3>
 <li><code>--ntasks-per-node=1</code> specifies that only one task should run per node.</li>
 </ul>
 <p><strong><u>NOTE:</u></strong> If your machine does not have the SLURM environment, you can also run the script directly from the command line. For example:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>nohup bash workflow_active_learning_dev.sh &amp;&gt;workflow.log &amp;
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>nohup bash workflow_active_learning_dev.sh &amp;&gt;workflow.log &amp;
 </code></pre></div>
-<h3 id="2-basic-setup">2. <strong>Basic Setup</strong></h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>cd $SLURM_SUBMIT_DIR 
+<h2 id="2-basic-setup">2. <strong>Basic Setup</strong></h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>cd $SLURM_SUBMIT_DIR 
 </code></pre></div>
 <p>Ensure the working directory is correct, and that all necessary files are present for the job.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  # Load the submit template
-<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>python_pynep=python  # Python executable for the deprecated pynep branch if needed
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  # Load the submit template
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>python_pynep=python  # Python executable for the deprecated pynep branch if needed
 </code></pre></div>
 <ul>
 <li><code>GPUMDkit_path</code> is the environment variable that stores the path for the <code>GPUMDkit</code> .</li>
 <li><code>python_pynep</code> points to the Python environment used for the deprecated <code>pynep</code>-related branch if needed.</li>
 </ul>
 <hr />
-<h3 id="3-variable-definitions">3. <strong>Variable Definitions</strong></h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>work_dir=${PWD}  # Set the working directory
-<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>prefix_name=LiF_iter01  # Prefix for calculations
-<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>min_dist=1.4  # Minimum atom distance
-<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a>box_limit=13  # Simulation box limit
-<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>max_fp_num=50  # Maximum number of single point calculations
-<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a>sample_method=pynep  # Sampling method (options: uniform, random, pynep)
-<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a>pynep_sample_dist=0.01  # Sampling distance for pynep
+<h2 id="3-variable-definitions">3. <strong>Variable Definitions</strong></h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>work_dir=${PWD}  # Set the working directory
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>prefix_name=LiF_iter01  # Prefix for calculations
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>min_dist=1.4  # Minimum atom distance
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>box_limit=13  # Simulation box limit
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>max_fp_num=50  # Maximum number of single point calculations
+<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>sample_method=pynep  # Sampling method (options: uniform, random, pynep)
+<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>pynep_sample_dist=0.01  # Sampling distance for pynep
 </code></pre></div>
 <p>You can customize:</p>
 <ul>
@@ -1567,20 +1608,20 @@ <h3 id="3-variable-definitions">3. <strong>Variable Definitions</strong></h3>
 <li><code>pynep_sample_dist</code> is the sampling distance for <code>pynep</code>.</li>
 </ul>
 <hr />
-<h3 id="4-check-required-files">4. <strong>Check Required Files</strong></h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ -f run.in ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>    # Check for the required files before proceeding.
-<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>else
-<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>    echo &quot;Please put nep.in nep.txt train.xyz run.in INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.&quot;
-<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>    exit 1
-<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>fi
+<h2 id="4-check-required-files">4. <strong>Check Required Files</strong></h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ -f run.in ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>    # Check for the required files before proceeding.
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>else
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>    echo &quot;Please put nep.in nep.txt train.xyz run.in INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.&quot;
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a>    exit 1
+<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>fi
 </code></pre></div>
 <p>Make sure the necessary files (<code>nep.txt</code>, <code>nep.in</code>, <code>train.xyz</code>, <code>run.in</code>, <code>INCAR</code>, <code>POTCAR</code>, <code>KPOINTS</code>) are available in the working directory. If any of these are missing, the script will terminate. <code>train.xyz</code> and <code>nep.txt</code> are used for <code>pynep</code> sampling, and <code>run.in</code> is the simulation parameters of MD in the current iteration.</p>
 <hr />
-<h3 id="5-file-organization">5. <strong>File Organization</strong></h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>mkdir 00.modev common
-<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>mv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common
-<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>cp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev
+<h2 id="5-file-organization">5. <strong>File Organization</strong></h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>mkdir 00.modev common
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>mv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>cp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev
 </code></pre></div>
 <p>The script organizes the working files into two folders:</p>
 <ul>
@@ -1588,53 +1629,53 @@ <h3 id="5-file-organization">5. <strong>File Organization</strong></h3>
 <li><code>common</code>: For shared resources such as <code>nep.txt</code>, <code>run.in</code>, and the structure files, etc.</li>
 </ul>
 <hr />
-<h3 id="6-molecular-dynamics-simulation-submission">6. <strong>Molecular Dynamics Simulation Submission</strong></h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>submit_gpumd_array modev ${sample_struct_num}
-<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>sbatch submit.slurm
+<h2 id="6-molecular-dynamics-simulation-submission">6. <strong>Molecular Dynamics Simulation Submission</strong></h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>submit_gpumd_array modev ${sample_struct_num}
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>sbatch submit.slurm
 </code></pre></div>
 <p>After preparing the input files, the script submits an array of molecular dynamics (MD) tasks using <code>submit_gpumd_array</code>.</p>
 <hr />
-<h3 id="7-monitoring-task-completion">7. <strong>Monitoring Task Completion</strong></h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>while true; do
-<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>    logs=$(find &quot;${work_dir}/00.modev/&quot; -type f -name log -path &quot;*/sample_*/log&quot;)
-<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>    finished_tasks_md=$(grep &quot;Finished running GPUMD.&quot; $logs | wc -l)
-<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>    error_tasks_md=$(grep &quot;Error&quot; $logs | wc -l)
-<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a>
-<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>    if [ &quot;$error_tasks_md&quot; -ne 0 ]; then
-<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a>        echo &quot;Error: MD simulation encountered an error.&quot;
-<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a>        exit 1
-<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a>    fi
-<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a>    if [ $finished_tasks_md -eq $sample_struct_num ]; then
-<a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a>        break
-<a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></a>    fi
-<a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a>    sleep 30
-<a id="__codelineno-8-14" name="__codelineno-8-14" href="#__codelineno-8-14"></a>done
+<h2 id="7-monitoring-task-completion">7. <strong>Monitoring Task Completion</strong></h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>while true; do
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>    logs=$(find &quot;${work_dir}/00.modev/&quot; -type f -name log -path &quot;*/sample_*/log&quot;)
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>    finished_tasks_md=$(grep &quot;Finished running GPUMD.&quot; $logs | wc -l)
+<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a>    error_tasks_md=$(grep &quot;Error&quot; $logs | wc -l)
+<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>
+<a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a>    if [ &quot;$error_tasks_md&quot; -ne 0 ]; then
+<a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a>        echo &quot;Error: MD simulation encountered an error.&quot;
+<a id="__codelineno-9-8" name="__codelineno-9-8" href="#__codelineno-9-8"></a>        exit 1
+<a id="__codelineno-9-9" name="__codelineno-9-9" href="#__codelineno-9-9"></a>    fi
+<a id="__codelineno-9-10" name="__codelineno-9-10" href="#__codelineno-9-10"></a>    if [ $finished_tasks_md -eq $sample_struct_num ]; then
+<a id="__codelineno-9-11" name="__codelineno-9-11" href="#__codelineno-9-11"></a>        break
+<a id="__codelineno-9-12" name="__codelineno-9-12" href="#__codelineno-9-12"></a>    fi
+<a id="__codelineno-9-13" name="__codelineno-9-13" href="#__codelineno-9-13"></a>    sleep 30
+<a id="__codelineno-9-14" name="__codelineno-9-14" href="#__codelineno-9-14"></a>done
 </code></pre></div>
 <p>The script continuously checks whether all MD tasks have finished by searching for a <code>Finished running GPUMD.</code> message in the logs. If an error is encountered, the script terminates.</p>
 <hr />
-<h3 id="8-analysis-and-filtering">8. <strong>Analysis and Filtering</strong></h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>mkdir ${work_dir}/01.select
-<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>...
+<h2 id="8-analysis-and-filtering">8. <strong>Analysis and Filtering</strong></h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>mkdir ${work_dir}/01.select
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>...
 </code></pre></div>
 <p>In the <code>01.select</code> folder, all structures in the trajectory file <code>dump.xyz</code> during the MD process will be analyzed and filtered to avoid the generation of non-physical structures as much as possible. Specifically, the <code>get_min_dist.py</code>, <code>filter_structures_by_distance.py</code> and <code>filter_exyz_by_box.py</code> scripts will be employed to check whether there are situations where the distance between atoms is too close or the simulated box exceeds the limit value, and such structures will be filtered out.</p>
 <hr />
-<h3 id="9-sampling-methods">9. <strong>Sampling Methods</strong></h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>case $sample_method in
-<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>    &quot;uniform&quot;)
-<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>    &quot;random&quot;)
-<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a>    &quot;pynep&quot;)
+<h2 id="9-sampling-methods">9. <strong>Sampling Methods</strong></h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>case $sample_method in
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>    &quot;uniform&quot;)
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>    &quot;random&quot;)
+<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a>    &quot;pynep&quot;)
 </code></pre></div>
 <p>The script supports three sampling methods: <code>uniform</code>, <code>random</code>, and <code>pynep</code>. It selects structures according to the chosen method and checks if the number exceeds <code>max_fp_num</code>, ensuring the final structure count is within limits.</p>
 <hr />
-<h3 id="10-scf-calculations">10. <strong>SCF Calculations</strong></h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>submit_vasp_array scf ${selected_struct_num} ${prefix_name}
+<h2 id="10-scf-calculations">10. <strong>SCF Calculations</strong></h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>submit_vasp_array scf ${selected_struct_num} ${prefix_name}
 </code></pre></div>
 <p>After sampling, SCF calculations are submitted using <code>submit_vasp_array</code>. The process is similar to the MD submission, but for SCF calculations.</p>
 <hr />
-<h3 id="11-prediction-step">11. <strong>Prediction Step</strong></h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>submit_nep_prediction
+<h2 id="11-prediction-step">11. <strong>Prediction Step</strong></h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>submit_nep_prediction
 </code></pre></div>
-<p>The final step involves submitting the NEP prediction task to check  the accuracy of the NEP model. </p>
+<p>The final step involves submitting the NEP prediction task to check the accuracy of the NEP model. </p>
 <hr />
 <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>
 
diff --git a/docs/htmls/en/analyzer_scripts.html b/docs/htmls/en/analyzer_scripts.html
index 07f5b94..b6bbf48 100644
--- a/docs/htmls/en/analyzer_scripts.html
+++ b/docs/htmls/en/analyzer_scripts.html
@@ -143,7 +143,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#overview" class="md-skip">
+        <a href="#what-it-does" class="md-skip">
           Skip to content
         </a>
       
@@ -628,6 +628,28 @@
     </label>
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
+        <li class="md-nav__item">
+  <a href="#what-it-does" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        What it does
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#before-you-start" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Before you start
+      
+    </span>
+  </a>
+  
+</li>
+      
         <li class="md-nav__item">
   <a href="#overview" class="md-nav__link">
     <span class="md-ellipsis">
@@ -637,6 +659,17 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#interactive-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive Mode
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -648,6 +681,17 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#chemical-species" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Chemical Species
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -670,6 +714,34 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="Minimum Distance Checks">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#without-pbc-fast" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Without PBC (Fast)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#with-pbc-accurate" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        With PBC (Accurate)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -745,14 +817,114 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#example-commands" class="md-nav__link">
+  <a href="#outlier-detection" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Outlier Detection
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#time-estimation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Time Estimation
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Time Estimation">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gpumd-remaining-time" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Example Commands
+        GPUMD Remaining Time
       
     </span>
   </a>
   
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#nep-remaining-time" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP Remaining Time
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#probability-density-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Probability Density Analysis
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-workflows" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example Workflows
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Example Workflows">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#structure-quality-check" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Structure Quality Check
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#structure-filtering-pipeline" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Structure Filtering Pipeline
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#diffusion-channel-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Diffusion Channel Analysis
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -1353,6 +1525,28 @@
     </label>
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
+        <li class="md-nav__item">
+  <a href="#what-it-does" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        What it does
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#before-you-start" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Before you start
+      
+    </span>
+  </a>
+  
+</li>
+      
         <li class="md-nav__item">
   <a href="#overview" class="md-nav__link">
     <span class="md-ellipsis">
@@ -1362,6 +1556,17 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#interactive-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive Mode
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1373,6 +1578,17 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#chemical-species" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Chemical Species
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1395,6 +1611,34 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="Minimum Distance Checks">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#without-pbc-fast" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Without PBC (Fast)
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#with-pbc-accurate" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        With PBC (Accurate)
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1470,14 +1714,114 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#example-commands" class="md-nav__link">
+  <a href="#outlier-detection" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Outlier Detection
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#time-estimation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Time Estimation
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Time Estimation">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gpumd-remaining-time" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        GPUMD Remaining Time
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#nep-remaining-time" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP Remaining Time
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#probability-density-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Probability Density Analysis
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#example-workflows" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Example Workflows
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Example Workflows">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#structure-quality-check" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Structure Quality Check
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#structure-filtering-pipeline" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Structure Filtering Pipeline
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#diffusion-channel-analysis" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Example Commands
+        Diffusion Channel Analysis
       
     </span>
   </a>
   
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -1502,10 +1846,14 @@
 
 <div align="center">
   <h1>🔍 Analyzer Scripts</h1>
-  <p style="text-align: justify;">Analyzer scripts provide structure statistics, distance checks, filters, and composition analysis for extxyz datasets.</p>
+  <p style="text-align: justify;">Analyzer scripts provide structure statistics, distance checks, filters, composition analysis, outlier detection, and time estimation for extxyz datasets.</p>
 </div>
 
-<p><strong>Script Location:</strong> <code>Scripts/analyzer/</code></p>
+<h2 id="what-it-does">What it does</h2>
+<p>This module helps you inspect, filter, and validate structure datasets. You can check composition, analyze property ranges, detect short contacts, filter structures by various criteria, find outliers in NEP training data, and estimate remaining simulation time.</p>
+<h2 id="before-you-start">Before you start</h2>
+<p><strong>Script location:</strong> <code>Scripts/analyzer/</code></p>
+<p>Make sure GPUMDkit is installed. See <a href="quick_start.html">Quick Start</a> for installation instructions.</p>
 <h2 id="overview">Overview</h2>
 <table>
 <thead>
@@ -1519,133 +1867,345 @@ <h2 id="overview">Overview</h2>
 <tr>
 <td>Composition</td>
 <td><code>gpumdkit.sh -analyze_comp train.xyz</code></td>
-<td>group structures by chemical composition</td>
+<td>Group structures by chemical composition</td>
 </tr>
 <tr>
 <td>Chemical species</td>
 <td><code>gpumdkit.sh -chem_species train.xyz</code></td>
-<td>list species in a file</td>
+<td>List species in a file</td>
 </tr>
 <tr>
 <td>Property range</td>
 <td><code>gpumdkit.sh -range train.xyz force</code></td>
-<td>inspect energy/force/virial range</td>
+<td>Inspect energy/force/virial range</td>
 </tr>
 <tr>
 <td>Minimum distance</td>
 <td><code>gpumdkit.sh -min_dist dump.xyz</code></td>
-<td>fast distance check without PBC</td>
+<td>Fast distance check without PBC</td>
 </tr>
 <tr>
 <td>Minimum distance with PBC</td>
 <td><code>gpumdkit.sh -min_dist_pbc dump.xyz</code></td>
-<td>accurate distance check with PBC</td>
+<td>Accurate distance check with PBC</td>
 </tr>
 <tr>
 <td>Charge balance</td>
 <td><code>gpumdkit.sh -cbc train.xyz</code></td>
-<td>oxidation-state balance check</td>
+<td>Oxidation-state balance check</td>
 </tr>
 <tr>
 <td>Distance filter</td>
 <td><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code></td>
-<td>remove structures with short contacts</td>
+<td>Remove structures with short contacts</td>
 </tr>
 <tr>
 <td>Box filter</td>
 <td><code>gpumdkit.sh -filter_box dump.xyz 13</code></td>
-<td>remove structures with too-large box edges</td>
+<td>Remove structures with too-large box edges</td>
 </tr>
 <tr>
 <td>Property filter</td>
 <td><code>gpumdkit.sh -filter_value train.xyz force 20</code></td>
-<td>filter by energy/force/virial threshold</td>
+<td>Filter by energy/force/virial threshold</td>
 </tr>
 <tr>
 <td>Pair-distance range</td>
 <td><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code></td>
-<td>extract structures by pair distance</td>
+<td>Extract structures by pair distance</td>
+</tr>
+<tr>
+<td>Outlier detection</td>
+<td>Menu 502</td>
+<td>Find high-RMSE structures in training set</td>
+</tr>
+<tr>
+<td>Probability density</td>
+<td><code>gpumdkit.sh -pda &lt;ref&gt; &lt;traj&gt; &lt;element&gt; &lt;interval&gt;</code></td>
+<td>3D probability density for diffusion channels</td>
+</tr>
+<tr>
+<td>GPUMD time</td>
+<td><code>gpumdkit.sh -time gpumd</code></td>
+<td>Estimate remaining GPUMD run time</td>
+</tr>
+<tr>
+<td>NEP time</td>
+<td><code>gpumdkit.sh -time nep</code></td>
+<td>Estimate remaining NEP training time</td>
 </tr>
 </tbody>
 </table>
+<hr />
+<h2 id="interactive-mode">Interactive Mode</h2>
+<p>Open GPUMDkit and choose <code>5) Analyzer</code>:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh
+</code></pre></div>
+<p>The analyzer menu is:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>+------------------------------------------------------+
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>|                    ANALYZER TOOLS                    |
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>+------------------------------------------------------+
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>| 501) Analyze composition of extxyz                   |
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>| 502) Find outliers of extxyz                         |
+<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>| 503) Analyze chemical species of extxyz              |
+<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a>| 504) Check charge balance of extxyz                  |
+<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a>| 505) Analyze energy/force/virial range               |
+<a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a>| 506) Filter structures by minimum distance           |
+<a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a>| 507) Get minimum interatomic distance                |
+<a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a>| 508) Probability density analysis                    |
+<a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a>+------------------------------------------------------+
+<a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a>| 000) Return to the main menu                         |
+<a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></a>+------------------------------------------------------+
+<a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a>Input the function number:
+</code></pre></div>
+<p>Most analyzer functions also have direct CLI shortcuts, which are listed in the overview table and in the sections below.</p>
+<hr />
 <h2 id="composition-analysis">Composition Analysis</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
+<p><code>analyze_composition.py</code> analyzes the composition of your extxyz file and lets you export subsets.</p>
+<p><strong>What it does:</strong> Groups structures by chemical composition and shows how many structures belong to each composition. You can export subsets by composition.</p>
+<p><strong>CLI mode:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
 </code></pre></div>
-<p>Example output:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>Index    Compositions           N atoms      Count
-<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>---------------------------------------------------
-<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>1        Li56O96Zr16La24        192          51
-<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>---------------------------------------------------
-<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>Enter index to export (e.g., &#39;1,2&#39;, &#39;2-3&#39;, &#39;all&#39;), or press Enter to skip:
+<p><strong>Interactive mode:</strong> Choose <code>501</code> from the analyzer menu.</p>
+<p><strong>Output example:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>Index    Compositions           N atoms      Count
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>---------------------------------------------------
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>1        Li56O96Zr16La24        192          51
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>---------------------------------------------------
+<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>Enter index to export (e.g., &#39;1,2&#39;, &#39;2-3&#39;, &#39;all&#39;), or press Enter to skip:
 </code></pre></div>
 <p>This is useful when <code>train.xyz</code> contains structures from different systems or different cell sizes. You can export a subset by composition from the interactive prompt.</p>
+<hr />
+<h2 id="chemical-species">Chemical Species</h2>
+<p><code>analyze_chem_species.py</code> lists all unique chemical species in an extxyz file.</p>
+<p><strong>Input file:</strong> <code>train.xyz</code> (extxyz format)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-chem_species<span class="w"> </span>train.xyz
+</code></pre></div>
+<hr />
 <h2 id="property-range-analysis">Property Range Analysis</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force
-<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>energy
-<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>virial
-<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist
+<p><code>energy_force_virial_analyzer.py</code> calculates and visualizes the range of properties from an extxyz file.</p>
+<p><strong>Input file:</strong> <code>train.xyz</code> (extxyz format)</p>
+<p><strong>Supported properties:</strong> <code>energy</code>, <code>force</code>, <code>virial</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>energy
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>virial
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist<span class="w">    </span><span class="c1"># Show histogram</span>
+</code></pre></div>
+<p><strong>Output example:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>Force range: 0.03210566767721861 to 9.230115912468435
 </code></pre></div>
-<p>Use <code>hist</code> to show a histogram of the selected property.</p>
+<p>With <code>hist</code> option:</p>
 <div align="center">
   <img src="../../Gallery/range_force.png" alt="Force range histogram" width="52%" />
 </div>
 
+<hr />
 <h2 id="minimum-distance-checks">Minimum Distance Checks</h2>
-<p>Fast check without PBC:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist<span class="w"> </span>dump.xyz
+<h3 id="without-pbc-fast">Without PBC (Fast)</h3>
+<p><code>get_min_dist.py</code> calculates minimum interatomic distances without considering periodic boundary conditions. Fast but may be inaccurate for periodic systems.</p>
+<p><strong>What it does:</strong> Reports the minimum distance between each pair of elements in every frame, ignoring periodic boundary conditions.</p>
+<p><strong>CLI mode:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist<span class="w"> </span>dump.xyz
 </code></pre></div>
-<p>Accurate check with PBC:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
+<p><strong>Interactive mode:</strong> Choose <code>507</code> from the analyzer menu.</p>
+<p><strong>Output example:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>+---------------------------+
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>|   PBC ignored for speed   |
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>| use -min_dist_pbc for PBC |
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>+---------------------------+
+<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a>Minimum interatomic distances:
+<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>+---------------------------+
+<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a>| Atom Pair |  Distance (Å) |
+<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a>+---------------------------+
+<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a>|   Li-Li   |     1.696     |
+<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a>|   Li-O    |     1.587     |
+<a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a>|   O-O     |     2.480     |
+<a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></a>+---------------------------+
+<a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a>Overall min_distance: 1.587 Å
 </code></pre></div>
-<p>Typical output:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>Minimum interatomic distances (with PBC):
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>+---------------------------+
-<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>| Atom Pair |  Distance (A) |
-<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>+---------------------------+
-<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>|   Li-Li   |     1.696     |
-<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>|   Li-O    |     1.587     |
-<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>|   O-O     |     2.355     |
-<a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a>+---------------------------+
-<a id="__codelineno-5-9" name="__codelineno-5-9" href="#__codelineno-5-9"></a>Overall min_distance: 1.587 A
+<p><strong>Notes:</strong> Use this for a quick check. For periodic systems, prefer <code>-min_dist_pbc</code> for accurate results.</p>
+<h3 id="with-pbc-accurate">With PBC (Accurate)</h3>
+<p><code>get_min_dist_pbc.py</code> calculates minimum interatomic distances considering periodic boundary conditions.</p>
+<p><strong>What it does:</strong> Reports the minimum distance between each pair of elements, accounting for periodic boundary conditions.</p>
+<p><strong>CLI mode:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
 </code></pre></div>
-<p>The PBC version considers periodic boundary conditions.</p>
+<p><strong>Interactive mode:</strong> Choose <code>507</code> from the analyzer menu and answer <code>y</code> when asked whether to consider PBC.</p>
+<p><strong>Output example:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>Minimum interatomic distances (with PBC):
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>+---------------------------+
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>| Atom Pair |  Distance (Å) |
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a>+---------------------------+
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>|   Li-Li   |     1.696     |
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>|   Li-O    |     1.587     |
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a>|   O-O     |     2.355     |
+<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>+---------------------------+
+<a id="__codelineno-10-9" name="__codelineno-10-9" href="#__codelineno-10-9"></a>Overall min_distance: 1.587 Å
+</code></pre></div>
+<hr />
 <h2 id="filtering-structures">Filtering Structures</h2>
 <h3 id="filter-by-minimum-distance">Filter by Minimum Distance</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
+<p><code>filter_structures_by_distance_pbc.py</code> removes structures with any interatomic distance below a threshold.</p>
+<p><strong>Input file:</strong> <code>dump.xyz</code> (extxyz format)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
 </code></pre></div>
-<p>This removes structures with any interatomic distance below <code>1.0 A</code>.</p>
+<p>This removes structures with any interatomic distance below <code>1.0 Å</code>.</p>
 <h3 id="filter-by-box-size">Filter by Box Size</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
+<p><code>filter_exyz_by_box.py</code> filters structures by box-edge length.</p>
+<p><strong>Input file:</strong> <code>dump.xyz</code> (extxyz format)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
 </code></pre></div>
-<p>This filters structures by box-edge length.</p>
+<p>This keeps structures where all box edges are below <code>13 Å</code>.</p>
 <h3 id="filter-by-property-value">Filter by Property Value</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span><span class="m">20</span>
-<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>energy<span class="w"> </span><span class="m">5</span>
+<p><code>filter_exyz_by_value.py</code> filters structures by energy, force, or virial threshold.</p>
+<p><strong>Input file:</strong> <code>train.xyz</code> (extxyz format)</p>
+<p><strong>Supported properties:</strong> <code>energy</code>, <code>force</code>, <code>virial</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span><span class="m">20</span>
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>energy<span class="w"> </span><span class="m">5</span>
 </code></pre></div>
+<p>This filters out structures with force components exceeding <code>20 eV/Å</code> (or energy exceeding <code>5 eV/atom</code>).</p>
 <h3 id="filter-by-pair-distance-range">Filter by Pair-Distance Range</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-filter_range<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>.8<span class="w"> </span><span class="m">2</span>.0
+<p><code>filter_dist_range.py</code> extracts structures where a specific element-pair distance falls within a given range.</p>
+<p><strong>Input file:</strong> <code>dump.xyz</code> (extxyz format)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-filter_range<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>.8<span class="w"> </span><span class="m">2</span>.0
 </code></pre></div>
-<p>This extracts structures where the Li-Li minimum distance is between <code>1.8 A</code> and <code>2.0 A</code>.</p>
+<p>This extracts structures where the Li-Li minimum distance is between <code>1.8 Å</code> and <code>2.0 Å</code>. Output: <code>filtered_Li_Li_1.8_2.0.xyz</code>.</p>
+<hr />
 <h2 id="charge-balance-check">Charge Balance Check</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-cbc<span class="w"> </span>train.xyz
+<p><code>charge_balance_check.py</code> checks the oxidation-state balance of structures.</p>
+<p><strong>Input file:</strong> <code>train.xyz</code> (extxyz format)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-cbc<span class="w"> </span>train.xyz
 </code></pre></div>
-<p>Outputs may include:</p>
+<p><strong>Output files:</strong></p>
 <ul>
-<li><code>balanced.xyz</code></li>
-<li><code>unbalanced.xyz</code></li>
-<li><code>indices.txt</code></li>
+<li><code>balanced.xyz</code> — structures with balanced charges</li>
+<li><code>unbalanced.xyz</code> — structures with unbalanced charges</li>
+<li><code>indices.txt</code> — indices of balanced structures</li>
 </ul>
 <p>This is intended for systems where common oxidation states are meaningful.</p>
-<h2 id="example-commands">Example Commands</h2>
-<p>Property and distance checks:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
-<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist
-<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>energy<span class="w"> </span>hist
-<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>train.xyz
+<hr />
+<h2 id="outlier-detection">Outlier Detection</h2>
+<p><code>find_outliers.py</code> finds outlier structures in NEP training data based on RMSE thresholds for energy, force, and stress.</p>
+<p><strong>Input files:</strong> <code>energy_train.out</code>, <code>force_train.out</code>, <code>stress_train.out</code>, <code>train.xyz</code></p>
+<p>These files are generated during NEP training. The script compares DFT vs NEP predictions and identifies structures with large errors.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a><span class="c1"># Interactive mode</span>
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w">    </span><span class="c1"># Select: 5) Analyzer → 502) Find outliers of extxyz</span>
+</code></pre></div>
+<p><strong>Interactive prompts:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>Enter energy RMSE threshold (meV/atom): 1
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>Enter force RMSE threshold (meV/Å): 60
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>Enter stress RMSE threshold (GPa): 0.03
+</code></pre></div>
+<p><strong>Output files:</strong></p>
+<ul>
+<li><code>selected.xyz</code> — structures exceeding the RMSE thresholds (outliers)</li>
+<li><code>remained.xyz</code> — structures within the thresholds</li>
+<li><code>selected_remained.png</code> — comparison plot</li>
+</ul>
+<p><strong>Use case:</strong> After NEP training, use this to identify problematic structures that contribute most to the error. Remove or improve these structures to enhance the training set.</p>
+<hr />
+<h2 id="time-estimation">Time Estimation</h2>
+<h3 id="gpumd-remaining-time">GPUMD Remaining Time</h3>
+<p><code>time_consuming_gpumd.sh</code> estimates the remaining time for a GPUMD simulation.</p>
+<p><strong>Input files:</strong> <code>run.in</code>, <code>thermo.out</code> (in the current GPUMD working directory)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-time<span class="w"> </span>gpumd
+</code></pre></div>
+<p><strong>Output example:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>----------------- System Information ----------------
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>total frames: 1050000
+<a id="__codelineno-19-3" name="__codelineno-19-3" href="#__codelineno-19-3"></a>-----------------------------------------------------
+<a id="__codelineno-19-4" name="__codelineno-19-4" href="#__codelineno-19-4"></a>Current Frame  Speed (steps/s)   Total Time       Time Left       Estimated End
+<a id="__codelineno-19-5" name="__codelineno-19-5" href="#__codelineno-19-5"></a>-------------   -------------   -------------   -------------   -----------------
+<a id="__codelineno-19-6" name="__codelineno-19-6" href="#__codelineno-19-6"></a>    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04
+<a id="__codelineno-19-7" name="__codelineno-19-7" href="#__codelineno-19-7"></a>    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56
+</code></pre></div>
+<h3 id="nep-remaining-time">NEP Remaining Time</h3>
+<p><code>time_consuming_nep.sh</code> estimates the remaining time for NEP training.</p>
+<p><strong>Input files:</strong> <code>loss.out</code> (in the current NEP working directory)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-time<span class="w"> </span>nep
+</code></pre></div>
+<p><strong>Output example:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>+-----------------+-----------+-----------------+---------------------+
+<a id="__codelineno-21-2" name="__codelineno-21-2" href="#__codelineno-21-2"></a>|       Step      | Time Diff |    Time Left    |    Finish Time      |
+<a id="__codelineno-21-3" name="__codelineno-21-3" href="#__codelineno-21-3"></a>+-----------------+-----------+-----------------+---------------------+
+<a id="__codelineno-21-4" name="__codelineno-21-4" href="#__codelineno-21-4"></a>| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |
+<a id="__codelineno-21-5" name="__codelineno-21-5" href="#__codelineno-21-5"></a>| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |
+<a id="__codelineno-21-6" name="__codelineno-21-6" href="#__codelineno-21-6"></a>| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |
+<a id="__codelineno-21-7" name="__codelineno-21-7" href="#__codelineno-21-7"></a>+-----------------+-----------+-----------------+---------------------+
+</code></pre></div>
+<hr />
+<h2 id="probability-density-analysis">Probability Density Analysis</h2>
+<p><code>probability_density_analysis.py</code> calculates 3D probability density of mobile ions for diffusion channel analysis.</p>
+<p><strong>Input files:</strong> Reference structure (POSCAR), trajectory file (extxyz)</p>
+<p><strong>CLI mode:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a>gpumdkit.sh<span class="w"> </span>-pda<span class="w"> </span>LLZO.vasp<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">0</span>.25
+</code></pre></div>
+<p><strong>Arguments:</strong></p>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>LLZO.vasp</code></td>
+<td>Reference structure (POSCAR format)</td>
+</tr>
+<tr>
+<td><code>dump.xyz</code></td>
+<td>Trajectory file (extxyz format)</td>
+</tr>
+<tr>
+<td><code>Li</code></td>
+<td>Target mobile species</td>
+</tr>
+<tr>
+<td><code>0.25</code></td>
+<td>Grid interval for the probability density (Å)</td>
+</tr>
+</tbody>
+</table>
+<p><strong>Output:</strong> <code>probability_density_0.25.vasp</code> — probability density grid in VASP format for visualization with VESTA or similar tools.</p>
+<p><strong>Visualization suggestions:</strong></p>
+<ol>
+<li>Open <code>probability_density_0.25.vasp</code> in VESTA</li>
+<li>Use "Edit → Data → Volumetric Data" to adjust isosurface levels</li>
+<li>Color the probability density by value to highlight preferred diffusion pathways</li>
+<li>Overlay with the crystal structure for context</li>
+</ol>
+<hr />
+<h2 id="example-workflows">Example Workflows</h2>
+<h3 id="structure-quality-check">Structure Quality Check</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-23-1" name="__codelineno-23-1" href="#__codelineno-23-1"></a><span class="c1"># 1. Check composition</span>
+<a id="__codelineno-23-2" name="__codelineno-23-2" href="#__codelineno-23-2"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
+<a id="__codelineno-23-3" name="__codelineno-23-3" href="#__codelineno-23-3"></a>
+<a id="__codelineno-23-4" name="__codelineno-23-4" href="#__codelineno-23-4"></a><span class="c1"># 2. Check energy/force range</span>
+<a id="__codelineno-23-5" name="__codelineno-23-5" href="#__codelineno-23-5"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist
+<a id="__codelineno-23-6" name="__codelineno-23-6" href="#__codelineno-23-6"></a>
+<a id="__codelineno-23-7" name="__codelineno-23-7" href="#__codelineno-23-7"></a><span class="c1"># 3. Check minimum distances</span>
+<a id="__codelineno-23-8" name="__codelineno-23-8" href="#__codelineno-23-8"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>train.xyz
+<a id="__codelineno-23-9" name="__codelineno-23-9" href="#__codelineno-23-9"></a>
+<a id="__codelineno-23-10" name="__codelineno-23-10" href="#__codelineno-23-10"></a><span class="c1"># 4. Find outliers (after NEP training)</span>
+<a id="__codelineno-23-11" name="__codelineno-23-11" href="#__codelineno-23-11"></a><span class="c1"># Interactive: 5) Analyzer → 502</span>
+</code></pre></div>
+<h3 id="structure-filtering-pipeline">Structure Filtering Pipeline</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-24-1" name="__codelineno-24-1" href="#__codelineno-24-1"></a><span class="c1"># 1. Filter by minimum distance</span>
+<a id="__codelineno-24-2" name="__codelineno-24-2" href="#__codelineno-24-2"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
+<a id="__codelineno-24-3" name="__codelineno-24-3" href="#__codelineno-24-3"></a>
+<a id="__codelineno-24-4" name="__codelineno-24-4" href="#__codelineno-24-4"></a><span class="c1"># 2. Filter by box size</span>
+<a id="__codelineno-24-5" name="__codelineno-24-5" href="#__codelineno-24-5"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>filtered_dist_pbc.xyz<span class="w"> </span><span class="m">13</span>
+<a id="__codelineno-24-6" name="__codelineno-24-6" href="#__codelineno-24-6"></a>
+<a id="__codelineno-24-7" name="__codelineno-24-7" href="#__codelineno-24-7"></a><span class="c1"># 3. Filter by force threshold</span>
+<a id="__codelineno-24-8" name="__codelineno-24-8" href="#__codelineno-24-8"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>filtered_box.xyz<span class="w"> </span>force<span class="w"> </span><span class="m">20</span>
 </code></pre></div>
-<p>Filtering examples:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
-<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>filtered_dist.xyz<span class="w"> </span><span class="m">13</span>
+<h3 id="diffusion-channel-analysis">Diffusion Channel Analysis</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-25-1" name="__codelineno-25-1" href="#__codelineno-25-1"></a><span class="c1"># 1. Calculate probability density</span>
+<a id="__codelineno-25-2" name="__codelineno-25-2" href="#__codelineno-25-2"></a>gpumdkit.sh<span class="w"> </span>-pda<span class="w"> </span>LLZO.vasp<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">0</span>.25
+<a id="__codelineno-25-3" name="__codelineno-25-3" href="#__codelineno-25-3"></a>
+<a id="__codelineno-25-4" name="__codelineno-25-4" href="#__codelineno-25-4"></a><span class="c1"># 2. Visualize with VESTA</span>
+<a id="__codelineno-25-5" name="__codelineno-25-5" href="#__codelineno-25-5"></a><span class="c1"># Open probability_density_0.25.vasp</span>
 </code></pre></div>
 
 
diff --git a/docs/htmls/en/calculator_scripts.html b/docs/htmls/en/calculator_scripts.html
index 1ab336f..3e5a28b 100644
--- a/docs/htmls/en/calculator_scripts.html
+++ b/docs/htmls/en/calculator_scripts.html
@@ -728,75 +728,25 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#ferroelectric-and-polar-material-tools" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        Ferroelectric and Polar Material Tools
-      
-    </span>
-  </a>
-  
-    <nav class="md-nav" aria-label="Ferroelectric and Polar Material Tools">
-      <ul class="md-nav__list">
-        
-          <li class="md-nav__item">
-  <a href="#build-neighbor-lists" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        Build Neighbor Lists
-      
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#calculate-displacements" class="md-nav__link">
+  <a href="#rdf-calculation-with-ovito" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Calculate Displacements
+        RDF Calculation with OVITO
       
     </span>
   </a>
   
 </li>
-        
-          <li class="md-nav__item">
-  <a href="#average-a-structure" class="md-nav__link">
-    <span class="md-ellipsis">
       
-        Average a Structure
-      
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#octahedral-tilt" class="md-nav__link">
+        <li class="md-nav__item">
+  <a href="#ferroelectric-and-polar-material-tools" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Octahedral Tilt
+        Ferroelectric and Polar Material Tools
       
     </span>
   </a>
   
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#abo3-polarization" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        ABO3 Polarization
-      
-    </span>
-  </a>
-  
-</li>
-        
-      </ul>
-    </nav>
-  
 </li>
       
     </ul>
@@ -1553,75 +1503,25 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#ferroelectric-and-polar-material-tools" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        Ferroelectric and Polar Material Tools
-      
-    </span>
-  </a>
-  
-    <nav class="md-nav" aria-label="Ferroelectric and Polar Material Tools">
-      <ul class="md-nav__list">
-        
-          <li class="md-nav__item">
-  <a href="#build-neighbor-lists" class="md-nav__link">
+  <a href="#rdf-calculation-with-ovito" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Build Neighbor Lists
+        RDF Calculation with OVITO
       
     </span>
   </a>
   
 </li>
-        
-          <li class="md-nav__item">
-  <a href="#calculate-displacements" class="md-nav__link">
-    <span class="md-ellipsis">
       
-        Calculate Displacements
-      
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#average-a-structure" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        Average a Structure
-      
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#octahedral-tilt" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        Octahedral Tilt
-      
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#abo3-polarization" class="md-nav__link">
+        <li class="md-nav__item">
+  <a href="#ferroelectric-and-polar-material-tools" class="md-nav__link">
     <span class="md-ellipsis">
       
-        ABO3 Polarization
+        Ferroelectric and Polar Material Tools
       
     </span>
   </a>
   
-</li>
-        
-      </ul>
-    </nav>
-  
 </li>
       
     </ul>
@@ -1697,28 +1597,28 @@ <h2 id="overview">Overview</h2>
 </tr>
 <tr>
 <td>Neighbor list</td>
-<td><code>gpumdkit.sh -calc nlist [args...]</code></td>
-<td>structure</td>
+<td><code>gpumdkit.sh -calc nlist ...</code></td>
+<td>see <a href="polar_material_analysis.html">Polar Material Analysis</a></td>
 </tr>
 <tr>
 <td>Displacement</td>
-<td><code>gpumdkit.sh -calc disp [args...]</code></td>
-<td>trajectory + neighbor list</td>
+<td><code>gpumdkit.sh -calc disp ...</code></td>
+<td>see <a href="polar_material_analysis.html">Polar Material Analysis</a></td>
 </tr>
 <tr>
 <td>Average structure</td>
-<td><code>gpumdkit.sh -calc avg-struct [args...]</code></td>
-<td>trajectory</td>
+<td><code>gpumdkit.sh -calc avg-struct ...</code></td>
+<td>see <a href="polar_material_analysis.html">Polar Material Analysis</a></td>
 </tr>
 <tr>
 <td>Octahedral tilt</td>
-<td><code>gpumdkit.sh -calc oct-tilt [args...]</code></td>
-<td>trajectory + B-O neighbor list</td>
+<td><code>gpumdkit.sh -calc oct-tilt ...</code></td>
+<td>see <a href="polar_material_analysis.html">Polar Material Analysis</a></td>
 </tr>
 <tr>
 <td>ABO3 polarization</td>
-<td><code>gpumdkit.sh -calc pol-abo3 [args...]</code></td>
-<td>trajectory + neighbor lists</td>
+<td><code>gpumdkit.sh -calc pol-abo3 ...</code></td>
+<td>see <a href="polar_material_analysis.html">Polar Material Analysis</a></td>
 </tr>
 </tbody>
 </table>
@@ -1883,12 +1783,18 @@ <h2 id="mean-square-displacement">Mean Square Displacement</h2>
 
 <h2 id="nep-property-prediction">NEP Property Prediction</h2>
 <p><code>calc_properties_with_nep.py</code> calculates energy, force, and stress for structures using a NEP model.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nep<span class="w"> </span>structures.xyz<span class="w"> </span>predictions.xyz<span class="w"> </span>nep.txt
+<p><strong>Dependency:</strong> <code>calorine</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>pip<span class="w"> </span>install<span class="w"> </span>calorine
+</code></pre></div>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nep<span class="w"> </span>structures.xyz<span class="w"> </span>predictions.xyz<span class="w"> </span>nep.txt
+</code></pre></div>
+<p>Use this function to run predictions with a trained NEP model. For best results, validate model quality on your target structures before relying on the output.</p>
+<p><strong>Tip:</strong> Before prediction, you may want to clean the extxyz metadata:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-clean_xyz<span class="w"> </span>train.xyz<span class="w"> </span>clean_train.xyz
 </code></pre></div>
-<p>This function is useful when you intentionally want to use a trained NEP model as a surrogate calculator. It should not be treated as a replacement for DFT unless the model quality has been carefully validated.</p>
 <h2 id="nep-descriptors">NEP Descriptors</h2>
 <p><code>calc_descriptors.py</code> extracts NEP descriptors for a selected element.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
 </code></pre></div>
 <p>Use cases:</p>
 <ul>
@@ -1897,8 +1803,8 @@ <h2 id="nep-descriptors">NEP Descriptors</h2>
 <li>inspect whether new data expands descriptor space.</li>
 </ul>
 <p>Plot descriptors with:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
-<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/des_umap.png" alt="Descriptor UMAP" width="52%" />
@@ -1906,8 +1812,8 @@ <h2 id="nep-descriptors">NEP Descriptors</h2>
 
 <h2 id="density-of-atomistic-states">Density of Atomistic States</h2>
 <p><code>calc_doas.py</code> calculates density of atomistic states (DOAS), following the idea proposed by <a href="https://doi.org/10.1002/anie.202215544">Wang et al.</a>.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>doas<span class="w"> </span>structures.xyz<span class="w"> </span>nep.txt<span class="w"> </span>doas.out
-<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>doas<span class="w"> </span>structures.xyz<span class="w"> </span>nep.txt<span class="w"> </span>doas.out
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
 </code></pre></div>
 <p>The script:</p>
 <ol>
@@ -1917,13 +1823,13 @@ <h2 id="density-of-atomistic-states">Density of Atomistic States</h2>
 <li>groups atomic energies by element;</li>
 <li>writes the grouped values to the output file.</li>
 </ol>
-<p>For very large systems, doing minimization and atomistic-energy extraction directly in GPUMD may be more efficient.</p>
+<p>For very large systems, running minimization and atomistic-energy extraction directly in GPUMD can be more efficient.</p>
 <div align="center">
   <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
 </div>
 
 <h2 id="neb-with-a-nep-model">NEB with a NEP Model</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>neb<span class="w"> </span>initial.xyz<span class="w"> </span>final.xyz<span class="w"> </span><span class="m">9</span><span class="w"> </span>nep.txt
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>neb<span class="w"> </span>initial.xyz<span class="w"> </span>final.xyz<span class="w"> </span><span class="m">9</span><span class="w"> </span>nep.txt
 </code></pre></div>
 <p>This runs a NEB calculation with <code>9</code> intermediate images. During execution, the script asks how atoms should be fixed:</p>
 <ul>
@@ -1933,7 +1839,11 @@ <h2 id="neb-with-a-nep-model">NEB with a NEP Model</h2>
 <li><code>position</code>: fix atoms inside a coordinate range.</li>
 </ul>
 <h2 id="structure-minimization">Structure Minimization</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>minimize<span class="w"> </span>POSCAR<span class="w"> </span>nep.txt<span class="w"> </span><span class="m">0</span>.01<span class="w"> </span><span class="m">1000</span>
+<p><code>calc_minimize.py</code> minimizes a structure using a NEP model through <code>calorine</code>.</p>
+<p><strong>Dependency:</strong> <code>calorine</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>pip<span class="w"> </span>install<span class="w"> </span>calorine
+</code></pre></div>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>minimize<span class="w"> </span>POSCAR<span class="w"> </span>nep.txt<span class="w"> </span><span class="m">0</span>.01<span class="w"> </span><span class="m">1000</span>
 </code></pre></div>
 <p>Arguments:</p>
 <table>
@@ -1967,32 +1877,48 @@ <h2 id="structure-minimization">Structure Minimization</h2>
 <li><code>minimize.xyz</code></li>
 <li><code>minimize.log</code></li>
 </ul>
-<h2 id="ferroelectric-and-polar-material-tools">Ferroelectric and Polar Material Tools</h2>
-<p>The following tools are useful for perovskite and polar-material analysis. They require <code>ferrodispcalc</code>:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
-</code></pre></div>
-<p><code>ferrodispcalc</code> currently has no associated paper to cite.</p>
-<h3 id="build-neighbor-lists">Build Neighbor Lists</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
-</code></pre></div>
-<p>This creates a neighbor-list file where each row stores one center atom and its nearest neighbor atoms.</p>
-<h3 id="calculate-displacements">Calculate Displacements</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+<h2 id="rdf-calculation-with-ovito">RDF Calculation with OVITO</h2>
+<p><code>rdf_calculator_ovito.py</code> calculates radial distribution function using OVITO's analysis tools.</p>
+<p><strong>Dependency:</strong> OVITO</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>pip<span class="w"> </span>install<span class="w"> </span>ovito
 </code></pre></div>
-<p>Use <code>-l 0.2</code> to analyze the last 20% of frames. Use <code>-s</code>, <code>-t</code>, and <code>-p</code> if you want an explicit slice.</p>
-<h3 id="average-a-structure">Average a Structure</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+<p><strong>Input file:</strong> Structure file (single frame or trajectory)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>python<span class="w"> </span>Scripts/calculators/rdf_calculator_ovito.py<span class="w"> </span>trajectory.xyz<span class="w"> </span><span class="m">6</span>.0<span class="w"> </span><span class="m">400</span>
 </code></pre></div>
-<p>This is useful before displacement or polarization analysis when a representative averaged structure is needed.</p>
-<h3 id="octahedral-tilt">Octahedral Tilt</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>octahedral_tilt.dat
+<p><strong>Parameters:</strong></p>
+<table>
+<thead>
+<tr>
+<th>Argument</th>
+<th>Meaning</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>trajectory.xyz</code></td>
+<td>Input structure file</td>
+</tr>
+<tr>
+<td><code>6.0</code></td>
+<td>Maximum distance for RDF calculation (Å)</td>
+</tr>
+<tr>
+<td><code>400</code></td>
+<td>Number of histogram bins</td>
+</tr>
+</tbody>
+</table>
+<p><strong>Visualization:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf
 </code></pre></div>
-<p>The neighbor list should usually contain six B-O neighbors for each B-site center in an <code>ABO3</code>-like structure.</p>
-<h3 id="abo3-polarization">ABO3 Polarization</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
-<a id="__codelineno-21-2" name="__codelineno-21-2" href="#__codelineno-21-2"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-o<span class="w"> </span>polarization.dat
+<p><strong>Note:</strong> It is recommended to use the <code>compute_rdf</code> command directly in GPUMD when possible.</p>
+<hr />
+<h2 id="ferroelectric-and-polar-material-tools">Ferroelectric and Polar Material Tools</h2>
+<p>Options <code>406–410</code> cover perovskite and polar-material analysis: neighbor lists, local displacements, averaged structures, octahedral tilt, and ABO3 polarization. These tools are built on <code>ferrodispcalc</code>.</p>
+<p><strong>Dependency:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
 </code></pre></div>
-<p>The <code>--bec</code> values should be chosen according to your model or reference data. The tool is designed for <code>ABO3</code>-type local polarization analysis.</p>
+<p>For complete argument lists, real-world workflow examples (PbTiO3 phase transition, PTO/STO superlattice topology, etc.), see <strong><a href="polar_material_analysis.html">Polar Material Analysis</a></strong>.</p>
 
 
 
diff --git a/docs/htmls/en/command_reference.html b/docs/htmls/en/command_reference.html
index 67cb6c9..897633e 100644
--- a/docs/htmls/en/command_reference.html
+++ b/docs/htmls/en/command_reference.html
@@ -1434,8 +1434,8 @@ <h2 id="gpumdkitsh-h-output"><code>gpumdkit.sh -h</code> Output</h2>
 <a id="__codelineno-0-25" name="__codelineno-0-25" href="#__codelineno-0-25"></a>| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
 <a id="__codelineno-0-26" name="__codelineno-0-26" href="#__codelineno-0-26"></a>| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 <a id="__codelineno-0-27" name="__codelineno-0-27" href="#__codelineno-0-27"></a>| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-<a id="__codelineno-0-28" name="__codelineno-0-28" href="#__codelineno-0-28"></a>| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-<a id="__codelineno-0-29" name="__codelineno-0-29" href="#__codelineno-0-29"></a>| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
+<a id="__codelineno-0-28" name="__codelineno-0-28" href="#__codelineno-0-28"></a>| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
+<a id="__codelineno-0-29" name="__codelineno-0-29" href="#__codelineno-0-29"></a>| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
 <a id="__codelineno-0-30" name="__codelineno-0-30" href="#__codelineno-0-30"></a>+-------------------------------------------------------------------------------------------------------+
 <a id="__codelineno-0-31" name="__codelineno-0-31" href="#__codelineno-0-31"></a>| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |
 <a id="__codelineno-0-32" name="__codelineno-0-32" href="#__codelineno-0-32"></a>+-------------------------------------------------------------------------------------------------------+
diff --git a/docs/htmls/en/contributing_to_gpumdkit.html b/docs/htmls/en/contributing_to_gpumdkit.html
index 7c46b72..39b22fb 100644
--- a/docs/htmls/en/contributing_to_gpumdkit.html
+++ b/docs/htmls/en/contributing_to_gpumdkit.html
@@ -1727,7 +1727,16 @@ <h1>🤝 Contributing to GPUMDkit</h1>
   <p style="text-align: justify;">Thank you for your interest in contributing to <strong>GPUMDkit</strong>! We appreciate your time and effort in helping improve this toolkit.</p>
 </div>
 
+<p align="center">
+  <strong>English</strong>
+  &nbsp;·&nbsp;
+  <a href="../zh/贡献指南.md">简体中文</a>
+</p>
+
 <p><code>GPUMDkit</code> is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.</p>
+<blockquote>
+<p><strong>Note</strong>: The authoritative version of this document is <a href="https://github.com/zhyan0603/GPUMDkit/blob/main/CONTRIBUTING.md"><code>CONTRIBUTING.md</code></a> in the repository root. This tutorial page mirrors its content.</p>
+</blockquote>
 <hr />
 <h2 id="table-of-contents">Table of Contents</h2>
 <ul>
@@ -1784,7 +1793,9 @@ <h3 id="code-style">Code Style</h3>
 <h3 id="documentation">Documentation</h3>
 <ul>
 <li>Ensure that help messages (e.g., <code>-h</code> flags) are clear and accurate.</li>
-<li>Documentation files in the <code>docs/</code> directory will be updated by the maintainers, so you generally don't need to modify them.</li>
+<li>Tutorial documentation lives in <code>docs/tutorials/en/</code> (English) and <code>docs/tutorials/zh/</code> (Chinese).
+  If you add a new feature, consider updating the relevant tutorial page.</li>
+<li>After editing tutorial markdown files, rebuild the HTML with <code>mkdocs build -f docs/mkdocs.yml</code>.</li>
 </ul>
 <hr />
 <h2 id="reporting-bugs">Reporting Bugs</h2>
@@ -1834,7 +1845,8 @@ <h3 id="create-a-feature-branch">Create a Feature Branch</h3>
 <h3 id="making-changes">Making Changes</h3>
 <p>The structure of <code>GPUMDkit</code> consists of:
 - <strong><code>gpumdkit.sh</code></strong>: Main entry point (Bash script) handling both interactive menu mode and command-line mode
-- <strong><code>Scripts/</code></strong>: Python utility scripts organized by functionality
+- <strong><code>install.sh</code></strong>: Installation script that sets up environment variables and shell configuration
+- <strong><code>Scripts/</code></strong>: Python and Bash implementation scripts organized by functionality
   - <code>plt_scripts/</code>: Plotting scripts
   - <code>calculators/</code>: Calculation utilities
   - <code>format_conversion/</code>: Format conversion tools
@@ -1850,7 +1862,12 @@ <h3 id="making-changes">Making Changes</h3>
   - <code>f5_analyzers.sh</code>
   - <code>f6_plots.sh</code>
   - <code>f7_utilities.sh</code>
-- <strong><code>docs/</code></strong>: Documentation files</p>
+- <strong><code>skills/</code></strong>: AI agent skill definitions (SKILL.md files for opencode/Claude Code integration)
+- <strong><code>docs/</code></strong>: Documentation files
+  - <code>tutorials/en/</code> and <code>tutorials/zh/</code>: Bilingual tutorial pages
+  - <code>mkdocs.yml</code>: MkDocs configuration for building tutorial HTML
+  - <code>command_reference.tsv</code>: Machine-readable command reference
+  - <code>htmls/</code>: Generated HTML output from MkDocs</p>
 <h4 id="interactive-mode-contributions">Interactive Mode Contributions</h4>
 <p>To add a new feature accessible through the interactive menu:</p>
 <ol>
@@ -1871,18 +1888,18 @@ <h4 id="interactive-mode-contributions">Interactive Mode Contributions</h4>
 </li>
 </ol>
 <p>Add a new function:
-   <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="k">function</span><span class="w"> </span>f106_new_converter<span class="o">(){</span>
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="k">function</span><span class="w"> </span>f111_new_converter<span class="o">(){</span>
 <a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
 <a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Calling the script in Scripts/format_conversion |&quot;</span>
 <a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Script: new_converter.py                        |&quot;</span>
 <a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Developer: Your Name (your@email.com)           |&quot;</span>
 <a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
-<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Input the required parameters:&quot;</span>
+<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Input &lt;required_param1&gt; &lt;required_param2&gt;&quot;</span>
 <a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Example: input.xyz output.lmp&quot;</span>
 <a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ------------&gt;&gt;&quot;</span>
-<a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="s2">&quot; &quot;</span><span class="w"> </span>converter_params
+<a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a><span class="nb">read</span><span class="w"> </span>-r<span class="w"> </span>-a<span class="w"> </span>converter_args
 <a id="__codelineno-6-11" name="__codelineno-6-11" href="#__codelineno-6-11"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ---------------------------------------------------&quot;</span>
-<a id="__codelineno-6-12" name="__codelineno-6-12" href="#__codelineno-6-12"></a>python<span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/Scripts/format_conversion/new_converter.py<span class="w"> </span><span class="si">${</span><span class="nv">converter_params</span><span class="si">}</span>
+<a id="__codelineno-6-12" name="__codelineno-6-12" href="#__codelineno-6-12"></a>python<span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/Scripts/format_conversion/new_converter.py<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">converter_args</span><span class="p">[@]</span><span class="si">}</span><span class="s2">&quot;</span>
 <a id="__codelineno-6-13" name="__codelineno-6-13" href="#__codelineno-6-13"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Code path: </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span><span class="s2">/Scripts/format_conversion/new_converter.py&quot;</span>
 <a id="__codelineno-6-14" name="__codelineno-6-14" href="#__codelineno-6-14"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ---------------------------------------------------&quot;</span>
 <a id="__codelineno-6-15" name="__codelineno-6-15" href="#__codelineno-6-15"></a><span class="o">}</span>
@@ -1893,7 +1910,7 @@ <h4 id="interactive-mode-contributions">Interactive Mode Contributions</h4>
    <div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># Find the menu() function and update it if needed</span>
 <a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="c1"># Find the array_choice array and add your new choice number</span>
 <a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="nv">array_choice</span><span class="o">=(</span>
-<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="w">    </span><span class="s2">&quot;0&quot;</span><span class="w"> </span><span class="s2">&quot;1&quot;</span><span class="w"> </span><span class="s2">&quot;101&quot;</span><span class="w"> </span><span class="s2">&quot;102&quot;</span><span class="w"> </span><span class="s2">&quot;103&quot;</span><span class="w"> </span><span class="s2">&quot;104&quot;</span><span class="w"> </span><span class="s2">&quot;105&quot;</span><span class="w"> </span><span class="s2">&quot;106&quot;</span><span class="w">  </span><span class="c1"># Added &quot;106&quot;</span>
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="w">    </span><span class="s2">&quot;0&quot;</span><span class="w"> </span><span class="s2">&quot;1&quot;</span><span class="w"> </span><span class="s2">&quot;101&quot;</span><span class="w"> </span><span class="s2">&quot;102&quot;</span><span class="w"> </span><span class="s2">&quot;103&quot;</span><span class="w"> </span><span class="s2">&quot;104&quot;</span><span class="w"> </span><span class="s2">&quot;105&quot;</span><span class="w"> </span><span class="s2">&quot;106&quot;</span><span class="w"> </span><span class="s2">&quot;107&quot;</span><span class="w"> </span><span class="s2">&quot;108&quot;</span><span class="w"> </span><span class="s2">&quot;109&quot;</span><span class="w"> </span><span class="s2">&quot;110&quot;</span><span class="w"> </span><span class="s2">&quot;111&quot;</span><span class="w">  </span><span class="c1"># Added &quot;111&quot;</span>
 <a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a><span class="w">    </span><span class="c1"># ... rest of choices</span>
 <a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a><span class="o">)</span>
 </code></pre></div></p>
@@ -1907,9 +1924,9 @@ <h4 id="interactive-mode-contributions">Interactive Mode Contributions</h4>
 <a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a><span class="w">        </span><span class="nb">source</span><span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/src/f1_format_conversions.sh
 <a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a><span class="w">        </span><span class="k">case</span><span class="w"> </span><span class="nv">$choice</span><span class="w"> </span><span class="k">in</span>
 <a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="w">            </span><span class="s2">&quot;1&quot;</span><span class="o">)</span><span class="w"> </span>f1_format_conversion<span class="w"> </span><span class="p">;;</span>
-<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a><span class="w">            </span><span class="s2">&quot;101&quot;</span><span class="o">)</span><span class="w"> </span>f101_out2xyz<span class="w"> </span><span class="p">;;</span>
-<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a><span class="w">            </span><span class="c1"># ... existing cases ...</span>
-<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a><span class="w">            </span><span class="s2">&quot;106&quot;</span><span class="o">)</span><span class="w"> </span>f106_new_converter<span class="w"> </span><span class="p">;;</span><span class="w">  </span><span class="c1"># Add your case</span>
+<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a><span class="w">             </span><span class="s2">&quot;101&quot;</span><span class="o">)</span><span class="w"> </span>f101_out2xyz<span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a><span class="w">             </span><span class="c1"># ... existing cases ...</span>
+<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a><span class="w">             </span><span class="s2">&quot;111&quot;</span><span class="o">)</span><span class="w"> </span>f111_new_converter<span class="w"> </span><span class="p">;;</span><span class="w">  </span><span class="c1"># Add your case</span>
 <a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a><span class="w">        </span><span class="k">esac</span><span class="w"> </span><span class="p">;;</span>
 <a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></a><span class="w">    </span><span class="c1"># ...</span>
 <a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a><span class="k">esac</span>
@@ -1930,39 +1947,41 @@ <h4 id="command-line-mode-contributions">Command-Line Mode Contributions</h4>
    <div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="c1"># Example: Scripts/analyzer/analyze_bonds.py</span>
 <a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a><span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
 <a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>
-<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="k">def</span><span class="w"> </span><span class="nf">main</span><span class="p">():</span>
-<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">3</span><span class="p">:</span>
-<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;&quot;</span><span class="p">)</span>
-<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a>        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0&quot;</span><span class="p">)</span>
-<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>        <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
-<a id="__codelineno-10-9" name="__codelineno-10-9" href="#__codelineno-10-9"></a>
-<a id="__codelineno-10-10" name="__codelineno-10-10" href="#__codelineno-10-10"></a>    <span class="n">input_file</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-<a id="__codelineno-10-11" name="__codelineno-10-11" href="#__codelineno-10-11"></a>    <span class="n">cutoff</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
-<a id="__codelineno-10-12" name="__codelineno-10-12" href="#__codelineno-10-12"></a>
-<a id="__codelineno-10-13" name="__codelineno-10-13" href="#__codelineno-10-13"></a>    <span class="c1"># Your implementation here</span>
-<a id="__codelineno-10-14" name="__codelineno-10-14" href="#__codelineno-10-14"></a>
-<a id="__codelineno-10-15" name="__codelineno-10-15" href="#__codelineno-10-15"></a><span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
-<a id="__codelineno-10-16" name="__codelineno-10-16" href="#__codelineno-10-16"></a>    <span class="n">main</span><span class="p">()</span>
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">3</span><span class="p">:</span>
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;&quot;</span><span class="p">)</span>
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0&quot;</span><span class="p">)</span>
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a>    <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
+<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>
+<a id="__codelineno-10-9" name="__codelineno-10-9" href="#__codelineno-10-9"></a><span class="n">input_file</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<a id="__codelineno-10-10" name="__codelineno-10-10" href="#__codelineno-10-10"></a><span class="n">cutoff</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+<a id="__codelineno-10-11" name="__codelineno-10-11" href="#__codelineno-10-11"></a>
+<a id="__codelineno-10-12" name="__codelineno-10-12" href="#__codelineno-10-12"></a><span class="c1"># Your implementation here</span>
 </code></pre></div></p>
 </li>
+</ol>
+<blockquote>
+<p><strong>Note</strong>: GPUMDkit Python scripts are designed to run directly (not imported as modules).
+You may use a <code>main()</code> function with <code>if __name__ == "__main__":</code> guard if you prefer,
+but it is not required. Most existing scripts execute at module level.</p>
+</blockquote>
+<ol>
 <li>
 <p><strong>Add the command-line flag handler</strong> in <code>gpumdkit.sh</code>:
-   <div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="c1"># Find the command-line parsing section (after line ~167)</span>
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="c1"># Find the command-line parsing section (the large &quot;case $1 in&quot; block)</span>
 <a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="c1"># Add your new flag in the appropriate location</span>
 <a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>
 <a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a><span class="k">case</span><span class="w"> </span><span class="nv">$1</span><span class="w"> </span><span class="k">in</span>
 <a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="w">    </span><span class="c1"># ... existing cases ...</span>
 <a id="__codelineno-11-6" name="__codelineno-11-6" href="#__codelineno-11-6"></a><span class="w">    </span>-analyze_bonds<span class="o">)</span>
-<a id="__codelineno-11-7" name="__codelineno-11-7" href="#__codelineno-11-7"></a><span class="w">        </span><span class="k">if</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$3</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span>
-<a id="__codelineno-11-8" name="__codelineno-11-8" href="#__codelineno-11-8"></a><span class="w">            </span>python<span class="w"> </span><span class="si">${</span><span class="nv">analyzer_path</span><span class="si">}</span>/analyze_bonds.py<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$3</span><span class="s2">&quot;</span>
+<a id="__codelineno-11-7" name="__codelineno-11-7" href="#__codelineno-11-7"></a><span class="w">        </span><span class="k">if</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="o">[</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span>!<span class="o">=</span><span class="w"> </span><span class="s2">&quot;-h&quot;</span><span class="w"> </span><span class="o">]</span><span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$3</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span>
+<a id="__codelineno-11-8" name="__codelineno-11-8" href="#__codelineno-11-8"></a><span class="w">            </span>python<span class="w"> </span><span class="si">${</span><span class="nv">analyzer_path</span><span class="si">}</span>/analyze_bonds.py<span class="w"> </span><span class="nv">$2</span><span class="w"> </span><span class="nv">$3</span>
 <a id="__codelineno-11-9" name="__codelineno-11-9" href="#__codelineno-11-9"></a><span class="w">        </span><span class="k">else</span>
 <a id="__codelineno-11-10" name="__codelineno-11-10" href="#__codelineno-11-10"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;&quot;</span>
 <a id="__codelineno-11-11" name="__codelineno-11-11" href="#__codelineno-11-11"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0&quot;</span>
 <a id="__codelineno-11-12" name="__codelineno-11-12" href="#__codelineno-11-12"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Code path: </span><span class="si">${</span><span class="nv">analyzer_path</span><span class="si">}</span><span class="s2">/analyze_bonds.py&quot;</span>
-<a id="__codelineno-11-13" name="__codelineno-11-13" href="#__codelineno-11-13"></a><span class="w">            </span><span class="nb">exit</span><span class="w"> </span><span class="m">1</span>
-<a id="__codelineno-11-14" name="__codelineno-11-14" href="#__codelineno-11-14"></a><span class="w">        </span><span class="k">fi</span><span class="w"> </span><span class="p">;;</span>
-<a id="__codelineno-11-15" name="__codelineno-11-15" href="#__codelineno-11-15"></a><span class="w">    </span><span class="c1"># ... rest of cases ...</span>
-<a id="__codelineno-11-16" name="__codelineno-11-16" href="#__codelineno-11-16"></a><span class="k">esac</span>
+<a id="__codelineno-11-13" name="__codelineno-11-13" href="#__codelineno-11-13"></a><span class="w">        </span><span class="k">fi</span><span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-11-14" name="__codelineno-11-14" href="#__codelineno-11-14"></a><span class="w">    </span><span class="c1"># ... rest of cases ...</span>
+<a id="__codelineno-11-15" name="__codelineno-11-15" href="#__codelineno-11-15"></a><span class="k">esac</span>
 </code></pre></div></p>
 </li>
 <li>
@@ -1983,50 +2002,87 @@ <h4 id="updating-tab-completion">Updating Tab Completion</h4>
 </code></pre></div>
 <p>Add your new flag to the <code>opts</code> variable:
 <div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a><span class="c1"># Find the line with local opts=...</span>
-<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a><span class="nb">local</span><span class="w"> </span><span class="nv">opts</span><span class="o">=</span><span class="s2">&quot;-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ...&quot;</span>
-<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a><span class="c1">#                                                      ^^^^^^^^^^^^^^ Add your flag here</span>
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a><span class="nb">local</span><span class="w"> </span><span class="nv">opts</span><span class="o">=</span><span class="s2">&quot;-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...&quot;</span>
+<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a><span class="c1">#                                                        Add your flag here</span>
+</code></pre></div></p>
+<p>If your flag requires file arguments, add it to the existing file-completion case:
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a><span class="c1"># Find the case for file-requiring flags and add yours with |</span>
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>-out2xyz<span class="p">|</span>-out2exyz<span class="p">|</span>-...<span class="p">|</span>-your_new_flag<span class="o">)</span>
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a><span class="w">    </span><span class="nv">COMPREPLY</span><span class="o">=(</span><span class="k">$(</span><span class="nb">compgen</span><span class="w"> </span>-f<span class="w"> </span>--<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$cur</span><span class="s2">&quot;</span><span class="k">)</span><span class="o">)</span><span class="w"> </span><span class="p">;;</span>
 </code></pre></div></p>
-<p>If your flag accepts secondary options (like <code>-plt</code> or <code>-calc</code>), add a case for it:
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a><span class="k">case</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$prev</span><span class="s2">&quot;</span><span class="w"> </span><span class="k">in</span>
-<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="w">    </span><span class="c1"># ... existing cases ...</span>
-<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a><span class="w">    </span>-analyze_bonds<span class="o">)</span>
-<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a><span class="w">        </span><span class="nv">COMPREPLY</span><span class="o">=(</span><span class="k">$(</span><span class="nb">compgen</span><span class="w"> </span>-f<span class="w"> </span>--<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$cur</span><span class="s2">&quot;</span><span class="k">)</span><span class="o">)</span><span class="w">  </span><span class="c1"># Complete with filenames</span>
-<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a><span class="w">        </span><span class="p">;;</span>
-<a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a><span class="w">    </span><span class="c1"># ... rest of cases ...</span>
-<a id="__codelineno-15-7" name="__codelineno-15-7" href="#__codelineno-15-7"></a><span class="k">esac</span>
+<p>If your flag accepts secondary options (like <code>-plt</code> or <code>-calc</code>), add a new case:
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a><span class="k">case</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$prev</span><span class="s2">&quot;</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a><span class="w">    </span><span class="c1"># ... existing cases ...</span>
+<a id="__codelineno-16-3" name="__codelineno-16-3" href="#__codelineno-16-3"></a><span class="w">    </span>-your_new_flag<span class="o">)</span>
+<a id="__codelineno-16-4" name="__codelineno-16-4" href="#__codelineno-16-4"></a><span class="w">        </span><span class="nv">COMPREPLY</span><span class="o">=(</span><span class="k">$(</span><span class="nb">compgen</span><span class="w"> </span>-W<span class="w"> </span><span class="s2">&quot;option1 option2 option3&quot;</span><span class="w"> </span>--<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$cur</span><span class="s2">&quot;</span><span class="k">)</span><span class="o">)</span><span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-16-5" name="__codelineno-16-5" href="#__codelineno-16-5"></a><span class="w">    </span><span class="c1"># ... rest of cases ...</span>
+<a id="__codelineno-16-6" name="__codelineno-16-6" href="#__codelineno-16-6"></a><span class="k">esac</span>
 </code></pre></div></p>
 <h3 id="code-style-and-best-practices">Code Style and Best Practices</h3>
 <ul>
 <li><strong>Shell Scripts</strong>:</li>
 <li>Use <code>${variable}</code> for variable expansion</li>
+<li>Use <code>[ ! -z "$var" ]</code> for non-empty checks (project convention)</li>
+<li>Interactive functions should follow the banner format:
+    <div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Calling the script in Scripts/&lt;category&gt;        |&quot;</span>
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Script: &lt;script_name&gt;.py                        |&quot;</span>
+<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Developer: &lt;Name&gt; (&lt;email&gt;)                     |&quot;</span>
+<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
+</code></pre></div></li>
+<li>Use <code>read -r -a varname</code> for multi-word input, then pass with <code>"${varname[@]}"</code></li>
 <li>
-<p>Write code that is clear and easy to maintain</p>
+<p>Shell scripts in <code>src/</code> should start with a file header block:
+    <div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a><span class="c1"># ============================================================</span>
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a><span class="c1"># GPUMDkit &lt;module name&gt; module</span>
+<a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a><span class="c1"># Repository: https://github.com/zhyan0603/GPUMDkit</span>
+<a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a><span class="c1"># Author: &lt;Name&gt; (&lt;email&gt;)</span>
+<a id="__codelineno-18-5" name="__codelineno-18-5" href="#__codelineno-18-5"></a><span class="c1"># ============================================================</span>
+</code></pre></div></p>
 </li>
 <li>
 <p><strong>Python Scripts</strong>:</p>
 </li>
 <li>Write clear, maintainable code</li>
 <li>Use meaningful variable names</li>
+<li>Use <code>sys.argv</code> for argument parsing (consistent with most existing scripts)</li>
+<li>Provide clear usage messages with <code>print("Usage: ...")</code> and <code>print("Example: ...")</code></li>
+<li>If your script uses heavy/special packages (<code>NepTrain</code>, <code>calorine</code>, <code>dpdata</code>), add a
+    <code>print_dependency_notice()</code> function to inform users about citation recommendations</li>
 </ul>
 <h3 id="testing-your-changes">Testing Your Changes</h3>
-<p>Before submitting your contribution:</p>
+<p>Before submitting your contribution, run the relevant validation commands:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a><span class="c1"># Shell syntax checks (always run these)</span>
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>bash<span class="w"> </span>-n<span class="w"> </span>gpumdkit.sh
+<a id="__codelineno-19-3" name="__codelineno-19-3" href="#__codelineno-19-3"></a>find<span class="w"> </span>src<span class="w"> </span>Scripts<span class="w"> </span>-name<span class="w"> </span><span class="s1">&#39;*.sh&#39;</span><span class="w"> </span>-exec<span class="w"> </span>bash<span class="w"> </span>-n<span class="w"> </span><span class="o">{}</span><span class="w"> </span>+
+<a id="__codelineno-19-4" name="__codelineno-19-4" href="#__codelineno-19-4"></a>
+<a id="__codelineno-19-5" name="__codelineno-19-5" href="#__codelineno-19-5"></a><span class="c1"># Python syntax checks (for modified Python files)</span>
+<a id="__codelineno-19-6" name="__codelineno-19-6" href="#__codelineno-19-6"></a>python3<span class="w"> </span>-m<span class="w"> </span>py_compile<span class="w"> </span>path/to/modified_script.py
+<a id="__codelineno-19-7" name="__codelineno-19-7" href="#__codelineno-19-7"></a>
+<a id="__codelineno-19-8" name="__codelineno-19-8" href="#__codelineno-19-8"></a><span class="c1"># MkDocs build (if you modified documentation)</span>
+<a id="__codelineno-19-9" name="__codelineno-19-9" href="#__codelineno-19-9"></a>mkdocs<span class="w"> </span>build<span class="w"> </span>-f<span class="w"> </span>docs/mkdocs.yml
+<a id="__codelineno-19-10" name="__codelineno-19-10" href="#__codelineno-19-10"></a>
+<a id="__codelineno-19-11" name="__codelineno-19-11" href="#__codelineno-19-11"></a><span class="c1"># Check for trailing whitespace issues</span>
+<a id="__codelineno-19-12" name="__codelineno-19-12" href="#__codelineno-19-12"></a>git<span class="w"> </span>diff<span class="w"> </span>--check
+</code></pre></div>
+<p>Then test functionality:</p>
 <ol>
 <li>
 <p><strong>Test interactive mode</strong> (if applicable):
-   <div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh
-<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a><span class="c1"># Navigate to your new feature and test it thoroughly</span>
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh
+<a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a><span class="c1"># Navigate to your new feature and test it thoroughly</span>
 </code></pre></div></p>
 </li>
 <li>
 <p><strong>Test command-line mode</strong> (if applicable):
-   <div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span><span class="o">[</span>arguments<span class="o">]</span>
-<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span>-h<span class="w">  </span><span class="c1"># Test help message</span>
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span><span class="o">[</span>arguments<span class="o">]</span>
+<a id="__codelineno-21-2" name="__codelineno-21-2" href="#__codelineno-21-2"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span>-h<span class="w">  </span><span class="c1"># Test help message</span>
 </code></pre></div></p>
 </li>
 <li>
 <p><strong>Test tab completion</strong> (if you modified <code>completion.sh</code>):
-   <div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a><span class="nb">source</span><span class="w"> </span>Scripts/utils/completion.sh
-<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-&lt;TAB&gt;<span class="w">  </span><span class="c1"># Should show your new flag</span>
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a><span class="nb">source</span><span class="w"> </span>Scripts/utils/completion.sh
+<a id="__codelineno-22-2" name="__codelineno-22-2" href="#__codelineno-22-2"></a>gpumdkit.sh<span class="w"> </span>-&lt;TAB&gt;<span class="w">  </span><span class="c1"># Should show your new flag</span>
 </code></pre></div></p>
 </li>
 <li>
@@ -2047,19 +2103,19 @@ <h3 id="push-and-open-a-pull-request">Push and Open a Pull Request</h3>
 <ol>
 <li>
 <p><strong>Commit your changes</strong>:
-   <div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>git<span class="w"> </span>add<span class="w"> </span>.
-<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>git<span class="w"> </span>commit<span class="w"> </span>-m<span class="w"> </span><span class="s2">&quot;your descriptive message&quot;</span>
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-23-1" name="__codelineno-23-1" href="#__codelineno-23-1"></a>git<span class="w"> </span>add<span class="w"> </span>.
+<a id="__codelineno-23-2" name="__codelineno-23-2" href="#__codelineno-23-2"></a>git<span class="w"> </span>commit<span class="w"> </span>-m<span class="w"> </span><span class="s2">&quot;your descriptive message&quot;</span>
 </code></pre></div></p>
 </li>
 <li>
-<p><strong>Keep your branch updated</strong> with the upstream <code>main</code> branch:
-   <div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>git<span class="w"> </span>fetch<span class="w"> </span>upstream
-<a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a>git<span class="w"> </span>rebase<span class="w"> </span>upstream/main
+<p><strong>Keep your branch updated</strong> with the latest <code>dev</code> branch:
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-24-1" name="__codelineno-24-1" href="#__codelineno-24-1"></a>git<span class="w"> </span>fetch<span class="w"> </span>origin
+<a id="__codelineno-24-2" name="__codelineno-24-2" href="#__codelineno-24-2"></a>git<span class="w"> </span>rebase<span class="w"> </span>origin/dev
 </code></pre></div></p>
 </li>
 <li>
 <p><strong>Push your branch</strong> to your fork:
-   <div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>git<span class="w"> </span>push<span class="w"> </span>origin<span class="w"> </span>your-branch-name
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-25-1" name="__codelineno-25-1" href="#__codelineno-25-1"></a>git<span class="w"> </span>push<span class="w"> </span>origin<span class="w"> </span>your-branch-name
 </code></pre></div></p>
 </li>
 <li>
@@ -2098,7 +2154,7 @@ <h2 id="questions-or-need-help">Questions or Need Help?</h2>
 <li><strong>Contact maintainers</strong>: Reach out to the core developers listed in the README</li>
 </ul>
 <hr />
-<p>Thank you again for contributing to <code>GPUMDkit</code>! Your efforts help make this toolkit better for the entire GPUMD and NEP community. 🚀</p>
+<p>Thank you again for contributing to <code>GPUMDkit</code>! Your efforts help make this toolkit better for the entire GPUMD and NEP community.</p>
 
 
 
diff --git a/docs/htmls/en/custom_commands.html b/docs/htmls/en/custom_commands.html
index c12059e..b72fd19 100644
--- a/docs/htmls/en/custom_commands.html
+++ b/docs/htmls/en/custom_commands.html
@@ -1519,7 +1519,7 @@ <h3 id="command-with-required-arguments">Command with Required Arguments</h3>
 <a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Hello, </span><span class="si">${</span><span class="nv">name</span><span class="si">}</span><span class="s2">!&quot;</span>
 <a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="o">}</span>
 </code></pre></div>
-<p>and you can add a argument, for example: <code>gpumdkit.sh -greet Zihan</code>, then you will see:</p>
+<p>and you can add an argument, for example: <code>gpumdkit.sh -greet Zihan</code>, then you will see:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>Hello, Zihan!
 </code></pre></div>
 <p><strong>Passing arguments</strong>: Use <code>"$@"</code> to forward all arguments safely. Use <code>${@:1}</code> when you need to refer to arguments starting from the first one. </p>
diff --git a/docs/htmls/en/format_conversion.html b/docs/htmls/en/format_conversion.html
index deee4c3..cf278a4 100644
--- a/docs/htmls/en/format_conversion.html
+++ b/docs/htmls/en/format_conversion.html
@@ -143,7 +143,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#overview" class="md-skip">
+        <a href="#what-it-does" class="md-skip">
           Skip to content
         </a>
       
@@ -517,10 +517,32 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#overview" class="md-nav__link">
+  <a href="#what-it-does" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Overview
+        What it does
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#before-you-start" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Before you start
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#supported-formats" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Supported formats
       
     </span>
   </a>
@@ -692,6 +714,39 @@
     </span>
   </a>
   
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#split-multi-frame-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Split multi-frame extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#mtp-conversion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MTP conversion
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#abacus-conversion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        ABACUS conversion
+      
+    </span>
+  </a>
+  
 </li>
         
       </ul>
@@ -1432,10 +1487,32 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#overview" class="md-nav__link">
+  <a href="#what-it-does" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        What it does
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#before-you-start" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Before you start
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#supported-formats" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Overview
+        Supported formats
       
     </span>
   </a>
@@ -1607,6 +1684,39 @@
     </span>
   </a>
   
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#split-multi-frame-extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Split multi-frame extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#mtp-conversion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MTP conversion
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#abacus-conversion" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        ABACUS conversion
+      
+    </span>
+  </a>
+  
 </li>
         
       </ul>
@@ -1661,8 +1771,12 @@ <h1>🔄 Format Conversion</h1>
   <p style="text-align: justify;">GPUMDkit contains utilities for converting common atomistic simulation formats, with extra handling for metadata such as group labels, weights, and frame extraction.</p>
 </div>
 
-<p><strong>Script Location:</strong> <code>Scripts/format_conversion/</code></p>
-<h2 id="overview">Overview</h2>
+<h2 id="what-it-does">What it does</h2>
+<p>This module converts structure and trajectory files between common formats used in computational materials science. It supports VASP, LAMMPS, CP2K, ABACUS, CIF, ASE trajectories, and extxyz. It also provides tools for adding group labels, weights, extracting frames, and replicating structures.</p>
+<h2 id="before-you-start">Before you start</h2>
+<p><strong>Script location:</strong> <code>Scripts/format_conversion/</code></p>
+<p>Make sure GPUMDkit is installed. See <a href="quick_start.html">Quick Start</a> for installation instructions.</p>
+<h2 id="supported-formats">Supported formats</h2>
 <p>The format conversion module covers:</p>
 <ul>
 <li><strong>VASP</strong>: <code>POSCAR</code>, <code>CONTCAR</code>, <code>OUTCAR</code>, <code>XDATCAR</code></li>
@@ -1870,13 +1984,14 @@ <h2 id="quick-command-reference">Quick Command Reference</h2>
 </table>
 <h2 id="common-examples">Common Examples</h2>
 <h3 id="convert-vasp-calculations-to-extxyz">Convert VASP calculations to extxyz</h3>
-<p>If each calculation directory contains an <code>OUTCAR</code>, run:</p>
+<p><strong>What it does:</strong> Searches a directory for VASP OUTCAR files and converts them into a single extxyz file for NEP training or analysis.</p>
+<p><strong>CLI mode:</strong></p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-out2xyz<span class="w"> </span>./vasp_results/
 </code></pre></div>
-<p>The shell version searches the target directory and converts VASP results into an extxyz file suitable for later analysis. If you prefer the Python implementation:</p>
+<p>The shell version searches the target directory and converts VASP results into an extxyz file. If you prefer the Python implementation:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-out2exyz<span class="w"> </span>./vasp_results/
 </code></pre></div>
-<p>From interactive mode, choose <code>101</code>. You will see:</p>
+<p><strong>Interactive mode:</strong> Choose <code>101</code> from the format conversion menu. You will see:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>&gt;-------------------------------------------------&lt;
 <a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>| Calling the script in Scripts/format_conversion |
 <a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>| Script: out2xyz.sh                              |
@@ -1886,12 +2001,14 @@ <h3 id="convert-vasp-calculations-to-extxyz">Convert VASP calculations to extxyz
 <a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>Example: ./
 <a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a>------------&gt;&gt;
 </code></pre></div>
+<p><strong>Output:</strong> An extxyz file containing the converted structures, suitable for NEP training or further analysis.</p>
 <h3 id="add-group-labels">Add group labels</h3>
-<p>Some GPUMD-related workflows use group labels for atom grouping, for example in species-specific MSD or diffusion calculations.</p>
+<p><strong>What it does:</strong> Adds atom group labels to a structure file. Group labels are required by some GPUMD-related workflows, such as species-specific MSD or diffusion calculations.</p>
+<p><strong>CLI mode:</strong></p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
 </code></pre></div>
 <p>This command reads the input structure and writes an extxyz file with group information.</p>
-<p>From interactive mode, choose <code>106</code>. You will see:</p>
+<p><strong>Interactive mode:</strong> Choose <code>106</code> from the format conversion menu. You will see:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>&gt;-------------------------------------------------&lt;
 <a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>| Calling the script in Scripts/format_conversion |
 <a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>| Script: add_groups.py                           |
@@ -1901,6 +2018,7 @@ <h3 id="add-group-labels">Add group labels</h3>
 <a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a>Example: POSCAR Li Y Cl
 <a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>------------&gt;&gt;
 </code></pre></div>
+<p><strong>Output:</strong> An extxyz file with group labels added.</p>
 <h2 id="script-details">Script Details</h2>
 <h3 id="poscar-to-extxyz">POSCAR to extxyz</h3>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
@@ -1947,6 +2065,29 @@ <h3 id="extract-one-frame">Extract one frame</h3>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-get_frame<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1000</span>
 </code></pre></div>
 <p>This extracts frame index <code>1000</code> from an extxyz trajectory.</p>
+<h3 id="split-multi-frame-extxyz">Split multi-frame extxyz</h3>
+<p><code>split_single_xyz.py</code> splits an extxyz file into individual frames, each written to a separate file.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>python<span class="w"> </span>Scripts/format_conversion/split_single_xyz.py<span class="w"> </span>dump.xyz
+</code></pre></div>
+<p>This creates <code>model_0.xyz</code>, <code>model_1.xyz</code>, ... for each frame in the trajectory.</p>
+<h3 id="mtp-conversion">MTP conversion</h3>
+<p>Convert MTP <code>.cfg</code> format to extxyz:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w">    </span><span class="c1"># Select: 1) Format Conversion → 102</span>
+</code></pre></div>
+<p>Interactive prompt:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;
+<a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a>Example: train.cfg Pd Ag
+<a id="__codelineno-20-3" name="__codelineno-20-3" href="#__codelineno-20-3"></a>------------&gt;&gt;
+</code></pre></div>
+<h3 id="abacus-conversion">ABACUS conversion</h3>
+<p>Convert ABACUS output to extxyz:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w">    </span><span class="c1"># Select: 1) Format Conversion → 104</span>
+</code></pre></div>
+<p>The menu offers two options:</p>
+<ol>
+<li>SCF output (<code>running_scf.log</code>)</li>
+<li>MD output (<code>running_md.log</code>)</li>
+</ol>
 <h2 id="common-mistakes">Common Mistakes</h2>
 <table>
 <thead>
diff --git a/docs/htmls/en/index.html b/docs/htmls/en/index.html
index bab137d..b8c871b 100644
--- a/docs/htmls/en/index.html
+++ b/docs/htmls/en/index.html
@@ -143,7 +143,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#what-is-gpumdkit" class="md-skip">
+        <a href="#what-it-does" class="md-skip">
           Skip to content
         </a>
       
@@ -433,10 +433,10 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#what-is-gpumdkit" class="md-nav__link">
+  <a href="#what-it-does" class="md-nav__link">
     <span class="md-ellipsis">
       
-        What is GPUMDkit?
+        What it does
       
     </span>
   </a>
@@ -444,33 +444,33 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#quick-start" class="md-nav__link">
+  <a href="#common-tasks" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Quick Start
+        Common Tasks
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="Quick Start">
-      <ul class="md-nav__list">
-        
-          <li class="md-nav__item">
-  <a href="#installation" class="md-nav__link">
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#before-you-start" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Installation
+        Before you start
       
     </span>
   </a>
   
-</li>
+    <nav class="md-nav" aria-label="Before you start">
+      <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#dependencies" class="md-nav__link">
+  <a href="#installation" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Dependencies
+        Installation
       
     </span>
   </a>
@@ -478,10 +478,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#usage" class="md-nav__link">
+  <a href="#dependencies" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Usage
+        Dependencies
       
     </span>
   </a>
@@ -494,21 +494,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#tutorials" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        Tutorials
-      
-    </span>
-  </a>
-  
-</li>
-      
-        <li class="md-nav__item">
-  <a href="#example-convert-vasp-outcars" class="md-nav__link">
+  <a href="#interactive-mode" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Example: Convert VASP OUTCARs
+        Interactive mode
       
     </span>
   </a>
@@ -516,10 +505,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#example-plot-nep-results" class="md-nav__link">
+  <a href="#cli-mode" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Example: Plot NEP Results
+        CLI mode
       
     </span>
   </a>
@@ -527,10 +516,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#example-ionic-conductivity" class="md-nav__link">
+  <a href="#module-overview" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Example: Ionic Conductivity
+        Module Overview
       
     </span>
   </a>
@@ -538,10 +527,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#module-overview" class="md-nav__link">
+  <a href="#all-tutorials" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Module Overview
+        All Tutorials
       
     </span>
   </a>
@@ -1354,10 +1343,10 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#what-is-gpumdkit" class="md-nav__link">
+  <a href="#what-it-does" class="md-nav__link">
     <span class="md-ellipsis">
       
-        What is GPUMDkit?
+        What it does
       
     </span>
   </a>
@@ -1365,33 +1354,33 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#quick-start" class="md-nav__link">
+  <a href="#common-tasks" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Quick Start
+        Common Tasks
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="Quick Start">
-      <ul class="md-nav__list">
-        
-          <li class="md-nav__item">
-  <a href="#installation" class="md-nav__link">
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#before-you-start" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Installation
+        Before you start
       
     </span>
   </a>
   
-</li>
+    <nav class="md-nav" aria-label="Before you start">
+      <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#dependencies" class="md-nav__link">
+  <a href="#installation" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Dependencies
+        Installation
       
     </span>
   </a>
@@ -1399,10 +1388,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#usage" class="md-nav__link">
+  <a href="#dependencies" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Usage
+        Dependencies
       
     </span>
   </a>
@@ -1415,10 +1404,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#tutorials" class="md-nav__link">
+  <a href="#interactive-mode" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Tutorials
+        Interactive mode
       
     </span>
   </a>
@@ -1426,10 +1415,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#example-convert-vasp-outcars" class="md-nav__link">
+  <a href="#cli-mode" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Example: Convert VASP OUTCARs
+        CLI mode
       
     </span>
   </a>
@@ -1437,21 +1426,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#example-plot-nep-results" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        Example: Plot NEP Results
-      
-    </span>
-  </a>
-  
-</li>
-      
-        <li class="md-nav__item">
-  <a href="#example-ionic-conductivity" class="md-nav__link">
+  <a href="#module-overview" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Example: Ionic Conductivity
+        Module Overview
       
     </span>
   </a>
@@ -1459,10 +1437,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#module-overview" class="md-nav__link">
+  <a href="#all-tutorials" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Module Overview
+        All Tutorials
       
     </span>
   </a>
@@ -1505,108 +1483,79 @@ <h1>📚 GPUMDkit Tutorials</h1>
   <p style="text-align: justify;">Welcome to <strong>GPUMDkit</strong>, a command-line toolkit for GPUMD and NEP.</p>
 </div>
 
-<h2 id="what-is-gpumdkit">What is GPUMDkit?</h2>
-<p>GPUMDkit streamlines common tasks in computational materials science:</p>
-<ul>
-<li><strong>Format Conversion</strong>: Convert between VASP, LAMMPS, CP2K, ABACUS, CIF, and extxyz formats</li>
-<li><strong>Visualization</strong>: Plotting tools for NEP training, MD simulations, and analysis</li>
-<li><strong>Calculators</strong>: Compute ionic conductivity, descriptors, MSD, NEB, and more</li>
-<li><strong>Analyzers</strong>: Structure validation, filtering, composition analysis</li>
-<li><strong>Workflows</strong>: Batch processing for DFT and MD simulations</li>
-<li><strong>Sampling</strong>: Structure selection using uniform, random, or FPS methods</li>
-</ul>
-<h2 id="quick-start">Quick Start</h2>
-<h3 id="installation">Installation</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
-<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
-<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="nb">source</span><span class="w"> </span>./install.sh
-</code></pre></div>
-<h3 id="dependencies">Dependencies</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>gpumdkit<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12
-<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>gpumdkit
-<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>pip<span class="w"> </span>install<span class="w"> </span>neptrain<span class="w"> </span>dpdata<span class="w"> </span>calorine
-</code></pre></div>
-<h3 id="usage">Usage</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="c1"># Interactive mode</span>
-<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh
-<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
-<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="c1"># Command-line mode</span>
-<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>gpumdkit.sh<span class="w"> </span>-&lt;option&gt;<span class="w"> </span><span class="o">[</span>args...<span class="o">]</span>
-<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>
-<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a><span class="c1"># Get help</span>
-<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>gpumdkit.sh<span class="w"> </span>-h
-</code></pre></div>
-<h2 id="tutorials">Tutorials</h2>
+<h2 id="what-it-does">What it does</h2>
+<p>GPUMDkit helps you perform common tasks in computational materials science without writing custom scripts. It supports format conversion, structure analysis, property calculation, visualization, and batch workflows — all from one command-line tool.</p>
+<h2 id="common-tasks">Common Tasks</h2>
 <table>
 <thead>
 <tr>
+<th>I want to...</th>
 <th>Tutorial</th>
-<th>Description</th>
 </tr>
 </thead>
 <tbody>
 <tr>
+<td>Install GPUMDkit and run my first command</td>
 <td><a href="quick_start.html">Quick Start</a></td>
-<td>Installation and first steps</td>
 </tr>
 <tr>
-<td><a href="command_reference.html">Command Reference</a></td>
-<td>One-page CLI and menu reference</td>
+<td>Convert VASP, LAMMPS, CP2K, or CIF files to extxyz</td>
+<td><a href="format_conversion.html">Format Conversion</a></td>
 </tr>
 <tr>
-<td><a href="format_conversion.html">Format Conversion</a></td>
-<td>Convert between file formats</td>
+<td>Check structure distances, filter datasets, or find outliers</td>
+<td><a href="analyzer_scripts.html">Analyzer Scripts</a></td>
 </tr>
 <tr>
+<td>Calculate MSD, ionic conductivity, or descriptors</td>
 <td><a href="calculator_scripts.html">Calculator Scripts</a></td>
-<td>Compute material properties</td>
 </tr>
 <tr>
-<td><a href="analyzer_scripts.html">Analyzer Scripts</a></td>
-<td>Structure analysis and validation</td>
+<td>Analyze polar materials, ferroelectrics, or ABO3 systems</td>
+<td><a href="polar_material_analysis.html">Polar Material Analysis</a></td>
 </tr>
 <tr>
+<td>Plot NEP training results or thermodynamic data</td>
 <td><a href="plot_scripts.html">Plot Scripts</a></td>
-<td>Plotting and visualization</td>
 </tr>
 <tr>
+<td>Run batch DFT or MD simulations</td>
 <td><a href="workflow_scripts.html">Workflow Scripts</a></td>
-<td>Batch processing and automation</td>
 </tr>
 <tr>
+<td>Select representative structures from a dataset</td>
 <td><a href="structure_sampling.html">Structure Sampling</a></td>
-<td>Structure selection methods</td>
 </tr>
 <tr>
+<td>Add my own shortcuts to GPUMDkit</td>
 <td><a href="custom_commands.html">Custom Commands</a></td>
-<td>User-defined GPUMDkit shortcuts</td>
-</tr>
-<tr>
-<td><a href="active_learning_workflow.html">Active Learning Workflow</a></td>
-<td>Batch active-learning workflow notes</td>
-</tr>
-<tr>
-<td><a href="polar_material_analysis.html">Polar Material Analysis</a></td>
-<td>Ferroelectric and polarization tools</td>
-</tr>
-<tr>
-<td><a href="contributing_to_gpumdkit.html">Contributing to GPUMDkit</a></td>
-<td>Development notes</td>
 </tr>
 </tbody>
 </table>
-<h2 id="example-convert-vasp-outcars">Example: Convert VASP OUTCARs</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-out2xyz<span class="w"> </span>./vasp_results/
+<h2 id="before-you-start">Before you start</h2>
+<h3 id="installation">Installation</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="nb">source</span><span class="w"> </span>./install.sh
+</code></pre></div>
+<h3 id="dependencies">Dependencies</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>gpumdkit<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>gpumdkit
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>pip<span class="w"> </span>install<span class="w"> </span>neptrain<span class="w"> </span>dpdata<span class="w"> </span>calorine
 </code></pre></div>
-<h2 id="example-plot-nep-results">Example: Plot NEP Results</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
-<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>prediction
+<h2 id="interactive-mode">Interactive mode</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh
 </code></pre></div>
-<h2 id="example-ionic-conductivity">Example: Ionic Conductivity</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>trajectory.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>ionic-cond<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>
-<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<p>This opens a menu where you can select modules by number.</p>
+<h2 id="cli-mode">CLI mode</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-&lt;option&gt;<span class="w"> </span><span class="o">[</span>args...<span class="o">]</span>
 </code></pre></div>
+<p>For example:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>trajectory.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
+</code></pre></div>
+<p>Use <code>gpumdkit.sh -h</code> to see all available options.</p>
 <h2 id="module-overview">Module Overview</h2>
 <table>
 <thead>
@@ -1662,6 +1611,65 @@ <h2 id="module-overview">Module Overview</h2>
 </tr>
 </tbody>
 </table>
+<h2 id="all-tutorials">All Tutorials</h2>
+<table>
+<thead>
+<tr>
+<th>Tutorial</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><a href="quick_start.html">Quick Start</a></td>
+<td>Installation and first steps</td>
+</tr>
+<tr>
+<td><a href="command_reference.html">Command Reference</a></td>
+<td>One-page CLI and menu reference</td>
+</tr>
+<tr>
+<td><a href="format_conversion.html">Format Conversion</a></td>
+<td>Convert between file formats</td>
+</tr>
+<tr>
+<td><a href="calculator_scripts.html">Calculator Scripts</a></td>
+<td>Compute material properties</td>
+</tr>
+<tr>
+<td><a href="analyzer_scripts.html">Analyzer Scripts</a></td>
+<td>Structure analysis and validation</td>
+</tr>
+<tr>
+<td><a href="plot_scripts.html">Plot Scripts</a></td>
+<td>Plotting and visualization</td>
+</tr>
+<tr>
+<td><a href="workflow_scripts.html">Workflow Scripts</a></td>
+<td>Batch processing and automation</td>
+</tr>
+<tr>
+<td><a href="structure_sampling.html">Structure Sampling</a></td>
+<td>Structure selection methods</td>
+</tr>
+<tr>
+<td><a href="custom_commands.html">Custom Commands</a></td>
+<td>User-defined GPUMDkit shortcuts</td>
+</tr>
+<tr>
+<td><a href="active_learning_workflow.html">Active Learning Workflow</a></td>
+<td>Batch active-learning workflow notes</td>
+</tr>
+<tr>
+<td><a href="polar_material_analysis.html">Polar Material Analysis</a></td>
+<td>Ferroelectric and polarization tools</td>
+</tr>
+<tr>
+<td><a href="contributing_to_gpumdkit.html">Contributing to GPUMDkit</a></td>
+<td>Development notes</td>
+</tr>
+</tbody>
+</table>
 <h2 id="links">Links</h2>
 <ul>
 <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li>
diff --git a/docs/htmls/en/plot_scripts.html b/docs/htmls/en/plot_scripts.html
index 6221af3..4a26f0e 100644
--- a/docs/htmls/en/plot_scripts.html
+++ b/docs/htmls/en/plot_scripts.html
@@ -680,10 +680,10 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#training-results" class="md-nav__link">
+  <a href="#plt_trainpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Training Results
+        plt_train.py
       
     </span>
   </a>
@@ -691,10 +691,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#prediction-results" class="md-nav__link">
+  <a href="#plt_predictionpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Prediction Results
+        plt_prediction.py
       
     </span>
   </a>
@@ -702,10 +702,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#traintest-comparison" class="md-nav__link">
+  <a href="#plt_train_testpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Train/Test Comparison
+        plt_train_test.py
       
     </span>
   </a>
@@ -713,10 +713,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#density-parity-plot" class="md-nav__link">
+  <a href="#plt_parity_densitypy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Density Parity Plot
+        plt_parity_density.py
       
     </span>
   </a>
@@ -724,10 +724,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#force-error-analysis" class="md-nav__link">
+  <a href="#plt_force_errorspy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Force Error Analysis
+        plt_force_errors.py
       
     </span>
   </a>
@@ -735,10 +735,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#restart-parameters" class="md-nav__link">
+  <a href="#plt_learning_ratepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Restart Parameters
+        plt_learning_rate.py
       
     </span>
   </a>
@@ -746,34 +746,44 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#charge-and-born-effective-charge" class="md-nav__link">
+  <a href="#plt_nep_restartpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Charge and Born Effective Charge
+        plt_nep_restart.py
       
     </span>
   </a>
   
 </li>
         
-      </ul>
-    </nav>
+          <li class="md-nav__item">
+  <a href="#plt_chargepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_charge.py
+      
+    </span>
+  </a>
   
 </li>
-      
-        <li class="md-nav__item">
-  <a href="#molecular-dynamics-and-thermodynamics" class="md-nav__link">
+        
+          <li class="md-nav__item">
+  <a href="#plt_born_chargepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Molecular Dynamics and Thermodynamics
+        plt_born_charge.py
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="Molecular Dynamics and Thermodynamics">
-      <ul class="md-nav__list">
+</li>
         
-          <li class="md-nav__item">
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
   <a href="#thermodynamic-properties" class="md-nav__link">
     <span class="md-ellipsis">
       
@@ -782,13 +792,14 @@
     </span>
   </a>
   
-</li>
+    <nav class="md-nav" aria-label="Thermodynamic Properties">
+      <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#radial-distribution-function" class="md-nav__link">
+  <a href="#plt_thermopy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Radial Distribution Function
+        plt_thermo.py
       
     </span>
   </a>
@@ -796,10 +807,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#velocity-autocorrelation-and-pdos" class="md-nav__link">
+  <a href="#plt_thermo2py-plt_thermo3py" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Velocity Autocorrelation and PDOS
+        plt_thermo2.py &amp; plt_thermo3.py
       
     </span>
   </a>
@@ -824,10 +835,10 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#mean-square-displacement" class="md-nav__link">
+  <a href="#plt_msdpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Mean Square Displacement
+        plt_msd.py
       
     </span>
   </a>
@@ -835,10 +846,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#msd-for-all-species" class="md-nav__link">
+  <a href="#plt_msd_allpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        MSD for All Species
+        plt_msd_all.py
       
     </span>
   </a>
@@ -846,10 +857,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#msd-convergence-check" class="md-nav__link">
+  <a href="#plt_msd_convergence_checkpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        MSD Convergence Check
+        plt_msd_convergence_check.py
       
     </span>
   </a>
@@ -857,10 +868,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#self-diffusion-coefficient" class="md-nav__link">
+  <a href="#plt_sdcpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Self-Diffusion Coefficient
+        plt_sdc.py
       
     </span>
   </a>
@@ -868,10 +879,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#arrhenius-diffusivity" class="md-nav__link">
+  <a href="#plt_arrhenius_dpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Arrhenius Diffusivity
+        plt_arrhenius_d.py
       
     </span>
   </a>
@@ -879,10 +890,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#arrhenius-ionic-conductivity" class="md-nav__link">
+  <a href="#plt_arrhenius_sigmapy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Arrhenius Ionic Conductivity
+        plt_arrhenius_sigma.py
       
     </span>
   </a>
@@ -907,10 +918,82 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#emd" class="md-nav__link">
+  <a href="#plt_emdpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_emd.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_nemdpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_nemd.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_hnemdpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_hnemd.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#structural-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Structural Analysis
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Structural Analysis">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_rdfpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_rdf.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_rdf_pmfpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_rdf_pmf.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_vacpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        EMD
+        plt_vac.py
       
     </span>
   </a>
@@ -918,10 +1001,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#nemd" class="md-nav__link">
+  <a href="#plt_cohesivepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        NEMD
+        plt_cohesive.py
       
     </span>
   </a>
@@ -929,10 +1012,38 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#hnemd" class="md-nav__link">
+  <a href="#plt_net_forcepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        HNEMD
+        plt_net_force.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#phonons" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Phonons
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Phonons">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_pdospy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_pdos.py
       
     </span>
   </a>
@@ -957,10 +1068,10 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#descriptor-visualization" class="md-nav__link">
+  <a href="#plt_descriptorspy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Descriptor Visualization
+        plt_descriptors.py
       
     </span>
   </a>
@@ -968,10 +1079,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#dimer-curve" class="md-nav__link">
+  <a href="#plt_descriptors_comparepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Dimer Curve
+        plt_descriptors_compare.py
       
     </span>
   </a>
@@ -979,10 +1090,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#density-of-atomistic-states" class="md-nav__link">
+  <a href="#plt_dimerpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Density of Atomistic States
+        plt_dimer.py
       
     </span>
   </a>
@@ -990,10 +1101,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#net-force-distribution" class="md-nav__link">
+  <a href="#plt_doaspy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Net Force Distribution
+        plt_doas.py
       
     </span>
   </a>
@@ -1621,10 +1732,10 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#training-results" class="md-nav__link">
+  <a href="#plt_trainpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Training Results
+        plt_train.py
       
     </span>
   </a>
@@ -1632,10 +1743,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#prediction-results" class="md-nav__link">
+  <a href="#plt_predictionpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Prediction Results
+        plt_prediction.py
       
     </span>
   </a>
@@ -1643,10 +1754,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#traintest-comparison" class="md-nav__link">
+  <a href="#plt_train_testpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Train/Test Comparison
+        plt_train_test.py
       
     </span>
   </a>
@@ -1654,10 +1765,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#density-parity-plot" class="md-nav__link">
+  <a href="#plt_parity_densitypy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Density Parity Plot
+        plt_parity_density.py
       
     </span>
   </a>
@@ -1665,10 +1776,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#force-error-analysis" class="md-nav__link">
+  <a href="#plt_force_errorspy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Force Error Analysis
+        plt_force_errors.py
       
     </span>
   </a>
@@ -1676,10 +1787,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#restart-parameters" class="md-nav__link">
+  <a href="#plt_learning_ratepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Restart Parameters
+        plt_learning_rate.py
       
     </span>
   </a>
@@ -1687,34 +1798,44 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#charge-and-born-effective-charge" class="md-nav__link">
+  <a href="#plt_nep_restartpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Charge and Born Effective Charge
+        plt_nep_restart.py
       
     </span>
   </a>
   
 </li>
         
-      </ul>
-    </nav>
+          <li class="md-nav__item">
+  <a href="#plt_chargepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_charge.py
+      
+    </span>
+  </a>
   
 </li>
-      
-        <li class="md-nav__item">
-  <a href="#molecular-dynamics-and-thermodynamics" class="md-nav__link">
+        
+          <li class="md-nav__item">
+  <a href="#plt_born_chargepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Molecular Dynamics and Thermodynamics
+        plt_born_charge.py
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="Molecular Dynamics and Thermodynamics">
-      <ul class="md-nav__list">
+</li>
         
-          <li class="md-nav__item">
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
   <a href="#thermodynamic-properties" class="md-nav__link">
     <span class="md-ellipsis">
       
@@ -1723,13 +1844,14 @@
     </span>
   </a>
   
-</li>
+    <nav class="md-nav" aria-label="Thermodynamic Properties">
+      <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#radial-distribution-function" class="md-nav__link">
+  <a href="#plt_thermopy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Radial Distribution Function
+        plt_thermo.py
       
     </span>
   </a>
@@ -1737,10 +1859,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#velocity-autocorrelation-and-pdos" class="md-nav__link">
+  <a href="#plt_thermo2py-plt_thermo3py" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Velocity Autocorrelation and PDOS
+        plt_thermo2.py &amp; plt_thermo3.py
       
     </span>
   </a>
@@ -1765,10 +1887,10 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#mean-square-displacement" class="md-nav__link">
+  <a href="#plt_msdpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Mean Square Displacement
+        plt_msd.py
       
     </span>
   </a>
@@ -1776,10 +1898,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#msd-for-all-species" class="md-nav__link">
+  <a href="#plt_msd_allpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        MSD for All Species
+        plt_msd_all.py
       
     </span>
   </a>
@@ -1787,10 +1909,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#msd-convergence-check" class="md-nav__link">
+  <a href="#plt_msd_convergence_checkpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        MSD Convergence Check
+        plt_msd_convergence_check.py
       
     </span>
   </a>
@@ -1798,10 +1920,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#self-diffusion-coefficient" class="md-nav__link">
+  <a href="#plt_sdcpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Self-Diffusion Coefficient
+        plt_sdc.py
       
     </span>
   </a>
@@ -1809,10 +1931,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#arrhenius-diffusivity" class="md-nav__link">
+  <a href="#plt_arrhenius_dpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Arrhenius Diffusivity
+        plt_arrhenius_d.py
       
     </span>
   </a>
@@ -1820,10 +1942,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#arrhenius-ionic-conductivity" class="md-nav__link">
+  <a href="#plt_arrhenius_sigmapy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Arrhenius Ionic Conductivity
+        plt_arrhenius_sigma.py
       
     </span>
   </a>
@@ -1848,10 +1970,10 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#emd" class="md-nav__link">
+  <a href="#plt_emdpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        EMD
+        plt_emd.py
       
     </span>
   </a>
@@ -1859,10 +1981,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#nemd" class="md-nav__link">
+  <a href="#plt_nemdpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        NEMD
+        plt_nemd.py
       
     </span>
   </a>
@@ -1870,10 +1992,110 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#hnemd" class="md-nav__link">
+  <a href="#plt_hnemdpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        HNEMD
+        plt_hnemd.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#structural-analysis" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Structural Analysis
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Structural Analysis">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_rdfpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_rdf.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_rdf_pmfpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_rdf_pmf.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_vacpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_vac.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_cohesivepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_cohesive.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_net_forcepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_net_force.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#phonons" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Phonons
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Phonons">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_pdospy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_pdos.py
       
     </span>
   </a>
@@ -1898,10 +2120,10 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#descriptor-visualization" class="md-nav__link">
+  <a href="#plt_descriptorspy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Descriptor Visualization
+        plt_descriptors.py
       
     </span>
   </a>
@@ -1909,10 +2131,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#dimer-curve" class="md-nav__link">
+  <a href="#plt_descriptors_comparepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Dimer Curve
+        plt_descriptors_compare.py
       
     </span>
   </a>
@@ -1920,10 +2142,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#density-of-atomistic-states" class="md-nav__link">
+  <a href="#plt_dimerpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Density of Atomistic States
+        plt_dimer.py
       
     </span>
   </a>
@@ -1931,10 +2153,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#net-force-distribution" class="md-nav__link">
+  <a href="#plt_doaspy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Net Force Distribution
+        plt_doas.py
       
     </span>
   </a>
@@ -1990,251 +2212,417 @@
 
 <div align="center">
   <h1>📊 Plot Scripts</h1>
-  <p style="text-align: justify;">The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators.</p>
+  <p style="text-align: justify;">The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators. All plots can be displayed interactively or saved as high-resolution PNG files.</p>
 </div>
 
 <p><strong>Script Location:</strong> <code>Scripts/plt_scripts/</code></p>
 <h2 id="quick-access">Quick Access</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w">          </span><span class="c1"># show all plotting options</span>
-<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w">   </span><span class="c1"># generate a plot</span>
-<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>save
-<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>-h
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w">              </span><span class="c1"># Show all plotting options</span>
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w">       </span><span class="c1"># Generate a plot</span>
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>save<span class="w">  </span><span class="c1"># Save plot as PNG</span>
+<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>-h<span class="w">    </span><span class="c1"># Show help for a specific plot type</span>
+</code></pre></div>
+<p>Running <code>gpumdkit.sh -plt</code> prints the plotting command menu:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>|                                    NEP Training &amp; Evaluation                                  |
+<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a>|  train          - NEP training results           prediction     - NEP prediction results      |
+<a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a>|  train_test     - NEP train and test results     parity_density - Parity density plot         |
+<a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a>|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |
+<a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a>|  charge         - Charge distribution            born_charge    - Born effective charges      |
+<a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a>|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |
+<a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a>|  des            - Descriptors                    lr             - Learning rate for gnep      |
+<a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a>|                                     Diffusion &amp; Transport                                     |
+<a id="__codelineno-1-16" name="__codelineno-1-16" href="#__codelineno-1-16"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-17" name="__codelineno-1-17" href="#__codelineno-1-17"></a>|  msd            - Mean square displacement       msd_conv       - MSD convergence             |
+<a id="__codelineno-1-18" name="__codelineno-1-18" href="#__codelineno-1-18"></a>|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |
+<a id="__codelineno-1-19" name="__codelineno-1-19" href="#__codelineno-1-19"></a>|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|
+<a id="__codelineno-1-20" name="__codelineno-1-20" href="#__codelineno-1-20"></a>|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |
+<a id="__codelineno-1-21" name="__codelineno-1-21" href="#__codelineno-1-21"></a>|  D_xyz          - Directional Arrhenius D                                                     |
+<a id="__codelineno-1-22" name="__codelineno-1-22" href="#__codelineno-1-22"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-23" name="__codelineno-1-23" href="#__codelineno-1-23"></a>|                                    MD &amp; Structural Analysis                                   |
+<a id="__codelineno-1-24" name="__codelineno-1-24" href="#__codelineno-1-24"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-25" name="__codelineno-1-25" href="#__codelineno-1-25"></a>|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |
+<a id="__codelineno-1-26" name="__codelineno-1-26" href="#__codelineno-1-26"></a>|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
+<a id="__codelineno-1-27" name="__codelineno-1-27" href="#__codelineno-1-27"></a>|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
+<a id="__codelineno-1-28" name="__codelineno-1-28" href="#__codelineno-1-28"></a>|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
+<a id="__codelineno-1-29" name="__codelineno-1-29" href="#__codelineno-1-29"></a>|  doas           - Density of atomistic states                                                 |
+<a id="__codelineno-1-30" name="__codelineno-1-30" href="#__codelineno-1-30"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-31" name="__codelineno-1-31" href="#__codelineno-1-31"></a>|                                        Heat Transport                                         |
+<a id="__codelineno-1-32" name="__codelineno-1-32" href="#__codelineno-1-32"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-33" name="__codelineno-1-33" href="#__codelineno-1-33"></a>|  emd            - EMD results                    nemd           - NEMD results                |
+<a id="__codelineno-1-34" name="__codelineno-1-34" href="#__codelineno-1-34"></a>|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |
+<a id="__codelineno-1-35" name="__codelineno-1-35" href="#__codelineno-1-35"></a>+-----------------------------------------------------------------------------------------------+
 </code></pre></div>
+<hr />
 <h2 id="nep-training-and-prediction">NEP Training and Prediction</h2>
-<h3 id="training-results">Training Results</h3>
-<p><code>plt_train.py</code> visualizes NEP training progress, including loss curves and parity plots for energy, force, and virial/stress.</p>
-<p><strong>Input files:</strong></p>
-<ul>
-<li><code>loss.out</code></li>
-<li><code>energy_train.out</code></li>
-<li><code>force_train.out</code></li>
-<li><code>virial_train.out</code></li>
-</ul>
-<p><strong>Usage:</strong></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<h3 id="plt_trainpy">plt_train.py</h3>
+<p>Visualizes NEP training progress including loss curves, RMSE evolution, and parity plots comparing DFT vs NEP predictions for energy, forces, and stresses.</p>
+<p><strong>Input Files:</strong> <code>loss.out</code>, <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/train.png" alt="NEP training results" width="75%" />
 </div>
 
-<h3 id="prediction-results">Prediction Results</h3>
-<p><code>plt_prediction.py</code> visualizes prediction/test-set results.</p>
-<p><strong>Input files:</strong></p>
-<ul>
-<li><code>energy_test.out</code></li>
-<li><code>force_test.out</code></li>
-<li><code>virial_test.out</code></li>
-</ul>
-<p><strong>Usage:</strong></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>prediction
-<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
+<hr />
+<h3 id="plt_predictionpy">plt_prediction.py</h3>
+<p>Visualizes NEP prediction results on the test set.</p>
+<p><strong>Input Files:</strong> <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>prediction
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span><span class="w">         </span><span class="c1"># Alternative command</span>
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/prediction.png" alt="NEP prediction results" width="75%" />
 </div>
 
-<h3 id="traintest-comparison">Train/Test Comparison</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train_test
+<hr />
+<h3 id="plt_train_testpy">plt_train_test.py</h3>
+<p>Creates combined parity plots for both training and testing datasets.</p>
+<p><strong>Input Files:</strong> <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code>, <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train_test
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/train_test.png" alt="NEP train and test comparison" width="75%" />
 </div>
 
-<h3 id="density-parity-plot">Density Parity Plot</h3>
-<p>For large datasets, density-based parity plots are often easier to read than raw scatter plots.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>parity_density
+<hr />
+<h3 id="plt_parity_densitypy">plt_parity_density.py</h3>
+<p>Generates density-based parity plots for energies, forces, and stresses. Useful for large datasets where scatter plots become unreadable.</p>
+<p><strong>Input Files:</strong> <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>parity_density
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/parity_plot_density.png" alt="Parity density plot" width="70%" />
 </div>
 
-<h3 id="force-error-analysis">Force Error Analysis</h3>
-<p><code>plt_force_errors.py</code> plots force magnitude and angular errors following the analysis style proposed by <a href="https://doi.org/10.1038/s41524-023-01123-3">Liu et al.</a>.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>force_errors
+<hr />
+<h3 id="plt_force_errorspy">plt_force_errors.py</h3>
+<p>Plots force error evaluation metrics as proposed by <a href="https://doi.org/10.1038/s41524-023-01123-3">Liu et al.</a>.</p>
+<p><strong>Input File:</strong> <code>force_train.out</code></p>
+<p><strong>Metrics Displayed:</strong>
+- Force magnitude errors (delta_F)
+- Force angle errors (delta_theta)
+- Distribution of errors</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>force_errors
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/force_errors.png" alt="Force error analysis" width="70%" />
 </div>
 
-<h3 id="restart-parameters">Restart Parameters</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>restart
+<hr />
+<h3 id="plt_learning_ratepy">plt_learning_rate.py</h3>
+<p>Visualizes learning rate during <code>gnep</code> training.</p>
+<p><strong>Input File:</strong> <code>loss.out</code></p>
+<p><strong>Note:</strong> Only for the <code>gnep</code> training process.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>lr
+</code></pre></div>
+<hr />
+<h3 id="plt_nep_restartpy">plt_nep_restart.py</h3>
+<p>Visualizes parameters stored in the <code>nep.restart</code> file.</p>
+<p><strong>Input File:</strong> <code>nep.restart</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>restart
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/nep_restart.png" alt="NEP restart parameters" width="60%" />
 </div>
 
-<h3 id="charge-and-born-effective-charge">Charge and Born Effective Charge</h3>
-<p>For qNEP charge output:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>charge
+<hr />
+<h3 id="plt_chargepy">plt_charge.py</h3>
+<p>Plots charge distribution from <code>qNEP</code> model.</p>
+<p><strong>Input File:</strong> <code>charge_train.out</code></p>
+<p><strong>Important:</strong> Ensure consistency between training set and charge output atom ordering. Use full batch training or run prediction step first.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>charge
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/charge.png" alt="Charge distribution" width="45%" />
 </div>
 
-<p>For Born effective charge prediction:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>born_charge
-<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>bec
+<hr />
+<h3 id="plt_born_chargepy">plt_born_charge.py</h3>
+<p>Creates parity plots for Born effective charges (BEC) on training and testing datasets. Structures with all-zero reference BEC are filtered out.</p>
+<p><strong>Input Files:</strong> <code>bec_train.out</code>, <code>bec_test.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>born_charge
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>bec<span class="w">          </span><span class="c1"># Alternative command</span>
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/born_charge.png" alt="Born effective charge parity plot" width="45%" />
 </div>
 
-<h2 id="molecular-dynamics-and-thermodynamics">Molecular Dynamics and Thermodynamics</h2>
-<h3 id="thermodynamic-properties">Thermodynamic Properties</h3>
-<p><code>plt_thermo.py</code> reads <code>thermo.out</code> and plots temperature, potential energy, pressure, and other thermodynamic quantities.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
-<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo2
-<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo3
+<hr />
+<h2 id="thermodynamic-properties">Thermodynamic Properties</h2>
+<h3 id="plt_thermopy">plt_thermo.py</h3>
+<p>Primary script for comprehensive thermodynamic property visualization.</p>
+<p><strong>Input File:</strong> <code>thermo.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/thermo.png" alt="Thermo plot" width="75%" />
 </div>
 
-<h3 id="radial-distribution-function">Radial Distribution Function</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf
-<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf<span class="w"> </span>&lt;column&gt;
+<hr />
+<h3 id="plt_thermo2py-plt_thermo3py">plt_thermo2.py &amp; plt_thermo3.py</h3>
+<p>Alternative thermodynamic visualization with different styles.</p>
+<p><strong>Input File:</strong> <code>thermo.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo2
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo3
 </code></pre></div>
-<p>Full RDF output:</p>
-<div align="center">
-  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
-</div>
-
-<p>Single pair RDF:</p>
-<div align="center">
-  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
-</div>
-
-<h3 id="velocity-autocorrelation-and-pdos">Velocity Autocorrelation and PDOS</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos
-<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos<span class="w"> </span>save
-</code></pre></div>
-<p><strong>Input files:</strong> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></p>
-<div align="center">
-  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
-</div>
-
-<p>Heat capacity output:</p>
-<div align="center">
-  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
-</div>
-
+<hr />
 <h2 id="diffusion-and-ionic-transport">Diffusion and Ionic Transport</h2>
-<h3 id="mean-square-displacement">Mean Square Displacement</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<h3 id="plt_msdpy">plt_msd.py</h3>
+<p>Plots mean square displacement (MSD) for all directions.</p>
+<p><strong>Input File:</strong> <code>msd.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/msd.png" alt="Mean square displacement" width="48%" />
 </div>
 
-<h3 id="msd-for-all-species">MSD for All Species</h3>
-<p>Use this when <code>compute_msd</code> in <code>run.in</code> was configured with <code>all_groups</code>.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd_all<span class="w"> </span>msd.out<span class="w"> </span>Li<span class="w"> </span>P<span class="w"> </span>S
+<hr />
+<h3 id="plt_msd_allpy">plt_msd_all.py</h3>
+<p>Plots MSD for all atomic species separately when using <code>all_groups</code> in GPUMD.</p>
+<p><strong>Input File:</strong> <code>msd.out</code> (computed with <code>all_groups</code> option)</p>
+<p><strong>Requirements:</strong> Must use <code>all_groups</code> in the <code>compute_msd</code> command in <code>run.in</code>.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd_all<span class="w"> </span>msd.out<span class="w"> </span>Li<span class="w"> </span>P<span class="w"> </span>S
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/msd_all.png" alt="MSD for all species" width="48%" />
 </div>
 
-<h3 id="msd-convergence-check">MSD Convergence Check</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd_conv
+<hr />
+<h3 id="plt_msd_convergence_checkpy">plt_msd_convergence_check.py</h3>
+<p>Checks convergence of MSD calculations across different time windows.</p>
+<p><strong>Input File:</strong> <code>msd_step*.out</code> (computed with <code>save_every</code> option)</p>
+<p><strong>Requirements:</strong> Use <code>save_every</code> in the <code>compute_msd</code> command.</p>
+<p><strong>Purpose:</strong> Verify MSD has converged sufficiently for accurate diffusion coefficient calculation.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd_conv
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/msd_convergence.png" alt="MSD convergence" width="48%" />
 </div>
 
-<h3 id="self-diffusion-coefficient">Self-Diffusion Coefficient</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+<hr />
+<h3 id="plt_sdcpy">plt_sdc.py</h3>
+<p>Plots self-diffusion coefficient (SDC) vs time.</p>
+<p><strong>Input File:</strong> <code>msd.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/sdc.png" alt="Self-diffusion coefficient" width="48%" />
 </div>
 
-<h3 id="arrhenius-diffusivity">Arrhenius Diffusivity</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_d
-<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>D
+<hr />
+<h3 id="plt_arrhenius_dpy">plt_arrhenius_d.py</h3>
+<p>Creates Arrhenius plot for diffusivity (log10 D vs 1000/T).</p>
+<p><strong>Input Files:</strong> <code>*K/msd.out</code> files (each temperature subdirectory should contain an <code>msd.out</code>)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_d
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>D<span class="w">             </span><span class="c1"># Alternative command</span>
+</code></pre></div>
+<p><strong>Output example:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>T: 300K, D_total: 1.001e-07 cm2/s
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>T: 350K, D_total: 4.184e-07 cm2/s
+<a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a>T: 400K, D_total: 1.027e-06 cm2/s
+<a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a>Ea: 0.230 eV
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/Arrhenius_D.png" alt="Arrhenius diffusivity" width="58%" />
 </div>
 
-<p>Example output:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>T: 300K, D_total: 1.001e-07 cm2/s
-<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>T: 350K, D_total: 4.184e-07 cm2/s
-<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>T: 400K, D_total: 1.027e-06 cm2/s
-<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a>Ea: 0.230 eV
-</code></pre></div>
-<h3 id="arrhenius-ionic-conductivity">Arrhenius Ionic Conductivity</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_sigma
-<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sigma
+<hr />
+<h3 id="plt_arrhenius_sigmapy">plt_arrhenius_sigma.py</h3>
+<p>Creates Arrhenius plot for ionic conductivity (ln(σ·T) vs 1000/T).</p>
+<p><strong>Input Files:</strong> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> (each temperature subdirectory)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_sigma
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sigma<span class="w">         </span><span class="c1"># Alternative command</span>
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/Arrhenius_sigma.png" alt="Arrhenius ionic conductivity" width="58%" />
 </div>
 
+<hr />
 <h2 id="heat-transport">Heat Transport</h2>
-<h3 id="emd">EMD</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>emd<span class="w"> </span>x
+<h3 id="plt_emdpy">plt_emd.py</h3>
+<p>Analyzes and plots thermal conductivity from equilibrium molecular dynamics (EMD).</p>
+<p><strong>Input Files:</strong> EMD output files from GPUMD</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>emd<span class="w"> </span>x<span class="w">        </span><span class="c1"># for x direction</span>
 </code></pre></div>
 <div align="center">
-  <img src="../../Gallery/emd.png" alt="EMD thermal conductivity" width="72%" />
+  <img src="../../Gallery/emd.png" alt="EMD thermal conductivity" width="70%" />
 </div>
 
-<h3 id="nemd">NEMD</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>nemd<span class="w"> </span><span class="o">[</span>real_length<span class="o">]</span><span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
-</code></pre></div>
-<p>Parameter notes:</p>
+<hr />
+<h3 id="plt_nemdpy">plt_nemd.py</h3>
+<p>Visualizes non-equilibrium molecular dynamics (NEMD) thermal transport properties.</p>
+<p><strong>Input Files:</strong> NEMD output files from GPUMD</p>
+<p><strong>Parameters:</strong></p>
 <table>
 <thead>
 <tr>
 <th>Parameter</th>
-<th>Meaning</th>
+<th>Description</th>
 </tr>
 </thead>
 <tbody>
 <tr>
 <td><code>real_length</code></td>
-<td>real length of heat-transfer zone in nm; use <code>Auto</code> for automatic calculation</td>
+<td>Real length of heat transfer zone in nm (set to <code>Auto</code> for auto-calculation)</td>
 </tr>
 <tr>
 <td><code>scale_eff_size</code></td>
-<td>scale factor for effective cross-sectional area</td>
+<td>Scale factor for effective cross-sectional area (default: 1). For 3D bulk: use 1. For low-dimensional systems with vacuum: S_box / S_eff</td>
 </tr>
 <tr>
 <td><code>cutoff_freq</code></td>
-<td>cutoff frequency for SHC calculation in THz</td>
+<td>Cutoff frequency for SHC calculation in THz (default: 60)</td>
 </tr>
 <tr>
 <td><code>save</code></td>
-<td>optional flag to save the figure</td>
+<td>Optional, save the plot as <code>nemd.png</code></td>
 </tr>
 </tbody>
 </table>
+<p><strong>Note:</strong> If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>nemd<span class="w"> </span><span class="o">[</span>real_length<span class="o">]</span><span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
+</code></pre></div>
 <div align="center">
-  <img src="../../Gallery/nemd.png" alt="NEMD results" width="72%" />
+  <img src="../../Gallery/nemd.png" alt="NEMD results" width="70%" />
 </div>
 
-<h3 id="hnemd">HNEMD</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>hnemd<span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
+<hr />
+<h3 id="plt_hnemdpy">plt_hnemd.py</h3>
+<p>Plots homogeneous non-equilibrium molecular dynamics (HNEMD) results.</p>
+<p><strong>Input Files:</strong> HNEMD output files from GPUMD</p>
+<p><strong>Parameters:</strong></p>
+<table>
+<thead>
+<tr>
+<th>Parameter</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>scale_eff_size</code></td>
+<td>Scale factor for effective cross-sectional area (default: 1)</td>
+</tr>
+<tr>
+<td><code>cutoff_freq</code></td>
+<td>Cutoff frequency for SHC calculation in THz (default: 60)</td>
+</tr>
+<tr>
+<td><code>save</code></td>
+<td>Optional, save the plot as <code>hnemd.png</code></td>
+</tr>
+</tbody>
+</table>
+<p><strong>Note:</strong> If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>hnemd<span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
 </code></pre></div>
 <div align="center">
-  <img src="../../Gallery/hnemd.png" alt="HNEMD results" width="72%" />
+  <img src="../../Gallery/hnemd.png" alt="HNEMD results" width="70%" />
 </div>
 
-<h2 id="descriptor-dimer-and-extra-analysis">Descriptor, Dimer, and Extra Analysis</h2>
-<h3 id="descriptor-visualization">Descriptor Visualization</h3>
-<p>First calculate descriptors:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
+<hr />
+<h2 id="structural-analysis">Structural Analysis</h2>
+<h3 id="plt_rdfpy">plt_rdf.py</h3>
+<p>Plots radial distribution function (RDF) showing pair correlations.</p>
+<p><strong>Input File:</strong> <code>rdf.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-23-1" name="__codelineno-23-1" href="#__codelineno-23-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf<span class="w">               </span><span class="c1"># Plot all RDF pairs</span>
+<a id="__codelineno-23-2" name="__codelineno-23-2" href="#__codelineno-23-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf<span class="w"> </span>&lt;column&gt;<span class="w">      </span><span class="c1"># Plot specific pair</span>
+</code></pre></div>
+<p><strong>Full RDF output:</strong></p>
+<div align="center">
+  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
+</div>
+
+<p><strong>Single pair RDF:</strong></p>
+<div align="center">
+  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
+</div>
+
+<hr />
+<h3 id="plt_rdf_pmfpy">plt_rdf_pmf.py</h3>
+<p>Plots RDF combined with potential of mean force (PMF).</p>
+<p><strong>Input File:</strong> <code>rdf.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-24-1" name="__codelineno-24-1" href="#__codelineno-24-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf_pmf
+</code></pre></div>
+<hr />
+<h3 id="plt_vacpy">plt_vac.py</h3>
+<p>Plots velocity autocorrelation function (VAC). Useful for analyzing phonon properties and atomic dynamics.</p>
+<p><strong>Input File:</strong> <code>sdc.out</code> (the VAC columns are read from this file by the plotting script)</p>
+<p><strong>Output:</strong> Interactive plot or <code>vac.png</code> (with <code>save</code> option)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-25-1" name="__codelineno-25-1" href="#__codelineno-25-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>vac
+</code></pre></div>
+<hr />
+<h3 id="plt_cohesivepy">plt_cohesive.py</h3>
+<p>Plots cohesive energy curve from <code>cohesive.out</code>. Useful for analyzing lattice stability and equilibrium lattice constants.</p>
+<p><strong>Input File:</strong> <code>cohesive.out</code> (isotropic scaling factor vs cohesive energy)</p>
+<p><strong>Output:</strong> Interactive plot or <code>cohesive.png</code> (with <code>save</code> option)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-26-1" name="__codelineno-26-1" href="#__codelineno-26-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>cohesive
+</code></pre></div>
+<hr />
+<h3 id="plt_net_forcepy">plt_net_force.py</h3>
+<p>Plots distribution of net forces on structures, useful for identifying problematic configurations.</p>
+<p><strong>Input File:</strong> <code>train.xyz</code> (extxyz format)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-27-1" name="__codelineno-27-1" href="#__codelineno-27-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>net_force<span class="w"> </span>train.xyz
+</code></pre></div>
+<p><strong>Reference:</strong> <a href="https://arxiv.org/abs/2510.19774">arXiv:2510.19774</a></p>
+<div align="center">
+  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
+</div>
+
+<hr />
+<h2 id="phonons">Phonons</h2>
+<h3 id="plt_pdospy">plt_pdos.py</h3>
+<p>Calculates and plots normalized VAC, PDOS, and Heat Capacity (Cv).</p>
+<p><strong>Input Files:</strong> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-28-1" name="__codelineno-28-1" href="#__codelineno-28-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos
+<a id="__codelineno-28-2" name="__codelineno-28-2" href="#__codelineno-28-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos<span class="w"> </span>save
 </code></pre></div>
-<p>Then visualize:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-23-1" name="__codelineno-23-1" href="#__codelineno-23-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
-<a id="__codelineno-23-2" name="__codelineno-23-2" href="#__codelineno-23-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
+<div align="center">
+  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
+</div>
+
+<p>Heat capacity output:</p>
+<div align="center">
+  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
+</div>
+
+<hr />
+<h2 id="descriptor-dimer-and-extra-analysis">Descriptor, Dimer, and Extra Analysis</h2>
+<h3 id="plt_descriptorspy">plt_descriptors.py</h3>
+<p>Visualizes high-dimensional NEP descriptors using dimensionality reduction (PCA or UMAP).</p>
+<p><strong>Input File:</strong> <code>descriptors.npy</code> (generated by <code>gpumdkit.sh -calc des</code>)</p>
+<p><strong>Methods:</strong>
+- <code>pca</code> — Principal Component Analysis
+- <code>umap</code> — Uniform Manifold Approximation and Projection</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-29-1" name="__codelineno-29-1" href="#__codelineno-29-1"></a><span class="c1"># First generate descriptors</span>
+<a id="__codelineno-29-2" name="__codelineno-29-2" href="#__codelineno-29-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
+<a id="__codelineno-29-3" name="__codelineno-29-3" href="#__codelineno-29-3"></a>
+<a id="__codelineno-29-4" name="__codelineno-29-4" href="#__codelineno-29-4"></a><span class="c1"># Then visualize</span>
+<a id="__codelineno-29-5" name="__codelineno-29-5" href="#__codelineno-29-5"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
+<a id="__codelineno-29-6" name="__codelineno-29-6" href="#__codelineno-29-6"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/des_umap.png" alt="UMAP descriptor visualization" width="52%" />
 </div>
 
-<h3 id="dimer-curve">Dimer Curve</h3>
-<p><code>plt_dimer.py</code> places two atoms in a large cubic box and calculates energy/force as a function of dimer distance using a NEP model.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-24-1" name="__codelineno-24-1" href="#__codelineno-24-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span>nep.txt
+<hr />
+<h3 id="plt_descriptors_comparepy">plt_descriptors_compare.py</h3>
+<p>Compares descriptors from multiple training sets or models.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-30-1" name="__codelineno-30-1" href="#__codelineno-30-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des_compare
+</code></pre></div>
+<hr />
+<h3 id="plt_dimerpy">plt_dimer.py</h3>
+<p>Plots dimer interaction curves. Two atoms are placed in a cubic box (30 Å) and the potential energy and force are calculated as a function of dimer distance using a NEP model.</p>
+<p><strong>Input File:</strong> <code>nep.txt</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-31-1" name="__codelineno-31-1" href="#__codelineno-31-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>&lt;element1&gt;<span class="w"> </span>&lt;element2&gt;<span class="w"> </span>&lt;nep_model&gt;
+<a id="__codelineno-31-2" name="__codelineno-31-2" href="#__codelineno-31-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span>nep.txt
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/dimer_nep.png" alt="Dimer NEP curve" width="45%" />
@@ -2242,41 +2630,40 @@ <h3 id="dimer-curve">Dimer Curve</h3>
 </div>
 
 <p><strong>Reference:</strong> <a href="https://doi.org/10.1021/acs.jcim.5c02335">J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</a></p>
-<h3 id="density-of-atomistic-states">Density of Atomistic States</h3>
-<p><code>plt_doas.py</code> plots the density of atomistic states proposed by <a href="https://doi.org/10.1002/anie.202215544">Wang et al.</a>.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-25-1" name="__codelineno-25-1" href="#__codelineno-25-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
+<hr />
+<h3 id="plt_doaspy">plt_doas.py</h3>
+<p>Plots density of atomistic states (DOAS) proposed by <a href="https://doi.org/10.1002/anie.202215544">Wang et al.</a>.</p>
+<p><strong>Input File:</strong> <code>doas.out</code> (calculated by <code>gpumdkit.sh -calc doas</code>)</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-32-1" name="__codelineno-32-1" href="#__codelineno-32-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>&lt;doas.out&gt;<span class="w"> </span>&lt;species&gt;
+<a id="__codelineno-32-2" name="__codelineno-32-2" href="#__codelineno-32-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
 </div>
 
-<h3 id="net-force-distribution">Net Force Distribution</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-26-1" name="__codelineno-26-1" href="#__codelineno-26-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>net_force<span class="w"> </span>train.xyz
-</code></pre></div>
-<p><strong>Reference:</strong> <a href="https://arxiv.org/abs/2510.19774">arXiv:2510.19774</a></p>
-<div align="center">
-  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
-</div>
-
+<hr />
 <h2 id="plane-grid-plot-for-polar-materials">Plane-Grid Plot for Polar Materials</h2>
-<p>This workflow maps displacement or polarization data onto a grid and plots selected plane profiles.</p>
-<p>Typical upstream steps:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-27-1" name="__codelineno-27-1" href="#__codelineno-27-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span><span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
-<a id="__codelineno-27-2" name="__codelineno-27-2" href="#__codelineno-27-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Pb_Sr-O.dat<span class="w"> </span>-o<span class="w"> </span>displacements.dat
-<a id="__codelineno-27-3" name="__codelineno-27-3" href="#__codelineno-27-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+<p>This workflow maps displacement or polarization data onto a grid and plots selected plane profiles. For detailed usage and real-world examples, see <strong><a href="polar_material_analysis.html">Polar Material Analysis</a></strong>.</p>
+<p><strong>Dependency:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-33-1" name="__codelineno-33-1" href="#__codelineno-33-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
 </code></pre></div>
-<p>Plot:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-28-1" name="__codelineno-28-1" href="#__codelineno-28-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr
-<a id="__codelineno-28-2" name="__codelineno-28-2" href="#__codelineno-28-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span>
+<p><strong>Typical upstream steps:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-34-1" name="__codelineno-34-1" href="#__codelineno-34-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span><span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
+<a id="__codelineno-34-2" name="__codelineno-34-2" href="#__codelineno-34-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Pb_Sr-O.dat<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+<a id="__codelineno-34-3" name="__codelineno-34-3" href="#__codelineno-34-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
 </code></pre></div>
-<p>This function requires <code>ferrodispcalc</code>.</p>
+<p><strong>Usage:</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-35-1" name="__codelineno-35-1" href="#__codelineno-35-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr
+<a id="__codelineno-35-2" name="__codelineno-35-2" href="#__codelineno-35-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span>
+</code></pre></div>
+<hr />
 <h2 id="quick-reference-table">Quick Reference Table</h2>
 <table>
 <thead>
 <tr>
 <th>Command</th>
 <th>Input File(s)</th>
-<th>Purpose</th>
+<th>Description</th>
 </tr>
 </thead>
 <tbody>
@@ -2286,38 +2673,123 @@ <h2 id="quick-reference-table">Quick Reference Table</h2>
 <td>NEP training plots</td>
 </tr>
 <tr>
-<td><code>prediction</code></td>
+<td><code>prediction</code> / <code>test</code></td>
 <td><code>*_test.out</code></td>
 <td>NEP prediction plots</td>
 </tr>
 <tr>
 <td><code>train_test</code></td>
-<td>train/test outputs</td>
-<td>combined parity plots</td>
+<td><code>*_train.out</code>, <code>*_test.out</code></td>
+<td>Combined parity plots</td>
+</tr>
+<tr>
+<td><code>parity_density</code></td>
+<td><code>*_train.out</code></td>
+<td>Density-based parity plots</td>
+</tr>
+<tr>
+<td><code>force_errors</code></td>
+<td><code>force_train.out</code></td>
+<td>Force error metrics</td>
+</tr>
+<tr>
+<td><code>lr</code></td>
+<td><code>loss.out</code> (gnep)</td>
+<td>Learning rate</td>
+</tr>
+<tr>
+<td><code>restart</code></td>
+<td><code>nep.restart</code></td>
+<td>Restart file parameters</td>
+</tr>
+<tr>
+<td><code>charge</code></td>
+<td><code>charge_train.out</code></td>
+<td>Charge distribution</td>
+</tr>
+<tr>
+<td><code>born_charge</code> / <code>bec</code></td>
+<td><code>bec_train.out</code>, <code>bec_test.out</code></td>
+<td>Born effective charges</td>
 </tr>
 <tr>
 <td><code>thermo</code></td>
 <td><code>thermo.out</code></td>
-<td>thermodynamic properties</td>
+<td>Thermodynamic properties</td>
 </tr>
 <tr>
 <td><code>msd</code></td>
 <td><code>msd.out</code></td>
-<td>mean square displacement</td>
+<td>Mean square displacement</td>
+</tr>
+<tr>
+<td><code>msd_all</code></td>
+<td><code>msd.out</code> (all_groups)</td>
+<td>MSD for all species</td>
+</tr>
+<tr>
+<td><code>msd_conv</code></td>
+<td><code>msd_step*.out</code></td>
+<td>MSD convergence check</td>
 </tr>
 <tr>
 <td><code>sdc</code></td>
 <td><code>msd.out</code></td>
-<td>self-diffusion coefficient</td>
+<td>Self-diffusion coefficient</td>
+</tr>
+<tr>
+<td><code>arrhenius_d</code> / <code>D</code></td>
+<td><code>*K/msd.out</code></td>
+<td>Arrhenius diffusivity</td>
+</tr>
+<tr>
+<td><code>arrhenius_sigma</code> / <code>sigma</code></td>
+<td><code>*K/{model.xyz, run.in, thermo.out, msd.out}</code></td>
+<td>Arrhenius ionic conductivity</td>
 </tr>
 <tr>
 <td><code>rdf</code></td>
 <td><code>rdf.out</code></td>
-<td>radial distribution function</td>
+<td>Radial distribution function</td>
+</tr>
+<tr>
+<td><code>rdf_pmf</code></td>
+<td><code>rdf.out</code></td>
+<td>RDF + potential of mean force</td>
+</tr>
+<tr>
+<td><code>vac</code></td>
+<td><code>sdc.out</code></td>
+<td>Velocity autocorrelation</td>
+</tr>
+<tr>
+<td><code>cohesive</code></td>
+<td><code>cohesive.out</code></td>
+<td>Cohesive energy curve</td>
+</tr>
+<tr>
+<td><code>net_force</code></td>
+<td><code>train.xyz</code></td>
+<td>Net force distribution</td>
+</tr>
+<tr>
+<td><code>doas</code></td>
+<td><code>doas.out</code></td>
+<td>Density of atomistic states</td>
+</tr>
+<tr>
+<td><code>des</code></td>
+<td><code>descriptors.npy</code></td>
+<td>Descriptor PCA/UMAP</td>
+</tr>
+<tr>
+<td><code>dimer</code></td>
+<td><code>nep.txt</code></td>
+<td>Dimer energy/force curve</td>
 </tr>
 <tr>
 <td><code>pdos</code></td>
-<td><code>dos.out</code>, <code>mvac.out</code></td>
+<td><code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></td>
 <td>VAC and PDOS</td>
 </tr>
 <tr>
@@ -2336,24 +2808,9 @@ <h2 id="quick-reference-table">Quick Reference Table</h2>
 <td>HNEMD thermal transport</td>
 </tr>
 <tr>
-<td><code>des</code></td>
-<td><code>descriptors.npy</code></td>
-<td>descriptor PCA/UMAP</td>
-</tr>
-<tr>
-<td><code>dimer</code></td>
-<td><code>nep.txt</code></td>
-<td>dimer energy/force curve</td>
-</tr>
-<tr>
-<td><code>doas</code></td>
-<td><code>doas.out</code></td>
-<td>density of atomistic states</td>
-</tr>
-<tr>
-<td><code>net_force</code></td>
-<td><code>train.xyz</code></td>
-<td>net force distribution</td>
+<td><code>viscosity</code></td>
+<td>Viscosity outputs</td>
+<td>Viscosity</td>
 </tr>
 </tbody>
 </table>
diff --git a/docs/htmls/en/polar_material_analysis.html b/docs/htmls/en/polar_material_analysis.html
index 9778142..9646805 100644
--- a/docs/htmls/en/polar_material_analysis.html
+++ b/docs/htmls/en/polar_material_analysis.html
@@ -143,7 +143,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#dependency" class="md-skip">
+        <a href="#overview" class="md-skip">
           Skip to content
         </a>
       
@@ -740,6 +740,17 @@
     </label>
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
+        <li class="md-nav__item">
+  <a href="#overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
         <li class="md-nav__item">
   <a href="#dependency" class="md-nav__link">
     <span class="md-ellipsis">
@@ -1698,6 +1709,17 @@
     </label>
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
+        <li class="md-nav__item">
+  <a href="#overview" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Overview
+      
+    </span>
+  </a>
+  
+</li>
+      
         <li class="md-nav__item">
   <a href="#dependency" class="md-nav__link">
     <span class="md-ellipsis">
@@ -2202,30 +2224,103 @@ <h1>🧲 Polar Material Analysis</h1>
 <li><code>oct-tilt</code> is for octahedral environments (requires 6 neighbors around each center).</li>
 <li><code>pol-abo3</code> is specific to <code>ABO3</code> polarization analysis.</li>
 </ul>
+<h2 id="overview">Overview</h2>
+<table>
+<thead>
+<tr>
+<th>Step</th>
+<th>CLI Command</th>
+<th>Main Input</th>
+<th>Output</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>Build neighbor list</td>
+<td><code>gpumdkit.sh -calc nlist ...</code></td>
+<td><code>model.xyz</code></td>
+<td><code>nl-*.dat</code></td>
+</tr>
+<tr>
+<td>Calculate displacement</td>
+<td><code>gpumdkit.sh -calc disp ...</code></td>
+<td>trajectory + <code>nl-*.dat</code></td>
+<td><code>displacements.dat</code></td>
+</tr>
+<tr>
+<td>Average trajectory</td>
+<td><code>gpumdkit.sh -calc avg-struct ...</code></td>
+<td>trajectory</td>
+<td>averaged extxyz</td>
+</tr>
+<tr>
+<td>Octahedral tilt</td>
+<td><code>gpumdkit.sh -calc oct-tilt ...</code></td>
+<td>trajectory + B-O neighbor list</td>
+<td>tilt-angle table</td>
+</tr>
+<tr>
+<td>ABO3 polarization</td>
+<td><code>gpumdkit.sh -calc pol-abo3 ...</code></td>
+<td>trajectory + neighbor lists</td>
+<td>polarization table</td>
+</tr>
+<tr>
+<td>Plane-grid plot</td>
+<td><code>gpumdkit.sh -plt plane-grid ...</code></td>
+<td>structure + displacement data</td>
+<td>plane profile plot</td>
+</tr>
+</tbody>
+</table>
 <h2 id="dependency">Dependency</h2>
 <p>These scripts require <code>ferrodispcalc</code>:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
 </code></pre></div>
 <h2 id="interactive-mode-entry">Interactive mode entry</h2>
 <p>Options <code>406-410</code> are the core functions for this tutorial. The sections below explain when to use each one and how to run it.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="c1"># choose 4) Calculators</span>
+</code></pre></div>
+<p>The calculator menu is:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>|                     CALCULATOR TOOLS                     |
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>| 401) Calc ionic conductivity                             |
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>| 402) Calc properties by nep                              |
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>| 403) Calc descriptors of specific elements               |
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>| 404) Calc density of atomistic states (DOAS)             |
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>| 405) Calc nudged elastic band (NEB) by nep               |
+<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>| 406) Build neighbor list                                 |
+<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a>| 407) Calc displacement from trajectory                   |
+<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a>| 408) Calc averaged structure                             |
+<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a>| 409) Calc octahedral tilt                                |
+<a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a>| 410) Calc polarization for ABO3                          |
+<a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a>| 411) Minimize structure by nep                           |
+<a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a>| 412) Calc mean square displacement (MSD) from trajectory |
+<a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-17" name="__codelineno-2-17" href="#__codelineno-2-17"></a>| 000) Return to the main menu                             |
+<a id="__codelineno-2-18" name="__codelineno-2-18" href="#__codelineno-2-18"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-19" name="__codelineno-2-19" href="#__codelineno-2-19"></a>Input the function number:
+</code></pre></div>
 <p>For full argument details, use:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-h
-<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-h
-<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-h
-<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-h
-<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-h
-<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-h
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-h
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-h
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-h
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-h
+<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-h
+<a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-h
 </code></pre></div>
 <h2 id="406-build-neighbor-list-calc_neighbor_listpy">406) Build neighbor list (<code>calc_neighbor_list.py</code>)</h2>
 <p>Build neighbor lists for selected center and neighbor elements.</p>
 <p>When to use it:
 This is usually the first step before <code>disp</code>, <code>oct-tilt</code>, and <code>pol-abo3</code>, because those scripts read <code>nl-*.dat</code> neighbor files.</p>
 <h3 id="usage">Usage</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="c1"># Example 1: Ti-O nearest 6 neighbors for octahedral analysis</span>
-<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
-<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
-<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="c1"># Example 2: Pb/Sr-O nearest 12 neighbors for A-site centered analysis</span>
-<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="c1"># Example 1: Ti-O nearest 6 neighbors for octahedral analysis</span>
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="c1"># Example 2: Pb/Sr-O nearest 12 neighbors for A-site centered analysis</span>
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
 </code></pre></div>
 <h3 id="arguments-complete">Arguments (complete)</h3>
 <ul>
@@ -2254,11 +2349,11 @@ <h3 id="output-file">Output file</h3>
 <h2 id="407-calc-displacement-from-trajectory-calc_displacementpy">407) Calc displacement from trajectory (<code>calc_displacement.py</code>)</h2>
 <p>Compute local displacement vectors from a trajectory/model and a neighbor list.</p>
 <h3 id="usage_1">Usage</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># Example 1: single-frame displacement from model.xyz</span>
-<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>disp_model.dat
-<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>
-<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="c1"># Example 2: use the last 20% frames in movie.xyz</span>
-<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="c1"># Example 1: single-frame displacement from model.xyz</span>
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>disp_model.dat
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="c1"># Example 2: use the last 20% frames in movie.xyz</span>
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>displacements.dat
 </code></pre></div>
 <h3 id="arguments-complete_1">Arguments (complete)</h3>
 <ul>
@@ -2278,7 +2373,7 @@ <h3 id="arguments-complete_1">Arguments (complete)</h3>
   Select trailing frames.
   Integer: last <code>N</code> frames.
   <code>0 &lt; value &lt; 1</code>: last ratio of frames.</li>
-<li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
+<li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
 </ul>
 <h3 id="output-file_1">Output file</h3>
 <ul>
@@ -2289,11 +2384,11 @@ <h2 id="408-calc-averaged-structure-calc_averaged_structurepy">408) Calc average
 <p>Generate one averaged structure from selected trajectory frames.
 Use this after equilibration. For a solid near equilibrium, average a frame window at the target temperature and analyze that representative structure instead of processing every snapshot.</p>
 <h3 id="usage_2">Usage</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="c1"># Example 1: average all frames</span>
-<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
-<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>
-<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="c1"># Example 2: average selected frames (100:500:2)</span>
-<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-s<span class="w"> </span><span class="m">100</span><span class="w"> </span>-t<span class="w"> </span><span class="m">500</span><span class="w"> </span>-p<span class="w"> </span><span class="m">2</span><span class="w"> </span>-o<span class="w"> </span>avg_slice.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="c1"># Example 1: average all frames</span>
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="c1"># Example 2: average selected frames (100:500:2)</span>
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-s<span class="w"> </span><span class="m">100</span><span class="w"> </span>-t<span class="w"> </span><span class="m">500</span><span class="w"> </span>-p<span class="w"> </span><span class="m">2</span><span class="w"> </span>-o<span class="w"> </span>avg_slice.xyz
 </code></pre></div>
 <h3 id="arguments-complete_2">Arguments (complete)</h3>
 <ul>
@@ -2309,7 +2404,7 @@ <h3 id="arguments-complete_2">Arguments (complete)</h3>
   Slice step. Default: <code>1</code>.</li>
 <li><code>-l, --last</code>:
   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li>
-<li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
+<li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
 </ul>
 <h3 id="output-file_2">Output file</h3>
 <ul>
@@ -2320,11 +2415,11 @@ <h2 id="409-calc-octahedral-tilt-calc_oct_tiltpy">409) Calc octahedral tilt (<co
 <p>Calculate octahedral tilt angles from a B-O neighbor list.
 This is commonly used to analyze octahedral rotation patterns in <code>ABO3</code> systems, such as <code>SrTiO3</code> and <code>PbZrO3</code>.</p>
 <h3 id="usage_3">Usage</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="c1"># Example 1: octahedral tilt of the TiO6 octahedra from a single frame</span>
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>oct_tilt_model.dat
-<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>
-<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="c1"># Example 2: octahedral tilt of the TiO6 octahedra from the last 20% trajectory frames</span>
-<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>octahedral_tilt.dat
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># Example 1: octahedral tilt of the TiO6 octahedra from a single frame</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>oct_tilt_model.dat
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="c1"># Example 2: octahedral tilt of the TiO6 octahedra from the last 20% trajectory frames</span>
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>octahedral_tilt.dat
 </code></pre></div>
 <h3 id="arguments-complete_3">Arguments (complete)</h3>
 <ul>
@@ -2342,7 +2437,7 @@ <h3 id="arguments-complete_3">Arguments (complete)</h3>
   Slice step. Default: <code>1</code>.</li>
 <li><code>-l, --last</code>:
   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li>
-<li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
+<li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
 </ul>
 <h3 id="output-file_3">Output file</h3>
 <ul>
@@ -2352,13 +2447,13 @@ <h3 id="output-file_3">Output file</h3>
 <h2 id="410-calc-polarization-for-abo3-calc_polarization_abo3py">410) Calc polarization for ABO3 (<code>calc_polarization_abo3.py</code>)</h2>
 <p>Calculate local polarization vectors for <code>ABO3</code> systems.</p>
 <h3 id="usage_4">Usage</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="c1"># Example 1: single-frame ABO3 polarization</span>
-<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
-<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Sr</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-o<span class="w"> </span>polarization_model.dat
-<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>
-<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="c1"># Example 2: trajectory polarization on a selected frame window</span>
-<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
-<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-s<span class="w"> </span><span class="m">200</span><span class="w"> </span>-t<span class="w"> </span><span class="m">600</span><span class="w"> </span>-p<span class="w"> </span><span class="m">5</span><span class="w"> </span>-o<span class="w"> </span>polarization_slice.dat
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="c1"># Example 1: single-frame ABO3 polarization</span>
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Sr</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-o<span class="w"> </span>polarization_model.dat
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>
+<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a><span class="c1"># Example 2: trajectory polarization on a selected frame window</span>
+<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-s<span class="w"> </span><span class="m">200</span><span class="w"> </span>-t<span class="w"> </span><span class="m">600</span><span class="w"> </span>-p<span class="w"> </span><span class="m">5</span><span class="w"> </span>-o<span class="w"> </span>polarization_slice.dat
 </code></pre></div>
 <h3 id="arguments-complete_4">Arguments (complete)</h3>
 <ul>
@@ -2381,7 +2476,7 @@ <h3 id="arguments-complete_4">Arguments (complete)</h3>
   Slice step. Default: <code>1</code>.</li>
 <li><code>-l, --last</code>:
   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li>
-<li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
+<li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li>
 </ul>
 <p>Important checks:</p>
 <ul>
@@ -2395,11 +2490,11 @@ <h3 id="output-file_4">Output file</h3>
 </ul>
 <h3 id="plane-grid-visualization-plt_plane_gridpy">Plane-grid visualization (<code>plt_plane_grid.py</code>)</h3>
 <p>You can visualize either <code>displacements.dat</code> or <code>polarization.dat</code>:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># Example 1: displacement map on Ti sites, first XY layer</span>
-<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span>
-<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>
-<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="c1"># Example 2: polarization map on Pb sites, XZ and YZ layers</span>
-<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>polarization.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span>--select-yz<span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">4</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="c1"># Example 1: displacement map on Ti sites, first XY layer</span>
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span>
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>
+<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a><span class="c1"># Example 2: polarization map on Pb sites, XZ and YZ layers</span>
+<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>polarization.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span>--select-yz<span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">4</span>
 </code></pre></div>
 <p>Arguments (complete):</p>
 <ul>
@@ -2430,7 +2525,7 @@ <h3 id="plane-grid-visualization-plt_plane_gridpy">Plane-grid visualization (<co
 <li>Saves figures as <code>XY_*.png</code>, <code>XZ_*.png</code>, <code>YZ_*.png</code>.</li>
 </ul>
 <div align="center">
-    <img src="../Gallery/PTO_STO_superlattice.png" alt="PTO_STO" width="65%" />
+    <img src="../../Gallery/PTO_STO_superlattice.png" alt="PTO_STO" width="65%" />
 </div>
 
 <h2 id="output-files-at-a-glance">Output files at a glance</h2>
@@ -2478,89 +2573,89 @@ <h2 id="output-files-at-a-glance">Output files at a glance</h2>
 <h2 id="real-examples">Real Examples</h2>
 <h3 id="temperature-driven-ferroelectric-to-paraelectric-phase-transition-for-pbtio3">Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3</h3>
 <p>Assume all files are in the current directory <code>./</code>:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>./
-<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>├── model.xyz
-<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>├── 300K.xyz
-<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>├── 350K.xyz
-<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a>├── 400K.xyz
-<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>├── ...
-<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a>└── 800K.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>./
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>├── model.xyz
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>├── 300K.xyz
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a>├── 350K.xyz
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>├── 400K.xyz
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>├── ...
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a>└── 800K.xyz
 </code></pre></div>
 <p><code>model.xyz</code> is the initial structure used to run MD simulations. Each <code>TEMP K.xyz</code> is a trajectory at that temperature.</p>
 <h4 id="step-1-get-averaged-structures-from-the-last-half-of-each-trajectory">Step 1: get averaged structures from the last half of each trajectory</h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
-<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
-<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span>
-<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a><span class="k">done</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span>
+<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a><span class="k">done</span>
 </code></pre></div>
 <p>This writes <code>300K-avg.xyz</code>, <code>350K-avg.xyz</code>, ..., <code>800K-avg.xyz</code>.</p>
 <h4 id="step-2-build-neighbor-lists-from-modelxyz">Step 2: build neighbor lists from <code>model.xyz</code></h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="c1"># B-O list: for each Ti, find the nearest 6 O atoms</span>
-<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
-<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>
-<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="c1"># A-O list: for each Pb, find the nearest 12 O atoms</span>
-<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Pb-O.dat
-<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>
-<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a><span class="c1"># B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms</span>
-<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">5</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">8</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>Pb<span class="w"> </span>-o<span class="w"> </span>nl-Ti-Pb.dat
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="c1"># B-O list: for each Ti, find the nearest 6 O atoms</span>
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a>
+<a id="__codelineno-12-4" name="__codelineno-12-4" href="#__codelineno-12-4"></a><span class="c1"># A-O list: for each Pb, find the nearest 12 O atoms</span>
+<a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Pb-O.dat
+<a id="__codelineno-12-6" name="__codelineno-12-6" href="#__codelineno-12-6"></a>
+<a id="__codelineno-12-7" name="__codelineno-12-7" href="#__codelineno-12-7"></a><span class="c1"># B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms</span>
+<a id="__codelineno-12-8" name="__codelineno-12-8" href="#__codelineno-12-8"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">5</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">8</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>Pb<span class="w"> </span>-o<span class="w"> </span>nl-Ti-Pb.dat
 </code></pre></div>
 <h4 id="step-3-compute-displacement-and-polarization-for-each-temperature">Step 3: compute displacement and polarization for each temperature</h4>
 <p>Use Born effective charges (BEC), not nominal ionic charges. For PbTiO3 in this example:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="n">PTO</span> <span class="o">=</span> <span class="p">{</span>
-<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>    <span class="s1">&#39;Pb&#39;</span><span class="p">:</span> <span class="mf">3.44</span><span class="p">,</span>
-<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>    <span class="s1">&#39;Ti&#39;</span><span class="p">:</span> <span class="mf">5.18</span><span class="p">,</span>
-<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a>    <span class="s1">&#39;O&#39;</span><span class="p">:</span> <span class="o">-</span><span class="p">(</span><span class="mf">3.44</span> <span class="o">+</span> <span class="mf">5.18</span><span class="p">)</span> <span class="o">/</span> <span class="mi">3</span>
-<a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="p">}</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="n">PTO</span> <span class="o">=</span> <span class="p">{</span>
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>    <span class="s1">&#39;Pb&#39;</span><span class="p">:</span> <span class="mf">3.44</span><span class="p">,</span>
+<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>    <span class="s1">&#39;Ti&#39;</span><span class="p">:</span> <span class="mf">5.18</span><span class="p">,</span>
+<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a>    <span class="s1">&#39;O&#39;</span><span class="p">:</span> <span class="o">-</span><span class="p">(</span><span class="mf">3.44</span> <span class="o">+</span> <span class="mf">5.18</span><span class="p">)</span> <span class="o">/</span> <span class="mi">3</span>
+<a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a><span class="p">}</span>
 </code></pre></div>
 <p>You can obtain BEC from your own DFPT calculation or from literature values. Thus use following commands to compute local displacement and polarization:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
-<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
-<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span>
-<a id="__codelineno-12-4" name="__codelineno-12-4" href="#__codelineno-12-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
-<a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a><span class="w">    </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">3</span>.44<span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">5</span>.18<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.8733333333<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span>
-<a id="__codelineno-12-6" name="__codelineno-12-6" href="#__codelineno-12-6"></a><span class="k">done</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span>
+<a id="__codelineno-14-4" name="__codelineno-14-4" href="#__codelineno-14-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-14-5" name="__codelineno-14-5" href="#__codelineno-14-5"></a><span class="w">    </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">3</span>.44<span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">5</span>.18<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.8733333333<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span>
+<a id="__codelineno-14-6" name="__codelineno-14-6" href="#__codelineno-14-6"></a><span class="k">done</span>
 </code></pre></div>
 <h4 id="step-4-plot-displacement-and-polarization-maps-in-real-space">Step 4: plot displacement and polarization maps in real space</h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
-<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
-<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp&quot;</span>
-<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol&quot;</span>
-<a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a><span class="k">done</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp&quot;</span>
+<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol&quot;</span>
+<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a><span class="k">done</span>
 </code></pre></div>
 <h4 id="step-5-build-a-temperature-order-parameter-curve">Step 5: build a temperature-order-parameter curve</h4>
 <p>By analyzing the lattice of each temperature-averaged structure together with its polarization (<code>XX-pol.dat</code>), we can obtain the following figure:</p>
 <div align="center">
-    <img src="../Gallery/PTO-temp.png" alt="PTO-temp" width="65%" />
+    <img src="../../Gallery/PTO-temp.png" alt="PTO-temp" width="65%" />
 </div>
 
 <p>The trend shows a clear phase transition around <code>600 K</code>, where the polarization vanishes.</p>
 <h3 id="topological-structure-in-pbtio3srtio3-superlattice">Topological structure in PbTiO3/SrTiO3 superlattice</h3>
 <p>Assume <code>movie.xyz</code> is the trajectory of the PbTiO3/SrTiO3 superlattice in the current directory.</p>
 <h4 id="step-1-build-an-averaged-structure-from-the-last-25-frames">Step 1: build an averaged structure from the last 25% frames</h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>model-avg.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>model-avg.xyz
 </code></pre></div>
 <h4 id="step-2-build-the-ti-neighbor-list">Step 2: build the Ti neighbor list</h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
 </code></pre></div>
 <h4 id="step-3-plot-the-plane-grid-map">Step 3: plot the plane-grid map</h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>disp-last25.dat
-<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-d<span class="w"> </span>disp-last25.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span>-o<span class="w"> </span>plot-topology
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>disp-last25.dat
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-d<span class="w"> </span>disp-last25.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span>-o<span class="w"> </span>plot-topology
 </code></pre></div>
 <div align="center">
-    <img src="../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
+    <img src="../../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
 </div>
 
-<p>This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero. By analyzing how polarization varies around the vortex core, you can estimate the local dielectric response, but that is beyond the scope of this tutorial.</p>
-<p>Note: this figure uses a different colormap from the default GPUMDkit plotting style. The default output does not look exactly the same, but you can get this style with small plotting-script changes.</p>
+<p>This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero.</p>
+<p>Note: the example figure uses a custom colormap. The default GPUMDkit output uses a different style, which can be adjusted by editing the plotting script.</p>
 <h3 id="other-systems">Other Systems</h3>
 <h4 id="organic-inorganic-hybrid-ferroelectrics">Organic-inorganic hybrid ferroelectrics</h4>
 <p>In many organic-inorganic ferroelectrics, polarization is strongly tied to anisotropic molecular units. A practical way to track molecular orientation is to use bond vectors.</p>
 <p>For TMCM-CdCl3, you can use the C-Cl bond direction of the TMCM molecule as an orientation proxy, then use it to estimate the polarization state:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a><span class="c1"># Find the nearest Cl around each C (tune cutoff if needed)</span>
-<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">3</span><span class="w"> </span>-n<span class="w"> </span><span class="m">1</span><span class="w"> </span>-C<span class="w"> </span>C<span class="w"> </span>-E<span class="w"> </span>Cl<span class="w"> </span>-o<span class="w"> </span>nl-C-Cl.dat
-<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>
-<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a><span class="c1"># Compute C-Cl bond vectors from the trajectory</span>
-<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-C-Cl.dat<span class="w"> </span>-o<span class="w"> </span>ccl_vectors.dat
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a><span class="c1"># Find the nearest Cl around each C (tune cutoff if needed)</span>
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">3</span><span class="w"> </span>-n<span class="w"> </span><span class="m">1</span><span class="w"> </span>-C<span class="w"> </span>C<span class="w"> </span>-E<span class="w"> </span>Cl<span class="w"> </span>-o<span class="w"> </span>nl-C-Cl.dat
+<a id="__codelineno-19-3" name="__codelineno-19-3" href="#__codelineno-19-3"></a>
+<a id="__codelineno-19-4" name="__codelineno-19-4" href="#__codelineno-19-4"></a><span class="c1"># Compute C-Cl bond vectors from the trajectory</span>
+<a id="__codelineno-19-5" name="__codelineno-19-5" href="#__codelineno-19-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-C-Cl.dat<span class="w"> </span>-o<span class="w"> </span>ccl_vectors.dat
 </code></pre></div>
 <p><code>ccl_vectors.dat</code> can then be analyzed as an orientation order parameter. More details could be found at: Phys. Rev. Lett. 136, 016801</p>
 <h4 id="other-ferroelectric-families">Other ferroelectric families</h4>
diff --git a/docs/htmls/en/quick_start.html b/docs/htmls/en/quick_start.html
index 9a10029..006095f 100644
--- a/docs/htmls/en/quick_start.html
+++ b/docs/htmls/en/quick_start.html
@@ -143,7 +143,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#1-prepare-a-python-environment" class="md-skip">
+        <a href="#what-it-does" class="md-skip">
           Skip to content
         </a>
       
@@ -461,10 +461,10 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#1-prepare-a-python-environment" class="md-nav__link">
+  <a href="#what-it-does" class="md-nav__link">
     <span class="md-ellipsis">
       
-        1. Prepare a Python Environment
+        What it does
       
     </span>
   </a>
@@ -472,33 +472,33 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#2-install-gpumdkit" class="md-nav__link">
+  <a href="#before-you-start" class="md-nav__link">
     <span class="md-ellipsis">
       
-        2. Install GPUMDkit
+        Before you start
       
     </span>
   </a>
   
-</li>
-      
-        <li class="md-nav__item">
-  <a href="#3-usage-modes" class="md-nav__link">
+    <nav class="md-nav" aria-label="Before you start">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#1-prepare-a-python-environment" class="md-nav__link">
     <span class="md-ellipsis">
       
-        3. Usage Modes
+        1. Prepare a Python environment
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="3. Usage Modes">
-      <ul class="md-nav__list">
+</li>
         
           <li class="md-nav__item">
-  <a href="#interactive-mode" class="md-nav__link">
+  <a href="#2-install-gpumdkit" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Interactive Mode
+        2. Install GPUMDkit
       
     </span>
   </a>
@@ -506,10 +506,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#command-line-mode" class="md-nav__link">
+  <a href="#3-verify-the-installation" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Command-Line Mode
+        3. Verify the installation
       
     </span>
   </a>
@@ -522,22 +522,44 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#4-practical-examples" class="md-nav__link">
+  <a href="#interactive-mode" class="md-nav__link">
     <span class="md-ellipsis">
       
-        4. Practical Examples
+        Interactive mode
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="4. Practical Examples">
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#cli-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        CLI mode
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#common-examples" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Common examples
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Common examples">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#convert-poscar-to-extxyz" class="md-nav__link">
+  <a href="#convert-a-poscar-to-extxyz" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Convert POSCAR to extxyz
+        Convert a POSCAR to extxyz
       
     </span>
   </a>
@@ -548,7 +570,7 @@
   <a href="#add-gpumd-group-labels" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Add GPUMD Group Labels
+        Add GPUMD group labels
       
     </span>
   </a>
@@ -559,7 +581,7 @@
   <a href="#plot-nep-training-results" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Plot NEP Training Results
+        Plot NEP training results
       
     </span>
   </a>
@@ -570,7 +592,7 @@
   <a href="#plot-nep-test-results" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Plot NEP Test Results
+        Plot NEP test results
       
     </span>
   </a>
@@ -581,7 +603,7 @@
   <a href="#plot-thermodynamic-data" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Plot Thermodynamic Data
+        Plot thermodynamic data
       
     </span>
   </a>
@@ -592,7 +614,7 @@
   <a href="#plot-msd-and-self-diffusion-coefficient" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Plot MSD and Self-Diffusion Coefficient
+        Plot MSD and self-diffusion coefficient
       
     </span>
   </a>
@@ -605,10 +627,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#5-help" class="md-nav__link">
+  <a href="#notes" class="md-nav__link">
     <span class="md-ellipsis">
       
-        5. Help
+        Notes
       
     </span>
   </a>
@@ -1382,10 +1404,10 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#1-prepare-a-python-environment" class="md-nav__link">
+  <a href="#what-it-does" class="md-nav__link">
     <span class="md-ellipsis">
       
-        1. Prepare a Python Environment
+        What it does
       
     </span>
   </a>
@@ -1393,33 +1415,33 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#2-install-gpumdkit" class="md-nav__link">
+  <a href="#before-you-start" class="md-nav__link">
     <span class="md-ellipsis">
       
-        2. Install GPUMDkit
+        Before you start
       
     </span>
   </a>
   
-</li>
-      
-        <li class="md-nav__item">
-  <a href="#3-usage-modes" class="md-nav__link">
+    <nav class="md-nav" aria-label="Before you start">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#1-prepare-a-python-environment" class="md-nav__link">
     <span class="md-ellipsis">
       
-        3. Usage Modes
+        1. Prepare a Python environment
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="3. Usage Modes">
-      <ul class="md-nav__list">
+</li>
         
           <li class="md-nav__item">
-  <a href="#interactive-mode" class="md-nav__link">
+  <a href="#2-install-gpumdkit" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Interactive Mode
+        2. Install GPUMDkit
       
     </span>
   </a>
@@ -1427,10 +1449,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#command-line-mode" class="md-nav__link">
+  <a href="#3-verify-the-installation" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Command-Line Mode
+        3. Verify the installation
       
     </span>
   </a>
@@ -1443,22 +1465,44 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#4-practical-examples" class="md-nav__link">
+  <a href="#interactive-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Interactive mode
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#cli-mode" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        CLI mode
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#common-examples" class="md-nav__link">
     <span class="md-ellipsis">
       
-        4. Practical Examples
+        Common examples
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="4. Practical Examples">
+    <nav class="md-nav" aria-label="Common examples">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#convert-poscar-to-extxyz" class="md-nav__link">
+  <a href="#convert-a-poscar-to-extxyz" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Convert POSCAR to extxyz
+        Convert a POSCAR to extxyz
       
     </span>
   </a>
@@ -1469,7 +1513,7 @@
   <a href="#add-gpumd-group-labels" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Add GPUMD Group Labels
+        Add GPUMD group labels
       
     </span>
   </a>
@@ -1480,7 +1524,7 @@
   <a href="#plot-nep-training-results" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Plot NEP Training Results
+        Plot NEP training results
       
     </span>
   </a>
@@ -1491,7 +1535,7 @@
   <a href="#plot-nep-test-results" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Plot NEP Test Results
+        Plot NEP test results
       
     </span>
   </a>
@@ -1502,7 +1546,7 @@
   <a href="#plot-thermodynamic-data" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Plot Thermodynamic Data
+        Plot thermodynamic data
       
     </span>
   </a>
@@ -1513,7 +1557,7 @@
   <a href="#plot-msd-and-self-diffusion-coefficient" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Plot MSD and Self-Diffusion Coefficient
+        Plot MSD and self-diffusion coefficient
       
     </span>
   </a>
@@ -1526,10 +1570,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#5-help" class="md-nav__link">
+  <a href="#notes" class="md-nav__link">
     <span class="md-ellipsis">
       
-        5. Help
+        Notes
       
     </span>
   </a>
@@ -1558,170 +1602,136 @@
 
 <div align="center">
   <h1>🚀 Quick Start</h1>
-  <p style="text-align: justify;">This page introduces the basic installation and several common commands. GPUMDkit can be used through the interactive menu or by direct command-line options.</p>
+  <p style="text-align: justify;">This page helps you install GPUMDkit and run your first commands. You can use GPUMDkit through an interactive menu or direct command-line options.</p>
 </div>
 
-<h2 id="1-prepare-a-python-environment">1. Prepare a Python Environment</h2>
-<p>You can use a clean conda environment:</p>
+<h2 id="what-it-does">What it does</h2>
+<p>GPUMDkit provides a single entry point for common tasks in computational materials science — format conversion, structure analysis, property calculation, and visualization — without writing custom scripts.</p>
+<h2 id="before-you-start">Before you start</h2>
+<h3 id="1-prepare-a-python-environment">1. Prepare a Python environment</h3>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>gpumdkit<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12
 <a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>gpumdkit
 </code></pre></div>
-<p>Some optional functions use additional packages:</p>
+<p>Some optional functions require additional packages:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>pip<span class="w"> </span>install<span class="w"> </span>neptrain<span class="w"> </span>dpdata<span class="w"> </span>calorine
 </code></pre></div>
 <p>Other Python dependencies are loaded by the corresponding scripts. If a package is missing, Python will report it when that function is used.</p>
-<h2 id="2-install-gpumdkit">2. Install GPUMDkit</h2>
-<p>Clone the repository:</p>
+<h3 id="2-install-gpumdkit">2. Install GPUMDkit</h3>
+<p>Clone the repository and run the installer:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
 <a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
-</code></pre></div>
-<p>Run the installer:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="nb">source</span><span class="w"> </span>./install.sh
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a><span class="nb">source</span><span class="w"> </span>./install.sh
 </code></pre></div>
 <p>The installer writes <code>GPUMDkit_path</code> and <code>PATH</code> settings to your shell configuration and loads them for the current shell. It writes to <code>~/.bashrc</code> by default; if the current shell is zsh, it writes to <code>~/.zshrc</code>. If an existing GPUMDkit path is found, the installer prints the old path and asks whether to replace it. Before changing the rc file, it creates a backup.</p>
 <p>Typical installation output:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>======================================================
-<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>  GPUMDkit Installation
-<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>======================================================
-<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a> [1/4] Detecting GPUMDkit directory...
-<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>       /path/to/GPUMDkit
-<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a> [2/4] Detecting shell configuration...
-<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a>       Target: /Users/you/.bashrc
-<a id="__codelineno-4-8" name="__codelineno-4-8" href="#__codelineno-4-8"></a>       Adding environment variables to /Users/you/.bashrc
-<a id="__codelineno-4-9" name="__codelineno-4-9" href="#__codelineno-4-9"></a>       Success: Environment variables added.
-<a id="__codelineno-4-10" name="__codelineno-4-10" href="#__codelineno-4-10"></a> [3/4] Setting executable permissions...
-<a id="__codelineno-4-11" name="__codelineno-4-11" href="#__codelineno-4-11"></a>       Added executable permission to gpumdkit.sh
-<a id="__codelineno-4-12" name="__codelineno-4-12" href="#__codelineno-4-12"></a> [4/4] Loading environment...
-<a id="__codelineno-4-13" name="__codelineno-4-13" href="#__codelineno-4-13"></a>
-<a id="__codelineno-4-14" name="__codelineno-4-14" href="#__codelineno-4-14"></a>======================================================
-<a id="__codelineno-4-15" name="__codelineno-4-15" href="#__codelineno-4-15"></a>  Installation Complete!  GPUMDkit is ready to use.
-<a id="__codelineno-4-16" name="__codelineno-4-16" href="#__codelineno-4-16"></a>======================================================
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>======================================================
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>  GPUMDkit Installation
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>======================================================
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a> [1/4] Detecting GPUMDkit directory...
+<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>       /path/to/GPUMDkit
+<a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a> [2/4] Detecting shell configuration...
+<a id="__codelineno-3-7" name="__codelineno-3-7" href="#__codelineno-3-7"></a>       Target: /Users/you/.bashrc
+<a id="__codelineno-3-8" name="__codelineno-3-8" href="#__codelineno-3-8"></a>       Adding environment variables to /Users/you/.bashrc
+<a id="__codelineno-3-9" name="__codelineno-3-9" href="#__codelineno-3-9"></a>       Success: Environment variables added.
+<a id="__codelineno-3-10" name="__codelineno-3-10" href="#__codelineno-3-10"></a> [3/4] Setting executable permissions...
+<a id="__codelineno-3-11" name="__codelineno-3-11" href="#__codelineno-3-11"></a>       Added executable permission to gpumdkit.sh
+<a id="__codelineno-3-12" name="__codelineno-3-12" href="#__codelineno-3-12"></a> [4/4] Loading environment...
+<a id="__codelineno-3-13" name="__codelineno-3-13" href="#__codelineno-3-13"></a>
+<a id="__codelineno-3-14" name="__codelineno-3-14" href="#__codelineno-3-14"></a>======================================================
+<a id="__codelineno-3-15" name="__codelineno-3-15" href="#__codelineno-3-15"></a>  Installation Complete!  GPUMDkit is ready to use.
+<a id="__codelineno-3-16" name="__codelineno-3-16" href="#__codelineno-3-16"></a>======================================================
 </code></pre></div>
 <p>If GPUMDkit was installed before, you may see:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>Existing GPUMDkit configuration found.
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>Existing path(s):
-<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>  - /old/path/to/GPUMDkit
-<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>New path:
-<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>  - /new/path/to/GPUMDkit
-<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>
-<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>Replace the existing GPUMDkit configuration with the new path? [y/N]:
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>Existing GPUMDkit configuration found.
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>Existing path(s):
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>  - /old/path/to/GPUMDkit
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a>New path:
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>  - /new/path/to/GPUMDkit
+<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a>
+<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a>Replace the existing GPUMDkit configuration with the new path? [y/N]:
 </code></pre></div>
-<p>Check the command:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-h
+<h3 id="3-verify-the-installation">3. Verify the installation</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-h
 </code></pre></div>
-<p>The help table:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
-<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>|                                          MAIN FUNCTIONS                                               |
-<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a>| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |
-<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a>| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |
-<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
-<a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a>|                                         FORMAT CONVERSION                                             |
-<a id="__codelineno-7-11" name="__codelineno-7-11" href="#__codelineno-7-11"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a>| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |
-<a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a>| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |
-<a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a>| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |
-<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a>| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |
-<a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a>| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |
-<a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a>| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |
-<a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a>| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
-<a id="__codelineno-7-19" name="__codelineno-7-19" href="#__codelineno-7-19"></a>| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
-<a id="__codelineno-7-20" name="__codelineno-7-20" href="#__codelineno-7-20"></a>| -frame_range  Extract frames by range         |                                                       |
-<a id="__codelineno-7-21" name="__codelineno-7-21" href="#__codelineno-7-21"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-22" name="__codelineno-7-22" href="#__codelineno-7-22"></a>|                                            ANALYSIS                                                   |
-<a id="__codelineno-7-23" name="__codelineno-7-23" href="#__codelineno-7-23"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-24" name="__codelineno-7-24" href="#__codelineno-7-24"></a>| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
-<a id="__codelineno-7-25" name="__codelineno-7-25" href="#__codelineno-7-25"></a>| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
-<a id="__codelineno-7-26" name="__codelineno-7-26" href="#__codelineno-7-26"></a>| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
-<a id="__codelineno-7-27" name="__codelineno-7-27" href="#__codelineno-7-27"></a>| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-<a id="__codelineno-7-28" name="__codelineno-7-28" href="#__codelineno-7-28"></a>| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-<a id="__codelineno-7-29" name="__codelineno-7-29" href="#__codelineno-7-29"></a>| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
-<a id="__codelineno-7-30" name="__codelineno-7-30" href="#__codelineno-7-30"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-31" name="__codelineno-7-31" href="#__codelineno-7-31"></a>| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |
-<a id="__codelineno-7-32" name="__codelineno-7-32" href="#__codelineno-7-32"></a>+-------------------------------------------------------------------------------------------------------+
+<p>This prints a help table listing all available options.</p>
+<h2 id="interactive-mode">Interactive mode</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh
 </code></pre></div>
-<h2 id="3-usage-modes">3. Usage Modes</h2>
-<h3 id="interactive-mode">Interactive Mode</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh
+<p>This opens the main menu:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>           ____ ____  _   _ __  __ ____  _    _ _
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>         | |  _| |_) | | | | |\/| | | | | |/ / | __|
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
+<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a>
+<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a>          GPUMDkit Version 1.5.6 (dev) (2026-06-17)
+<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+<a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a> Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA
+<a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a>
+<a id="__codelineno-7-11" name="__codelineno-7-11" href="#__codelineno-7-11"></a> ---------------------- GPUMD ------------------------
+<a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a> 1) Format Conversion          2) Sample Structures
+<a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a> 3) Workflow                   4) Calculators
+<a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a> 5) Analyzer                   6) Visualization
+<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a> 7) Utilities                  8) Developing...
+<a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a> 0) Exit
+<a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a> ------------&gt;&gt;
+<a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a> Input the function number:
 </code></pre></div>
-<p>Main menu:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>           ____ ____  _   _ __  __ ____  _    _ _
-<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
-<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>         | |  _| |_) | | | | |\/| | | | | |/ / | __|
-<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a>         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_
-<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
-<a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a>
-<a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a>          GPUMDkit Version 1.5.6 (dev) (2026-06-17)
-<a id="__codelineno-9-8" name="__codelineno-9-8" href="#__codelineno-9-8"></a>    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
-<a id="__codelineno-9-9" name="__codelineno-9-9" href="#__codelineno-9-9"></a> Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA
-<a id="__codelineno-9-10" name="__codelineno-9-10" href="#__codelineno-9-10"></a>
-<a id="__codelineno-9-11" name="__codelineno-9-11" href="#__codelineno-9-11"></a> ---------------------- GPUMD ------------------------
-<a id="__codelineno-9-12" name="__codelineno-9-12" href="#__codelineno-9-12"></a> 1) Format Conversion          2) Sample Structures
-<a id="__codelineno-9-13" name="__codelineno-9-13" href="#__codelineno-9-13"></a> 3) Workflow                   4) Calculators
-<a id="__codelineno-9-14" name="__codelineno-9-14" href="#__codelineno-9-14"></a> 5) Analyzer                   6) Visualization
-<a id="__codelineno-9-15" name="__codelineno-9-15" href="#__codelineno-9-15"></a> 7) Utilities                  8) Developing...
-<a id="__codelineno-9-16" name="__codelineno-9-16" href="#__codelineno-9-16"></a> 0) Exit
-<a id="__codelineno-9-17" name="__codelineno-9-17" href="#__codelineno-9-17"></a> ------------&gt;&gt;
-<a id="__codelineno-9-18" name="__codelineno-9-18" href="#__codelineno-9-18"></a> Input the function number:
-</code></pre></div>
-<h3 id="command-line-mode">Command-Line Mode</h3>
+<p>Select a module by number. Each module provides sub-menus with specific functions.</p>
+<h2 id="cli-mode">CLI mode</h2>
 <p>Direct commands use fixed positional arguments:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
-<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
-<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-&lt;option&gt;<span class="w"> </span><span class="o">[</span>args...<span class="o">]</span>
 </code></pre></div>
-<p>For example:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<p>Examples:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>trajectory.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
 </code></pre></div>
-<p>means reading <code>POSCAR</code> and writing <code>model.xyz</code>.</p>
-<h2 id="4-practical-examples">4. Practical Examples</h2>
-<h3 id="convert-poscar-to-extxyz">Convert POSCAR to extxyz</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<p>The first example reads <code>POSCAR</code> and writes <code>model.xyz</code>.</p>
+<h2 id="common-examples">Common examples</h2>
+<h3 id="convert-a-poscar-to-extxyz">Convert a POSCAR to extxyz</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
 </code></pre></div>
-<h3 id="add-gpumd-group-labels">Add GPUMD Group Labels</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
+<h3 id="add-gpumd-group-labels">Add GPUMD group labels</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
 </code></pre></div>
-<p>Group labels are used by some GPUMD-related workflows and analyses that need atom grouping, such as species-specific MSD or diffusion calculations.</p>
-<h3 id="plot-nep-training-results">Plot NEP Training Results</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<p>Group labels are used by some GPUMD-related workflows that need atom grouping, such as species-specific MSD or diffusion calculations.</p>
+<h3 id="plot-nep-training-results">Plot NEP training results</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/train.png" alt="NEP training results" width="72%" />
 </div>
 
-<h3 id="plot-nep-test-results">Plot NEP Test Results</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
+<h3 id="plot-nep-test-results">Plot NEP test results</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/prediction.png" alt="NEP test results" width="72%" />
 </div>
 
-<h3 id="plot-thermodynamic-data">Plot Thermodynamic Data</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+<h3 id="plot-thermodynamic-data">Plot thermodynamic data</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/thermo.png" alt="Thermo plot" width="72%" />
 </div>
 
-<h3 id="plot-msd-and-self-diffusion-coefficient">Plot MSD and Self-Diffusion Coefficient</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
-<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+<h3 id="plot-msd-and-self-diffusion-coefficient">Plot MSD and self-diffusion coefficient</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
   <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
 </div>
 
-<h2 id="5-help">5. Help</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-h
-<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>-h
-<a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>-h
-<a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train<span class="w"> </span>-h
-<a id="__codelineno-18-5" name="__codelineno-18-5" href="#__codelineno-18-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>-h
-</code></pre></div>
+<h2 id="notes">Notes</h2>
+<ul>
+<li>Use <code>gpumdkit.sh -h</code> to see all available options.</li>
+<li>Use <code>gpumdkit.sh -&lt;option&gt; -h</code> to get help for a specific option (e.g., <code>gpumdkit.sh -plt train -h</code>).</li>
+<li>For detailed usage of each module, see the corresponding tutorial pages linked in the <a href="index.html">index</a>.</li>
+</ul>
 
 
 
diff --git a/docs/htmls/en/structure_sampling.html b/docs/htmls/en/structure_sampling.html
index b591fa6..43b3ec7 100644
--- a/docs/htmls/en/structure_sampling.html
+++ b/docs/htmls/en/structure_sampling.html
@@ -586,6 +586,45 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="Deprecated PyNEP FPS">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#serial-pynep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Serial PyNEP
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#parallel-pynep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Parallel PyNEP
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gpumdkit-entry" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        GPUMDkit Entry
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1367,6 +1406,45 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="Deprecated PyNEP FPS">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#serial-pynep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Serial PyNEP
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#parallel-pynep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Parallel PyNEP
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gpumdkit-entry" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        GPUMDkit Entry
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1606,7 +1684,7 @@ <h2 id="farthest-point-sampling-with-neptrain">Farthest Point Sampling with NepT
 </code></pre></div>
 <p>This function requires the <code>NepTrain</code> package. If you use this function, we recommend citing the NepTrain paper printed by the script.</p>
 <h2 id="deprecated-pynep-fps">Deprecated PyNEP FPS</h2>
-<p>PyNEP FPS is kept for compatibility, but it is only exposed through the direct <code>-pynep</code> entry:</p>
+<p>PyNEP FPS is kept for compatibility, but it is only exposed through the direct <code>-pynep</code> entry.</p>
 <p>If you choose <code>202</code> from the interactive menu, it prints:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>+-------------------------------------------------+
 <a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>| Function 202 is no longer supported here.       |
@@ -1616,21 +1694,29 @@ <h2 id="deprecated-pynep-fps">Deprecated PyNEP FPS</h2>
 <a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a>|                 gpumdkit.sh -pynep              |
 <a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a>+-------------------------------------------------+
 </code></pre></div>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pynep
+<h3 id="serial-pynep">Serial PyNEP</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>python<span class="w"> </span>Scripts/sample_structures/pynep_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
+</code></pre></div>
+<h3 id="parallel-pynep">Parallel PyNEP</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>python<span class="w"> </span>Scripts/sample_structures/parallel_pynep_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt<span class="w"> </span><span class="m">8</span>
+</code></pre></div>
+<p>The last argument is the number of CPU threads.</p>
+<h3 id="gpumdkit-entry">GPUMDkit Entry</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-pynep
 </code></pre></div>
 <p>Then input:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>dump.xyz train.xyz nep.txt 8
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>dump.xyz train.xyz nep.txt 8
 </code></pre></div>
 <p>This entry requires <code>pynep</code> and is kept for compatibility.</p>
 <h2 id="structure-perturbation">Structure Perturbation</h2>
 <p>Use perturbation when you want to generate initial structures around a known configuration.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>python<span class="w"> </span>Scripts/sample_structures/perturb_structure.py<span class="w"> </span>POSCAR<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">0</span>.03<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>uniform
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>python<span class="w"> </span>Scripts/sample_structures/perturb_structure.py<span class="w"> </span>POSCAR<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">0</span>.03<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>uniform
 </code></pre></div>
 <p>From interactive mode, choose <code>204</code>. You will see:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;
-<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>The default parameters for perturb are 20 0.03 0.2 uniform
-<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>Example: POSCAR 20 0.03 0.2 uniform
-<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a>------------&gt;&gt;
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>The default parameters for perturb are 20 0.03 0.2 uniform
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a>Example: POSCAR 20 0.03 0.2 uniform
+<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a>------------&gt;&gt;
 </code></pre></div>
 <p>Arguments:</p>
 <table>
@@ -1667,18 +1753,18 @@ <h2 id="structure-perturbation">Structure Perturbation</h2>
 <ul>
 <li><code>POSCAR_01.vasp</code>, <code>POSCAR_02.vasp</code>, ...</li>
 </ul>
-<p>This function requires <code>dpdata</code>.</p>
+<p>This function requires <code>dpdata</code>. If you use this function, we recommend citing the dpdata package.</p>
 <h2 id="force-deviation-selection">Force-Deviation Selection</h2>
 <p>Use this together with the GPUMD <code>active</code> command. The <code>active</code> command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. <code>select_max_modev.py</code> selects structures with large force deviations from <code>active.out</code> and <code>active.xyz</code>, then writes them to <code>selected.xyz</code>.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>python<span class="w"> </span>Scripts/sample_structures/select_max_modev.py<span class="w"> </span><span class="m">200</span><span class="w"> </span><span class="m">0</span>.15
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>python<span class="w"> </span>Scripts/sample_structures/select_max_modev.py<span class="w"> </span><span class="m">200</span><span class="w"> </span><span class="m">0</span>.15
 </code></pre></div>
 <p>From interactive mode, choose <code>205</code>. You will see:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>+----------------------------------------------------+
-<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>| Select max force deviation structs from active.xyz |
-<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a>|     generated by the active command in gpumd.      |
-<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a>+----------------------------------------------------+
-<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a>Input &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)
-<a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a>------------&gt;&gt;
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>+----------------------------------------------------+
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>| Select max force deviation structs from active.xyz |
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>|     generated by the active command in gpumd.      |
+<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a>+----------------------------------------------------+
+<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a>Input &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)
+<a id="__codelineno-17-6" name="__codelineno-17-6" href="#__codelineno-17-6"></a>------------&gt;&gt;
 </code></pre></div>
 <p>Arguments:</p>
 <table>
@@ -1710,14 +1796,14 @@ <h2 id="force-deviation-selection">Force-Deviation Selection</h2>
 </ul>
 <h2 id="frame-range-extraction">Frame Range Extraction</h2>
 <p>Use this to extract a fraction of a trajectory:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>python<span class="w"> </span>Scripts/sample_structures/frame_range.py<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span>.8
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>python<span class="w"> </span>Scripts/sample_structures/frame_range.py<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span>.8
 </code></pre></div>
 <p>This writes frames from 0% to 80% of the trajectory.</p>
 <h2 id="example-commands">Example Commands</h2>
 <p>An example sequence using several sampling-related tools:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
-<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
-<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
+<a id="__codelineno-19-3" name="__codelineno-19-3" href="#__codelineno-19-3"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
 </code></pre></div>
 <h2 id="common-mistakes">Common Mistakes</h2>
 <table>
diff --git a/docs/htmls/en/workflow_scripts.html b/docs/htmls/en/workflow_scripts.html
index 35f0f81..699b6b8 100644
--- a/docs/htmls/en/workflow_scripts.html
+++ b/docs/htmls/en/workflow_scripts.html
@@ -1502,7 +1502,19 @@ <h2 id="interactive-entry">Interactive Entry</h2>
 <p>Choose:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>3) Workflow
 </code></pre></div>
-<p>Typical workflow menu:</p>
+<p>The workflow menu looks like:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>+---------------------------------------------------------+
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>|                      WORKFLOW TOOLS                     |
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>+---------------------------------------------------------+
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>| 301) SCF batch pretreatment                             |
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>| 302) MD sample batch pretreatment (gpumd)               |
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>| 303) MD sample batch pretreatment (lmp)                 |
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>+---------------------------------------------------------+
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>| 000) Return to the main menu                            |
+<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>+---------------------------------------------------------+
+<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a>Input the function number:
+</code></pre></div>
+<p>Available entries:</p>
 <table>
 <thead>
 <tr>
@@ -1515,17 +1527,17 @@ <h2 id="interactive-entry">Interactive Entry</h2>
 <tr>
 <td>301</td>
 <td>SCF batch pretreatment</td>
-<td>prepare single-point DFT calculations</td>
+<td>Prepare single-point DFT calculations</td>
 </tr>
 <tr>
 <td>302</td>
 <td>MD sample batch pretreatment (GPUMD)</td>
-<td>prepare GPUMD sampling calculations</td>
+<td>Prepare GPUMD sampling calculations</td>
 </tr>
 <tr>
 <td>303</td>
 <td>MD sample batch pretreatment (LAMMPS)</td>
-<td>prepare LAMMPS sampling calculations</td>
+<td>Prepare LAMMPS sampling calculations</td>
 </tr>
 </tbody>
 </table>
@@ -1533,8 +1545,8 @@ <h2 id="scf-batch-pretreatment">SCF Batch Pretreatment</h2>
 <p>Use this when you have many structures and want to prepare single-point DFT calculations.</p>
 <h3 id="vasp">VASP</h3>
 <p>Interactive mode:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh
-<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="c1"># choose 3 -&gt; 301 -&gt; VASP</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a><span class="c1"># choose 3 -&gt; 301 -&gt; VASP</span>
 </code></pre></div>
 <p>Before running, put structure files in the current directory. The script checks files in this order:</p>
 <ol>
@@ -1544,91 +1556,91 @@ <h3 id="vasp">VASP</h3>
 <li>if no <code>.vasp</code> file exists and multiple <code>.xyz</code> files exist, it asks you to choose one.</li>
 </ol>
 <p>Typical input directory before running:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>current directory/
-<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>├── POSCAR_1.vasp
-<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>├── POSCAR_2.vasp
-<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>└── POSCAR_3.vasp
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>current directory/
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>├── POSCAR_1.vasp
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>├── POSCAR_2.vasp
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a>└── POSCAR_3.vasp
 </code></pre></div>
 <p>or:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>current directory/
-<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>└── sampled.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>current directory/
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>└── sampled.xyz
 </code></pre></div>
 <p>After running, the script creates:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>current directory/
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>├── struct_fp/
-<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>│   ├── POSCAR_1.vasp
-<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>│   ├── POSCAR_2.vasp
-<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>│   └── ...
-<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>├── fp/
-<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>├── &lt;prefix&gt;_1/
-<a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a>├── &lt;prefix&gt;_2/
-<a id="__codelineno-5-9" name="__codelineno-5-9" href="#__codelineno-5-9"></a>└── presub.sh
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>current directory/
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>├── struct_fp/
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>│   ├── POSCAR_1.vasp
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>│   ├── POSCAR_2.vasp
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a>│   └── ...
+<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>├── fp/
+<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a>├── &lt;prefix&gt;_1/
+<a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a>├── &lt;prefix&gt;_2/
+<a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a>└── presub.sh
 </code></pre></div>
 <p>You must place <code>INCAR</code>, <code>POTCAR</code>, and <code>KPOINTS</code> in the generated <code>fp/</code> directory after the script creates it. The calculation folders link to files in <code>fp/</code>.</p>
 <p>The <code>prefix</code> you input during the workflow becomes the calculation folder prefix. When <code>out2xyz</code> is later used to extract results, the folder name is stored as <code>config_type</code> in the extxyz file, which makes it easier to trace where each structure came from.</p>
 <h3 id="cp2k">CP2K</h3>
 <p>CP2K SCF batch pretreatment is available from the workflow menu and can also be called directly:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh
-<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="c1"># choose 3 -&gt; 301 -&gt; CP2K</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="c1"># choose 3 -&gt; 301 -&gt; CP2K</span>
 </code></pre></div>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>python<span class="w"> </span>Scripts/workflow/scf_batch_pretreatment_cp2k.py<span class="w"> </span>train.xyz<span class="w"> </span>template.inp<span class="w"> </span>calc
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>python<span class="w"> </span>Scripts/workflow/scf_batch_pretreatment_cp2k.py<span class="w"> </span>train.xyz<span class="w"> </span>template.inp<span class="w"> </span>calc
 </code></pre></div>
 <p>The interactive wrapper asks for:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;
 </code></pre></div>
 <p>Example:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>dump.xyz template.inp H2O
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>dump.xyz template.inp H2O
 </code></pre></div>
 <p>The template should be configured to read coordinates from <code>pos.xyz</code>. A reference template is available at:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>Scripts/workflow/cp2k_template.inp
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>Scripts/workflow/cp2k_template.inp
 </code></pre></div>
 <p>The script creates <code>&lt;prefix&gt;_&lt;index&gt;/</code> directories, writes <code>input.inp</code>, and writes <code>pos.xyz</code> for each structure.</p>
 <h2 id="md-sampling-pretreatment">MD Sampling Pretreatment</h2>
 <h3 id="gpumd">GPUMD</h3>
 <p>Interactive mode:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh
-<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="c1"># choose 3 -&gt; 302</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a><span class="c1"># choose 3 -&gt; 302</span>
 </code></pre></div>
 <p>Typical preparation:
 Before running, put <code>.vasp</code> files or one extxyz file in the current directory. The detection order is the same as the VASP SCF workflow: <code>.vasp</code> files are preferred; if multiple <code>.xyz</code> files are found without <code>.vasp</code>, the script asks you to choose one.</p>
 <p>Typical input directory:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>current directory/
-<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>├── POSCAR_1.vasp
-<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a>└── POSCAR_2.vasp
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>current directory/
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>├── POSCAR_1.vasp
+<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>└── POSCAR_2.vasp
 </code></pre></div>
 <p>or:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>current directory/
-<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>└── dump.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>current directory/
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>└── dump.xyz
 </code></pre></div>
 <p>After running, the script creates:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>current directory/
-<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>├── struct_md/
-<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a>│   ├── model_1.xyz
-<a id="__codelineno-14-4" name="__codelineno-14-4" href="#__codelineno-14-4"></a>│   ├── model_2.xyz
-<a id="__codelineno-14-5" name="__codelineno-14-5" href="#__codelineno-14-5"></a>│   └── ...
-<a id="__codelineno-14-6" name="__codelineno-14-6" href="#__codelineno-14-6"></a>├── md/
-<a id="__codelineno-14-7" name="__codelineno-14-7" href="#__codelineno-14-7"></a>├── sample_1/
-<a id="__codelineno-14-8" name="__codelineno-14-8" href="#__codelineno-14-8"></a>├── sample_2/
-<a id="__codelineno-14-9" name="__codelineno-14-9" href="#__codelineno-14-9"></a>└── presub.sh
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>current directory/
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>├── struct_md/
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a>│   ├── model_1.xyz
+<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a>│   ├── model_2.xyz
+<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a>│   └── ...
+<a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a>├── md/
+<a id="__codelineno-15-7" name="__codelineno-15-7" href="#__codelineno-15-7"></a>├── sample_1/
+<a id="__codelineno-15-8" name="__codelineno-15-8" href="#__codelineno-15-8"></a>├── sample_2/
+<a id="__codelineno-15-9" name="__codelineno-15-9" href="#__codelineno-15-9"></a>└── presub.sh
 </code></pre></div>
 <p>You must place <code>nep.txt</code> and <code>run_*.in</code> files in the generated <code>md/</code> directory. The script links <code>run_1.in</code> to <code>sample_1/run.in</code>, <code>run_2.in</code> to <code>sample_2/run.in</code>, and so on.</p>
 <h3 id="lammps">LAMMPS</h3>
 <p>Interactive mode:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh
-<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="c1"># choose 3 -&gt; 303</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a><span class="c1"># choose 3 -&gt; 303</span>
 </code></pre></div>
 <p>Typical preparation:
 Before running, put <code>.vasp</code> files or one extxyz file in the current directory. <code>.vasp</code> files are preferred when both formats exist.</p>
 <p>After running, the script creates LAMMPS data files in <code>struct_md/</code>, sample folders, and an <code>md/</code> directory:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>current directory/
-<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>├── struct_md/
-<a id="__codelineno-16-3" name="__codelineno-16-3" href="#__codelineno-16-3"></a>│   ├── lammps_1.data
-<a id="__codelineno-16-4" name="__codelineno-16-4" href="#__codelineno-16-4"></a>│   ├── lammps_2.data
-<a id="__codelineno-16-5" name="__codelineno-16-5" href="#__codelineno-16-5"></a>│   └── ...
-<a id="__codelineno-16-6" name="__codelineno-16-6" href="#__codelineno-16-6"></a>├── md/
-<a id="__codelineno-16-7" name="__codelineno-16-7" href="#__codelineno-16-7"></a>├── sample_1/
-<a id="__codelineno-16-8" name="__codelineno-16-8" href="#__codelineno-16-8"></a>├── sample_2/
-<a id="__codelineno-16-9" name="__codelineno-16-9" href="#__codelineno-16-9"></a>└── presub.sh
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>current directory/
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>├── struct_md/
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>│   ├── lammps_1.data
+<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a>│   ├── lammps_2.data
+<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a>│   └── ...
+<a id="__codelineno-17-6" name="__codelineno-17-6" href="#__codelineno-17-6"></a>├── md/
+<a id="__codelineno-17-7" name="__codelineno-17-7" href="#__codelineno-17-7"></a>├── sample_1/
+<a id="__codelineno-17-8" name="__codelineno-17-8" href="#__codelineno-17-8"></a>├── sample_2/
+<a id="__codelineno-17-9" name="__codelineno-17-9" href="#__codelineno-17-9"></a>└── presub.sh
 </code></pre></div>
 <p>You must place <code>lmprun.in</code> and <code>nep.txt</code> in the generated <code>md/</code> directory.</p>
 <h2 id="active-learning-style-workflow">Active-Learning Style Workflow</h2>
@@ -1646,12 +1658,12 @@ <h2 id="active-learning-style-workflow">Active-Learning Style Workflow</h2>
 <p>For the development active-learning script, see <a href="active_learning_workflow.html">Active Learning</a>.</p>
 <h2 id="template-based-temperature-series">Template-Based Temperature Series</h2>
 <p>For a simple temperature series, a shell loop is often enough:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a><span class="k">for</span><span class="w"> </span>temp<span class="w"> </span><span class="k">in</span><span class="w"> </span><span class="m">300</span><span class="w"> </span><span class="m">500</span><span class="w"> </span><span class="m">700</span><span class="w"> </span><span class="m">900</span><span class="p">;</span><span class="w"> </span><span class="k">do</span>
-<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a><span class="w">    </span>mkdir<span class="w"> </span>-p<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K&quot;</span>
-<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a><span class="w">    </span>cp<span class="w"> </span>model.xyz<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/&quot;</span>
-<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a><span class="w">    </span>cp<span class="w"> </span>nep.txt<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/&quot;</span>
-<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a><span class="w">    </span>sed<span class="w"> </span><span class="s2">&quot;s/TEMPERATURE/</span><span class="nv">$temp</span><span class="s2">/g&quot;</span><span class="w"> </span>run_template.in<span class="w"> </span>&gt;<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/run.in&quot;</span>
-<a id="__codelineno-17-6" name="__codelineno-17-6" href="#__codelineno-17-6"></a><span class="k">done</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a><span class="k">for</span><span class="w"> </span>temp<span class="w"> </span><span class="k">in</span><span class="w"> </span><span class="m">300</span><span class="w"> </span><span class="m">500</span><span class="w"> </span><span class="m">700</span><span class="w"> </span><span class="m">900</span><span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a><span class="w">    </span>mkdir<span class="w"> </span>-p<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K&quot;</span>
+<a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a><span class="w">    </span>cp<span class="w"> </span>model.xyz<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/&quot;</span>
+<a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a><span class="w">    </span>cp<span class="w"> </span>nep.txt<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/&quot;</span>
+<a id="__codelineno-18-5" name="__codelineno-18-5" href="#__codelineno-18-5"></a><span class="w">    </span>sed<span class="w"> </span><span class="s2">&quot;s/TEMPERATURE/</span><span class="nv">$temp</span><span class="s2">/g&quot;</span><span class="w"> </span>run_template.in<span class="w"> </span>&gt;<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/run.in&quot;</span>
+<a id="__codelineno-18-6" name="__codelineno-18-6" href="#__codelineno-18-6"></a><span class="k">done</span>
 </code></pre></div>
 <p>Then submit the generated folders according to your local cluster system.</p>
 <h2 id="practical-notes">Practical Notes</h2>
diff --git a/docs/htmls/search/search_index.json b/docs/htmls/search/search_index.json
index 64c023b..e731dbe 100644
--- a/docs/htmls/search/search_index.json
+++ b/docs/htmls/search/search_index.json
@@ -1 +1 @@
-{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"],"fields":{"title":{"boost":1000.0},"text":{"boost":1.0},"tags":{"boost":1000000.0}}},"docs":[{"location":"index.html","title":"Home","text":"\ud83d\udcda GPUMDkit Documentation <p>A practical bilingual tutorial for GPUMDkit, covering installation, command-line tools, interactive workflows, plotting, and analysis utilities.</p>"},{"location":"index.html#language","title":"Language","text":"Language Start Here Command Reference English GPUMDkit Tutorials Command Reference \u7b80\u4f53\u4e2d\u6587 GPUMDkit \u6559\u7a0b \u547d\u4ee4\u53c2\u8003"},{"location":"index.html#what-you-can-learn-here","title":"What You Can Learn Here","text":"<p>This documentation is organized as a practical tutorial rather than only a command list. New users are encouraged to start from the overview and quick start pages, then move to the topic that matches their task.</p> Topic What it Covers Quick Start Installation, environment setup, interactive mode, direct command mode Format Conversion VASP, LAMMPS, CP2K, ABACUS, CIF, extxyz, group labels, weights Sampling Uniform/random sampling, NepTrain FPS, perturbation, force-deviation selection Calculators MSD, ionic conductivity, NEP prediction, descriptors, DOAS, NEB, polarization tools Analyzers Composition checks, distance checks, filters, property range analysis Visualization NEP training plots, MD plots, transport plots, thermal transport plots, example figures Workflows Batch DFT/MD processing and active-learning style workflows <p>For complex operations, use the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>For common operations with fixed arguments, use direct command-line mode:</p> <pre><code>gpumdkit.sh -h\ngpumdkit.sh -plt -h\ngpumdkit.sh -calc -h\n</code></pre>"},{"location":"en/index.html","title":"GPUMDkit Tutorials","text":"\ud83d\udcda GPUMDkit Tutorials <p>Welcome to GPUMDkit, a command-line toolkit for GPUMD and NEP.</p>"},{"location":"en/index.html#what-is-gpumdkit","title":"What is GPUMDkit?","text":"<p>GPUMDkit streamlines common tasks in computational materials science:</p> <ul> <li>Format Conversion: Convert between VASP, LAMMPS, CP2K, ABACUS, CIF, and extxyz formats</li> <li>Visualization: Plotting tools for NEP training, MD simulations, and analysis</li> <li>Calculators: Compute ionic conductivity, descriptors, MSD, NEB, and more</li> <li>Analyzers: Structure validation, filtering, composition analysis</li> <li>Workflows: Batch processing for DFT and MD simulations</li> <li>Sampling: Structure selection using uniform, random, or FPS methods</li> </ul>"},{"location":"en/index.html#quick-start","title":"Quick Start","text":""},{"location":"en/index.html#installation","title":"Installation","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"en/index.html#dependencies","title":"Dependencies","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"en/index.html#usage","title":"Usage","text":"<pre><code># Interactive mode\ngpumdkit.sh\n\n# Command-line mode\ngpumdkit.sh -&lt;option&gt; [args...]\n\n# Get help\ngpumdkit.sh -h\n</code></pre>"},{"location":"en/index.html#tutorials","title":"Tutorials","text":"Tutorial Description Quick Start Installation and first steps Command Reference One-page CLI and menu reference Format Conversion Convert between file formats Calculator Scripts Compute material properties Analyzer Scripts Structure analysis and validation Plot Scripts Plotting and visualization Workflow Scripts Batch processing and automation Structure Sampling Structure selection methods Custom Commands User-defined GPUMDkit shortcuts Active Learning Workflow Batch active-learning workflow notes Polar Material Analysis Ferroelectric and polarization tools Contributing to GPUMDkit Development notes"},{"location":"en/index.html#example-convert-vasp-outcars","title":"Example: Convert VASP OUTCARs","text":"<pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre>"},{"location":"en/index.html#example-plot-nep-results","title":"Example: Plot NEP Results","text":"<pre><code>gpumdkit.sh -plt train\ngpumdkit.sh -plt prediction\n</code></pre>"},{"location":"en/index.html#example-ionic-conductivity","title":"Example: Ionic Conductivity","text":"<pre><code>gpumdkit.sh -calc msd trajectory.xyz Li 10\ngpumdkit.sh -calc ionic-cond Li 1\ngpumdkit.sh -plt msd\n</code></pre>"},{"location":"en/index.html#module-overview","title":"Module Overview","text":"Module Menu CLI Description Format Conversion 1 <code>-out2xyz</code>, <code>-pos2exyz</code> File conversion Sample Structures 2 <code>-neptrain</code>, interactive menu Structure sampling Workflow 3 - Batch processing Calculators 4 <code>-calc &lt;type&gt;</code> Property calculations Analyzer 5 <code>-range</code>, <code>-min_dist</code> Structure analysis Visualization 6 <code>-plt &lt;type&gt;</code> Plotting tools Utilities 7 <code>-time</code>, <code>-clean</code> Utility functions"},{"location":"en/index.html#links","title":"Links","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>Documentation: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"en/active_learning_workflow.html","title":"Active Learning Workflow","text":"\ud83d\udd01 Active Learning Workflow <p>This tutorial explains the steps and considerations involved in the <code>workflow_active_learning_dev.sh</code> script. The workflow is used to generate, select, and analyze molecular structures, followed by simulations and data collection.</p>"},{"location":"en/active_learning_workflow.html#overview","title":"Overview","text":"<p>This script is designed to handle molecular dynamics simulations, sampling, and SCF (self-consistent field) calculations for NEP. Below is a step-by-step guide explaining how the script works and what each part does.</p>"},{"location":"en/active_learning_workflow.html#1-slurm-directives","title":"1. SLURM Directives","text":"<pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>The SLURM directives are used to define how the job will be submitted to the cluster:</p> <ul> <li><code>#SBATCH -p</code> defines the partition, in this case, it's <code>intel-sc3</code> and <code>intel-sc3-32c</code>.</li> <li><code>#SBATCH -q</code> specifies the queue, in this case, <code>huge</code>.</li> <li><code>#SBATCH -N</code> allocates 1 node for the job.</li> <li><code>#SBATCH -J</code> names the job <code>workflow</code>.</li> <li><code>#SBATCH -o</code> defines the output log file as <code>workflow.log</code>.</li> <li><code>--ntasks-per-node=1</code> specifies that only one task should run per node.</li> </ul> <p>NOTE: If your machine does not have the SLURM environment, you can also run the script directly from the command line. For example:</p> <pre><code>nohup bash workflow_active_learning_dev.sh &amp;&gt;workflow.log &amp;\n</code></pre>"},{"location":"en/active_learning_workflow.html#2-basic-setup","title":"2. Basic Setup","text":"<pre><code>cd $SLURM_SUBMIT_DIR \n</code></pre> <p>Ensure the working directory is correct, and that all necessary files are present for the job.</p> <pre><code>source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  # Load the submit template\npython_pynep=python  # Python executable for the deprecated pynep branch if needed\n</code></pre> <ul> <li><code>GPUMDkit_path</code> is the environment variable that stores the path for the <code>GPUMDkit</code> .</li> <li><code>python_pynep</code> points to the Python environment used for the deprecated <code>pynep</code>-related branch if needed.</li> </ul>"},{"location":"en/active_learning_workflow.html#3-variable-definitions","title":"3. Variable Definitions","text":"<pre><code>work_dir=${PWD}  # Set the working directory\nprefix_name=LiF_iter01  # Prefix for calculations\nmin_dist=1.4  # Minimum atom distance\nbox_limit=13  # Simulation box limit\nmax_fp_num=50  # Maximum number of single point calculations\nsample_method=pynep  # Sampling method (options: uniform, random, pynep)\npynep_sample_dist=0.01  # Sampling distance for pynep\n</code></pre> <p>You can customize:</p> <ul> <li><code>prefix_name</code> to reflect the name of your current work.</li> <li><code>min_dist</code>, <code>box_limit</code>, and <code>max_fp_num</code> based on your own system.</li> <li><code>sample_method</code> (choose between <code>uniform</code>, <code>random</code>, or <code>pynep</code>).</li> <li><code>pynep_sample_dist</code> is the sampling distance for <code>pynep</code>.</li> </ul>"},{"location":"en/active_learning_workflow.html#4-check-required-files","title":"4. Check Required Files","text":"<pre><code>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ -f run.in ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then\n    # Check for the required files before proceeding.\nelse\n    echo \"Please put nep.in nep.txt train.xyz run.in INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.\"\n    exit 1\nfi\n</code></pre> <p>Make sure the necessary files (<code>nep.txt</code>, <code>nep.in</code>, <code>train.xyz</code>, <code>run.in</code>, <code>INCAR</code>, <code>POTCAR</code>, <code>KPOINTS</code>) are available in the working directory. If any of these are missing, the script will terminate. <code>train.xyz</code> and <code>nep.txt</code> are used for <code>pynep</code> sampling, and <code>run.in</code> is the simulation parameters of MD in the current iteration.</p>"},{"location":"en/active_learning_workflow.html#5-file-organization","title":"5. File Organization","text":"<pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <p>The script organizes the working files into two folders:</p> <ul> <li><code>00.modev</code>: For molecular dynamics simulation.</li> <li><code>common</code>: For shared resources such as <code>nep.txt</code>, <code>run.in</code>, and the structure files, etc.</li> </ul>"},{"location":"en/active_learning_workflow.html#6-molecular-dynamics-simulation-submission","title":"6. Molecular Dynamics Simulation Submission","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>After preparing the input files, the script submits an array of molecular dynamics (MD) tasks using <code>submit_gpumd_array</code>.</p>"},{"location":"en/active_learning_workflow.html#7-monitoring-task-completion","title":"7. Monitoring Task Completion","text":"<pre><code>while true; do\n    logs=$(find \"${work_dir}/00.modev/\" -type f -name log -path \"*/sample_*/log\")\n    finished_tasks_md=$(grep \"Finished running GPUMD.\" $logs | wc -l)\n    error_tasks_md=$(grep \"Error\" $logs | wc -l)\n\n    if [ \"$error_tasks_md\" -ne 0 ]; then\n        echo \"Error: MD simulation encountered an error.\"\n        exit 1\n    fi\n    if [ $finished_tasks_md -eq $sample_struct_num ]; then\n        break\n    fi\n    sleep 30\ndone\n</code></pre> <p>The script continuously checks whether all MD tasks have finished by searching for a <code>Finished running GPUMD.</code> message in the logs. If an error is encountered, the script terminates.</p>"},{"location":"en/active_learning_workflow.html#8-analysis-and-filtering","title":"8. Analysis and Filtering","text":"<pre><code>mkdir ${work_dir}/01.select\n...\n</code></pre> <p>In the <code>01.select</code> folder, all structures in the trajectory file <code>dump.xyz</code> during the MD process will be analyzed and filtered to avoid the generation of non-physical structures as much as possible. Specifically, the <code>get_min_dist.py</code>, <code>filter_structures_by_distance.py</code> and <code>filter_exyz_by_box.py</code> scripts will be employed to check whether there are situations where the distance between atoms is too close or the simulated box exceeds the limit value, and such structures will be filtered out.</p>"},{"location":"en/active_learning_workflow.html#9-sampling-methods","title":"9. Sampling Methods","text":"<pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <p>The script supports three sampling methods: <code>uniform</code>, <code>random</code>, and <code>pynep</code>. It selects structures according to the chosen method and checks if the number exceeds <code>max_fp_num</code>, ensuring the final structure count is within limits.</p>"},{"location":"en/active_learning_workflow.html#10-scf-calculations","title":"10. SCF Calculations","text":"<pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>After sampling, SCF calculations are submitted using <code>submit_vasp_array</code>. The process is similar to the MD submission, but for SCF calculations.</p>"},{"location":"en/active_learning_workflow.html#11-prediction-step","title":"11. Prediction Step","text":"<pre><code>submit_nep_prediction\n</code></pre> <p>The final step involves submitting the NEP prediction task to check  the accuracy of the NEP model. </p> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/analyzer_scripts.html","title":"Analyzer Scripts","text":"\ud83d\udd0d Analyzer Scripts <p>Analyzer scripts provide structure statistics, distance checks, filters, and composition analysis for extxyz datasets.</p> <p>Script Location: <code>Scripts/analyzer/</code></p>"},{"location":"en/analyzer_scripts.html#overview","title":"Overview","text":"Task Command Purpose Composition <code>gpumdkit.sh -analyze_comp train.xyz</code> group structures by chemical composition Chemical species <code>gpumdkit.sh -chem_species train.xyz</code> list species in a file Property range <code>gpumdkit.sh -range train.xyz force</code> inspect energy/force/virial range Minimum distance <code>gpumdkit.sh -min_dist dump.xyz</code> fast distance check without PBC Minimum distance with PBC <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> accurate distance check with PBC Charge balance <code>gpumdkit.sh -cbc train.xyz</code> oxidation-state balance check Distance filter <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> remove structures with short contacts Box filter <code>gpumdkit.sh -filter_box dump.xyz 13</code> remove structures with too-large box edges Property filter <code>gpumdkit.sh -filter_value train.xyz force 20</code> filter by energy/force/virial threshold Pair-distance range <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> extract structures by pair distance"},{"location":"en/analyzer_scripts.html#composition-analysis","title":"Composition Analysis","text":"<pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>Example output:</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>This is useful when <code>train.xyz</code> contains structures from different systems or different cell sizes. You can export a subset by composition from the interactive prompt.</p>"},{"location":"en/analyzer_scripts.html#property-range-analysis","title":"Property Range Analysis","text":"<pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist\n</code></pre> <p>Use <code>hist</code> to show a histogram of the selected property.</p>"},{"location":"en/analyzer_scripts.html#minimum-distance-checks","title":"Minimum Distance Checks","text":"<p>Fast check without PBC:</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>Accurate check with PBC:</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>Typical output:</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (A) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 A\n</code></pre> <p>The PBC version considers periodic boundary conditions.</p>"},{"location":"en/analyzer_scripts.html#filtering-structures","title":"Filtering Structures","text":""},{"location":"en/analyzer_scripts.html#filter-by-minimum-distance","title":"Filter by Minimum Distance","text":"<pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>This removes structures with any interatomic distance below <code>1.0 A</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-box-size","title":"Filter by Box Size","text":"<pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>This filters structures by box-edge length.</p>"},{"location":"en/analyzer_scripts.html#filter-by-property-value","title":"Filter by Property Value","text":"<pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre>"},{"location":"en/analyzer_scripts.html#filter-by-pair-distance-range","title":"Filter by Pair-Distance Range","text":"<pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>This extracts structures where the Li-Li minimum distance is between <code>1.8 A</code> and <code>2.0 A</code>.</p>"},{"location":"en/analyzer_scripts.html#charge-balance-check","title":"Charge Balance Check","text":"<pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>Outputs may include:</p> <ul> <li><code>balanced.xyz</code></li> <li><code>unbalanced.xyz</code></li> <li><code>indices.txt</code></li> </ul> <p>This is intended for systems where common oxidation states are meaningful.</p>"},{"location":"en/analyzer_scripts.html#example-commands","title":"Example Commands","text":"<p>Property and distance checks:</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\ngpumdkit.sh -range train.xyz force hist\ngpumdkit.sh -range train.xyz energy hist\ngpumdkit.sh -min_dist_pbc train.xyz\n</code></pre> <p>Filtering examples:</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\ngpumdkit.sh -filter_box filtered_dist.xyz 13\n</code></pre>"},{"location":"en/calculator_scripts.html","title":"Calculator Scripts","text":"\ud83e\uddee Calculator Scripts <p>The calculator module contains scripts for computing properties from MD trajectories, NEP models, and structure files.</p> <p>Script Location: <code>Scripts/calculators/</code></p>"},{"location":"en/calculator_scripts.html#overview","title":"Overview","text":"Task Command Main Input Ionic conductivity <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>, <code>thermo.out</code>, <code>model.xyz</code> MSD from trajectory <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz trajectory NEP prediction <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP model NEP descriptors <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP model DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP model NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> initial/final structures Minimization <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> structure + NEP model Neighbor list <code>gpumdkit.sh -calc nlist [args...]</code> structure Displacement <code>gpumdkit.sh -calc disp [args...]</code> trajectory + neighbor list Average structure <code>gpumdkit.sh -calc avg-struct [args...]</code> trajectory Octahedral tilt <code>gpumdkit.sh -calc oct-tilt [args...]</code> trajectory + B-O neighbor list ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 [args...]</code> trajectory + neighbor lists <p>For a full command list:</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>The command-line help table looks like:</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>In interactive mode, choose <code>4) Calculators</code>. The menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"en/calculator_scripts.html#ionic-conductivity","title":"Ionic Conductivity","text":"<p><code>calc_ion_conductivity.py</code> calculates ionic diffusivity and conductivity from <code>msd.out</code>.</p>"},{"location":"en/calculator_scripts.html#required-and-optional-files","title":"Required and Optional Files","text":"File Role <code>msd.out</code> Required MSD data <code>thermo.out</code> Optional, used for automatic temperature detection <code>model.xyz</code> Optional, used for volume and ion-count detection <code>run.in</code> Optional, used to detect replication"},{"location":"en/calculator_scripts.html#usage","title":"Usage","text":"<pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>From interactive mode, choose <code>401</code>. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>If automatic files are missing, the script will ask for temperature, volume, and ion count interactively.</p> <p>Interactive prompts in manual mode look like:</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre>"},{"location":"en/calculator_scripts.html#example-output","title":"Example Output","text":"<pre><code>Diffusivity (D):\n  D_x: 4.153e-07 cm^2/s\n  D_y: 4.174e-07 cm^2/s\n  D_z: 2.610e-07 cm^2/s\n  D_total: 3.646e-07 cm^2/s\n------------------------------\nIonic Conductivity:\n  Sigma_x: 2.576e-02 mS/cm\n  Sigma_y: 2.589e-02 mS/cm\n  Sigma_z: 1.619e-02 mS/cm\n  Sigma_total: 2.261e-02 mS/cm\n</code></pre>"},{"location":"en/calculator_scripts.html#mean-square-displacement","title":"Mean Square Displacement","text":"<p><code>calc_msd.py</code> computes MSD directly from an extxyz trajectory.</p> <pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>From interactive mode, choose <code>412</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>Li</code> target mobile species <code>10</code> time interval between frames, in fs <code>5000</code> optional maximum correlation steps <p>Output:</p> <ul> <li><code>msd.out</code></li> </ul> <p>The beginning of <code>msd.out</code> is a text table with time and MSD columns. After generating it, use the plot commands below.</p> <p>You can then plot:</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-property-prediction","title":"NEP Property Prediction","text":"<p><code>calc_properties_with_nep.py</code> calculates energy, force, and stress for structures using a NEP model.</p> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>This function is useful when you intentionally want to use a trained NEP model as a surrogate calculator. It should not be treated as a replacement for DFT unless the model quality has been carefully validated.</p>"},{"location":"en/calculator_scripts.html#nep-descriptors","title":"NEP Descriptors","text":"<p><code>calc_descriptors.py</code> extracts NEP descriptors for a selected element.</p> <pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>Use cases:</p> <ul> <li>visualize chemical environments with PCA/UMAP;</li> <li>compare training and candidate structures;</li> <li>inspect whether new data expands descriptor space.</li> </ul> <p>Plot descriptors with:</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/calculator_scripts.html#density-of-atomistic-states","title":"Density of Atomistic States","text":"<p><code>calc_doas.py</code> calculates density of atomistic states (DOAS), following the idea proposed by Wang et al..</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>The script:</p> <ol> <li>reads all structures;</li> <li>relaxes each structure with a NEP calculator;</li> <li>extracts per-atom energies;</li> <li>groups atomic energies by element;</li> <li>writes the grouped values to the output file.</li> </ol> <p>For very large systems, doing minimization and atomistic-energy extraction directly in GPUMD may be more efficient.</p>"},{"location":"en/calculator_scripts.html#neb-with-a-nep-model","title":"NEB with a NEP Model","text":"<pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>This runs a NEB calculation with <code>9</code> intermediate images. During execution, the script asks how atoms should be fixed:</p> <ul> <li><code>none</code>: no atoms fixed;</li> <li><code>index</code>: fix atoms by index;</li> <li><code>element</code>: fix all atoms of one element;</li> <li><code>position</code>: fix atoms inside a coordinate range.</li> </ul>"},{"location":"en/calculator_scripts.html#structure-minimization","title":"Structure Minimization","text":"<pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input structure, POSCAR/CONTCAR or extxyz <code>nep.txt</code> NEP model <code>0.01</code> optional force convergence threshold in eV/Ang <code>1000</code> optional maximum optimization steps <p>Output:</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"en/calculator_scripts.html#ferroelectric-and-polar-material-tools","title":"Ferroelectric and Polar Material Tools","text":"<p>The following tools are useful for perovskite and polar-material analysis. They require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p><code>ferrodispcalc</code> currently has no associated paper to cite.</p>"},{"location":"en/calculator_scripts.html#build-neighbor-lists","title":"Build Neighbor Lists","text":"<pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre> <p>This creates a neighbor-list file where each row stores one center atom and its nearest neighbor atoms.</p>"},{"location":"en/calculator_scripts.html#calculate-displacements","title":"Calculate Displacements","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre> <p>Use <code>-l 0.2</code> to analyze the last 20% of frames. Use <code>-s</code>, <code>-t</code>, and <code>-p</code> if you want an explicit slice.</p>"},{"location":"en/calculator_scripts.html#average-a-structure","title":"Average a Structure","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>This is useful before displacement or polarization analysis when a representative averaged structure is needed.</p>"},{"location":"en/calculator_scripts.html#octahedral-tilt","title":"Octahedral Tilt","text":"<pre><code>gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre> <p>The neighbor list should usually contain six B-O neighbors for each B-site center in an <code>ABO3</code>-like structure.</p>"},{"location":"en/calculator_scripts.html#abo3-polarization","title":"ABO3 Polarization","text":"<pre><code>gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -o polarization.dat\n</code></pre> <p>The <code>--bec</code> values should be chosen according to your model or reference data. The tool is designed for <code>ABO3</code>-type local polarization analysis.</p>"},{"location":"en/command_reference.html","title":"Command Reference","text":"\ud83d\udccb Command Reference <p>This page lists the stable GPUMDkit command-line shortcuts. Interactive mode is available for workflows with many choices.</p> <p>The source table is maintained in <code>docs/command_reference.tsv</code>.</p>"},{"location":"en/command_reference.html#gpumdkitsh-h-output","title":"<code>gpumdkit.sh -h</code> Output","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |\n| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/command_reference.html#main","title":"Main","text":"Command Syntax Description <code>-h</code> <code>gpumdkit.sh -h</code> Show general help <code>-update</code> <code>gpumdkit.sh -update</code> Update GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> Clean extra files in the current directory"},{"location":"en/command_reference.html#format-conversion","title":"Format Conversion","text":"Command Syntax Description <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR to extxyz, shell version <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR to extxyz, Python version <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K output to xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR to extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF to POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF to extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR to extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz frames to POSCAR files <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR to LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump to extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory to extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> Replicate by cell factors <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> Replicate toward a target atom count <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> Add GPUMD group labels <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> Add structure weights <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> Extract one frame <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> Remove extra extxyz properties <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> Extract frames by fractional range"},{"location":"en/command_reference.html#calculators","title":"Calculators","text":"Command Syntax Description <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> Ionic conductivity <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP property prediction <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP descriptors <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> Density of atomistic states <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> NEB with a NEP model <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> Structure minimization <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> MSD from trajectory <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> Neighbor lists <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> Displacements <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> Averaged structure <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> Octahedral tilt <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 local polarization"},{"location":"en/command_reference.html#analyzers","title":"Analyzers","text":"Command Syntax Description <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> Property range analysis <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> Composition analysis <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> Chemical species list <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> Charge-balance check <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> Minimum distance without PBC <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> Minimum distance with PBC <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> Distance filtering <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> PBC-aware distance filtering <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> Box-edge filtering <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> Property threshold filtering <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> Element-pair distance range filtering <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> Probability density analysis"},{"location":"en/command_reference.html#visualization","title":"Visualization","text":"<p>Use:</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>Common types include <code>train</code>, <code>prediction</code>, <code>thermo</code>, <code>msd</code>, <code>sdc</code>, <code>rdf</code>, <code>emd</code>, <code>nemd</code>, <code>hnemd</code>, <code>pdos</code>, and <code>plane-grid</code>.</p>"},{"location":"en/command_reference.html#utilities","title":"Utilities","text":"Command Syntax Description <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> Monitor GPUMD or NEP progress <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> Modify NEP models interactively <code>-pynep</code> <code>gpumdkit.sh -pynep</code> Deprecated PyNEP FPS sampling"},{"location":"en/contributing_to_gpumdkit.html","title":"Contributing to GPUMDkit","text":"\ud83e\udd1d Contributing to GPUMDkit <p>Thank you for your interest in contributing to GPUMDkit! We appreciate your time and effort in helping improve this toolkit.</p> <p><code>GPUMDkit</code> is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.</p>"},{"location":"en/contributing_to_gpumdkit.html#table-of-contents","title":"Table of Contents","text":"<ul> <li>Development Restrictions and Guidelines</li> <li>Reporting Bugs</li> <li>Suggesting Features</li> <li>Contributing Code</li> <li>Fork and Clone the Repository</li> <li>Create a Feature Branch</li> <li>Making Changes<ul> <li>Interactive Mode Contributions</li> <li>Command-Line Mode Contributions</li> <li>Updating Tab Completion</li> </ul> </li> <li>Code Style and Best Practices</li> <li>Testing Your Changes</li> <li>Commit Messages</li> <li>Push and Open a Pull Request</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#development-restrictions-and-guidelines","title":"Development Restrictions and Guidelines","text":"<p>To maintain code quality and consistency across the project, please adhere to these guidelines:</p>"},{"location":"en/contributing_to_gpumdkit.html#language-requirements","title":"Language Requirements","text":"<ul> <li>All code should be written in English: This includes variable names, function names, comments, docstrings, commit messages, and documentation.</li> <li>While we understand that contributors come from diverse backgrounds, using English ensures that the codebase is accessible to the widest possible audience.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#modularity-and-reusability","title":"Modularity and Reusability","text":"<ul> <li>Write modular and reusable code: Functions and scripts should be designed with flexibility in mind.</li> <li>Prefer passing parameters over hardcoding values: Use function arguments, command-line parameters, or configuration files instead of hardcoded values. However, some filenames are required to be fixed by GPUMD and NEP programs (e.g., <code>train.xyz</code>, <code>thermo.out</code>), and these can be hardcoded as needed.</li> <li>Example:    <pre><code># Good: accepts parameters\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # processing logic\n}\n\n# Avoid: hardcoded values (unless required by GPUMD/NEP)\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # processing logic\n}\n</code></pre></li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#code-style","title":"Code Style","text":"<ul> <li>Write code that is clear and easy for others to maintain and modify.</li> <li>Use meaningful variable and function names.</li> <li>Add comments where necessary to explain complex logic.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#documentation","title":"Documentation","text":"<ul> <li>Ensure that help messages (e.g., <code>-h</code> flags) are clear and accurate.</li> <li>Documentation files in the <code>docs/</code> directory will be updated by the maintainers, so you generally don't need to modify them.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#reporting-bugs","title":"Reporting Bugs","text":"<p>If you encounter a bug, please help us fix it by reporting it through GitHub Issues:</p> <ol> <li>Search existing issues to see if the bug has already been reported.</li> <li>Open a new issue if it hasn't been reported yet: Create an Issue</li> <li>Describe the problem in detail and provide test files if possible.</li> </ol> <p>You can also reach out to us through: - QQ Group: 825696376 - Email: yanzihan@westlake.edu.cn - Script Developer: Contact the developer listed in the script header</p>"},{"location":"en/contributing_to_gpumdkit.html#suggesting-features","title":"Suggesting Features","text":"<p>We welcome feature suggestions! To propose a new feature:</p> <ol> <li>Search existing issues to see if someone has already suggested it.</li> <li>Open a new feature request: Create a Feature Request and mention @zhyan0603</li> <li>Describe what you need clearly and explain how it would be useful.</li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#contributing-code","title":"Contributing Code","text":""},{"location":"en/contributing_to_gpumdkit.html#fork-and-clone-the-repository","title":"Fork and Clone the Repository","text":"<ol> <li> <p>Fork the repository on GitHub by clicking the \"Fork\" button at the top right of the repository page.</p> </li> <li> <p>Clone your fork to your local machine:</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>Set up the upstream remote to keep your fork in sync:    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#create-a-feature-branch","title":"Create a Feature Branch","text":"<p>Create a new branch for your changes:</p> <pre><code># Create and checkout a new branch from main\ngit checkout -b your-branch-name\n</code></pre> <p>Name your branch as you prefer.</p>"},{"location":"en/contributing_to_gpumdkit.html#making-changes","title":"Making Changes","text":"<p>The structure of <code>GPUMDkit</code> consists of: - <code>gpumdkit.sh</code>: Main entry point (Bash script) handling both interactive menu mode and command-line mode - <code>Scripts/</code>: Python utility scripts organized by functionality   - <code>plt_scripts/</code>: Plotting scripts   - <code>calculators/</code>: Calculation utilities   - <code>format_conversion/</code>: Format conversion tools   - <code>workflow/</code>: Workflow automation   - <code>sample_structures/</code>: Structure sampling utilities   - <code>analyzer/</code>: Analysis tools   - <code>utils/</code>: Utility functions (including <code>completion.sh</code> for tab completion) - <code>src/</code>: Shell scripts containing menu functions for interactive mode   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>docs/</code>: Documentation files</p>"},{"location":"en/contributing_to_gpumdkit.html#interactive-mode-contributions","title":"Interactive Mode Contributions","text":"<p>To add a new feature accessible through the interactive menu:</p> <ol> <li>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:</li> </ol> <pre><code># Example: Add a new format conversion script\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>Implement your functionality following the modularity guidelines (accept parameters, avoid hardcoding).</p> </li> <li> <p>Add a wrapper function in the corresponding <code>src/</code> file:    <pre><code># Example: Edit src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>Add a new function:    <pre><code>function f106_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input the required parameters:\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -p \" \" converter_params\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py ${converter_params}\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>Update the menu display in <code>gpumdkit.sh</code>:    <pre><code># Find the menu() function and update it if needed\n# Find the array_choice array and add your new choice number\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\"  # Added \"106\"\n    # ... rest of choices\n)\n</code></pre></p> </li> <li> <p>Add the case statement in <code>gpumdkit.sh</code>:    <pre><code># In the main() function, find the appropriate case statement\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n            \"101\") f101_out2xyz ;;\n            # ... existing cases ...\n            \"106\") f106_new_converter ;;  # Add your case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#command-line-mode-contributions","title":"Command-Line Mode Contributions","text":"<p>To add a new command-line flag or subcommand:</p> <ol> <li> <p>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:    <pre><code># Example: Add a new analyzer script\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>Implement your functionality with clear parameter requirements:    <pre><code># Example: Scripts/analyzer/analyze_bonds.py\nimport sys\n\ndef main():\n    if len(sys.argv) != 3:\n        print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n        print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n        sys.exit(1)\n\n    input_file = sys.argv[1]\n    cutoff = float(sys.argv[2])\n\n    # Your implementation here\n\nif __name__ == \"__main__\":\n    main()\n</code></pre></p> </li> <li> <p>Add the command-line flag handler in <code>gpumdkit.sh</code>:    <pre><code># Find the command-line parsing section (after line ~167)\n# Add your new flag in the appropriate location\n\ncase $1 in\n    # ... existing cases ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py \"$2\" \"$3\"\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n            exit 1\n        fi ;;\n    # ... rest of cases ...\nesac\n</code></pre></p> </li> <li> <p>Update the help information in <code>gpumdkit.sh</code>:    <pre><code># Find the help_info_table() function and add your command\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... rest of help table ...\n}\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#updating-tab-completion","title":"Updating Tab Completion","text":"<p>When adding new command-line flags, update the tab completion script:</p> <pre><code># Edit Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>Add your new flag to the <code>opts</code> variable: <pre><code># Find the line with local opts=...\nlocal opts=\"-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ...\"\n#                                                      ^^^^^^^^^^^^^^ Add your flag here\n</code></pre></p> <p>If your flag accepts secondary options (like <code>-plt</code> or <code>-calc</code>), add a case for it: <pre><code>case \"$prev\" in\n    # ... existing cases ...\n    -analyze_bonds)\n        COMPREPLY=($(compgen -f -- \"$cur\"))  # Complete with filenames\n        ;;\n    # ... rest of cases ...\nesac\n</code></pre></p>"},{"location":"en/contributing_to_gpumdkit.html#code-style-and-best-practices","title":"Code Style and Best Practices","text":"<ul> <li>Shell Scripts:</li> <li>Use <code>${variable}</code> for variable expansion</li> <li> <p>Write code that is clear and easy to maintain</p> </li> <li> <p>Python Scripts:</p> </li> <li>Write clear, maintainable code</li> <li>Use meaningful variable names</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#testing-your-changes","title":"Testing Your Changes","text":"<p>Before submitting your contribution:</p> <ol> <li> <p>Test interactive mode (if applicable):    <pre><code>gpumdkit.sh\n# Navigate to your new feature and test it thoroughly\n</code></pre></p> </li> <li> <p>Test command-line mode (if applicable):    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # Test help message\n</code></pre></p> </li> <li> <p>Test tab completion (if you modified <code>completion.sh</code>):    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # Should show your new flag\n</code></pre></p> </li> <li> <p>Test with various inputs:</p> </li> <li>Test with typical inputs</li> <li>Test with edge cases (empty files, large files, etc.)</li> <li> <p>Test error handling (missing files, invalid parameters)</p> </li> <li> <p>Verify no regressions: Ensure existing functionality still works correctly.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#commit-messages","title":"Commit Messages","text":"<p>Write clear, descriptive commit messages that explain what you changed. There are no strict format requirements - just make sure your message is understandable.</p>"},{"location":"en/contributing_to_gpumdkit.html#push-and-open-a-pull-request","title":"Push and Open a Pull Request","text":"<ol> <li> <p>Commit your changes:    <pre><code>git add .\ngit commit -m \"your descriptive message\"\n</code></pre></p> </li> <li> <p>Keep your branch updated with the upstream <code>main</code> branch:    <pre><code>git fetch upstream\ngit rebase upstream/main\n</code></pre></p> </li> <li> <p>Push your branch to your fork:    <pre><code>git push origin your-branch-name\n</code></pre></p> </li> <li> <p>Open a Pull Request:</p> </li> <li>Go to the GPUMDkit repository</li> <li>Click \"Pull Requests\" \u2192 \"New Pull Request\"</li> <li>Set the base branch to <code>dev</code> for code review</li> <li>Set the compare branch to your feature branch</li> <li> <p>Fill in the PR description with:</p> <ul> <li>Title: Brief description of changes</li> <li>Description: Detailed explanation of what changed and why</li> <li>Testing: Describe how you tested the changes</li> </ul> </li> <li> <p>Respond to review feedback:</p> </li> <li>Be open to suggestions and constructive criticism</li> <li>Make requested changes promptly</li> <li> <p>Push additional commits to your branch (they'll automatically appear in the PR)</p> </li> <li> <p>After approval: A maintainer will merge your PR.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#questions-or-need-help","title":"Questions or Need Help?","text":"<p>If you have questions about contributing or need help with your contribution:</p> <ul> <li>Open a discussion: Use GitHub Discussions for general questions</li> <li>Ask in an issue: Comment on related issues for specific questions</li> <li>Contact maintainers: Reach out to the core developers listed in the README</li> </ul> <p>Thank you again for contributing to <code>GPUMDkit</code>! Your efforts help make this toolkit better for the entire GPUMD and NEP community. \ud83d\ude80</p>"},{"location":"en/custom_commands.html","title":"Custom Commands","text":"\ud83d\udd27 Custom Commands <p>GPUMDkit allows users to extend the command-line interface with custom commands. Define shortcuts for frequently used scripts in your ~/.gpumdkit.in file.</p>"},{"location":"en/custom_commands.html#setup","title":"Setup","text":"<p>Create or edit <code>~/.gpumdkit.in</code>: <pre><code>vi ~/.gpumdkit.in\n</code></pre></p> <p>Define custom functions with the <code>custom_</code> prefix.</p>"},{"location":"en/custom_commands.html#examples","title":"Examples","text":""},{"location":"en/custom_commands.html#simple-greeting","title":"Simple Greeting","text":"<p>Write the following codes in your <code>~/.gpumdkit.in</code> </p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>and run <code>gpumdkit.sh -hello</code>, you will see:</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"en/custom_commands.html#command-with-required-arguments","title":"Command with Required Arguments","text":"<p>For the following function:</p> <pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>and you can add a argument, for example: <code>gpumdkit.sh -greet Zihan</code>, then you will see:</p> <pre><code>Hello, Zihan!\n</code></pre> <p>Passing arguments: Use <code>\"$@\"</code> to forward all arguments safely. Use <code>${@:1}</code> when you need to refer to arguments starting from the first one. </p>"},{"location":"en/custom_commands.html#calling-an-external-script","title":"Calling an External Script","text":"<p>If you want to call an external script like <code>gpumdkit.sh</code>.</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>and run <code>gpumdkit.sh -nepanalyse</code></p>"},{"location":"en/custom_commands.html#advanced-examples","title":"Advanced Examples","text":""},{"location":"en/custom_commands.html#batch-processing","title":"Batch Processing","text":"<p>Process multiple files: <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -batch_plot dir1 dir2 dir3</code></p>"},{"location":"en/custom_commands.html#analysis-pipeline","title":"Analysis Pipeline","text":"<p>Combine multiple operations: <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -analyze_training train.xyz</code></p>"},{"location":"en/custom_commands.html#custom-workflow","title":"Custom Workflow","text":"<p>Automate common workflow: <pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    # Convert VASP outputs\n    gpumdkit.sh -out2xyz ./\n\n    # Filter outliers\n    gpumdkit.sh -filter_value train.xyz force 30\n\n    # Check quality\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -prep_training</code></p>"},{"location":"en/custom_commands.html#tips","title":"Tips","text":"<ul> <li>Use descriptive names: <code>custom_analyze_nep_training</code> is clearer than <code>custom_ant</code></li> <li>Add help messages: Echo usage info when no arguments provided</li> <li>Error handling: Check if required files exist before processing</li> <li>Forward arguments safely: Use <code>\"$@\"</code> to preserve spaces and special characters</li> </ul> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/format_conversion.html","title":"Format Conversion","text":"\ud83d\udd04 Format Conversion <p>GPUMDkit contains utilities for converting common atomistic simulation formats, with extra handling for metadata such as group labels, weights, and frame extraction.</p> <p>Script Location: <code>Scripts/format_conversion/</code></p>"},{"location":"en/format_conversion.html#overview","title":"Overview","text":"<p>The format conversion module covers:</p> <ul> <li>VASP: <code>POSCAR</code>, <code>CONTCAR</code>, <code>OUTCAR</code>, <code>XDATCAR</code></li> <li>LAMMPS: data files and dump trajectories</li> <li>CP2K: output logs, position, force, and cell files</li> <li>ABACUS: SCF/MD logs</li> <li>CIF: crystallographic structure files</li> <li>ASE trajectory: <code>.traj</code></li> <li>extxyz: a common structure format for GPUMD and NEP</li> </ul>"},{"location":"en/format_conversion.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>1) Format Conversion\n</code></pre> <p>The format conversion menu is:</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"en/format_conversion.html#what-each-entry-does","title":"What Each Entry Does","text":"Entry Function When to Use <code>101</code> VASP OUTCAR to extxyz, shell version convert VASP calculation directories <code>102</code> MTP cfg to extxyz convert MTP training data <code>103</code> CP2K to extxyz choose CP2K log/inp route or pos/frc/cell route <code>104</code> ABACUS to extxyz convert ABACUS SCF or MD output <code>105</code> extxyz to POSCAR write each extxyz frame as a POSCAR-style file <code>106</code> add group labels add atom group labels for GPUMD-related workflows <code>107</code> add weights assign training weights in extxyz <code>108</code> extract frame export one frame from an extxyz trajectory <code>109</code> clean XYZ info remove extra extxyz properties <code>110</code> replicate structure build supercells by factors or target atom count <code>out2exyz</code> OUTCAR to extxyz, Python version alternative VASP OUTCAR converter <code>pos2exyz</code> POSCAR to extxyz convert a single structure <code>cif2pos</code> CIF to POSCAR prepare VASP input from CIF <code>cif2exyz</code> CIF to extxyz prepare GPUMDkit input from CIF <code>xdat2exyz</code> XDATCAR to extxyz convert VASP MD trajectory <code>pos2lmp</code> POSCAR to LAMMPS data prepare LAMMPS input <code>lmp2exyz</code> LAMMPS dump to extxyz convert LAMMPS trajectory <code>traj2exyz</code> ASE traj to extxyz convert ASE trajectory"},{"location":"en/format_conversion.html#quick-command-reference","title":"Quick Command Reference","text":"Source Target Command OUTCAR directory extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR directory extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> extxyz POSCAR files <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"en/format_conversion.html#common-examples","title":"Common Examples","text":""},{"location":"en/format_conversion.html#convert-vasp-calculations-to-extxyz","title":"Convert VASP calculations to extxyz","text":"<p>If each calculation directory contains an <code>OUTCAR</code>, run:</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>The shell version searches the target directory and converts VASP results into an extxyz file suitable for later analysis. If you prefer the Python implementation:</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>From interactive mode, choose <code>101</code>. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#add-group-labels","title":"Add group labels","text":"<p>Some GPUMD-related workflows use group labels for atom grouping, for example in species-specific MSD or diffusion calculations.</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>This command reads the input structure and writes an extxyz file with group information.</p> <p>From interactive mode, choose <code>106</code>. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#script-details","title":"Script Details","text":""},{"location":"en/format_conversion.html#poscar-to-extxyz","title":"POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>Use this when you have a single VASP structure and want an extxyz output.</p> <p>Interactive keyword: <code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#extxyz-to-poscar","title":"extxyz to POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>This converts all frames in an extxyz file into <code>POSCAR_*.vasp</code> files. Frame indices are 0-based in most GPUMDkit scripts, but output filenames are meant for direct inspection and batch calculations.</p> <p>Interactive entry: <code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#lammps-dump-to-extxyz","title":"LAMMPS dump to extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>The element symbols must match the LAMMPS atom type IDs. For example, if type <code>1</code> is Li, type <code>2</code> is Y, and type <code>3</code> is Cl, the order should be <code>Li Y Cl</code>.</p> <p>Interactive keyword: <code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#cif-conversion","title":"CIF conversion","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>Use <code>-cif2pos</code> if you want a VASP-style structure, and <code>-cif2exyz</code> if the next step is GPUMDkit analysis.</p>"},{"location":"en/format_conversion.html#add-weights","title":"Add weights","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>This is useful when you want some structures to have a different training weight in a NEP dataset.</p>"},{"location":"en/format_conversion.html#replicate-structures","title":"Replicate structures","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>The first form uses explicit replication factors. The second form tries to build a supercell close to a target atom count.</p>"},{"location":"en/format_conversion.html#extract-one-frame","title":"Extract one frame","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>This extracts frame index <code>1000</code> from an extxyz trajectory.</p>"},{"location":"en/format_conversion.html#common-mistakes","title":"Common Mistakes","text":"Problem What to Check LAMMPS elements are wrong Check the element order passed after the dump file A trajectory has strange metadata Try <code>-clean_xyz input.xyz clean.xyz</code> A converted structure looks shifted Inspect PBC/cell information in the source file Frame extraction gives the wrong structure Remember that frame indices are 0-based"},{"location":"en/format_conversion.html#notes","title":"Notes","text":"<p>If a Python package required by a specific converter is missing, Python will report it when that converter is used.</p>"},{"location":"en/plot_scripts.html","title":"Plot Scripts","text":"\ud83d\udcca Plot Scripts <p>The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators.</p> <p>Script Location: <code>Scripts/plt_scripts/</code></p>"},{"location":"en/plot_scripts.html#quick-access","title":"Quick Access","text":"<pre><code>gpumdkit.sh -plt          # show all plotting options\ngpumdkit.sh -plt &lt;type&gt;   # generate a plot\ngpumdkit.sh -plt &lt;type&gt; save\ngpumdkit.sh -plt &lt;type&gt; -h\n</code></pre>"},{"location":"en/plot_scripts.html#nep-training-and-prediction","title":"NEP Training and Prediction","text":""},{"location":"en/plot_scripts.html#training-results","title":"Training Results","text":"<p><code>plt_train.py</code> visualizes NEP training progress, including loss curves and parity plots for energy, force, and virial/stress.</p> <p>Input files:</p> <ul> <li><code>loss.out</code></li> <li><code>energy_train.out</code></li> <li><code>force_train.out</code></li> <li><code>virial_train.out</code></li> </ul> <p>Usage:</p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/plot_scripts.html#prediction-results","title":"Prediction Results","text":"<p><code>plt_prediction.py</code> visualizes prediction/test-set results.</p> <p>Input files:</p> <ul> <li><code>energy_test.out</code></li> <li><code>force_test.out</code></li> <li><code>virial_test.out</code></li> </ul> <p>Usage:</p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test\n</code></pre>"},{"location":"en/plot_scripts.html#traintest-comparison","title":"Train/Test Comparison","text":"<pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"en/plot_scripts.html#density-parity-plot","title":"Density Parity Plot","text":"<p>For large datasets, density-based parity plots are often easier to read than raw scatter plots.</p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"en/plot_scripts.html#force-error-analysis","title":"Force Error Analysis","text":"<p><code>plt_force_errors.py</code> plots force magnitude and angular errors following the analysis style proposed by Liu et al..</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"en/plot_scripts.html#restart-parameters","title":"Restart Parameters","text":"<pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"en/plot_scripts.html#charge-and-born-effective-charge","title":"Charge and Born Effective Charge","text":"<p>For qNEP charge output:</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre> <p>For Born effective charge prediction:</p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec\n</code></pre>"},{"location":"en/plot_scripts.html#molecular-dynamics-and-thermodynamics","title":"Molecular Dynamics and Thermodynamics","text":""},{"location":"en/plot_scripts.html#thermodynamic-properties","title":"Thermodynamic Properties","text":"<p><code>plt_thermo.py</code> reads <code>thermo.out</code> and plots temperature, potential energy, pressure, and other thermodynamic quantities.</p> <pre><code>gpumdkit.sh -plt thermo\ngpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"en/plot_scripts.html#radial-distribution-function","title":"Radial Distribution Function","text":"<pre><code>gpumdkit.sh -plt rdf\ngpumdkit.sh -plt rdf &lt;column&gt;\n</code></pre> <p>Full RDF output:</p> <p>Single pair RDF:</p>"},{"location":"en/plot_scripts.html#velocity-autocorrelation-and-pdos","title":"Velocity Autocorrelation and PDOS","text":"<pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>Input files: <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></p> <p>Heat capacity output:</p>"},{"location":"en/plot_scripts.html#diffusion-and-ionic-transport","title":"Diffusion and Ionic Transport","text":""},{"location":"en/plot_scripts.html#mean-square-displacement","title":"Mean Square Displacement","text":"<pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"en/plot_scripts.html#msd-for-all-species","title":"MSD for All Species","text":"<p>Use this when <code>compute_msd</code> in <code>run.in</code> was configured with <code>all_groups</code>.</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"en/plot_scripts.html#msd-convergence-check","title":"MSD Convergence Check","text":"<pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"en/plot_scripts.html#self-diffusion-coefficient","title":"Self-Diffusion Coefficient","text":"<pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/plot_scripts.html#arrhenius-diffusivity","title":"Arrhenius Diffusivity","text":"<pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D\n</code></pre> <p>Example output:</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"en/plot_scripts.html#arrhenius-ionic-conductivity","title":"Arrhenius Ionic Conductivity","text":"<pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma\n</code></pre>"},{"location":"en/plot_scripts.html#heat-transport","title":"Heat Transport","text":""},{"location":"en/plot_scripts.html#emd","title":"EMD","text":"<pre><code>gpumdkit.sh -plt emd x\n</code></pre>"},{"location":"en/plot_scripts.html#nemd","title":"NEMD","text":"<pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre> <p>Parameter notes:</p> Parameter Meaning <code>real_length</code> real length of heat-transfer zone in nm; use <code>Auto</code> for automatic calculation <code>scale_eff_size</code> scale factor for effective cross-sectional area <code>cutoff_freq</code> cutoff frequency for SHC calculation in THz <code>save</code> optional flag to save the figure"},{"location":"en/plot_scripts.html#hnemd","title":"HNEMD","text":"<pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#descriptor-dimer-and-extra-analysis","title":"Descriptor, Dimer, and Extra Analysis","text":""},{"location":"en/plot_scripts.html#descriptor-visualization","title":"Descriptor Visualization","text":"<p>First calculate descriptors:</p> <pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>Then visualize:</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/plot_scripts.html#dimer-curve","title":"Dimer Curve","text":"<p><code>plt_dimer.py</code> places two atoms in a large cubic box and calculates energy/force as a function of dimer distance using a NEP model.</p> <pre><code>gpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>Reference: J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"en/plot_scripts.html#density-of-atomistic-states","title":"Density of Atomistic States","text":"<p><code>plt_doas.py</code> plots the density of atomistic states proposed by Wang et al..</p> <pre><code>gpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"en/plot_scripts.html#net-force-distribution","title":"Net Force Distribution","text":"<pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>Reference: arXiv:2510.19774</p>"},{"location":"en/plot_scripts.html#plane-grid-plot-for-polar-materials","title":"Plane-Grid Plot for Polar Materials","text":"<p>This workflow maps displacement or polarization data onto a grid and plots selected plane profiles.</p> <p>Typical upstream steps:</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>Plot:</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre> <p>This function requires <code>ferrodispcalc</code>.</p>"},{"location":"en/plot_scripts.html#quick-reference-table","title":"Quick Reference Table","text":"Command Input File(s) Purpose <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP training plots <code>prediction</code> <code>*_test.out</code> NEP prediction plots <code>train_test</code> train/test outputs combined parity plots <code>thermo</code> <code>thermo.out</code> thermodynamic properties <code>msd</code> <code>msd.out</code> mean square displacement <code>sdc</code> <code>msd.out</code> self-diffusion coefficient <code>rdf</code> <code>rdf.out</code> radial distribution function <code>pdos</code> <code>dos.out</code>, <code>mvac.out</code> VAC and PDOS <code>emd</code> EMD outputs EMD thermal conductivity <code>nemd</code> NEMD outputs NEMD thermal transport <code>hnemd</code> HNEMD outputs HNEMD thermal transport <code>des</code> <code>descriptors.npy</code> descriptor PCA/UMAP <code>dimer</code> <code>nep.txt</code> dimer energy/force curve <code>doas</code> <code>doas.out</code> density of atomistic states <code>net_force</code> <code>train.xyz</code> net force distribution"},{"location":"en/polar_material_analysis.html","title":"Polar Material Analysis","text":"\ud83e\uddf2 Polar Material Analysis <p>This tutorial covers GPUMDkit calculator options <code>406-410</code> and the <code>plane-grid</code> plotting workflow.</p> <p>Script Location: <code>Scripts/calculators/</code> and <code>Scripts/plt_scripts/</code></p> <p>This tutorial includes both general and system-specific tools:</p> <ul> <li><code>nlist</code>, <code>disp</code>, and <code>avg-struct</code> are broadly useful for structure/trajectory analysis.</li> <li><code>oct-tilt</code> is for octahedral environments (requires 6 neighbors around each center).</li> <li><code>pol-abo3</code> is specific to <code>ABO3</code> polarization analysis.</li> </ul>"},{"location":"en/polar_material_analysis.html#dependency","title":"Dependency","text":"<p>These scripts require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"en/polar_material_analysis.html#interactive-mode-entry","title":"Interactive mode entry","text":"<p>Options <code>406-410</code> are the core functions for this tutorial. The sections below explain when to use each one and how to run it.</p> <p>For full argument details, use:</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"en/polar_material_analysis.html#406-build-neighbor-list-calc_neighbor_listpy","title":"406) Build neighbor list (<code>calc_neighbor_list.py</code>)","text":"<p>Build neighbor lists for selected center and neighbor elements.</p> <p>When to use it: This is usually the first step before <code>disp</code>, <code>oct-tilt</code>, and <code>pol-abo3</code>, because those scripts read <code>nl-*.dat</code> neighbor files.</p>"},{"location":"en/polar_material_analysis.html#usage","title":"Usage","text":"<pre><code># Example 1: Ti-O nearest 6 neighbors for octahedral analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# Example 2: Pb/Sr-O nearest 12 neighbors for A-site centered analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input structure file. Default: <code>model.xyz</code>.</li> <li><code>-x, --index</code>:   Frame index to read from input. Default: <code>0</code>.</li> <li><code>-c, --cutoff</code> (required):   Neighbor search cutoff (Angstrom).</li> <li><code>-n, --neighbor-num</code> (required):   Number of neighbors per center.</li> <li><code>-d, --defect</code>:   Defect mode. If enabled and neighbors are insufficient, missing slots are filled with the center index.</li> <li><code>-C, --center-elements</code> (required):   Center species list.</li> <li><code>-E, --neighbor-elements</code> (required):   Neighbor species list.</li> <li><code>-o, --output</code>:   Output file path. Default: <code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file","title":"Output file","text":"<ul> <li>Main output: neighbor list text file (for example <code>nl-Ti-O.dat</code>).</li> <li>The file is a 2D integer array with shape <code>(n_center, neighbor_num + 1)</code>. Each row corresponds to one center atom: the first column is the center index, and the remaining columns are its neighbor indices (all 1-based).</li> </ul>"},{"location":"en/polar_material_analysis.html#407-calc-displacement-from-trajectory-calc_displacementpy","title":"407) Calc displacement from trajectory (<code>calc_displacement.py</code>)","text":"<p>Compute local displacement vectors from a trajectory/model and a neighbor list.</p>"},{"location":"en/polar_material_analysis.html#usage_1","title":"Usage","text":"<pre><code># Example 1: single-frame displacement from model.xyz\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# Example 2: use the last 20% frames in movie.xyz\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_1","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   Neighbor list file from <code>nlist</code>.</li> <li><code>-o, --output</code>:   Output file. Default: <code>displacements.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames.   Integer: last <code>N</code> frames.   <code>0 &lt; value &lt; 1</code>: last ratio of frames.</li> <li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_1","title":"Output file","text":"<ul> <li>Main output: <code>displacements.dat</code> (or your custom output name).</li> <li>The saved text file is a 2D array: for a single-frame input, its shape is <code>(n_center, 3)</code>; for a multi-frame input, it is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The three columns are <code>dx</code>, <code>dy</code>, and <code>dz</code> displacement components in Angstrom.</li> </ul>"},{"location":"en/polar_material_analysis.html#408-calc-averaged-structure-calc_averaged_structurepy","title":"408) Calc averaged structure (<code>calc_averaged_structure.py</code>)","text":"<p>Generate one averaged structure from selected trajectory frames. Use this after equilibration. For a solid near equilibrium, average a frame window at the target temperature and analyze that representative structure instead of processing every snapshot.</p>"},{"location":"en/polar_material_analysis.html#usage_2","title":"Usage","text":"<pre><code># Example 1: average all frames\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# Example 2: average selected frames (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_2","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input trajectory file. Default: <code>movie.xyz</code>.</li> <li><code>-o, --output</code>:   Output structure file. Default: <code>averaged_structure.xyz</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_2","title":"Output file","text":"<ul> <li>Main output: averaged single-frame extxyz file.</li> <li>Position averaging applies MIC/PBC correction relative to the first selected frame.</li> </ul>"},{"location":"en/polar_material_analysis.html#409-calc-octahedral-tilt-calc_oct_tiltpy","title":"409) Calc octahedral tilt (<code>calc_oct_tilt.py</code>)","text":"<p>Calculate octahedral tilt angles from a B-O neighbor list. This is commonly used to analyze octahedral rotation patterns in <code>ABO3</code> systems, such as <code>SrTiO3</code> and <code>PbZrO3</code>.</p>"},{"location":"en/polar_material_analysis.html#usage_3","title":"Usage","text":"<pre><code># Example 1: octahedral tilt of the TiO6 octahedra from a single frame\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# Example 2: octahedral tilt of the TiO6 octahedra from the last 20% trajectory frames\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_3","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   B-O neighbor list file.</li> <li><code>-o, --output</code>:   Output file. Default: <code>octahedral_tilt.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_3","title":"Output file","text":"<ul> <li>Main output: <code>octahedral_tilt.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>theta_x</code>, <code>theta_y</code>, <code>theta_z</code>, in degree): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#410-calc-polarization-for-abo3-calc_polarization_abo3py","title":"410) Calc polarization for ABO3 (<code>calc_polarization_abo3.py</code>)","text":"<p>Calculate local polarization vectors for <code>ABO3</code> systems.</p>"},{"location":"en/polar_material_analysis.html#usage_4","title":"Usage","text":"<pre><code># Example 1: single-frame ABO3 polarization\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# Example 2: trajectory polarization on a selected frame window\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_4","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>--nl-ba</code> (required):   B-A neighbor list.</li> <li><code>--nl-bo</code> (required):   B-O neighbor list.</li> <li><code>-o, --output</code>:   Output file. Default: <code>polarization.dat</code>.</li> <li><code>--bec</code> (required):   Born effective charge terms in <code>Element=value</code> format.   Example: <code>Pb=2.5 Ti=4.0 O=-2.0</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul> <p>Important checks:</p> <ul> <li><code>--bec</code> must include all element species in the input structure.</li> <li>Center atom indices in <code>--nl-ba</code> and <code>--nl-bo</code> must match.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_4","title":"Output file","text":"<ul> <li>Main output: <code>polarization.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>Px</code>, <code>Py</code>, <code>Pz</code>, in <code>C/m^2</code>): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The script prints a warning if the total Born charge is not balanced.</li> </ul>"},{"location":"en/polar_material_analysis.html#plane-grid-visualization-plt_plane_gridpy","title":"Plane-grid visualization (<code>plt_plane_grid.py</code>)","text":"<p>You can visualize either <code>displacements.dat</code> or <code>polarization.dat</code>:</p> <pre><code># Example 1: displacement map on Ti sites, first XY layer\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# Example 2: polarization map on Pb sites, XZ and YZ layers\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>Arguments (complete):</p> <ul> <li><code>-i, --input</code>:   Input xyz file for atomic layout and layering. Default: <code>model.xyz</code>.</li> <li><code>-d, --disp</code>:   Vector-field data file. Default: <code>displacements.dat</code>.</li> <li><code>-e, --elements</code> (required):   Center element symbols used to map vectors to lattice layers.</li> <li><code>-m, --tol</code>:   Layer tolerance for grid mapping. Default: <code>1.0</code>.</li> <li><code>-g, --target-size</code>:   Expected grid size as <code>nx ny nz</code>.</li> <li><code>-o, --save-dir</code>:   Figure output directory. Default: <code>plot</code>.</li> <li><code>-f, --frame</code>:   Frame index to visualize when vector data has multiple frames. Default: <code>0</code>.</li> <li><code>--select-xy</code>:   Selected XY layer indices.</li> <li><code>--select-xz</code>:   Selected XZ layer indices.</li> <li><code>--select-yz</code>:   Selected YZ layer indices.</li> </ul> <p>Output:</p> <ul> <li>Creates output directory if needed.</li> <li>Saves figures as <code>XY_*.png</code>, <code>XZ_*.png</code>, <code>YZ_*.png</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-files-at-a-glance","title":"Output files at a glance","text":"Script Main output What it stores <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based center index + neighbor indices <code>calc_displacement.py</code> <code>*.dat</code> Local displacement vectors (<code>dx dy dz</code>, Angstrom) <code>calc_averaged_structure.py</code> <code>*.xyz</code> One averaged structure <code>calc_oct_tilt.py</code> <code>*.dat</code> Octahedral tilt angles (<code>theta_x theta_y theta_z</code>, degree) <code>calc_polarization_abo3.py</code> <code>*.dat</code> Local polarization vectors (<code>Px Py Pz</code>, <code>C/m^2</code>) <code>plt_plane_grid.py</code> <code>plot/*.png</code> XY/XZ/YZ plane maps from vector-field data"},{"location":"en/polar_material_analysis.html#real-examples","title":"Real Examples","text":""},{"location":"en/polar_material_analysis.html#temperature-driven-ferroelectric-to-paraelectric-phase-transition-for-pbtio3","title":"Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3","text":"<p>Assume all files are in the current directory <code>./</code>:</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> is the initial structure used to run MD simulations. Each <code>TEMP K.xyz</code> is a trajectory at that temperature.</p>"},{"location":"en/polar_material_analysis.html#step-1-get-averaged-structures-from-the-last-half-of-each-trajectory","title":"Step 1: get averaged structures from the last half of each trajectory","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>This writes <code>300K-avg.xyz</code>, <code>350K-avg.xyz</code>, ..., <code>800K-avg.xyz</code>.</p>"},{"location":"en/polar_material_analysis.html#step-2-build-neighbor-lists-from-modelxyz","title":"Step 2: build neighbor lists from <code>model.xyz</code>","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-compute-displacement-and-polarization-for-each-temperature","title":"Step 3: compute displacement and polarization for each temperature","text":"<p>Use Born effective charges (BEC), not nominal ionic charges. For PbTiO3 in this example:</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>You can obtain BEC from your own DFPT calculation or from literature values. Thus use following commands to compute local displacement and polarization:</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-4-plot-displacement-and-polarization-maps-in-real-space","title":"Step 4: plot displacement and polarization maps in real space","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-5-build-a-temperature-order-parameter-curve","title":"Step 5: build a temperature-order-parameter curve","text":"<p>By analyzing the lattice of each temperature-averaged structure together with its polarization (<code>XX-pol.dat</code>), we can obtain the following figure:</p> <p>The trend shows a clear phase transition around <code>600 K</code>, where the polarization vanishes.</p>"},{"location":"en/polar_material_analysis.html#topological-structure-in-pbtio3srtio3-superlattice","title":"Topological structure in PbTiO3/SrTiO3 superlattice","text":"<p>Assume <code>movie.xyz</code> is the trajectory of the PbTiO3/SrTiO3 superlattice in the current directory.</p>"},{"location":"en/polar_material_analysis.html#step-1-build-an-averaged-structure-from-the-last-25-frames","title":"Step 1: build an averaged structure from the last 25% frames","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-2-build-the-ti-neighbor-list","title":"Step 2: build the Ti neighbor list","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-plot-the-plane-grid-map","title":"Step 3: plot the plane-grid map","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero. By analyzing how polarization varies around the vortex core, you can estimate the local dielectric response, but that is beyond the scope of this tutorial.</p> <p>Note: this figure uses a different colormap from the default GPUMDkit plotting style. The default output does not look exactly the same, but you can get this style with small plotting-script changes.</p>"},{"location":"en/polar_material_analysis.html#other-systems","title":"Other Systems","text":""},{"location":"en/polar_material_analysis.html#organic-inorganic-hybrid-ferroelectrics","title":"Organic-inorganic hybrid ferroelectrics","text":"<p>In many organic-inorganic ferroelectrics, polarization is strongly tied to anisotropic molecular units. A practical way to track molecular orientation is to use bond vectors.</p> <p>For TMCM-CdCl3, you can use the C-Cl bond direction of the TMCM molecule as an orientation proxy, then use it to estimate the polarization state:</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p><code>ccl_vectors.dat</code> can then be analyzed as an orientation order parameter. More details could be found at: Phys. Rev. Lett. 136, 016801</p>"},{"location":"en/polar_material_analysis.html#other-ferroelectric-families","title":"Other ferroelectric families","text":"<p>Beyond <code>ABO3</code>, <code>ferrodispcalc</code> can be adapted to many ferroelectric systems, including nitrides, hafnia-based compounds, organic-inorganic hybrids, and some 2D ferroelectrics.</p>"},{"location":"en/quick_start.html","title":"Quick Start","text":"\ud83d\ude80 Quick Start <p>This page introduces the basic installation and several common commands. GPUMDkit can be used through the interactive menu or by direct command-line options.</p>"},{"location":"en/quick_start.html#1-prepare-a-python-environment","title":"1. Prepare a Python Environment","text":"<p>You can use a clean conda environment:</p> <pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>Some optional functions use additional packages:</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>Other Python dependencies are loaded by the corresponding scripts. If a package is missing, Python will report it when that function is used.</p>"},{"location":"en/quick_start.html#2-install-gpumdkit","title":"2. Install GPUMDkit","text":"<p>Clone the repository:</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <p>Run the installer:</p> <pre><code>source ./install.sh\n</code></pre> <p>The installer writes <code>GPUMDkit_path</code> and <code>PATH</code> settings to your shell configuration and loads them for the current shell. It writes to <code>~/.bashrc</code> by default; if the current shell is zsh, it writes to <code>~/.zshrc</code>. If an existing GPUMDkit path is found, the installer prints the old path and asks whether to replace it. Before changing the rc file, it creates a backup.</p> <p>Typical installation output:</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>If GPUMDkit was installed before, you may see:</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre> <p>Check the command:</p> <pre><code>gpumdkit.sh -h\n</code></pre> <p>The help table:</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |\n| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/quick_start.html#3-usage-modes","title":"3. Usage Modes","text":""},{"location":"en/quick_start.html#interactive-mode","title":"Interactive Mode","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>Main menu:</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre>"},{"location":"en/quick_start.html#command-line-mode","title":"Command-Line Mode","text":"<p>Direct commands use fixed positional arguments:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -plt thermo\n</code></pre> <p>For example:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>means reading <code>POSCAR</code> and writing <code>model.xyz</code>.</p>"},{"location":"en/quick_start.html#4-practical-examples","title":"4. Practical Examples","text":""},{"location":"en/quick_start.html#convert-poscar-to-extxyz","title":"Convert POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"en/quick_start.html#add-gpumd-group-labels","title":"Add GPUMD Group Labels","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>Group labels are used by some GPUMD-related workflows and analyses that need atom grouping, such as species-specific MSD or diffusion calculations.</p>"},{"location":"en/quick_start.html#plot-nep-training-results","title":"Plot NEP Training Results","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/quick_start.html#plot-nep-test-results","title":"Plot NEP Test Results","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"en/quick_start.html#plot-thermodynamic-data","title":"Plot Thermodynamic Data","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/quick_start.html#plot-msd-and-self-diffusion-coefficient","title":"Plot MSD and Self-Diffusion Coefficient","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/quick_start.html#5-help","title":"5. Help","text":"<pre><code>gpumdkit.sh -h\ngpumdkit.sh -plt -h\ngpumdkit.sh -calc -h\ngpumdkit.sh -plt train -h\ngpumdkit.sh -calc msd -h\n</code></pre>"},{"location":"en/structure_sampling.html","title":"Structure Sampling","text":"\ud83d\udce6 Structure Sampling <p>Structure sampling is used to select, generate, or filter candidate configurations for NEP training and molecular dynamics workflows.</p> <p>Script Location: <code>Scripts/sample_structures/</code></p>"},{"location":"en/structure_sampling.html#interactive-mode","title":"Interactive Mode","text":"<p>Sampling tasks are usually easier to run from the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>2) Sample Structures\n</code></pre> <p>The menu is:</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Method Use Case 201 Uniform/random sampling quick frame selection from a trajectory 202 PyNEP notice prints a notice; use <code>gpumdkit.sh -pynep</code> to run PyNEP 203 NepTrain FPS descriptor-based FPS with NepTrain 204 Perturb structure generate perturbed structures from POSCAR/CONTCAR 205 Force-deviation selection select structures with high model deviation"},{"location":"en/structure_sampling.html#uniform-and-random-sampling","title":"Uniform and Random Sampling","text":"<p>From interactive mode, choose <code>201</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>Example input:</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>or:</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>uniform</code> / <code>random</code> sampling method <code>50</code> / <code>100</code> number of selected structures <code>500</code> optional number of initial frames to skip <p>Output:</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#farthest-point-sampling-with-neptrain","title":"Farthest Point Sampling with NepTrain","text":"<p>This entry uses NepTrain descriptors for FPS.</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>From interactive mode, choose <code>203</code>. You will see:</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>Inputs:</p> File Meaning <code>dump.xyz</code> candidate structures <code>train.xyz</code> existing training set <code>nep.txt</code> current NEP model used to compute descriptors <p>Outputs:</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>During execution, choose one of two selection modes:</p> <ol> <li>select until the descriptor distance is below a threshold;</li> <li>select a specified number of structures.</li> </ol> <p>The script then prints a selection prompt:</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>This function requires the <code>NepTrain</code> package. If you use this function, we recommend citing the NepTrain paper printed by the script.</p>"},{"location":"en/structure_sampling.html#deprecated-pynep-fps","title":"Deprecated PyNEP FPS","text":"<p>PyNEP FPS is kept for compatibility, but it is only exposed through the direct <code>-pynep</code> entry:</p> <p>If you choose <code>202</code> from the interactive menu, it prints:</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre> <pre><code>gpumdkit.sh -pynep\n</code></pre> <p>Then input:</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>This entry requires <code>pynep</code> and is kept for compatibility.</p>"},{"location":"en/structure_sampling.html#structure-perturbation","title":"Structure Perturbation","text":"<p>Use perturbation when you want to generate initial structures around a known configuration.</p> <pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>From interactive mode, choose <code>204</code>. You will see:</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input VASP structure <code>20</code> number of perturbed structures <code>0.03</code> cell perturbation fraction <code>0.2</code> atom perturbation distance in Angstrom <code>uniform</code> perturbation style: <code>normal</code>, <code>uniform</code>, or <code>const</code> <p>Output:</p> <ul> <li><code>POSCAR_01.vasp</code>, <code>POSCAR_02.vasp</code>, ...</li> </ul> <p>This function requires <code>dpdata</code>.</p>"},{"location":"en/structure_sampling.html#force-deviation-selection","title":"Force-Deviation Selection","text":"<p>Use this together with the GPUMD <code>active</code> command. The <code>active</code> command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. <code>select_max_modev.py</code> selects structures with large force deviations from <code>active.out</code> and <code>active.xyz</code>, then writes them to <code>selected.xyz</code>.</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>From interactive mode, choose <code>205</code>. You will see:</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>200</code> maximum number of structures to keep <code>0.15</code> minimum force deviation threshold <p>Required files:</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>Output:</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#frame-range-extraction","title":"Frame Range Extraction","text":"<p>Use this to extract a fraction of a trajectory:</p> <pre><code>python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>This writes frames from 0% to 80% of the trajectory.</p>"},{"location":"en/structure_sampling.html#example-commands","title":"Example Commands","text":"<p>An example sequence using several sampling-related tools:</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"en/structure_sampling.html#common-mistakes","title":"Common Mistakes","text":"Problem Recommendation FPS selects too many similar structures increase the distance threshold or select fewer structures Perturbed structures are unphysical reduce <code>cell_pert</code> and <code>atom_pert</code>, then check minimum distances <code>active.out</code> and <code>active.xyz</code> do not match regenerate both from the same GPUMD active run PCA plot looks strange check whether <code>nep.txt</code> matches the chemical species in both datasets"},{"location":"en/workflow_scripts.html","title":"Workflow Scripts","text":"\ud83d\udd27 Workflow Scripts <p>Workflow scripts automate repetitive preparation steps for DFT, MD, and NEP development.</p> <p>Script Location: <code>Scripts/workflow/</code></p>"},{"location":"en/workflow_scripts.html#interactive-entry","title":"Interactive Entry","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>3) Workflow\n</code></pre> <p>Typical workflow menu:</p> Menu Workflow Purpose 301 SCF batch pretreatment prepare single-point DFT calculations 302 MD sample batch pretreatment (GPUMD) prepare GPUMD sampling calculations 303 MD sample batch pretreatment (LAMMPS) prepare LAMMPS sampling calculations"},{"location":"en/workflow_scripts.html#scf-batch-pretreatment","title":"SCF Batch Pretreatment","text":"<p>Use this when you have many structures and want to prepare single-point DFT calculations.</p>"},{"location":"en/workflow_scripts.html#vasp","title":"VASP","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>Before running, put structure files in the current directory. The script checks files in this order:</p> <ol> <li>if one or more <code>.vasp</code> files exist, it processes <code>.vasp</code> files;</li> <li>if both <code>.vasp</code> and <code>.xyz</code> files exist, it prints a notice and only processes <code>.vasp</code> files;</li> <li>if no <code>.vasp</code> file exists and one <code>.xyz</code> file exists, it converts that extxyz file to POSCAR files;</li> <li>if no <code>.vasp</code> file exists and multiple <code>.xyz</code> files exist, it asks you to choose one.</li> </ol> <p>Typical input directory before running:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>INCAR</code>, <code>POTCAR</code>, and <code>KPOINTS</code> in the generated <code>fp/</code> directory after the script creates it. The calculation folders link to files in <code>fp/</code>.</p> <p>The <code>prefix</code> you input during the workflow becomes the calculation folder prefix. When <code>out2xyz</code> is later used to extract results, the folder name is stored as <code>config_type</code> in the extxyz file, which makes it easier to trace where each structure came from.</p>"},{"location":"en/workflow_scripts.html#cp2k","title":"CP2K","text":"<p>CP2K SCF batch pretreatment is available from the workflow menu and can also be called directly:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>The interactive wrapper asks for:</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>Example:</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>The template should be configured to read coordinates from <code>pos.xyz</code>. A reference template is available at:</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>The script creates <code>&lt;prefix&gt;_&lt;index&gt;/</code> directories, writes <code>input.inp</code>, and writes <code>pos.xyz</code> for each structure.</p>"},{"location":"en/workflow_scripts.html#md-sampling-pretreatment","title":"MD Sampling Pretreatment","text":""},{"location":"en/workflow_scripts.html#gpumd","title":"GPUMD","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 302\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. The detection order is the same as the VASP SCF workflow: <code>.vasp</code> files are preferred; if multiple <code>.xyz</code> files are found without <code>.vasp</code>, the script asks you to choose one.</p> <p>Typical input directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>nep.txt</code> and <code>run_*.in</code> files in the generated <code>md/</code> directory. The script links <code>run_1.in</code> to <code>sample_1/run.in</code>, <code>run_2.in</code> to <code>sample_2/run.in</code>, and so on.</p>"},{"location":"en/workflow_scripts.html#lammps","title":"LAMMPS","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 303\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. <code>.vasp</code> files are preferred when both formats exist.</p> <p>After running, the script creates LAMMPS data files in <code>struct_md/</code>, sample folders, and an <code>md/</code> directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>lmprun.in</code> and <code>nep.txt</code> in the generated <code>md/</code> directory.</p>"},{"location":"en/workflow_scripts.html#active-learning-style-workflow","title":"Active-Learning Style Workflow","text":"<p>A common NEP improvement loop is:</p> <ol> <li>run MD with the current <code>nep.txt</code>;</li> <li>collect <code>dump.xyz</code> or <code>active.xyz</code>;</li> <li>remove unphysical structures;</li> <li>select diverse or uncertain structures;</li> <li>run DFT single-point calculations;</li> <li>convert DFT results to extxyz;</li> <li>append new structures to <code>train.xyz</code>;</li> <li>retrain the NEP model.</li> </ol> <p>For the development active-learning script, see Active Learning.</p>"},{"location":"en/workflow_scripts.html#template-based-temperature-series","title":"Template-Based Temperature Series","text":"<p>For a simple temperature series, a shell loop is often enough:</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>Then submit the generated folders according to your local cluster system.</p>"},{"location":"en/workflow_scripts.html#practical-notes","title":"Practical Notes","text":"<ul> <li>Workflow scripts are cluster- and template-dependent. Always test with a small number of structures first.</li> <li>Keep template files (<code>INCAR</code>, <code>KPOINTS</code>, <code>POTCAR</code>, <code>run.in</code>, CP2K inputs) under version control if possible.</li> <li>Check generated folders before submitting a large batch.</li> <li>Use analyzers and sampling scripts before expensive DFT calculations.</li> </ul>"},{"location":"zh/index.html","title":"GPUMDkit \u6559\u7a0b","text":"\ud83d\udcda GPUMDkit \u6559\u7a0b <p>\u6b22\u8fce\u4f7f\u7528 GPUMDkit\uff0c\u8fd9\u662f\u4e00\u4e2a\u9762\u5411 GPUMD \u548c NEP \u7684\u547d\u4ee4\u884c\u5de5\u5177\u5305\u3002</p>"},{"location":"zh/index.html#gpumdkit","title":"\u4ec0\u4e48\u662f GPUMDkit\uff1f","text":"<p>GPUMDkit \u7b80\u5316\u4e86\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u7684\u5e38\u89c1\u4efb\u52a1\uff1a</p> <ul> <li>\u683c\u5f0f\u8f6c\u6362\uff1a\u5728 VASP\u3001LAMMPS\u3001CP2K\u3001ABACUS\u3001CIF \u548c extxyz \u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362</li> <li>\u53ef\u89c6\u5316\uff1a\u7528\u4e8e NEP \u8bad\u7ec3\u3001MD \u6a21\u62df\u548c\u5206\u6790\u7684\u7ed8\u56fe\u5de5\u5177</li> <li>\u8ba1\u7b97\u5668\uff1a\u8ba1\u7b97\u79bb\u5b50\u7535\u5bfc\u7387\u3001\u63cf\u8ff0\u7b26\u3001MSD\u3001NEB \u7b49</li> <li>\u5206\u6790\u5de5\u5177\uff1a\u7ed3\u6784\u9a8c\u8bc1\u3001\u8fc7\u6ee4\u3001\u6210\u5206\u5206\u6790</li> <li>\u5de5\u4f5c\u6d41\uff1aDFT \u548c MD \u6a21\u62df\u7684\u6279\u5904\u7406</li> <li>\u7ed3\u6784\u91c7\u6837\uff1a\u4f7f\u7528\u5747\u5300\u3001\u968f\u673a\u6216 FPS \u65b9\u6cd5\u9009\u62e9\u7ed3\u6784</li> </ul>"},{"location":"zh/index.html#_1","title":"\u5feb\u901f\u5f00\u59cb","text":""},{"location":"zh/index.html#_2","title":"\u5b89\u88c5","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"zh/index.html#_3","title":"\u4f9d\u8d56","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"zh/index.html#_4","title":"\u4f7f\u7528\u65b9\u6cd5","text":"<pre><code># \u4ea4\u4e92\u6a21\u5f0f\ngpumdkit.sh\n\n# \u547d\u4ee4\u884c\u6a21\u5f0f\ngpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n\n# \u83b7\u53d6\u5e2e\u52a9\ngpumdkit.sh -h\n</code></pre>"},{"location":"zh/index.html#_5","title":"\u6559\u7a0b\u5217\u8868","text":"\u6559\u7a0b \u63cf\u8ff0 \u5feb\u901f\u5165\u95e8 \u5b89\u88c5\u548c\u7b2c\u4e00\u6b65 \u547d\u4ee4\u53c2\u8003 \u5e38\u7528 CLI \u548c\u83dc\u5355\u5165\u53e3\u901f\u67e5 \u683c\u5f0f\u8f6c\u6362 \u5728\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362 \u8ba1\u7b97\u5668\u811a\u672c \u8ba1\u7b97\u6750\u6599\u5c5e\u6027 \u5206\u6790\u5de5\u5177 \u7ed3\u6784\u5206\u6790\u548c\u9a8c\u8bc1 \u7ed8\u56fe\u811a\u672c \u7ed8\u56fe\u548c\u53ef\u89c6\u5316 \u5de5\u4f5c\u6d41\u811a\u672c \u6279\u5904\u7406\u548c\u81ea\u52a8\u5316 \u7ed3\u6784\u91c7\u6837 \u7ed3\u6784\u9009\u62e9\u65b9\u6cd5 \u81ea\u5b9a\u4e49\u547d\u4ee4 \u7528\u6237\u81ea\u5b9a\u4e49 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 \u6279\u91cf\u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\u8bf4\u660e \u6781\u6027\u6750\u6599\u5206\u6790 \u94c1\u7535\u548c\u6781\u5316\u76f8\u5173\u5de5\u5177 \u8d21\u732e\u6307\u5357 \u5f00\u53d1\u548c\u8d21\u732e\u8bf4\u660e"},{"location":"zh/index.html#vasp-outcar","title":"\u793a\u4f8b\uff1a\u8f6c\u6362 VASP OUTCAR","text":"<pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre>"},{"location":"zh/index.html#nep","title":"\u793a\u4f8b\uff1a\u7ed8\u5236 NEP \u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt train\ngpumdkit.sh -plt prediction\n</code></pre>"},{"location":"zh/index.html#_6","title":"\u793a\u4f8b\uff1a\u79bb\u5b50\u7535\u5bfc\u7387","text":"<pre><code>gpumdkit.sh -calc msd trajectory.xyz Li 10\ngpumdkit.sh -calc ionic-cond Li 1\ngpumdkit.sh -plt msd\n</code></pre>"},{"location":"zh/index.html#_7","title":"\u6a21\u5757\u6982\u89c8","text":"\u6a21\u5757 \u83dc\u5355 CLI \u63cf\u8ff0 \u683c\u5f0f\u8f6c\u6362 1 <code>-out2xyz</code>, <code>-pos2exyz</code> \u6587\u4ef6\u8f6c\u6362 \u7ed3\u6784\u91c7\u6837 2 <code>-neptrain</code>\u3001\u4ea4\u4e92\u83dc\u5355 \u7ed3\u6784\u91c7\u6837 \u5de5\u4f5c\u6d41 3 - \u6279\u5904\u7406 \u8ba1\u7b97\u5668 4 <code>-calc &lt;\u7c7b\u578b&gt;</code> \u5c5e\u6027\u8ba1\u7b97 \u5206\u6790\u5de5\u5177 5 <code>-range</code>, <code>-min_dist</code> \u7ed3\u6784\u5206\u6790 \u53ef\u89c6\u5316 6 <code>-plt &lt;\u7c7b\u578b&gt;</code> \u7ed8\u56fe\u5de5\u5177 \u5b9e\u7528\u5de5\u5177 7 <code>-time</code>, <code>-clean</code> \u5b9e\u7528\u529f\u80fd"},{"location":"zh/index.html#_8","title":"\u94fe\u63a5","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>\u6587\u6863: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html","title":"\u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41","text":"\ud83d\udd01 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 <p><code>workflow_active_learning_dev.sh</code> \u7528\u4e8e\u7ec4\u7ec7\u4e00\u8f6e NEP \u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\uff1a\u8fd0\u884c GPUMD \u5206\u5b50\u52a8\u529b\u5b66\u3001\u7b5b\u9009\u7ed3\u6784\u3001\u62bd\u6837\u3001\u63d0\u4ea4\u7b2c\u4e00\u6027\u539f\u7406\u8ba1\u7b97\uff0c\u5e76\u8fdb\u884c NEP \u9884\u6d4b\u68c0\u67e5\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#_1","title":"\u6982\u89c8","text":"<p>\u8be5\u811a\u672c\u7528\u4e8e\u5904\u7406 NEP \u4e3b\u52a8\u5b66\u4e60\u4e2d\u5e38\u89c1\u7684\u4e00\u8f6e\u6d41\u7a0b\uff1a\u8fd0\u884c\u5206\u5b50\u52a8\u529b\u5b66\u3001\u7b5b\u9009\u7ed3\u6784\u3001\u62bd\u6837\u3001\u63d0\u4ea4 SCF \u8ba1\u7b97\uff0c\u5e76\u6574\u7406\u540e\u7eed prediction \u68c0\u67e5\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#1-slurm","title":"1. SLURM \u8bbe\u7f6e","text":"<p>\u811a\u672c\u5f00\u5934\u5305\u542b\u96c6\u7fa4\u63d0\u4ea4\u53c2\u6570\uff0c\u4f8b\u5982\uff1a</p> <pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>\u8fd9\u4e9b\u53c2\u6570\u9700\u8981\u6839\u636e\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u4fee\u6539\u3002\u5982\u679c\u6ca1\u6709 SLURM \u73af\u5883\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u540e\u53f0\u8fd0\u884c\uff1a</p> <pre><code>nohup bash workflow_active_learning_dev.sh &gt; workflow.log 2&gt;&amp;1 &amp;\n</code></pre>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#2","title":"2. \u57fa\u672c\u8bbe\u7f6e","text":"<p>\u811a\u672c\u4f1a\u8fdb\u5165\u63d0\u4ea4\u76ee\u5f55\uff0c\u5e76\u52a0\u8f7d\u63d0\u4ea4\u6a21\u677f\uff1a</p> <pre><code>cd $SLURM_SUBMIT_DIR\nsource ${GPUMDkit_path}/Scripts/workflow/submit_template.sh\npython_pynep=python\n</code></pre> <ul> <li><code>GPUMDkit_path</code> \u662f\u5b89\u88c5\u811a\u672c\u5199\u5165\u7684 GPUMDkit \u8def\u5f84\u3002</li> <li><code>python_pynep</code> \u4ec5\u7528\u4e8e\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#3","title":"3. \u4e3b\u8981\u53d8\u91cf","text":"<p>\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u9002\u5408\u5df2\u7ecf\u6709\u521d\u59cb <code>nep.txt</code>\u3001<code>nep.in</code>\u3001<code>train.xyz</code> \u548c GPUMD/DFT \u8f93\u5165\u6587\u4ef6\uff0c\u5e76\u5e0c\u671b\u5728\u96c6\u7fa4\u4e0a\u81ea\u52a8\u6269\u5c55\u8bad\u7ec3\u96c6\u7684\u60c5\u51b5\u3002</p> <p>\u811a\u672c\u5f00\u5934\u901a\u5e38\u9700\u8981\u6839\u636e\u4f53\u7cfb\u4fee\u6539\uff1a</p> <pre><code>work_dir=${PWD}\nprefix_name=LiF_iter01\nmin_dist=1.4\nbox_limit=13\nmax_fp_num=50\nsample_method=pynep\npynep_sample_dist=0.01\n</code></pre> <ul> <li><code>prefix_name</code> \u7528\u4e8e\u547d\u540d\u672c\u8f6e\u8ba1\u7b97\u3002</li> <li><code>min_dist</code> \u548c <code>box_limit</code> \u7528\u4e8e\u8fc7\u6ee4\u660e\u663e\u4e0d\u5408\u7406\u7684\u7ed3\u6784\u3002</li> <li><code>max_fp_num</code> \u63a7\u5236\u6700\u591a\u63d0\u4ea4\u591a\u5c11\u4e2a\u5355\u70b9\u8ba1\u7b97\u3002</li> <li><code>sample_method</code> \u53ef\u9009 <code>uniform</code>\u3001<code>random</code> \u6216 <code>pynep</code>\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#4","title":"4. \u68c0\u67e5\u8f93\u5165\u6587\u4ef6","text":"<p>\u5e38\u89c1\u8f93\u5165\u5305\u62ec\uff1a</p> <ul> <li><code>nep.txt</code></li> <li><code>nep.in</code></li> <li><code>train.xyz</code></li> <li><code>run.in</code></li> <li><code>INCAR</code></li> <li><code>POTCAR</code></li> <li><code>KPOINTS</code></li> <li>\u521d\u59cb\u91c7\u6837\u7ed3\u6784\u6587\u4ef6\uff0c\u4f8b\u5982 <code>sample_struct.xyz</code></li> </ul> <p>\u811a\u672c\u4f1a\u628a\u516c\u5171\u8f93\u5165\u79fb\u52a8\u5230 <code>common/</code>\uff0c\u5e76\u521b\u5efa <code>00.modev/</code>\u3001<code>01.select/</code> \u7b49\u5de5\u4f5c\u76ee\u5f55\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#5","title":"5. \u6587\u4ef6\u7ec4\u7ec7","text":"<p>\u811a\u672c\u4f1a\u521b\u5efa\u516c\u5171\u8f93\u5165\u76ee\u5f55\u548c MD \u76ee\u5f55\uff1a</p> <pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <ul> <li><code>00.modev</code>\uff1a\u7528\u4e8e\u8fd0\u884c GPUMD MD \u91c7\u6837\u3002</li> <li><code>common</code>\uff1a\u4fdd\u5b58 <code>nep.txt</code>\u3001<code>run.in</code>\u3001\u7ed3\u6784\u6587\u4ef6\u548c DFT \u8f93\u5165\u6587\u4ef6\u7b49\u516c\u5171\u8d44\u6e90\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#6-md","title":"6. \u63d0\u4ea4 MD \u4efb\u52a1","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>\u811a\u672c\u4f1a\u901a\u8fc7\u63d0\u4ea4\u6a21\u677f\u521b\u5efa\u6570\u7ec4\u4efb\u52a1\u3002\u4e0d\u540c\u96c6\u7fa4\u4e0a\u7684\u63d0\u4ea4\u547d\u4ee4\u548c\u6a21\u677f\u53ef\u80fd\u9700\u8981\u81ea\u5df1\u4fee\u6539\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#7","title":"7. \u68c0\u67e5\u4efb\u52a1\u5b8c\u6210","text":"<p>\u811a\u672c\u4f1a\u6301\u7eed\u68c0\u67e5 <code>00.modev/</code> \u4e0b\u5404\u4e2a <code>sample_*/log</code> \u6587\u4ef6\uff0c\u786e\u8ba4\u662f\u5426\u51fa\u73b0\uff1a</p> <pre><code>Finished running GPUMD.\n</code></pre> <p>\u5982\u679c\u53d1\u73b0 <code>Error</code>\uff0c\u811a\u672c\u4f1a\u505c\u6b62\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#8","title":"8. \u5206\u6790\u548c\u8fc7\u6ee4\u7ed3\u6784","text":"<p>MD \u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u8fdb\u5165 <code>01.select</code>\uff0c\u5bf9 <code>dump.xyz</code> \u4e2d\u7684\u7ed3\u6784\u8fdb\u884c\u7b5b\u9009\u3002\u5e38\u89c1\u68c0\u67e5\u5305\u62ec\uff1a</p> <ul> <li>\u6700\u5c0f\u539f\u5b50\u8ddd\u79bb\uff1b</li> <li>\u6a21\u62df\u76d2\u5b50\u8fb9\u957f\uff1b</li> <li>\u7ed3\u6784\u6570\u91cf\u662f\u5426\u8d85\u8fc7 <code>max_fp_num</code>\u3002</li> </ul> <p>\u8fd9\u4e9b\u6b65\u9aa4\u4f1a\u8c03\u7528 analyzer \u548c sample_structures \u4e2d\u7684\u811a\u672c\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#9","title":"9. \u62bd\u6837\u65b9\u6cd5","text":"<p>\u811a\u672c\u6839\u636e <code>sample_method</code> \u9009\u62e9\u62bd\u6837\u65b9\u5f0f\uff1a</p> <pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <ul> <li><code>uniform</code>\uff1a\u5747\u5300\u62bd\u5e27\uff1b</li> <li><code>random</code>\uff1a\u968f\u673a\u62bd\u5e27\uff1b</li> <li><code>pynep</code>\uff1a\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#10-scf","title":"10. \u63d0\u4ea4 SCF \u8ba1\u7b97","text":"<p>\u62bd\u6837\u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u63d0\u4ea4 VASP \u5355\u70b9\u8ba1\u7b97\uff1a</p> <pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>\u8fd9\u91cc\u7684 <code>prefix_name</code> \u4f1a\u7528\u4e8e\u8ba1\u7b97\u76ee\u5f55\u547d\u540d\uff0c\u4e5f\u65b9\u4fbf\u540e\u7eed\u8ffd\u8e2a\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#11-prediction","title":"11. Prediction \u6b65\u9aa4","text":"<p>\u6700\u540e\u811a\u672c\u4f1a\u63d0\u4ea4 NEP prediction\uff0c\u7528\u4e8e\u68c0\u67e5\u5f53\u524d\u6a21\u578b\u5728\u65b0\u589e\u7ed3\u6784\u4e0a\u7684\u8bef\u5dee\u3002</p> <p>\u8fd9\u4e2a\u811a\u672c\u548c\u8ba1\u7b97\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u4f7f\u7528\u524d\u5efa\u8bae\u5148\u7528\u5c0f\u4f53\u7cfb\u6216\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u4e00\u8f6e\uff0c\u5e76\u68c0\u67e5\u63d0\u4ea4\u6a21\u677f\u3001\u8def\u5f84\u548c\u8f93\u5165\u6587\u4ef6\u662f\u5426\u7b26\u5408\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html","title":"\u5206\u6790\u5de5\u5177","text":"\ud83d\udd0d \u5206\u6790\u5de5\u5177 <p>\u5206\u6790\u5de5\u5177\u7528\u4e8e\u5bf9 extxyz \u6570\u636e\u96c6\u8fdb\u884c\u7ed3\u6784\u7edf\u8ba1\u3001\u8ddd\u79bb\u68c0\u67e5\u3001\u8fc7\u6ee4\u548c\u7ec4\u5206\u5206\u6790\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/analyzer/</code></p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_1","title":"\u529f\u80fd\u6982\u89c8","text":"\u4efb\u52a1 \u547d\u4ee4 \u7528\u9014 \u7ec4\u5206\u5206\u6790 <code>gpumdkit.sh -analyze_comp train.xyz</code> \u6309\u5316\u5b66\u7ec4\u5206\u7edf\u8ba1\u7ed3\u6784 \u5143\u7d20\u5217\u8868 <code>gpumdkit.sh -chem_species train.xyz</code> \u67e5\u770b\u6587\u4ef6\u4e2d\u6709\u54ea\u4e9b\u5143\u7d20 \u6027\u8d28\u8303\u56f4 <code>gpumdkit.sh -range train.xyz force</code> \u68c0\u67e5\u80fd\u91cf/\u529b/virial \u8303\u56f4 \u6700\u5c0f\u8ddd\u79bb <code>gpumdkit.sh -min_dist dump.xyz</code> \u5feb\u901f\u68c0\u67e5\uff0c\u4e0d\u8003\u8651 PBC PBC \u6700\u5c0f\u8ddd\u79bb <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> \u8003\u8651 PBC \u7684\u8ddd\u79bb\u68c0\u67e5 \u7535\u8377\u5e73\u8861 <code>gpumdkit.sh -cbc train.xyz</code> \u68c0\u67e5\u5e38\u89c1\u6c27\u5316\u6001\u662f\u5426\u5e73\u8861 \u8ddd\u79bb\u8fc7\u6ee4 <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> \u5220\u9664\u77ed\u8ddd\u79bb\u7ed3\u6784 \u76d2\u5b50\u8fc7\u6ee4 <code>gpumdkit.sh -filter_box dump.xyz 13</code> \u5220\u9664\u76d2\u5b50\u8fb9\u957f\u8fc7\u5927\u7684\u7ed3\u6784 \u6570\u503c\u8fc7\u6ee4 <code>gpumdkit.sh -filter_value train.xyz force 20</code> \u6309\u6027\u8d28\u9608\u503c\u8fc7\u6ee4 \u5143\u7d20\u5bf9\u8ddd\u79bb <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> \u6309\u5143\u7d20\u5bf9\u8ddd\u79bb\u8303\u56f4\u63d0\u53d6"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_2","title":"\u7ec4\u5206\u5206\u6790","text":"<pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>\u793a\u4f8b\u8f93\u51fa\uff1a</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>\u5982\u679c\u4e00\u4e2a <code>train.xyz</code> \u4e2d\u6df7\u5408\u4e86\u591a\u4e2a\u4f53\u7cfb\u6216\u4e0d\u540c\u8d85\u80de\uff0c\u8fd9\u4e2a\u529f\u80fd\u5f88\u6709\u7528\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#virial","title":"\u80fd\u91cf/\u529b/virial \u8303\u56f4","text":"<pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist\n</code></pre> <p>\u4f7f\u7528 <code>hist</code> \u53ef\u4ee5\u753b\u51fa\u6240\u9009\u6027\u8d28\u7684\u76f4\u65b9\u56fe\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_3","title":"\u6700\u5c0f\u8ddd\u79bb\u68c0\u67e5","text":"<p>\u5feb\u901f\u7248\u672c\uff1a</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>\u8003\u8651 PBC \u7684\u7248\u672c\uff1a</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>PBC \u7248\u672c\u4f1a\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_4","title":"\u7ed3\u6784\u8fc7\u6ee4","text":"<p>\u6309\u6700\u5c0f\u8ddd\u79bb\u8fc7\u6ee4\uff1a</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>\u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4\uff1a</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>\u6309\u6027\u8d28\u503c\u8fc7\u6ee4\uff1a</p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\n</code></pre> <p>\u6309\u5143\u7d20\u5bf9\u8ddd\u79bb\u8303\u56f4\u63d0\u53d6\uff1a</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_5","title":"\u7535\u8377\u5e73\u8861\u68c0\u67e5","text":"<pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>\u53ef\u80fd\u8f93\u51fa\uff1a</p> <ul> <li><code>balanced.xyz</code></li> <li><code>unbalanced.xyz</code></li> <li><code>indices.txt</code></li> </ul> <p>\u8fd9\u4e2a\u529f\u80fd\u9002\u5408\u5e38\u89c1\u6c27\u5316\u6001\u6709\u610f\u4e49\u7684\u79bb\u5b50\u6750\u6599\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_6","title":"\u793a\u4f8b\u547d\u4ee4","text":"<p>\u6027\u8d28\u548c\u8ddd\u79bb\u68c0\u67e5\uff1a</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\ngpumdkit.sh -range train.xyz force hist\ngpumdkit.sh -range train.xyz energy hist\ngpumdkit.sh -min_dist_pbc train.xyz\n</code></pre> <p>\u8fc7\u6ee4\u793a\u4f8b\uff1a</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\ngpumdkit.sh -filter_box filtered_dist.xyz 13\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html","title":"\u547d\u4ee4\u53c2\u8003","text":"\ud83d\udccb \u547d\u4ee4\u53c2\u8003 <p>\u672c\u9875\u5217\u51fa GPUMDkit \u7a33\u5b9a\u7684\u547d\u4ee4\u884c\u5feb\u6377\u5165\u53e3\u3002\u5bf9\u4e8e\u53c2\u6570\u8f83\u591a\u3001\u9700\u8981\u9009\u62e9\u7684\u4efb\u52a1\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528\u4ea4\u4e92\u6a21\u5f0f\u3002</p> <p>\u6e90\u8868\u7ef4\u62a4\u5728 <code>docs/command_reference.tsv</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#gpumdkitsh-h","title":"<code>gpumdkit.sh -h</code> \u8f93\u51fa","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |\n| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_1","title":"\u4e3b\u547d\u4ee4","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-h</code> <code>gpumdkit.sh -h</code> \u663e\u793a\u901a\u7528\u5e2e\u52a9 <code>-update</code> <code>gpumdkit.sh -update</code> \u66f4\u65b0 GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> \u6e05\u7406\u5f53\u524d\u76ee\u5f55\u4e2d\u7684\u5197\u4f59\u6587\u4ef6"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_2","title":"\u683c\u5f0f\u8f6c\u6362","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K \u8f93\u51fa\u8f6c xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR \u8f6c extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF \u8f6c POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF \u8f6c extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR \u8f6c extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz \u591a\u5e27\u8f6c POSCAR \u6587\u4ef6 <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR \u8f6c LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump \u8f6c extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory \u8f6c extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> \u6309\u6676\u80de\u500d\u6570\u6269\u80de <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> \u6309\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> \u6dfb\u52a0 GPUMD group \u6807\u7b7e <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> \u6dfb\u52a0\u7ed3\u6784\u6743\u91cd <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> \u63d0\u53d6\u5355\u5e27 <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> \u6e05\u7406 extxyz \u5197\u4f59\u5c5e\u6027 <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> \u6309\u6bd4\u4f8b\u8303\u56f4\u63d0\u53d6\u5e27"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_3","title":"\u8ba1\u7b97\u5668","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> \u79bb\u5b50\u7535\u5bfc\u7387 <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP \u6027\u8d28\u9884\u6d4b <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP \u63cf\u8ff0\u7b26 <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u57fa\u4e8e NEP \u7684 NEB <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784\u4f18\u5316 <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> \u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> \u90bb\u5c45\u5217\u8868 <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> \u4f4d\u79fb <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> \u5e73\u5747\u7ed3\u6784 <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> \u516b\u9762\u4f53\u503e\u659c <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 \u5c40\u57df\u6781\u5316"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_4","title":"\u5206\u6790\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> \u6027\u8d28\u8303\u56f4\u5206\u6790 <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> \u6210\u5206\u5206\u6790 <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> \u5143\u7d20\u5217\u8868 <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> \u7535\u8377\u5e73\u8861\u68c0\u67e5 <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> \u65e0 PBC \u6700\u5c0f\u8ddd\u79bb <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> \u5e26 PBC \u6700\u5c0f\u8ddd\u79bb <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u5e26 PBC \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> \u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4 <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> \u6027\u8d28\u9608\u503c\u8fc7\u6ee4 <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> \u5143\u7d20\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4 <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> \u6982\u7387\u5bc6\u5ea6\u5206\u6790"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_5","title":"\u53ef\u89c6\u5316","text":"<p>\u4f7f\u7528\uff1a</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>\u5e38\u7528\u7c7b\u578b\u5305\u62ec <code>train</code>\u3001<code>prediction</code>\u3001<code>thermo</code>\u3001<code>msd</code>\u3001<code>sdc</code>\u3001<code>rdf</code>\u3001<code>emd</code>\u3001<code>nemd</code>\u3001<code>hnemd</code>\u3001<code>pdos</code> \u548c <code>plane-grid</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_6","title":"\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> \u76d1\u63a7 GPUMD \u6216 NEP \u8fdb\u5ea6 <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> \u4ea4\u4e92\u5f0f\u4fee\u6539 NEP \u6a21\u578b <code>-pynep</code> <code>gpumdkit.sh -pynep</code> \u5df2\u5f03\u7528\u7684 PyNEP FPS \u91c7\u6837"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html","title":"\u5de5\u4f5c\u6d41\u811a\u672c","text":"\ud83d\udd27 \u5de5\u4f5c\u6d41\u811a\u672c <p>\u5de5\u4f5c\u6d41\u811a\u672c\u7528\u4e8e\u81ea\u52a8\u5316\u91cd\u590d\u6027\u7684 DFT\u3001MD \u548c NEP \u6570\u636e\u51c6\u5907\u6b65\u9aa4\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_1","title":"\u4ea4\u4e92\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>3) Workflow\n</code></pre> <p>\u5e38\u89c1\u83dc\u5355\uff1a</p> \u83dc\u5355 \u5de5\u4f5c\u6d41 \u7528\u9014 301 SCF batch pretreatment \u51c6\u5907 DFT \u5355\u70b9\u8ba1\u7b97 302 MD sample batch pretreatment (GPUMD) \u51c6\u5907 GPUMD \u91c7\u6837\u8ba1\u7b97 303 MD sample batch pretreatment (LAMMPS) \u51c6\u5907 LAMMPS \u91c7\u6837\u8ba1\u7b97"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#scf","title":"SCF \u6279\u5904\u7406\u9884\u5904\u7406","text":"<p>\u9002\u7528\u4e8e\u5df2\u6709\u591a\u4e2a\u7ed3\u6784\uff0c\u9700\u8981\u51c6\u5907\u7b2c\u4e00\u6027\u539f\u7406\u5355\u70b9\u8ba1\u7b97\u7684\u60c5\u51b5\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#vasp","title":"VASP","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a\u7ed3\u6784\u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u811a\u672c\u6309\u4ee5\u4e0b\u987a\u5e8f\u68c0\u6d4b\uff1a</p> <ol> <li>\u5982\u679c\u5b58\u5728\u4e00\u4e2a\u6216\u591a\u4e2a <code>.vasp</code> \u6587\u4ef6\uff0c\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c <code>.vasp</code> \u548c <code>.xyz</code> \u540c\u65f6\u5b58\u5728\uff0c\u4f1a\u6253\u5370\u63d0\u793a\uff0c\u5e76\u53ea\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u53ea\u6709\u4e00\u4e2a <code>.xyz</code>\uff0c\u4f1a\u628a\u8fd9\u4e2a extxyz \u8f6c\u4e3a POSCAR \u6587\u4ef6\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</li> </ol> <p>\u8fd0\u884c\u524d\u7684\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>fp/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u7528\u6237\u628a <code>INCAR</code>\u3001<code>POTCAR</code>\u3001<code>KPOINTS</code> \u653e\u5230 <code>fp/</code> \u4e2d\uff0c\u8ba1\u7b97\u76ee\u5f55\u4f1a\u94fe\u63a5\u8fd9\u91cc\u7684\u6587\u4ef6\u3002</p> <p>\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u8f93\u5165\u7684 <code>prefix</code> \u4f1a\u4f5c\u4e3a\u8ba1\u7b97\u6587\u4ef6\u5939\u540d\u524d\u7f00\u3002\u540e\u7eed\u4f7f\u7528 <code>out2xyz</code> \u63d0\u53d6\u7ed3\u679c\u65f6\uff0c\u6587\u4ef6\u5939\u540d\u4f1a\u4f5c\u4e3a <code>config_type</code> \u5199\u5165 extxyz\uff0c\u4fbf\u4e8e\u4e4b\u540e\u68c0\u67e5\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#cp2k","title":"CP2K","text":"<p>CP2K \u53ef\u4ee5\u4ece\u4ea4\u4e92\u83dc\u5355\u8fdb\u5165\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u547d\u4ee4\u884c\u8c03\u7528\uff1a</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4f1a\u8981\u6c42\u8f93\u5165\uff1a</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>CP2K \u6a21\u677f\u5e94\u8bbe\u7f6e\u4e3a\u4ece <code>pos.xyz</code> \u8bfb\u53d6\u5750\u6807\u3002\u53c2\u8003\u6a21\u677f\u5728\uff1a</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>\u811a\u672c\u4f1a\u4e3a\u6bcf\u4e2a\u7ed3\u6784\u751f\u6210 <code>&lt;prefix&gt;_&lt;index&gt;/</code> \u76ee\u5f55\uff0c\u5e76\u5199\u5165 <code>input.inp</code> \u548c <code>pos.xyz</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#md","title":"MD \u91c7\u6837\u9884\u5904\u7406","text":""},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#gpumd","title":"GPUMD","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 302\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u68c0\u6d4b\u987a\u5e8f\u4e0e VASP SCF \u9884\u5904\u7406\u4e00\u81f4\uff1a\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</p> <p>\u8fd0\u884c\u524d\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>md/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>nep.txt</code> \u548c <code>run_*.in</code> \u653e\u5165 <code>md/</code>\u3002\u4f8b\u5982 <code>run_1.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_1/run.in</code>\uff0c<code>run_2.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_2/run.in</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#lammps","title":"LAMMPS","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 303\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\uff1b\u4e24\u79cd\u683c\u5f0f\u540c\u65f6\u5b58\u5728\u65f6\u4f18\u5148\u5904\u7406 <code>.vasp</code>\u3002</p> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>lmprun.in</code> \u548c <code>nep.txt</code> \u653e\u5230 <code>md/</code> \u4e2d\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_2","title":"\u4e3b\u52a8\u5b66\u4e60\u5f0f\u6d41\u7a0b","text":"<p>\u5e38\u89c1 NEP \u6570\u636e\u8fed\u4ee3\u6d41\u7a0b\uff1a</p> <ol> <li>\u4f7f\u7528\u5f53\u524d <code>nep.txt</code> \u8fd0\u884c MD\uff1b</li> <li>\u6536\u96c6 <code>dump.xyz</code> \u6216 <code>active.xyz</code>\uff1b</li> <li>\u5220\u9664\u660e\u663e\u4e0d\u5408\u7406\u7ed3\u6784\uff1b</li> <li>\u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\uff1b</li> <li>\u8fd0\u884c DFT \u5355\u70b9\uff1b</li> <li>\u5c06 DFT \u7ed3\u679c\u8f6c\u6362\u4e3a extxyz\uff1b</li> <li>\u8ffd\u52a0\u5230 <code>train.xyz</code>\uff1b</li> <li>\u91cd\u65b0\u8bad\u7ec3 NEP\u3002</li> </ol> <p>\u66f4\u5b8c\u6574\u7684\u5f00\u53d1\u7248\u4e3b\u52a8\u5b66\u4e60\u811a\u672c\u8bf4\u660e\u89c1 \u4e3b\u52a8\u5b66\u4e60\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_3","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u5de5\u4f5c\u6d41\u811a\u672c\u548c\u96c6\u7fa4\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u6279\u91cf\u63d0\u4ea4\u524d\u5148\u7528\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u3002</li> <li>\u6a21\u677f\u6587\u4ef6\u5982 <code>INCAR</code>\u3001<code>KPOINTS</code>\u3001<code>POTCAR</code>\u3001<code>run.in</code> \u5e94\u4ed4\u7ec6\u68c0\u67e5\u3002</li> <li>\u6279\u91cf DFT \u524d\u5148\u7528\u5206\u6790\u548c\u91c7\u6837\u811a\u672c\u6e05\u7406\u5019\u9009\u7ed3\u6784\u3002</li> </ul>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html","title":"\u5feb\u901f\u5165\u95e8","text":"\ud83d\ude80 \u5feb\u901f\u5165\u95e8 <p>\u672c\u9875\u4ecb\u7ecd GPUMDkit \u7684\u57fa\u672c\u5b89\u88c5\u65b9\u5f0f\u548c\u51e0\u4e2a\u5e38\u7528\u547d\u4ee4\u3002GPUMDkit \u65e2\u53ef\u4ee5\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u4f7f\u7528\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u901a\u8fc7\u547d\u4ee4\u884c\u9009\u9879\u8c03\u7528\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#1-python","title":"1. \u51c6\u5907 Python \u73af\u5883","text":"<p>\u53ef\u4ee5\u4f7f\u7528\u5e72\u51c0\u7684 conda \u73af\u5883\uff1a</p> <pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>\u90e8\u5206\u53ef\u9009\u529f\u80fd\u9700\u8981\u989d\u5916\u4f9d\u8d56\uff1a</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>\u5176\u4ed6 Python \u4f9d\u8d56\u7531\u5bf9\u5e94\u811a\u672c\u5728\u8fd0\u884c\u65f6\u5bfc\u5165\u3002\u5982\u679c\u7f3a\u5c11\u67d0\u4e2a\u5305\uff0c\u4f7f\u7528\u5bf9\u5e94\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u63d0\u793a\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#2-gpumdkit","title":"2. \u5b89\u88c5 GPUMDkit","text":"<p>\u514b\u9686\u4ed3\u5e93\uff1a</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <p>\u8fd0\u884c\u5b89\u88c5\u811a\u672c\uff1a</p> <pre><code>source ./install.sh\n</code></pre> <p>\u5b89\u88c5\u811a\u672c\u4f1a\u5199\u5165 <code>GPUMDkit_path</code> \u548c <code>PATH</code> \u8bbe\u7f6e\uff0c\u5e76\u5728\u5f53\u524d shell \u4e2d\u52a0\u8f7d\u3002\u9ed8\u8ba4\u5199\u5165 <code>~/.bashrc</code>\uff1b\u5982\u679c\u5f53\u524d shell \u662f zsh\uff0c\u5219\u5199\u5165 <code>~/.zshrc</code>\u3002\u5982\u679c\u68c0\u6d4b\u5230\u5df2\u6709 GPUMDkit \u8def\u5f84\uff0c\u5b89\u88c5\u811a\u672c\u4f1a\u6253\u5370\u65e7\u8def\u5f84\u5e76\u8be2\u95ee\u662f\u5426\u66ff\u6362\uff1b\u4fee\u6539 rc \u6587\u4ef6\u524d\u4f1a\u5148\u521b\u5efa\u5907\u4efd\u3002</p> <p>\u5178\u578b\u5b89\u88c5\u8f93\u51fa\uff1a</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>\u5982\u679c\u4e4b\u524d\u5df2\u7ecf\u5b89\u88c5\u8fc7 GPUMDkit\uff0c\u53ef\u80fd\u4f1a\u770b\u5230\uff1a</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre> <p>\u68c0\u67e5\u547d\u4ee4\uff1a</p> <pre><code>gpumdkit.sh -h\n</code></pre> <p>\u5e2e\u52a9\u8868\uff1a</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |\n| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#3","title":"3. \u4f7f\u7528\u65b9\u5f0f","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_1","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u4e3b\u83dc\u5355\uff1a</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_2","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<p>\u76f4\u63a5\u547d\u4ee4\u4f7f\u7528\u56fa\u5b9a\u7684\u4f4d\u7f6e\u53c2\u6570\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -plt thermo\n</code></pre> <p>\u4f8b\u5982\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>\u8868\u793a\u8bfb\u53d6 <code>POSCAR</code>\uff0c\u5199\u51fa <code>model.xyz</code>\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#4","title":"4. \u5b9e\u9645\u4f8b\u5b50","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#gpumd-group","title":"\u6dfb\u52a0 GPUMD group \u6807\u7b7e","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>group \u6807\u7b7e\u7528\u4e8e\u4e00\u4e9b\u9700\u8981\u539f\u5b50\u5206\u7ec4\u7684 GPUMD \u76f8\u5173\u6d41\u7a0b\u548c\u5206\u6790\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep","title":"\u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep_1","title":"\u7ed8\u5236 NEP \u6d4b\u8bd5\u96c6\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_3","title":"\u7ed8\u5236\u70ed\u529b\u5b66\u91cf","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#msd","title":"\u7ed8\u5236 MSD \u548c\u81ea\u6269\u6563\u7cfb\u6570","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#5","title":"5. \u83b7\u53d6\u5e2e\u52a9","text":"<pre><code>gpumdkit.sh -h\ngpumdkit.sh -plt -h\ngpumdkit.sh -calc -h\ngpumdkit.sh -plt train -h\ngpumdkit.sh -calc msd -h\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html","title":"\u6781\u6027\u6750\u6599\u5206\u6790","text":"\ud83e\uddf2 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u672c\u6559\u7a0b\u4ecb\u7ecd GPUMDkit \u4e2d\u8ba1\u7b97\u5668\u9009\u9879 <code>406-410</code>\uff0c\u4ee5\u53ca <code>plane-grid</code> \u7ed8\u56fe\u6d41\u7a0b\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code> \u548c <code>Scripts/plt_scripts/</code></p> <p>\u672c\u6559\u7a0b\u5305\u542b\u901a\u7528\u5de5\u5177\u548c\u4f53\u7cfb\u76f8\u5173\u5de5\u5177\uff1a</p> <ul> <li><code>nlist</code>\u3001<code>disp</code> \u548c <code>avg-struct</code> \u53ef\u5e7f\u6cdb\u7528\u4e8e\u7ed3\u6784\u548c\u8f68\u8ff9\u5206\u6790\u3002</li> <li><code>oct-tilt</code> \u7528\u4e8e\u516b\u9762\u4f53\u73af\u5883\u5206\u6790\uff0c\u9700\u8981\u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u5468\u56f4\u6709 6 \u4e2a\u8fd1\u90bb\u3002</li> <li><code>pol-abo3</code> \u4e13\u7528\u4e8e <code>ABO3</code> \u4f53\u7cfb\u7684\u6781\u5316\u5206\u6790\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_1","title":"\u4f9d\u8d56","text":"<p>\u8fd9\u4e9b\u811a\u672c\u9700\u8981 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_2","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<p>\u9009\u9879 <code>406-410</code> \u662f\u672c\u6559\u7a0b\u4e2d\u7684\u6838\u5fc3\u529f\u80fd\u3002\u4e0b\u9762\u5404\u8282\u4f1a\u8bf4\u660e\u6bcf\u4e2a\u529f\u80fd\u7684\u7528\u9014\u548c\u8fd0\u884c\u65b9\u5f0f\u3002</p> <p>\u5b8c\u6574\u53c2\u6570\u8bf4\u660e\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u547d\u4ee4\u67e5\u770b\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#406-calc_neighbor_listpy","title":"406) \u6784\u5efa\u8fd1\u90bb\u5217\u8868 (<code>calc_neighbor_list.py</code>)","text":"<p>\u4e3a\u6307\u5b9a\u4e2d\u5fc3\u5143\u7d20\u548c\u8fd1\u90bb\u5143\u7d20\u6784\u5efa\u8fd1\u90bb\u5217\u8868\u3002</p> <p>\u4f7f\u7528\u573a\u666f\uff1a \u8fd9\u901a\u5e38\u662f\u8fd0\u884c <code>disp</code>\u3001<code>oct-tilt</code> \u548c <code>pol-abo3</code> \u4e4b\u524d\u7684\u7b2c\u4e00\u6b65\uff0c\u56e0\u4e3a\u8fd9\u4e9b\u811a\u672c\u4f1a\u8bfb\u53d6 <code>nl-*.dat</code> \u8fd1\u90bb\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_3","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4e3a\u516b\u9762\u4f53\u5206\u6790\u6784\u5efa Ti-O \u6700\u8fd1 6 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# \u793a\u4f8b 2\uff1a\u4e3a A \u4f4d\u4e2d\u5fc3\u5206\u6790\u6784\u5efa Pb/Sr-O \u6700\u8fd1 12 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_4","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-x, --index</code>\uff1a   \u4ece\u8f93\u5165\u6587\u4ef6\u4e2d\u8bfb\u53d6\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-c, --cutoff</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u641c\u7d22\u622a\u65ad\u8ddd\u79bb\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> <li><code>-n, --neighbor-num</code>\uff08\u5fc5\u9700\uff09\uff1a   \u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u7684\u8fd1\u90bb\u6570\u91cf\u3002</li> <li><code>-d, --defect</code>\uff1a   \u7f3a\u9677\u6a21\u5f0f\u3002\u542f\u7528\u540e\uff0c\u5982\u679c\u8fd1\u90bb\u6570\u91cf\u4e0d\u8db3\uff0c\u7f3a\u5931\u4f4d\u7f6e\u4f1a\u7528\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u586b\u5145\u3002</li> <li><code>-C, --center-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u4e2d\u5fc3\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-E, --neighbor-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u8def\u5f84\u3002\u9ed8\u8ba4\u503c\uff1a<code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_5","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u8fd1\u90bb\u5217\u8868\u6587\u672c\u6587\u4ef6\uff0c\u4f8b\u5982 <code>nl-Ti-O.dat</code>\u3002</li> <li>\u6587\u4ef6\u662f\u4e00\u4e2a\u4e8c\u7ef4\u6574\u6570\u6570\u7ec4\uff0c\u5f62\u72b6\u4e3a <code>(n_center, neighbor_num + 1)</code>\u3002\u6bcf\u4e00\u884c\u5bf9\u5e94\u4e00\u4e2a\u4e2d\u5fc3\u539f\u5b50\uff1a\u7b2c\u4e00\u5217\u662f\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\uff0c\u540e\u7eed\u5217\u662f\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7\uff0c\u6240\u6709\u7f16\u53f7\u5747\u4e3a 1-based\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#407-calc_displacementpy","title":"407) \u4ece\u8f68\u8ff9\u8ba1\u7b97\u4f4d\u79fb (<code>calc_displacement.py</code>)","text":"<p>\u6839\u636e\u8f68\u8ff9\u6216\u6a21\u578b\u7ed3\u6784\u4ee5\u53ca\u8fd1\u90bb\u5217\u8868\uff0c\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_6","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece model.xyz \u8ba1\u7b97\u5355\u5e27\u4f4d\u79fb\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4f7f\u7528 movie.xyz \u7684\u6700\u540e 20% \u5e27\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_7","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7531 <code>nlist</code> \u751f\u6210\u7684\u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u90e8\u5206\u5e27\u3002   \u6574\u6570\u8868\u793a\u6700\u540e <code>N</code> \u5e27\uff1b   <code>0 &lt; value &lt; 1</code> \u8868\u793a\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_8","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>displacements.dat</code>\uff0c\u6216\u4f60\u6307\u5b9a\u7684\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e8c\u7ef4\u6570\u7ec4\uff1a\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u4e09\u5217\u5206\u522b\u4e3a <code>dx</code>\u3001<code>dy</code> \u548c <code>dz</code> \u4f4d\u79fb\u5206\u91cf\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#408-calc_averaged_structurepy","title":"408) \u8ba1\u7b97\u5e73\u5747\u7ed3\u6784 (<code>calc_averaged_structure.py</code>)","text":"<p>\u4ece\u9009\u5b9a\u8f68\u8ff9\u5e27\u751f\u6210\u4e00\u4e2a\u5e73\u5747\u7ed3\u6784\u3002 \u901a\u5e38\u53ef\u5728\u4f53\u7cfb\u5e73\u8861\u540e\u4f7f\u7528\uff1a\u5bf9\u4e8e\u63a5\u8fd1\u5e73\u8861\u7684\u56fa\u4f53\uff0c\u53ef\u4ee5\u5bf9\u76ee\u6807\u6e29\u5ea6\u4e0b\u7684\u4e00\u6bb5\u8f68\u8ff9\u53d6\u5e73\u5747\uff0c\u5e76\u5206\u6790\u8be5\u4ee3\u8868\u6027\u7ed3\u6784\uff0c\u800c\u4e0d\u662f\u9010\u5e27\u5904\u7406\u6bcf\u4e2a snapshot\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_9","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5e73\u5747\u6240\u6709\u5e27\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# \u793a\u4f8b 2\uff1a\u5e73\u5747\u9009\u5b9a\u5e27\u8303\u56f4 (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_10","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u8f68\u8ff9\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>movie.xyz</code>\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>averaged_structure.xyz</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_11","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u5355\u5e27\u5e73\u5747\u7ed3\u6784 extxyz \u6587\u4ef6\u3002</li> <li>\u4f4d\u7f6e\u5e73\u5747\u4f1a\u76f8\u5bf9\u4e8e\u6240\u9009\u7b2c\u4e00\u5e27\u8fdb\u884c MIC/PBC \u4fee\u6b63\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#409-calc_oct_tiltpy","title":"409) \u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c (<code>calc_oct_tilt.py</code>)","text":"<p>\u6839\u636e B-O \u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c\u89d2\u3002 \u8be5\u529f\u80fd\u5e38\u7528\u4e8e\u5206\u6790 <code>ABO3</code> \u4f53\u7cfb\u4e2d\u7684\u516b\u9762\u4f53\u8f6c\u52a8\u6a21\u5f0f\uff0c\u4f8b\u5982 <code>SrTiO3</code> \u548c <code>PbZrO3</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_12","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece\u5355\u5e27\u7ed3\u6784\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4ece\u8f68\u8ff9\u6700\u540e 20% \u5e27\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_13","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>octahedral_tilt.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_14","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>octahedral_tilt.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>theta_x</code>\u3001<code>theta_y</code>\u3001<code>theta_z</code>\uff0c\u5355\u4f4d\u4e3a degree\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#410-abo3-calc_polarization_abo3py","title":"410) \u8ba1\u7b97 ABO3 \u4f53\u7cfb\u6781\u5316 (<code>calc_polarization_abo3.py</code>)","text":"<p>\u8ba1\u7b97 <code>ABO3</code> \u4f53\u7cfb\u7684\u5c40\u57df\u6781\u5316\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_15","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5355\u5e27 ABO3 \u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# \u793a\u4f8b 2\uff1a\u9009\u5b9a\u8f68\u8ff9\u5e27\u8303\u56f4\u4e0a\u7684\u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_16","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>--nl-ba</code>\uff08\u5fc5\u9700\uff09\uff1a   B-A \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>--nl-bo</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>polarization.dat</code>\u3002</li> <li><code>--bec</code>\uff08\u5fc5\u9700\uff09\uff1a   Born \u6709\u6548\u7535\u8377\u9879\uff0c\u683c\u5f0f\u4e3a <code>Element=value</code>\u3002   \u793a\u4f8b\uff1a<code>Pb=2.5 Ti=4.0 O=-2.0</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul> <p>\u91cd\u8981\u68c0\u67e5\uff1a</p> <ul> <li><code>--bec</code> \u5fc5\u987b\u5305\u542b\u8f93\u5165\u7ed3\u6784\u4e2d\u7684\u6240\u6709\u5143\u7d20\u79cd\u7c7b\u3002</li> <li><code>--nl-ba</code> \u548c <code>--nl-bo</code> \u4e2d\u7684\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u5fc5\u987b\u5339\u914d\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_17","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>polarization.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>Px</code>\u3001<code>Py</code>\u3001<code>Pz</code>\uff0c\u5355\u4f4d\u4e3a <code>C/m^2</code>\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u5982\u679c\u603b Born \u7535\u8377\u4e0d\u5e73\u8861\uff0c\u811a\u672c\u4f1a\u6253\u5370 warning\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#plane-grid-plt_plane_gridpy","title":"Plane-grid \u53ef\u89c6\u5316 (<code>plt_plane_grid.py</code>)","text":"<p>\u4f60\u53ef\u4ee5\u53ef\u89c6\u5316 <code>displacements.dat</code> \u6216 <code>polarization.dat</code>\uff1a</p> <pre><code># \u793a\u4f8b 1\uff1aTi \u4f4d\u70b9\u4e0a\u7684\u4f4d\u79fb\u56fe\uff0c\u9009\u62e9\u7b2c\u4e00\u4e2a XY \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# \u793a\u4f8b 2\uff1aPb \u4f4d\u70b9\u4e0a\u7684\u6781\u5316\u56fe\uff0c\u9009\u62e9 XZ \u548c YZ \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>\u53c2\u6570\uff08\u5b8c\u6574\uff09\uff1a</p> <ul> <li><code>-i, --input</code>\uff1a   \u7528\u4e8e\u539f\u5b50\u5e03\u5c40\u548c\u5206\u5c42\u7684\u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-d, --disp</code>\uff1a   \u77e2\u91cf\u573a\u6570\u636e\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-e, --elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7528\u4e8e\u5c06\u77e2\u91cf\u6620\u5c04\u5230\u6676\u683c\u5c42\u4e0a\u7684\u4e2d\u5fc3\u5143\u7d20\u7b26\u53f7\u3002</li> <li><code>-m, --tol</code>\uff1a   \u7f51\u683c\u6620\u5c04\u7684\u5c42\u5bb9\u5dee\u3002\u9ed8\u8ba4\u503c\uff1a<code>1.0</code>\u3002</li> <li><code>-g, --target-size</code>\uff1a   \u671f\u671b\u7f51\u683c\u5927\u5c0f\uff0c\u683c\u5f0f\u4e3a <code>nx ny nz</code>\u3002</li> <li><code>-o, --save-dir</code>\uff1a   \u56fe\u7247\u8f93\u51fa\u76ee\u5f55\u3002\u9ed8\u8ba4\u503c\uff1a<code>plot</code>\u3002</li> <li><code>-f, --frame</code>\uff1a   \u5f53\u77e2\u91cf\u6570\u636e\u5305\u542b\u591a\u5e27\u65f6\uff0c\u8981\u53ef\u89c6\u5316\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>--select-xy</code>\uff1a   \u9009\u5b9a\u7684 XY \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-xz</code>\uff1a   \u9009\u5b9a\u7684 XZ \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-yz</code>\uff1a   \u9009\u5b9a\u7684 YZ \u5c42\u7f16\u53f7\u3002</li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li>\u5982\u679c\u9700\u8981\uff0c\u4f1a\u521b\u5efa\u8f93\u51fa\u76ee\u5f55\u3002</li> <li>\u56fe\u7247\u4fdd\u5b58\u4e3a <code>XY_*.png</code>\u3001<code>XZ_*.png</code>\u3001<code>YZ_*.png</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_18","title":"\u8f93\u51fa\u6587\u4ef6\u4e00\u89c8","text":"\u811a\u672c \u4e3b\u8981\u8f93\u51fa \u4fdd\u5b58\u5185\u5bb9 <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based \u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u548c\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7 <code>calc_displacement.py</code> <code>*.dat</code> \u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\uff08<code>dx dy dz</code>\uff0cAngstrom\uff09 <code>calc_averaged_structure.py</code> <code>*.xyz</code> \u4e00\u4e2a\u5e73\u5747\u7ed3\u6784 <code>calc_oct_tilt.py</code> <code>*.dat</code> \u516b\u9762\u4f53\u503e\u8f6c\u89d2\uff08<code>theta_x theta_y theta_z</code>\uff0cdegree\uff09 <code>calc_polarization_abo3.py</code> <code>*.dat</code> \u5c40\u57df\u6781\u5316\u77e2\u91cf\uff08<code>Px Py Pz</code>\uff0c<code>C/m^2</code>\uff09 <code>plt_plane_grid.py</code> <code>plot/*.png</code> \u6839\u636e\u77e2\u91cf\u573a\u6570\u636e\u7ed8\u5236\u7684 XY/XZ/YZ \u5e73\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_19","title":"\u771f\u5b9e\u6848\u4f8b","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3-","title":"PbTiO3 \u7684\u6e29\u5ea6\u9a71\u52a8\u94c1\u7535-\u987a\u7535\u76f8\u53d8","text":"<p>\u5047\u8bbe\u6240\u6709\u6587\u4ef6\u90fd\u4f4d\u4e8e\u5f53\u524d\u76ee\u5f55 <code>./</code>\uff1a</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> \u662f\u7528\u4e8e\u8fdb\u884c MD \u6a21\u62df\u7684\u521d\u59cb\u7ed3\u6784\u3002\u6bcf\u4e2a <code>TEMP K.xyz</code> \u662f\u5bf9\u5e94\u6e29\u5ea6\u4e0b\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1","title":"\u7b2c 1 \u6b65\uff1a\u4ece\u6bcf\u6761\u8f68\u8ff9\u7684\u540e\u534a\u6bb5\u5f97\u5230\u5e73\u5747\u7ed3\u6784","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>\u8fd9\u4f1a\u5199\u51fa <code>300K-avg.xyz</code>\u3001<code>350K-avg.xyz</code>\u3001...\u3001<code>800K-avg.xyz</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-modelxyz","title":"\u7b2c 2 \u6b65\uff1a\u57fa\u4e8e <code>model.xyz</code> \u6784\u5efa\u8fd1\u90bb\u5217\u8868","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3","title":"\u7b2c 3 \u6b65\uff1a\u4e3a\u6bcf\u4e2a\u6e29\u5ea6\u8ba1\u7b97\u4f4d\u79fb\u548c\u6781\u5316","text":"<p>\u8fd9\u91cc\u4f7f\u7528 Born \u6709\u6548\u7535\u8377\uff08BEC\uff09\uff0c\u4e0d\u662f\u540d\u4e49\u79bb\u5b50\u7535\u8377\u3002\u5bf9\u4e8e\u672c\u4f8b\u4e2d\u7684 PbTiO3\uff1a</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>\u4f60\u53ef\u4ee5\u4ece\u81ea\u5df1\u7684 DFPT \u8ba1\u7b97\u6216\u6587\u732e\u4e2d\u83b7\u5f97 BEC\u3002\u56e0\u6b64\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u548c\u6781\u5316\uff1a</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#4","title":"\u7b2c 4 \u6b65\uff1a\u7ed8\u5236\u5b9e\u7a7a\u95f4\u4f4d\u79fb\u548c\u6781\u5316\u56fe","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#5-","title":"\u7b2c 5 \u6b65\uff1a\u6784\u5efa\u6e29\u5ea6-\u5e8f\u53c2\u91cf\u66f2\u7ebf","text":"<p>\u7ed3\u5408\u6bcf\u4e2a\u6e29\u5ea6\u5e73\u5747\u7ed3\u6784\u7684\u6676\u683c\u4fe1\u606f\u548c\u6781\u5316\u6587\u4ef6\uff08<code>XX-pol.dat</code>\uff09\u8fdb\u884c\u5206\u6790\uff0c\u53ef\u4ee5\u5f97\u5230\u5982\u4e0b\u56fe\uff1a</p> <p>\u8be5\u8d8b\u52bf\u663e\u793a\u5728\u7ea6 <code>600 K</code> \u9644\u8fd1\u53d1\u751f\u660e\u663e\u76f8\u53d8\uff0c\u6b64\u65f6\u6781\u5316\u6d88\u5931\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3srtio3","title":"PbTiO3/SrTiO3 \u8d85\u6676\u683c\u4e2d\u7684\u62d3\u6251\u7ed3\u6784","text":"<p>\u5047\u8bbe <code>movie.xyz</code> \u662f\u5f53\u524d\u76ee\u5f55\u4e0b PbTiO3/SrTiO3 \u8d85\u6676\u683c\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1-25","title":"\u7b2c 1 \u6b65\uff1a\u4f7f\u7528\u6700\u540e 25% \u5e27\u6784\u5efa\u5e73\u5747\u7ed3\u6784","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-ti","title":"\u7b2c 2 \u6b65\uff1a\u6784\u5efa Ti \u8fd1\u90bb\u5217\u8868","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3-plane-grid","title":"\u7b2c 3 \u6b65\uff1a\u7ed8\u5236 plane-grid \u56fe","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>\u8fd9\u4f1a\u5f97\u5230\u4e0e\u524d\u9762\u5c55\u793a\u76f8\u4f3c\u7684\u56fe\u3002\u5728 PTO \u533a\u57df\u53ef\u4ee5\u770b\u5230\u7c7b\u4f3c\u6da1\u65cb\u7684\u6781\u5316\u56fe\u6837\uff0c\u800c STO \u533a\u57df\u7684\u6781\u5316\u63a5\u8fd1\u4e8e\u96f6\u3002\u901a\u8fc7\u5206\u6790\u6da1\u65cb\u6838\u9644\u8fd1\u6781\u5316\u7684\u53d8\u5316\uff0c\u53ef\u4ee5\u4f30\u8ba1\u5c40\u57df\u4ecb\u7535\u54cd\u5e94\uff0c\u4f46\u8fd9\u8d85\u51fa\u4e86\u672c\u6559\u7a0b\u8303\u56f4\u3002</p> <p>\u6ce8\u610f\uff1a\u8be5\u56fe\u4f7f\u7528\u7684 colormap \u4e0e GPUMDkit \u9ed8\u8ba4\u7ed8\u56fe\u98ce\u683c\u4e0d\u540c\u3002\u9ed8\u8ba4\u8f93\u51fa\u4e0d\u4f1a\u4e0e\u56fe\u4e2d\u5b8c\u5168\u4e00\u81f4\uff0c\u4f46\u53ef\u4ee5\u901a\u8fc7\u5c11\u91cf\u4fee\u6539\u7ed8\u56fe\u811a\u672c\u83b7\u5f97\u8fd9\u79cd\u98ce\u683c\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_20","title":"\u5176\u4ed6\u4f53\u7cfb","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#-","title":"\u6709\u673a-\u65e0\u673a\u6742\u5316\u94c1\u7535\u4f53","text":"<p>\u5728\u8bb8\u591a\u6709\u673a-\u65e0\u673a\u94c1\u7535\u4f53\u4e2d\uff0c\u6781\u5316\u4e0e\u5404\u5411\u5f02\u6027\u7684\u5206\u5b50\u5355\u5143\u5bc6\u5207\u76f8\u5173\u3002\u8ddf\u8e2a\u5206\u5b50\u53d6\u5411\u7684\u4e00\u79cd\u5b9e\u7528\u65b9\u6cd5\u662f\u4f7f\u7528\u952e\u77e2\u91cf\u3002</p> <p>\u5bf9\u4e8e TMCM-CdCl3\uff0c\u53ef\u4ee5\u4f7f\u7528 TMCM \u5206\u5b50\u4e2d\u7684 C-Cl \u952e\u65b9\u5411\u4f5c\u4e3a\u53d6\u5411\u4ee3\u7406\uff0c\u5e76\u636e\u6b64\u4f30\u8ba1\u6781\u5316\u6001\uff1a</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p>\u968f\u540e\u53ef\u4ee5\u628a <code>ccl_vectors.dat</code> \u4f5c\u4e3a\u53d6\u5411\u5e8f\u53c2\u91cf\u8fdb\u884c\u5206\u6790\u3002\u66f4\u591a\u7ec6\u8282\u53ef\u53c2\u8003\uff1aPhys. Rev. Lett. 136, 016801\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_21","title":"\u5176\u4ed6\u94c1\u7535\u6750\u6599\u5bb6\u65cf","text":"<p>\u9664 <code>ABO3</code> \u5916\uff0c<code>ferrodispcalc</code> \u4e5f\u53ef\u4ee5\u9002\u914d\u8bb8\u591a\u94c1\u7535\u4f53\u7cfb\uff0c\u5305\u62ec\u6c2e\u5316\u7269\u3001\u6c27\u5316\u94ea\u57fa\u5316\u5408\u7269\u3001\u6709\u673a-\u65e0\u673a\u6742\u5316\u4f53\u7cfb\u4ee5\u53ca\u90e8\u5206\u4e8c\u7ef4\u94c1\u7535\u6750\u6599\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html","title":"\u683c\u5f0f\u8f6c\u6362","text":"\ud83d\udd04 \u683c\u5f0f\u8f6c\u6362 <p>\u683c\u5f0f\u8f6c\u6362\u6a21\u5757\u7528\u4e8e\u5728\u5e38\u89c1\u539f\u5b50\u6a21\u62df\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362\uff0c\u540c\u65f6\u63d0\u4f9b group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u5e27\u63d0\u53d6\u7b49\u5143\u6570\u636e\u5904\u7406\u529f\u80fd\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/format_conversion/</code></p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_1","title":"\u652f\u6301\u7684\u683c\u5f0f","text":"<ul> <li>VASP\uff1a<code>POSCAR</code>\u3001<code>CONTCAR</code>\u3001<code>OUTCAR</code>\u3001<code>XDATCAR</code></li> <li>LAMMPS\uff1adata \u6587\u4ef6\u548c dump \u8f68\u8ff9</li> <li>CP2K\uff1a\u8f93\u51fa log\u3001\u5750\u6807\u3001\u529b\u548c\u6676\u80de\u6587\u4ef6</li> <li>ABACUS\uff1aSCF/MD \u8f93\u51fa</li> <li>CIF\uff1a\u6676\u4f53\u7ed3\u6784\u6587\u4ef6</li> <li>ASE trajectory\uff1a<code>.traj</code></li> <li>extxyz\uff1aGPUMD \u548c NEP \u5e38\u7528\u7684\u7ed3\u6784\u683c\u5f0f</li> </ul>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_2","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>1) Format Conversion\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_3","title":"\u6bcf\u4e2a\u5165\u53e3\u7684\u4f5c\u7528","text":"\u5165\u53e3 \u529f\u80fd \u9002\u7528\u573a\u666f <code>101</code> VASP OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c \u6279\u91cf\u8f6c\u6362 VASP \u8ba1\u7b97\u76ee\u5f55 <code>102</code> MTP cfg \u8f6c extxyz \u8f6c\u6362 MTP \u6570\u636e <code>103</code> CP2K \u8f6c extxyz \u53ef\u9009\u62e9 log/inp \u8def\u7ebf\u6216 pos/frc/cell \u8def\u7ebf <code>104</code> ABACUS \u8f6c extxyz \u8f6c\u6362 ABACUS SCF \u6216 MD \u8f93\u51fa <code>105</code> extxyz \u8f6c POSCAR \u5c06 extxyz \u6bcf\u4e00\u5e27\u5199\u6210 POSCAR <code>106</code> \u6dfb\u52a0 group \u6807\u7b7e \u4e3a GPUMD \u76f8\u5173\u6d41\u7a0b\u6dfb\u52a0\u539f\u5b50\u5206\u7ec4\u6807\u7b7e <code>107</code> \u6dfb\u52a0\u6743\u91cd \u4fee\u6539\u8bad\u7ec3\u96c6\u7ed3\u6784\u6743\u91cd <code>108</code> \u63d0\u53d6\u5355\u5e27 \u4ece extxyz \u8f68\u8ff9\u5bfc\u51fa\u67d0\u4e00\u5e27 <code>109</code> \u6e05\u7406 XYZ \u4fe1\u606f \u5220\u9664\u591a\u4f59 extxyz \u5c5e\u6027 <code>110</code> \u6269\u80de \u6309\u500d\u6570\u6216\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>out2exyz</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c VASP OUTCAR \u8f6c\u6362\u7684\u53e6\u4e00\u4e2a\u5165\u53e3 <code>pos2exyz</code> POSCAR \u8f6c extxyz \u8f6c\u6362\u5355\u4e2a\u7ed3\u6784 <code>cif2pos</code> CIF \u8f6c POSCAR \u4ece CIF \u51c6\u5907 VASP \u8f93\u5165 <code>cif2exyz</code> CIF \u8f6c extxyz \u4ece CIF \u51c6\u5907 GPUMDkit \u8f93\u5165 <code>xdat2exyz</code> XDATCAR \u8f6c extxyz \u8f6c\u6362 VASP MD \u8f68\u8ff9 <code>pos2lmp</code> POSCAR \u8f6c LAMMPS data \u51c6\u5907 LAMMPS \u8f93\u5165 <code>lmp2exyz</code> LAMMPS dump \u8f6c extxyz \u8f6c\u6362 LAMMPS \u8f68\u8ff9 <code>traj2exyz</code> ASE traj \u8f6c extxyz \u8f6c\u6362 ASE \u8f68\u8ff9"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_4","title":"\u5feb\u901f\u547d\u4ee4\u8868","text":"\u6765\u6e90 \u76ee\u6807 \u547d\u4ee4 OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz POSCAR model.xyz</code> extxyz POSCAR \u6587\u4ef6 <code>gpumdkit.sh -exyz2pos train.xyz</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_5","title":"\u5e38\u89c1\u4f8b\u5b50","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#vasp","title":"\u8f6c\u6362 VASP \u7ed3\u679c","text":"<p>\u5982\u679c\u6bcf\u4e2a\u8ba1\u7b97\u76ee\u5f55\u4e0b\u90fd\u6709 <code>OUTCAR</code>\uff1a</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>\u4e5f\u53ef\u4ee5\u4f7f\u7528 Python \u7248\u672c\uff1a</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>\u5728\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>101</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#group","title":"\u6dfb\u52a0 group \u6807\u7b7e","text":"<p>\u4e00\u4e9b GPUMD \u76f8\u5173\u6d41\u7a0b\u4f1a\u4f7f\u7528 group \u6807\u7b7e\u8fdb\u884c\u539f\u5b50\u5206\u7ec4\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>\u8be5\u547d\u4ee4\u8bfb\u53d6\u8f93\u5165\u7ed3\u6784\uff0c\u5e76\u5199\u51fa\u5e26 group \u4fe1\u606f\u7684 extxyz \u6587\u4ef6\u3002</p> <p>\u5728\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>106</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_6","title":"\u5e38\u7528\u811a\u672c\u8bf4\u660e","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>\u9002\u5408\u628a\u5355\u4e2a VASP \u7ed3\u6784\u8f6c\u6210 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz-poscar","title":"extxyz \u8f6c POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>\u4f1a\u5c06 extxyz \u4e2d\u6240\u6709\u5e27\u8f6c\u6362\u6210 <code>POSCAR_*.vasp</code> \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3\uff1a<code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#lammps-dump-extxyz","title":"LAMMPS dump \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>\u5143\u7d20\u987a\u5e8f\u5fc5\u987b\u5bf9\u5e94 LAMMPS \u4e2d\u7684 atom type ID\u3002\u4f8b\u5982 type 1 \u662f Li\u3001type 2 \u662f Y\u3001type 3 \u662f Cl\uff0c\u5219\u8f93\u5165 <code>Li Y Cl</code>\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#cif","title":"CIF \u8f6c\u6362","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>\u5982\u679c\u540e\u7eed\u9700\u8981 VASP \u8ba1\u7b97\uff0c\u4f7f\u7528 <code>-cif2pos</code>\uff1b\u5982\u679c\u540e\u7eed\u8981\u8fdb\u5165 GPUMDkit \u5206\u6790\uff0c\u4f7f\u7528 <code>-cif2exyz</code>\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_7","title":"\u6dfb\u52a0\u6743\u91cd","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>\u7528\u4e8e\u7ed9\u8bad\u7ec3\u96c6\u7ed3\u6784\u6dfb\u52a0\u6216\u4fee\u6539\u6743\u91cd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_8","title":"\u6269\u80de","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>\u7b2c\u4e00\u79cd\u6309\u6676\u80de\u500d\u6570\u6269\u80de\uff0c\u7b2c\u4e8c\u79cd\u6309\u76ee\u6807\u539f\u5b50\u6570\u81ea\u52a8\u9009\u62e9\u6269\u80de\u65b9\u5f0f\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_9","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae LAMMPS \u8f6c\u6362\u540e\u5143\u7d20\u4e0d\u5bf9 \u68c0\u67e5 dump \u6587\u4ef6\u540e\u7684\u5143\u7d20\u987a\u5e8f extxyz \u5143\u6570\u636e\u592a\u591a \u4f7f\u7528 <code>-clean_xyz input.xyz clean.xyz</code> \u63d0\u53d6\u5e27\u4e0d\u5bf9 \u6ce8\u610f\u5e27\u7d22\u5f15\u901a\u5e38\u4ece 0 \u5f00\u59cb"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_10","title":"\u8bf4\u660e","text":"<p>\u5982\u679c\u67d0\u4e2a\u8f6c\u6362\u811a\u672c\u7f3a\u5c11\u6240\u9700 Python \u5305\uff0c\u8fd0\u884c\u8be5\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u76f8\u5e94\u63d0\u793a\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html","title":"\u7ed3\u6784\u91c7\u6837","text":"\ud83d\udce6 \u7ed3\u6784\u91c7\u6837 <p>\u7ed3\u6784\u91c7\u6837\u7528\u4e8e\u4ece\u8f68\u8ff9\u4e2d\u9009\u62e9\u5019\u9009\u7ed3\u6784\u3001\u751f\u6210\u6270\u52a8\u7ed3\u6784\uff0c\u6216\u6839\u636e\u6a21\u578b\u504f\u5dee\u6311\u9009\u503c\u5f97\u8fdb\u4e00\u6b65\u8ba1\u7b97\u7684\u7ed3\u6784\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/sample_structures/</code></p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_1","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>2) Sample Structures\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u65b9\u6cd5 \u7528\u9014 201 uniform/random \u4ece\u8f68\u8ff9\u4e2d\u5747\u5300\u6216\u968f\u673a\u62bd\u5e27 202 PyNEP notice \u53ea\u6253\u5370\u63d0\u793a\uff1b\u771f\u6b63\u8fd0\u884c PyNEP \u8bf7\u7528 <code>gpumdkit.sh -pynep</code> 203 NepTrain FPS \u4f7f\u7528 NepTrain \u63cf\u8ff0\u7b26\u7684 FPS \u91c7\u6837 204 perturb \u4ece POSCAR/CONTCAR \u751f\u6210\u6270\u52a8\u7ed3\u6784 205 force deviation \u4ece active learning \u8f93\u51fa\u4e2d\u9009\u62e9\u9ad8\u504f\u5dee\u7ed3\u6784"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_2","title":"\u5747\u5300/\u968f\u673a\u91c7\u6837","text":"<p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>201</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>\u4f8b\u5982\u8f93\u5165\uff1a</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>\u6216\uff1a</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>uniform</code> / <code>random</code> \u91c7\u6837\u65b9\u6cd5 <code>50</code> / <code>100</code> \u91c7\u6837\u7ed3\u6784\u6570 <code>500</code> \u53ef\u9009\uff0c\u8df3\u8fc7\u524d 500 \u5e27 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#neptrain-fps","title":"NepTrain FPS","text":"<p>NepTrain \u7248\u672c\u7684 FPS\uff1a</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>203</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u5165\uff1a</p> \u6587\u4ef6 \u542b\u4e49 <code>dump.xyz</code> \u5019\u9009\u7ed3\u6784 <code>train.xyz</code> \u5f53\u524d\u8bad\u7ec3\u96c6 <code>nep.txt</code> \u7528\u4e8e\u8ba1\u7b97\u63cf\u8ff0\u7b26\u7684 NEP \u6a21\u578b <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>\u8fd0\u884c\u65f6\u53ef\u4ee5\u9009\u62e9\u6309\u6700\u5c0f\u8ddd\u79bb\u9608\u503c\u91c7\u6837\uff0c\u6216\u6307\u5b9a\u91c7\u6837\u7ed3\u6784\u6570\u3002\u811a\u672c\u968f\u540e\u4f1a\u6253\u5370\uff1a</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>NepTrain</code>\uff0c\u8fd0\u884c\u65f6\u4f1a\u63d0\u793a\u76f8\u5173\u5f15\u7528\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep","title":"PyNEP \u65e7\u5165\u53e3","text":"<p>PyNEP FPS \u4ecd\u7136\u4fdd\u7559\u517c\u5bb9\uff0c\u4f46\u53ea\u901a\u8fc7 <code>-pynep</code> \u5165\u53e3\u8c03\u7528\uff1a</p> <p>\u5982\u679c\u5728\u4ea4\u4e92\u83dc\u5355\u4e2d\u9009\u62e9 <code>202</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre> <pre><code>gpumdkit.sh -pynep\n</code></pre> <p>\u968f\u540e\u8f93\u5165\uff1a</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u8fd9\u4e2a\u5165\u53e3\u9700\u8981 <code>pynep</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_3","title":"\u7ed3\u6784\u6270\u52a8","text":"<pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>204</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>POSCAR</code> \u8f93\u5165\u7ed3\u6784 <code>20</code> \u751f\u6210\u7ed3\u6784\u6570 <code>0.03</code> \u6676\u80de\u6270\u52a8\u6bd4\u4f8b <code>0.2</code> \u539f\u5b50\u6270\u52a8\u8ddd\u79bb\uff0c\u5355\u4f4d Angstrom <code>uniform</code> \u6270\u52a8\u65b9\u5f0f\uff0c\u53ef\u9009 <code>normal</code>\u3001<code>uniform</code>\u3001<code>const</code> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>POSCAR_01.vasp</code>\u3001<code>POSCAR_02.vasp</code> \u7b49</li> </ul> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>dpdata</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_4","title":"\u6700\u5927\u529b\u504f\u5dee\u7ed3\u6784\u9009\u62e9","text":"<p>\u8be5\u529f\u80fd\u9700\u8981\u914d\u5408 GPUMD \u7684 <code>active</code> \u547d\u4ee4\u4f7f\u7528\u3002<code>active</code> \u901a\u8fc7\u59d4\u5458\u4f1a\u8bc4\u5ba1\u673a\u5236\uff0c\u8ba9\u591a\u6761\u52bf\u51fd\u6570\u5bf9\u540c\u4e00\u7ed3\u6784\u8fdb\u884c\u9884\u6d4b\uff0c\u5e76\u8bb0\u5f55\u6bcf\u4e2a\u7ed3\u6784\u7684\u6700\u5927\u529b\u504f\u5dee\u3002<code>select_max_modev.py</code> \u4f1a\u4ece <code>active.out</code> \u548c <code>active.xyz</code> \u4e2d\u9009\u62e9\u529b\u504f\u5dee\u8f83\u5927\u7684\u7ed3\u6784\uff0c\u5199\u5165 <code>selected.xyz</code>\u3002</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>205</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>\u9700\u8981\u5f53\u524d\u76ee\u5f55\u4e0b\u6709\uff1a</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_5","title":"\u793a\u4f8b\u547d\u4ee4","text":"<pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_6","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae FPS \u9009\u51fa\u592a\u591a\u76f8\u4f3c\u7ed3\u6784 \u8c03\u5927\u8ddd\u79bb\u9608\u503c\u6216\u9650\u5236\u6700\u5927\u9009\u62e9\u6570 \u6270\u52a8\u7ed3\u6784\u4e0d\u5408\u7406 \u51cf\u5c0f <code>cell_pert</code> \u548c <code>atom_pert</code> <code>active.out</code> \u548c <code>active.xyz</code> \u4e0d\u5339\u914d \u786e\u4fdd\u6765\u81ea\u540c\u4e00\u6b21 GPUMD active \u8fd0\u884c PCA \u56fe\u5f02\u5e38 \u68c0\u67e5 <code>nep.txt</code> \u662f\u5426\u548c\u4e24\u4e2a\u6570\u636e\u96c6\u5143\u7d20\u4e00\u81f4"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html","title":"\u7ed8\u56fe\u811a\u672c","text":"\ud83d\udcca \u7ed8\u56fe\u811a\u672c <p>\u7ed8\u56fe\u6a21\u5757\u7528\u4e8e\u53ef\u89c6\u5316 GPUMD\u3001NEP \u548c GPUMDkit \u8ba1\u7b97\u5668\u4ea7\u751f\u7684\u6570\u636e\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/plt_scripts/</code></p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_1","title":"\u5feb\u901f\u5165\u53e3","text":"<pre><code>gpumdkit.sh -plt\ngpumdkit.sh -plt &lt;type&gt;\ngpumdkit.sh -plt &lt;type&gt; save\ngpumdkit.sh -plt &lt;type&gt; -h\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u8bad\u7ec3\u4e0e\u9884\u6d4b","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_2","title":"\u8bad\u7ec3\u7ed3\u679c","text":"<p>\u8bfb\u53d6 <code>loss.out</code>\u3001<code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code>\uff0c\u7ed8\u5236 loss \u548c\u80fd\u91cf/\u529b/virial \u7684 parity plot\u3002</p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_3","title":"\u9884\u6d4b\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_4","title":"\u8bad\u7ec3/\u6d4b\u8bd5\u96c6\u5bf9\u6bd4","text":"<pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#parity-plot","title":"\u5bc6\u5ea6 parity plot","text":"<p>\u5927\u6570\u636e\u96c6\u6563\u70b9\u592a\u5bc6\u65f6\uff0c\u5bc6\u5ea6\u56fe\u66f4\u5bb9\u6613\u89c2\u5bdf\u8bef\u5dee\u5206\u5e03\uff1a</p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_5","title":"\u529b\u8bef\u5dee\u5206\u6790","text":"<p><code>plt_force_errors.py</code> \u53c2\u8003 Liu et al. \u7684\u65b9\u5f0f\u5206\u6790\u529b\u5927\u5c0f\u8bef\u5dee\u548c\u89d2\u5ea6\u8bef\u5dee\u3002</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#born","title":"\u7535\u8377\u548c Born \u6709\u6548\u7535\u8377","text":"<pre><code>gpumdkit.sh -plt charge\ngpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#md","title":"MD \u548c\u7ed3\u6784\u5206\u6790\u7ed8\u56fe","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_6","title":"\u70ed\u529b\u5b66\u91cf","text":"<pre><code>gpumdkit.sh -plt thermo\ngpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#rdf","title":"RDF","text":"<pre><code>gpumdkit.sh -plt rdf\ngpumdkit.sh -plt rdf &lt;column&gt;\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#vac-pdos","title":"VAC \u548c PDOS","text":"<pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>\u8f93\u5165\u6587\u4ef6\u901a\u5e38\u5305\u62ec <code>model.xyz</code>\u3001<code>run.in</code>\u3001<code>dos.out</code>\u3001<code>mvac.out</code>\u3002</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_7","title":"\u6269\u6563\u548c\u79bb\u5b50\u8f93\u8fd0","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\ngpumdkit.sh -plt msd_conv\ngpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt arrhenius_sigma\n</code></pre> <p>Arrhenius \u56fe\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_8","title":"\u70ed\u8f93\u8fd0","text":"<pre><code>gpumdkit.sh -plt emd x\ngpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\ngpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#dimer","title":"\u63cf\u8ff0\u7b26\u3001Dimer \u548c\u5176\u4ed6\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_9","title":"\u63cf\u8ff0\u7b26\u53ef\u89c6\u5316","text":"<pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#dimer_1","title":"Dimer \u66f2\u7ebf","text":"<pre><code>gpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>Reference: J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#doas","title":"DOAS","text":"<pre><code>gpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#net-force","title":"Net force","text":"<pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>Reference: arXiv:2510.19774</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_10","title":"\u5feb\u901f\u8868","text":"\u547d\u4ee4 \u8f93\u5165\u6587\u4ef6 \u7528\u9014 <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP \u8bad\u7ec3\u7ed3\u679c <code>prediction</code> <code>*_test.out</code> NEP \u9884\u6d4b\u7ed3\u679c <code>thermo</code> <code>thermo.out</code> \u70ed\u529b\u5b66\u91cf <code>msd</code> <code>msd.out</code> \u5747\u65b9\u4f4d\u79fb <code>sdc</code> <code>msd.out</code> \u81ea\u6269\u6563\u7cfb\u6570 <code>rdf</code> <code>rdf.out</code> \u5f84\u5411\u5206\u5e03\u51fd\u6570 <code>pdos</code> <code>dos.out</code>, <code>mvac.out</code> VAC \u548c PDOS <code>emd</code>/<code>nemd</code>/<code>hnemd</code> \u70ed\u8f93\u8fd0\u8f93\u51fa \u70ed\u5bfc\u7387\u5206\u6790 <code>des</code> <code>descriptors.npy</code> \u63cf\u8ff0\u7b26\u964d\u7ef4 <code>dimer</code> <code>nep.txt</code> \u4e8c\u805a\u4f53\u80fd\u91cf/\u529b\u66f2\u7ebf <code>doas</code> <code>doas.out</code> \u539f\u5b50\u6001\u5bc6\u5ea6"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html","title":"\u81ea\u5b9a\u4e49\u547d\u4ee4","text":"\ud83d\udd27 \u81ea\u5b9a\u4e49\u547d\u4ee4 <p>GPUMDkit \u652f\u6301\u4ece ~/.gpumdkit.in \u52a0\u8f7d\u81ea\u5b9a\u4e49\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u628a\u5e38\u7528\u811a\u672c\u6216\u5de5\u4f5c\u6d41\u5c01\u88c5\u6210 <code>custom_</code> \u5f00\u5934\u7684 Bash \u51fd\u6570\uff0c\u7136\u540e\u901a\u8fc7 <code>gpumdkit.sh -\u547d\u4ee4\u540d</code> \u8c03\u7528\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_1","title":"\u8bbe\u7f6e","text":"<p>\u7f16\u8f91\u914d\u7f6e\u6587\u4ef6\uff1a</p> <pre><code>vi ~/.gpumdkit.in\n</code></pre> <p>\u81ea\u5b9a\u4e49\u51fd\u6570\u9700\u8981\u4f7f\u7528 <code>custom_</code> \u524d\u7f00\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_2","title":"\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_3","title":"\u7b80\u5355\u95ee\u5019","text":"<p>\u5728 <code>~/.gpumdkit.in</code> \u4e2d\u5199\u5165\uff1a</p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>\u7136\u540e\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -hello\n</code></pre> <p>\u4f60\u4f1a\u770b\u5230\u7c7b\u4f3c\u8f93\u51fa\uff1a</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_4","title":"\u5e26\u5fc5\u9700\u53c2\u6570\u7684\u547d\u4ee4","text":"<pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -greet Zihan\n</code></pre> <p>\u8f93\u51fa\uff1a</p> <pre><code>Hello, Zihan!\n</code></pre> <p>\u4f20\u9012\u53c2\u6570\u65f6\uff0c\u53ef\u4ee5\u7528 <code>\"$@\"</code> \u5b89\u5168\u5730\u8f6c\u53d1\u6240\u6709\u53c2\u6570\uff1b\u5982\u679c\u9700\u8981\u4ece\u7b2c\u4e00\u4e2a\u53c2\u6570\u5f00\u59cb\u5f15\u7528\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528 <code>${@:1}</code>\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_5","title":"\u8c03\u7528\u5916\u90e8\u811a\u672c","text":"<p>\u5982\u679c\u5e0c\u671b\u50cf\u8c03\u7528 GPUMDkit \u5185\u7f6e\u547d\u4ee4\u4e00\u6837\u8c03\u7528\u81ea\u5df1\u7684\u811a\u672c\uff1a</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -nepanalyse\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_6","title":"\u8fdb\u9636\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_7","title":"\u6279\u5904\u7406\u7ed8\u56fe","text":"<p>\u5bf9\u591a\u4e2a\u76ee\u5f55\u6279\u91cf\u7ed8\u56fe\uff1a</p> <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -batch_plot dir1 dir2 dir3\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_8","title":"\u8bad\u7ec3\u96c6\u5206\u6790\u6d41\u7a0b","text":"<p>\u628a\u591a\u4e2a\u5206\u6790\u547d\u4ee4\u7ec4\u5408\u6210\u4e00\u4e2a\u5165\u53e3\uff1a</p> <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -analyze_training train.xyz\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_9","title":"\u81ea\u5b9a\u4e49\u6570\u636e\u51c6\u5907\u6d41\u7a0b","text":"<pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    gpumdkit.sh -out2xyz ./\n    gpumdkit.sh -filter_value train.xyz force 30\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -prep_training\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_10","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u547d\u4ee4\u540d\u5c3d\u91cf\u6e05\u695a\uff0c\u4f8b\u5982 <code>custom_analyze_training</code> \u6bd4 <code>custom_at</code> \u66f4\u5bb9\u6613\u7ef4\u62a4\u3002</li> <li>\u5bf9\u9700\u8981\u53c2\u6570\u7684\u547d\u4ee4\uff0c\u5efa\u8bae\u5728\u53c2\u6570\u4e3a\u7a7a\u65f6\u6253\u5370\u7528\u6cd5\u63d0\u793a\u3002</li> <li>\u8c03\u7528\u5916\u90e8\u811a\u672c\u65f6\uff0c\u5c3d\u91cf\u7528 <code>\"$@\"</code> \u4fdd\u7559\u53c2\u6570\u4e2d\u7684\u7a7a\u683c\u548c\u7279\u6b8a\u5b57\u7b26\u3002</li> <li>\u6279\u5904\u7406\u76ee\u5f55\u65f6\uff0c\u6ce8\u610f\u4f7f\u7528 <code>cd \"$dir\"</code>\uff0c\u907f\u514d\u8def\u5f84\u4e2d\u6709\u7a7a\u683c\u65f6\u51fa\u9519\u3002</li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html","title":"\u8ba1\u7b97\u5668\u811a\u672c","text":"\ud83e\uddee \u8ba1\u7b97\u5668\u811a\u672c <p>\u8ba1\u7b97\u5668\u6a21\u5757\u7528\u4e8e\u4ece MD \u8f68\u8ff9\u3001NEP \u6a21\u578b\u548c\u7ed3\u6784\u6587\u4ef6\u4e2d\u8ba1\u7b97\u6750\u6599\u6027\u8d28\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code></p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_1","title":"\u529f\u80fd\u6982\u89c8","text":"\u4efb\u52a1 \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u79bb\u5b50\u7535\u5bfc\u7387 <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>\u3001<code>thermo.out</code>\u3001<code>model.xyz</code> MSD <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz \u8f68\u8ff9 NEP \u9884\u6d4b <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP \u6a21\u578b NEP \u63cf\u8ff0\u7b26 <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP \u6a21\u578b DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP \u6a21\u578b NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u521d\u672b\u6001\u7ed3\u6784 \u7ed3\u6784\u4f18\u5316 <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784 + NEP \u6a21\u578b \u90bb\u5c45\u5217\u8868 <code>gpumdkit.sh -calc nlist [args...]</code> \u7ed3\u6784 \u4f4d\u79fb <code>gpumdkit.sh -calc disp [args...]</code> \u8f68\u8ff9 + \u90bb\u5c45\u5217\u8868 \u5e73\u5747\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct [args...]</code> \u8f68\u8ff9 \u516b\u9762\u4f53\u503e\u8f6c <code>gpumdkit.sh -calc oct-tilt [args...]</code> \u8f68\u8ff9 + B-O \u90bb\u5c45\u5217\u8868 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 [args...]</code> \u8f68\u8ff9 + \u90bb\u5c45\u5217\u8868 <p>\u67e5\u770b\u5b8c\u6574\u5e2e\u52a9\uff1a</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>\u547d\u4ee4\u884c\u5e2e\u52a9\u8868\u7c7b\u4f3c\uff1a</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>4) Calculators</code>\uff0c\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_2","title":"\u79bb\u5b50\u7535\u5bfc\u7387","text":"<pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>401</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>\u5e38\u7528\u8f93\u5165\u6587\u4ef6\uff1a</p> \u6587\u4ef6 \u4f5c\u7528 <code>msd.out</code> \u5fc5\u9700\uff0cMSD \u6570\u636e <code>thermo.out</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u6e29\u5ea6 <code>model.xyz</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u4f53\u79ef\u548c\u79bb\u5b50\u6570 <code>run.in</code> \u53ef\u9009\uff0c\u8bc6\u522b\u6269\u80de\u4fe1\u606f <p>\u5982\u679c\u7f3a\u5c11\u81ea\u52a8\u8bc6\u522b\u6240\u9700\u6587\u4ef6\uff0c\u811a\u672c\u4f1a\u4ea4\u4e92\u5f0f\u8be2\u95ee\u6e29\u5ea6\u3001\u4f53\u79ef\u548c\u79bb\u5b50\u6570\u3002</p> <p>\u624b\u52a8\u6a21\u5f0f\u7684\u63d0\u793a\u7c7b\u4f3c\uff1a</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#msd","title":"\u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD","text":"<pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>412</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>Li</code> \u76ee\u6807\u6269\u6563\u5143\u7d20 <code>10</code> \u5e27\u95f4\u9694\uff0c\u5355\u4f4d fs <code>5000</code> \u53ef\u9009\uff0c\u6700\u5927\u76f8\u5173\u6b65\u6570 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>msd.out</code></li> </ul> <p>\u968f\u540e\u53ef\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u9884\u6d4b\u6027\u8d28","text":"<pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>\u8be5\u529f\u80fd\u4f7f\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8ba1\u7b97\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u3002\u53ea\u6709\u5f53\u4f60\u786e\u8ba4\u6a21\u578b\u8d28\u91cf\u53ef\u9760\uff0c\u5e76\u660e\u786e\u5e0c\u671b\u4f7f\u7528 NEP \u4f5c\u4e3a\u66ff\u4ee3\u8ba1\u7b97\u5668\u65f6\uff0c\u624d\u5efa\u8bae\u4f7f\u7528\u5b83\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep_1","title":"NEP \u63cf\u8ff0\u7b26","text":"<pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>\u7528\u9014\u5305\u62ec\uff1a</p> <ul> <li>\u7528 PCA/UMAP \u53ef\u89c6\u5316\u5c40\u57df\u73af\u5883\uff1b</li> <li>\u6bd4\u8f83\u8bad\u7ec3\u96c6\u548c\u5019\u9009\u7ed3\u6784\uff1b</li> <li>\u5224\u65ad\u65b0\u6570\u636e\u662f\u5426\u6269\u5c55\u4e86\u63cf\u8ff0\u7b26\u7a7a\u95f4\u3002</li> </ul> <p>\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#doas","title":"DOAS","text":"<p><code>calc_doas.py</code> \u7528\u4e8e\u8ba1\u7b97 Wang et al. \u63d0\u51fa\u7684 density of atomistic states\u3002</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>\u811a\u672c\u4f1a\uff1a</p> <ol> <li>\u8bfb\u53d6\u6240\u6709\u7ed3\u6784\uff1b</li> <li>\u4f7f\u7528 NEP \u8fdb\u884c\u7ed3\u6784\u4f18\u5316\uff1b</li> <li>\u63d0\u53d6\u6bcf\u4e2a\u539f\u5b50\u7684\u80fd\u91cf\uff1b</li> <li>\u6309\u5143\u7d20\u5206\u7ec4\u8f93\u51fa\uff1b</li> <li>\u7528\u7ed8\u56fe\u811a\u672c\u53ef\u89c6\u5316\u5206\u5e03\u3002</li> </ol>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#neb","title":"NEB \u548c\u7ed3\u6784\u4f18\u5316","text":"<p>NEB\uff1a</p> <pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>\u7ed3\u6784\u4f18\u5316\uff1a</p> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>\u8f93\u51fa\u5305\u62ec\uff1a</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_3","title":"\u94c1\u7535\u548c\u6781\u6027\u6750\u6599\u5de5\u5177","text":"<p>\u8fd9\u4e9b\u5de5\u5177\u9700\u8981 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p><code>ferrodispcalc</code> \u76ee\u524d\u6ca1\u6709\u9700\u8981\u989d\u5916\u5f15\u7528\u7684\u8bba\u6587\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_4","title":"\u90bb\u5c45\u5217\u8868","text":"<pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_5","title":"\u4f4d\u79fb","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_6","title":"\u5e73\u5747\u7ed3\u6784","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_7","title":"\u516b\u9762\u4f53\u503e\u8f6c","text":"<pre><code>gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#abo3","title":"ABO3 \u5c40\u57df\u6781\u5316","text":"<pre><code>gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -o polarization.dat\n</code></pre> <p><code>--bec</code> \u5e94\u6839\u636e\u4f60\u7684\u4f53\u7cfb\u6216\u53c2\u8003\u6570\u636e\u8bbe\u7f6e\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html","title":"\u8d21\u732e\u6307\u5357","text":"\ud83e\udd1d \u8d21\u732e\u6307\u5357 <p>\u611f\u8c22\u4f60\u6709\u5174\u8da3\u4e3a GPUMDkit \u505a\u8d21\u732e\u3002\u6211\u4eec\u975e\u5e38\u611f\u8c22\u4f60\u613f\u610f\u82b1\u65f6\u95f4\u548c\u7cbe\u529b\u5e2e\u52a9\u6539\u8fdb\u8fd9\u4e2a\u5de5\u5177\u5305\u3002</p> <p><code>GPUMDkit</code> \u662f\u4e00\u4e2a\u5f00\u6e90\u8f6f\u4ef6\u5305\u3002\u65e0\u8bba\u662f\u4fee\u590d bug\u3001\u6dfb\u52a0\u65b0\u529f\u80fd\u3001\u6539\u8fdb\u6587\u6863\uff0c\u8fd8\u662f\u63d0\u51fa\u4f7f\u7528\u5efa\u8bae\uff0c\u6211\u4eec\u90fd\u6b22\u8fce\u793e\u533a\u8d21\u732e\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_1","title":"\u76ee\u5f55","text":"<ul> <li>\u5f00\u53d1\u9650\u5236\u548c\u6307\u5357</li> <li>\u62a5\u544a Bug</li> <li>\u63d0\u51fa\u529f\u80fd\u5efa\u8bae</li> <li>\u8d21\u732e\u4ee3\u7801</li> <li>Fork \u5e76\u514b\u9686\u4ed3\u5e93</li> <li>\u521b\u5efa\u529f\u80fd\u5206\u652f</li> <li>\u8fdb\u884c\u4fee\u6539</li> <li>\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e</li> <li>\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e</li> <li>\u66f4\u65b0 Tab \u8865\u5168</li> <li>\u4ee3\u7801\u98ce\u683c\u548c\u6700\u4f73\u5b9e\u8df5</li> <li>\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539</li> <li>\u63d0\u4ea4\u4fe1\u606f</li> <li>\u63a8\u9001\u5e76\u6253\u5f00 Pull Request</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_2","title":"\u5f00\u53d1\u9650\u5236\u548c\u6307\u5357","text":"<p>\u4e3a\u4e86\u4fdd\u6301\u9879\u76ee\u4ee3\u7801\u8d28\u91cf\u548c\u4e00\u81f4\u6027\uff0c\u8bf7\u9075\u5b88\u4ee5\u4e0b\u6307\u5357\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_3","title":"\u8bed\u8a00\u8981\u6c42","text":"<ul> <li>\u6240\u6709\u4ee3\u7801\u5e94\u4f7f\u7528\u82f1\u6587\u7f16\u5199\uff1a\u5305\u62ec\u53d8\u91cf\u540d\u3001\u51fd\u6570\u540d\u3001\u6ce8\u91ca\u3001docstring\u3001\u63d0\u4ea4\u4fe1\u606f\u548c\u6587\u6863\u3002</li> <li>\u6211\u4eec\u7406\u89e3\u8d21\u732e\u8005\u53ef\u80fd\u6765\u81ea\u4e0d\u540c\u80cc\u666f\uff0c\u4f46\u4f7f\u7528\u82f1\u6587\u53ef\u4ee5\u8ba9\u4ee3\u7801\u5e93\u5bf9\u66f4\u5e7f\u6cdb\u7684\u7528\u6237\u4fdd\u6301\u53ef\u8bfb\u548c\u53ef\u7ef4\u62a4\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_4","title":"\u6a21\u5757\u5316\u548c\u53ef\u590d\u7528\u6027","text":"<ul> <li>\u7f16\u5199\u6a21\u5757\u5316\u3001\u53ef\u590d\u7528\u7684\u4ee3\u7801\uff1a\u51fd\u6570\u548c\u811a\u672c\u5e94\u5c3d\u91cf\u5177\u6709\u7075\u6d3b\u6027\u3002</li> <li>\u4f18\u5148\u901a\u8fc7\u53c2\u6570\u4f20\u9012\u4fe1\u606f\uff0c\u907f\u514d\u786c\u7f16\u7801\uff1a\u4f7f\u7528\u51fd\u6570\u53c2\u6570\u3001\u547d\u4ee4\u884c\u53c2\u6570\u6216\u914d\u7f6e\u6587\u4ef6\uff0c\u800c\u4e0d\u662f\u628a\u6570\u503c\u76f4\u63a5\u5199\u6b7b\u3002\u4e0d\u8fc7\uff0c\u67d0\u4e9b\u6587\u4ef6\u540d\u662f GPUMD \u548c NEP \u7a0b\u5e8f\u56fa\u5b9a\u8981\u6c42\u7684\uff0c\u4f8b\u5982 <code>train.xyz</code>\u3001<code>thermo.out</code>\uff0c\u8fd9\u7c7b\u60c5\u51b5\u53ef\u4ee5\u6309\u9700\u8981\u4fdd\u7559\u56fa\u5b9a\u6587\u4ef6\u540d\u3002</li> <li>\u793a\u4f8b\uff1a</li> </ul> <pre><code># Good: accepts parameters\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # processing logic\n}\n\n# Avoid: hardcoded values (unless required by GPUMD/NEP)\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # processing logic\n}\n</code></pre>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_5","title":"\u4ee3\u7801\u98ce\u683c","text":"<ul> <li>\u7f16\u5199\u6e05\u6670\u3001\u6613\u4e8e\u4ed6\u4eba\u7ef4\u62a4\u548c\u4fee\u6539\u7684\u4ee3\u7801\u3002</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u540d\u548c\u51fd\u6570\u540d\u3002</li> <li>\u5728\u5fc5\u8981\u65f6\u6dfb\u52a0\u6ce8\u91ca\uff0c\u89e3\u91ca\u590d\u6742\u903b\u8f91\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_6","title":"\u6587\u6863","text":"<ul> <li>\u786e\u4fdd\u5e2e\u52a9\u4fe1\u606f\uff08\u4f8b\u5982 <code>-h</code> \u53c2\u6570\uff09\u6e05\u6670\u3001\u51c6\u786e\u3002</li> <li><code>docs/</code> \u76ee\u5f55\u4e2d\u7684\u6587\u6863\u901a\u5e38\u7531\u7ef4\u62a4\u8005\u66f4\u65b0\uff0c\u56e0\u6b64\u4e00\u822c\u4e0d\u9700\u8981\u8d21\u732e\u8005\u76f4\u63a5\u4fee\u6539\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#bug","title":"\u62a5\u544a Bug","text":"<p>\u5982\u679c\u4f60\u9047\u5230 bug\uff0c\u8bf7\u901a\u8fc7 GitHub Issues \u5e2e\u52a9\u6211\u4eec\u5b9a\u4f4d\u548c\u4fee\u590d\uff1a</p> <ol> <li>\u5148\u641c\u7d22\u5df2\u6709 issue\uff0c\u786e\u8ba4\u8fd9\u4e2a bug \u662f\u5426\u5df2\u7ecf\u88ab\u62a5\u544a\u8fc7\u3002</li> <li>\u5982\u679c\u8fd8\u6ca1\u6709\u62a5\u544a\uff0c\u8bf7\u521b\u5efa\u65b0 issue\uff1aCreate an Issue</li> <li>\u8be6\u7ec6\u63cf\u8ff0\u95ee\u9898\uff0c\u5982\u679c\u53ef\u4ee5\uff0c\u8bf7\u63d0\u4f9b\u6d4b\u8bd5\u6587\u4ef6\u3002</li> </ol> <p>\u4f60\u4e5f\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u65b9\u5f0f\u8054\u7cfb\u6211\u4eec\uff1a</p> <ul> <li>QQ \u7fa4\uff1a825696376</li> <li>Email\uff1ayanzihan@westlake.edu.cn</li> <li>\u811a\u672c\u5f00\u53d1\u8005\uff1a\u8054\u7cfb\u811a\u672c\u6587\u4ef6\u5934\u90e8\u5217\u51fa\u7684\u5f00\u53d1\u8005</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_7","title":"\u63d0\u51fa\u529f\u80fd\u5efa\u8bae","text":"<p>\u6211\u4eec\u6b22\u8fce\u65b0\u7684\u529f\u80fd\u5efa\u8bae\u3002\u63d0\u51fa\u65b0\u529f\u80fd\u65f6\uff0c\u53ef\u4ee5\u6309\u4ee5\u4e0b\u65b9\u5f0f\u8fdb\u884c\uff1a</p> <ol> <li>\u5148\u641c\u7d22\u5df2\u6709 issue\uff0c\u786e\u8ba4\u662f\u5426\u5df2\u7ecf\u6709\u4eba\u63d0\u51fa\u8fc7\u7c7b\u4f3c\u5efa\u8bae\u3002</li> <li>\u521b\u5efa\u65b0\u7684\u529f\u80fd\u8bf7\u6c42\uff1aCreate a Feature Request\uff0c\u5e76\u63d0\u53ca @zhyan0603\u3002</li> <li>\u6e05\u695a\u63cf\u8ff0\u4f60\u7684\u9700\u6c42\uff0c\u5e76\u8bf4\u660e\u5b83\u4e3a\u4ec0\u4e48\u6709\u7528\u3002</li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_8","title":"\u8d21\u732e\u4ee3\u7801","text":""},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#fork","title":"Fork \u5e76\u514b\u9686\u4ed3\u5e93","text":"<ol> <li> <p>\u5728 GitHub \u7684 GPUMDkit \u4ed3\u5e93\u9875\u9762\u53f3\u4e0a\u89d2\u70b9\u51fb \"Fork\"\uff0c\u5c06\u4ed3\u5e93 fork \u5230\u81ea\u5df1\u7684\u8d26\u53f7\u4e0b\u3002</p> </li> <li> <p>\u5c06\u4f60\u7684 fork \u514b\u9686\u5230\u672c\u5730\uff1a</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>\u8bbe\u7f6e upstream remote\uff0c\u65b9\u4fbf\u548c\u4e3b\u4ed3\u5e93\u4fdd\u6301\u540c\u6b65\uff1a</li> </ol> <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_9","title":"\u521b\u5efa\u529f\u80fd\u5206\u652f","text":"<p>\u4e3a\u4f60\u7684\u4fee\u6539\u521b\u5efa\u4e00\u4e2a\u65b0\u5206\u652f\uff1a</p> <pre><code># Create and checkout a new branch from main\ngit checkout -b your-branch-name\n</code></pre> <p>\u5206\u652f\u540d\u53ef\u4ee5\u6309\u4f60\u7684\u4e60\u60ef\u547d\u540d\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_10","title":"\u8fdb\u884c\u4fee\u6539","text":"<p><code>GPUMDkit</code> \u7684\u7ed3\u6784\u5305\u62ec\uff1a</p> <ul> <li><code>gpumdkit.sh</code>\uff1a\u4e3b\u5165\u53e3 Bash \u811a\u672c\uff0c\u8d1f\u8d23\u4ea4\u4e92\u83dc\u5355\u6a21\u5f0f\u548c\u547d\u4ee4\u884c\u6a21\u5f0f\u3002</li> <li><code>Scripts/</code>\uff1a\u6309\u529f\u80fd\u5206\u7c7b\u7ec4\u7ec7\u7684 Python \u5de5\u5177\u811a\u672c\u3002</li> <li><code>plt_scripts/</code>\uff1a\u7ed8\u56fe\u811a\u672c</li> <li><code>calculators/</code>\uff1a\u8ba1\u7b97\u5de5\u5177</li> <li><code>format_conversion/</code>\uff1a\u683c\u5f0f\u8f6c\u6362\u5de5\u5177</li> <li><code>workflow/</code>\uff1a\u5de5\u4f5c\u6d41\u81ea\u52a8\u5316</li> <li><code>sample_structures/</code>\uff1a\u7ed3\u6784\u91c7\u6837\u5de5\u5177</li> <li><code>analyzer/</code>\uff1a\u5206\u6790\u5de5\u5177</li> <li><code>utils/</code>\uff1a\u5b9e\u7528\u51fd\u6570\uff0c\u5305\u62ec\u7528\u4e8e Tab \u8865\u5168\u7684 <code>completion.sh</code></li> <li><code>src/</code>\uff1a\u5305\u542b\u4ea4\u4e92\u6a21\u5f0f\u83dc\u5355\u51fd\u6570\u7684 Shell \u811a\u672c\u3002</li> <li><code>f1_format_conversions.sh</code></li> <li><code>f2_sample_structures.sh</code></li> <li><code>f3_workflows.sh</code></li> <li><code>f4_calculators.sh</code></li> <li><code>f5_analyzers.sh</code></li> <li><code>f6_plots.sh</code></li> <li><code>f7_utilities.sh</code></li> <li><code>docs/</code>\uff1a\u6587\u6863\u6587\u4ef6\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_11","title":"\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e","text":"<p>\u5982\u679c\u8981\u6dfb\u52a0\u4e00\u4e2a\u53ef\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u8bbf\u95ee\u7684\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u5728\u5408\u9002\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a</li> </ol> <pre><code># Example: Add a new format conversion script\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u5e76\u9075\u5faa\u6a21\u5757\u5316\u6307\u5357\uff1a\u63a5\u53d7\u53c2\u6570\uff0c\u907f\u514d\u4e0d\u5fc5\u8981\u7684\u786c\u7f16\u7801\u3002</p> </li> <li> <p>\u5728\u5bf9\u5e94\u7684 <code>src/</code> \u6587\u4ef6\u4e2d\u6dfb\u52a0\u5305\u88c5\u51fd\u6570\uff1a</p> </li> </ol> <pre><code># Example: Edit src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre> <p>\u6dfb\u52a0\u4e00\u4e2a\u65b0\u51fd\u6570\uff1a</p> <pre><code>function f106_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input the required parameters:\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -p \" \" converter_params\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py ${converter_params}\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre> <ol> <li>\u66f4\u65b0 <code>gpumdkit.sh</code> \u4e2d\u7684\u83dc\u5355\u663e\u793a\uff1a</li> </ol> <pre><code># Find the menu() function and update it if needed\n# Find the array_choice array and add your new choice number\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\"  # Added \"106\"\n    # ... rest of choices\n)\n</code></pre> <ol> <li>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0 case \u5206\u652f\uff1a</li> </ol> <pre><code># In the main() function, find the appropriate case statement\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n            \"101\") f101_out2xyz ;;\n            # ... existing cases ...\n            \"106\") f106_new_converter ;;  # Add your case\n        esac ;;\n    # ...\nesac\n</code></pre>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_12","title":"\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e","text":"<p>\u5982\u679c\u8981\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c flag \u6216\u5b50\u547d\u4ee4\uff1a</p> <ol> <li>\u5728\u5408\u9002\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a</li> </ol> <pre><code># Example: Add a new analyzer script\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre> <ol> <li>\u5b9e\u73b0\u529f\u80fd\uff0c\u5e76\u660e\u786e\u53c2\u6570\u8981\u6c42\uff1a</li> </ol> <pre><code># Example: Scripts/analyzer/analyze_bonds.py\nimport sys\n\ndef main():\n    if len(sys.argv) != 3:\n        print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n        print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n        sys.exit(1)\n\n    input_file = sys.argv[1]\n    cutoff = float(sys.argv[2])\n\n    # Your implementation here\n\nif __name__ == \"__main__\":\n    main()\n</code></pre> <ol> <li>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0\u547d\u4ee4\u884c flag \u5904\u7406\u903b\u8f91\uff1a</li> </ol> <pre><code># Find the command-line parsing section (after line ~167)\n# Add your new flag in the appropriate location\n\ncase $1 in\n    # ... existing cases ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py \"$2\" \"$3\"\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n            exit 1\n        fi ;;\n    # ... rest of cases ...\nesac\n</code></pre> <ol> <li>\u66f4\u65b0 <code>gpumdkit.sh</code> \u4e2d\u7684\u5e2e\u52a9\u4fe1\u606f\uff1a</li> </ol> <pre><code># Find the help_info_table() function and add your command\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... rest of help table ...\n}\n</code></pre>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#tab","title":"\u66f4\u65b0 Tab \u8865\u5168","text":"<p>\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c flag \u65f6\uff0c\u8bf7\u66f4\u65b0 Tab \u8865\u5168\u811a\u672c\uff1a</p> <pre><code># Edit Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>\u5c06\u65b0\u7684 flag \u52a0\u5165 <code>opts</code> \u53d8\u91cf\uff1a</p> <pre><code># Find the line with local opts=...\nlocal opts=\"-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ...\"\n#                                                      ^^^^^^^^^^^^^^ Add your flag here\n</code></pre> <p>\u5982\u679c\u8fd9\u4e2a flag \u63a5\u53d7\u4e8c\u7ea7\u9009\u9879\uff0c\u4f8b\u5982 <code>-plt</code> \u6216 <code>-calc</code>\uff0c\u4e5f\u9700\u8981\u4e3a\u5b83\u6dfb\u52a0\u5bf9\u5e94\u7684 <code>case</code> \u5206\u652f\uff1a</p> <pre><code>case \"$prev\" in\n    # ... existing cases ...\n    -analyze_bonds)\n        COMPREPLY=($(compgen -f -- \"$cur\"))  # Complete with filenames\n        ;;\n    # ... rest of cases ...\nesac\n</code></pre>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_13","title":"\u4ee3\u7801\u98ce\u683c\u548c\u6700\u4f73\u5b9e\u8df5","text":"<ul> <li>Shell \u811a\u672c\uff1a</li> <li>\u4f7f\u7528 <code>${variable}</code> \u8fdb\u884c\u53d8\u91cf\u5c55\u5f00\u3002</li> <li> <p>\u7f16\u5199\u6e05\u6670\u3001\u6613\u7ef4\u62a4\u7684\u4ee3\u7801\u3002</p> </li> <li> <p>Python \u811a\u672c\uff1a</p> </li> <li>\u7f16\u5199\u6e05\u6670\u3001\u53ef\u7ef4\u62a4\u7684\u4ee3\u7801\u3002</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u540d\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_14","title":"\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539","text":"<p>\u63d0\u4ea4\u8d21\u732e\u524d\uff0c\u8bf7\u8fdb\u884c\u6d4b\u8bd5\uff1a</p> <ol> <li>\u6d4b\u8bd5\u4ea4\u4e92\u6a21\u5f0f\uff08\u5982\u679c\u9002\u7528\uff09\uff1a</li> </ol> <pre><code>gpumdkit.sh\n# Navigate to your new feature and test it thoroughly\n</code></pre> <ol> <li>\u6d4b\u8bd5\u547d\u4ee4\u884c\u6a21\u5f0f\uff08\u5982\u679c\u9002\u7528\uff09\uff1a</li> </ol> <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # Test help message\n</code></pre> <ol> <li>\u6d4b\u8bd5 Tab \u8865\u5168\uff08\u5982\u679c\u4fee\u6539\u4e86 <code>completion.sh</code>\uff09\uff1a</li> </ol> <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # Should show your new flag\n</code></pre> <ol> <li> <p>\u4f7f\u7528\u4e0d\u540c\u8f93\u5165\u6d4b\u8bd5\uff1a</p> </li> <li> <p>\u6d4b\u8bd5\u5e38\u89c4\u8f93\u5165\u3002</p> </li> <li>\u6d4b\u8bd5\u8fb9\u754c\u60c5\u51b5\uff0c\u4f8b\u5982\u7a7a\u6587\u4ef6\u3001\u5927\u6587\u4ef6\u7b49\u3002</li> <li> <p>\u6d4b\u8bd5\u9519\u8bef\u5904\u7406\uff0c\u4f8b\u5982\u7f3a\u5c11\u6587\u4ef6\u3001\u53c2\u6570\u65e0\u6548\u7b49\u3002</p> </li> <li> <p>\u786e\u8ba4\u6ca1\u6709\u56de\u5f52\u95ee\u9898\uff1a\u786e\u4fdd\u5df2\u6709\u529f\u80fd\u4ecd\u7136\u53ef\u4ee5\u6b63\u5e38\u5de5\u4f5c\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_15","title":"\u63d0\u4ea4\u4fe1\u606f","text":"<p>\u63d0\u4ea4\u4fe1\u606f\u5e94\u6e05\u695a\u3001\u5177\u4f53\uff0c\u8bf4\u660e\u4f60\u4fee\u6539\u4e86\u4ec0\u4e48\u3002\u4e0d\u8981\u6c42\u4e25\u683c\u683c\u5f0f\uff0c\u4f46\u9700\u8981\u8ba9\u4ed6\u4eba\u80fd\u591f\u7406\u89e3\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#pull-request","title":"\u63a8\u9001\u5e76\u6253\u5f00 Pull Request","text":"<ol> <li>\u63d0\u4ea4\u4f60\u7684\u4fee\u6539\uff1a</li> </ol> <pre><code>git add .\ngit commit -m \"your descriptive message\"\n</code></pre> <ol> <li>\u8ba9\u4f60\u7684\u5206\u652f\u4e0e upstream <code>main</code> \u5206\u652f\u4fdd\u6301\u540c\u6b65\uff1a</li> </ol> <pre><code>git fetch upstream\ngit rebase upstream/main\n</code></pre> <ol> <li>\u5c06\u5206\u652f\u63a8\u9001\u5230\u4f60\u7684 fork\uff1a</li> </ol> <pre><code>git push origin your-branch-name\n</code></pre> <ol> <li> <p>\u6253\u5f00 Pull Request\uff1a</p> </li> <li> <p>\u8fdb\u5165 GPUMDkit repository\u3002</p> </li> <li>\u70b9\u51fb \"Pull Requests\" -&gt; \"New Pull Request\"\u3002</li> <li>\u5c06 base branch \u8bbe\u7f6e\u4e3a <code>dev</code>\uff0c\u7528\u4e8e\u4ee3\u7801\u5ba1\u67e5\u3002</li> <li>\u5c06 compare branch \u8bbe\u7f6e\u4e3a\u4f60\u7684\u529f\u80fd\u5206\u652f\u3002</li> <li> <p>\u586b\u5199 PR \u63cf\u8ff0\uff0c\u5305\u62ec\uff1a</p> <ul> <li>Title\uff1a\u7b80\u8981\u63cf\u8ff0\u4fee\u6539\u5185\u5bb9\u3002</li> <li>Description\uff1a\u8be6\u7ec6\u8bf4\u660e\u4fee\u6539\u4e86\u4ec0\u4e48\u4ee5\u53ca\u4e3a\u4ec0\u4e48\u4fee\u6539\u3002</li> <li>Testing\uff1a\u8bf4\u660e\u4f60\u5982\u4f55\u6d4b\u8bd5\u8fd9\u4e9b\u4fee\u6539\u3002</li> </ul> </li> <li> <p>\u56de\u5e94\u5ba1\u67e5\u610f\u89c1\uff1a</p> </li> <li> <p>\u63a5\u53d7\u5efa\u8bae\u548c\u5efa\u8bbe\u6027\u610f\u89c1\u3002</p> </li> <li>\u53ca\u65f6\u5b8c\u6210\u8981\u6c42\u7684\u4fee\u6539\u3002</li> <li> <p>\u5c06\u989d\u5916\u63d0\u4ea4\u63a8\u9001\u5230\u4f60\u7684\u5206\u652f\uff0c\u5b83\u4eec\u4f1a\u81ea\u52a8\u663e\u793a\u5728 PR \u4e2d\u3002</p> </li> <li> <p>\u5ba1\u67e5\u901a\u8fc7\u540e\uff1a\u7ef4\u62a4\u8005\u4f1a\u5408\u5e76\u4f60\u7684 PR\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_16","title":"\u6709\u95ee\u9898\u6216\u9700\u8981\u5e2e\u52a9\uff1f","text":"<p>\u5982\u679c\u4f60\u5bf9\u8d21\u732e\u6d41\u7a0b\u6709\u7591\u95ee\uff0c\u6216\u9700\u8981\u5e2e\u52a9\uff1a</p> <ul> <li>\u6253\u5f00\u8ba8\u8bba\uff1a\u4e00\u822c\u95ee\u9898\u53ef\u4ee5\u4f7f\u7528 GitHub Discussions\u3002</li> <li>\u5728 issue \u4e2d\u63d0\u95ee\uff1a\u4e0e\u5177\u4f53\u95ee\u9898\u76f8\u5173\u7684\u5185\u5bb9\u53ef\u4ee5\u5728\u5bf9\u5e94 issue \u4e0b\u8bc4\u8bba\u3002</li> <li>\u8054\u7cfb\u7ef4\u62a4\u8005\uff1a\u8054\u7cfb README \u4e2d\u5217\u51fa\u7684\u6838\u5fc3\u5f00\u53d1\u8005\u3002</li> </ul> <p>\u518d\u6b21\u611f\u8c22\u4f60\u4e3a <code>GPUMDkit</code> \u505a\u8d21\u732e\u3002\u4f60\u7684\u5de5\u4f5c\u4f1a\u5e2e\u52a9\u6574\u4e2a GPUMD \u548c NEP \u793e\u533a\u66f4\u597d\u5730\u4f7f\u7528\u8fd9\u4e2a\u5de5\u5177\u5305\u3002</p>"}]}
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+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"],"fields":{"title":{"boost":1000.0},"text":{"boost":1.0},"tags":{"boost":1000000.0}}},"docs":[{"location":"index.html","title":"Home","text":"\ud83d\udcda GPUMDkit Documentation <p>A practical bilingual tutorial for GPUMDkit, covering installation, command-line tools, interactive workflows, plotting, and analysis utilities.</p>"},{"location":"index.html#language","title":"Language","text":"Language Start Here Command Reference English GPUMDkit Tutorials Command Reference \u7b80\u4f53\u4e2d\u6587 GPUMDkit \u6559\u7a0b \u547d\u4ee4\u53c2\u8003"},{"location":"index.html#what-you-can-learn-here","title":"What You Can Learn Here","text":"<p>This documentation is organized as a practical tutorial rather than only a command list. New users are encouraged to start from the overview and quick start pages, then move to the topic that matches their task.</p> Topic What it Covers Quick Start Installation, environment setup, interactive mode, direct command mode Format Conversion VASP, LAMMPS, CP2K, ABACUS, CIF, extxyz, group labels, weights Sampling Uniform/random sampling, NepTrain FPS, perturbation, force-deviation selection Calculators MSD, ionic conductivity, NEP prediction, descriptors, DOAS, NEB, polarization tools Analyzers Composition checks, distance checks, filters, property range analysis Visualization NEP training plots, MD plots, transport plots, thermal transport plots, example figures Workflows Batch DFT/MD processing and active-learning style workflows <p>For complex operations, use the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>For common operations with fixed arguments, use direct command-line mode:</p> <pre><code>gpumdkit.sh -h\ngpumdkit.sh -plt -h\ngpumdkit.sh -calc -h\n</code></pre>"},{"location":"en/index.html","title":"GPUMDkit Tutorials","text":"\ud83d\udcda GPUMDkit Tutorials <p>Welcome to GPUMDkit, a command-line toolkit for GPUMD and NEP.</p>"},{"location":"en/index.html#what-it-does","title":"What it does","text":"<p>GPUMDkit helps you perform common tasks in computational materials science without writing custom scripts. It supports format conversion, structure analysis, property calculation, visualization, and batch workflows \u2014 all from one command-line tool.</p>"},{"location":"en/index.html#common-tasks","title":"Common Tasks","text":"I want to... Tutorial Install GPUMDkit and run my first command Quick Start Convert VASP, LAMMPS, CP2K, or CIF files to extxyz Format Conversion Check structure distances, filter datasets, or find outliers Analyzer Scripts Calculate MSD, ionic conductivity, or descriptors Calculator Scripts Analyze polar materials, ferroelectrics, or ABO3 systems Polar Material Analysis Plot NEP training results or thermodynamic data Plot Scripts Run batch DFT or MD simulations Workflow Scripts Select representative structures from a dataset Structure Sampling Add my own shortcuts to GPUMDkit Custom Commands"},{"location":"en/index.html#before-you-start","title":"Before you start","text":""},{"location":"en/index.html#installation","title":"Installation","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"en/index.html#dependencies","title":"Dependencies","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"en/index.html#interactive-mode","title":"Interactive mode","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>This opens a menu where you can select modules by number.</p>"},{"location":"en/index.html#cli-mode","title":"CLI mode","text":"<pre><code>gpumdkit.sh -&lt;option&gt; [args...]\n</code></pre> <p>For example:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>Use <code>gpumdkit.sh -h</code> to see all available options.</p>"},{"location":"en/index.html#module-overview","title":"Module Overview","text":"Module Menu CLI Description Format Conversion 1 <code>-out2xyz</code>, <code>-pos2exyz</code> File conversion Sample Structures 2 <code>-neptrain</code>, interactive menu Structure sampling Workflow 3 - Batch processing Calculators 4 <code>-calc &lt;type&gt;</code> Property calculations Analyzer 5 <code>-range</code>, <code>-min_dist</code> Structure analysis Visualization 6 <code>-plt &lt;type&gt;</code> Plotting tools Utilities 7 <code>-time</code>, <code>-clean</code> Utility functions"},{"location":"en/index.html#all-tutorials","title":"All Tutorials","text":"Tutorial Description Quick Start Installation and first steps Command Reference One-page CLI and menu reference Format Conversion Convert between file formats Calculator Scripts Compute material properties Analyzer Scripts Structure analysis and validation Plot Scripts Plotting and visualization Workflow Scripts Batch processing and automation Structure Sampling Structure selection methods Custom Commands User-defined GPUMDkit shortcuts Active Learning Workflow Batch active-learning workflow notes Polar Material Analysis Ferroelectric and polarization tools Contributing to GPUMDkit Development notes"},{"location":"en/index.html#links","title":"Links","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>Documentation: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"en/active_learning_workflow.html","title":"Active Learning Workflow","text":"\ud83d\udd01 Active Learning Workflow <p>This tutorial explains the steps and considerations involved in the <code>workflow_active_learning_dev.sh</code> script. The workflow is used to generate, select, and analyze molecular structures, followed by simulations and data collection.</p> <p>Script Location: <code>Scripts/workflow/</code></p>"},{"location":"en/active_learning_workflow.html#overview","title":"Overview","text":"<p>This script automates one iteration of NEP active learning. The typical workflow includes:</p> Step Action Purpose 1 Run MD simulations Generate candidate structures with current NEP model 2 Filter structures Remove unphysical configurations (short distances, large boxes) 3 Sample structures Select diverse or uncertain structures for DFT 4 Run SCF calculations Compute DFT reference energies/forces 5 NEP prediction Check model accuracy on new structures <p>Unlike menu-driven modules, this workflow is a shell script that you customize and run directly:</p> <pre><code>bash Scripts/workflow/workflow_active_learning_dev.sh\n</code></pre> <p>The sections below explain the main blocks in the script and what each part does.</p>"},{"location":"en/active_learning_workflow.html#1-slurm-directives","title":"1. SLURM Directives","text":"<pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>The SLURM directives are used to define how the job will be submitted to the cluster:</p> <ul> <li><code>#SBATCH -p</code> defines the partition, in this case, it's <code>intel-sc3</code> and <code>intel-sc3-32c</code>.</li> <li><code>#SBATCH -q</code> specifies the queue, in this case, <code>huge</code>.</li> <li><code>#SBATCH -N</code> allocates 1 node for the job.</li> <li><code>#SBATCH -J</code> names the job <code>workflow</code>.</li> <li><code>#SBATCH -o</code> defines the output log file as <code>workflow.log</code>.</li> <li><code>--ntasks-per-node=1</code> specifies that only one task should run per node.</li> </ul> <p>NOTE: If your machine does not have the SLURM environment, you can also run the script directly from the command line. For example:</p> <pre><code>nohup bash workflow_active_learning_dev.sh &amp;&gt;workflow.log &amp;\n</code></pre>"},{"location":"en/active_learning_workflow.html#2-basic-setup","title":"2. Basic Setup","text":"<pre><code>cd $SLURM_SUBMIT_DIR \n</code></pre> <p>Ensure the working directory is correct, and that all necessary files are present for the job.</p> <pre><code>source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  # Load the submit template\npython_pynep=python  # Python executable for the deprecated pynep branch if needed\n</code></pre> <ul> <li><code>GPUMDkit_path</code> is the environment variable that stores the path for the <code>GPUMDkit</code> .</li> <li><code>python_pynep</code> points to the Python environment used for the deprecated <code>pynep</code>-related branch if needed.</li> </ul>"},{"location":"en/active_learning_workflow.html#3-variable-definitions","title":"3. Variable Definitions","text":"<pre><code>work_dir=${PWD}  # Set the working directory\nprefix_name=LiF_iter01  # Prefix for calculations\nmin_dist=1.4  # Minimum atom distance\nbox_limit=13  # Simulation box limit\nmax_fp_num=50  # Maximum number of single point calculations\nsample_method=pynep  # Sampling method (options: uniform, random, pynep)\npynep_sample_dist=0.01  # Sampling distance for pynep\n</code></pre> <p>You can customize:</p> <ul> <li><code>prefix_name</code> to reflect the name of your current work.</li> <li><code>min_dist</code>, <code>box_limit</code>, and <code>max_fp_num</code> based on your own system.</li> <li><code>sample_method</code> (choose between <code>uniform</code>, <code>random</code>, or <code>pynep</code>).</li> <li><code>pynep_sample_dist</code> is the sampling distance for <code>pynep</code>.</li> </ul>"},{"location":"en/active_learning_workflow.html#4-check-required-files","title":"4. Check Required Files","text":"<pre><code>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ -f run.in ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then\n    # Check for the required files before proceeding.\nelse\n    echo \"Please put nep.in nep.txt train.xyz run.in INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.\"\n    exit 1\nfi\n</code></pre> <p>Make sure the necessary files (<code>nep.txt</code>, <code>nep.in</code>, <code>train.xyz</code>, <code>run.in</code>, <code>INCAR</code>, <code>POTCAR</code>, <code>KPOINTS</code>) are available in the working directory. If any of these are missing, the script will terminate. <code>train.xyz</code> and <code>nep.txt</code> are used for <code>pynep</code> sampling, and <code>run.in</code> is the simulation parameters of MD in the current iteration.</p>"},{"location":"en/active_learning_workflow.html#5-file-organization","title":"5. File Organization","text":"<pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <p>The script organizes the working files into two folders:</p> <ul> <li><code>00.modev</code>: For molecular dynamics simulation.</li> <li><code>common</code>: For shared resources such as <code>nep.txt</code>, <code>run.in</code>, and the structure files, etc.</li> </ul>"},{"location":"en/active_learning_workflow.html#6-molecular-dynamics-simulation-submission","title":"6. Molecular Dynamics Simulation Submission","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>After preparing the input files, the script submits an array of molecular dynamics (MD) tasks using <code>submit_gpumd_array</code>.</p>"},{"location":"en/active_learning_workflow.html#7-monitoring-task-completion","title":"7. Monitoring Task Completion","text":"<pre><code>while true; do\n    logs=$(find \"${work_dir}/00.modev/\" -type f -name log -path \"*/sample_*/log\")\n    finished_tasks_md=$(grep \"Finished running GPUMD.\" $logs | wc -l)\n    error_tasks_md=$(grep \"Error\" $logs | wc -l)\n\n    if [ \"$error_tasks_md\" -ne 0 ]; then\n        echo \"Error: MD simulation encountered an error.\"\n        exit 1\n    fi\n    if [ $finished_tasks_md -eq $sample_struct_num ]; then\n        break\n    fi\n    sleep 30\ndone\n</code></pre> <p>The script continuously checks whether all MD tasks have finished by searching for a <code>Finished running GPUMD.</code> message in the logs. If an error is encountered, the script terminates.</p>"},{"location":"en/active_learning_workflow.html#8-analysis-and-filtering","title":"8. Analysis and Filtering","text":"<pre><code>mkdir ${work_dir}/01.select\n...\n</code></pre> <p>In the <code>01.select</code> folder, all structures in the trajectory file <code>dump.xyz</code> during the MD process will be analyzed and filtered to avoid the generation of non-physical structures as much as possible. Specifically, the <code>get_min_dist.py</code>, <code>filter_structures_by_distance.py</code> and <code>filter_exyz_by_box.py</code> scripts will be employed to check whether there are situations where the distance between atoms is too close or the simulated box exceeds the limit value, and such structures will be filtered out.</p>"},{"location":"en/active_learning_workflow.html#9-sampling-methods","title":"9. Sampling Methods","text":"<pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <p>The script supports three sampling methods: <code>uniform</code>, <code>random</code>, and <code>pynep</code>. It selects structures according to the chosen method and checks if the number exceeds <code>max_fp_num</code>, ensuring the final structure count is within limits.</p>"},{"location":"en/active_learning_workflow.html#10-scf-calculations","title":"10. SCF Calculations","text":"<pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>After sampling, SCF calculations are submitted using <code>submit_vasp_array</code>. The process is similar to the MD submission, but for SCF calculations.</p>"},{"location":"en/active_learning_workflow.html#11-prediction-step","title":"11. Prediction Step","text":"<pre><code>submit_nep_prediction\n</code></pre> <p>The final step involves submitting the NEP prediction task to check the accuracy of the NEP model. </p> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/analyzer_scripts.html","title":"Analyzer Scripts","text":"\ud83d\udd0d Analyzer Scripts <p>Analyzer scripts provide structure statistics, distance checks, filters, composition analysis, outlier detection, and time estimation for extxyz datasets.</p>"},{"location":"en/analyzer_scripts.html#what-it-does","title":"What it does","text":"<p>This module helps you inspect, filter, and validate structure datasets. You can check composition, analyze property ranges, detect short contacts, filter structures by various criteria, find outliers in NEP training data, and estimate remaining simulation time.</p>"},{"location":"en/analyzer_scripts.html#before-you-start","title":"Before you start","text":"<p>Script location: <code>Scripts/analyzer/</code></p> <p>Make sure GPUMDkit is installed. See Quick Start for installation instructions.</p>"},{"location":"en/analyzer_scripts.html#overview","title":"Overview","text":"Task Command Purpose Composition <code>gpumdkit.sh -analyze_comp train.xyz</code> Group structures by chemical composition Chemical species <code>gpumdkit.sh -chem_species train.xyz</code> List species in a file Property range <code>gpumdkit.sh -range train.xyz force</code> Inspect energy/force/virial range Minimum distance <code>gpumdkit.sh -min_dist dump.xyz</code> Fast distance check without PBC Minimum distance with PBC <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> Accurate distance check with PBC Charge balance <code>gpumdkit.sh -cbc train.xyz</code> Oxidation-state balance check Distance filter <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> Remove structures with short contacts Box filter <code>gpumdkit.sh -filter_box dump.xyz 13</code> Remove structures with too-large box edges Property filter <code>gpumdkit.sh -filter_value train.xyz force 20</code> Filter by energy/force/virial threshold Pair-distance range <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> Extract structures by pair distance Outlier detection Menu 502 Find high-RMSE structures in training set Probability density <code>gpumdkit.sh -pda &lt;ref&gt; &lt;traj&gt; &lt;element&gt; &lt;interval&gt;</code> 3D probability density for diffusion channels GPUMD time <code>gpumdkit.sh -time gpumd</code> Estimate remaining GPUMD run time NEP time <code>gpumdkit.sh -time nep</code> Estimate remaining NEP training time"},{"location":"en/analyzer_scripts.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit and choose <code>5) Analyzer</code>:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>The analyzer menu is:</p> <pre><code>+------------------------------------------------------+\n|                    ANALYZER TOOLS                    |\n+------------------------------------------------------+\n| 501) Analyze composition of extxyz                   |\n| 502) Find outliers of extxyz                         |\n| 503) Analyze chemical species of extxyz              |\n| 504) Check charge balance of extxyz                  |\n| 505) Analyze energy/force/virial range               |\n| 506) Filter structures by minimum distance           |\n| 507) Get minimum interatomic distance                |\n| 508) Probability density analysis                    |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Most analyzer functions also have direct CLI shortcuts, which are listed in the overview table and in the sections below.</p>"},{"location":"en/analyzer_scripts.html#composition-analysis","title":"Composition Analysis","text":"<p><code>analyze_composition.py</code> analyzes the composition of your extxyz file and lets you export subsets.</p> <p>What it does: Groups structures by chemical composition and shows how many structures belong to each composition. You can export subsets by composition.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>Interactive mode: Choose <code>501</code> from the analyzer menu.</p> <p>Output example:</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>This is useful when <code>train.xyz</code> contains structures from different systems or different cell sizes. You can export a subset by composition from the interactive prompt.</p>"},{"location":"en/analyzer_scripts.html#chemical-species","title":"Chemical Species","text":"<p><code>analyze_chem_species.py</code> lists all unique chemical species in an extxyz file.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -chem_species train.xyz\n</code></pre>"},{"location":"en/analyzer_scripts.html#property-range-analysis","title":"Property Range Analysis","text":"<p><code>energy_force_virial_analyzer.py</code> calculates and visualizes the range of properties from an extxyz file.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <p>Supported properties: <code>energy</code>, <code>force</code>, <code>virial</code></p> <pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist    # Show histogram\n</code></pre> <p>Output example:</p> <pre><code>Force range: 0.03210566767721861 to 9.230115912468435\n</code></pre> <p>With <code>hist</code> option:</p>"},{"location":"en/analyzer_scripts.html#minimum-distance-checks","title":"Minimum Distance Checks","text":""},{"location":"en/analyzer_scripts.html#without-pbc-fast","title":"Without PBC (Fast)","text":"<p><code>get_min_dist.py</code> calculates minimum interatomic distances without considering periodic boundary conditions. Fast but may be inaccurate for periodic systems.</p> <p>What it does: Reports the minimum distance between each pair of elements in every frame, ignoring periodic boundary conditions.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>Interactive mode: Choose <code>507</code> from the analyzer menu.</p> <p>Output example:</p> <pre><code>+---------------------------+\n|   PBC ignored for speed   |\n| use -min_dist_pbc for PBC |\n+---------------------------+\nMinimum interatomic distances:\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.480     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre> <p>Notes: Use this for a quick check. For periodic systems, prefer <code>-min_dist_pbc</code> for accurate results.</p>"},{"location":"en/analyzer_scripts.html#with-pbc-accurate","title":"With PBC (Accurate)","text":"<p><code>get_min_dist_pbc.py</code> calculates minimum interatomic distances considering periodic boundary conditions.</p> <p>What it does: Reports the minimum distance between each pair of elements, accounting for periodic boundary conditions.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>Interactive mode: Choose <code>507</code> from the analyzer menu and answer <code>y</code> when asked whether to consider PBC.</p> <p>Output example:</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre>"},{"location":"en/analyzer_scripts.html#filtering-structures","title":"Filtering Structures","text":""},{"location":"en/analyzer_scripts.html#filter-by-minimum-distance","title":"Filter by Minimum Distance","text":"<p><code>filter_structures_by_distance_pbc.py</code> removes structures with any interatomic distance below a threshold.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>This removes structures with any interatomic distance below <code>1.0 \u00c5</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-box-size","title":"Filter by Box Size","text":"<p><code>filter_exyz_by_box.py</code> filters structures by box-edge length.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>This keeps structures where all box edges are below <code>13 \u00c5</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-property-value","title":"Filter by Property Value","text":"<p><code>filter_exyz_by_value.py</code> filters structures by energy, force, or virial threshold.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <p>Supported properties: <code>energy</code>, <code>force</code>, <code>virial</code></p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre> <p>This filters out structures with force components exceeding <code>20 eV/\u00c5</code> (or energy exceeding <code>5 eV/atom</code>).</p>"},{"location":"en/analyzer_scripts.html#filter-by-pair-distance-range","title":"Filter by Pair-Distance Range","text":"<p><code>filter_dist_range.py</code> extracts structures where a specific element-pair distance falls within a given range.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>This extracts structures where the Li-Li minimum distance is between <code>1.8 \u00c5</code> and <code>2.0 \u00c5</code>. Output: <code>filtered_Li_Li_1.8_2.0.xyz</code>.</p>"},{"location":"en/analyzer_scripts.html#charge-balance-check","title":"Charge Balance Check","text":"<p><code>charge_balance_check.py</code> checks the oxidation-state balance of structures.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>Output files:</p> <ul> <li><code>balanced.xyz</code> \u2014 structures with balanced charges</li> <li><code>unbalanced.xyz</code> \u2014 structures with unbalanced charges</li> <li><code>indices.txt</code> \u2014 indices of balanced structures</li> </ul> <p>This is intended for systems where common oxidation states are meaningful.</p>"},{"location":"en/analyzer_scripts.html#outlier-detection","title":"Outlier Detection","text":"<p><code>find_outliers.py</code> finds outlier structures in NEP training data based on RMSE thresholds for energy, force, and stress.</p> <p>Input files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>stress_train.out</code>, <code>train.xyz</code></p> <p>These files are generated during NEP training. The script compares DFT vs NEP predictions and identifies structures with large errors.</p> <pre><code># Interactive mode\ngpumdkit.sh    # Select: 5) Analyzer \u2192 502) Find outliers of extxyz\n</code></pre> <p>Interactive prompts:</p> <pre><code>Enter energy RMSE threshold (meV/atom): 1\nEnter force RMSE threshold (meV/\u00c5): 60\nEnter stress RMSE threshold (GPa): 0.03\n</code></pre> <p>Output files:</p> <ul> <li><code>selected.xyz</code> \u2014 structures exceeding the RMSE thresholds (outliers)</li> <li><code>remained.xyz</code> \u2014 structures within the thresholds</li> <li><code>selected_remained.png</code> \u2014 comparison plot</li> </ul> <p>Use case: After NEP training, use this to identify problematic structures that contribute most to the error. Remove or improve these structures to enhance the training set.</p>"},{"location":"en/analyzer_scripts.html#time-estimation","title":"Time Estimation","text":""},{"location":"en/analyzer_scripts.html#gpumd-remaining-time","title":"GPUMD Remaining Time","text":"<p><code>time_consuming_gpumd.sh</code> estimates the remaining time for a GPUMD simulation.</p> <p>Input files: <code>run.in</code>, <code>thermo.out</code> (in the current GPUMD working directory)</p> <pre><code>gpumdkit.sh -time gpumd\n</code></pre> <p>Output example:</p> <pre><code>----------------- System Information ----------------\ntotal frames: 1050000\n-----------------------------------------------------\nCurrent Frame  Speed (steps/s)   Total Time       Time Left       Estimated End\n-------------   -------------   -------------   -------------   -----------------\n    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04\n    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56\n</code></pre>"},{"location":"en/analyzer_scripts.html#nep-remaining-time","title":"NEP Remaining Time","text":"<p><code>time_consuming_nep.sh</code> estimates the remaining time for NEP training.</p> <p>Input files: <code>loss.out</code> (in the current NEP working directory)</p> <pre><code>gpumdkit.sh -time nep\n</code></pre> <p>Output example:</p> <pre><code>+-----------------+-----------+-----------------+---------------------+\n|       Step      | Time Diff |    Time Left    |    Finish Time      |\n+-----------------+-----------+-----------------+---------------------+\n| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |\n| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |\n| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |\n+-----------------+-----------+-----------------+---------------------+\n</code></pre>"},{"location":"en/analyzer_scripts.html#probability-density-analysis","title":"Probability Density Analysis","text":"<p><code>probability_density_analysis.py</code> calculates 3D probability density of mobile ions for diffusion channel analysis.</p> <p>Input files: Reference structure (POSCAR), trajectory file (extxyz)</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n</code></pre> <p>Arguments:</p> Argument Meaning <code>LLZO.vasp</code> Reference structure (POSCAR format) <code>dump.xyz</code> Trajectory file (extxyz format) <code>Li</code> Target mobile species <code>0.25</code> Grid interval for the probability density (\u00c5) <p>Output: <code>probability_density_0.25.vasp</code> \u2014 probability density grid in VASP format for visualization with VESTA or similar tools.</p> <p>Visualization suggestions:</p> <ol> <li>Open <code>probability_density_0.25.vasp</code> in VESTA</li> <li>Use \"Edit \u2192 Data \u2192 Volumetric Data\" to adjust isosurface levels</li> <li>Color the probability density by value to highlight preferred diffusion pathways</li> <li>Overlay with the crystal structure for context</li> </ol>"},{"location":"en/analyzer_scripts.html#example-workflows","title":"Example Workflows","text":""},{"location":"en/analyzer_scripts.html#structure-quality-check","title":"Structure Quality Check","text":"<pre><code># 1. Check composition\ngpumdkit.sh -analyze_comp train.xyz\n\n# 2. Check energy/force range\ngpumdkit.sh -range train.xyz force hist\n\n# 3. Check minimum distances\ngpumdkit.sh -min_dist_pbc train.xyz\n\n# 4. Find outliers (after NEP training)\n# Interactive: 5) Analyzer \u2192 502\n</code></pre>"},{"location":"en/analyzer_scripts.html#structure-filtering-pipeline","title":"Structure Filtering Pipeline","text":"<pre><code># 1. Filter by minimum distance\ngpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n\n# 2. Filter by box size\ngpumdkit.sh -filter_box filtered_dist_pbc.xyz 13\n\n# 3. Filter by force threshold\ngpumdkit.sh -filter_value filtered_box.xyz force 20\n</code></pre>"},{"location":"en/analyzer_scripts.html#diffusion-channel-analysis","title":"Diffusion Channel Analysis","text":"<pre><code># 1. Calculate probability density\ngpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n\n# 2. Visualize with VESTA\n# Open probability_density_0.25.vasp\n</code></pre>"},{"location":"en/calculator_scripts.html","title":"Calculator Scripts","text":"\ud83e\uddee Calculator Scripts <p>The calculator module contains scripts for computing properties from MD trajectories, NEP models, and structure files.</p> <p>Script Location: <code>Scripts/calculators/</code></p>"},{"location":"en/calculator_scripts.html#overview","title":"Overview","text":"Task Command Main Input Ionic conductivity <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>, <code>thermo.out</code>, <code>model.xyz</code> MSD from trajectory <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz trajectory NEP prediction <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP model NEP descriptors <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP model DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP model NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> initial/final structures Minimization <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> structure + NEP model Neighbor list <code>gpumdkit.sh -calc nlist ...</code> see Polar Material Analysis Displacement <code>gpumdkit.sh -calc disp ...</code> see Polar Material Analysis Average structure <code>gpumdkit.sh -calc avg-struct ...</code> see Polar Material Analysis Octahedral tilt <code>gpumdkit.sh -calc oct-tilt ...</code> see Polar Material Analysis ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 ...</code> see Polar Material Analysis <p>For a full command list:</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>The command-line help table looks like:</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>In interactive mode, choose <code>4) Calculators</code>. The menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"en/calculator_scripts.html#ionic-conductivity","title":"Ionic Conductivity","text":"<p><code>calc_ion_conductivity.py</code> calculates ionic diffusivity and conductivity from <code>msd.out</code>.</p>"},{"location":"en/calculator_scripts.html#required-and-optional-files","title":"Required and Optional Files","text":"File Role <code>msd.out</code> Required MSD data <code>thermo.out</code> Optional, used for automatic temperature detection <code>model.xyz</code> Optional, used for volume and ion-count detection <code>run.in</code> Optional, used to detect replication"},{"location":"en/calculator_scripts.html#usage","title":"Usage","text":"<pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>From interactive mode, choose <code>401</code>. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>If automatic files are missing, the script will ask for temperature, volume, and ion count interactively.</p> <p>Interactive prompts in manual mode look like:</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre>"},{"location":"en/calculator_scripts.html#example-output","title":"Example Output","text":"<pre><code>Diffusivity (D):\n  D_x: 4.153e-07 cm^2/s\n  D_y: 4.174e-07 cm^2/s\n  D_z: 2.610e-07 cm^2/s\n  D_total: 3.646e-07 cm^2/s\n------------------------------\nIonic Conductivity:\n  Sigma_x: 2.576e-02 mS/cm\n  Sigma_y: 2.589e-02 mS/cm\n  Sigma_z: 1.619e-02 mS/cm\n  Sigma_total: 2.261e-02 mS/cm\n</code></pre>"},{"location":"en/calculator_scripts.html#mean-square-displacement","title":"Mean Square Displacement","text":"<p><code>calc_msd.py</code> computes MSD directly from an extxyz trajectory.</p> <pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>From interactive mode, choose <code>412</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>Li</code> target mobile species <code>10</code> time interval between frames, in fs <code>5000</code> optional maximum correlation steps <p>Output:</p> <ul> <li><code>msd.out</code></li> </ul> <p>The beginning of <code>msd.out</code> is a text table with time and MSD columns. After generating it, use the plot commands below.</p> <p>You can then plot:</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-property-prediction","title":"NEP Property Prediction","text":"<p><code>calc_properties_with_nep.py</code> calculates energy, force, and stress for structures using a NEP model.</p> <p>Dependency: <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>Use this function to run predictions with a trained NEP model. For best results, validate model quality on your target structures before relying on the output.</p> <p>Tip: Before prediction, you may want to clean the extxyz metadata:</p> <pre><code>gpumdkit.sh -clean_xyz train.xyz clean_train.xyz\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-descriptors","title":"NEP Descriptors","text":"<p><code>calc_descriptors.py</code> extracts NEP descriptors for a selected element.</p> <pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>Use cases:</p> <ul> <li>visualize chemical environments with PCA/UMAP;</li> <li>compare training and candidate structures;</li> <li>inspect whether new data expands descriptor space.</li> </ul> <p>Plot descriptors with:</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/calculator_scripts.html#density-of-atomistic-states","title":"Density of Atomistic States","text":"<p><code>calc_doas.py</code> calculates density of atomistic states (DOAS), following the idea proposed by Wang et al..</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>The script:</p> <ol> <li>reads all structures;</li> <li>relaxes each structure with a NEP calculator;</li> <li>extracts per-atom energies;</li> <li>groups atomic energies by element;</li> <li>writes the grouped values to the output file.</li> </ol> <p>For very large systems, running minimization and atomistic-energy extraction directly in GPUMD can be more efficient.</p>"},{"location":"en/calculator_scripts.html#neb-with-a-nep-model","title":"NEB with a NEP Model","text":"<pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>This runs a NEB calculation with <code>9</code> intermediate images. During execution, the script asks how atoms should be fixed:</p> <ul> <li><code>none</code>: no atoms fixed;</li> <li><code>index</code>: fix atoms by index;</li> <li><code>element</code>: fix all atoms of one element;</li> <li><code>position</code>: fix atoms inside a coordinate range.</li> </ul>"},{"location":"en/calculator_scripts.html#structure-minimization","title":"Structure Minimization","text":"<p><code>calc_minimize.py</code> minimizes a structure using a NEP model through <code>calorine</code>.</p> <p>Dependency: <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input structure, POSCAR/CONTCAR or extxyz <code>nep.txt</code> NEP model <code>0.01</code> optional force convergence threshold in eV/Ang <code>1000</code> optional maximum optimization steps <p>Output:</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"en/calculator_scripts.html#rdf-calculation-with-ovito","title":"RDF Calculation with OVITO","text":"<p><code>rdf_calculator_ovito.py</code> calculates radial distribution function using OVITO's analysis tools.</p> <p>Dependency: OVITO</p> <pre><code>pip install ovito\n</code></pre> <p>Input file: Structure file (single frame or trajectory)</p> <pre><code>python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400\n</code></pre> <p>Parameters:</p> Argument Meaning <code>trajectory.xyz</code> Input structure file <code>6.0</code> Maximum distance for RDF calculation (\u00c5) <code>400</code> Number of histogram bins <p>Visualization:</p> <pre><code>gpumdkit.sh -plt rdf\n</code></pre> <p>Note: It is recommended to use the <code>compute_rdf</code> command directly in GPUMD when possible.</p>"},{"location":"en/calculator_scripts.html#ferroelectric-and-polar-material-tools","title":"Ferroelectric and Polar Material Tools","text":"<p>Options <code>406\u2013410</code> cover perovskite and polar-material analysis: neighbor lists, local displacements, averaged structures, octahedral tilt, and ABO3 polarization. These tools are built on <code>ferrodispcalc</code>.</p> <p>Dependency:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>For complete argument lists, real-world workflow examples (PbTiO3 phase transition, PTO/STO superlattice topology, etc.), see Polar Material Analysis.</p>"},{"location":"en/command_reference.html","title":"Command Reference","text":"\ud83d\udccb Command Reference <p>This page lists the stable GPUMDkit command-line shortcuts. Interactive mode is available for workflows with many choices.</p> <p>The source table is maintained in <code>docs/command_reference.tsv</code>.</p>"},{"location":"en/command_reference.html#gpumdkitsh-h-output","title":"<code>gpumdkit.sh -h</code> Output","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |\n| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/command_reference.html#main","title":"Main","text":"Command Syntax Description <code>-h</code> <code>gpumdkit.sh -h</code> Show general help <code>-update</code> <code>gpumdkit.sh -update</code> Update GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> Clean extra files in the current directory"},{"location":"en/command_reference.html#format-conversion","title":"Format Conversion","text":"Command Syntax Description <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR to extxyz, shell version <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR to extxyz, Python version <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K output to xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR to extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF to POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF to extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR to extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz frames to POSCAR files <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR to LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump to extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory to extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> Replicate by cell factors <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> Replicate toward a target atom count <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> Add GPUMD group labels <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> Add structure weights <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> Extract one frame <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> Remove extra extxyz properties <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> Extract frames by fractional range"},{"location":"en/command_reference.html#calculators","title":"Calculators","text":"Command Syntax Description <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> Ionic conductivity <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP property prediction <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP descriptors <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> Density of atomistic states <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> NEB with a NEP model <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> Structure minimization <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> MSD from trajectory <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> Neighbor lists <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> Displacements <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> Averaged structure <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> Octahedral tilt <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 local polarization"},{"location":"en/command_reference.html#analyzers","title":"Analyzers","text":"Command Syntax Description <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> Property range analysis <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> Composition analysis <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> Chemical species list <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> Charge-balance check <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> Minimum distance without PBC <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> Minimum distance with PBC <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> Distance filtering <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> PBC-aware distance filtering <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> Box-edge filtering <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> Property threshold filtering <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> Element-pair distance range filtering <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> Probability density analysis"},{"location":"en/command_reference.html#visualization","title":"Visualization","text":"<p>Use:</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>Common types include <code>train</code>, <code>prediction</code>, <code>thermo</code>, <code>msd</code>, <code>sdc</code>, <code>rdf</code>, <code>emd</code>, <code>nemd</code>, <code>hnemd</code>, <code>pdos</code>, and <code>plane-grid</code>.</p>"},{"location":"en/command_reference.html#utilities","title":"Utilities","text":"Command Syntax Description <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> Monitor GPUMD or NEP progress <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> Modify NEP models interactively <code>-pynep</code> <code>gpumdkit.sh -pynep</code> Deprecated PyNEP FPS sampling"},{"location":"en/contributing_to_gpumdkit.html","title":"Contributing to GPUMDkit","text":"\ud83e\udd1d Contributing to GPUMDkit <p>Thank you for your interest in contributing to GPUMDkit! We appreciate your time and effort in helping improve this toolkit.</p> <p> English   \u00a0\u00b7\u00a0   \u7b80\u4f53\u4e2d\u6587 </p> <p><code>GPUMDkit</code> is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.</p> <p>Note: The authoritative version of this document is <code>CONTRIBUTING.md</code> in the repository root. This tutorial page mirrors its content.</p>"},{"location":"en/contributing_to_gpumdkit.html#table-of-contents","title":"Table of Contents","text":"<ul> <li>Development Restrictions and Guidelines</li> <li>Reporting Bugs</li> <li>Suggesting Features</li> <li>Contributing Code</li> <li>Fork and Clone the Repository</li> <li>Create a Feature Branch</li> <li>Making Changes<ul> <li>Interactive Mode Contributions</li> <li>Command-Line Mode Contributions</li> <li>Updating Tab Completion</li> </ul> </li> <li>Code Style and Best Practices</li> <li>Testing Your Changes</li> <li>Commit Messages</li> <li>Push and Open a Pull Request</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#development-restrictions-and-guidelines","title":"Development Restrictions and Guidelines","text":"<p>To maintain code quality and consistency across the project, please adhere to these guidelines:</p>"},{"location":"en/contributing_to_gpumdkit.html#language-requirements","title":"Language Requirements","text":"<ul> <li>All code should be written in English: This includes variable names, function names, comments, docstrings, commit messages, and documentation.</li> <li>While we understand that contributors come from diverse backgrounds, using English ensures that the codebase is accessible to the widest possible audience.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#modularity-and-reusability","title":"Modularity and Reusability","text":"<ul> <li>Write modular and reusable code: Functions and scripts should be designed with flexibility in mind.</li> <li>Prefer passing parameters over hardcoding values: Use function arguments, command-line parameters, or configuration files instead of hardcoded values. However, some filenames are required to be fixed by GPUMD and NEP programs (e.g., <code>train.xyz</code>, <code>thermo.out</code>), and these can be hardcoded as needed.</li> <li>Example:    <pre><code># Good: accepts parameters\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # processing logic\n}\n\n# Avoid: hardcoded values (unless required by GPUMD/NEP)\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # processing logic\n}\n</code></pre></li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#code-style","title":"Code Style","text":"<ul> <li>Write code that is clear and easy for others to maintain and modify.</li> <li>Use meaningful variable and function names.</li> <li>Add comments where necessary to explain complex logic.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#documentation","title":"Documentation","text":"<ul> <li>Ensure that help messages (e.g., <code>-h</code> flags) are clear and accurate.</li> <li>Tutorial documentation lives in <code>docs/tutorials/en/</code> (English) and <code>docs/tutorials/zh/</code> (Chinese).   If you add a new feature, consider updating the relevant tutorial page.</li> <li>After editing tutorial markdown files, rebuild the HTML with <code>mkdocs build -f docs/mkdocs.yml</code>.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#reporting-bugs","title":"Reporting Bugs","text":"<p>If you encounter a bug, please help us fix it by reporting it through GitHub Issues:</p> <ol> <li>Search existing issues to see if the bug has already been reported.</li> <li>Open a new issue if it hasn't been reported yet: Create an Issue</li> <li>Describe the problem in detail and provide test files if possible.</li> </ol> <p>You can also reach out to us through: - QQ Group: 825696376 - Email: yanzihan@westlake.edu.cn - Script Developer: Contact the developer listed in the script header</p>"},{"location":"en/contributing_to_gpumdkit.html#suggesting-features","title":"Suggesting Features","text":"<p>We welcome feature suggestions! To propose a new feature:</p> <ol> <li>Search existing issues to see if someone has already suggested it.</li> <li>Open a new feature request: Create a Feature Request and mention @zhyan0603</li> <li>Describe what you need clearly and explain how it would be useful.</li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#contributing-code","title":"Contributing Code","text":""},{"location":"en/contributing_to_gpumdkit.html#fork-and-clone-the-repository","title":"Fork and Clone the Repository","text":"<ol> <li> <p>Fork the repository on GitHub by clicking the \"Fork\" button at the top right of the repository page.</p> </li> <li> <p>Clone your fork to your local machine:</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>Set up the upstream remote to keep your fork in sync:    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#create-a-feature-branch","title":"Create a Feature Branch","text":"<p>Create a new branch for your changes:</p> <pre><code># Create and checkout a new branch from main\ngit checkout -b your-branch-name\n</code></pre> <p>Name your branch as you prefer.</p>"},{"location":"en/contributing_to_gpumdkit.html#making-changes","title":"Making Changes","text":"<p>The structure of <code>GPUMDkit</code> consists of: - <code>gpumdkit.sh</code>: Main entry point (Bash script) handling both interactive menu mode and command-line mode - <code>install.sh</code>: Installation script that sets up environment variables and shell configuration - <code>Scripts/</code>: Python and Bash implementation scripts organized by functionality   - <code>plt_scripts/</code>: Plotting scripts   - <code>calculators/</code>: Calculation utilities   - <code>format_conversion/</code>: Format conversion tools   - <code>workflow/</code>: Workflow automation   - <code>sample_structures/</code>: Structure sampling utilities   - <code>analyzer/</code>: Analysis tools   - <code>utils/</code>: Utility functions (including <code>completion.sh</code> for tab completion) - <code>src/</code>: Shell scripts containing menu functions for interactive mode   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>skills/</code>: AI agent skill definitions (SKILL.md files for opencode/Claude Code integration) - <code>docs/</code>: Documentation files   - <code>tutorials/en/</code> and <code>tutorials/zh/</code>: Bilingual tutorial pages   - <code>mkdocs.yml</code>: MkDocs configuration for building tutorial HTML   - <code>command_reference.tsv</code>: Machine-readable command reference   - <code>htmls/</code>: Generated HTML output from MkDocs</p>"},{"location":"en/contributing_to_gpumdkit.html#interactive-mode-contributions","title":"Interactive Mode Contributions","text":"<p>To add a new feature accessible through the interactive menu:</p> <ol> <li>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:</li> </ol> <pre><code># Example: Add a new format conversion script\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>Implement your functionality following the modularity guidelines (accept parameters, avoid hardcoding).</p> </li> <li> <p>Add a wrapper function in the corresponding <code>src/</code> file:    <pre><code># Example: Edit src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>Add a new function:    <pre><code>function f111_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input &lt;required_param1&gt; &lt;required_param2&gt;\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -r -a converter_args\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py \"${converter_args[@]}\"\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>Update the menu display in <code>gpumdkit.sh</code>:    <pre><code># Find the menu() function and update it if needed\n# Find the array_choice array and add your new choice number\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\" \"107\" \"108\" \"109\" \"110\" \"111\"  # Added \"111\"\n    # ... rest of choices\n)\n</code></pre></p> </li> <li> <p>Add the case statement in <code>gpumdkit.sh</code>:    <pre><code># In the main() function, find the appropriate case statement\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n             \"101\") f101_out2xyz ;;\n             # ... existing cases ...\n             \"111\") f111_new_converter ;;  # Add your case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#command-line-mode-contributions","title":"Command-Line Mode Contributions","text":"<p>To add a new command-line flag or subcommand:</p> <ol> <li> <p>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:    <pre><code># Example: Add a new analyzer script\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>Implement your functionality with clear parameter requirements:    <pre><code># Example: Scripts/analyzer/analyze_bonds.py\nimport sys\n\nif len(sys.argv) != 3:\n    print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n    print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n    sys.exit(1)\n\ninput_file = sys.argv[1]\ncutoff = float(sys.argv[2])\n\n# Your implementation here\n</code></pre></p> </li> </ol> <p>Note: GPUMDkit Python scripts are designed to run directly (not imported as modules). You may use a <code>main()</code> function with <code>if __name__ == \"__main__\":</code> guard if you prefer, but it is not required. Most existing scripts execute at module level.</p> <ol> <li> <p>Add the command-line flag handler in <code>gpumdkit.sh</code>:    <pre><code># Find the command-line parsing section (the large \"case $1 in\" block)\n# Add your new flag in the appropriate location\n\ncase $1 in\n    # ... existing cases ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ \"$2\" != \"-h\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py $2 $3\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n        fi ;;\n    # ... rest of cases ...\nesac\n</code></pre></p> </li> <li> <p>Update the help information in <code>gpumdkit.sh</code>:    <pre><code># Find the help_info_table() function and add your command\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... rest of help table ...\n}\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#updating-tab-completion","title":"Updating Tab Completion","text":"<p>When adding new command-line flags, update the tab completion script:</p> <pre><code># Edit Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>Add your new flag to the <code>opts</code> variable: <pre><code># Find the line with local opts=...\nlocal opts=\"-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...\"\n#                                                        Add your flag here\n</code></pre></p> <p>If your flag requires file arguments, add it to the existing file-completion case: <pre><code># Find the case for file-requiring flags and add yours with |\n-out2xyz|-out2exyz|-...|-your_new_flag)\n    COMPREPLY=($(compgen -f -- \"$cur\")) ;;\n</code></pre></p> <p>If your flag accepts secondary options (like <code>-plt</code> or <code>-calc</code>), add a new case: <pre><code>case \"$prev\" in\n    # ... existing cases ...\n    -your_new_flag)\n        COMPREPLY=($(compgen -W \"option1 option2 option3\" -- \"$cur\")) ;;\n    # ... rest of cases ...\nesac\n</code></pre></p>"},{"location":"en/contributing_to_gpumdkit.html#code-style-and-best-practices","title":"Code Style and Best Practices","text":"<ul> <li>Shell Scripts:</li> <li>Use <code>${variable}</code> for variable expansion</li> <li>Use <code>[ ! -z \"$var\" ]</code> for non-empty checks (project convention)</li> <li>Interactive functions should follow the banner format:     <pre><code>echo \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/&lt;category&gt;        |\"\necho \" | Script: &lt;script_name&gt;.py                        |\"\necho \" | Developer: &lt;Name&gt; (&lt;email&gt;)                     |\"\necho \" &gt;-------------------------------------------------&lt;\"\n</code></pre></li> <li>Use <code>read -r -a varname</code> for multi-word input, then pass with <code>\"${varname[@]}\"</code></li> <li> <p>Shell scripts in <code>src/</code> should start with a file header block:     <pre><code># ============================================================\n# GPUMDkit &lt;module name&gt; module\n# Repository: https://github.com/zhyan0603/GPUMDkit\n# Author: &lt;Name&gt; (&lt;email&gt;)\n# ============================================================\n</code></pre></p> </li> <li> <p>Python Scripts:</p> </li> <li>Write clear, maintainable code</li> <li>Use meaningful variable names</li> <li>Use <code>sys.argv</code> for argument parsing (consistent with most existing scripts)</li> <li>Provide clear usage messages with <code>print(\"Usage: ...\")</code> and <code>print(\"Example: ...\")</code></li> <li>If your script uses heavy/special packages (<code>NepTrain</code>, <code>calorine</code>, <code>dpdata</code>), add a     <code>print_dependency_notice()</code> function to inform users about citation recommendations</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#testing-your-changes","title":"Testing Your Changes","text":"<p>Before submitting your contribution, run the relevant validation commands:</p> <pre><code># Shell syntax checks (always run these)\nbash -n gpumdkit.sh\nfind src Scripts -name '*.sh' -exec bash -n {} +\n\n# Python syntax checks (for modified Python files)\npython3 -m py_compile path/to/modified_script.py\n\n# MkDocs build (if you modified documentation)\nmkdocs build -f docs/mkdocs.yml\n\n# Check for trailing whitespace issues\ngit diff --check\n</code></pre> <p>Then test functionality:</p> <ol> <li> <p>Test interactive mode (if applicable):    <pre><code>gpumdkit.sh\n# Navigate to your new feature and test it thoroughly\n</code></pre></p> </li> <li> <p>Test command-line mode (if applicable):    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # Test help message\n</code></pre></p> </li> <li> <p>Test tab completion (if you modified <code>completion.sh</code>):    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # Should show your new flag\n</code></pre></p> </li> <li> <p>Test with various inputs:</p> </li> <li>Test with typical inputs</li> <li>Test with edge cases (empty files, large files, etc.)</li> <li> <p>Test error handling (missing files, invalid parameters)</p> </li> <li> <p>Verify no regressions: Ensure existing functionality still works correctly.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#commit-messages","title":"Commit Messages","text":"<p>Write clear, descriptive commit messages that explain what you changed. There are no strict format requirements - just make sure your message is understandable.</p>"},{"location":"en/contributing_to_gpumdkit.html#push-and-open-a-pull-request","title":"Push and Open a Pull Request","text":"<ol> <li> <p>Commit your changes:    <pre><code>git add .\ngit commit -m \"your descriptive message\"\n</code></pre></p> </li> <li> <p>Keep your branch updated with the latest <code>dev</code> branch:    <pre><code>git fetch origin\ngit rebase origin/dev\n</code></pre></p> </li> <li> <p>Push your branch to your fork:    <pre><code>git push origin your-branch-name\n</code></pre></p> </li> <li> <p>Open a Pull Request:</p> </li> <li>Go to the GPUMDkit repository</li> <li>Click \"Pull Requests\" \u2192 \"New Pull Request\"</li> <li>Set the base branch to <code>dev</code> for code review</li> <li>Set the compare branch to your feature branch</li> <li> <p>Fill in the PR description with:</p> <ul> <li>Title: Brief description of changes</li> <li>Description: Detailed explanation of what changed and why</li> <li>Testing: Describe how you tested the changes</li> </ul> </li> <li> <p>Respond to review feedback:</p> </li> <li>Be open to suggestions and constructive criticism</li> <li>Make requested changes promptly</li> <li> <p>Push additional commits to your branch (they'll automatically appear in the PR)</p> </li> <li> <p>After approval: A maintainer will merge your PR.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#questions-or-need-help","title":"Questions or Need Help?","text":"<p>If you have questions about contributing or need help with your contribution:</p> <ul> <li>Open a discussion: Use GitHub Discussions for general questions</li> <li>Ask in an issue: Comment on related issues for specific questions</li> <li>Contact maintainers: Reach out to the core developers listed in the README</li> </ul> <p>Thank you again for contributing to <code>GPUMDkit</code>! Your efforts help make this toolkit better for the entire GPUMD and NEP community.</p>"},{"location":"en/custom_commands.html","title":"Custom Commands","text":"\ud83d\udd27 Custom Commands <p>GPUMDkit allows users to extend the command-line interface with custom commands. Define shortcuts for frequently used scripts in your ~/.gpumdkit.in file.</p>"},{"location":"en/custom_commands.html#setup","title":"Setup","text":"<p>Create or edit <code>~/.gpumdkit.in</code>: <pre><code>vi ~/.gpumdkit.in\n</code></pre></p> <p>Define custom functions with the <code>custom_</code> prefix.</p>"},{"location":"en/custom_commands.html#examples","title":"Examples","text":""},{"location":"en/custom_commands.html#simple-greeting","title":"Simple Greeting","text":"<p>Write the following codes in your <code>~/.gpumdkit.in</code> </p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>and run <code>gpumdkit.sh -hello</code>, you will see:</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"en/custom_commands.html#command-with-required-arguments","title":"Command with Required Arguments","text":"<p>For the following function:</p> <pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>and you can add an argument, for example: <code>gpumdkit.sh -greet Zihan</code>, then you will see:</p> <pre><code>Hello, Zihan!\n</code></pre> <p>Passing arguments: Use <code>\"$@\"</code> to forward all arguments safely. Use <code>${@:1}</code> when you need to refer to arguments starting from the first one. </p>"},{"location":"en/custom_commands.html#calling-an-external-script","title":"Calling an External Script","text":"<p>If you want to call an external script like <code>gpumdkit.sh</code>.</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>and run <code>gpumdkit.sh -nepanalyse</code></p>"},{"location":"en/custom_commands.html#advanced-examples","title":"Advanced Examples","text":""},{"location":"en/custom_commands.html#batch-processing","title":"Batch Processing","text":"<p>Process multiple files: <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -batch_plot dir1 dir2 dir3</code></p>"},{"location":"en/custom_commands.html#analysis-pipeline","title":"Analysis Pipeline","text":"<p>Combine multiple operations: <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -analyze_training train.xyz</code></p>"},{"location":"en/custom_commands.html#custom-workflow","title":"Custom Workflow","text":"<p>Automate common workflow: <pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    # Convert VASP outputs\n    gpumdkit.sh -out2xyz ./\n\n    # Filter outliers\n    gpumdkit.sh -filter_value train.xyz force 30\n\n    # Check quality\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -prep_training</code></p>"},{"location":"en/custom_commands.html#tips","title":"Tips","text":"<ul> <li>Use descriptive names: <code>custom_analyze_nep_training</code> is clearer than <code>custom_ant</code></li> <li>Add help messages: Echo usage info when no arguments provided</li> <li>Error handling: Check if required files exist before processing</li> <li>Forward arguments safely: Use <code>\"$@\"</code> to preserve spaces and special characters</li> </ul> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/format_conversion.html","title":"Format Conversion","text":"\ud83d\udd04 Format Conversion <p>GPUMDkit contains utilities for converting common atomistic simulation formats, with extra handling for metadata such as group labels, weights, and frame extraction.</p>"},{"location":"en/format_conversion.html#what-it-does","title":"What it does","text":"<p>This module converts structure and trajectory files between common formats used in computational materials science. It supports VASP, LAMMPS, CP2K, ABACUS, CIF, ASE trajectories, and extxyz. It also provides tools for adding group labels, weights, extracting frames, and replicating structures.</p>"},{"location":"en/format_conversion.html#before-you-start","title":"Before you start","text":"<p>Script location: <code>Scripts/format_conversion/</code></p> <p>Make sure GPUMDkit is installed. See Quick Start for installation instructions.</p>"},{"location":"en/format_conversion.html#supported-formats","title":"Supported formats","text":"<p>The format conversion module covers:</p> <ul> <li>VASP: <code>POSCAR</code>, <code>CONTCAR</code>, <code>OUTCAR</code>, <code>XDATCAR</code></li> <li>LAMMPS: data files and dump trajectories</li> <li>CP2K: output logs, position, force, and cell files</li> <li>ABACUS: SCF/MD logs</li> <li>CIF: crystallographic structure files</li> <li>ASE trajectory: <code>.traj</code></li> <li>extxyz: a common structure format for GPUMD and NEP</li> </ul>"},{"location":"en/format_conversion.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>1) Format Conversion\n</code></pre> <p>The format conversion menu is:</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"en/format_conversion.html#what-each-entry-does","title":"What Each Entry Does","text":"Entry Function When to Use <code>101</code> VASP OUTCAR to extxyz, shell version convert VASP calculation directories <code>102</code> MTP cfg to extxyz convert MTP training data <code>103</code> CP2K to extxyz choose CP2K log/inp route or pos/frc/cell route <code>104</code> ABACUS to extxyz convert ABACUS SCF or MD output <code>105</code> extxyz to POSCAR write each extxyz frame as a POSCAR-style file <code>106</code> add group labels add atom group labels for GPUMD-related workflows <code>107</code> add weights assign training weights in extxyz <code>108</code> extract frame export one frame from an extxyz trajectory <code>109</code> clean XYZ info remove extra extxyz properties <code>110</code> replicate structure build supercells by factors or target atom count <code>out2exyz</code> OUTCAR to extxyz, Python version alternative VASP OUTCAR converter <code>pos2exyz</code> POSCAR to extxyz convert a single structure <code>cif2pos</code> CIF to POSCAR prepare VASP input from CIF <code>cif2exyz</code> CIF to extxyz prepare GPUMDkit input from CIF <code>xdat2exyz</code> XDATCAR to extxyz convert VASP MD trajectory <code>pos2lmp</code> POSCAR to LAMMPS data prepare LAMMPS input <code>lmp2exyz</code> LAMMPS dump to extxyz convert LAMMPS trajectory <code>traj2exyz</code> ASE traj to extxyz convert ASE trajectory"},{"location":"en/format_conversion.html#quick-command-reference","title":"Quick Command Reference","text":"Source Target Command OUTCAR directory extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR directory extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> extxyz POSCAR files <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"en/format_conversion.html#common-examples","title":"Common Examples","text":""},{"location":"en/format_conversion.html#convert-vasp-calculations-to-extxyz","title":"Convert VASP calculations to extxyz","text":"<p>What it does: Searches a directory for VASP OUTCAR files and converts them into a single extxyz file for NEP training or analysis.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>The shell version searches the target directory and converts VASP results into an extxyz file. If you prefer the Python implementation:</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>Interactive mode: Choose <code>101</code> from the format conversion menu. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre> <p>Output: An extxyz file containing the converted structures, suitable for NEP training or further analysis.</p>"},{"location":"en/format_conversion.html#add-group-labels","title":"Add group labels","text":"<p>What it does: Adds atom group labels to a structure file. Group labels are required by some GPUMD-related workflows, such as species-specific MSD or diffusion calculations.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>This command reads the input structure and writes an extxyz file with group information.</p> <p>Interactive mode: Choose <code>106</code> from the format conversion menu. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre> <p>Output: An extxyz file with group labels added.</p>"},{"location":"en/format_conversion.html#script-details","title":"Script Details","text":""},{"location":"en/format_conversion.html#poscar-to-extxyz","title":"POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>Use this when you have a single VASP structure and want an extxyz output.</p> <p>Interactive keyword: <code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#extxyz-to-poscar","title":"extxyz to POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>This converts all frames in an extxyz file into <code>POSCAR_*.vasp</code> files. Frame indices are 0-based in most GPUMDkit scripts, but output filenames are meant for direct inspection and batch calculations.</p> <p>Interactive entry: <code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#lammps-dump-to-extxyz","title":"LAMMPS dump to extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>The element symbols must match the LAMMPS atom type IDs. For example, if type <code>1</code> is Li, type <code>2</code> is Y, and type <code>3</code> is Cl, the order should be <code>Li Y Cl</code>.</p> <p>Interactive keyword: <code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#cif-conversion","title":"CIF conversion","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>Use <code>-cif2pos</code> if you want a VASP-style structure, and <code>-cif2exyz</code> if the next step is GPUMDkit analysis.</p>"},{"location":"en/format_conversion.html#add-weights","title":"Add weights","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>This is useful when you want some structures to have a different training weight in a NEP dataset.</p>"},{"location":"en/format_conversion.html#replicate-structures","title":"Replicate structures","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>The first form uses explicit replication factors. The second form tries to build a supercell close to a target atom count.</p>"},{"location":"en/format_conversion.html#extract-one-frame","title":"Extract one frame","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>This extracts frame index <code>1000</code> from an extxyz trajectory.</p>"},{"location":"en/format_conversion.html#split-multi-frame-extxyz","title":"Split multi-frame extxyz","text":"<p><code>split_single_xyz.py</code> splits an extxyz file into individual frames, each written to a separate file.</p> <pre><code>python Scripts/format_conversion/split_single_xyz.py dump.xyz\n</code></pre> <p>This creates <code>model_0.xyz</code>, <code>model_1.xyz</code>, ... for each frame in the trajectory.</p>"},{"location":"en/format_conversion.html#mtp-conversion","title":"MTP conversion","text":"<p>Convert MTP <code>.cfg</code> format to extxyz:</p> <pre><code>gpumdkit.sh    # Select: 1) Format Conversion \u2192 102\n</code></pre> <p>Interactive prompt:</p> <pre><code>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;\nExample: train.cfg Pd Ag\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#abacus-conversion","title":"ABACUS conversion","text":"<p>Convert ABACUS output to extxyz:</p> <pre><code>gpumdkit.sh    # Select: 1) Format Conversion \u2192 104\n</code></pre> <p>The menu offers two options:</p> <ol> <li>SCF output (<code>running_scf.log</code>)</li> <li>MD output (<code>running_md.log</code>)</li> </ol>"},{"location":"en/format_conversion.html#common-mistakes","title":"Common Mistakes","text":"Problem What to Check LAMMPS elements are wrong Check the element order passed after the dump file A trajectory has strange metadata Try <code>-clean_xyz input.xyz clean.xyz</code> A converted structure looks shifted Inspect PBC/cell information in the source file Frame extraction gives the wrong structure Remember that frame indices are 0-based"},{"location":"en/format_conversion.html#notes","title":"Notes","text":"<p>If a Python package required by a specific converter is missing, Python will report it when that converter is used.</p>"},{"location":"en/plot_scripts.html","title":"Plot Scripts","text":"\ud83d\udcca Plot Scripts <p>The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators. All plots can be displayed interactively or saved as high-resolution PNG files.</p> <p>Script Location: <code>Scripts/plt_scripts/</code></p>"},{"location":"en/plot_scripts.html#quick-access","title":"Quick Access","text":"<pre><code>gpumdkit.sh -plt              # Show all plotting options\ngpumdkit.sh -plt &lt;type&gt;       # Generate a plot\ngpumdkit.sh -plt &lt;type&gt; save  # Save plot as PNG\ngpumdkit.sh -plt &lt;type&gt; -h    # Show help for a specific plot type\n</code></pre> <p>Running <code>gpumdkit.sh -plt</code> prints the plotting command menu:</p> <pre><code>+-----------------------------------------------------------------------------------------------+\n|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |\n+-----------------------------------------------------------------------------------------------+\n|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |\n+-----------------------------------------------------------------------------------------------+\n|                                    NEP Training &amp; Evaluation                                  |\n+-----------------------------------------------------------------------------------------------+\n|  train          - NEP training results           prediction     - NEP prediction results      |\n|  train_test     - NEP train and test results     parity_density - Parity density plot         |\n|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |\n|  charge         - Charge distribution            born_charge    - Born effective charges      |\n|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |\n|  des            - Descriptors                    lr             - Learning rate for gnep      |\n+-----------------------------------------------------------------------------------------------+\n|                                     Diffusion &amp; Transport                                     |\n+-----------------------------------------------------------------------------------------------+\n|  msd            - Mean square displacement       msd_conv       - MSD convergence             |\n|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |\n|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|\n|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |\n|  D_xyz          - Directional Arrhenius D                                                     |\n+-----------------------------------------------------------------------------------------------+\n|                                    MD &amp; Structural Analysis                                   |\n+-----------------------------------------------------------------------------------------------+\n|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |\n|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |\n|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |\n|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |\n|  doas           - Density of atomistic states                                                 |\n+-----------------------------------------------------------------------------------------------+\n|                                        Heat Transport                                         |\n+-----------------------------------------------------------------------------------------------+\n|  emd            - EMD results                    nemd           - NEMD results                |\n|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |\n+-----------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/plot_scripts.html#nep-training-and-prediction","title":"NEP Training and Prediction","text":""},{"location":"en/plot_scripts.html#plt_trainpy","title":"plt_train.py","text":"<p>Visualizes NEP training progress including loss curves, RMSE evolution, and parity plots comparing DFT vs NEP predictions for energy, forces, and stresses.</p> <p>Input Files: <code>loss.out</code>, <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/plot_scripts.html#plt_predictionpy","title":"plt_prediction.py","text":"<p>Visualizes NEP prediction results on the test set.</p> <p>Input Files: <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test         # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#plt_train_testpy","title":"plt_train_test.py","text":"<p>Creates combined parity plots for both training and testing datasets.</p> <p>Input Files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code>, <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"en/plot_scripts.html#plt_parity_densitypy","title":"plt_parity_density.py","text":"<p>Generates density-based parity plots for energies, forces, and stresses. Useful for large datasets where scatter plots become unreadable.</p> <p>Input Files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"en/plot_scripts.html#plt_force_errorspy","title":"plt_force_errors.py","text":"<p>Plots force error evaluation metrics as proposed by Liu et al..</p> <p>Input File: <code>force_train.out</code></p> <p>Metrics Displayed: - Force magnitude errors (delta_F) - Force angle errors (delta_theta) - Distribution of errors</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"en/plot_scripts.html#plt_learning_ratepy","title":"plt_learning_rate.py","text":"<p>Visualizes learning rate during <code>gnep</code> training.</p> <p>Input File: <code>loss.out</code></p> <p>Note: Only for the <code>gnep</code> training process.</p> <pre><code>gpumdkit.sh -plt lr\n</code></pre>"},{"location":"en/plot_scripts.html#plt_nep_restartpy","title":"plt_nep_restart.py","text":"<p>Visualizes parameters stored in the <code>nep.restart</code> file.</p> <p>Input File: <code>nep.restart</code></p> <pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"en/plot_scripts.html#plt_chargepy","title":"plt_charge.py","text":"<p>Plots charge distribution from <code>qNEP</code> model.</p> <p>Input File: <code>charge_train.out</code></p> <p>Important: Ensure consistency between training set and charge output atom ordering. Use full batch training or run prediction step first.</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre>"},{"location":"en/plot_scripts.html#plt_born_chargepy","title":"plt_born_charge.py","text":"<p>Creates parity plots for Born effective charges (BEC) on training and testing datasets. Structures with all-zero reference BEC are filtered out.</p> <p>Input Files: <code>bec_train.out</code>, <code>bec_test.out</code></p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec          # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#thermodynamic-properties","title":"Thermodynamic Properties","text":""},{"location":"en/plot_scripts.html#plt_thermopy","title":"plt_thermo.py","text":"<p>Primary script for comprehensive thermodynamic property visualization.</p> <p>Input File: <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/plot_scripts.html#plt_thermo2py-plt_thermo3py","title":"plt_thermo2.py &amp; plt_thermo3.py","text":"<p>Alternative thermodynamic visualization with different styles.</p> <p>Input File: <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"en/plot_scripts.html#diffusion-and-ionic-transport","title":"Diffusion and Ionic Transport","text":""},{"location":"en/plot_scripts.html#plt_msdpy","title":"plt_msd.py","text":"<p>Plots mean square displacement (MSD) for all directions.</p> <p>Input File: <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"en/plot_scripts.html#plt_msd_allpy","title":"plt_msd_all.py","text":"<p>Plots MSD for all atomic species separately when using <code>all_groups</code> in GPUMD.</p> <p>Input File: <code>msd.out</code> (computed with <code>all_groups</code> option)</p> <p>Requirements: Must use <code>all_groups</code> in the <code>compute_msd</code> command in <code>run.in</code>.</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"en/plot_scripts.html#plt_msd_convergence_checkpy","title":"plt_msd_convergence_check.py","text":"<p>Checks convergence of MSD calculations across different time windows.</p> <p>Input File: <code>msd_step*.out</code> (computed with <code>save_every</code> option)</p> <p>Requirements: Use <code>save_every</code> in the <code>compute_msd</code> command.</p> <p>Purpose: Verify MSD has converged sufficiently for accurate diffusion coefficient calculation.</p> <pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"en/plot_scripts.html#plt_sdcpy","title":"plt_sdc.py","text":"<p>Plots self-diffusion coefficient (SDC) vs time.</p> <p>Input File: <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/plot_scripts.html#plt_arrhenius_dpy","title":"plt_arrhenius_d.py","text":"<p>Creates Arrhenius plot for diffusivity (log10 D vs 1000/T).</p> <p>Input Files: <code>*K/msd.out</code> files (each temperature subdirectory should contain an <code>msd.out</code>)</p> <pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D             # Alternative command\n</code></pre> <p>Output example:</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"en/plot_scripts.html#plt_arrhenius_sigmapy","title":"plt_arrhenius_sigma.py","text":"<p>Creates Arrhenius plot for ionic conductivity (ln(\u03c3\u00b7T) vs 1000/T).</p> <p>Input Files: <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> (each temperature subdirectory)</p> <pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma         # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#heat-transport","title":"Heat Transport","text":""},{"location":"en/plot_scripts.html#plt_emdpy","title":"plt_emd.py","text":"<p>Analyzes and plots thermal conductivity from equilibrium molecular dynamics (EMD).</p> <p>Input Files: EMD output files from GPUMD</p> <pre><code>gpumdkit.sh -plt emd x        # for x direction\n</code></pre>"},{"location":"en/plot_scripts.html#plt_nemdpy","title":"plt_nemd.py","text":"<p>Visualizes non-equilibrium molecular dynamics (NEMD) thermal transport properties.</p> <p>Input Files: NEMD output files from GPUMD</p> <p>Parameters:</p> Parameter Description <code>real_length</code> Real length of heat transfer zone in nm (set to <code>Auto</code> for auto-calculation) <code>scale_eff_size</code> Scale factor for effective cross-sectional area (default: 1). For 3D bulk: use 1. For low-dimensional systems with vacuum: S_box / S_eff <code>cutoff_freq</code> Cutoff frequency for SHC calculation in THz (default: 60) <code>save</code> Optional, save the plot as <code>nemd.png</code> <p>Note: If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p> <pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#plt_hnemdpy","title":"plt_hnemd.py","text":"<p>Plots homogeneous non-equilibrium molecular dynamics (HNEMD) results.</p> <p>Input Files: HNEMD output files from GPUMD</p> <p>Parameters:</p> Parameter Description <code>scale_eff_size</code> Scale factor for effective cross-sectional area (default: 1) <code>cutoff_freq</code> Cutoff frequency for SHC calculation in THz (default: 60) <code>save</code> Optional, save the plot as <code>hnemd.png</code> <p>Note: If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p> <pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#structural-analysis","title":"Structural Analysis","text":""},{"location":"en/plot_scripts.html#plt_rdfpy","title":"plt_rdf.py","text":"<p>Plots radial distribution function (RDF) showing pair correlations.</p> <p>Input File: <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf               # Plot all RDF pairs\ngpumdkit.sh -plt rdf &lt;column&gt;      # Plot specific pair\n</code></pre> <p>Full RDF output:</p> <p>Single pair RDF:</p>"},{"location":"en/plot_scripts.html#plt_rdf_pmfpy","title":"plt_rdf_pmf.py","text":"<p>Plots RDF combined with potential of mean force (PMF).</p> <p>Input File: <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf_pmf\n</code></pre>"},{"location":"en/plot_scripts.html#plt_vacpy","title":"plt_vac.py","text":"<p>Plots velocity autocorrelation function (VAC). Useful for analyzing phonon properties and atomic dynamics.</p> <p>Input File: <code>sdc.out</code> (the VAC columns are read from this file by the plotting script)</p> <p>Output: Interactive plot or <code>vac.png</code> (with <code>save</code> option)</p> <pre><code>gpumdkit.sh -plt vac\n</code></pre>"},{"location":"en/plot_scripts.html#plt_cohesivepy","title":"plt_cohesive.py","text":"<p>Plots cohesive energy curve from <code>cohesive.out</code>. Useful for analyzing lattice stability and equilibrium lattice constants.</p> <p>Input File: <code>cohesive.out</code> (isotropic scaling factor vs cohesive energy)</p> <p>Output: Interactive plot or <code>cohesive.png</code> (with <code>save</code> option)</p> <pre><code>gpumdkit.sh -plt cohesive\n</code></pre>"},{"location":"en/plot_scripts.html#plt_net_forcepy","title":"plt_net_force.py","text":"<p>Plots distribution of net forces on structures, useful for identifying problematic configurations.</p> <p>Input File: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>Reference: arXiv:2510.19774</p>"},{"location":"en/plot_scripts.html#phonons","title":"Phonons","text":""},{"location":"en/plot_scripts.html#plt_pdospy","title":"plt_pdos.py","text":"<p>Calculates and plots normalized VAC, PDOS, and Heat Capacity (Cv).</p> <p>Input Files: <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></p> <pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>Heat capacity output:</p>"},{"location":"en/plot_scripts.html#descriptor-dimer-and-extra-analysis","title":"Descriptor, Dimer, and Extra Analysis","text":""},{"location":"en/plot_scripts.html#plt_descriptorspy","title":"plt_descriptors.py","text":"<p>Visualizes high-dimensional NEP descriptors using dimensionality reduction (PCA or UMAP).</p> <p>Input File: <code>descriptors.npy</code> (generated by <code>gpumdkit.sh -calc des</code>)</p> <p>Methods: - <code>pca</code> \u2014 Principal Component Analysis - <code>umap</code> \u2014 Uniform Manifold Approximation and Projection</p> <pre><code># First generate descriptors\ngpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n\n# Then visualize\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/plot_scripts.html#plt_descriptors_comparepy","title":"plt_descriptors_compare.py","text":"<p>Compares descriptors from multiple training sets or models.</p> <pre><code>gpumdkit.sh -plt des_compare\n</code></pre>"},{"location":"en/plot_scripts.html#plt_dimerpy","title":"plt_dimer.py","text":"<p>Plots dimer interaction curves. Two atoms are placed in a cubic box (30 \u00c5) and the potential energy and force are calculated as a function of dimer distance using a NEP model.</p> <p>Input File: <code>nep.txt</code></p> <pre><code>gpumdkit.sh -plt dimer &lt;element1&gt; &lt;element2&gt; &lt;nep_model&gt;\ngpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>Reference: J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"en/plot_scripts.html#plt_doaspy","title":"plt_doas.py","text":"<p>Plots density of atomistic states (DOAS) proposed by Wang et al..</p> <p>Input File: <code>doas.out</code> (calculated by <code>gpumdkit.sh -calc doas</code>)</p> <pre><code>gpumdkit.sh -plt doas &lt;doas.out&gt; &lt;species&gt;\ngpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"en/plot_scripts.html#plane-grid-plot-for-polar-materials","title":"Plane-Grid Plot for Polar Materials","text":"<p>This workflow maps displacement or polarization data onto a grid and plots selected plane profiles. For detailed usage and real-world examples, see Polar Material Analysis.</p> <p>Dependency:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>Typical upstream steps:</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>Usage:</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre>"},{"location":"en/plot_scripts.html#quick-reference-table","title":"Quick Reference Table","text":"Command Input File(s) Description <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP training plots <code>prediction</code> / <code>test</code> <code>*_test.out</code> NEP prediction plots <code>train_test</code> <code>*_train.out</code>, <code>*_test.out</code> Combined parity plots <code>parity_density</code> <code>*_train.out</code> Density-based parity plots <code>force_errors</code> <code>force_train.out</code> Force error metrics <code>lr</code> <code>loss.out</code> (gnep) Learning rate <code>restart</code> <code>nep.restart</code> Restart file parameters <code>charge</code> <code>charge_train.out</code> Charge distribution <code>born_charge</code> / <code>bec</code> <code>bec_train.out</code>, <code>bec_test.out</code> Born effective charges <code>thermo</code> <code>thermo.out</code> Thermodynamic properties <code>msd</code> <code>msd.out</code> Mean square displacement <code>msd_all</code> <code>msd.out</code> (all_groups) MSD for all species <code>msd_conv</code> <code>msd_step*.out</code> MSD convergence check <code>sdc</code> <code>msd.out</code> Self-diffusion coefficient <code>arrhenius_d</code> / <code>D</code> <code>*K/msd.out</code> Arrhenius diffusivity <code>arrhenius_sigma</code> / <code>sigma</code> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> Arrhenius ionic conductivity <code>rdf</code> <code>rdf.out</code> Radial distribution function <code>rdf_pmf</code> <code>rdf.out</code> RDF + potential of mean force <code>vac</code> <code>sdc.out</code> Velocity autocorrelation <code>cohesive</code> <code>cohesive.out</code> Cohesive energy curve <code>net_force</code> <code>train.xyz</code> Net force distribution <code>doas</code> <code>doas.out</code> Density of atomistic states <code>des</code> <code>descriptors.npy</code> Descriptor PCA/UMAP <code>dimer</code> <code>nep.txt</code> Dimer energy/force curve <code>pdos</code> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code> VAC and PDOS <code>emd</code> EMD outputs EMD thermal conductivity <code>nemd</code> NEMD outputs NEMD thermal transport <code>hnemd</code> HNEMD outputs HNEMD thermal transport <code>viscosity</code> Viscosity outputs Viscosity"},{"location":"en/polar_material_analysis.html","title":"Polar Material Analysis","text":"\ud83e\uddf2 Polar Material Analysis <p>This tutorial covers GPUMDkit calculator options <code>406-410</code> and the <code>plane-grid</code> plotting workflow.</p> <p>Script Location: <code>Scripts/calculators/</code> and <code>Scripts/plt_scripts/</code></p> <p>This tutorial includes both general and system-specific tools:</p> <ul> <li><code>nlist</code>, <code>disp</code>, and <code>avg-struct</code> are broadly useful for structure/trajectory analysis.</li> <li><code>oct-tilt</code> is for octahedral environments (requires 6 neighbors around each center).</li> <li><code>pol-abo3</code> is specific to <code>ABO3</code> polarization analysis.</li> </ul>"},{"location":"en/polar_material_analysis.html#overview","title":"Overview","text":"Step CLI Command Main Input Output Build neighbor list <code>gpumdkit.sh -calc nlist ...</code> <code>model.xyz</code> <code>nl-*.dat</code> Calculate displacement <code>gpumdkit.sh -calc disp ...</code> trajectory + <code>nl-*.dat</code> <code>displacements.dat</code> Average trajectory <code>gpumdkit.sh -calc avg-struct ...</code> trajectory averaged extxyz Octahedral tilt <code>gpumdkit.sh -calc oct-tilt ...</code> trajectory + B-O neighbor list tilt-angle table ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 ...</code> trajectory + neighbor lists polarization table Plane-grid plot <code>gpumdkit.sh -plt plane-grid ...</code> structure + displacement data plane profile plot"},{"location":"en/polar_material_analysis.html#dependency","title":"Dependency","text":"<p>These scripts require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"en/polar_material_analysis.html#interactive-mode-entry","title":"Interactive mode entry","text":"<p>Options <code>406-410</code> are the core functions for this tutorial. The sections below explain when to use each one and how to run it.</p> <pre><code>gpumdkit.sh\n# choose 4) Calculators\n</code></pre> <p>The calculator menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre> <p>For full argument details, use:</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"en/polar_material_analysis.html#406-build-neighbor-list-calc_neighbor_listpy","title":"406) Build neighbor list (<code>calc_neighbor_list.py</code>)","text":"<p>Build neighbor lists for selected center and neighbor elements.</p> <p>When to use it: This is usually the first step before <code>disp</code>, <code>oct-tilt</code>, and <code>pol-abo3</code>, because those scripts read <code>nl-*.dat</code> neighbor files.</p>"},{"location":"en/polar_material_analysis.html#usage","title":"Usage","text":"<pre><code># Example 1: Ti-O nearest 6 neighbors for octahedral analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# Example 2: Pb/Sr-O nearest 12 neighbors for A-site centered analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input structure file. Default: <code>model.xyz</code>.</li> <li><code>-x, --index</code>:   Frame index to read from input. Default: <code>0</code>.</li> <li><code>-c, --cutoff</code> (required):   Neighbor search cutoff (Angstrom).</li> <li><code>-n, --neighbor-num</code> (required):   Number of neighbors per center.</li> <li><code>-d, --defect</code>:   Defect mode. If enabled and neighbors are insufficient, missing slots are filled with the center index.</li> <li><code>-C, --center-elements</code> (required):   Center species list.</li> <li><code>-E, --neighbor-elements</code> (required):   Neighbor species list.</li> <li><code>-o, --output</code>:   Output file path. Default: <code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file","title":"Output file","text":"<ul> <li>Main output: neighbor list text file (for example <code>nl-Ti-O.dat</code>).</li> <li>The file is a 2D integer array with shape <code>(n_center, neighbor_num + 1)</code>. Each row corresponds to one center atom: the first column is the center index, and the remaining columns are its neighbor indices (all 1-based).</li> </ul>"},{"location":"en/polar_material_analysis.html#407-calc-displacement-from-trajectory-calc_displacementpy","title":"407) Calc displacement from trajectory (<code>calc_displacement.py</code>)","text":"<p>Compute local displacement vectors from a trajectory/model and a neighbor list.</p>"},{"location":"en/polar_material_analysis.html#usage_1","title":"Usage","text":"<pre><code># Example 1: single-frame displacement from model.xyz\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# Example 2: use the last 20% frames in movie.xyz\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_1","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   Neighbor list file from <code>nlist</code>.</li> <li><code>-o, --output</code>:   Output file. Default: <code>displacements.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames.   Integer: last <code>N</code> frames.   <code>0 &lt; value &lt; 1</code>: last ratio of frames.</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_1","title":"Output file","text":"<ul> <li>Main output: <code>displacements.dat</code> (or your custom output name).</li> <li>The saved text file is a 2D array: for a single-frame input, its shape is <code>(n_center, 3)</code>; for a multi-frame input, it is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The three columns are <code>dx</code>, <code>dy</code>, and <code>dz</code> displacement components in Angstrom.</li> </ul>"},{"location":"en/polar_material_analysis.html#408-calc-averaged-structure-calc_averaged_structurepy","title":"408) Calc averaged structure (<code>calc_averaged_structure.py</code>)","text":"<p>Generate one averaged structure from selected trajectory frames. Use this after equilibration. For a solid near equilibrium, average a frame window at the target temperature and analyze that representative structure instead of processing every snapshot.</p>"},{"location":"en/polar_material_analysis.html#usage_2","title":"Usage","text":"<pre><code># Example 1: average all frames\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# Example 2: average selected frames (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_2","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input trajectory file. Default: <code>movie.xyz</code>.</li> <li><code>-o, --output</code>:   Output structure file. Default: <code>averaged_structure.xyz</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_2","title":"Output file","text":"<ul> <li>Main output: averaged single-frame extxyz file.</li> <li>Position averaging applies MIC/PBC correction relative to the first selected frame.</li> </ul>"},{"location":"en/polar_material_analysis.html#409-calc-octahedral-tilt-calc_oct_tiltpy","title":"409) Calc octahedral tilt (<code>calc_oct_tilt.py</code>)","text":"<p>Calculate octahedral tilt angles from a B-O neighbor list. This is commonly used to analyze octahedral rotation patterns in <code>ABO3</code> systems, such as <code>SrTiO3</code> and <code>PbZrO3</code>.</p>"},{"location":"en/polar_material_analysis.html#usage_3","title":"Usage","text":"<pre><code># Example 1: octahedral tilt of the TiO6 octahedra from a single frame\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# Example 2: octahedral tilt of the TiO6 octahedra from the last 20% trajectory frames\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_3","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   B-O neighbor list file.</li> <li><code>-o, --output</code>:   Output file. Default: <code>octahedral_tilt.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_3","title":"Output file","text":"<ul> <li>Main output: <code>octahedral_tilt.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>theta_x</code>, <code>theta_y</code>, <code>theta_z</code>, in degree): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#410-calc-polarization-for-abo3-calc_polarization_abo3py","title":"410) Calc polarization for ABO3 (<code>calc_polarization_abo3.py</code>)","text":"<p>Calculate local polarization vectors for <code>ABO3</code> systems.</p>"},{"location":"en/polar_material_analysis.html#usage_4","title":"Usage","text":"<pre><code># Example 1: single-frame ABO3 polarization\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# Example 2: trajectory polarization on a selected frame window\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_4","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>--nl-ba</code> (required):   B-A neighbor list.</li> <li><code>--nl-bo</code> (required):   B-O neighbor list.</li> <li><code>-o, --output</code>:   Output file. Default: <code>polarization.dat</code>.</li> <li><code>--bec</code> (required):   Born effective charge terms in <code>Element=value</code> format.   Example: <code>Pb=2.5 Ti=4.0 O=-2.0</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul> <p>Important checks:</p> <ul> <li><code>--bec</code> must include all element species in the input structure.</li> <li>Center atom indices in <code>--nl-ba</code> and <code>--nl-bo</code> must match.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_4","title":"Output file","text":"<ul> <li>Main output: <code>polarization.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>Px</code>, <code>Py</code>, <code>Pz</code>, in <code>C/m^2</code>): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The script prints a warning if the total Born charge is not balanced.</li> </ul>"},{"location":"en/polar_material_analysis.html#plane-grid-visualization-plt_plane_gridpy","title":"Plane-grid visualization (<code>plt_plane_grid.py</code>)","text":"<p>You can visualize either <code>displacements.dat</code> or <code>polarization.dat</code>:</p> <pre><code># Example 1: displacement map on Ti sites, first XY layer\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# Example 2: polarization map on Pb sites, XZ and YZ layers\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>Arguments (complete):</p> <ul> <li><code>-i, --input</code>:   Input xyz file for atomic layout and layering. Default: <code>model.xyz</code>.</li> <li><code>-d, --disp</code>:   Vector-field data file. Default: <code>displacements.dat</code>.</li> <li><code>-e, --elements</code> (required):   Center element symbols used to map vectors to lattice layers.</li> <li><code>-m, --tol</code>:   Layer tolerance for grid mapping. Default: <code>1.0</code>.</li> <li><code>-g, --target-size</code>:   Expected grid size as <code>nx ny nz</code>.</li> <li><code>-o, --save-dir</code>:   Figure output directory. Default: <code>plot</code>.</li> <li><code>-f, --frame</code>:   Frame index to visualize when vector data has multiple frames. Default: <code>0</code>.</li> <li><code>--select-xy</code>:   Selected XY layer indices.</li> <li><code>--select-xz</code>:   Selected XZ layer indices.</li> <li><code>--select-yz</code>:   Selected YZ layer indices.</li> </ul> <p>Output:</p> <ul> <li>Creates output directory if needed.</li> <li>Saves figures as <code>XY_*.png</code>, <code>XZ_*.png</code>, <code>YZ_*.png</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-files-at-a-glance","title":"Output files at a glance","text":"Script Main output What it stores <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based center index + neighbor indices <code>calc_displacement.py</code> <code>*.dat</code> Local displacement vectors (<code>dx dy dz</code>, Angstrom) <code>calc_averaged_structure.py</code> <code>*.xyz</code> One averaged structure <code>calc_oct_tilt.py</code> <code>*.dat</code> Octahedral tilt angles (<code>theta_x theta_y theta_z</code>, degree) <code>calc_polarization_abo3.py</code> <code>*.dat</code> Local polarization vectors (<code>Px Py Pz</code>, <code>C/m^2</code>) <code>plt_plane_grid.py</code> <code>plot/*.png</code> XY/XZ/YZ plane maps from vector-field data"},{"location":"en/polar_material_analysis.html#real-examples","title":"Real Examples","text":""},{"location":"en/polar_material_analysis.html#temperature-driven-ferroelectric-to-paraelectric-phase-transition-for-pbtio3","title":"Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3","text":"<p>Assume all files are in the current directory <code>./</code>:</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> is the initial structure used to run MD simulations. Each <code>TEMP K.xyz</code> is a trajectory at that temperature.</p>"},{"location":"en/polar_material_analysis.html#step-1-get-averaged-structures-from-the-last-half-of-each-trajectory","title":"Step 1: get averaged structures from the last half of each trajectory","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>This writes <code>300K-avg.xyz</code>, <code>350K-avg.xyz</code>, ..., <code>800K-avg.xyz</code>.</p>"},{"location":"en/polar_material_analysis.html#step-2-build-neighbor-lists-from-modelxyz","title":"Step 2: build neighbor lists from <code>model.xyz</code>","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-compute-displacement-and-polarization-for-each-temperature","title":"Step 3: compute displacement and polarization for each temperature","text":"<p>Use Born effective charges (BEC), not nominal ionic charges. For PbTiO3 in this example:</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>You can obtain BEC from your own DFPT calculation or from literature values. Thus use following commands to compute local displacement and polarization:</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-4-plot-displacement-and-polarization-maps-in-real-space","title":"Step 4: plot displacement and polarization maps in real space","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-5-build-a-temperature-order-parameter-curve","title":"Step 5: build a temperature-order-parameter curve","text":"<p>By analyzing the lattice of each temperature-averaged structure together with its polarization (<code>XX-pol.dat</code>), we can obtain the following figure:</p> <p>The trend shows a clear phase transition around <code>600 K</code>, where the polarization vanishes.</p>"},{"location":"en/polar_material_analysis.html#topological-structure-in-pbtio3srtio3-superlattice","title":"Topological structure in PbTiO3/SrTiO3 superlattice","text":"<p>Assume <code>movie.xyz</code> is the trajectory of the PbTiO3/SrTiO3 superlattice in the current directory.</p>"},{"location":"en/polar_material_analysis.html#step-1-build-an-averaged-structure-from-the-last-25-frames","title":"Step 1: build an averaged structure from the last 25% frames","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-2-build-the-ti-neighbor-list","title":"Step 2: build the Ti neighbor list","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-plot-the-plane-grid-map","title":"Step 3: plot the plane-grid map","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero.</p> <p>Note: the example figure uses a custom colormap. The default GPUMDkit output uses a different style, which can be adjusted by editing the plotting script.</p>"},{"location":"en/polar_material_analysis.html#other-systems","title":"Other Systems","text":""},{"location":"en/polar_material_analysis.html#organic-inorganic-hybrid-ferroelectrics","title":"Organic-inorganic hybrid ferroelectrics","text":"<p>In many organic-inorganic ferroelectrics, polarization is strongly tied to anisotropic molecular units. A practical way to track molecular orientation is to use bond vectors.</p> <p>For TMCM-CdCl3, you can use the C-Cl bond direction of the TMCM molecule as an orientation proxy, then use it to estimate the polarization state:</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p><code>ccl_vectors.dat</code> can then be analyzed as an orientation order parameter. More details could be found at: Phys. Rev. Lett. 136, 016801</p>"},{"location":"en/polar_material_analysis.html#other-ferroelectric-families","title":"Other ferroelectric families","text":"<p>Beyond <code>ABO3</code>, <code>ferrodispcalc</code> can be adapted to many ferroelectric systems, including nitrides, hafnia-based compounds, organic-inorganic hybrids, and some 2D ferroelectrics.</p>"},{"location":"en/quick_start.html","title":"Quick Start","text":"\ud83d\ude80 Quick Start <p>This page helps you install GPUMDkit and run your first commands. You can use GPUMDkit through an interactive menu or direct command-line options.</p>"},{"location":"en/quick_start.html#what-it-does","title":"What it does","text":"<p>GPUMDkit provides a single entry point for common tasks in computational materials science \u2014 format conversion, structure analysis, property calculation, and visualization \u2014 without writing custom scripts.</p>"},{"location":"en/quick_start.html#before-you-start","title":"Before you start","text":""},{"location":"en/quick_start.html#1-prepare-a-python-environment","title":"1. Prepare a Python environment","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>Some optional functions require additional packages:</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>Other Python dependencies are loaded by the corresponding scripts. If a package is missing, Python will report it when that function is used.</p>"},{"location":"en/quick_start.html#2-install-gpumdkit","title":"2. Install GPUMDkit","text":"<p>Clone the repository and run the installer:</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre> <p>The installer writes <code>GPUMDkit_path</code> and <code>PATH</code> settings to your shell configuration and loads them for the current shell. It writes to <code>~/.bashrc</code> by default; if the current shell is zsh, it writes to <code>~/.zshrc</code>. If an existing GPUMDkit path is found, the installer prints the old path and asks whether to replace it. Before changing the rc file, it creates a backup.</p> <p>Typical installation output:</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>If GPUMDkit was installed before, you may see:</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre>"},{"location":"en/quick_start.html#3-verify-the-installation","title":"3. Verify the installation","text":"<pre><code>gpumdkit.sh -h\n</code></pre> <p>This prints a help table listing all available options.</p>"},{"location":"en/quick_start.html#interactive-mode","title":"Interactive mode","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>This opens the main menu:</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre> <p>Select a module by number. Each module provides sub-menus with specific functions.</p>"},{"location":"en/quick_start.html#cli-mode","title":"CLI mode","text":"<p>Direct commands use fixed positional arguments:</p> <pre><code>gpumdkit.sh -&lt;option&gt; [args...]\n</code></pre> <p>Examples:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>The first example reads <code>POSCAR</code> and writes <code>model.xyz</code>.</p>"},{"location":"en/quick_start.html#common-examples","title":"Common examples","text":""},{"location":"en/quick_start.html#convert-a-poscar-to-extxyz","title":"Convert a POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"en/quick_start.html#add-gpumd-group-labels","title":"Add GPUMD group labels","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>Group labels are used by some GPUMD-related workflows that need atom grouping, such as species-specific MSD or diffusion calculations.</p>"},{"location":"en/quick_start.html#plot-nep-training-results","title":"Plot NEP training results","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/quick_start.html#plot-nep-test-results","title":"Plot NEP test results","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"en/quick_start.html#plot-thermodynamic-data","title":"Plot thermodynamic data","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/quick_start.html#plot-msd-and-self-diffusion-coefficient","title":"Plot MSD and self-diffusion coefficient","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/quick_start.html#notes","title":"Notes","text":"<ul> <li>Use <code>gpumdkit.sh -h</code> to see all available options.</li> <li>Use <code>gpumdkit.sh -&lt;option&gt; -h</code> to get help for a specific option (e.g., <code>gpumdkit.sh -plt train -h</code>).</li> <li>For detailed usage of each module, see the corresponding tutorial pages linked in the index.</li> </ul>"},{"location":"en/structure_sampling.html","title":"Structure Sampling","text":"\ud83d\udce6 Structure Sampling <p>Structure sampling is used to select, generate, or filter candidate configurations for NEP training and molecular dynamics workflows.</p> <p>Script Location: <code>Scripts/sample_structures/</code></p>"},{"location":"en/structure_sampling.html#interactive-mode","title":"Interactive Mode","text":"<p>Sampling tasks are usually easier to run from the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>2) Sample Structures\n</code></pre> <p>The menu is:</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Method Use Case 201 Uniform/random sampling quick frame selection from a trajectory 202 PyNEP notice prints a notice; use <code>gpumdkit.sh -pynep</code> to run PyNEP 203 NepTrain FPS descriptor-based FPS with NepTrain 204 Perturb structure generate perturbed structures from POSCAR/CONTCAR 205 Force-deviation selection select structures with high model deviation"},{"location":"en/structure_sampling.html#uniform-and-random-sampling","title":"Uniform and Random Sampling","text":"<p>From interactive mode, choose <code>201</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>Example input:</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>or:</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>uniform</code> / <code>random</code> sampling method <code>50</code> / <code>100</code> number of selected structures <code>500</code> optional number of initial frames to skip <p>Output:</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#farthest-point-sampling-with-neptrain","title":"Farthest Point Sampling with NepTrain","text":"<p>This entry uses NepTrain descriptors for FPS.</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>From interactive mode, choose <code>203</code>. You will see:</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>Inputs:</p> File Meaning <code>dump.xyz</code> candidate structures <code>train.xyz</code> existing training set <code>nep.txt</code> current NEP model used to compute descriptors <p>Outputs:</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>During execution, choose one of two selection modes:</p> <ol> <li>select until the descriptor distance is below a threshold;</li> <li>select a specified number of structures.</li> </ol> <p>The script then prints a selection prompt:</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>This function requires the <code>NepTrain</code> package. If you use this function, we recommend citing the NepTrain paper printed by the script.</p>"},{"location":"en/structure_sampling.html#deprecated-pynep-fps","title":"Deprecated PyNEP FPS","text":"<p>PyNEP FPS is kept for compatibility, but it is only exposed through the direct <code>-pynep</code> entry.</p> <p>If you choose <code>202</code> from the interactive menu, it prints:</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre>"},{"location":"en/structure_sampling.html#serial-pynep","title":"Serial PyNEP","text":"<pre><code>python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"en/structure_sampling.html#parallel-pynep","title":"Parallel PyNEP","text":"<pre><code>python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8\n</code></pre> <p>The last argument is the number of CPU threads.</p>"},{"location":"en/structure_sampling.html#gpumdkit-entry","title":"GPUMDkit Entry","text":"<pre><code>gpumdkit.sh -pynep\n</code></pre> <p>Then input:</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>This entry requires <code>pynep</code> and is kept for compatibility.</p>"},{"location":"en/structure_sampling.html#structure-perturbation","title":"Structure Perturbation","text":"<p>Use perturbation when you want to generate initial structures around a known configuration.</p> <pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>From interactive mode, choose <code>204</code>. You will see:</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input VASP structure <code>20</code> number of perturbed structures <code>0.03</code> cell perturbation fraction <code>0.2</code> atom perturbation distance in Angstrom <code>uniform</code> perturbation style: <code>normal</code>, <code>uniform</code>, or <code>const</code> <p>Output:</p> <ul> <li><code>POSCAR_01.vasp</code>, <code>POSCAR_02.vasp</code>, ...</li> </ul> <p>This function requires <code>dpdata</code>. If you use this function, we recommend citing the dpdata package.</p>"},{"location":"en/structure_sampling.html#force-deviation-selection","title":"Force-Deviation Selection","text":"<p>Use this together with the GPUMD <code>active</code> command. The <code>active</code> command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. <code>select_max_modev.py</code> selects structures with large force deviations from <code>active.out</code> and <code>active.xyz</code>, then writes them to <code>selected.xyz</code>.</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>From interactive mode, choose <code>205</code>. You will see:</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>200</code> maximum number of structures to keep <code>0.15</code> minimum force deviation threshold <p>Required files:</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>Output:</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#frame-range-extraction","title":"Frame Range Extraction","text":"<p>Use this to extract a fraction of a trajectory:</p> <pre><code>python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>This writes frames from 0% to 80% of the trajectory.</p>"},{"location":"en/structure_sampling.html#example-commands","title":"Example Commands","text":"<p>An example sequence using several sampling-related tools:</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"en/structure_sampling.html#common-mistakes","title":"Common Mistakes","text":"Problem Recommendation FPS selects too many similar structures increase the distance threshold or select fewer structures Perturbed structures are unphysical reduce <code>cell_pert</code> and <code>atom_pert</code>, then check minimum distances <code>active.out</code> and <code>active.xyz</code> do not match regenerate both from the same GPUMD active run PCA plot looks strange check whether <code>nep.txt</code> matches the chemical species in both datasets"},{"location":"en/workflow_scripts.html","title":"Workflow Scripts","text":"\ud83d\udd27 Workflow Scripts <p>Workflow scripts automate repetitive preparation steps for DFT, MD, and NEP development.</p> <p>Script Location: <code>Scripts/workflow/</code></p>"},{"location":"en/workflow_scripts.html#interactive-entry","title":"Interactive Entry","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>3) Workflow\n</code></pre> <p>The workflow menu looks like:</p> <pre><code>+---------------------------------------------------------+\n|                      WORKFLOW TOOLS                     |\n+---------------------------------------------------------+\n| 301) SCF batch pretreatment                             |\n| 302) MD sample batch pretreatment (gpumd)               |\n| 303) MD sample batch pretreatment (lmp)                 |\n+---------------------------------------------------------+\n| 000) Return to the main menu                            |\n+---------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Workflow Purpose 301 SCF batch pretreatment Prepare single-point DFT calculations 302 MD sample batch pretreatment (GPUMD) Prepare GPUMD sampling calculations 303 MD sample batch pretreatment (LAMMPS) Prepare LAMMPS sampling calculations"},{"location":"en/workflow_scripts.html#scf-batch-pretreatment","title":"SCF Batch Pretreatment","text":"<p>Use this when you have many structures and want to prepare single-point DFT calculations.</p>"},{"location":"en/workflow_scripts.html#vasp","title":"VASP","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>Before running, put structure files in the current directory. The script checks files in this order:</p> <ol> <li>if one or more <code>.vasp</code> files exist, it processes <code>.vasp</code> files;</li> <li>if both <code>.vasp</code> and <code>.xyz</code> files exist, it prints a notice and only processes <code>.vasp</code> files;</li> <li>if no <code>.vasp</code> file exists and one <code>.xyz</code> file exists, it converts that extxyz file to POSCAR files;</li> <li>if no <code>.vasp</code> file exists and multiple <code>.xyz</code> files exist, it asks you to choose one.</li> </ol> <p>Typical input directory before running:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>INCAR</code>, <code>POTCAR</code>, and <code>KPOINTS</code> in the generated <code>fp/</code> directory after the script creates it. The calculation folders link to files in <code>fp/</code>.</p> <p>The <code>prefix</code> you input during the workflow becomes the calculation folder prefix. When <code>out2xyz</code> is later used to extract results, the folder name is stored as <code>config_type</code> in the extxyz file, which makes it easier to trace where each structure came from.</p>"},{"location":"en/workflow_scripts.html#cp2k","title":"CP2K","text":"<p>CP2K SCF batch pretreatment is available from the workflow menu and can also be called directly:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>The interactive wrapper asks for:</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>Example:</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>The template should be configured to read coordinates from <code>pos.xyz</code>. A reference template is available at:</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>The script creates <code>&lt;prefix&gt;_&lt;index&gt;/</code> directories, writes <code>input.inp</code>, and writes <code>pos.xyz</code> for each structure.</p>"},{"location":"en/workflow_scripts.html#md-sampling-pretreatment","title":"MD Sampling Pretreatment","text":""},{"location":"en/workflow_scripts.html#gpumd","title":"GPUMD","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 302\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. The detection order is the same as the VASP SCF workflow: <code>.vasp</code> files are preferred; if multiple <code>.xyz</code> files are found without <code>.vasp</code>, the script asks you to choose one.</p> <p>Typical input directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>nep.txt</code> and <code>run_*.in</code> files in the generated <code>md/</code> directory. The script links <code>run_1.in</code> to <code>sample_1/run.in</code>, <code>run_2.in</code> to <code>sample_2/run.in</code>, and so on.</p>"},{"location":"en/workflow_scripts.html#lammps","title":"LAMMPS","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 303\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. <code>.vasp</code> files are preferred when both formats exist.</p> <p>After running, the script creates LAMMPS data files in <code>struct_md/</code>, sample folders, and an <code>md/</code> directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>lmprun.in</code> and <code>nep.txt</code> in the generated <code>md/</code> directory.</p>"},{"location":"en/workflow_scripts.html#active-learning-style-workflow","title":"Active-Learning Style Workflow","text":"<p>A common NEP improvement loop is:</p> <ol> <li>run MD with the current <code>nep.txt</code>;</li> <li>collect <code>dump.xyz</code> or <code>active.xyz</code>;</li> <li>remove unphysical structures;</li> <li>select diverse or uncertain structures;</li> <li>run DFT single-point calculations;</li> <li>convert DFT results to extxyz;</li> <li>append new structures to <code>train.xyz</code>;</li> <li>retrain the NEP model.</li> </ol> <p>For the development active-learning script, see Active Learning.</p>"},{"location":"en/workflow_scripts.html#template-based-temperature-series","title":"Template-Based Temperature Series","text":"<p>For a simple temperature series, a shell loop is often enough:</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>Then submit the generated folders according to your local cluster system.</p>"},{"location":"en/workflow_scripts.html#practical-notes","title":"Practical Notes","text":"<ul> <li>Workflow scripts are cluster- and template-dependent. Always test with a small number of structures first.</li> <li>Keep template files (<code>INCAR</code>, <code>KPOINTS</code>, <code>POTCAR</code>, <code>run.in</code>, CP2K inputs) under version control if possible.</li> <li>Check generated folders before submitting a large batch.</li> <li>Use analyzers and sampling scripts before expensive DFT calculations.</li> </ul>"},{"location":"zh/index.html","title":"GPUMDkit \u6559\u7a0b","text":"\ud83d\udcda GPUMDkit \u6559\u7a0b <p>\u6b22\u8fce\u4f7f\u7528 GPUMDkit\uff0c\u8fd9\u662f\u4e00\u4e2a\u9762\u5411 GPUMD \u548c NEP \u7684\u547d\u4ee4\u884c\u5de5\u5177\u5305\u3002</p>"},{"location":"zh/index.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>GPUMDkit \u5e2e\u52a9\u4f60\u5728\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u7814\u7a76\u4e2d\u5b8c\u6210\u5e38\u89c1\u4efb\u52a1\uff0c\u65e0\u9700\u7f16\u5199\u81ea\u5b9a\u4e49\u811a\u672c\u3002\u5b83\u652f\u6301\u683c\u5f0f\u8f6c\u6362\u3001\u7ed3\u6784\u5206\u6790\u3001\u6027\u8d28\u8ba1\u7b97\u3001\u53ef\u89c6\u5316\u548c\u6279\u91cf\u5de5\u4f5c\u6d41\u2014\u2014\u5168\u90e8\u901a\u8fc7\u4e00\u4e2a\u547d\u4ee4\u884c\u5de5\u5177\u5b8c\u6210\u3002</p>"},{"location":"zh/index.html#_2","title":"\u5e38\u89c1\u4efb\u52a1","text":"\u6211\u60f3\u8981... \u6559\u7a0b \u5b89\u88c5 GPUMDkit \u5e76\u8fd0\u884c\u7b2c\u4e00\u4e2a\u547d\u4ee4 \u5feb\u901f\u5165\u95e8 \u5c06 VASP\u3001LAMMPS\u3001CP2K \u6216 CIF \u6587\u4ef6\u8f6c\u6362\u4e3a extxyz \u683c\u5f0f\u8f6c\u6362 \u68c0\u67e5\u7ed3\u6784\u8ddd\u79bb\u3001\u8fc7\u6ee4\u6570\u636e\u96c6\u6216\u67e5\u627e\u5f02\u5e38\u503c \u5206\u6790\u5de5\u5177 \u8ba1\u7b97 MSD\u3001\u79bb\u5b50\u7535\u5bfc\u7387\u6216\u63cf\u8ff0\u7b26 \u8ba1\u7b97\u5668\u811a\u672c \u5206\u6790\u6781\u6027\u6750\u6599\u3001\u94c1\u7535\u4f53\u6216 ABO3 \u4f53\u7cfb \u6781\u6027\u6750\u6599\u5206\u6790 \u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c\u6216\u70ed\u529b\u5b66\u6570\u636e \u7ed8\u56fe\u811a\u672c \u8fd0\u884c\u6279\u91cf DFT \u6216 MD \u6a21\u62df \u5de5\u4f5c\u6d41\u811a\u672c \u4ece\u6570\u636e\u96c6\u4e2d\u9009\u62e9\u4ee3\u8868\u6027\u7ed3\u6784 \u7ed3\u6784\u91c7\u6837 \u6dfb\u52a0\u81ea\u5df1\u7684 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u81ea\u5b9a\u4e49\u547d\u4ee4"},{"location":"zh/index.html#_3","title":"\u51c6\u5907\u5de5\u4f5c","text":""},{"location":"zh/index.html#_4","title":"\u5b89\u88c5","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"zh/index.html#_5","title":"\u4f9d\u8d56","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"zh/index.html#_6","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u6253\u5f00\u83dc\u5355\u540e\uff0c\u6309\u6570\u5b57\u9009\u62e9\u6a21\u5757\u3002</p>"},{"location":"zh/index.html#_7","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n</code></pre> <p>\u4f8b\u5982\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>\u4f7f\u7528 <code>gpumdkit.sh -h</code> \u67e5\u770b\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</p>"},{"location":"zh/index.html#_8","title":"\u6a21\u5757\u6982\u89c8","text":"\u6a21\u5757 \u83dc\u5355 CLI \u63cf\u8ff0 \u683c\u5f0f\u8f6c\u6362 1 <code>-out2xyz</code>, <code>-pos2exyz</code> \u6587\u4ef6\u8f6c\u6362 \u7ed3\u6784\u91c7\u6837 2 <code>-neptrain</code>\u3001\u4ea4\u4e92\u83dc\u5355 \u7ed3\u6784\u91c7\u6837 \u5de5\u4f5c\u6d41 3 - \u6279\u5904\u7406 \u8ba1\u7b97\u5668 4 <code>-calc &lt;\u7c7b\u578b&gt;</code> \u5c5e\u6027\u8ba1\u7b97 \u5206\u6790\u5de5\u5177 5 <code>-range</code>, <code>-min_dist</code> \u7ed3\u6784\u5206\u6790 \u53ef\u89c6\u5316 6 <code>-plt &lt;\u7c7b\u578b&gt;</code> \u7ed8\u56fe\u5de5\u5177 \u5b9e\u7528\u5de5\u5177 7 <code>-time</code>, <code>-clean</code> \u5b9e\u7528\u529f\u80fd"},{"location":"zh/index.html#_9","title":"\u5168\u90e8\u6559\u7a0b","text":"\u6559\u7a0b \u63cf\u8ff0 \u5feb\u901f\u5165\u95e8 \u5b89\u88c5\u548c\u7b2c\u4e00\u6b65 \u547d\u4ee4\u53c2\u8003 \u5e38\u7528 CLI \u548c\u83dc\u5355\u5165\u53e3\u901f\u67e5 \u683c\u5f0f\u8f6c\u6362 \u5728\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362 \u8ba1\u7b97\u5668\u811a\u672c \u8ba1\u7b97\u6750\u6599\u5c5e\u6027 \u5206\u6790\u5de5\u5177 \u7ed3\u6784\u5206\u6790\u548c\u9a8c\u8bc1 \u7ed8\u56fe\u811a\u672c \u7ed8\u56fe\u548c\u53ef\u89c6\u5316 \u5de5\u4f5c\u6d41\u811a\u672c \u6279\u5904\u7406\u548c\u81ea\u52a8\u5316 \u7ed3\u6784\u91c7\u6837 \u7ed3\u6784\u9009\u62e9\u65b9\u6cd5 \u81ea\u5b9a\u4e49\u547d\u4ee4 \u7528\u6237\u81ea\u5b9a\u4e49 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 \u6279\u91cf\u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\u8bf4\u660e \u6781\u6027\u6750\u6599\u5206\u6790 \u94c1\u7535\u548c\u6781\u5316\u76f8\u5173\u5de5\u5177 \u8d21\u732e\u6307\u5357 \u5f00\u53d1\u548c\u8d21\u732e\u8bf4\u660e"},{"location":"zh/index.html#_10","title":"\u94fe\u63a5","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>\u6587\u6863: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html","title":"\u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41","text":"\ud83d\udd01 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 <p><code>workflow_active_learning_dev.sh</code> \u7528\u4e8e\u7ec4\u7ec7\u4e00\u8f6e NEP \u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\uff1a\u8fd0\u884c GPUMD \u5206\u5b50\u52a8\u529b\u5b66\u3001\u7b5b\u9009\u7ed3\u6784\u3001\u62bd\u6837\u3001\u63d0\u4ea4\u7b2c\u4e00\u6027\u539f\u7406\u8ba1\u7b97\uff0c\u5e76\u8fdb\u884c NEP \u9884\u6d4b\u68c0\u67e5\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#_1","title":"\u6982\u89c8","text":"<p>\u8be5\u811a\u672c\u81ea\u52a8\u5316\u4e86 NEP \u4e3b\u52a8\u5b66\u4e60\u7684\u4e00\u8f6e\u8fed\u4ee3\u3002\u5178\u578b\u6d41\u7a0b\u5305\u62ec\uff1a</p> \u6b65\u9aa4 \u64cd\u4f5c \u76ee\u7684 1 \u8fd0\u884c MD \u6a21\u62df \u4f7f\u7528\u5f53\u524d NEP \u6a21\u578b\u751f\u6210\u5019\u9009\u7ed3\u6784 2 \u8fc7\u6ee4\u7ed3\u6784 \u79fb\u9664\u4e0d\u5408\u7406\u7684\u6784\u578b\uff08\u77ed\u8ddd\u79bb\u3001\u5927\u76d2\u5b50\uff09 3 \u91c7\u6837\u7ed3\u6784 \u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\u8fdb\u884c DFT \u8ba1\u7b97 4 \u8fd0\u884c SCF \u8ba1\u7b97 \u8ba1\u7b97 DFT \u53c2\u8003\u80fd\u91cf/\u529b 5 NEP \u9884\u6d4b \u68c0\u67e5\u6a21\u578b\u5728\u65b0\u7ed3\u6784\u4e0a\u7684\u7cbe\u5ea6 <p>\u4e0e\u83dc\u5355\u9a71\u52a8\u7684\u6a21\u5757\u4e0d\u540c\uff0c\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u662f\u4e00\u4e2a\u9700\u8981\u6309\u4f53\u7cfb\u4fee\u6539\u540e\u76f4\u63a5\u8fd0\u884c\u7684 shell \u811a\u672c\uff1a</p> <pre><code>bash Scripts/workflow/workflow_active_learning_dev.sh\n</code></pre> <p>\u4e0b\u9762\u6309\u811a\u672c\u4e2d\u7684\u4e3b\u8981\u4ee3\u7801\u5757\u8bf4\u660e\u6bcf\u4e00\u6b65\u7684\u4f5c\u7528\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#1-slurm","title":"1. SLURM \u8bbe\u7f6e","text":"<p>\u811a\u672c\u5f00\u5934\u5305\u542b\u96c6\u7fa4\u63d0\u4ea4\u53c2\u6570\uff0c\u4f8b\u5982\uff1a</p> <pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>\u8fd9\u4e9b\u53c2\u6570\u9700\u8981\u6839\u636e\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u4fee\u6539\u3002\u5982\u679c\u6ca1\u6709 SLURM \u73af\u5883\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u540e\u53f0\u8fd0\u884c\uff1a</p> <pre><code>nohup bash workflow_active_learning_dev.sh &gt; workflow.log 2&gt;&amp;1 &amp;\n</code></pre>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#2","title":"2. \u57fa\u672c\u8bbe\u7f6e","text":"<p>\u811a\u672c\u4f1a\u8fdb\u5165\u63d0\u4ea4\u76ee\u5f55\uff0c\u5e76\u52a0\u8f7d\u63d0\u4ea4\u6a21\u677f\uff1a</p> <pre><code>cd $SLURM_SUBMIT_DIR\nsource ${GPUMDkit_path}/Scripts/workflow/submit_template.sh\npython_pynep=python\n</code></pre> <ul> <li><code>GPUMDkit_path</code> \u662f\u5b89\u88c5\u811a\u672c\u5199\u5165\u7684 GPUMDkit \u8def\u5f84\u3002</li> <li><code>python_pynep</code> \u4ec5\u7528\u4e8e\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#3","title":"3. \u4e3b\u8981\u53d8\u91cf","text":"<p>\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u9002\u5408\u5df2\u7ecf\u6709\u521d\u59cb <code>nep.txt</code>\u3001<code>nep.in</code>\u3001<code>train.xyz</code> \u548c GPUMD/DFT \u8f93\u5165\u6587\u4ef6\uff0c\u5e76\u5e0c\u671b\u5728\u96c6\u7fa4\u4e0a\u81ea\u52a8\u6269\u5c55\u8bad\u7ec3\u96c6\u7684\u60c5\u51b5\u3002</p> <p>\u811a\u672c\u5f00\u5934\u901a\u5e38\u9700\u8981\u6839\u636e\u4f53\u7cfb\u4fee\u6539\uff1a</p> <pre><code>work_dir=${PWD}\nprefix_name=LiF_iter01\nmin_dist=1.4\nbox_limit=13\nmax_fp_num=50\nsample_method=pynep\npynep_sample_dist=0.01\n</code></pre> <ul> <li><code>prefix_name</code> \u7528\u4e8e\u547d\u540d\u672c\u8f6e\u8ba1\u7b97\u3002</li> <li><code>min_dist</code> \u548c <code>box_limit</code> \u7528\u4e8e\u8fc7\u6ee4\u660e\u663e\u4e0d\u5408\u7406\u7684\u7ed3\u6784\u3002</li> <li><code>max_fp_num</code> \u63a7\u5236\u6700\u591a\u63d0\u4ea4\u591a\u5c11\u4e2a\u5355\u70b9\u8ba1\u7b97\u3002</li> <li><code>sample_method</code> \u53ef\u9009 <code>uniform</code>\u3001<code>random</code> \u6216 <code>pynep</code>\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#4","title":"4. \u68c0\u67e5\u8f93\u5165\u6587\u4ef6","text":"<p>\u5e38\u89c1\u8f93\u5165\u5305\u62ec\uff1a</p> <ul> <li><code>nep.txt</code></li> <li><code>nep.in</code></li> <li><code>train.xyz</code></li> <li><code>run.in</code></li> <li><code>INCAR</code></li> <li><code>POTCAR</code></li> <li><code>KPOINTS</code></li> <li>\u521d\u59cb\u91c7\u6837\u7ed3\u6784\u6587\u4ef6\uff0c\u4f8b\u5982 <code>sample_struct.xyz</code></li> </ul> <p>\u811a\u672c\u4f1a\u628a\u516c\u5171\u8f93\u5165\u79fb\u52a8\u5230 <code>common/</code>\uff0c\u5e76\u521b\u5efa <code>00.modev/</code>\u3001<code>01.select/</code> \u7b49\u5de5\u4f5c\u76ee\u5f55\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#5","title":"5. \u6587\u4ef6\u7ec4\u7ec7","text":"<p>\u811a\u672c\u4f1a\u521b\u5efa\u516c\u5171\u8f93\u5165\u76ee\u5f55\u548c MD \u76ee\u5f55\uff1a</p> <pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <ul> <li><code>00.modev</code>\uff1a\u7528\u4e8e\u8fd0\u884c GPUMD MD \u91c7\u6837\u3002</li> <li><code>common</code>\uff1a\u4fdd\u5b58 <code>nep.txt</code>\u3001<code>run.in</code>\u3001\u7ed3\u6784\u6587\u4ef6\u548c DFT \u8f93\u5165\u6587\u4ef6\u7b49\u516c\u5171\u8d44\u6e90\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#6-md","title":"6. \u63d0\u4ea4 MD \u4efb\u52a1","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>\u811a\u672c\u4f1a\u901a\u8fc7\u63d0\u4ea4\u6a21\u677f\u521b\u5efa\u6570\u7ec4\u4efb\u52a1\u3002\u4e0d\u540c\u96c6\u7fa4\u4e0a\u7684\u63d0\u4ea4\u547d\u4ee4\u548c\u6a21\u677f\u53ef\u80fd\u9700\u8981\u81ea\u5df1\u4fee\u6539\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#7","title":"7. \u68c0\u67e5\u4efb\u52a1\u5b8c\u6210","text":"<p>\u811a\u672c\u4f1a\u6301\u7eed\u68c0\u67e5 <code>00.modev/</code> \u4e0b\u5404\u4e2a <code>sample_*/log</code> \u6587\u4ef6\uff0c\u786e\u8ba4\u662f\u5426\u51fa\u73b0\uff1a</p> <pre><code>Finished running GPUMD.\n</code></pre> <p>\u5982\u679c\u53d1\u73b0 <code>Error</code>\uff0c\u811a\u672c\u4f1a\u505c\u6b62\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#8","title":"8. \u5206\u6790\u548c\u8fc7\u6ee4\u7ed3\u6784","text":"<p>MD \u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u8fdb\u5165 <code>01.select</code>\uff0c\u5bf9 <code>dump.xyz</code> \u4e2d\u7684\u7ed3\u6784\u8fdb\u884c\u7b5b\u9009\u3002\u5e38\u89c1\u68c0\u67e5\u5305\u62ec\uff1a</p> <ul> <li>\u6700\u5c0f\u539f\u5b50\u8ddd\u79bb\uff1b</li> <li>\u6a21\u62df\u76d2\u5b50\u8fb9\u957f\uff1b</li> <li>\u7ed3\u6784\u6570\u91cf\u662f\u5426\u8d85\u8fc7 <code>max_fp_num</code>\u3002</li> </ul> <p>\u8fd9\u4e9b\u6b65\u9aa4\u4f1a\u8c03\u7528 analyzer \u548c sample_structures \u4e2d\u7684\u811a\u672c\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#9","title":"9. \u62bd\u6837\u65b9\u6cd5","text":"<p>\u811a\u672c\u6839\u636e <code>sample_method</code> \u9009\u62e9\u62bd\u6837\u65b9\u5f0f\uff1a</p> <pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <ul> <li><code>uniform</code>\uff1a\u5747\u5300\u62bd\u5e27\uff1b</li> <li><code>random</code>\uff1a\u968f\u673a\u62bd\u5e27\uff1b</li> <li><code>pynep</code>\uff1a\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#10-scf","title":"10. \u63d0\u4ea4 SCF \u8ba1\u7b97","text":"<p>\u62bd\u6837\u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u63d0\u4ea4 VASP \u5355\u70b9\u8ba1\u7b97\uff1a</p> <pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>\u8fd9\u91cc\u7684 <code>prefix_name</code> \u4f1a\u7528\u4e8e\u8ba1\u7b97\u76ee\u5f55\u547d\u540d\uff0c\u4e5f\u65b9\u4fbf\u540e\u7eed\u8ffd\u8e2a\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#11-prediction","title":"11. Prediction \u6b65\u9aa4","text":"<p>\u6700\u540e\u811a\u672c\u4f1a\u63d0\u4ea4 NEP prediction\uff0c\u7528\u4e8e\u68c0\u67e5\u5f53\u524d\u6a21\u578b\u5728\u65b0\u589e\u7ed3\u6784\u4e0a\u7684\u8bef\u5dee\u3002</p> <p>\u8fd9\u4e2a\u811a\u672c\u548c\u8ba1\u7b97\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u4f7f\u7528\u524d\u5efa\u8bae\u5148\u7528\u5c0f\u4f53\u7cfb\u6216\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u4e00\u8f6e\uff0c\u5e76\u68c0\u67e5\u63d0\u4ea4\u6a21\u677f\u3001\u8def\u5f84\u548c\u8f93\u5165\u6587\u4ef6\u662f\u5426\u7b26\u5408\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html","title":"\u5206\u6790\u5de5\u5177","text":"\ud83d\udd0d \u5206\u6790\u5de5\u5177 <p>\u5206\u6790\u811a\u672c\u4e3a extxyz \u6570\u636e\u96c6\u63d0\u4f9b\u7ed3\u6784\u7edf\u8ba1\u3001\u8ddd\u79bb\u68c0\u67e5\u3001\u8fc7\u6ee4\u3001\u6210\u5206\u5206\u6790\u3001\u5f02\u5e38\u68c0\u6d4b\u548c\u65f6\u95f4\u4f30\u7b97\u529f\u80fd\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>\u672c\u6a21\u5757\u5e2e\u52a9\u4f60\u68c0\u67e5\u3001\u8fc7\u6ee4\u548c\u9a8c\u8bc1\u7ed3\u6784\u6570\u636e\u96c6\u3002\u53ef\u4ee5\u68c0\u67e5\u6210\u5206\u3001\u5206\u6790\u6027\u8d28\u8303\u56f4\u3001\u68c0\u6d4b\u77ed\u8ddd\u79bb\u63a5\u89e6\u3001\u6309\u5404\u79cd\u6761\u4ef6\u8fc7\u6ee4\u7ed3\u6784\u3001\u67e5\u627e NEP \u8bad\u7ec3\u6570\u636e\u4e2d\u7684\u5f02\u5e38\u503c\uff0c\u4ee5\u53ca\u4f30\u7b97\u5269\u4f59\u6a21\u62df\u65f6\u95f4\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":"<p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/analyzer/</code></p> <p>\u786e\u4fdd\u5df2\u5b89\u88c5 GPUMDkit\u3002\u5b89\u88c5\u8bf4\u660e\u8bf7\u53c2\u89c1\u5feb\u901f\u5165\u95e8\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_3","title":"\u6982\u89c8","text":"\u4efb\u52a1 \u547d\u4ee4 \u7528\u9014 \u6210\u5206\u5206\u6790 <code>gpumdkit.sh -analyze_comp train.xyz</code> \u6309\u5316\u5b66\u6210\u5206\u5206\u7ec4 \u5316\u5b66\u7269\u79cd <code>gpumdkit.sh -chem_species train.xyz</code> \u5217\u51fa\u6587\u4ef6\u4e2d\u7684\u5143\u7d20 \u6027\u8d28\u8303\u56f4 <code>gpumdkit.sh -range train.xyz force</code> \u68c0\u67e5\u80fd\u91cf/\u529b/virial \u8303\u56f4 \u6700\u77ed\u8ddd\u79bb <code>gpumdkit.sh -min_dist dump.xyz</code> \u5feb\u901f\u8ddd\u79bb\u68c0\u67e5\uff08\u65e0 PBC\uff09 \u6700\u77ed\u8ddd\u79bb\uff08PBC\uff09 <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> \u51c6\u786e\u8ddd\u79bb\u68c0\u67e5\uff08\u542b PBC\uff09 \u7535\u8377\u5e73\u8861 <code>gpumdkit.sh -cbc train.xyz</code> \u6c27\u5316\u6001\u5e73\u8861\u68c0\u67e5 \u8ddd\u79bb\u8fc7\u6ee4 <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> \u79fb\u9664\u77ed\u8ddd\u79bb\u63a5\u89e6\u7684\u7ed3\u6784 \u76d2\u5b50\u8fc7\u6ee4 <code>gpumdkit.sh -filter_box dump.xyz 13</code> \u79fb\u9664\u76d2\u5b50\u8fc7\u5927\u7684\u7ed3\u6784 \u6027\u8d28\u8fc7\u6ee4 <code>gpumdkit.sh -filter_value train.xyz force 20</code> \u6309\u80fd\u91cf/\u529b/virial \u9608\u503c\u8fc7\u6ee4 \u5bf9\u8ddd\u79bb\u8303\u56f4 <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> \u6309\u5bf9\u8ddd\u79bb\u63d0\u53d6\u7ed3\u6784 \u5f02\u5e38\u68c0\u6d4b \u83dc\u5355 502 \u67e5\u627e\u8bad\u7ec3\u96c6\u4e2d\u9ad8 RMSE \u7684\u7ed3\u6784 \u6982\u7387\u5bc6\u5ea6 <code>gpumdkit.sh -pda &lt;\u53c2\u8003\u7ed3\u6784&gt; &lt;\u8f68\u8ff9&gt; &lt;\u5143\u7d20&gt; &lt;\u7f51\u683c\u95f4\u8ddd&gt;</code> 3D \u6982\u7387\u5bc6\u5ea6\u5206\u6790\u6269\u6563\u901a\u9053 GPUMD \u65f6\u95f4 <code>gpumdkit.sh -time gpumd</code> \u4f30\u7b97 GPUMD \u5269\u4f59\u8fd0\u884c\u65f6\u95f4 NEP \u65f6\u95f4 <code>gpumdkit.sh -time nep</code> \u4f30\u7b97 NEP \u5269\u4f59\u8bad\u7ec3\u65f6\u95f4"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_4","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit \u5e76\u9009\u62e9 <code>5) Analyzer</code>\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u5206\u6790\u5de5\u5177\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                    ANALYZER TOOLS                    |\n+------------------------------------------------------+\n| 501) Analyze composition of extxyz                   |\n| 502) Find outliers of extxyz                         |\n| 503) Analyze chemical species of extxyz              |\n| 504) Check charge balance of extxyz                  |\n| 505) Analyze energy/force/virial range               |\n| 506) Filter structures by minimum distance           |\n| 507) Get minimum interatomic distance                |\n| 508) Probability density analysis                    |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5927\u591a\u6570\u5206\u6790\u529f\u80fd\u4e5f\u63d0\u4f9b\u76f4\u63a5 CLI \u8c03\u7528\u65b9\u5f0f\uff0c\u6982\u89c8\u8868\u548c\u540e\u7eed\u5c0f\u8282\u4e2d\u5217\u51fa\u4e86\u5e38\u7528\u547d\u4ee4\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_5","title":"\u6210\u5206\u5206\u6790","text":"<p><code>analyze_composition.py</code> \u5206\u6790 extxyz \u6587\u4ef6\u7684\u6210\u5206\uff0c\u5e76\u5141\u8bb8\u5bfc\u51fa\u5b50\u96c6\u3002</p> <p>\u529f\u80fd\uff1a \u6309\u5316\u5b66\u6210\u5206\u5bf9\u7ed3\u6784\u5206\u7ec4\uff0c\u5e76\u663e\u793a\u6bcf\u79cd\u6210\u5206\u7684\u7ed3\u6784\u6570\u91cf\u3002\u53ef\u4ee5\u6309\u6210\u5206\u5bfc\u51fa\u5b50\u96c6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>501</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>\u5f53 <code>train.xyz</code> \u5305\u542b\u4e0d\u540c\u4f53\u7cfb\u6216\u4e0d\u540c\u5c3a\u5bf8\u7684\u7ed3\u6784\u65f6\u5f88\u6709\u7528\u3002\u53ef\u4ee5\u4ece\u4ea4\u4e92\u63d0\u793a\u4e2d\u6309\u6210\u5206\u5bfc\u51fa\u5b50\u96c6\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_6","title":"\u5316\u5b66\u7269\u79cd","text":"<p><code>analyze_chem_species.py</code> \u5217\u51fa extxyz \u6587\u4ef6\u4e2d\u6240\u6709\u552f\u4e00\u7684\u5316\u5b66\u7269\u79cd\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -chem_species train.xyz\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_7","title":"\u6027\u8d28\u8303\u56f4\u5206\u6790","text":"<p><code>energy_force_virial_analyzer.py</code> \u8ba1\u7b97\u5e76\u53ef\u89c6\u5316 extxyz \u6587\u4ef6\u4e2d\u6027\u8d28\u7684\u8303\u56f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <p>\u652f\u6301\u7684\u6027\u8d28\uff1a <code>energy</code>\u3001<code>force</code>\u3001<code>virial</code></p> <pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist    # \u663e\u793a\u76f4\u65b9\u56fe\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Force range: 0.03210566767721861 to 9.230115912468435\n</code></pre> <p>\u4f7f\u7528 <code>hist</code> \u9009\u9879\uff1a</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_8","title":"\u6700\u77ed\u8ddd\u79bb\u68c0\u67e5","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#pbc","title":"\u65e0 PBC\uff08\u5feb\u901f\uff09","text":"<p><code>get_min_dist.py</code> \u8ba1\u7b97\u4e0d\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u7684\u6700\u77ed\u539f\u5b50\u95f4\u8ddd\u3002\u901f\u5ea6\u5feb\uff0c\u4f46\u5bf9\u5468\u671f\u6027\u4f53\u7cfb\u53ef\u80fd\u4e0d\u51c6\u786e\u3002</p> <p>\u529f\u80fd\uff1a \u62a5\u544a\u6bcf\u5e27\u4e2d\u6bcf\u5bf9\u5143\u7d20\u4e4b\u95f4\u7684\u6700\u77ed\u8ddd\u79bb\uff0c\u5ffd\u7565\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>507</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>+---------------------------+\n|   PBC ignored for speed   |\n| use -min_dist_pbc for PBC |\n+---------------------------+\nMinimum interatomic distances:\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.480     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre> <p>\u8bf4\u660e\uff1a \u7528\u4e8e\u5feb\u901f\u68c0\u67e5\u3002\u5bf9\u4e8e\u5468\u671f\u6027\u4f53\u7cfb\uff0c\u5efa\u8bae\u4f7f\u7528 <code>-min_dist_pbc</code> \u83b7\u5f97\u51c6\u786e\u7ed3\u679c\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#pbc_1","title":"\u542b PBC\uff08\u51c6\u786e\uff09","text":"<p><code>get_min_dist_pbc.py</code> \u8ba1\u7b97\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u7684\u6700\u77ed\u539f\u5b50\u95f4\u8ddd\u3002</p> <p>\u529f\u80fd\uff1a \u62a5\u544a\u6bcf\u5bf9\u5143\u7d20\u4e4b\u95f4\u7684\u6700\u77ed\u8ddd\u79bb\uff0c\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>507</code>\uff0c\u5f53\u63d0\u793a\u662f\u5426\u8003\u8651 PBC \u65f6\u8f93\u5165 <code>y</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_9","title":"\u7ed3\u6784\u8fc7\u6ee4","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_10","title":"\u6309\u6700\u77ed\u8ddd\u79bb\u8fc7\u6ee4","text":"<p><code>filter_structures_by_distance_pbc.py</code> \u79fb\u9664\u4efb\u4f55\u539f\u5b50\u95f4\u8ddd\u4f4e\u4e8e\u9608\u503c\u7684\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>\u79fb\u9664\u4efb\u4f55\u539f\u5b50\u95f4\u8ddd\u4f4e\u4e8e <code>1.0 \u00c5</code> \u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_11","title":"\u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4","text":"<p><code>filter_exyz_by_box.py</code> \u6309\u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>\u4fdd\u7559\u6240\u6709\u76d2\u5b50\u8fb9\u957f\u4f4e\u4e8e <code>13 \u00c5</code> \u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_12","title":"\u6309\u6027\u8d28\u503c\u8fc7\u6ee4","text":"<p><code>filter_exyz_by_value.py</code> \u6309\u80fd\u91cf\u3001\u529b\u6216 virial \u9608\u503c\u8fc7\u6ee4\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <p>\u652f\u6301\u7684\u6027\u8d28\uff1a <code>energy</code>\u3001<code>force</code>\u3001<code>virial</code></p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre> <p>\u8fc7\u6ee4\u6389\u529b\u5206\u91cf\u8d85\u8fc7 <code>20 eV/\u00c5</code>\uff08\u6216\u80fd\u91cf\u8d85\u8fc7 <code>5 eV/atom</code>\uff09\u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_13","title":"\u6309\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4","text":"<p><code>filter_dist_range.py</code> \u63d0\u53d6\u7279\u5b9a\u5143\u7d20\u5bf9\u8ddd\u79bb\u5728\u7ed9\u5b9a\u8303\u56f4\u5185\u7684\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>\u63d0\u53d6 Li-Li \u6700\u77ed\u8ddd\u79bb\u5728 <code>1.8 \u00c5</code> \u5230 <code>2.0 \u00c5</code> \u4e4b\u95f4\u7684\u7ed3\u6784\u3002\u8f93\u51fa\uff1a<code>filtered_Li_Li_1.8_2.0.xyz</code>\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_14","title":"\u7535\u8377\u5e73\u8861\u68c0\u67e5","text":"<p><code>charge_balance_check.py</code> \u68c0\u67e5\u7ed3\u6784\u7684\u6c27\u5316\u6001\u5e73\u8861\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>\u8f93\u51fa\u6587\u4ef6\uff1a</p> <ul> <li><code>balanced.xyz</code> \u2014 \u7535\u8377\u5e73\u8861\u7684\u7ed3\u6784</li> <li><code>unbalanced.xyz</code> \u2014 \u7535\u8377\u4e0d\u5e73\u8861\u7684\u7ed3\u6784</li> <li><code>indices.txt</code> \u2014 \u5e73\u8861\u7ed3\u6784\u7684\u7d22\u5f15</li> </ul> <p>\u9002\u7528\u4e8e\u5177\u6709\u660e\u786e\u6c27\u5316\u6001\u7684\u4f53\u7cfb\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_15","title":"\u5f02\u5e38\u68c0\u6d4b","text":"<p><code>find_outliers.py</code> \u57fa\u4e8e\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u7684 RMSE \u9608\u503c\u67e5\u627e NEP \u8bad\u7ec3\u6570\u636e\u4e2d\u7684\u5f02\u5e38\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>stress_train.out</code>\u3001<code>train.xyz</code></p> <p>\u8fd9\u4e9b\u6587\u4ef6\u5728 NEP \u8bad\u7ec3\u8fc7\u7a0b\u4e2d\u751f\u6210\u3002\u811a\u672c\u6bd4\u8f83 DFT \u4e0e NEP \u7684\u9884\u6d4b\uff0c\u8bc6\u522b\u8bef\u5dee\u8f83\u5927\u7684\u7ed3\u6784\u3002</p> <pre><code># \u4ea4\u4e92\u6a21\u5f0f\ngpumdkit.sh    # \u9009\u62e9\uff1a5) \u5206\u6790\u5de5\u5177 \u2192 502) \u67e5\u627e\u5f02\u5e38\u7ed3\u6784\n</code></pre> <p>\u4ea4\u4e92\u63d0\u793a\uff1a</p> <pre><code>Enter energy RMSE threshold (meV/atom): 1\nEnter force RMSE threshold (meV/\u00c5): 60\nEnter stress RMSE threshold (GPa): 0.03\n</code></pre> <p>\u8f93\u51fa\u6587\u4ef6\uff1a</p> <ul> <li><code>selected.xyz</code> \u2014 \u8d85\u8fc7 RMSE \u9608\u503c\u7684\u7ed3\u6784\uff08\u5f02\u5e38\u503c\uff09</li> <li><code>remained.xyz</code> \u2014 \u5728\u9608\u503c\u5185\u7684\u7ed3\u6784</li> <li><code>selected_remained.png</code> \u2014 \u5bf9\u6bd4\u56fe</li> </ul> <p>\u7528\u9014\uff1a NEP \u8bad\u7ec3\u540e\uff0c\u7528\u6b64\u5de5\u5177\u8bc6\u522b\u5bf9\u8bef\u5dee\u8d21\u732e\u6700\u5927\u7684\u95ee\u9898\u7ed3\u6784\u3002\u79fb\u9664\u6216\u6539\u8fdb\u8fd9\u4e9b\u7ed3\u6784\u4ee5\u63d0\u5347\u8bad\u7ec3\u96c6\u8d28\u91cf\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_16","title":"\u65f6\u95f4\u4f30\u7b97","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#gpumd","title":"GPUMD \u5269\u4f59\u65f6\u95f4","text":"<p><code>time_consuming_gpumd.sh</code> \u4f30\u7b97 GPUMD \u6a21\u62df\u7684\u5269\u4f59\u65f6\u95f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>run.in</code>\u3001<code>thermo.out</code>\uff08\u5728\u5f53\u524d GPUMD \u5de5\u4f5c\u76ee\u5f55\u4e2d\uff09</p> <pre><code>gpumdkit.sh -time gpumd\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>----------------- System Information ----------------\ntotal frames: 1050000\n-----------------------------------------------------\nCurrent Frame  Speed (steps/s)   Total Time       Time Left       Estimated End\n-------------   -------------   -------------   -------------   -----------------\n    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04\n    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#nep","title":"NEP \u5269\u4f59\u65f6\u95f4","text":"<p><code>time_consuming_nep.sh</code> \u4f30\u7b97 NEP \u8bad\u7ec3\u7684\u5269\u4f59\u65f6\u95f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code>\uff08\u5728\u5f53\u524d NEP \u5de5\u4f5c\u76ee\u5f55\u4e2d\uff09</p> <pre><code>gpumdkit.sh -time nep\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>+-----------------+-----------+-----------------+---------------------+\n|       Step      | Time Diff |    Time Left    |    Finish Time      |\n+-----------------+-----------+-----------------+---------------------+\n| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |\n| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |\n| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |\n+-----------------+-----------+-----------------+---------------------+\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_17","title":"\u6982\u7387\u5bc6\u5ea6\u5206\u6790","text":"<p><code>probability_density_analysis.py</code> \u8ba1\u7b97\u79fb\u52a8\u79bb\u5b50\u7684 3D \u6982\u7387\u5bc6\u5ea6\uff0c\u7528\u4e8e\u6269\u6563\u901a\u9053\u5206\u6790\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a \u53c2\u8003\u7ed3\u6784\uff08POSCAR\uff09\u3001\u8f68\u8ff9\u6587\u4ef6\uff08extxyz\uff09</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n</code></pre> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>LLZO.vasp</code> \u53c2\u8003\u7ed3\u6784\uff08POSCAR \u683c\u5f0f\uff09 <code>dump.xyz</code> \u8f68\u8ff9\u6587\u4ef6\uff08extxyz \u683c\u5f0f\uff09 <code>Li</code> \u76ee\u6807\u79fb\u52a8\u79bb\u5b50 <code>0.25</code> \u6982\u7387\u5bc6\u5ea6\u7f51\u683c\u95f4\u8ddd\uff08\u00c5\uff09 <p>\u8f93\u51fa\uff1a <code>probability_density_0.25.vasp</code> \u2014 VASP \u683c\u5f0f\u7684\u6982\u7387\u5bc6\u5ea6\u7f51\u683c\uff0c\u53ef\u7528 VESTA \u7b49\u5de5\u5177\u53ef\u89c6\u5316\u3002</p> <p>\u53ef\u89c6\u5316\u5efa\u8bae\uff1a</p> <ol> <li>\u5728 VESTA \u4e2d\u6253\u5f00 <code>probability_density_0.25.vasp</code></li> <li>\u4f7f\u7528 \"Edit \u2192 Data \u2192 Volumetric Data\" \u8c03\u6574\u7b49\u503c\u9762\u7ea7\u522b</li> <li>\u6309\u6570\u503c\u5bf9\u6982\u7387\u5bc6\u5ea6\u7740\u8272\uff0c\u4ee5\u7a81\u51fa\u4f18\u9009\u6269\u6563\u8def\u5f84</li> <li>\u53e0\u52a0\u6676\u4f53\u7ed3\u6784\u4f5c\u4e3a\u53c2\u8003</li> </ol>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_18","title":"\u793a\u4f8b\u5de5\u4f5c\u6d41","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_19","title":"\u7ed3\u6784\u8d28\u91cf\u68c0\u67e5","text":"<pre><code># 1. \u68c0\u67e5\u6210\u5206\ngpumdkit.sh -analyze_comp train.xyz\n\n# 2. \u68c0\u67e5\u80fd\u91cf/\u529b\u8303\u56f4\ngpumdkit.sh -range train.xyz force hist\n\n# 3. \u68c0\u67e5\u6700\u77ed\u8ddd\u79bb\ngpumdkit.sh -min_dist_pbc train.xyz\n\n# 4. \u67e5\u627e\u5f02\u5e38\u503c\uff08NEP \u8bad\u7ec3\u540e\uff09\n# \u4ea4\u4e92\uff1a5) \u5206\u6790\u5de5\u5177 \u2192 502\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_20","title":"\u7ed3\u6784\u8fc7\u6ee4\u6d41\u6c34\u7ebf","text":"<pre><code># 1. \u6309\u6700\u77ed\u8ddd\u79bb\u8fc7\u6ee4\ngpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n\n# 2. \u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4\ngpumdkit.sh -filter_box filtered_dist_pbc.xyz 13\n\n# 3. \u6309\u529b\u9608\u503c\u8fc7\u6ee4\ngpumdkit.sh -filter_value filtered_box.xyz force 20\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_21","title":"\u6269\u6563\u901a\u9053\u5206\u6790","text":"<pre><code># 1. \u8ba1\u7b97\u6982\u7387\u5bc6\u5ea6\ngpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n\n# 2. \u7528 VESTA \u53ef\u89c6\u5316\n# \u6253\u5f00 probability_density_0.25.vasp\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html","title":"\u547d\u4ee4\u53c2\u8003","text":"\ud83d\udccb \u547d\u4ee4\u53c2\u8003 <p>\u672c\u9875\u5217\u51fa GPUMDkit \u7a33\u5b9a\u7684\u547d\u4ee4\u884c\u5feb\u6377\u5165\u53e3\u3002\u5bf9\u4e8e\u53c2\u6570\u8f83\u591a\u3001\u9700\u8981\u9009\u62e9\u7684\u4efb\u52a1\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528\u4ea4\u4e92\u6a21\u5f0f\u3002</p> <p>\u6e90\u8868\u7ef4\u62a4\u5728 <code>docs/command_reference.tsv</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#gpumdkitsh-h","title":"<code>gpumdkit.sh -h</code> \u8f93\u51fa","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |\n| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_1","title":"\u4e3b\u547d\u4ee4","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-h</code> <code>gpumdkit.sh -h</code> \u663e\u793a\u901a\u7528\u5e2e\u52a9 <code>-update</code> <code>gpumdkit.sh -update</code> \u66f4\u65b0 GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> \u6e05\u7406\u5f53\u524d\u76ee\u5f55\u4e2d\u7684\u5197\u4f59\u6587\u4ef6"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_2","title":"\u683c\u5f0f\u8f6c\u6362","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K \u8f93\u51fa\u8f6c xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR \u8f6c extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF \u8f6c POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF \u8f6c extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR \u8f6c extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz \u591a\u5e27\u8f6c POSCAR \u6587\u4ef6 <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR \u8f6c LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump \u8f6c extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory \u8f6c extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> \u6309\u6676\u80de\u500d\u6570\u6269\u80de <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> \u6309\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> \u6dfb\u52a0 GPUMD group \u6807\u7b7e <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> \u6dfb\u52a0\u7ed3\u6784\u6743\u91cd <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> \u63d0\u53d6\u5355\u5e27 <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> \u6e05\u7406 extxyz \u5197\u4f59\u5c5e\u6027 <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> \u6309\u6bd4\u4f8b\u8303\u56f4\u63d0\u53d6\u5e27"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_3","title":"\u8ba1\u7b97\u5668","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> \u79bb\u5b50\u7535\u5bfc\u7387 <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP \u6027\u8d28\u9884\u6d4b <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP \u63cf\u8ff0\u7b26 <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u57fa\u4e8e NEP \u7684 NEB <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784\u4f18\u5316 <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> \u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> \u90bb\u5c45\u5217\u8868 <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> \u4f4d\u79fb <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> \u5e73\u5747\u7ed3\u6784 <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> \u516b\u9762\u4f53\u503e\u659c <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 \u5c40\u57df\u6781\u5316"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_4","title":"\u5206\u6790\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> \u6027\u8d28\u8303\u56f4\u5206\u6790 <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> \u6210\u5206\u5206\u6790 <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> \u5143\u7d20\u5217\u8868 <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> \u7535\u8377\u5e73\u8861\u68c0\u67e5 <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> \u65e0 PBC \u6700\u5c0f\u8ddd\u79bb <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> \u5e26 PBC \u6700\u5c0f\u8ddd\u79bb <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u5e26 PBC \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> \u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4 <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> \u6027\u8d28\u9608\u503c\u8fc7\u6ee4 <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> \u5143\u7d20\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4 <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> \u6982\u7387\u5bc6\u5ea6\u5206\u6790"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_5","title":"\u53ef\u89c6\u5316","text":"<p>\u4f7f\u7528\uff1a</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>\u5e38\u7528\u7c7b\u578b\u5305\u62ec <code>train</code>\u3001<code>prediction</code>\u3001<code>thermo</code>\u3001<code>msd</code>\u3001<code>sdc</code>\u3001<code>rdf</code>\u3001<code>emd</code>\u3001<code>nemd</code>\u3001<code>hnemd</code>\u3001<code>pdos</code> \u548c <code>plane-grid</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_6","title":"\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> \u76d1\u63a7 GPUMD \u6216 NEP \u8fdb\u5ea6 <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> \u4ea4\u4e92\u5f0f\u4fee\u6539 NEP \u6a21\u578b <code>-pynep</code> <code>gpumdkit.sh -pynep</code> \u5df2\u5f03\u7528\u7684 PyNEP FPS \u91c7\u6837"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html","title":"\u5de5\u4f5c\u6d41\u811a\u672c","text":"\ud83d\udd27 \u5de5\u4f5c\u6d41\u811a\u672c <p>\u5de5\u4f5c\u6d41\u811a\u672c\u7528\u4e8e\u81ea\u52a8\u5316\u91cd\u590d\u6027\u7684 DFT\u3001MD \u548c NEP \u6570\u636e\u51c6\u5907\u6b65\u9aa4\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_1","title":"\u4ea4\u4e92\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>3) Workflow\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+---------------------------------------------------------+\n|                      WORKFLOW TOOLS                     |\n+---------------------------------------------------------+\n| 301) SCF batch pretreatment                             |\n| 302) MD sample batch pretreatment (gpumd)               |\n| 303) MD sample batch pretreatment (lmp)                 |\n+---------------------------------------------------------+\n| 000) Return to the main menu                            |\n+---------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u5de5\u4f5c\u6d41 \u7528\u9014 301 SCF batch pretreatment \u51c6\u5907 DFT \u5355\u70b9\u8ba1\u7b97 302 MD sample batch pretreatment (GPUMD) \u51c6\u5907 GPUMD \u91c7\u6837\u8ba1\u7b97 303 MD sample batch pretreatment (LAMMPS) \u51c6\u5907 LAMMPS \u91c7\u6837\u8ba1\u7b97"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#scf","title":"SCF \u6279\u5904\u7406\u9884\u5904\u7406","text":"<p>\u9002\u7528\u4e8e\u5df2\u6709\u591a\u4e2a\u7ed3\u6784\uff0c\u9700\u8981\u51c6\u5907\u7b2c\u4e00\u6027\u539f\u7406\u5355\u70b9\u8ba1\u7b97\u7684\u60c5\u51b5\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#vasp","title":"VASP","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a\u7ed3\u6784\u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u811a\u672c\u6309\u4ee5\u4e0b\u987a\u5e8f\u68c0\u6d4b\uff1a</p> <ol> <li>\u5982\u679c\u5b58\u5728\u4e00\u4e2a\u6216\u591a\u4e2a <code>.vasp</code> \u6587\u4ef6\uff0c\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c <code>.vasp</code> \u548c <code>.xyz</code> \u540c\u65f6\u5b58\u5728\uff0c\u4f1a\u6253\u5370\u63d0\u793a\uff0c\u5e76\u53ea\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u53ea\u6709\u4e00\u4e2a <code>.xyz</code>\uff0c\u4f1a\u628a\u8fd9\u4e2a extxyz \u8f6c\u4e3a POSCAR \u6587\u4ef6\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</li> </ol> <p>\u8fd0\u884c\u524d\u7684\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>fp/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u7528\u6237\u628a <code>INCAR</code>\u3001<code>POTCAR</code>\u3001<code>KPOINTS</code> \u653e\u5230 <code>fp/</code> \u4e2d\uff0c\u8ba1\u7b97\u76ee\u5f55\u4f1a\u94fe\u63a5\u8fd9\u91cc\u7684\u6587\u4ef6\u3002</p> <p>\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u8f93\u5165\u7684 <code>prefix</code> \u4f1a\u4f5c\u4e3a\u8ba1\u7b97\u6587\u4ef6\u5939\u540d\u524d\u7f00\u3002\u540e\u7eed\u4f7f\u7528 <code>out2xyz</code> \u63d0\u53d6\u7ed3\u679c\u65f6\uff0c\u6587\u4ef6\u5939\u540d\u4f1a\u4f5c\u4e3a <code>config_type</code> \u5199\u5165 extxyz\uff0c\u4fbf\u4e8e\u4e4b\u540e\u68c0\u67e5\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#cp2k","title":"CP2K","text":"<p>CP2K \u53ef\u4ee5\u4ece\u4ea4\u4e92\u83dc\u5355\u8fdb\u5165\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u547d\u4ee4\u884c\u8c03\u7528\uff1a</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4f1a\u8981\u6c42\u8f93\u5165\uff1a</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>CP2K \u6a21\u677f\u5e94\u8bbe\u7f6e\u4e3a\u4ece <code>pos.xyz</code> \u8bfb\u53d6\u5750\u6807\u3002\u53c2\u8003\u6a21\u677f\u5728\uff1a</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>\u811a\u672c\u4f1a\u4e3a\u6bcf\u4e2a\u7ed3\u6784\u751f\u6210 <code>&lt;prefix&gt;_&lt;index&gt;/</code> \u76ee\u5f55\uff0c\u5e76\u5199\u5165 <code>input.inp</code> \u548c <code>pos.xyz</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#md","title":"MD \u91c7\u6837\u9884\u5904\u7406","text":""},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#gpumd","title":"GPUMD","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 302\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u68c0\u6d4b\u987a\u5e8f\u4e0e VASP SCF \u9884\u5904\u7406\u4e00\u81f4\uff1a\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</p> <p>\u8fd0\u884c\u524d\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>md/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>nep.txt</code> \u548c <code>run_*.in</code> \u653e\u5165 <code>md/</code>\u3002\u4f8b\u5982 <code>run_1.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_1/run.in</code>\uff0c<code>run_2.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_2/run.in</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#lammps","title":"LAMMPS","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 303\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\uff1b\u4e24\u79cd\u683c\u5f0f\u540c\u65f6\u5b58\u5728\u65f6\u4f18\u5148\u5904\u7406 <code>.vasp</code>\u3002</p> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>lmprun.in</code> \u548c <code>nep.txt</code> \u653e\u5230 <code>md/</code> \u4e2d\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_2","title":"\u4e3b\u52a8\u5b66\u4e60\u5f0f\u6d41\u7a0b","text":"<p>\u5e38\u89c1 NEP \u6570\u636e\u8fed\u4ee3\u6d41\u7a0b\uff1a</p> <ol> <li>\u4f7f\u7528\u5f53\u524d <code>nep.txt</code> \u8fd0\u884c MD\uff1b</li> <li>\u6536\u96c6 <code>dump.xyz</code> \u6216 <code>active.xyz</code>\uff1b</li> <li>\u5220\u9664\u660e\u663e\u4e0d\u5408\u7406\u7ed3\u6784\uff1b</li> <li>\u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\uff1b</li> <li>\u8fd0\u884c DFT \u5355\u70b9\uff1b</li> <li>\u5c06 DFT \u7ed3\u679c\u8f6c\u6362\u4e3a extxyz\uff1b</li> <li>\u8ffd\u52a0\u5230 <code>train.xyz</code>\uff1b</li> <li>\u91cd\u65b0\u8bad\u7ec3 NEP\u3002</li> </ol> <p>\u66f4\u5b8c\u6574\u7684\u5f00\u53d1\u7248\u4e3b\u52a8\u5b66\u4e60\u811a\u672c\u8bf4\u660e\u89c1 \u4e3b\u52a8\u5b66\u4e60\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_3","title":"\u57fa\u4e8e\u6a21\u677f\u7684\u6e29\u5ea6\u7cfb\u5217","text":"<p>\u5bf9\u4e8e\u7b80\u5355\u7684\u6e29\u5ea6\u7cfb\u5217\u6a21\u62df\uff0c\u4f7f\u7528 shell \u5faa\u73af\u5373\u53ef\uff1a</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>\u7136\u540e\u6839\u636e\u4f60\u7684\u96c6\u7fa4\u7cfb\u7edf\u63d0\u4ea4\u751f\u6210\u7684\u6587\u4ef6\u5939\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_4","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u5de5\u4f5c\u6d41\u811a\u672c\u548c\u96c6\u7fa4\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u6279\u91cf\u63d0\u4ea4\u524d\u5148\u7528\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u3002</li> <li>\u6a21\u677f\u6587\u4ef6\u5982 <code>INCAR</code>\u3001<code>KPOINTS</code>\u3001<code>POTCAR</code>\u3001<code>run.in</code> \u5e94\u4ed4\u7ec6\u68c0\u67e5\u3002</li> <li>\u6279\u91cf DFT \u524d\u5148\u7528\u5206\u6790\u548c\u91c7\u6837\u811a\u672c\u6e05\u7406\u5019\u9009\u7ed3\u6784\u3002</li> </ul>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html","title":"\u5feb\u901f\u5165\u95e8","text":"\ud83d\ude80 \u5feb\u901f\u5165\u95e8 <p>\u672c\u9875\u5e2e\u52a9\u4f60\u5b89\u88c5 GPUMDkit \u5e76\u8fd0\u884c\u7b2c\u4e00\u4e2a\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u6216\u76f4\u63a5\u4f7f\u7528\u547d\u4ee4\u884c\u9009\u9879\u6765\u4f7f\u7528 GPUMDkit\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>GPUMDkit \u4e3a\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u7684\u5e38\u89c1\u4efb\u52a1\u63d0\u4f9b\u7edf\u4e00\u5165\u53e3\u2014\u2014\u683c\u5f0f\u8f6c\u6362\u3001\u7ed3\u6784\u5206\u6790\u3001\u6027\u8d28\u8ba1\u7b97\u548c\u53ef\u89c6\u5316\u2014\u2014\u65e0\u9700\u7f16\u5199\u81ea\u5b9a\u4e49\u811a\u672c\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#1-python","title":"1. \u51c6\u5907 Python \u73af\u5883","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>\u90e8\u5206\u53ef\u9009\u529f\u80fd\u9700\u8981\u989d\u5916\u4f9d\u8d56\uff1a</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>\u5176\u4ed6 Python \u4f9d\u8d56\u7531\u5bf9\u5e94\u811a\u672c\u5728\u8fd0\u884c\u65f6\u5bfc\u5165\u3002\u5982\u679c\u7f3a\u5c11\u67d0\u4e2a\u5305\uff0c\u4f7f\u7528\u5bf9\u5e94\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u63d0\u793a\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#2-gpumdkit","title":"2. \u5b89\u88c5 GPUMDkit","text":"<p>\u514b\u9686\u4ed3\u5e93\u5e76\u8fd0\u884c\u5b89\u88c5\u811a\u672c\uff1a</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre> <p>\u5b89\u88c5\u811a\u672c\u4f1a\u5199\u5165 <code>GPUMDkit_path</code> \u548c <code>PATH</code> \u8bbe\u7f6e\uff0c\u5e76\u5728\u5f53\u524d shell \u4e2d\u52a0\u8f7d\u3002\u9ed8\u8ba4\u5199\u5165 <code>~/.bashrc</code>\uff1b\u5982\u679c\u5f53\u524d shell \u662f zsh\uff0c\u5219\u5199\u5165 <code>~/.zshrc</code>\u3002\u5982\u679c\u68c0\u6d4b\u5230\u5df2\u6709 GPUMDkit \u8def\u5f84\uff0c\u5b89\u88c5\u811a\u672c\u4f1a\u6253\u5370\u65e7\u8def\u5f84\u5e76\u8be2\u95ee\u662f\u5426\u66ff\u6362\uff1b\u4fee\u6539 rc \u6587\u4ef6\u524d\u4f1a\u5148\u521b\u5efa\u5907\u4efd\u3002</p> <p>\u5178\u578b\u5b89\u88c5\u8f93\u51fa\uff1a</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>\u5982\u679c\u4e4b\u524d\u5df2\u7ecf\u5b89\u88c5\u8fc7 GPUMDkit\uff0c\u53ef\u80fd\u4f1a\u770b\u5230\uff1a</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#3","title":"3. \u9a8c\u8bc1\u5b89\u88c5","text":"<pre><code>gpumdkit.sh -h\n</code></pre> <p>\u6b64\u547d\u4ee4\u4f1a\u6253\u5370\u5e2e\u52a9\u8868\uff0c\u5217\u51fa\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_3","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u6253\u5f00\u4e3b\u83dc\u5355\uff1a</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre> <p>\u6309\u6570\u5b57\u9009\u62e9\u6a21\u5757\u3002\u6bcf\u4e2a\u6a21\u5757\u63d0\u4f9b\u5305\u542b\u5177\u4f53\u529f\u80fd\u7684\u5b50\u83dc\u5355\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_4","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<p>\u76f4\u63a5\u547d\u4ee4\u4f7f\u7528\u56fa\u5b9a\u7684\u4f4d\u7f6e\u53c2\u6570\uff1a</p> <pre><code>gpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>\u7b2c\u4e00\u4e2a\u793a\u4f8b\u8bfb\u53d6 <code>POSCAR</code>\uff0c\u5199\u51fa <code>model.xyz</code>\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_5","title":"\u5e38\u89c1\u793a\u4f8b","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#gpumd-group","title":"\u6dfb\u52a0 GPUMD group \u6807\u7b7e","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>group \u6807\u7b7e\u7528\u4e8e\u4e00\u4e9b\u9700\u8981\u539f\u5b50\u5206\u7ec4\u7684 GPUMD \u76f8\u5173\u6d41\u7a0b\u548c\u5206\u6790\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep","title":"\u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep_1","title":"\u7ed8\u5236 NEP \u6d4b\u8bd5\u96c6\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_6","title":"\u7ed8\u5236\u70ed\u529b\u5b66\u91cf","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#msd","title":"\u7ed8\u5236 MSD \u548c\u81ea\u6269\u6563\u7cfb\u6570","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_7","title":"\u8bf4\u660e","text":"<ul> <li>\u4f7f\u7528 <code>gpumdkit.sh -h</code> \u67e5\u770b\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</li> <li>\u4f7f\u7528 <code>gpumdkit.sh -&lt;\u9009\u9879&gt; -h</code> \u83b7\u53d6\u7279\u5b9a\u9009\u9879\u7684\u5e2e\u52a9\uff08\u4f8b\u5982 <code>gpumdkit.sh -plt train -h</code>\uff09\u3002</li> <li>\u5404\u6a21\u5757\u7684\u8be6\u7ec6\u7528\u6cd5\u8bf7\u53c2\u89c1\u9996\u9875\u4e2d\u94fe\u63a5\u7684\u5bf9\u5e94\u6559\u7a0b\u9875\u9762\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html","title":"\u6781\u6027\u6750\u6599\u5206\u6790","text":"\ud83e\uddf2 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u672c\u6559\u7a0b\u4ecb\u7ecd GPUMDkit \u4e2d\u8ba1\u7b97\u5668\u9009\u9879 <code>406-410</code>\uff0c\u4ee5\u53ca <code>plane-grid</code> \u7ed8\u56fe\u6d41\u7a0b\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code> \u548c <code>Scripts/plt_scripts/</code></p> <p>\u672c\u6559\u7a0b\u5305\u542b\u901a\u7528\u5de5\u5177\u548c\u4f53\u7cfb\u76f8\u5173\u5de5\u5177\uff1a</p> <ul> <li><code>nlist</code>\u3001<code>disp</code> \u548c <code>avg-struct</code> \u53ef\u5e7f\u6cdb\u7528\u4e8e\u7ed3\u6784\u548c\u8f68\u8ff9\u5206\u6790\u3002</li> <li><code>oct-tilt</code> \u7528\u4e8e\u516b\u9762\u4f53\u73af\u5883\u5206\u6790\uff0c\u9700\u8981\u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u5468\u56f4\u6709 6 \u4e2a\u8fd1\u90bb\u3002</li> <li><code>pol-abo3</code> \u4e13\u7528\u4e8e <code>ABO3</code> \u4f53\u7cfb\u7684\u6781\u5316\u5206\u6790\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_1","title":"\u6982\u89c8","text":"\u6b65\u9aa4 CLI \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u8f93\u51fa \u6784\u5efa\u8fd1\u90bb\u5217\u8868 <code>gpumdkit.sh -calc nlist ...</code> <code>model.xyz</code> <code>nl-*.dat</code> \u8ba1\u7b97\u4f4d\u79fb <code>gpumdkit.sh -calc disp ...</code> \u8f68\u8ff9 + <code>nl-*.dat</code> <code>displacements.dat</code> \u5e73\u5747\u8f68\u8ff9\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct ...</code> \u8f68\u8ff9 \u5e73\u5747\u7ed3\u6784 extxyz \u516b\u9762\u4f53\u503e\u659c <code>gpumdkit.sh -calc oct-tilt ...</code> \u8f68\u8ff9 + B-O \u8fd1\u90bb\u5217\u8868 \u503e\u659c\u89d2\u6570\u636e\u8868 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 ...</code> \u8f68\u8ff9 + \u8fd1\u90bb\u5217\u8868 \u6781\u5316\u6570\u636e\u8868 plane-grid \u7ed8\u56fe <code>gpumdkit.sh -plt plane-grid ...</code> \u7ed3\u6784 + \u4f4d\u79fb\u6570\u636e \u5e73\u9762\u5256\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_2","title":"\u4f9d\u8d56","text":"<p>\u8fd9\u4e9b\u811a\u672c\u9700\u8981 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_3","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<p>\u9009\u9879 <code>406-410</code> \u662f\u672c\u6559\u7a0b\u4e2d\u7684\u6838\u5fc3\u529f\u80fd\u3002\u4e0b\u9762\u5404\u8282\u4f1a\u8bf4\u660e\u6bcf\u4e2a\u529f\u80fd\u7684\u7528\u9014\u548c\u8fd0\u884c\u65b9\u5f0f\u3002</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 4) Calculators\n</code></pre> <p>\u8ba1\u7b97\u5668\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5b8c\u6574\u53c2\u6570\u8bf4\u660e\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u547d\u4ee4\u67e5\u770b\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#406-calc_neighbor_listpy","title":"406) \u6784\u5efa\u8fd1\u90bb\u5217\u8868 (<code>calc_neighbor_list.py</code>)","text":"<p>\u4e3a\u6307\u5b9a\u4e2d\u5fc3\u5143\u7d20\u548c\u8fd1\u90bb\u5143\u7d20\u6784\u5efa\u8fd1\u90bb\u5217\u8868\u3002</p> <p>\u4f7f\u7528\u573a\u666f\uff1a \u8fd9\u901a\u5e38\u662f\u8fd0\u884c <code>disp</code>\u3001<code>oct-tilt</code> \u548c <code>pol-abo3</code> \u4e4b\u524d\u7684\u7b2c\u4e00\u6b65\uff0c\u56e0\u4e3a\u8fd9\u4e9b\u811a\u672c\u4f1a\u8bfb\u53d6 <code>nl-*.dat</code> \u8fd1\u90bb\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_4","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4e3a\u516b\u9762\u4f53\u5206\u6790\u6784\u5efa Ti-O \u6700\u8fd1 6 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# \u793a\u4f8b 2\uff1a\u4e3a A \u4f4d\u4e2d\u5fc3\u5206\u6790\u6784\u5efa Pb/Sr-O \u6700\u8fd1 12 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_5","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-x, --index</code>\uff1a   \u4ece\u8f93\u5165\u6587\u4ef6\u4e2d\u8bfb\u53d6\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-c, --cutoff</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u641c\u7d22\u622a\u65ad\u8ddd\u79bb\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> <li><code>-n, --neighbor-num</code>\uff08\u5fc5\u9700\uff09\uff1a   \u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u7684\u8fd1\u90bb\u6570\u91cf\u3002</li> <li><code>-d, --defect</code>\uff1a   \u7f3a\u9677\u6a21\u5f0f\u3002\u542f\u7528\u540e\uff0c\u5982\u679c\u8fd1\u90bb\u6570\u91cf\u4e0d\u8db3\uff0c\u7f3a\u5931\u4f4d\u7f6e\u4f1a\u7528\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u586b\u5145\u3002</li> <li><code>-C, --center-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u4e2d\u5fc3\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-E, --neighbor-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u8def\u5f84\u3002\u9ed8\u8ba4\u503c\uff1a<code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_6","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u8fd1\u90bb\u5217\u8868\u6587\u672c\u6587\u4ef6\uff0c\u4f8b\u5982 <code>nl-Ti-O.dat</code>\u3002</li> <li>\u6587\u4ef6\u662f\u4e00\u4e2a\u4e8c\u7ef4\u6574\u6570\u6570\u7ec4\uff0c\u5f62\u72b6\u4e3a <code>(n_center, neighbor_num + 1)</code>\u3002\u6bcf\u4e00\u884c\u5bf9\u5e94\u4e00\u4e2a\u4e2d\u5fc3\u539f\u5b50\uff1a\u7b2c\u4e00\u5217\u662f\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\uff0c\u540e\u7eed\u5217\u662f\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7\uff0c\u6240\u6709\u7f16\u53f7\u5747\u4e3a 1-based\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#407-calc_displacementpy","title":"407) \u4ece\u8f68\u8ff9\u8ba1\u7b97\u4f4d\u79fb (<code>calc_displacement.py</code>)","text":"<p>\u6839\u636e\u8f68\u8ff9\u6216\u6a21\u578b\u7ed3\u6784\u4ee5\u53ca\u8fd1\u90bb\u5217\u8868\uff0c\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_7","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece model.xyz \u8ba1\u7b97\u5355\u5e27\u4f4d\u79fb\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4f7f\u7528 movie.xyz \u7684\u6700\u540e 20% \u5e27\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_8","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7531 <code>nlist</code> \u751f\u6210\u7684\u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u90e8\u5206\u5e27\u3002   \u6574\u6570\u8868\u793a\u6700\u540e <code>N</code> \u5e27\uff1b   <code>0 &lt; value &lt; 1</code> \u8868\u793a\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_9","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>displacements.dat</code>\uff0c\u6216\u4f60\u6307\u5b9a\u7684\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e8c\u7ef4\u6570\u7ec4\uff1a\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u4e09\u5217\u5206\u522b\u4e3a <code>dx</code>\u3001<code>dy</code> \u548c <code>dz</code> \u4f4d\u79fb\u5206\u91cf\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#408-calc_averaged_structurepy","title":"408) \u8ba1\u7b97\u5e73\u5747\u7ed3\u6784 (<code>calc_averaged_structure.py</code>)","text":"<p>\u4ece\u9009\u5b9a\u8f68\u8ff9\u5e27\u751f\u6210\u4e00\u4e2a\u5e73\u5747\u7ed3\u6784\u3002 \u901a\u5e38\u53ef\u5728\u4f53\u7cfb\u5e73\u8861\u540e\u4f7f\u7528\uff1a\u5bf9\u4e8e\u63a5\u8fd1\u5e73\u8861\u7684\u56fa\u4f53\uff0c\u53ef\u4ee5\u5bf9\u76ee\u6807\u6e29\u5ea6\u4e0b\u7684\u4e00\u6bb5\u8f68\u8ff9\u53d6\u5e73\u5747\uff0c\u5e76\u5206\u6790\u8be5\u4ee3\u8868\u6027\u7ed3\u6784\uff0c\u800c\u4e0d\u662f\u9010\u5e27\u5904\u7406\u6bcf\u4e2a snapshot\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_10","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5e73\u5747\u6240\u6709\u5e27\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# \u793a\u4f8b 2\uff1a\u5e73\u5747\u9009\u5b9a\u5e27\u8303\u56f4 (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_11","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u8f68\u8ff9\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>movie.xyz</code>\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>averaged_structure.xyz</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_12","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u5355\u5e27\u5e73\u5747\u7ed3\u6784 extxyz \u6587\u4ef6\u3002</li> <li>\u4f4d\u7f6e\u5e73\u5747\u4f1a\u76f8\u5bf9\u4e8e\u6240\u9009\u7b2c\u4e00\u5e27\u8fdb\u884c MIC/PBC \u4fee\u6b63\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#409-calc_oct_tiltpy","title":"409) \u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c (<code>calc_oct_tilt.py</code>)","text":"<p>\u6839\u636e B-O \u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c\u89d2\u3002 \u8be5\u529f\u80fd\u5e38\u7528\u4e8e\u5206\u6790 <code>ABO3</code> \u4f53\u7cfb\u4e2d\u7684\u516b\u9762\u4f53\u8f6c\u52a8\u6a21\u5f0f\uff0c\u4f8b\u5982 <code>SrTiO3</code> \u548c <code>PbZrO3</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_13","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece\u5355\u5e27\u7ed3\u6784\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4ece\u8f68\u8ff9\u6700\u540e 20% \u5e27\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_14","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>octahedral_tilt.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_15","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>octahedral_tilt.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>theta_x</code>\u3001<code>theta_y</code>\u3001<code>theta_z</code>\uff0c\u5355\u4f4d\u4e3a degree\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#410-abo3-calc_polarization_abo3py","title":"410) \u8ba1\u7b97 ABO3 \u4f53\u7cfb\u6781\u5316 (<code>calc_polarization_abo3.py</code>)","text":"<p>\u8ba1\u7b97 <code>ABO3</code> \u4f53\u7cfb\u7684\u5c40\u57df\u6781\u5316\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_16","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5355\u5e27 ABO3 \u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# \u793a\u4f8b 2\uff1a\u9009\u5b9a\u8f68\u8ff9\u5e27\u8303\u56f4\u4e0a\u7684\u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_17","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>--nl-ba</code>\uff08\u5fc5\u9700\uff09\uff1a   B-A \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>--nl-bo</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>polarization.dat</code>\u3002</li> <li><code>--bec</code>\uff08\u5fc5\u9700\uff09\uff1a   Born \u6709\u6548\u7535\u8377\u9879\uff0c\u683c\u5f0f\u4e3a <code>Element=value</code>\u3002   \u793a\u4f8b\uff1a<code>Pb=2.5 Ti=4.0 O=-2.0</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul> <p>\u91cd\u8981\u68c0\u67e5\uff1a</p> <ul> <li><code>--bec</code> \u5fc5\u987b\u5305\u542b\u8f93\u5165\u7ed3\u6784\u4e2d\u7684\u6240\u6709\u5143\u7d20\u79cd\u7c7b\u3002</li> <li><code>--nl-ba</code> \u548c <code>--nl-bo</code> \u4e2d\u7684\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u5fc5\u987b\u5339\u914d\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_18","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>polarization.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>Px</code>\u3001<code>Py</code>\u3001<code>Pz</code>\uff0c\u5355\u4f4d\u4e3a <code>C/m^2</code>\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u5982\u679c\u603b Born \u7535\u8377\u4e0d\u5e73\u8861\uff0c\u811a\u672c\u4f1a\u6253\u5370 warning\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#plane-grid-plt_plane_gridpy","title":"Plane-grid \u53ef\u89c6\u5316 (<code>plt_plane_grid.py</code>)","text":"<p>\u4f60\u53ef\u4ee5\u53ef\u89c6\u5316 <code>displacements.dat</code> \u6216 <code>polarization.dat</code>\uff1a</p> <pre><code># \u793a\u4f8b 1\uff1aTi \u4f4d\u70b9\u4e0a\u7684\u4f4d\u79fb\u56fe\uff0c\u9009\u62e9\u7b2c\u4e00\u4e2a XY \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# \u793a\u4f8b 2\uff1aPb \u4f4d\u70b9\u4e0a\u7684\u6781\u5316\u56fe\uff0c\u9009\u62e9 XZ \u548c YZ \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>\u53c2\u6570\uff08\u5b8c\u6574\uff09\uff1a</p> <ul> <li><code>-i, --input</code>\uff1a   \u7528\u4e8e\u539f\u5b50\u5e03\u5c40\u548c\u5206\u5c42\u7684\u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-d, --disp</code>\uff1a   \u77e2\u91cf\u573a\u6570\u636e\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-e, --elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7528\u4e8e\u5c06\u77e2\u91cf\u6620\u5c04\u5230\u6676\u683c\u5c42\u4e0a\u7684\u4e2d\u5fc3\u5143\u7d20\u7b26\u53f7\u3002</li> <li><code>-m, --tol</code>\uff1a   \u7f51\u683c\u6620\u5c04\u7684\u5c42\u5bb9\u5dee\u3002\u9ed8\u8ba4\u503c\uff1a<code>1.0</code>\u3002</li> <li><code>-g, --target-size</code>\uff1a   \u671f\u671b\u7f51\u683c\u5927\u5c0f\uff0c\u683c\u5f0f\u4e3a <code>nx ny nz</code>\u3002</li> <li><code>-o, --save-dir</code>\uff1a   \u56fe\u7247\u8f93\u51fa\u76ee\u5f55\u3002\u9ed8\u8ba4\u503c\uff1a<code>plot</code>\u3002</li> <li><code>-f, --frame</code>\uff1a   \u5f53\u77e2\u91cf\u6570\u636e\u5305\u542b\u591a\u5e27\u65f6\uff0c\u8981\u53ef\u89c6\u5316\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>--select-xy</code>\uff1a   \u9009\u5b9a\u7684 XY \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-xz</code>\uff1a   \u9009\u5b9a\u7684 XZ \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-yz</code>\uff1a   \u9009\u5b9a\u7684 YZ \u5c42\u7f16\u53f7\u3002</li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li>\u5982\u679c\u9700\u8981\uff0c\u4f1a\u521b\u5efa\u8f93\u51fa\u76ee\u5f55\u3002</li> <li>\u56fe\u7247\u4fdd\u5b58\u4e3a <code>XY_*.png</code>\u3001<code>XZ_*.png</code>\u3001<code>YZ_*.png</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_19","title":"\u8f93\u51fa\u6587\u4ef6\u4e00\u89c8","text":"\u811a\u672c \u4e3b\u8981\u8f93\u51fa \u4fdd\u5b58\u5185\u5bb9 <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based \u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u548c\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7 <code>calc_displacement.py</code> <code>*.dat</code> \u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\uff08<code>dx dy dz</code>\uff0cAngstrom\uff09 <code>calc_averaged_structure.py</code> <code>*.xyz</code> \u4e00\u4e2a\u5e73\u5747\u7ed3\u6784 <code>calc_oct_tilt.py</code> <code>*.dat</code> \u516b\u9762\u4f53\u503e\u8f6c\u89d2\uff08<code>theta_x theta_y theta_z</code>\uff0cdegree\uff09 <code>calc_polarization_abo3.py</code> <code>*.dat</code> \u5c40\u57df\u6781\u5316\u77e2\u91cf\uff08<code>Px Py Pz</code>\uff0c<code>C/m^2</code>\uff09 <code>plt_plane_grid.py</code> <code>plot/*.png</code> \u6839\u636e\u77e2\u91cf\u573a\u6570\u636e\u7ed8\u5236\u7684 XY/XZ/YZ \u5e73\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_20","title":"\u771f\u5b9e\u6848\u4f8b","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3-","title":"PbTiO3 \u7684\u6e29\u5ea6\u9a71\u52a8\u94c1\u7535-\u987a\u7535\u76f8\u53d8","text":"<p>\u5047\u8bbe\u6240\u6709\u6587\u4ef6\u90fd\u4f4d\u4e8e\u5f53\u524d\u76ee\u5f55 <code>./</code>\uff1a</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> \u662f\u7528\u4e8e\u8fdb\u884c MD \u6a21\u62df\u7684\u521d\u59cb\u7ed3\u6784\u3002\u6bcf\u4e2a <code>TEMP K.xyz</code> \u662f\u5bf9\u5e94\u6e29\u5ea6\u4e0b\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1","title":"\u7b2c 1 \u6b65\uff1a\u4ece\u6bcf\u6761\u8f68\u8ff9\u7684\u540e\u534a\u6bb5\u5f97\u5230\u5e73\u5747\u7ed3\u6784","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>\u8fd9\u4f1a\u5199\u51fa <code>300K-avg.xyz</code>\u3001<code>350K-avg.xyz</code>\u3001...\u3001<code>800K-avg.xyz</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-modelxyz","title":"\u7b2c 2 \u6b65\uff1a\u57fa\u4e8e <code>model.xyz</code> \u6784\u5efa\u8fd1\u90bb\u5217\u8868","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3","title":"\u7b2c 3 \u6b65\uff1a\u4e3a\u6bcf\u4e2a\u6e29\u5ea6\u8ba1\u7b97\u4f4d\u79fb\u548c\u6781\u5316","text":"<p>\u8fd9\u91cc\u4f7f\u7528 Born \u6709\u6548\u7535\u8377\uff08BEC\uff09\uff0c\u4e0d\u662f\u540d\u4e49\u79bb\u5b50\u7535\u8377\u3002\u5bf9\u4e8e\u672c\u4f8b\u4e2d\u7684 PbTiO3\uff1a</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>\u4f60\u53ef\u4ee5\u4ece\u81ea\u5df1\u7684 DFPT \u8ba1\u7b97\u6216\u6587\u732e\u4e2d\u83b7\u5f97 BEC\u3002\u56e0\u6b64\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u548c\u6781\u5316\uff1a</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#4","title":"\u7b2c 4 \u6b65\uff1a\u7ed8\u5236\u5b9e\u7a7a\u95f4\u4f4d\u79fb\u548c\u6781\u5316\u56fe","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#5-","title":"\u7b2c 5 \u6b65\uff1a\u6784\u5efa\u6e29\u5ea6-\u5e8f\u53c2\u91cf\u66f2\u7ebf","text":"<p>\u7ed3\u5408\u6bcf\u4e2a\u6e29\u5ea6\u5e73\u5747\u7ed3\u6784\u7684\u6676\u683c\u4fe1\u606f\u548c\u6781\u5316\u6587\u4ef6\uff08<code>XX-pol.dat</code>\uff09\u8fdb\u884c\u5206\u6790\uff0c\u53ef\u4ee5\u5f97\u5230\u5982\u4e0b\u56fe\uff1a</p> <p>\u8be5\u8d8b\u52bf\u663e\u793a\u5728\u7ea6 <code>600 K</code> \u9644\u8fd1\u53d1\u751f\u660e\u663e\u76f8\u53d8\uff0c\u6b64\u65f6\u6781\u5316\u6d88\u5931\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3srtio3","title":"PbTiO3/SrTiO3 \u8d85\u6676\u683c\u4e2d\u7684\u62d3\u6251\u7ed3\u6784","text":"<p>\u5047\u8bbe <code>movie.xyz</code> \u662f\u5f53\u524d\u76ee\u5f55\u4e0b PbTiO3/SrTiO3 \u8d85\u6676\u683c\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1-25","title":"\u7b2c 1 \u6b65\uff1a\u4f7f\u7528\u6700\u540e 25% \u5e27\u6784\u5efa\u5e73\u5747\u7ed3\u6784","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-ti","title":"\u7b2c 2 \u6b65\uff1a\u6784\u5efa Ti \u8fd1\u90bb\u5217\u8868","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3-plane-grid","title":"\u7b2c 3 \u6b65\uff1a\u7ed8\u5236 plane-grid \u56fe","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>\u8fd9\u4f1a\u5f97\u5230\u4e0e\u524d\u9762\u5c55\u793a\u76f8\u4f3c\u7684\u56fe\u3002\u5728 PTO \u533a\u57df\u53ef\u4ee5\u770b\u5230\u7c7b\u4f3c\u6da1\u65cb\u7684\u6781\u5316\u56fe\u6837\uff0c\u800c STO \u533a\u57df\u7684\u6781\u5316\u63a5\u8fd1\u4e8e\u96f6\u3002</p> <p>\u6ce8\u610f\uff1a\u793a\u4f8b\u56fe\u4f7f\u7528\u4e86\u81ea\u5b9a\u4e49 colormap\u3002GPUMDkit \u9ed8\u8ba4\u8f93\u51fa\u4f7f\u7528\u4e0d\u540c\u98ce\u683c\uff0c\u53ef\u901a\u8fc7\u4fee\u6539\u7ed8\u56fe\u811a\u672c\u8fdb\u884c\u8c03\u6574\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_21","title":"\u5176\u4ed6\u4f53\u7cfb","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#-","title":"\u6709\u673a-\u65e0\u673a\u6742\u5316\u94c1\u7535\u4f53","text":"<p>\u5728\u8bb8\u591a\u6709\u673a-\u65e0\u673a\u94c1\u7535\u4f53\u4e2d\uff0c\u6781\u5316\u4e0e\u5404\u5411\u5f02\u6027\u7684\u5206\u5b50\u5355\u5143\u5bc6\u5207\u76f8\u5173\u3002\u8ddf\u8e2a\u5206\u5b50\u53d6\u5411\u7684\u4e00\u79cd\u5b9e\u7528\u65b9\u6cd5\u662f\u4f7f\u7528\u952e\u77e2\u91cf\u3002</p> <p>\u5bf9\u4e8e TMCM-CdCl3\uff0c\u53ef\u4ee5\u4f7f\u7528 TMCM \u5206\u5b50\u4e2d\u7684 C-Cl \u952e\u65b9\u5411\u4f5c\u4e3a\u53d6\u5411\u4ee3\u7406\uff0c\u5e76\u636e\u6b64\u4f30\u8ba1\u6781\u5316\u6001\uff1a</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p>\u968f\u540e\u53ef\u4ee5\u628a <code>ccl_vectors.dat</code> \u4f5c\u4e3a\u53d6\u5411\u5e8f\u53c2\u91cf\u8fdb\u884c\u5206\u6790\u3002\u66f4\u591a\u7ec6\u8282\u53ef\u53c2\u8003\uff1aPhys. Rev. Lett. 136, 016801\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_22","title":"\u5176\u4ed6\u94c1\u7535\u6750\u6599\u5bb6\u65cf","text":"<p>\u9664 <code>ABO3</code> \u5916\uff0c<code>ferrodispcalc</code> \u4e5f\u53ef\u4ee5\u9002\u914d\u8bb8\u591a\u94c1\u7535\u4f53\u7cfb\uff0c\u5305\u62ec\u6c2e\u5316\u7269\u3001\u6c27\u5316\u94ea\u57fa\u5316\u5408\u7269\u3001\u6709\u673a-\u65e0\u673a\u6742\u5316\u4f53\u7cfb\u4ee5\u53ca\u90e8\u5206\u4e8c\u7ef4\u94c1\u7535\u6750\u6599\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html","title":"\u683c\u5f0f\u8f6c\u6362","text":"\ud83d\udd04 \u683c\u5f0f\u8f6c\u6362 <p>\u683c\u5f0f\u8f6c\u6362\u6a21\u5757\u7528\u4e8e\u5728\u5e38\u89c1\u539f\u5b50\u6a21\u62df\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362\uff0c\u540c\u65f6\u63d0\u4f9b group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u5e27\u63d0\u53d6\u7b49\u5143\u6570\u636e\u5904\u7406\u529f\u80fd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>\u672c\u6a21\u5757\u5728\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u5e38\u7528\u7684\u7ed3\u6784\u548c\u8f68\u8ff9\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8fdb\u884c\u8f6c\u6362\u3002\u652f\u6301 VASP\u3001LAMMPS\u3001CP2K\u3001ABACUS\u3001CIF\u3001ASE \u8f68\u8ff9\u548c extxyz \u683c\u5f0f\u3002\u8fd8\u63d0\u4f9b\u6dfb\u52a0 group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u63d0\u53d6\u5e27\u548c\u6269\u80de\u7b49\u5de5\u5177\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":"<p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/format_conversion/</code></p> <p>\u786e\u4fdd\u5df2\u5b89\u88c5 GPUMDkit\u3002\u5b89\u88c5\u8bf4\u660e\u8bf7\u53c2\u89c1\u5feb\u901f\u5165\u95e8\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_3","title":"\u652f\u6301\u7684\u683c\u5f0f","text":"<ul> <li>VASP\uff1a<code>POSCAR</code>\u3001<code>CONTCAR</code>\u3001<code>OUTCAR</code>\u3001<code>XDATCAR</code></li> <li>LAMMPS\uff1adata \u6587\u4ef6\u548c dump \u8f68\u8ff9</li> <li>CP2K\uff1a\u8f93\u51fa log\u3001\u5750\u6807\u3001\u529b\u548c\u6676\u80de\u6587\u4ef6</li> <li>ABACUS\uff1aSCF/MD \u8f93\u51fa</li> <li>CIF\uff1a\u6676\u4f53\u7ed3\u6784\u6587\u4ef6</li> <li>ASE trajectory\uff1a<code>.traj</code></li> <li>extxyz\uff1aGPUMD \u548c NEP \u5e38\u7528\u7684\u7ed3\u6784\u683c\u5f0f</li> </ul>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_4","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>1) Format Conversion\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_5","title":"\u6bcf\u4e2a\u5165\u53e3\u7684\u4f5c\u7528","text":"\u5165\u53e3 \u529f\u80fd \u9002\u7528\u573a\u666f <code>101</code> VASP OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c \u6279\u91cf\u8f6c\u6362 VASP \u8ba1\u7b97\u76ee\u5f55 <code>102</code> MTP cfg \u8f6c extxyz \u8f6c\u6362 MTP \u6570\u636e <code>103</code> CP2K \u8f6c extxyz \u53ef\u9009\u62e9 log/inp \u8def\u7ebf\u6216 pos/frc/cell \u8def\u7ebf <code>104</code> ABACUS \u8f6c extxyz \u8f6c\u6362 ABACUS SCF \u6216 MD \u8f93\u51fa <code>105</code> extxyz \u8f6c POSCAR \u5c06 extxyz \u6bcf\u4e00\u5e27\u5199\u6210 POSCAR <code>106</code> \u6dfb\u52a0 group \u6807\u7b7e \u4e3a GPUMD \u76f8\u5173\u6d41\u7a0b\u6dfb\u52a0\u539f\u5b50\u5206\u7ec4\u6807\u7b7e <code>107</code> \u6dfb\u52a0\u6743\u91cd \u4fee\u6539\u8bad\u7ec3\u96c6\u7ed3\u6784\u6743\u91cd <code>108</code> \u63d0\u53d6\u5355\u5e27 \u4ece extxyz \u8f68\u8ff9\u5bfc\u51fa\u67d0\u4e00\u5e27 <code>109</code> \u6e05\u7406 XYZ \u4fe1\u606f \u5220\u9664\u591a\u4f59 extxyz \u5c5e\u6027 <code>110</code> \u6269\u80de \u6309\u500d\u6570\u6216\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>out2exyz</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c VASP OUTCAR \u8f6c\u6362\u7684\u53e6\u4e00\u4e2a\u5165\u53e3 <code>pos2exyz</code> POSCAR \u8f6c extxyz \u8f6c\u6362\u5355\u4e2a\u7ed3\u6784 <code>cif2pos</code> CIF \u8f6c POSCAR \u4ece CIF \u51c6\u5907 VASP \u8f93\u5165 <code>cif2exyz</code> CIF \u8f6c extxyz \u4ece CIF \u51c6\u5907 GPUMDkit \u8f93\u5165 <code>xdat2exyz</code> XDATCAR \u8f6c extxyz \u8f6c\u6362 VASP MD \u8f68\u8ff9 <code>pos2lmp</code> POSCAR \u8f6c LAMMPS data \u51c6\u5907 LAMMPS \u8f93\u5165 <code>lmp2exyz</code> LAMMPS dump \u8f6c extxyz \u8f6c\u6362 LAMMPS \u8f68\u8ff9 <code>traj2exyz</code> ASE traj \u8f6c extxyz \u8f6c\u6362 ASE \u8f68\u8ff9"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_6","title":"\u5feb\u901f\u547d\u4ee4\u8868","text":"\u6765\u6e90 \u76ee\u6807 \u547d\u4ee4 OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz POSCAR model.xyz</code> extxyz POSCAR \u6587\u4ef6 <code>gpumdkit.sh -exyz2pos train.xyz</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_7","title":"\u5e38\u89c1\u4f8b\u5b50","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#vasp","title":"\u8f6c\u6362 VASP \u7ed3\u679c","text":"<p>\u529f\u80fd\uff1a \u5728\u76ee\u5f55\u4e2d\u641c\u7d22 VASP OUTCAR \u6587\u4ef6\uff0c\u5e76\u5c06\u5b83\u4eec\u8f6c\u6362\u4e3a\u5355\u4e2a extxyz \u6587\u4ef6\uff0c\u7528\u4e8e NEP \u8bad\u7ec3\u6216\u5206\u6790\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>\u4e5f\u53ef\u4ee5\u4f7f\u7528 Python \u7248\u672c\uff1a</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u683c\u5f0f\u8f6c\u6362\u83dc\u5355\u4e2d\u9009\u62e9 <code>101</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u51fa\uff1a \u5305\u542b\u8f6c\u6362\u540e\u7ed3\u6784\u7684 extxyz \u6587\u4ef6\uff0c\u53ef\u7528\u4e8e NEP \u8bad\u7ec3\u6216\u8fdb\u4e00\u6b65\u5206\u6790\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#group","title":"\u6dfb\u52a0 group \u6807\u7b7e","text":"<p>\u529f\u80fd\uff1a \u4e3a\u7ed3\u6784\u6587\u4ef6\u6dfb\u52a0\u539f\u5b50 group \u6807\u7b7e\u3002\u4e00\u4e9b GPUMD \u76f8\u5173\u6d41\u7a0b\u9700\u8981 group \u6807\u7b7e\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>\u8be5\u547d\u4ee4\u8bfb\u53d6\u8f93\u5165\u7ed3\u6784\uff0c\u5e76\u5199\u51fa\u5e26 group \u4fe1\u606f\u7684 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u683c\u5f0f\u8f6c\u6362\u83dc\u5355\u4e2d\u9009\u62e9 <code>106</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u51fa\uff1a \u6dfb\u52a0\u4e86 group \u6807\u7b7e\u7684 extxyz \u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_8","title":"\u5e38\u7528\u811a\u672c\u8bf4\u660e","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>\u9002\u5408\u628a\u5355\u4e2a VASP \u7ed3\u6784\u8f6c\u6210 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz-poscar","title":"extxyz \u8f6c POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>\u4f1a\u5c06 extxyz \u4e2d\u6240\u6709\u5e27\u8f6c\u6362\u6210 <code>POSCAR_*.vasp</code> \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3\uff1a<code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#lammps-dump-extxyz","title":"LAMMPS dump \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>\u5143\u7d20\u987a\u5e8f\u5fc5\u987b\u5bf9\u5e94 LAMMPS \u4e2d\u7684 atom type ID\u3002\u4f8b\u5982 type 1 \u662f Li\u3001type 2 \u662f Y\u3001type 3 \u662f Cl\uff0c\u5219\u8f93\u5165 <code>Li Y Cl</code>\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#cif","title":"CIF \u8f6c\u6362","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>\u5982\u679c\u540e\u7eed\u9700\u8981 VASP \u8ba1\u7b97\uff0c\u4f7f\u7528 <code>-cif2pos</code>\uff1b\u5982\u679c\u540e\u7eed\u8981\u8fdb\u5165 GPUMDkit \u5206\u6790\uff0c\u4f7f\u7528 <code>-cif2exyz</code>\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_9","title":"\u6dfb\u52a0\u6743\u91cd","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>\u7528\u4e8e\u7ed9\u8bad\u7ec3\u96c6\u7ed3\u6784\u6dfb\u52a0\u6216\u4fee\u6539\u6743\u91cd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_10","title":"\u6269\u80de","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>\u7b2c\u4e00\u79cd\u6309\u6676\u80de\u500d\u6570\u6269\u80de\uff0c\u7b2c\u4e8c\u79cd\u6309\u76ee\u6807\u539f\u5b50\u6570\u81ea\u52a8\u9009\u62e9\u6269\u80de\u65b9\u5f0f\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_11","title":"\u63d0\u53d6\u5355\u5e27","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>\u4ece extxyz \u8f68\u8ff9\u4e2d\u63d0\u53d6\u7b2c <code>1000</code> \u5e27\uff08\u7d22\u5f15\u4ece 0 \u5f00\u59cb\uff09\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz","title":"\u62c6\u5206\u591a\u5e27 extxyz","text":"<p><code>split_single_xyz.py</code> \u5c06\u591a\u5e27 extxyz \u6587\u4ef6\u62c6\u5206\u4e3a\u5355\u5e27\u6587\u4ef6\u3002</p> <pre><code>python Scripts/format_conversion/split_single_xyz.py dump.xyz\n</code></pre> <p>\u751f\u6210 <code>model_0.xyz</code>\u3001<code>model_1.xyz</code>\u3001... \u7b49\u5355\u5e27\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#mtp","title":"MTP \u8f6c\u6362","text":"<p>\u5c06 MTP <code>.cfg</code> \u683c\u5f0f\u8f6c\u6362\u4e3a extxyz\uff1a</p> <pre><code>gpumdkit.sh    # \u9009\u62e9\uff1a1) \u683c\u5f0f\u8f6c\u6362 \u2192 102\n</code></pre> <p>\u4ea4\u4e92\u63d0\u793a\uff1a</p> <pre><code>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;\nExample: train.cfg Pd Ag\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#abacus","title":"ABACUS \u8f6c\u6362","text":"<p>\u5c06 ABACUS \u8f93\u51fa\u8f6c\u6362\u4e3a extxyz\uff1a</p> <pre><code>gpumdkit.sh    # \u9009\u62e9\uff1a1) \u683c\u5f0f\u8f6c\u6362 \u2192 104\n</code></pre> <p>\u83dc\u5355\u63d0\u4f9b\u4e24\u4e2a\u9009\u9879\uff1a</p> <ol> <li>SCF \u8f93\u51fa\uff08<code>running_scf.log</code>\uff09</li> <li>MD \u8f93\u51fa\uff08<code>running_md.log</code>\uff09</li> </ol>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_12","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae LAMMPS \u8f6c\u6362\u540e\u5143\u7d20\u4e0d\u5bf9 \u68c0\u67e5 dump \u6587\u4ef6\u540e\u7684\u5143\u7d20\u987a\u5e8f extxyz \u5143\u6570\u636e\u592a\u591a \u4f7f\u7528 <code>-clean_xyz input.xyz clean.xyz</code> \u63d0\u53d6\u5e27\u4e0d\u5bf9 \u6ce8\u610f\u5e27\u7d22\u5f15\u901a\u5e38\u4ece 0 \u5f00\u59cb"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_13","title":"\u8bf4\u660e","text":"<p>\u5982\u679c\u67d0\u4e2a\u8f6c\u6362\u811a\u672c\u7f3a\u5c11\u6240\u9700 Python \u5305\uff0c\u8fd0\u884c\u8be5\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u76f8\u5e94\u63d0\u793a\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html","title":"\u7ed3\u6784\u91c7\u6837","text":"\ud83d\udce6 \u7ed3\u6784\u91c7\u6837 <p>\u7ed3\u6784\u91c7\u6837\u7528\u4e8e\u4ece\u8f68\u8ff9\u4e2d\u9009\u62e9\u5019\u9009\u7ed3\u6784\u3001\u751f\u6210\u6270\u52a8\u7ed3\u6784\uff0c\u6216\u6839\u636e\u6a21\u578b\u504f\u5dee\u6311\u9009\u503c\u5f97\u8fdb\u4e00\u6b65\u8ba1\u7b97\u7684\u7ed3\u6784\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/sample_structures/</code></p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_1","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>2) Sample Structures\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u65b9\u6cd5 \u7528\u9014 201 uniform/random \u4ece\u8f68\u8ff9\u4e2d\u5747\u5300\u6216\u968f\u673a\u62bd\u5e27 202 PyNEP notice \u53ea\u6253\u5370\u63d0\u793a\uff1b\u771f\u6b63\u8fd0\u884c PyNEP \u8bf7\u7528 <code>gpumdkit.sh -pynep</code> 203 NepTrain FPS \u4f7f\u7528 NepTrain \u63cf\u8ff0\u7b26\u7684 FPS \u91c7\u6837 204 perturb \u4ece POSCAR/CONTCAR \u751f\u6210\u6270\u52a8\u7ed3\u6784 205 force deviation \u4ece active learning \u8f93\u51fa\u4e2d\u9009\u62e9\u9ad8\u504f\u5dee\u7ed3\u6784"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_2","title":"\u5747\u5300/\u968f\u673a\u91c7\u6837","text":"<p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>201</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>\u4f8b\u5982\u8f93\u5165\uff1a</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>\u6216\uff1a</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>uniform</code> / <code>random</code> \u91c7\u6837\u65b9\u6cd5 <code>50</code> / <code>100</code> \u91c7\u6837\u7ed3\u6784\u6570 <code>500</code> \u53ef\u9009\uff0c\u8df3\u8fc7\u524d 500 \u5e27 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#neptrain-fps","title":"NepTrain FPS","text":"<p>NepTrain \u7248\u672c\u7684 FPS\uff1a</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>203</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u5165\uff1a</p> \u6587\u4ef6 \u542b\u4e49 <code>dump.xyz</code> \u5019\u9009\u7ed3\u6784 <code>train.xyz</code> \u5f53\u524d\u8bad\u7ec3\u96c6 <code>nep.txt</code> \u7528\u4e8e\u8ba1\u7b97\u63cf\u8ff0\u7b26\u7684 NEP \u6a21\u578b <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>\u8fd0\u884c\u65f6\u53ef\u4ee5\u9009\u62e9\u6309\u6700\u5c0f\u8ddd\u79bb\u9608\u503c\u91c7\u6837\uff0c\u6216\u6307\u5b9a\u91c7\u6837\u7ed3\u6784\u6570\u3002\u811a\u672c\u968f\u540e\u4f1a\u6253\u5370\uff1a</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>NepTrain</code>\uff0c\u8fd0\u884c\u65f6\u4f1a\u63d0\u793a\u76f8\u5173\u5f15\u7528\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep","title":"PyNEP \u65e7\u5165\u53e3","text":"<p>PyNEP FPS \u4ecd\u7136\u4fdd\u7559\u517c\u5bb9\uff0c\u4f46\u53ea\u901a\u8fc7 <code>-pynep</code> \u5165\u53e3\u8c03\u7528\u3002</p> <p>\u5982\u679c\u5728\u4ea4\u4e92\u83dc\u5355\u4e2d\u9009\u62e9 <code>202</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep_1","title":"\u4e32\u884c PyNEP","text":"<pre><code>python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep_2","title":"\u5e76\u884c PyNEP","text":"<pre><code>python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u6700\u540e\u4e00\u4e2a\u53c2\u6570\u662f CPU \u7ebf\u7a0b\u6570\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#gpumdkit","title":"GPUMDkit \u5165\u53e3","text":"<pre><code>gpumdkit.sh -pynep\n</code></pre> <p>\u968f\u540e\u8f93\u5165\uff1a</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u8fd9\u4e2a\u5165\u53e3\u9700\u8981 <code>pynep</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_3","title":"\u7ed3\u6784\u6270\u52a8","text":"<pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>204</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>POSCAR</code> \u8f93\u5165\u7ed3\u6784 <code>20</code> \u751f\u6210\u7ed3\u6784\u6570 <code>0.03</code> \u6676\u80de\u6270\u52a8\u6bd4\u4f8b <code>0.2</code> \u539f\u5b50\u6270\u52a8\u8ddd\u79bb\uff0c\u5355\u4f4d Angstrom <code>uniform</code> \u6270\u52a8\u65b9\u5f0f\uff0c\u53ef\u9009 <code>normal</code>\u3001<code>uniform</code>\u3001<code>const</code> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>POSCAR_01.vasp</code>\u3001<code>POSCAR_02.vasp</code> \u7b49</li> </ul> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>dpdata</code>\u3002\u4f7f\u7528\u6b64\u529f\u80fd\u65f6\u5efa\u8bae\u5f15\u7528 dpdata \u5305\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_4","title":"\u6700\u5927\u529b\u504f\u5dee\u7ed3\u6784\u9009\u62e9","text":"<p>\u8be5\u529f\u80fd\u9700\u8981\u914d\u5408 GPUMD \u7684 <code>active</code> \u547d\u4ee4\u4f7f\u7528\u3002<code>active</code> \u901a\u8fc7\u59d4\u5458\u4f1a\u8bc4\u5ba1\u673a\u5236\uff0c\u8ba9\u591a\u6761\u52bf\u51fd\u6570\u5bf9\u540c\u4e00\u7ed3\u6784\u8fdb\u884c\u9884\u6d4b\uff0c\u5e76\u8bb0\u5f55\u6bcf\u4e2a\u7ed3\u6784\u7684\u6700\u5927\u529b\u504f\u5dee\u3002<code>select_max_modev.py</code> \u4f1a\u4ece <code>active.out</code> \u548c <code>active.xyz</code> \u4e2d\u9009\u62e9\u529b\u504f\u5dee\u8f83\u5927\u7684\u7ed3\u6784\uff0c\u5199\u5165 <code>selected.xyz</code>\u3002</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>205</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>\u9700\u8981\u5f53\u524d\u76ee\u5f55\u4e0b\u6709\uff1a</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_5","title":"\u5e27\u8303\u56f4\u63d0\u53d6","text":"<p>\u63d0\u53d6\u8f68\u8ff9\u7684\u4e00\u90e8\u5206\u5e27\uff1a</p> <pre><code>python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>\u8fd9\u4f1a\u5199\u5165\u8f68\u8ff9 0% \u5230 80% \u7684\u5e27\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_6","title":"\u793a\u4f8b\u547d\u4ee4","text":"<pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_7","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae FPS \u9009\u51fa\u592a\u591a\u76f8\u4f3c\u7ed3\u6784 \u8c03\u5927\u8ddd\u79bb\u9608\u503c\u6216\u9650\u5236\u6700\u5927\u9009\u62e9\u6570 \u6270\u52a8\u7ed3\u6784\u4e0d\u5408\u7406 \u51cf\u5c0f <code>cell_pert</code> \u548c <code>atom_pert</code> <code>active.out</code> \u548c <code>active.xyz</code> \u4e0d\u5339\u914d \u786e\u4fdd\u6765\u81ea\u540c\u4e00\u6b21 GPUMD active \u8fd0\u884c PCA \u56fe\u5f02\u5e38 \u68c0\u67e5 <code>nep.txt</code> \u662f\u5426\u548c\u4e24\u4e2a\u6570\u636e\u96c6\u5143\u7d20\u4e00\u81f4"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html","title":"\u7ed8\u56fe\u811a\u672c","text":"\ud83d\udcca \u7ed8\u56fe\u811a\u672c <p>\u7ed8\u56fe\u6a21\u5757\u5305\u542b\u4e00\u7cfb\u5217 Python \u811a\u672c\uff0c\u7528\u4e8e\u53ef\u89c6\u5316 GPUMD\u3001NEP \u548c GPUMDkit \u8ba1\u7b97\u5668\u4ea7\u751f\u7684\u6570\u636e\u3002\u6240\u6709\u56fe\u8868\u5747\u53ef\u4ea4\u4e92\u663e\u793a\u6216\u4fdd\u5b58\u4e3a\u9ad8\u5206\u8fa8\u7387 PNG \u6587\u4ef6\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/plt_scripts/</code></p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_1","title":"\u5feb\u901f\u5165\u53e3","text":"<pre><code>gpumdkit.sh -plt              # \u663e\u793a\u6240\u6709\u7ed8\u56fe\u9009\u9879\ngpumdkit.sh -plt &lt;type&gt;       # \u751f\u6210\u6307\u5b9a\u56fe\u8868\ngpumdkit.sh -plt &lt;type&gt; save  # \u4fdd\u5b58\u4e3a PNG\ngpumdkit.sh -plt &lt;type&gt; -h    # \u663e\u793a\u7279\u5b9a\u56fe\u8868\u7684\u5e2e\u52a9\n</code></pre> <p>\u8fd0\u884c <code>gpumdkit.sh -plt</code> \u4f1a\u663e\u793a\u7ed8\u56fe\u547d\u4ee4\u83dc\u5355\uff1a</p> <pre><code>+-----------------------------------------------------------------------------------------------+\n|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |\n+-----------------------------------------------------------------------------------------------+\n|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |\n+-----------------------------------------------------------------------------------------------+\n|                                    NEP Training &amp; Evaluation                                  |\n+-----------------------------------------------------------------------------------------------+\n|  train          - NEP training results           prediction     - NEP prediction results      |\n|  train_test     - NEP train and test results     parity_density - Parity density plot         |\n|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |\n|  charge         - Charge distribution            born_charge    - Born effective charges      |\n|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |\n|  des            - Descriptors                    lr             - Learning rate for gnep      |\n+-----------------------------------------------------------------------------------------------+\n|                                     Diffusion &amp; Transport                                     |\n+-----------------------------------------------------------------------------------------------+\n|  msd            - Mean square displacement       msd_conv       - MSD convergence             |\n|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |\n|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|\n|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |\n|  D_xyz          - Directional Arrhenius D                                                     |\n+-----------------------------------------------------------------------------------------------+\n|                                    MD &amp; Structural Analysis                                   |\n+-----------------------------------------------------------------------------------------------+\n|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |\n|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |\n|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |\n|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |\n|  doas           - Density of atomistic states                                                 |\n+-----------------------------------------------------------------------------------------------+\n|                                        Heat Transport                                         |\n+-----------------------------------------------------------------------------------------------+\n|  emd            - EMD results                    nemd           - NEMD results                |\n|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |\n+-----------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u8bad\u7ec3\u4e0e\u9884\u6d4b","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_trainpy","title":"plt_train.py","text":"<p>\u53ef\u89c6\u5316 NEP \u8bad\u7ec3\u8fc7\u7a0b\uff0c\u5305\u62ec loss \u66f2\u7ebf\u3001RMSE \u6f14\u5316\uff0c\u4ee5\u53ca\u80fd\u91cf/\u529b/virial \u7684 DFT vs NEP parity plot\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code>\u3001<code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_predictionpy","title":"plt_prediction.py","text":"<p>\u53ef\u89c6\u5316\u6d4b\u8bd5\u96c6\u4e0a\u7684 NEP \u9884\u6d4b\u7ed3\u679c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_test.out</code>\u3001<code>force_test.out</code>\u3001<code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test         # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_train_testpy","title":"plt_train_test.py","text":"<p>\u5c06\u8bad\u7ec3\u96c6\u548c\u6d4b\u8bd5\u96c6\u7684 parity plot \u5408\u5e76\u663e\u793a\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code>\u3001<code>energy_test.out</code>\u3001<code>force_test.out</code>\u3001<code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_parity_densitypy","title":"plt_parity_density.py","text":"<p>\u751f\u6210\u57fa\u4e8e\u5bc6\u5ea6\u7684 parity plot\uff0c\u9002\u7528\u4e8e\u5927\u6570\u636e\u96c6\uff08\u6563\u70b9\u56fe\u8fc7\u4e8e\u5bc6\u96c6\u65f6\u66f4\u6613\u9605\u8bfb\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_force_errorspy","title":"plt_force_errors.py","text":"<p>\u53c2\u8003 Liu et al. \u7684\u65b9\u6cd5\u7ed8\u5236\u529b\u8bef\u5dee\u8bc4\u4f30\u6307\u6807\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>force_train.out</code></p> <p>\u663e\u793a\u6307\u6807\uff1a - \u529b\u5927\u5c0f\u8bef\u5dee (delta_F) - \u529b\u89d2\u5ea6\u8bef\u5dee (delta_theta) - \u8bef\u5dee\u5206\u5e03</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_learning_ratepy","title":"plt_learning_rate.py","text":"<p>\u53ef\u89c6\u5316 <code>gnep</code> \u8bad\u7ec3\u8fc7\u7a0b\u4e2d\u7684\u5b66\u4e60\u7387\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code></p> <p>\u6ce8\u610f\uff1a \u4ec5\u9002\u7528\u4e8e <code>gnep</code> \u8bad\u7ec3\u8fc7\u7a0b\u3002</p> <pre><code>gpumdkit.sh -plt lr\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_nep_restartpy","title":"plt_nep_restart.py","text":"<p>\u53ef\u89c6\u5316 <code>nep.restart</code> \u6587\u4ef6\u4e2d\u5b58\u50a8\u7684\u53c2\u6570\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>nep.restart</code></p> <pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_chargepy","title":"plt_charge.py","text":"<p>\u7ed8\u5236 <code>qNEP</code> \u6a21\u578b\u7684\u7535\u8377\u5206\u5e03\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>charge_train.out</code></p> <p>\u91cd\u8981\u63d0\u793a\uff1a \u786e\u4fdd\u8bad\u7ec3\u96c6\u548c\u7535\u8377\u8f93\u51fa\u7684\u539f\u5b50\u6392\u5e8f\u4e00\u81f4\u3002\u5efa\u8bae\u4f7f\u7528\u5168 batch \u8bad\u7ec3\u6216\u5148\u8fd0\u884c\u9884\u6d4b\u6b65\u9aa4\u3002</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_born_chargepy","title":"plt_born_charge.py","text":"<p>\u4e3a\u8bad\u7ec3\u96c6\u548c\u6d4b\u8bd5\u96c6\u521b\u5efa Born \u6709\u6548\u7535\u8377 (BEC) \u7684 parity plot\u3002\u5168\u96f6\u53c2\u8003 BEC \u7684\u7ed3\u6784\u4f1a\u88ab\u8fc7\u6ee4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>bec_train.out</code>\u3001<code>bec_test.out</code></p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec          # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_2","title":"\u70ed\u529b\u5b66\u91cf","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_thermopy","title":"plt_thermo.py","text":"<p>\u7efc\u5408\u53ef\u89c6\u5316\u70ed\u529b\u5b66\u6027\u8d28\u7684\u4e3b\u811a\u672c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_thermo2py-plt_thermo3py","title":"plt_thermo2.py &amp; plt_thermo3.py","text":"<p>\u4e0d\u540c\u98ce\u683c\u7684\u70ed\u529b\u5b66\u91cf\u53ef\u89c6\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_3","title":"\u6269\u6563\u548c\u79bb\u5b50\u8f93\u8fd0","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msdpy","title":"plt_msd.py","text":"<p>\u7ed8\u5236\u5404\u65b9\u5411\u7684\u5747\u65b9\u4f4d\u79fb (MSD)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msd_allpy","title":"plt_msd_all.py","text":"<p>\u5f53 GPUMD \u4e2d\u4f7f\u7528 <code>all_groups</code> \u65f6\uff0c\u5206\u522b\u7ed8\u5236\u6bcf\u79cd\u539f\u5b50\u7684 MSD\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code>\uff08\u9700\u8981\u4f7f\u7528 <code>all_groups</code> \u9009\u9879\u8ba1\u7b97\uff09</p> <p>\u8981\u6c42\uff1a <code>run.in</code> \u4e2d\u7684 <code>compute_msd</code> \u547d\u4ee4\u5fc5\u987b\u4f7f\u7528 <code>all_groups</code>\u3002</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msd_convergence_checkpy","title":"plt_msd_convergence_check.py","text":"<p>\u68c0\u67e5\u4e0d\u540c\u65f6\u95f4\u7a97\u53e3\u4e0b MSD \u8ba1\u7b97\u7684\u6536\u655b\u6027\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd_step*.out</code>\uff08\u9700\u8981\u5728 <code>compute_msd</code> \u4e2d\u4f7f\u7528 <code>save_every</code> \u9009\u9879\uff09</p> <p>\u8981\u6c42\uff1a \u5728 <code>compute_msd</code> \u547d\u4ee4\u4e2d\u4f7f\u7528 <code>save_every</code>\u3002</p> <p>\u7528\u9014\uff1a \u9a8c\u8bc1 MSD \u662f\u5426\u5df2\u5145\u5206\u6536\u655b\u4ee5\u51c6\u786e\u8ba1\u7b97\u6269\u6563\u7cfb\u6570\u3002</p> <pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_sdcpy","title":"plt_sdc.py","text":"<p>\u7ed8\u5236\u81ea\u6269\u6563\u7cfb\u6570 (SDC) \u968f\u65f6\u95f4\u7684\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_arrhenius_dpy","title":"plt_arrhenius_d.py","text":"<p>\u521b\u5efa Arrhenius \u6269\u6563\u7cfb\u6570\u56fe\uff08log10 D vs 1000/T\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>*K/msd.out</code>\uff08\u6bcf\u4e2a\u6e29\u5ea6\u5b50\u76ee\u5f55\u4e0b\u7684 <code>msd.out</code>\uff09</p> <pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D             # \u66ff\u4ee3\u547d\u4ee4\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_arrhenius_sigmapy","title":"plt_arrhenius_sigma.py","text":"<p>\u521b\u5efa Arrhenius \u79bb\u5b50\u7535\u5bfc\u7387\u56fe\uff08ln(\u03c3\u00b7T) vs 1000/T\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code>\uff08\u6bcf\u4e2a\u6e29\u5ea6\u5b50\u76ee\u5f55\uff09</p> <pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma         # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_4","title":"\u70ed\u8f93\u8fd0","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_emdpy","title":"plt_emd.py","text":"<p>\u5206\u6790\u5e76\u7ed8\u5236\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (EMD) \u70ed\u5bfc\u7387\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 EMD \u8f93\u51fa\u6587\u4ef6</p> <pre><code>gpumdkit.sh -plt emd x        # x \u65b9\u5411\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_nemdpy","title":"plt_nemd.py","text":"<p>\u53ef\u89c6\u5316\u975e\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (NEMD) \u70ed\u8f93\u8fd0\u6027\u8d28\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 NEMD \u8f93\u51fa\u6587\u4ef6</p> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u8bf4\u660e <code>real_length</code> \u4f20\u70ed\u533a\u5b9e\u9645\u957f\u5ea6\uff08nm\uff09\uff0c\u8bbe\u4e3a <code>Auto</code> \u53ef\u81ea\u52a8\u8ba1\u7b97 <code>scale_eff_size</code> \u6709\u6548\u622a\u9762\u79ef\u7f29\u653e\u56e0\u5b50\uff08\u9ed8\u8ba4\uff1a1\uff09\u3002\u4e09\u7ef4\u4f53\u76f8\u7528 1\uff1b\u542b\u771f\u7a7a\u5c42\u7684\u4f4e\u7ef4\u4f53\u7cfb\u7528 S_box / S_eff <code>cutoff_freq</code> SHC \u8ba1\u7b97\u7684\u622a\u6b62\u9891\u7387\uff08THz\uff0c\u9ed8\u8ba4\uff1a60\uff09 <code>save</code> \u53ef\u9009\uff0c\u4fdd\u5b58\u56fe\u7247\u4e3a <code>nemd.png</code> <p>\u6ce8\u610f\uff1a \u5982\u679c\u6ca1\u6709 SHC \u6570\u636e\uff0c\u4f7f\u7528 <code>save</code> \u65f6\u8bf7\u5c06 <code>scale_eff_size</code> \u548c <code>cutoff_freq</code> \u8bbe\u4e3a\u4efb\u610f\u5360\u4f4d\u6570\u5b57\u3002</p> <pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_hnemdpy","title":"plt_hnemd.py","text":"<p>\u7ed8\u5236\u975e\u5747\u5300\u975e\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (HNEMD) \u7ed3\u679c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 HNEMD \u8f93\u51fa\u6587\u4ef6</p> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u8bf4\u660e <code>scale_eff_size</code> \u6709\u6548\u622a\u9762\u79ef\u7f29\u653e\u56e0\u5b50\uff08\u9ed8\u8ba4\uff1a1\uff09 <code>cutoff_freq</code> SHC \u8ba1\u7b97\u7684\u622a\u6b62\u9891\u7387\uff08THz\uff0c\u9ed8\u8ba4\uff1a60\uff09 <code>save</code> \u53ef\u9009\uff0c\u4fdd\u5b58\u56fe\u7247\u4e3a <code>hnemd.png</code> <p>\u6ce8\u610f\uff1a \u5982\u679c\u6ca1\u6709 SHC \u6570\u636e\uff0c\u4f7f\u7528 <code>save</code> \u65f6\u8bf7\u5c06 <code>scale_eff_size</code> \u548c <code>cutoff_freq</code> \u8bbe\u4e3a\u4efb\u610f\u5360\u4f4d\u6570\u5b57\u3002</p> <pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_5","title":"\u7ed3\u6784\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_rdfpy","title":"plt_rdf.py","text":"<p>\u7ed8\u5236\u5f84\u5411\u5206\u5e03\u51fd\u6570 (RDF)\uff0c\u5c55\u793a\u539f\u5b50\u5bf9\u5173\u8054\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf               # \u663e\u793a\u6240\u6709 RDF \u5bf9\ngpumdkit.sh -plt rdf &lt;column&gt;      # \u663e\u793a\u7279\u5b9a\u5bf9\n</code></pre> <p>\u5b8c\u6574 RDF \u8f93\u51fa\uff1a</p> <p>\u5355\u5bf9 RDF\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_rdf_pmfpy","title":"plt_rdf_pmf.py","text":"<p>\u7ed8\u5236 RDF \u4e0e\u5e73\u5747\u529b\u52bf (PMF) \u7684\u7ec4\u5408\u56fe\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf_pmf\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_vacpy","title":"plt_vac.py","text":"<p>\u7ed8\u5236\u901f\u5ea6\u81ea\u76f8\u5173\u51fd\u6570 (VAC)\u3002\u53ef\u7528\u4e8e\u5206\u6790\u58f0\u5b50\u6027\u8d28\u548c\u539f\u5b50\u52a8\u529b\u5b66\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>sdc.out</code>\uff08\u7ed8\u56fe\u811a\u672c\u4f1a\u4ece\u8be5\u6587\u4ef6\u4e2d\u8bfb\u53d6 VAC \u76f8\u5173\u5217\uff09</p> <p>\u8f93\u51fa\uff1a \u4ea4\u4e92\u5f0f\u56fe\u8868\u6216 <code>vac.png</code>\uff08\u4f7f\u7528 <code>save</code> \u9009\u9879\u65f6\uff09</p> <pre><code>gpumdkit.sh -plt vac\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_cohesivepy","title":"plt_cohesive.py","text":"<p>\u4ece <code>cohesive.out</code> \u7ed8\u5236\u5185\u805a\u80fd\u66f2\u7ebf\u3002\u53ef\u7528\u4e8e\u5206\u6790\u6676\u683c\u7a33\u5b9a\u6027\u548c\u5e73\u8861\u6676\u683c\u5e38\u6570\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>cohesive.out</code>\uff08\u5404\u5411\u540c\u6027\u7f29\u653e\u56e0\u5b50 vs \u5185\u805a\u80fd\uff09</p> <p>\u8f93\u51fa\uff1a \u4ea4\u4e92\u5f0f\u56fe\u8868\u6216 <code>cohesive.png</code>\uff08\u4f7f\u7528 <code>save</code> \u9009\u9879\u65f6\uff09</p> <pre><code>gpumdkit.sh -plt cohesive\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_net_forcepy","title":"plt_net_force.py","text":"<p>\u7ed8\u5236\u7ed3\u6784\u4e0a\u7684\u51c0\u529b\u5206\u5e03\uff0c\u53ef\u7528\u4e8e\u8bc6\u522b\u95ee\u9898\u6784\u578b\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>\u53c2\u8003\u6587\u732e\uff1a arXiv:2510.19774</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_6","title":"\u58f0\u5b50","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_pdospy","title":"plt_pdos.py","text":"<p>\u8ba1\u7b97\u5e76\u7ed8\u5236\u5f52\u4e00\u5316\u7684\u901f\u5ea6\u81ea\u76f8\u5173\u51fd\u6570 (VAC)\u3001\u58f0\u5b50\u6001\u5bc6\u5ea6 (PDOS) \u548c\u70ed\u5bb9 (Cv)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>model.xyz</code>\u3001<code>run.in</code>\u3001<code>dos.out</code>\u3001<code>mvac.out</code></p> <pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>\u70ed\u5bb9\u8f93\u51fa\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#dimer","title":"\u63cf\u8ff0\u7b26\u3001Dimer \u548c\u5176\u4ed6\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_descriptorspy","title":"plt_descriptors.py","text":"<p>\u4f7f\u7528\u964d\u7ef4\u65b9\u6cd5\uff08PCA \u6216 UMAP\uff09\u53ef\u89c6\u5316\u9ad8\u7ef4 NEP \u63cf\u8ff0\u7b26\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>descriptors.npy</code>\uff08\u7531 <code>gpumdkit.sh -calc des</code> \u751f\u6210\uff09</p> <p>\u65b9\u6cd5\uff1a - <code>pca</code> \u2014 \u4e3b\u6210\u5206\u5206\u6790 - <code>umap</code> \u2014 \u7edf\u4e00\u6d41\u5f62\u903c\u8fd1\u4e0e\u6295\u5f71</p> <pre><code># \u5148\u8ba1\u7b97\u63cf\u8ff0\u7b26\ngpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n\n# \u518d\u53ef\u89c6\u5316\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_descriptors_comparepy","title":"plt_descriptors_compare.py","text":"<p>\u6bd4\u8f83\u591a\u4e2a\u8bad\u7ec3\u96c6\u6216\u6a21\u578b\u7684\u63cf\u8ff0\u7b26\u3002</p> <pre><code>gpumdkit.sh -plt des_compare\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_dimerpy","title":"plt_dimer.py","text":"<p>\u7ed8\u5236\u4e8c\u805a\u4f53\u76f8\u4e92\u4f5c\u7528\u66f2\u7ebf\u3002\u5c06\u4e24\u4e2a\u539f\u5b50\u653e\u5165\u7acb\u65b9\u76d2\u5b50\uff0830 \u00c5\uff09\uff0c\u4f7f\u7528 NEP \u6a21\u578b\u8ba1\u7b97\u52bf\u80fd\u548c\u529b\u968f\u8ddd\u79bb\u7684\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>nep.txt</code></p> <pre><code>gpumdkit.sh -plt dimer &lt;element1&gt; &lt;element2&gt; &lt;nep_model&gt;\ngpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>\u53c2\u8003\u6587\u732e\uff1a J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_doaspy","title":"plt_doas.py","text":"<p>\u7ed8\u5236 Wang et al. \u63d0\u51fa\u7684\u539f\u5b50\u6001\u5bc6\u5ea6 (DOAS)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>doas.out</code>\uff08\u7531 <code>gpumdkit.sh -calc doas</code> \u8ba1\u7b97\uff09</p> <pre><code>gpumdkit.sh -plt doas &lt;doas.out&gt; &lt;species&gt;\ngpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plane-grid","title":"\u6781\u6027\u6750\u6599\u7684 Plane-Grid \u7ed8\u56fe","text":"<p>\u6b64\u5de5\u4f5c\u6d41\u5c06\u4f4d\u79fb\u6216\u6781\u5316\u6570\u636e\u6620\u5c04\u5230\u7f51\u683c\u4e0a\uff0c\u5e76\u7ed8\u5236\u9009\u5b9a\u5e73\u9762\u7684\u8f6e\u5ed3\u3002\u8be6\u7ec6\u7528\u6cd5\u548c\u5b9e\u9645\u6848\u4f8b\u8bf7\u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790\u3002</p> <p>\u4f9d\u8d56\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>\u5178\u578b\u524d\u7f6e\u6b65\u9aa4\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>\u4f7f\u7528\u65b9\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_7","title":"\u5feb\u901f\u53c2\u8003\u8868","text":"\u547d\u4ee4 \u8f93\u5165\u6587\u4ef6 \u7528\u9014 <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP \u8bad\u7ec3\u7ed3\u679c <code>prediction</code> / <code>test</code> <code>*_test.out</code> NEP \u9884\u6d4b\u7ed3\u679c <code>train_test</code> <code>*_train.out</code>, <code>*_test.out</code> \u5408\u5e76 parity plot <code>parity_density</code> <code>*_train.out</code> \u5bc6\u5ea6 parity plot <code>force_errors</code> <code>force_train.out</code> \u529b\u8bef\u5dee\u6307\u6807 <code>lr</code> <code>loss.out</code> (gnep) \u5b66\u4e60\u7387 <code>restart</code> <code>nep.restart</code> \u91cd\u542f\u6587\u4ef6\u53c2\u6570 <code>charge</code> <code>charge_train.out</code> \u7535\u8377\u5206\u5e03 <code>born_charge</code> / <code>bec</code> <code>bec_train.out</code>, <code>bec_test.out</code> Born \u6709\u6548\u7535\u8377 <code>thermo</code> <code>thermo.out</code> \u70ed\u529b\u5b66\u91cf <code>msd</code> <code>msd.out</code> \u5747\u65b9\u4f4d\u79fb <code>msd_all</code> <code>msd.out</code> (all_groups) \u5168\u7ec4\u5206 MSD <code>msd_conv</code> <code>msd_step*.out</code> MSD \u6536\u655b\u6027\u68c0\u67e5 <code>sdc</code> <code>msd.out</code> \u81ea\u6269\u6563\u7cfb\u6570 <code>arrhenius_d</code> / <code>D</code> <code>*K/msd.out</code> Arrhenius \u6269\u6563\u7cfb\u6570 <code>arrhenius_sigma</code> / <code>sigma</code> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> Arrhenius \u79bb\u5b50\u7535\u5bfc\u7387 <code>rdf</code> <code>rdf.out</code> \u5f84\u5411\u5206\u5e03\u51fd\u6570 <code>rdf_pmf</code> <code>rdf.out</code> RDF + \u5e73\u5747\u529b\u52bf <code>vac</code> <code>sdc.out</code> \u901f\u5ea6\u81ea\u76f8\u5173 <code>cohesive</code> <code>cohesive.out</code> \u5185\u805a\u80fd\u66f2\u7ebf <code>net_force</code> <code>train.xyz</code> \u51c0\u529b\u5206\u5e03 <code>doas</code> <code>doas.out</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>des</code> <code>descriptors.npy</code> \u63cf\u8ff0\u7b26 PCA/UMAP <code>dimer</code> <code>nep.txt</code> \u4e8c\u805a\u4f53\u80fd\u91cf/\u529b\u66f2\u7ebf <code>pdos</code> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code> VAC \u548c PDOS <code>emd</code> EMD \u8f93\u51fa EMD \u70ed\u5bfc\u7387 <code>nemd</code> NEMD \u8f93\u51fa NEMD \u70ed\u8f93\u8fd0 <code>hnemd</code> HNEMD \u8f93\u51fa HNEMD \u70ed\u8f93\u8fd0 <code>viscosity</code> \u7c98\u5ea6\u8f93\u51fa \u7c98\u5ea6"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html","title":"\u81ea\u5b9a\u4e49\u547d\u4ee4","text":"\ud83d\udd27 \u81ea\u5b9a\u4e49\u547d\u4ee4 <p>GPUMDkit \u652f\u6301\u4ece ~/.gpumdkit.in \u52a0\u8f7d\u81ea\u5b9a\u4e49\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u628a\u5e38\u7528\u811a\u672c\u6216\u5de5\u4f5c\u6d41\u5c01\u88c5\u6210 <code>custom_</code> \u5f00\u5934\u7684 Bash \u51fd\u6570\uff0c\u7136\u540e\u901a\u8fc7 <code>gpumdkit.sh -\u547d\u4ee4\u540d</code> \u8c03\u7528\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_1","title":"\u8bbe\u7f6e","text":"<p>\u7f16\u8f91\u914d\u7f6e\u6587\u4ef6\uff1a</p> <pre><code>vi ~/.gpumdkit.in\n</code></pre> <p>\u81ea\u5b9a\u4e49\u51fd\u6570\u9700\u8981\u4f7f\u7528 <code>custom_</code> \u524d\u7f00\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_2","title":"\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_3","title":"\u7b80\u5355\u95ee\u5019","text":"<p>\u5728 <code>~/.gpumdkit.in</code> \u4e2d\u5199\u5165\uff1a</p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>\u7136\u540e\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -hello\n</code></pre> <p>\u4f60\u4f1a\u770b\u5230\u7c7b\u4f3c\u8f93\u51fa\uff1a</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_4","title":"\u5e26\u5fc5\u9700\u53c2\u6570\u7684\u547d\u4ee4","text":"<pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -greet Zihan\n</code></pre> <p>\u8f93\u51fa\uff1a</p> <pre><code>Hello, Zihan!\n</code></pre> <p>\u4f20\u9012\u53c2\u6570\u65f6\uff0c\u53ef\u4ee5\u7528 <code>\"$@\"</code> \u5b89\u5168\u5730\u8f6c\u53d1\u6240\u6709\u53c2\u6570\uff1b\u5982\u679c\u9700\u8981\u4ece\u7b2c\u4e00\u4e2a\u53c2\u6570\u5f00\u59cb\u5f15\u7528\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528 <code>${@:1}</code>\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_5","title":"\u8c03\u7528\u5916\u90e8\u811a\u672c","text":"<p>\u5982\u679c\u5e0c\u671b\u50cf\u8c03\u7528 GPUMDkit \u5185\u7f6e\u547d\u4ee4\u4e00\u6837\u8c03\u7528\u81ea\u5df1\u7684\u811a\u672c\uff1a</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -nepanalyse\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_6","title":"\u8fdb\u9636\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_7","title":"\u6279\u5904\u7406\u7ed8\u56fe","text":"<p>\u5bf9\u591a\u4e2a\u76ee\u5f55\u6279\u91cf\u7ed8\u56fe\uff1a</p> <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -batch_plot dir1 dir2 dir3\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_8","title":"\u8bad\u7ec3\u96c6\u5206\u6790\u6d41\u7a0b","text":"<p>\u628a\u591a\u4e2a\u5206\u6790\u547d\u4ee4\u7ec4\u5408\u6210\u4e00\u4e2a\u5165\u53e3\uff1a</p> <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -analyze_training train.xyz\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_9","title":"\u81ea\u5b9a\u4e49\u6570\u636e\u51c6\u5907\u6d41\u7a0b","text":"<pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    gpumdkit.sh -out2xyz ./\n    gpumdkit.sh -filter_value train.xyz force 30\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -prep_training\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_10","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u547d\u4ee4\u540d\u5c3d\u91cf\u6e05\u695a\uff0c\u4f8b\u5982 <code>custom_analyze_training</code> \u6bd4 <code>custom_at</code> \u66f4\u5bb9\u6613\u7ef4\u62a4\u3002</li> <li>\u5bf9\u9700\u8981\u53c2\u6570\u7684\u547d\u4ee4\uff0c\u5efa\u8bae\u5728\u53c2\u6570\u4e3a\u7a7a\u65f6\u6253\u5370\u7528\u6cd5\u63d0\u793a\u3002</li> <li>\u8c03\u7528\u5916\u90e8\u811a\u672c\u65f6\uff0c\u5c3d\u91cf\u7528 <code>\"$@\"</code> \u4fdd\u7559\u53c2\u6570\u4e2d\u7684\u7a7a\u683c\u548c\u7279\u6b8a\u5b57\u7b26\u3002</li> <li>\u6279\u5904\u7406\u76ee\u5f55\u65f6\uff0c\u6ce8\u610f\u4f7f\u7528 <code>cd \"$dir\"</code>\uff0c\u907f\u514d\u8def\u5f84\u4e2d\u6709\u7a7a\u683c\u65f6\u51fa\u9519\u3002</li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html","title":"\u8ba1\u7b97\u5668\u811a\u672c","text":"\ud83e\uddee \u8ba1\u7b97\u5668\u811a\u672c <p>\u8ba1\u7b97\u5668\u6a21\u5757\u7528\u4e8e\u4ece MD \u8f68\u8ff9\u3001NEP \u6a21\u578b\u548c\u7ed3\u6784\u6587\u4ef6\u4e2d\u8ba1\u7b97\u6750\u6599\u6027\u8d28\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code></p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_1","title":"\u529f\u80fd\u6982\u89c8","text":"\u4efb\u52a1 \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u79bb\u5b50\u7535\u5bfc\u7387 <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>\u3001<code>thermo.out</code>\u3001<code>model.xyz</code> MSD <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz \u8f68\u8ff9 NEP \u9884\u6d4b <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP \u6a21\u578b NEP \u63cf\u8ff0\u7b26 <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP \u6a21\u578b DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP \u6a21\u578b NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u521d\u672b\u6001\u7ed3\u6784 \u7ed3\u6784\u4f18\u5316 <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784 + NEP \u6a21\u578b \u90bb\u5c45\u5217\u8868 <code>gpumdkit.sh -calc nlist ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u4f4d\u79fb <code>gpumdkit.sh -calc disp ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u5e73\u5747\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u516b\u9762\u4f53\u503e\u8f6c <code>gpumdkit.sh -calc oct-tilt ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u67e5\u770b\u5b8c\u6574\u5e2e\u52a9\uff1a</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>\u547d\u4ee4\u884c\u5e2e\u52a9\u8868\u7c7b\u4f3c\uff1a</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>4) Calculators</code>\uff0c\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_2","title":"\u79bb\u5b50\u7535\u5bfc\u7387","text":"<pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>401</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>\u5e38\u7528\u8f93\u5165\u6587\u4ef6\uff1a</p> \u6587\u4ef6 \u4f5c\u7528 <code>msd.out</code> \u5fc5\u9700\uff0cMSD \u6570\u636e <code>thermo.out</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u6e29\u5ea6 <code>model.xyz</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u4f53\u79ef\u548c\u79bb\u5b50\u6570 <code>run.in</code> \u53ef\u9009\uff0c\u8bc6\u522b\u6269\u80de\u4fe1\u606f <p>\u5982\u679c\u7f3a\u5c11\u81ea\u52a8\u8bc6\u522b\u6240\u9700\u6587\u4ef6\uff0c\u811a\u672c\u4f1a\u4ea4\u4e92\u5f0f\u8be2\u95ee\u6e29\u5ea6\u3001\u4f53\u79ef\u548c\u79bb\u5b50\u6570\u3002</p> <p>\u624b\u52a8\u6a21\u5f0f\u7684\u63d0\u793a\u7c7b\u4f3c\uff1a</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#msd","title":"\u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD","text":"<pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>412</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>Li</code> \u76ee\u6807\u6269\u6563\u5143\u7d20 <code>10</code> \u5e27\u95f4\u9694\uff0c\u5355\u4f4d fs <code>5000</code> \u53ef\u9009\uff0c\u6700\u5927\u76f8\u5173\u6b65\u6570 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>msd.out</code></li> </ul> <p>\u968f\u540e\u53ef\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u9884\u6d4b\u6027\u8d28","text":"<p><code>calc_properties_with_nep.py</code> \u4f7f\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8ba1\u7b97\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u3002</p> <p>\u4f9d\u8d56\uff1a <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>\u4f7f\u7528\u6b64\u529f\u80fd\u53ef\u4ee5\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8fdb\u884c\u9884\u6d4b\u3002\u5efa\u8bae\u5728\u4f7f\u7528\u524d\u5148\u9a8c\u8bc1\u6a21\u578b\u5728\u76ee\u6807\u7ed3\u6784\u4e0a\u7684\u9884\u6d4b\u8d28\u91cf\u3002</p> <p>\u63d0\u793a\uff1a \u9884\u6d4b\u524d\u53ef\u4ee5\u6e05\u7406 extxyz \u5143\u6570\u636e\uff1a</p> <pre><code>gpumdkit.sh -clean_xyz train.xyz clean_train.xyz\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep_1","title":"NEP \u63cf\u8ff0\u7b26","text":"<pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>\u7528\u9014\u5305\u62ec\uff1a</p> <ul> <li>\u7528 PCA/UMAP \u53ef\u89c6\u5316\u5c40\u57df\u73af\u5883\uff1b</li> <li>\u6bd4\u8f83\u8bad\u7ec3\u96c6\u548c\u5019\u9009\u7ed3\u6784\uff1b</li> <li>\u5224\u65ad\u65b0\u6570\u636e\u662f\u5426\u6269\u5c55\u4e86\u63cf\u8ff0\u7b26\u7a7a\u95f4\u3002</li> </ul> <p>\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#doas","title":"DOAS","text":"<p><code>calc_doas.py</code> \u7528\u4e8e\u8ba1\u7b97 Wang et al. \u63d0\u51fa\u7684 density of atomistic states\u3002</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>\u811a\u672c\u4f1a\uff1a</p> <ol> <li>\u8bfb\u53d6\u6240\u6709\u7ed3\u6784\uff1b</li> <li>\u4f7f\u7528 NEP \u8fdb\u884c\u7ed3\u6784\u4f18\u5316\uff1b</li> <li>\u63d0\u53d6\u6bcf\u4e2a\u539f\u5b50\u7684\u80fd\u91cf\uff1b</li> <li>\u6309\u5143\u7d20\u5206\u7ec4\u8f93\u51fa\uff1b</li> <li>\u7528\u7ed8\u56fe\u811a\u672c\u53ef\u89c6\u5316\u5206\u5e03\u3002</li> </ol>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#neb","title":"NEB \u548c\u7ed3\u6784\u4f18\u5316","text":"<p>NEB\uff1a</p> <pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>\u7ed3\u6784\u4f18\u5316\uff08\u901a\u8fc7 <code>calorine</code>\uff09\uff1a</p> <p>\u4f9d\u8d56\uff1a <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>\u8f93\u51fa\u5305\u62ec\uff1a</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#ovito-rdf","title":"\u4f7f\u7528 OVITO \u8ba1\u7b97 RDF","text":"<p><code>rdf_calculator_ovito.py</code> \u4f7f\u7528 OVITO \u7684\u5206\u6790\u5de5\u5177\u8ba1\u7b97\u5f84\u5411\u5206\u5e03\u51fd\u6570\u3002</p> <p>\u4f9d\u8d56\uff1a OVITO</p> <pre><code>pip install ovito\n</code></pre> <p>\u8f93\u5165\u6587\u4ef6\uff1a \u7ed3\u6784\u6587\u4ef6\uff08\u5355\u5e27\u6216\u8f68\u8ff9\uff09</p> <pre><code>python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400\n</code></pre> <p>\u53c2\u6570\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>trajectory.xyz</code> \u8f93\u5165\u7ed3\u6784\u6587\u4ef6 <code>6.0</code> RDF \u8ba1\u7b97\u7684\u6700\u5927\u8ddd\u79bb\uff08\u00c5\uff09 <code>400</code> \u76f4\u65b9\u56fe\u7684\u5206\u7bb1\u6570 <p>\u53ef\u89c6\u5316\uff1a</p> <pre><code>gpumdkit.sh -plt rdf\n</code></pre> <p>\u6ce8\u610f\uff1a \u5efa\u8bae\u4f18\u5148\u4f7f\u7528 GPUMD \u4e2d\u7684 <code>compute_rdf</code> \u547d\u4ee4\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_3","title":"\u94c1\u7535\u548c\u6781\u6027\u6750\u6599\u5de5\u5177","text":"<p>\u9009\u9879 <code>406\u2013410</code> \u6db5\u76d6\u9499\u949b\u77ff\u548c\u6781\u6027\u6750\u6599\u5206\u6790\uff1a\u8fd1\u90bb\u5217\u8868\u3001\u5c40\u57df\u4f4d\u79fb\u3001\u5e73\u5747\u7ed3\u6784\u3001\u516b\u9762\u4f53\u503e\u8f6c\u548c ABO3 \u6781\u5316\u3002\u8fd9\u4e9b\u5de5\u5177\u57fa\u4e8e <code>ferrodispcalc</code>\u3002</p> <p>\u4f9d\u8d56\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>\u5b8c\u6574\u53c2\u6570\u5217\u8868\u548c\u771f\u5b9e\u5de5\u4f5c\u6d41\u6848\u4f8b\uff08PbTiO3 \u76f8\u53d8\u3001PTO/STO \u8d85\u6676\u683c\u62d3\u6251\u7b49\uff09\u8bf7\u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html","title":"\u8d21\u732e\u6307\u5357","text":"\ud83e\udd1d \u4e3a GPUMDkit \u8d21\u732e\u4ee3\u7801 <p>\u611f\u8c22\u4f60\u6709\u5174\u8da3\u4e3a GPUMDkit \u505a\u51fa\u8d21\u732e\uff01\u6211\u4eec\u611f\u8c22\u4f60\u4e3a\u6539\u5584\u8fd9\u4e2a\u5de5\u5177\u5305\u6240\u4ed8\u51fa\u7684\u65f6\u95f4\u548c\u52aa\u529b\u3002</p> <p> English   \u00a0\u00b7\u00a0   \u7b80\u4f53\u4e2d\u6587 </p> <p><code>GPUMDkit</code> \u662f\u4e00\u4e2a\u5f00\u6e90\u9879\u76ee\uff0c\u6211\u4eec\u6b22\u8fce\u793e\u533a\u7684\u5404\u79cd\u8d21\u732e\uff0c\u65e0\u8bba\u662f\u4fee\u590d bug\u3001\u6dfb\u52a0\u65b0\u529f\u80fd\u3001\u6539\u8fdb\u6587\u6863\u8fd8\u662f\u63d0\u51fa\u5efa\u8bae\u3002</p> <p>\u6ce8\u610f\uff1a\u672c\u6587\u6863\u7684\u6743\u5a01\u7248\u672c\u4f4d\u4e8e\u4ed3\u5e93\u6839\u76ee\u5f55\u7684 <code>CONTRIBUTING.md</code>\u3002\u672c\u6559\u7a0b\u9875\u9762\u540c\u6b65\u5176\u5185\u5bb9\u3002\u4e2d\u6587\u7248\u8bf7\u53c2\u89c1 <code>docs/CONTRIBUTING_zh-CN.md</code>\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_1","title":"\u76ee\u5f55","text":"<ul> <li>\u5f00\u53d1\u89c4\u8303\u4e0e\u51c6\u5219</li> <li>\u62a5\u544a\u95ee\u9898</li> <li>\u529f\u80fd\u5efa\u8bae</li> <li>\u8d21\u732e\u4ee3\u7801</li> <li>Fork \u5e76\u514b\u9686\u4ed3\u5e93</li> <li>\u521b\u5efa\u529f\u80fd\u5206\u652f</li> <li>\u8fdb\u884c\u4fee\u6539<ul> <li>\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e</li> <li>\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e</li> <li>\u66f4\u65b0 Tab \u8865\u5168</li> </ul> </li> <li>\u4ee3\u7801\u98ce\u683c\u4e0e\u6700\u4f73\u5b9e\u8df5</li> <li>\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539</li> <li>\u63d0\u4ea4\u4fe1\u606f</li> <li>\u63a8\u9001\u5e76\u521b\u5efa Pull Request</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_2","title":"\u5f00\u53d1\u89c4\u8303\u4e0e\u51c6\u5219","text":"<p>\u4e3a\u4fdd\u6301\u4ee3\u7801\u8d28\u91cf\u548c\u9879\u76ee\u4e00\u81f4\u6027\uff0c\u8bf7\u9075\u5faa\u4ee5\u4e0b\u51c6\u5219\uff1a</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_3","title":"\u8bed\u8a00\u8981\u6c42","text":"<ul> <li>\u6240\u6709\u4ee3\u7801\u5e94\u4f7f\u7528\u82f1\u6587\u7f16\u5199\uff1a\u5305\u62ec\u53d8\u91cf\u540d\u3001\u51fd\u6570\u540d\u3001\u6ce8\u91ca\u3001\u6587\u6863\u5b57\u7b26\u4e32\u3001\u63d0\u4ea4\u4fe1\u606f\u548c\u6587\u6863\u3002</li> <li>\u867d\u7136\u6211\u4eec\u7406\u89e3\u8d21\u732e\u8005\u6765\u81ea\u4e0d\u540c\u80cc\u666f\uff0c\u4f46\u4f7f\u7528\u82f1\u6587\u80fd\u786e\u4fdd\u4ee3\u7801\u5e93\u5bf9\u6700\u5e7f\u6cdb\u7684\u7528\u6237\u7fa4\u4f53\u53ef\u8bbf\u95ee\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_4","title":"\u6a21\u5757\u5316\u4e0e\u53ef\u590d\u7528\u6027","text":"<ul> <li>\u7f16\u5199\u6a21\u5757\u5316\u548c\u53ef\u590d\u7528\u7684\u4ee3\u7801\uff1a\u51fd\u6570\u548c\u811a\u672c\u7684\u8bbe\u8ba1\u5e94\u5177\u6709\u7075\u6d3b\u6027\u3002</li> <li>\u4f18\u5148\u4f20\u9012\u53c2\u6570\u800c\u975e\u786c\u7f16\u7801\u503c\uff1a\u4f7f\u7528\u51fd\u6570\u53c2\u6570\u3001\u547d\u4ee4\u884c\u53c2\u6570\u6216\u914d\u7f6e\u6587\u4ef6\u6765\u66ff\u4ee3\u786c\u7f16\u7801\u503c\u3002\u4f46\u67d0\u4e9b\u6587\u4ef6\u540d\u7531 GPUMD \u548c NEP \u7a0b\u5e8f\u56fa\u5b9a\u8981\u6c42\uff08\u5982 <code>train.xyz</code>\u3001<code>thermo.out</code>\uff09\uff0c\u8fd9\u4e9b\u53ef\u4ee5\u6309\u9700\u786c\u7f16\u7801\u3002</li> <li>\u793a\u4f8b\uff1a   <pre><code># \u597d\u7684\u505a\u6cd5\uff1a\u63a5\u53d7\u53c2\u6570\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # \u5904\u7406\u903b\u8f91\n}\n\n# \u907f\u514d\uff1a\u786c\u7f16\u7801\u503c\uff08\u9664\u975e GPUMD/NEP \u8981\u6c42\uff09\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # \u5904\u7406\u903b\u8f91\n}\n</code></pre></li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_5","title":"\u4ee3\u7801\u98ce\u683c","text":"<ul> <li>\u7f16\u5199\u6e05\u6670\u3001\u6613\u4e8e\u4ed6\u4eba\u7ef4\u62a4\u548c\u4fee\u6539\u7684\u4ee3\u7801\u3002</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u548c\u51fd\u6570\u540d\u3002</li> <li>\u5728\u5fc5\u8981\u5904\u6dfb\u52a0\u6ce8\u91ca\u4ee5\u89e3\u91ca\u590d\u6742\u903b\u8f91\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_6","title":"\u6587\u6863","text":"<ul> <li>\u786e\u4fdd\u5e2e\u52a9\u4fe1\u606f\uff08\u5982 <code>-h</code> \u6807\u5fd7\uff09\u6e05\u6670\u51c6\u786e\u3002</li> <li>\u6559\u7a0b\u6587\u6863\u4f4d\u4e8e <code>docs/tutorials/en/</code>\uff08\u82f1\u6587\uff09\u548c <code>docs/tutorials/zh/</code>\uff08\u4e2d\u6587\uff09\u3002\u5982\u679c\u4f60\u6dfb\u52a0\u4e86\u65b0\u529f\u80fd\uff0c\u8bf7\u8003\u8651\u66f4\u65b0\u76f8\u5173\u6559\u7a0b\u9875\u9762\u3002</li> <li>\u7f16\u8f91\u6559\u7a0b Markdown \u6587\u4ef6\u540e\uff0c\u4f7f\u7528 <code>mkdocs build -f docs/mkdocs.yml</code> \u91cd\u65b0\u6784\u5efa HTML\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_7","title":"\u62a5\u544a\u95ee\u9898","text":"<p>\u5982\u679c\u4f60\u9047\u5230 bug\uff0c\u8bf7\u901a\u8fc7 GitHub Issues \u5e2e\u52a9\u6211\u4eec\u4fee\u590d\uff1a</p> <ol> <li>\u641c\u7d22\u73b0\u6709 issues \u67e5\u770b\u8be5 bug \u662f\u5426\u5df2\u88ab\u62a5\u544a\u3002</li> <li>\u521b\u5efa\u65b0 issue\uff08\u5982\u679c\u5c1a\u672a\u88ab\u62a5\u544a\uff09\uff1a\u521b\u5efa Issue</li> <li>\u8be6\u7ec6\u63cf\u8ff0\u95ee\u9898\uff0c\u5982\u679c\u53ef\u80fd\u8bf7\u63d0\u4f9b\u6d4b\u8bd5\u6587\u4ef6\u3002</li> </ol> <p>\u4f60\u4e5f\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u65b9\u5f0f\u8054\u7cfb\u6211\u4eec\uff1a - QQ \u7fa4\uff1a825696376 - \u90ae\u7bb1\uff1ayanzihan@westlake.edu.cn - \u811a\u672c\u5f00\u53d1\u8005\uff1a\u8054\u7cfb\u811a\u672c\u5934\u90e8\u5217\u51fa\u7684\u5f00\u53d1\u8005</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_8","title":"\u529f\u80fd\u5efa\u8bae","text":"<p>\u6211\u4eec\u6b22\u8fce\u529f\u80fd\u5efa\u8bae\uff01\u63d0\u51fa\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u641c\u7d22\u73b0\u6709 issues \u67e5\u770b\u662f\u5426\u5df2\u6709\u4eba\u63d0\u51fa\u3002</li> <li>\u521b\u5efa\u65b0\u529f\u80fd\u8bf7\u6c42\uff1a\u521b\u5efa\u529f\u80fd\u8bf7\u6c42 \u5e76 mention @zhyan0603</li> <li>\u6e05\u695a\u63cf\u8ff0\u4f60\u7684\u9700\u6c42 \u5e76\u89e3\u91ca\u5176\u7528\u9014\u3002</li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_9","title":"\u8d21\u732e\u4ee3\u7801","text":""},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#fork","title":"Fork \u5e76\u514b\u9686\u4ed3\u5e93","text":"<ol> <li> <p>\u5728 GitHub \u4e0a Fork \u4ed3\u5e93\uff0c\u70b9\u51fb \u4ed3\u5e93\u9875\u9762 \u53f3\u4e0a\u89d2\u7684 \"Fork\" \u6309\u94ae\u3002</p> </li> <li> <p>\u514b\u9686\u4f60\u7684 fork \u5230\u672c\u5730\uff1a</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>\u8bbe\u7f6e upstream remote \u4ee5\u4fdd\u6301 fork \u540c\u6b65\uff1a    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_10","title":"\u521b\u5efa\u529f\u80fd\u5206\u652f","text":"<p>\u4e3a\u4f60\u7684\u4fee\u6539\u521b\u5efa\u65b0\u5206\u652f\uff1a</p> <pre><code># \u4ece main \u521b\u5efa\u5e76\u5207\u6362\u5230\u65b0\u5206\u652f\ngit checkout -b your-branch-name\n</code></pre> <p>\u5206\u652f\u540d\u79f0\u968f\u610f\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_11","title":"\u8fdb\u884c\u4fee\u6539","text":"<p><code>GPUMDkit</code> \u7684\u7ed3\u6784\u5305\u62ec\uff1a - <code>gpumdkit.sh</code>\uff1a\u4e3b\u5165\u53e3\uff08Bash \u811a\u672c\uff09\uff0c\u5904\u7406\u4ea4\u4e92\u83dc\u5355\u6a21\u5f0f\u548c\u547d\u4ee4\u884c\u6a21\u5f0f - <code>install.sh</code>\uff1a\u5b89\u88c5\u811a\u672c\uff0c\u8bbe\u7f6e\u73af\u5883\u53d8\u91cf\u548c shell \u914d\u7f6e - <code>Scripts/</code>\uff1a\u6309\u529f\u80fd\u7ec4\u7ec7\u7684 Python \u548c Bash \u5b9e\u73b0\u811a\u672c   - <code>plt_scripts/</code>\uff1a\u7ed8\u56fe\u811a\u672c   - <code>calculators/</code>\uff1a\u8ba1\u7b97\u5de5\u5177   - <code>format_conversion/</code>\uff1a\u683c\u5f0f\u8f6c\u6362\u5de5\u5177   - <code>workflow/</code>\uff1a\u5de5\u4f5c\u6d41\u81ea\u52a8\u5316   - <code>sample_structures/</code>\uff1a\u7ed3\u6784\u91c7\u6837\u5de5\u5177   - <code>analyzer/</code>\uff1a\u5206\u6790\u5de5\u5177   - <code>utils/</code>\uff1a\u5b9e\u7528\u51fd\u6570\uff08\u5305\u62ec <code>completion.sh</code> Tab \u8865\u5168\uff09 - <code>src/</code>\uff1a\u4ea4\u4e92\u6a21\u5f0f\u83dc\u5355\u51fd\u6570\u7684 Shell \u811a\u672c   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>skills/</code>\uff1aAI agent \u6280\u80fd\u5b9a\u4e49\uff08\u7528\u4e8e opencode/Claude Code \u96c6\u6210\u7684 SKILL.md \u6587\u4ef6\uff09 - <code>docs/</code>\uff1a\u6587\u6863\u6587\u4ef6   - <code>tutorials/en/</code> \u548c <code>tutorials/zh/</code>\uff1a\u53cc\u8bed\u6559\u7a0b\u9875\u9762   - <code>mkdocs.yml</code>\uff1a\u6784\u5efa\u6559\u7a0b HTML \u7684 MkDocs \u914d\u7f6e   - <code>command_reference.tsv</code>\uff1a\u673a\u5668\u53ef\u8bfb\u7684\u547d\u4ee4\u53c2\u8003   - <code>htmls/</code>\uff1aMkDocs \u751f\u6210\u7684 HTML \u8f93\u51fa</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_12","title":"\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e","text":"<p>\u8981\u6dfb\u52a0\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u8bbf\u95ee\u7684\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u5728\u76f8\u5e94\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a</li> </ol> <pre><code># \u793a\u4f8b\uff1a\u6dfb\u52a0\u65b0\u7684\u683c\u5f0f\u8f6c\u6362\u811a\u672c\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u9075\u5faa\u6a21\u5757\u5316\u51c6\u5219\uff08\u63a5\u53d7\u53c2\u6570\uff0c\u907f\u514d\u786c\u7f16\u7801\uff09\u3002</p> </li> <li> <p>\u5728\u76f8\u5e94\u7684 <code>src/</code> \u6587\u4ef6\u4e2d\u6dfb\u52a0\u5305\u88c5\u51fd\u6570\uff1a    <pre><code># \u793a\u4f8b\uff1a\u7f16\u8f91 src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>\u6dfb\u52a0\u65b0\u51fd\u6570\uff1a    <pre><code>function f111_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input &lt;required_param1&gt; &lt;required_param2&gt;\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -r -a converter_args\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py \"${converter_args[@]}\"\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u66f4\u65b0\u83dc\u5355\u663e\u793a\uff1a    <pre><code># \u627e\u5230 menu() \u51fd\u6570\u5e76\u6309\u9700\u66f4\u65b0\n# \u627e\u5230 array_choice \u6570\u7ec4\u5e76\u6dfb\u52a0\u4f60\u7684\u65b0\u9009\u62e9\u7f16\u53f7\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\" \"107\" \"108\" \"109\" \"110\" \"111\"  # \u6dfb\u52a0 \"111\"\n    # ... \u5176\u4f59\u9009\u62e9\n)\n</code></pre></p> </li> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0 case \u8bed\u53e5\uff1a    <pre><code># \u5728 main() \u51fd\u6570\u4e2d\u627e\u5230\u76f8\u5e94\u7684 case \u8bed\u53e5\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n            \"101\") f101_out2xyz ;;\n            # ... \u73b0\u6709 case ...\n            \"111\") f111_new_converter ;;  # \u6dfb\u52a0\u4f60\u7684 case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_13","title":"\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e","text":"<p>\u8981\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c\u6807\u5fd7\u6216\u5b50\u547d\u4ee4\uff1a</p> <ol> <li> <p>\u5728\u76f8\u5e94\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a    <pre><code># \u793a\u4f8b\uff1a\u6dfb\u52a0\u65b0\u7684\u5206\u6790\u5668\u811a\u672c\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u660e\u786e\u53c2\u6570\u8981\u6c42\uff1a    <pre><code># \u793a\u4f8b\uff1aScripts/analyzer/analyze_bonds.py\nimport sys\n\nif len(sys.argv) != 3:\n    print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n    print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n    sys.exit(1)\n\ninput_file = sys.argv[1]\ncutoff = float(sys.argv[2])\n\n# \u4f60\u7684\u5b9e\u73b0\n</code></pre></p> </li> </ol> <p>\u6ce8\u610f\uff1aGPUMDkit Python \u811a\u672c\u8bbe\u8ba1\u4e3a\u76f4\u63a5\u8fd0\u884c\uff08\u4e0d\u4f5c\u4e3a\u6a21\u5757\u5bfc\u5165\uff09\u3002 \u5982\u679c\u4f60\u613f\u610f\uff0c\u53ef\u4ee5\u4f7f\u7528 <code>main()</code> \u51fd\u6570\u914d\u5408 <code>if __name__ == \"__main__\":</code> \u4fdd\u62a4\uff0c \u4f46\u8fd9\u4e0d\u662f\u5fc5\u9700\u7684\u3002\u5927\u591a\u6570\u73b0\u6709\u811a\u672c\u5728\u6a21\u5757\u7ea7\u522b\u6267\u884c\u3002</p> <ol> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0\u547d\u4ee4\u884c\u6807\u5fd7\u5904\u7406\uff1a    <pre><code># \u627e\u5230\u547d\u4ee4\u884c\u89e3\u6790\u90e8\u5206\uff08\u5927\u7684 \"case $1 in\" \u5757\uff09\n# \u5728\u9002\u5f53\u4f4d\u7f6e\u6dfb\u52a0\u4f60\u7684\u65b0\u6807\u5fd7\n\ncase $1 in\n    # ... \u73b0\u6709 case ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ \"$2\" != \"-h\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py $2 $3\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n        fi ;;\n    # ... \u5176\u4f59 case ...\nesac\n</code></pre></p> </li> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u66f4\u65b0\u5e2e\u52a9\u4fe1\u606f\uff1a    <pre><code># \u627e\u5230 help_info_table() \u51fd\u6570\u5e76\u6dfb\u52a0\u4f60\u7684\u547d\u4ee4\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... \u5176\u4f59\u5e2e\u52a9\u8868 ...\n}\n</code></pre></p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#tab","title":"\u66f4\u65b0 Tab \u8865\u5168","text":"<p>\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c\u6807\u5fd7\u65f6\uff0c\u66f4\u65b0 Tab \u8865\u5168\u811a\u672c\uff1a</p> <pre><code># \u7f16\u8f91 Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>\u5c06\u4f60\u7684\u65b0\u6807\u5fd7\u6dfb\u52a0\u5230 <code>opts</code> \u53d8\u91cf\uff1a <pre><code># \u627e\u5230 local opts=... \u884c\nlocal opts=\"-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...\"\n#                                                        \u5728\u6b64\u6dfb\u52a0\u4f60\u7684\u6807\u5fd7\n</code></pre></p> <p>\u5982\u679c\u4f60\u7684\u6807\u5fd7\u9700\u8981\u6587\u4ef6\u53c2\u6570\uff0c\u5c06\u5176\u6dfb\u52a0\u5230\u73b0\u6709\u7684\u6587\u4ef6\u8865\u5168 case \u4e2d\uff1a <pre><code># \u627e\u5230\u9700\u8981\u6587\u4ef6\u53c2\u6570\u7684 case \u5e76\u7528 | \u6dfb\u52a0\u4f60\u7684\u6807\u5fd7\n-out2xyz|-out2exyz|-...|-your_new_flag)\n    COMPREPLY=($(compgen -f -- \"$cur\")) ;;\n</code></pre></p> <p>\u5982\u679c\u4f60\u7684\u6807\u5fd7\u63a5\u53d7\u4e8c\u7ea7\u9009\u9879\uff08\u5982 <code>-plt</code> \u6216 <code>-calc</code>\uff09\uff0c\u6dfb\u52a0\u65b0 case\uff1a <pre><code>case \"$prev\" in\n    # ... \u73b0\u6709 case ...\n    -your_new_flag)\n        COMPREPLY=($(compgen -W \"option1 option2 option3\" -- \"$cur\")) ;;\n    # ... \u5176\u4f59 case ...\nesac\n</code></pre></p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_14","title":"\u4ee3\u7801\u98ce\u683c\u4e0e\u6700\u4f73\u5b9e\u8df5","text":"<ul> <li>Shell \u811a\u672c\uff1a</li> <li>\u4f7f\u7528 <code>${variable}</code> \u8fdb\u884c\u53d8\u91cf\u5c55\u5f00</li> <li>\u4f7f\u7528 <code>[ ! -z \"$var\" ]</code> \u8fdb\u884c\u975e\u7a7a\u68c0\u67e5\uff08\u9879\u76ee\u7ea6\u5b9a\uff09</li> <li>\u4ea4\u4e92\u51fd\u6570\u5e94\u9075\u5faa banner \u683c\u5f0f\uff1a     <pre><code>echo \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/&lt;category&gt;        |\"\necho \" | Script: &lt;script_name&gt;.py                        |\"\necho \" | Developer: &lt;Name&gt; (&lt;email&gt;)                     |\"\necho \" &gt;-------------------------------------------------&lt;\"\n</code></pre></li> <li>\u4f7f\u7528 <code>read -r -a varname</code> \u8bfb\u53d6\u591a\u8bcd\u8f93\u5165\uff0c\u7136\u540e\u7528 <code>\"${varname[@]}\"</code> \u4f20\u9012</li> <li> <p><code>src/</code> \u4e2d\u7684 Shell \u811a\u672c\u5e94\u4ee5\u6587\u4ef6\u5934\u6ce8\u91ca\u5757\u5f00\u59cb\uff1a     <pre><code># ============================================================\n# GPUMDkit &lt;module name&gt; module\n# Repository: https://github.com/zhyan0603/GPUMDkit\n# Author: &lt;Name&gt; (&lt;email&gt;)\n# ============================================================\n</code></pre></p> </li> <li> <p>Python \u811a\u672c\uff1a</p> </li> <li>\u7f16\u5199\u6e05\u6670\u3001\u53ef\u7ef4\u62a4\u7684\u4ee3\u7801</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u540d</li> <li>\u4f7f\u7528 <code>sys.argv</code> \u8fdb\u884c\u53c2\u6570\u89e3\u6790\uff08\u4e0e\u5927\u591a\u6570\u73b0\u6709\u811a\u672c\u4e00\u81f4\uff09</li> <li>\u63d0\u4f9b\u6e05\u6670\u7684\u4f7f\u7528\u4fe1\u606f\uff1a<code>print(\"Usage: ...\")</code> \u548c <code>print(\"Example: ...\")</code></li> <li>\u5982\u679c\u4f60\u7684\u811a\u672c\u4f7f\u7528\u91cd\u578b/\u7279\u6b8a\u5305\uff08<code>NepTrain</code>\u3001<code>calorine</code>\u3001<code>dpdata</code>\uff09\uff0c\u8bf7\u6dfb\u52a0     <code>print_dependency_notice()</code> \u51fd\u6570\u4ee5\u901a\u77e5\u7528\u6237\u5f15\u7528\u5efa\u8bae</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_15","title":"\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539","text":"<p>\u63d0\u4ea4\u8d21\u732e\u524d\uff0c\u8fd0\u884c\u76f8\u5173\u9a8c\u8bc1\u547d\u4ee4\uff1a</p> <pre><code># Shell \u8bed\u6cd5\u68c0\u67e5\uff08\u59cb\u7ec8\u8fd0\u884c\uff09\nbash -n gpumdkit.sh\nfind src Scripts -name '*.sh' -exec bash -n {} +\n\n# Python \u8bed\u6cd5\u68c0\u67e5\uff08\u9488\u5bf9\u4fee\u6539\u7684 Python \u6587\u4ef6\uff09\npython3 -m py_compile path/to/modified_script.py\n\n# MkDocs \u6784\u5efa\uff08\u5982\u679c\u4fee\u6539\u4e86\u6587\u6863\uff09\nmkdocs build -f docs/mkdocs.yml\n\n# \u68c0\u67e5\u5c3e\u968f\u7a7a\u683c\u95ee\u9898\ngit diff --check\n</code></pre> <p>\u7136\u540e\u6d4b\u8bd5\u529f\u80fd\uff1a</p> <ol> <li> <p>\u6d4b\u8bd5\u4ea4\u4e92\u6a21\u5f0f\uff08\u5982\u9002\u7528\uff09\uff1a    <pre><code>gpumdkit.sh\n# \u5bfc\u822a\u5230\u4f60\u7684\u65b0\u529f\u80fd\u5e76\u5145\u5206\u6d4b\u8bd5\n</code></pre></p> </li> <li> <p>\u6d4b\u8bd5\u547d\u4ee4\u884c\u6a21\u5f0f\uff08\u5982\u9002\u7528\uff09\uff1a    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # \u6d4b\u8bd5\u5e2e\u52a9\u4fe1\u606f\n</code></pre></p> </li> <li> <p>\u6d4b\u8bd5 Tab \u8865\u5168\uff08\u5982\u679c\u4f60\u4fee\u6539\u4e86 <code>completion.sh</code>\uff09\uff1a    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # \u5e94\u663e\u793a\u4f60\u7684\u65b0\u6807\u5fd7\n</code></pre></p> </li> <li> <p>\u7528\u5404\u79cd\u8f93\u5165\u6d4b\u8bd5\uff1a</p> </li> <li>\u7528\u5178\u578b\u8f93\u5165\u6d4b\u8bd5</li> <li>\u7528\u8fb9\u7f18\u60c5\u51b5\u6d4b\u8bd5\uff08\u7a7a\u6587\u4ef6\u3001\u5927\u6587\u4ef6\u7b49\uff09</li> <li> <p>\u6d4b\u8bd5\u9519\u8bef\u5904\u7406\uff08\u7f3a\u5c11\u6587\u4ef6\u3001\u65e0\u6548\u53c2\u6570\uff09</p> </li> <li> <p>\u9a8c\u8bc1\u65e0\u56de\u5f52\uff1a\u786e\u4fdd\u73b0\u6709\u529f\u80fd\u4ecd\u7136\u6b63\u5e38\u5de5\u4f5c\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_16","title":"\u63d0\u4ea4\u4fe1\u606f","text":"<p>\u7f16\u5199\u6e05\u6670\u3001\u63cf\u8ff0\u6027\u7684\u63d0\u4ea4\u4fe1\u606f\u6765\u89e3\u91ca\u4f60\u505a\u4e86\u4ec0\u4e48\u66f4\u6539\u3002\u6ca1\u6709\u4e25\u683c\u7684\u683c\u5f0f\u8981\u6c42\u2014\u2014\u53ea\u8981\u786e\u4fdd\u4f60\u7684\u4fe1\u606f\u662f\u53ef\u7406\u89e3\u7684\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#pull-request","title":"\u63a8\u9001\u5e76\u521b\u5efa Pull Request","text":"<ol> <li> <p>\u63d0\u4ea4\u4f60\u7684\u4fee\u6539\uff1a    <pre><code>git add .\ngit commit -m \"\u4f60\u7684\u63cf\u8ff0\u6027\u4fe1\u606f\"\n</code></pre></p> </li> <li> <p>\u4fdd\u6301\u4f60\u7684\u5206\u652f\u4e0e\u6700\u65b0\u7684 <code>dev</code> \u5206\u652f\u540c\u6b65\uff1a    <pre><code>git fetch origin\ngit rebase origin/dev\n</code></pre></p> </li> <li> <p>\u63a8\u9001\u4f60\u7684\u5206\u652f\u5230\u4f60\u7684 fork\uff1a    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<p>\u63a8\u9001\u989d\u5916\u63d0\u4ea4\u5230\u4f60\u7684\u5206\u652f\uff08\u5b83\u4eec\u4f1a\u81ea\u52a8\u51fa\u73b0\u5728 PR \u4e2d\uff09</p> </li> <li> <p>\u6279\u51c6\u540e\uff1a\u7ef4\u62a4\u8005\u5c06\u5408\u5e76\u4f60\u7684 PR\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_17","title":"\u6709\u95ee\u9898\u6216\u9700\u8981\u5e2e\u52a9\uff1f","text":"<p>\u5982\u679c\u4f60\u5bf9\u8d21\u732e\u6709\u7591\u95ee\u6216\u9700\u8981\u5e2e\u52a9\uff1a</p> <ul> <li>\u53d1\u8d77\u8ba8\u8bba\uff1a\u4f7f\u7528 GitHub Discussions \u63d0\u51fa\u4e00\u822c\u6027\u95ee\u9898</li> <li>\u5728 issue \u4e2d\u63d0\u95ee\uff1a\u5728\u76f8\u5173 issue \u4e2d\u8bc4\u8bba\u4ee5\u83b7\u53d6\u5177\u4f53\u95ee\u9898\u7684\u5e2e\u52a9</li> <li>\u8054\u7cfb\u7ef4\u62a4\u8005\uff1a\u8054\u7cfb README \u4e2d\u5217\u51fa\u7684\u6838\u5fc3\u5f00\u53d1\u8005</li> </ul> <p>\u518d\u6b21\u611f\u8c22\u4f60\u4e3a <code>GPUMDkit</code> 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\ No newline at end of file
diff --git a/docs/htmls/sitemap.xml b/docs/htmls/sitemap.xml
index 82522c9..28a7dd6 100644
--- a/docs/htmls/sitemap.xml
+++ b/docs/htmls/sitemap.xml
@@ -2,110 +2,110 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/index.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/index.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/active_learning_workflow.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/analyzer_scripts.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/calculator_scripts.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/command_reference.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/contributing_to_gpumdkit.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/custom_commands.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/format_conversion.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/plot_scripts.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
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     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/polar_material_analysis.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/quick_start.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/structure_sampling.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/workflow_scripts.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/index.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
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     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html</loc>
-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
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-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
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-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
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     <url>
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-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
     <url>
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-         <lastmod>2026-06-28</lastmod>
+         <lastmod>2026-06-30</lastmod>
     </url>
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\ No newline at end of file
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diff --git a/docs/htmls/zh/index.html b/docs/htmls/zh/index.html
index e0b8e55..3add00d 100644
--- a/docs/htmls/zh/index.html
+++ b/docs/htmls/zh/index.html
@@ -143,7 +143,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#gpumdkit" class="md-skip">
+        <a href="#_1" class="md-skip">
           Skip to content
         </a>
       
@@ -851,10 +851,10 @@
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         <li class="md-nav__item">
-  <a href="#gpumdkit" class="md-nav__link">
+  <a href="#_1" class="md-nav__link">
     <span class="md-ellipsis">
       
-        什么是 GPUMDkit？
+        功能简介
       
     </span>
   </a>
@@ -862,33 +862,33 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_1" class="md-nav__link">
+  <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
-        快速开始
+        常见任务
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="快速开始">
-      <ul class="md-nav__list">
-        
-          <li class="md-nav__item">
-  <a href="#_2" class="md-nav__link">
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
     <span class="md-ellipsis">
       
-        安装
+        准备工作
       
     </span>
   </a>
   
-</li>
+    <nav class="md-nav" aria-label="准备工作">
+      <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
+  <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
-        依赖
+        安装
       
     </span>
   </a>
@@ -896,10 +896,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
+  <a href="#_5" class="md-nav__link">
     <span class="md-ellipsis">
       
-        使用方法
+        依赖
       
     </span>
   </a>
@@ -912,21 +912,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        教程列表
-      
-    </span>
-  </a>
-  
-</li>
-      
-        <li class="md-nav__item">
-  <a href="#vasp-outcar" class="md-nav__link">
+  <a href="#_6" class="md-nav__link">
     <span class="md-ellipsis">
       
-        示例：转换 VASP OUTCAR
+        交互模式
       
     </span>
   </a>
@@ -934,10 +923,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#nep" class="md-nav__link">
+  <a href="#_7" class="md-nav__link">
     <span class="md-ellipsis">
       
-        示例：绘制 NEP 结果
+        命令行模式
       
     </span>
   </a>
@@ -945,10 +934,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
+  <a href="#_8" class="md-nav__link">
     <span class="md-ellipsis">
       
-        示例：离子电导率
+        模块概览
       
     </span>
   </a>
@@ -956,10 +945,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
+  <a href="#_9" class="md-nav__link">
     <span class="md-ellipsis">
       
-        模块概览
+        全部教程
       
     </span>
   </a>
@@ -967,7 +956,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_8" class="md-nav__link">
+  <a href="#_10" class="md-nav__link">
     <span class="md-ellipsis">
       
         链接
@@ -1354,10 +1343,10 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#gpumdkit" class="md-nav__link">
+  <a href="#_1" class="md-nav__link">
     <span class="md-ellipsis">
       
-        什么是 GPUMDkit？
+        功能简介
       
     </span>
   </a>
@@ -1365,33 +1354,33 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_1" class="md-nav__link">
+  <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
-        快速开始
+        常见任务
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="快速开始">
-      <ul class="md-nav__list">
-        
-          <li class="md-nav__item">
-  <a href="#_2" class="md-nav__link">
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
     <span class="md-ellipsis">
       
-        安装
+        准备工作
       
     </span>
   </a>
   
-</li>
+    <nav class="md-nav" aria-label="准备工作">
+      <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
+  <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
-        依赖
+        安装
       
     </span>
   </a>
@@ -1399,10 +1388,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
+  <a href="#_5" class="md-nav__link">
     <span class="md-ellipsis">
       
-        使用方法
+        依赖
       
     </span>
   </a>
@@ -1415,21 +1404,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        教程列表
-      
-    </span>
-  </a>
-  
-</li>
-      
-        <li class="md-nav__item">
-  <a href="#vasp-outcar" class="md-nav__link">
+  <a href="#_6" class="md-nav__link">
     <span class="md-ellipsis">
       
-        示例：转换 VASP OUTCAR
+        交互模式
       
     </span>
   </a>
@@ -1437,10 +1415,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#nep" class="md-nav__link">
+  <a href="#_7" class="md-nav__link">
     <span class="md-ellipsis">
       
-        示例：绘制 NEP 结果
+        命令行模式
       
     </span>
   </a>
@@ -1448,10 +1426,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
+  <a href="#_8" class="md-nav__link">
     <span class="md-ellipsis">
       
-        示例：离子电导率
+        模块概览
       
     </span>
   </a>
@@ -1459,10 +1437,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
+  <a href="#_9" class="md-nav__link">
     <span class="md-ellipsis">
       
-        模块概览
+        全部教程
       
     </span>
   </a>
@@ -1470,7 +1448,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_8" class="md-nav__link">
+  <a href="#_10" class="md-nav__link">
     <span class="md-ellipsis">
       
         链接
@@ -1505,109 +1483,80 @@ <h1>📚 GPUMDkit 教程</h1>
   <p style="text-align: justify;">欢迎使用 <strong>GPUMDkit</strong>，这是一个面向 GPUMD 和 NEP 的命令行工具包。</p>
 </div>
 
-<h2 id="gpumdkit">什么是 GPUMDkit？</h2>
-<p>GPUMDkit 简化了计算材料科学中的常见任务：</p>
-<ul>
-<li><strong>格式转换</strong>：在 VASP、LAMMPS、CP2K、ABACUS、CIF 和 extxyz 格式之间转换</li>
-<li><strong>可视化</strong>：用于 NEP 训练、MD 模拟和分析的绘图工具</li>
-<li><strong>计算器</strong>：计算离子电导率、描述符、MSD、NEB 等</li>
-<li><strong>分析工具</strong>：结构验证、过滤、成分分析</li>
-<li><strong>工作流</strong>：DFT 和 MD 模拟的批处理</li>
-<li><strong>结构采样</strong>：使用均匀、随机或 FPS 方法选择结构</li>
-</ul>
-<h2 id="_1">快速开始</h2>
-<h3 id="_2">安装</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
-<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
-<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="nb">source</span><span class="w"> </span>./install.sh
-</code></pre></div>
-<h3 id="_3">依赖</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>gpumdkit<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12
-<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>gpumdkit
-<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>pip<span class="w"> </span>install<span class="w"> </span>neptrain<span class="w"> </span>dpdata<span class="w"> </span>calorine
-</code></pre></div>
-<h3 id="_4">使用方法</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="c1"># 交互模式</span>
-<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh
-<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
-<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="c1"># 命令行模式</span>
-<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>gpumdkit.sh<span class="w"> </span>-&lt;选项&gt;<span class="w"> </span><span class="o">[</span>参数...<span class="o">]</span>
-<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>
-<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a><span class="c1"># 获取帮助</span>
-<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>gpumdkit.sh<span class="w"> </span>-h
-</code></pre></div>
-<h2 id="_5">教程列表</h2>
+<h2 id="_1">功能简介</h2>
+<p>GPUMDkit 帮助你在计算材料科学研究中完成常见任务，无需编写自定义脚本。它支持格式转换、结构分析、性质计算、可视化和批量工作流——全部通过一个命令行工具完成。</p>
+<h2 id="_2">常见任务</h2>
 <table>
 <thead>
 <tr>
+<th>我想要...</th>
 <th>教程</th>
-<th>描述</th>
 </tr>
 </thead>
 <tbody>
 <tr>
+<td>安装 GPUMDkit 并运行第一个命令</td>
 <td><a href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html">快速入门</a></td>
-<td>安装和第一步</td>
 </tr>
 <tr>
-<td><a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html">命令参考</a></td>
-<td>常用 CLI 和菜单入口速查</td>
+<td>将 VASP、LAMMPS、CP2K 或 CIF 文件转换为 extxyz</td>
+<td><a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html">格式转换</a></td>
 </tr>
 <tr>
-<td><a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html">格式转换</a></td>
-<td>在文件格式之间转换</td>
+<td>检查结构距离、过滤数据集或查找异常值</td>
+<td><a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html">分析工具</a></td>
 </tr>
 <tr>
+<td>计算 MSD、离子电导率或描述符</td>
 <td><a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html">计算器脚本</a></td>
-<td>计算材料属性</td>
 </tr>
 <tr>
-<td><a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html">分析工具</a></td>
-<td>结构分析和验证</td>
+<td>分析极性材料、铁电体或 ABO3 体系</td>
+<td><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
 </tr>
 <tr>
+<td>绘制 NEP 训练结果或热力学数据</td>
 <td><a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html">绘图脚本</a></td>
-<td>绘图和可视化</td>
 </tr>
 <tr>
+<td>运行批量 DFT 或 MD 模拟</td>
 <td><a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html">工作流脚本</a></td>
-<td>批处理和自动化</td>
 </tr>
 <tr>
+<td>从数据集中选择代表性结构</td>
 <td><a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html">结构采样</a></td>
-<td>结构选择方法</td>
 </tr>
 <tr>
+<td>添加自己的 GPUMDkit 快捷命令</td>
 <td><a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html">自定义命令</a></td>
-<td>用户自定义 GPUMDkit 快捷命令</td>
-</tr>
-<tr>
-<td><a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html">主动学习工作流</a></td>
-<td>批量主动学习流程说明</td>
-</tr>
-<tr>
-<td><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
-<td>铁电和极化相关工具</td>
-</tr>
-<tr>
-<td><a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html">贡献指南</a></td>
-<td>开发和贡献说明</td>
 </tr>
 </tbody>
 </table>
-<h2 id="vasp-outcar">示例：转换 VASP OUTCAR</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-out2xyz<span class="w"> </span>./vasp_results/
+<h2 id="_3">准备工作</h2>
+<h3 id="_4">安装</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="nb">source</span><span class="w"> </span>./install.sh
+</code></pre></div>
+<h3 id="_5">依赖</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>gpumdkit<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>gpumdkit
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>pip<span class="w"> </span>install<span class="w"> </span>neptrain<span class="w"> </span>dpdata<span class="w"> </span>calorine
 </code></pre></div>
-<h2 id="nep">示例：绘制 NEP 结果</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
-<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>prediction
+<h2 id="_6">交互模式</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh
 </code></pre></div>
-<h2 id="_6">示例：离子电导率</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>trajectory.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>ionic-cond<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>
-<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<p>打开菜单后，按数字选择模块。</p>
+<h2 id="_7">命令行模式</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-&lt;选项&gt;<span class="w"> </span><span class="o">[</span>参数...<span class="o">]</span>
 </code></pre></div>
-<h2 id="_7">模块概览</h2>
+<p>例如：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>trajectory.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
+</code></pre></div>
+<p>使用 <code>gpumdkit.sh -h</code> 查看所有可用选项。</p>
+<h2 id="_8">模块概览</h2>
 <table>
 <thead>
 <tr>
@@ -1662,7 +1611,66 @@ <h2 id="_7">模块概览</h2>
 </tr>
 </tbody>
 </table>
-<h2 id="_8">链接</h2>
+<h2 id="_9">全部教程</h2>
+<table>
+<thead>
+<tr>
+<th>教程</th>
+<th>描述</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><a href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html">快速入门</a></td>
+<td>安装和第一步</td>
+</tr>
+<tr>
+<td><a href="%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html">命令参考</a></td>
+<td>常用 CLI 和菜单入口速查</td>
+</tr>
+<tr>
+<td><a href="%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html">格式转换</a></td>
+<td>在文件格式之间转换</td>
+</tr>
+<tr>
+<td><a href="%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html">计算器脚本</a></td>
+<td>计算材料属性</td>
+</tr>
+<tr>
+<td><a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html">分析工具</a></td>
+<td>结构分析和验证</td>
+</tr>
+<tr>
+<td><a href="%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html">绘图脚本</a></td>
+<td>绘图和可视化</td>
+</tr>
+<tr>
+<td><a href="%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html">工作流脚本</a></td>
+<td>批处理和自动化</td>
+</tr>
+<tr>
+<td><a href="%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html">结构采样</a></td>
+<td>结构选择方法</td>
+</tr>
+<tr>
+<td><a href="%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html">自定义命令</a></td>
+<td>用户自定义 GPUMDkit 快捷命令</td>
+</tr>
+<tr>
+<td><a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html">主动学习工作流</a></td>
+<td>批量主动学习流程说明</td>
+</tr>
+<tr>
+<td><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
+<td>铁电和极化相关工具</td>
+</tr>
+<tr>
+<td><a href="%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html">贡献指南</a></td>
+<td>开发和贡献说明</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_10">链接</h2>
 <ul>
 <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li>
 <li>文档: https://zhyan0603.github.io/GPUMDkit/</li>
diff --git "a/docs/htmls/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.html" "b/docs/htmls/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.html"
index 011de30..49b05be 100644
--- "a/docs/htmls/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.html"
+++ "b/docs/htmls/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.html"
@@ -1515,26 +1515,67 @@ <h1>🔁 主动学习工作流</h1>
   <p style="text-align: justify;"><code>workflow_active_learning_dev.sh</code> 用于组织一轮 NEP 主动学习流程：运行 GPUMD 分子动力学、筛选结构、抽样、提交第一性原理计算，并进行 NEP 预测检查。</p>
 </div>
 
-<h3 id="_1">概览</h3>
-<p>该脚本用于处理 NEP 主动学习中常见的一轮流程：运行分子动力学、筛选结构、抽样、提交 SCF 计算，并整理后续 prediction 检查。</p>
+<p><strong>脚本位置：</strong> <code>Scripts/workflow/</code></p>
+<h2 id="_1">概览</h2>
+<p>该脚本自动化了 NEP 主动学习的一轮迭代。典型流程包括：</p>
+<table>
+<thead>
+<tr>
+<th>步骤</th>
+<th>操作</th>
+<th>目的</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>1</td>
+<td>运行 MD 模拟</td>
+<td>使用当前 NEP 模型生成候选结构</td>
+</tr>
+<tr>
+<td>2</td>
+<td>过滤结构</td>
+<td>移除不合理的构型（短距离、大盒子）</td>
+</tr>
+<tr>
+<td>3</td>
+<td>采样结构</td>
+<td>选择多样性高或偏差大的结构进行 DFT 计算</td>
+</tr>
+<tr>
+<td>4</td>
+<td>运行 SCF 计算</td>
+<td>计算 DFT 参考能量/力</td>
+</tr>
+<tr>
+<td>5</td>
+<td>NEP 预测</td>
+<td>检查模型在新结构上的精度</td>
+</tr>
+</tbody>
+</table>
+<p>与菜单驱动的模块不同，这个工作流是一个需要按体系修改后直接运行的 shell 脚本：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>bash<span class="w"> </span>Scripts/workflow/workflow_active_learning_dev.sh
+</code></pre></div>
+<p>下面按脚本中的主要代码块说明每一步的作用。</p>
 <h2 id="1-slurm">1. SLURM 设置</h2>
 <p>脚本开头包含集群提交参数，例如：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="ch">#!/bin/bash -l</span>
-<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="c1">#SBATCH -p intel-sc3,intel-sc3-32c</span>
-<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="c1">#SBATCH -q huge</span>
-<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a><span class="c1">#SBATCH -N 1</span>
-<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a><span class="c1">#SBATCH -J workflow</span>
-<a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a><span class="c1">#SBATCH -o workflow.log</span>
-<a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a><span class="c1">#SBATCH --ntasks-per-node=1</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="ch">#!/bin/bash -l</span>
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="c1">#SBATCH -p intel-sc3,intel-sc3-32c</span>
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="c1">#SBATCH -q huge</span>
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a><span class="c1">#SBATCH -N 1</span>
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a><span class="c1">#SBATCH -J workflow</span>
+<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a><span class="c1">#SBATCH -o workflow.log</span>
+<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a><span class="c1">#SBATCH --ntasks-per-node=1</span>
 </code></pre></div>
 <p>这些参数需要根据自己的集群环境修改。如果没有 SLURM 环境，也可以直接后台运行：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>nohup<span class="w"> </span>bash<span class="w"> </span>workflow_active_learning_dev.sh<span class="w"> </span>&gt;<span class="w"> </span>workflow.log<span class="w"> </span><span class="m">2</span>&gt;<span class="p">&amp;</span><span class="m">1</span><span class="w"> </span><span class="p">&amp;</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>nohup<span class="w"> </span>bash<span class="w"> </span>workflow_active_learning_dev.sh<span class="w"> </span>&gt;<span class="w"> </span>workflow.log<span class="w"> </span><span class="m">2</span>&gt;<span class="p">&amp;</span><span class="m">1</span><span class="w"> </span><span class="p">&amp;</span>
 </code></pre></div>
 <h2 id="2">2. 基本设置</h2>
 <p>脚本会进入提交目录，并加载提交模板：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="nb">cd</span><span class="w"> </span><span class="nv">$SLURM_SUBMIT_DIR</span>
-<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="nb">source</span><span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/Scripts/workflow/submit_template.sh
-<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a><span class="nv">python_pynep</span><span class="o">=</span>python
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="nb">cd</span><span class="w"> </span><span class="nv">$SLURM_SUBMIT_DIR</span>
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a><span class="nb">source</span><span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/Scripts/workflow/submit_template.sh
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a><span class="nv">python_pynep</span><span class="o">=</span>python
 </code></pre></div>
 <ul>
 <li><code>GPUMDkit_path</code> 是安装脚本写入的 GPUMDkit 路径。</li>
@@ -1543,13 +1584,13 @@ <h2 id="2">2. 基本设置</h2>
 <h2 id="3">3. 主要变量</h2>
 <p>这个工作流适合已经有初始 <code>nep.txt</code>、<code>nep.in</code>、<code>train.xyz</code> 和 GPUMD/DFT 输入文件，并希望在集群上自动扩展训练集的情况。</p>
 <p>脚本开头通常需要根据体系修改：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="nv">work_dir</span><span class="o">=</span><span class="si">${</span><span class="nv">PWD</span><span class="si">}</span>
-<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a><span class="nv">prefix_name</span><span class="o">=</span>LiF_iter01
-<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a><span class="nv">min_dist</span><span class="o">=</span><span class="m">1</span>.4
-<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="nv">box_limit</span><span class="o">=</span><span class="m">13</span>
-<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a><span class="nv">max_fp_num</span><span class="o">=</span><span class="m">50</span>
-<a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a><span class="nv">sample_method</span><span class="o">=</span>pynep
-<a id="__codelineno-3-7" name="__codelineno-3-7" href="#__codelineno-3-7"></a><span class="nv">pynep_sample_dist</span><span class="o">=</span><span class="m">0</span>.01
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="nv">work_dir</span><span class="o">=</span><span class="si">${</span><span class="nv">PWD</span><span class="si">}</span>
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a><span class="nv">prefix_name</span><span class="o">=</span>LiF_iter01
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a><span class="nv">min_dist</span><span class="o">=</span><span class="m">1</span>.4
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="nv">box_limit</span><span class="o">=</span><span class="m">13</span>
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a><span class="nv">max_fp_num</span><span class="o">=</span><span class="m">50</span>
+<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a><span class="nv">sample_method</span><span class="o">=</span>pynep
+<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a><span class="nv">pynep_sample_dist</span><span class="o">=</span><span class="m">0</span>.01
 </code></pre></div>
 <ul>
 <li><code>prefix_name</code> 用于命名本轮计算。</li>
@@ -1572,22 +1613,22 @@ <h2 id="4">4. 检查输入文件</h2>
 <p>脚本会把公共输入移动到 <code>common/</code>，并创建 <code>00.modev/</code>、<code>01.select/</code> 等工作目录。</p>
 <h2 id="5">5. 文件组织</h2>
 <p>脚本会创建公共输入目录和 MD 目录：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>mkdir<span class="w"> </span><span class="m">00</span>.modev<span class="w"> </span>common
-<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>mv<span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/<span class="o">{</span>nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR<span class="o">}</span><span class="w"> </span>./common
-<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>cp<span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/common/<span class="nv">$sample_xyz_file</span><span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/00.modev
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>mkdir<span class="w"> </span><span class="m">00</span>.modev<span class="w"> </span>common
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>mv<span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/<span class="o">{</span>nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR<span class="o">}</span><span class="w"> </span>./common
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>cp<span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/common/<span class="nv">$sample_xyz_file</span><span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/00.modev
 </code></pre></div>
 <ul>
 <li><code>00.modev</code>：用于运行 GPUMD MD 采样。</li>
 <li><code>common</code>：保存 <code>nep.txt</code>、<code>run.in</code>、结构文件和 DFT 输入文件等公共资源。</li>
 </ul>
 <h2 id="6-md">6. 提交 MD 任务</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>submit_gpumd_array<span class="w"> </span>modev<span class="w"> </span><span class="si">${</span><span class="nv">sample_struct_num</span><span class="si">}</span>
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>sbatch<span class="w"> </span>submit.slurm
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>submit_gpumd_array<span class="w"> </span>modev<span class="w"> </span><span class="si">${</span><span class="nv">sample_struct_num</span><span class="si">}</span>
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>sbatch<span class="w"> </span>submit.slurm
 </code></pre></div>
 <p>脚本会通过提交模板创建数组任务。不同集群上的提交命令和模板可能需要自己修改。</p>
 <h2 id="7">7. 检查任务完成</h2>
 <p>脚本会持续检查 <code>00.modev/</code> 下各个 <code>sample_*/log</code> 文件，确认是否出现：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>Finished<span class="w"> </span>running<span class="w"> </span>GPUMD.
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>Finished<span class="w"> </span>running<span class="w"> </span>GPUMD.
 </code></pre></div>
 <p>如果发现 <code>Error</code>，脚本会停止。</p>
 <h2 id="8">8. 分析和过滤结构</h2>
@@ -1600,10 +1641,10 @@ <h2 id="8">8. 分析和过滤结构</h2>
 <p>这些步骤会调用 analyzer 和 sample_structures 中的脚本。</p>
 <h2 id="9">9. 抽样方法</h2>
 <p>脚本根据 <code>sample_method</code> 选择抽样方式：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="k">case</span><span class="w"> </span><span class="nv">$sample_method</span><span class="w"> </span><span class="k">in</span>
-<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="w">    </span><span class="s2">&quot;uniform&quot;</span><span class="o">)</span>
-<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="w">    </span><span class="s2">&quot;random&quot;</span><span class="o">)</span>
-<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="w">    </span><span class="s2">&quot;pynep&quot;</span><span class="o">)</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="k">case</span><span class="w"> </span><span class="nv">$sample_method</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a><span class="w">    </span><span class="s2">&quot;uniform&quot;</span><span class="o">)</span>
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a><span class="w">    </span><span class="s2">&quot;random&quot;</span><span class="o">)</span>
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="w">    </span><span class="s2">&quot;pynep&quot;</span><span class="o">)</span>
 </code></pre></div>
 <ul>
 <li><code>uniform</code>：均匀抽帧；</li>
@@ -1612,7 +1653,7 @@ <h2 id="9">9. 抽样方法</h2>
 </ul>
 <h2 id="10-scf">10. 提交 SCF 计算</h2>
 <p>抽样完成后，脚本会提交 VASP 单点计算：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>submit_vasp_array<span class="w"> </span>scf<span class="w"> </span><span class="si">${</span><span class="nv">selected_struct_num</span><span class="si">}</span><span class="w"> </span><span class="si">${</span><span class="nv">prefix_name</span><span class="si">}</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>submit_vasp_array<span class="w"> </span>scf<span class="w"> </span><span class="si">${</span><span class="nv">selected_struct_num</span><span class="si">}</span><span class="w"> </span><span class="si">${</span><span class="nv">prefix_name</span><span class="si">}</span>
 </code></pre></div>
 <p>这里的 <code>prefix_name</code> 会用于计算目录命名，也方便后续追踪结构来源。</p>
 <h2 id="11-prediction">11. Prediction 步骤</h2>
diff --git "a/docs/htmls/zh/\345\210\206\346\236\220\345\267\245\345\205\267.html" "b/docs/htmls/zh/\345\210\206\346\236\220\345\267\245\345\205\267.html"
index 81f7946..e4b3b95 100644
--- "a/docs/htmls/zh/\345\210\206\346\236\220\345\267\245\345\205\267.html"
+++ "b/docs/htmls/zh/\345\210\206\346\236\220\345\267\245\345\205\267.html"
@@ -1050,7 +1050,7 @@
   <a href="#_1" class="md-nav__link">
     <span class="md-ellipsis">
       
-        功能概览
+        功能简介
       
     </span>
   </a>
@@ -1061,7 +1061,7 @@
   <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
-        组分分析
+        准备工作
       
     </span>
   </a>
@@ -1069,10 +1069,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#virial" class="md-nav__link">
+  <a href="#_3" class="md-nav__link">
     <span class="md-ellipsis">
       
-        能量/力/virial 范围
+        概览
       
     </span>
   </a>
@@ -1080,10 +1080,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
+  <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
-        最小距离检查
+        交互模式
       
     </span>
   </a>
@@ -1091,7 +1091,79 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        成分分析
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        化学物种
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        性质范围分析
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        最短距离检查
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="最短距离检查">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#pbc" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        无 PBC（快速）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#pbc_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        含 PBC（准确）
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
     <span class="md-ellipsis">
       
         结构过滤
@@ -1099,10 +1171,60 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="结构过滤">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        按最短距离过滤
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_11" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        按盒子大小过滤
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        按性质值过滤
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        按对距离范围过滤
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
+  <a href="#_14" class="md-nav__link">
     <span class="md-ellipsis">
       
         电荷平衡检查
@@ -1113,14 +1235,114 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
+  <a href="#_15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        异常检测
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_16" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        时间估算
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="时间估算">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gpumd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        GPUMD 剩余时间
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#nep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP 剩余时间
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_17" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        概率密度分析
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_18" class="md-nav__link">
     <span class="md-ellipsis">
       
-        示例命令
+        示例工作流
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="示例工作流">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_19" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        结构质量检查
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_20" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        结构过滤流水线
       
     </span>
   </a>
   
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_21" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        扩散通道分析
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -1307,7 +1529,7 @@
   <a href="#_1" class="md-nav__link">
     <span class="md-ellipsis">
       
-        功能概览
+        功能简介
       
     </span>
   </a>
@@ -1318,7 +1540,7 @@
   <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
-        组分分析
+        准备工作
       
     </span>
   </a>
@@ -1326,10 +1548,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#virial" class="md-nav__link">
+  <a href="#_3" class="md-nav__link">
     <span class="md-ellipsis">
       
-        能量/力/virial 范围
+        概览
       
     </span>
   </a>
@@ -1337,10 +1559,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
+  <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
-        最小距离检查
+        交互模式
       
     </span>
   </a>
@@ -1348,7 +1570,79 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        成分分析
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        化学物种
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        性质范围分析
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_8" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        最短距离检查
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="最短距离检查">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#pbc" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        无 PBC（快速）
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#pbc_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        含 PBC（准确）
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_9" class="md-nav__link">
     <span class="md-ellipsis">
       
         结构过滤
@@ -1356,10 +1650,60 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="结构过滤">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_10" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        按最短距离过滤
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_11" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        按盒子大小过滤
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_12" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        按性质值过滤
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_13" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        按对距离范围过滤
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
+  <a href="#_14" class="md-nav__link">
     <span class="md-ellipsis">
       
         电荷平衡检查
@@ -1370,14 +1714,114 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
+  <a href="#_15" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        异常检测
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_16" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        时间估算
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="时间估算">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gpumd" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        GPUMD 剩余时间
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#nep" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        NEP 剩余时间
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_17" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        概率密度分析
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_18" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例工作流
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="示例工作流">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#_19" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        结构质量检查
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_20" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        结构过滤流水线
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_21" class="md-nav__link">
     <span class="md-ellipsis">
       
-        示例命令
+        扩散通道分析
       
     </span>
   </a>
   
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -1402,11 +1846,15 @@
 
 <div align="center">
   <h1>🔍 分析工具</h1>
-  <p style="text-align: justify;">分析工具用于对 extxyz 数据集进行结构统计、距离检查、过滤和组分分析。</p>
+  <p style="text-align: justify;">分析脚本为 extxyz 数据集提供结构统计、距离检查、过滤、成分分析、异常检测和时间估算功能。</p>
 </div>
 
+<h2 id="_1">功能简介</h2>
+<p>本模块帮助你检查、过滤和验证结构数据集。可以检查成分、分析性质范围、检测短距离接触、按各种条件过滤结构、查找 NEP 训练数据中的异常值，以及估算剩余模拟时间。</p>
+<h2 id="_2">准备工作</h2>
 <p><strong>脚本位置：</strong> <code>Scripts/analyzer/</code></p>
-<h2 id="_1">功能概览</h2>
+<p>确保已安装 GPUMDkit。安装说明请参见<a href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html">快速入门</a>。</p>
+<h2 id="_3">概览</h2>
 <table>
 <thead>
 <tr>
@@ -1417,14 +1865,14 @@ <h2 id="_1">功能概览</h2>
 </thead>
 <tbody>
 <tr>
-<td>组分分析</td>
+<td>成分分析</td>
 <td><code>gpumdkit.sh -analyze_comp train.xyz</code></td>
-<td>按化学组分统计结构</td>
+<td>按化学成分分组</td>
 </tr>
 <tr>
-<td>元素列表</td>
+<td>化学物种</td>
 <td><code>gpumdkit.sh -chem_species train.xyz</code></td>
-<td>查看文件中有哪些元素</td>
+<td>列出文件中的元素</td>
 </tr>
 <tr>
 <td>性质范围</td>
@@ -1432,105 +1880,332 @@ <h2 id="_1">功能概览</h2>
 <td>检查能量/力/virial 范围</td>
 </tr>
 <tr>
-<td>最小距离</td>
+<td>最短距离</td>
 <td><code>gpumdkit.sh -min_dist dump.xyz</code></td>
-<td>快速检查，不考虑 PBC</td>
+<td>快速距离检查（无 PBC）</td>
 </tr>
 <tr>
-<td>PBC 最小距离</td>
+<td>最短距离（PBC）</td>
 <td><code>gpumdkit.sh -min_dist_pbc dump.xyz</code></td>
-<td>考虑 PBC 的距离检查</td>
+<td>准确距离检查（含 PBC）</td>
 </tr>
 <tr>
 <td>电荷平衡</td>
 <td><code>gpumdkit.sh -cbc train.xyz</code></td>
-<td>检查常见氧化态是否平衡</td>
+<td>氧化态平衡检查</td>
 </tr>
 <tr>
 <td>距离过滤</td>
 <td><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code></td>
-<td>删除短距离结构</td>
+<td>移除短距离接触的结构</td>
 </tr>
 <tr>
 <td>盒子过滤</td>
 <td><code>gpumdkit.sh -filter_box dump.xyz 13</code></td>
-<td>删除盒子边长过大的结构</td>
+<td>移除盒子过大的结构</td>
 </tr>
 <tr>
-<td>数值过滤</td>
+<td>性质过滤</td>
 <td><code>gpumdkit.sh -filter_value train.xyz force 20</code></td>
-<td>按性质阈值过滤</td>
+<td>按能量/力/virial 阈值过滤</td>
 </tr>
 <tr>
-<td>元素对距离</td>
+<td>对距离范围</td>
 <td><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code></td>
-<td>按元素对距离范围提取</td>
+<td>按对距离提取结构</td>
+</tr>
+<tr>
+<td>异常检测</td>
+<td>菜单 502</td>
+<td>查找训练集中高 RMSE 的结构</td>
+</tr>
+<tr>
+<td>概率密度</td>
+<td><code>gpumdkit.sh -pda &lt;参考结构&gt; &lt;轨迹&gt; &lt;元素&gt; &lt;网格间距&gt;</code></td>
+<td>3D 概率密度分析扩散通道</td>
+</tr>
+<tr>
+<td>GPUMD 时间</td>
+<td><code>gpumdkit.sh -time gpumd</code></td>
+<td>估算 GPUMD 剩余运行时间</td>
+</tr>
+<tr>
+<td>NEP 时间</td>
+<td><code>gpumdkit.sh -time nep</code></td>
+<td>估算 NEP 剩余训练时间</td>
 </tr>
 </tbody>
 </table>
-<h2 id="_2">组分分析</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
+<hr />
+<h2 id="_4">交互模式</h2>
+<p>打开 GPUMDkit 并选择 <code>5) Analyzer</code>：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh
+</code></pre></div>
+<p>分析工具菜单如下：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>+------------------------------------------------------+
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>|                    ANALYZER TOOLS                    |
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>+------------------------------------------------------+
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>| 501) Analyze composition of extxyz                   |
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>| 502) Find outliers of extxyz                         |
+<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>| 503) Analyze chemical species of extxyz              |
+<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a>| 504) Check charge balance of extxyz                  |
+<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a>| 505) Analyze energy/force/virial range               |
+<a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a>| 506) Filter structures by minimum distance           |
+<a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a>| 507) Get minimum interatomic distance                |
+<a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a>| 508) Probability density analysis                    |
+<a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a>+------------------------------------------------------+
+<a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a>| 000) Return to the main menu                         |
+<a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></a>+------------------------------------------------------+
+<a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a>Input the function number:
+</code></pre></div>
+<p>大多数分析功能也提供直接 CLI 调用方式，概览表和后续小节中列出了常用命令。</p>
+<hr />
+<h2 id="_5">成分分析</h2>
+<p><code>analyze_composition.py</code> 分析 extxyz 文件的成分，并允许导出子集。</p>
+<p><strong>功能：</strong> 按化学成分对结构分组，并显示每种成分的结构数量。可以按成分导出子集。</p>
+<p><strong>命令行模式：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
 </code></pre></div>
-<p>示例输出：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>Index    Compositions           N atoms      Count
-<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>---------------------------------------------------
-<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>1        Li56O96Zr16La24        192          51
-<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>---------------------------------------------------
-<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>Enter index to export (e.g., &#39;1,2&#39;, &#39;2-3&#39;, &#39;all&#39;), or press Enter to skip:
+<p><strong>交互模式：</strong> 在分析工具菜单中选择 <code>501</code>。</p>
+<p><strong>输出示例：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>Index    Compositions           N atoms      Count
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>---------------------------------------------------
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>1        Li56O96Zr16La24        192          51
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>---------------------------------------------------
+<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>Enter index to export (e.g., &#39;1,2&#39;, &#39;2-3&#39;, &#39;all&#39;), or press Enter to skip:
 </code></pre></div>
-<p>如果一个 <code>train.xyz</code> 中混合了多个体系或不同超胞，这个功能很有用。</p>
-<h2 id="virial">能量/力/virial 范围</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force
-<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>energy
-<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>virial
-<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist
+<p>当 <code>train.xyz</code> 包含不同体系或不同尺寸的结构时很有用。可以从交互提示中按成分导出子集。</p>
+<hr />
+<h2 id="_6">化学物种</h2>
+<p><code>analyze_chem_species.py</code> 列出 extxyz 文件中所有唯一的化学物种。</p>
+<p><strong>输入文件：</strong> <code>train.xyz</code>（extxyz 格式）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-chem_species<span class="w"> </span>train.xyz
 </code></pre></div>
-<p>使用 <code>hist</code> 可以画出所选性质的直方图。</p>
+<hr />
+<h2 id="_7">性质范围分析</h2>
+<p><code>energy_force_virial_analyzer.py</code> 计算并可视化 extxyz 文件中性质的范围。</p>
+<p><strong>输入文件：</strong> <code>train.xyz</code>（extxyz 格式）</p>
+<p><strong>支持的性质：</strong> <code>energy</code>、<code>force</code>、<code>virial</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>energy
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>virial
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist<span class="w">    </span><span class="c1"># 显示直方图</span>
+</code></pre></div>
+<p><strong>输出示例：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>Force range: 0.03210566767721861 to 9.230115912468435
+</code></pre></div>
+<p>使用 <code>hist</code> 选项：</p>
 <div align="center">
   <img src="../../Gallery/range_force.png" alt="Force range histogram" width="52%" />
 </div>
 
-<h2 id="_3">最小距离检查</h2>
-<p>快速版本：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist<span class="w"> </span>dump.xyz
+<hr />
+<h2 id="_8">最短距离检查</h2>
+<h3 id="pbc">无 PBC（快速）</h3>
+<p><code>get_min_dist.py</code> 计算不考虑周期性边界条件的最短原子间距。速度快，但对周期性体系可能不准确。</p>
+<p><strong>功能：</strong> 报告每帧中每对元素之间的最短距离，忽略周期性边界条件。</p>
+<p><strong>命令行模式：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist<span class="w"> </span>dump.xyz
+</code></pre></div>
+<p><strong>交互模式：</strong> 在分析工具菜单中选择 <code>507</code>。</p>
+<p><strong>输出示例：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>+---------------------------+
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>|   PBC ignored for speed   |
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>| use -min_dist_pbc for PBC |
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>+---------------------------+
+<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a>Minimum interatomic distances:
+<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>+---------------------------+
+<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a>| Atom Pair |  Distance (Å) |
+<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a>+---------------------------+
+<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a>|   Li-Li   |     1.696     |
+<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a>|   Li-O    |     1.587     |
+<a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a>|   O-O     |     2.480     |
+<a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></a>+---------------------------+
+<a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a>Overall min_distance: 1.587 Å
 </code></pre></div>
-<p>考虑 PBC 的版本：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
+<p><strong>说明：</strong> 用于快速检查。对于周期性体系，建议使用 <code>-min_dist_pbc</code> 获得准确结果。</p>
+<h3 id="pbc_1">含 PBC（准确）</h3>
+<p><code>get_min_dist_pbc.py</code> 计算考虑周期性边界条件的最短原子间距。</p>
+<p><strong>功能：</strong> 报告每对元素之间的最短距离，考虑周期性边界条件。</p>
+<p><strong>命令行模式：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
 </code></pre></div>
-<p>PBC 版本会考虑周期性边界条件。</p>
-<h2 id="_4">结构过滤</h2>
-<p>按最小距离过滤：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
+<p><strong>交互模式：</strong> 在分析工具菜单中选择 <code>507</code>，当提示是否考虑 PBC 时输入 <code>y</code>。</p>
+<p><strong>输出示例：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>Minimum interatomic distances (with PBC):
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>+---------------------------+
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>| Atom Pair |  Distance (Å) |
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a>+---------------------------+
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>|   Li-Li   |     1.696     |
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>|   Li-O    |     1.587     |
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a>|   O-O     |     2.355     |
+<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>+---------------------------+
+<a id="__codelineno-10-9" name="__codelineno-10-9" href="#__codelineno-10-9"></a>Overall min_distance: 1.587 Å
 </code></pre></div>
-<p>按盒子大小过滤：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
+<hr />
+<h2 id="_9">结构过滤</h2>
+<h3 id="_10">按最短距离过滤</h3>
+<p><code>filter_structures_by_distance_pbc.py</code> 移除任何原子间距低于阈值的结构。</p>
+<p><strong>输入文件：</strong> <code>dump.xyz</code>（extxyz 格式）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
+</code></pre></div>
+<p>移除任何原子间距低于 <code>1.0 Å</code> 的结构。</p>
+<h3 id="_11">按盒子大小过滤</h3>
+<p><code>filter_exyz_by_box.py</code> 按盒子边长过滤结构。</p>
+<p><strong>输入文件：</strong> <code>dump.xyz</code>（extxyz 格式）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
 </code></pre></div>
-<p>按性质值过滤：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span><span class="m">20</span>
+<p>保留所有盒子边长低于 <code>13 Å</code> 的结构。</p>
+<h3 id="_12">按性质值过滤</h3>
+<p><code>filter_exyz_by_value.py</code> 按能量、力或 virial 阈值过滤结构。</p>
+<p><strong>输入文件：</strong> <code>train.xyz</code>（extxyz 格式）</p>
+<p><strong>支持的性质：</strong> <code>energy</code>、<code>force</code>、<code>virial</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span><span class="m">20</span>
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>train.xyz<span class="w"> </span>energy<span class="w"> </span><span class="m">5</span>
 </code></pre></div>
-<p>按元素对距离范围提取：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-filter_range<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>.8<span class="w"> </span><span class="m">2</span>.0
+<p>过滤掉力分量超过 <code>20 eV/Å</code>（或能量超过 <code>5 eV/atom</code>）的结构。</p>
+<h3 id="_13">按对距离范围过滤</h3>
+<p><code>filter_dist_range.py</code> 提取特定元素对距离在给定范围内的结构。</p>
+<p><strong>输入文件：</strong> <code>dump.xyz</code>（extxyz 格式）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-filter_range<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>.8<span class="w"> </span><span class="m">2</span>.0
 </code></pre></div>
-<h2 id="_5">电荷平衡检查</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-cbc<span class="w"> </span>train.xyz
+<p>提取 Li-Li 最短距离在 <code>1.8 Å</code> 到 <code>2.0 Å</code> 之间的结构。输出：<code>filtered_Li_Li_1.8_2.0.xyz</code>。</p>
+<hr />
+<h2 id="_14">电荷平衡检查</h2>
+<p><code>charge_balance_check.py</code> 检查结构的氧化态平衡。</p>
+<p><strong>输入文件：</strong> <code>train.xyz</code>（extxyz 格式）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-cbc<span class="w"> </span>train.xyz
 </code></pre></div>
-<p>可能输出：</p>
+<p><strong>输出文件：</strong></p>
 <ul>
-<li><code>balanced.xyz</code></li>
-<li><code>unbalanced.xyz</code></li>
-<li><code>indices.txt</code></li>
+<li><code>balanced.xyz</code> — 电荷平衡的结构</li>
+<li><code>unbalanced.xyz</code> — 电荷不平衡的结构</li>
+<li><code>indices.txt</code> — 平衡结构的索引</li>
 </ul>
-<p>这个功能适合常见氧化态有意义的离子材料。</p>
-<h2 id="_6">示例命令</h2>
-<p>性质和距离检查：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
-<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist
-<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>energy<span class="w"> </span>hist
-<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>train.xyz
+<p>适用于具有明确氧化态的体系。</p>
+<hr />
+<h2 id="_15">异常检测</h2>
+<p><code>find_outliers.py</code> 基于能量、力和应力的 RMSE 阈值查找 NEP 训练数据中的异常结构。</p>
+<p><strong>输入文件：</strong> <code>energy_train.out</code>、<code>force_train.out</code>、<code>stress_train.out</code>、<code>train.xyz</code></p>
+<p>这些文件在 NEP 训练过程中生成。脚本比较 DFT 与 NEP 的预测，识别误差较大的结构。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a><span class="c1"># 交互模式</span>
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w">    </span><span class="c1"># 选择：5) 分析工具 → 502) 查找异常结构</span>
 </code></pre></div>
-<p>过滤示例：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
-<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>filtered_dist.xyz<span class="w"> </span><span class="m">13</span>
+<p><strong>交互提示：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>Enter energy RMSE threshold (meV/atom): 1
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>Enter force RMSE threshold (meV/Å): 60
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>Enter stress RMSE threshold (GPa): 0.03
+</code></pre></div>
+<p><strong>输出文件：</strong></p>
+<ul>
+<li><code>selected.xyz</code> — 超过 RMSE 阈值的结构（异常值）</li>
+<li><code>remained.xyz</code> — 在阈值内的结构</li>
+<li><code>selected_remained.png</code> — 对比图</li>
+</ul>
+<p><strong>用途：</strong> NEP 训练后，用此工具识别对误差贡献最大的问题结构。移除或改进这些结构以提升训练集质量。</p>
+<hr />
+<h2 id="_16">时间估算</h2>
+<h3 id="gpumd">GPUMD 剩余时间</h3>
+<p><code>time_consuming_gpumd.sh</code> 估算 GPUMD 模拟的剩余时间。</p>
+<p><strong>输入文件：</strong> <code>run.in</code>、<code>thermo.out</code>（在当前 GPUMD 工作目录中）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-time<span class="w"> </span>gpumd
+</code></pre></div>
+<p><strong>输出示例：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>----------------- System Information ----------------
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>total frames: 1050000
+<a id="__codelineno-19-3" name="__codelineno-19-3" href="#__codelineno-19-3"></a>-----------------------------------------------------
+<a id="__codelineno-19-4" name="__codelineno-19-4" href="#__codelineno-19-4"></a>Current Frame  Speed (steps/s)   Total Time       Time Left       Estimated End
+<a id="__codelineno-19-5" name="__codelineno-19-5" href="#__codelineno-19-5"></a>-------------   -------------   -------------   -------------   -----------------
+<a id="__codelineno-19-6" name="__codelineno-19-6" href="#__codelineno-19-6"></a>    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04
+<a id="__codelineno-19-7" name="__codelineno-19-7" href="#__codelineno-19-7"></a>    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56
+</code></pre></div>
+<h3 id="nep">NEP 剩余时间</h3>
+<p><code>time_consuming_nep.sh</code> 估算 NEP 训练的剩余时间。</p>
+<p><strong>输入文件：</strong> <code>loss.out</code>（在当前 NEP 工作目录中）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-time<span class="w"> </span>nep
+</code></pre></div>
+<p><strong>输出示例：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>+-----------------+-----------+-----------------+---------------------+
+<a id="__codelineno-21-2" name="__codelineno-21-2" href="#__codelineno-21-2"></a>|       Step      | Time Diff |    Time Left    |    Finish Time      |
+<a id="__codelineno-21-3" name="__codelineno-21-3" href="#__codelineno-21-3"></a>+-----------------+-----------+-----------------+---------------------+
+<a id="__codelineno-21-4" name="__codelineno-21-4" href="#__codelineno-21-4"></a>| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |
+<a id="__codelineno-21-5" name="__codelineno-21-5" href="#__codelineno-21-5"></a>| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |
+<a id="__codelineno-21-6" name="__codelineno-21-6" href="#__codelineno-21-6"></a>| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |
+<a id="__codelineno-21-7" name="__codelineno-21-7" href="#__codelineno-21-7"></a>+-----------------+-----------+-----------------+---------------------+
+</code></pre></div>
+<hr />
+<h2 id="_17">概率密度分析</h2>
+<p><code>probability_density_analysis.py</code> 计算移动离子的 3D 概率密度，用于扩散通道分析。</p>
+<p><strong>输入文件：</strong> 参考结构（POSCAR）、轨迹文件（extxyz）</p>
+<p><strong>命令行模式：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a>gpumdkit.sh<span class="w"> </span>-pda<span class="w"> </span>LLZO.vasp<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">0</span>.25
+</code></pre></div>
+<p><strong>参数说明：</strong></p>
+<table>
+<thead>
+<tr>
+<th>参数</th>
+<th>含义</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>LLZO.vasp</code></td>
+<td>参考结构（POSCAR 格式）</td>
+</tr>
+<tr>
+<td><code>dump.xyz</code></td>
+<td>轨迹文件（extxyz 格式）</td>
+</tr>
+<tr>
+<td><code>Li</code></td>
+<td>目标移动离子</td>
+</tr>
+<tr>
+<td><code>0.25</code></td>
+<td>概率密度网格间距（Å）</td>
+</tr>
+</tbody>
+</table>
+<p><strong>输出：</strong> <code>probability_density_0.25.vasp</code> — VASP 格式的概率密度网格，可用 VESTA 等工具可视化。</p>
+<p><strong>可视化建议：</strong></p>
+<ol>
+<li>在 VESTA 中打开 <code>probability_density_0.25.vasp</code></li>
+<li>使用 "Edit → Data → Volumetric Data" 调整等值面级别</li>
+<li>按数值对概率密度着色，以突出优选扩散路径</li>
+<li>叠加晶体结构作为参考</li>
+</ol>
+<hr />
+<h2 id="_18">示例工作流</h2>
+<h3 id="_19">结构质量检查</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-23-1" name="__codelineno-23-1" href="#__codelineno-23-1"></a><span class="c1"># 1. 检查成分</span>
+<a id="__codelineno-23-2" name="__codelineno-23-2" href="#__codelineno-23-2"></a>gpumdkit.sh<span class="w"> </span>-analyze_comp<span class="w"> </span>train.xyz
+<a id="__codelineno-23-3" name="__codelineno-23-3" href="#__codelineno-23-3"></a>
+<a id="__codelineno-23-4" name="__codelineno-23-4" href="#__codelineno-23-4"></a><span class="c1"># 2. 检查能量/力范围</span>
+<a id="__codelineno-23-5" name="__codelineno-23-5" href="#__codelineno-23-5"></a>gpumdkit.sh<span class="w"> </span>-range<span class="w"> </span>train.xyz<span class="w"> </span>force<span class="w"> </span>hist
+<a id="__codelineno-23-6" name="__codelineno-23-6" href="#__codelineno-23-6"></a>
+<a id="__codelineno-23-7" name="__codelineno-23-7" href="#__codelineno-23-7"></a><span class="c1"># 3. 检查最短距离</span>
+<a id="__codelineno-23-8" name="__codelineno-23-8" href="#__codelineno-23-8"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>train.xyz
+<a id="__codelineno-23-9" name="__codelineno-23-9" href="#__codelineno-23-9"></a>
+<a id="__codelineno-23-10" name="__codelineno-23-10" href="#__codelineno-23-10"></a><span class="c1"># 4. 查找异常值（NEP 训练后）</span>
+<a id="__codelineno-23-11" name="__codelineno-23-11" href="#__codelineno-23-11"></a><span class="c1"># 交互：5) 分析工具 → 502</span>
+</code></pre></div>
+<h3 id="_20">结构过滤流水线</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-24-1" name="__codelineno-24-1" href="#__codelineno-24-1"></a><span class="c1"># 1. 按最短距离过滤</span>
+<a id="__codelineno-24-2" name="__codelineno-24-2" href="#__codelineno-24-2"></a>gpumdkit.sh<span class="w"> </span>-filter_dist_pbc<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1</span>.0
+<a id="__codelineno-24-3" name="__codelineno-24-3" href="#__codelineno-24-3"></a>
+<a id="__codelineno-24-4" name="__codelineno-24-4" href="#__codelineno-24-4"></a><span class="c1"># 2. 按盒子大小过滤</span>
+<a id="__codelineno-24-5" name="__codelineno-24-5" href="#__codelineno-24-5"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>filtered_dist_pbc.xyz<span class="w"> </span><span class="m">13</span>
+<a id="__codelineno-24-6" name="__codelineno-24-6" href="#__codelineno-24-6"></a>
+<a id="__codelineno-24-7" name="__codelineno-24-7" href="#__codelineno-24-7"></a><span class="c1"># 3. 按力阈值过滤</span>
+<a id="__codelineno-24-8" name="__codelineno-24-8" href="#__codelineno-24-8"></a>gpumdkit.sh<span class="w"> </span>-filter_value<span class="w"> </span>filtered_box.xyz<span class="w"> </span>force<span class="w"> </span><span class="m">20</span>
+</code></pre></div>
+<h3 id="_21">扩散通道分析</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-25-1" name="__codelineno-25-1" href="#__codelineno-25-1"></a><span class="c1"># 1. 计算概率密度</span>
+<a id="__codelineno-25-2" name="__codelineno-25-2" href="#__codelineno-25-2"></a>gpumdkit.sh<span class="w"> </span>-pda<span class="w"> </span>LLZO.vasp<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">0</span>.25
+<a id="__codelineno-25-3" name="__codelineno-25-3" href="#__codelineno-25-3"></a>
+<a id="__codelineno-25-4" name="__codelineno-25-4" href="#__codelineno-25-4"></a><span class="c1"># 2. 用 VESTA 可视化</span>
+<a id="__codelineno-25-5" name="__codelineno-25-5" href="#__codelineno-25-5"></a><span class="c1"># 打开 probability_density_0.25.vasp</span>
 </code></pre></div>
 
 
diff --git "a/docs/htmls/zh/\345\221\275\344\273\244\345\217\202\350\200\203.html" "b/docs/htmls/zh/\345\221\275\344\273\244\345\217\202\350\200\203.html"
index 927f08f..69657a5 100644
--- "a/docs/htmls/zh/\345\221\275\344\273\244\345\217\202\350\200\203.html"
+++ "b/docs/htmls/zh/\345\221\275\344\273\244\345\217\202\350\200\203.html"
@@ -1434,8 +1434,8 @@ <h2 id="gpumdkitsh-h"><code>gpumdkit.sh -h</code> 输出</h2>
 <a id="__codelineno-0-25" name="__codelineno-0-25" href="#__codelineno-0-25"></a>| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
 <a id="__codelineno-0-26" name="__codelineno-0-26" href="#__codelineno-0-26"></a>| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 <a id="__codelineno-0-27" name="__codelineno-0-27" href="#__codelineno-0-27"></a>| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-<a id="__codelineno-0-28" name="__codelineno-0-28" href="#__codelineno-0-28"></a>| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-<a id="__codelineno-0-29" name="__codelineno-0-29" href="#__codelineno-0-29"></a>| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
+<a id="__codelineno-0-28" name="__codelineno-0-28" href="#__codelineno-0-28"></a>| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
+<a id="__codelineno-0-29" name="__codelineno-0-29" href="#__codelineno-0-29"></a>| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
 <a id="__codelineno-0-30" name="__codelineno-0-30" href="#__codelineno-0-30"></a>+-------------------------------------------------------------------------------------------------------+
 <a id="__codelineno-0-31" name="__codelineno-0-31" href="#__codelineno-0-31"></a>| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |
 <a id="__codelineno-0-32" name="__codelineno-0-32" href="#__codelineno-0-32"></a>+-------------------------------------------------------------------------------------------------------+
diff --git "a/docs/htmls/zh/\345\267\245\344\275\234\346\265\201\350\204\232\346\234\254.html" "b/docs/htmls/zh/\345\267\245\344\275\234\346\265\201\350\204\232\346\234\254.html"
index e2d2e4a..a4f4c34 100644
--- "a/docs/htmls/zh/\345\267\245\344\275\234\346\265\201\350\204\232\346\234\254.html"
+++ "b/docs/htmls/zh/\345\267\245\344\275\234\346\265\201\350\204\232\346\234\254.html"
@@ -1092,6 +1092,17 @@
       
         <li class="md-nav__item">
   <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        基于模板的温度系列
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
         使用建议
@@ -1439,6 +1450,17 @@
       
         <li class="md-nav__item">
   <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        基于模板的温度系列
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
         使用建议
@@ -1480,7 +1502,19 @@ <h2 id="_1">交互入口</h2>
 <p>选择：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>3) Workflow
 </code></pre></div>
-<p>常见菜单：</p>
+<p>菜单如下：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>+---------------------------------------------------------+
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>|                      WORKFLOW TOOLS                     |
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>+---------------------------------------------------------+
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>| 301) SCF batch pretreatment                             |
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>| 302) MD sample batch pretreatment (gpumd)               |
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>| 303) MD sample batch pretreatment (lmp)                 |
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>+---------------------------------------------------------+
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>| 000) Return to the main menu                            |
+<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>+---------------------------------------------------------+
+<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a>Input the function number:
+</code></pre></div>
+<p>常用功能：</p>
 <table>
 <thead>
 <tr>
@@ -1510,8 +1544,8 @@ <h2 id="_1">交互入口</h2>
 <h2 id="scf">SCF 批处理预处理</h2>
 <p>适用于已有多个结构，需要准备第一性原理单点计算的情况。</p>
 <h3 id="vasp">VASP</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh
-<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="c1"># 选择 3 -&gt; 301 -&gt; VASP</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a><span class="c1"># 选择 3 -&gt; 301 -&gt; VASP</span>
 </code></pre></div>
 <p>运行前，把结构文件放在当前目录。脚本按以下顺序检测：</p>
 <ol>
@@ -1521,87 +1555,87 @@ <h3 id="vasp">VASP</h3>
 <li>如果没有 <code>.vasp</code> 且存在多个 <code>.xyz</code>，会让用户选择一个。</li>
 </ol>
 <p>运行前的典型目录：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>current directory/
-<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>├── POSCAR_1.vasp
-<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>├── POSCAR_2.vasp
-<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>└── POSCAR_3.vasp
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>current directory/
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>├── POSCAR_1.vasp
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>├── POSCAR_2.vasp
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a>└── POSCAR_3.vasp
 </code></pre></div>
 <p>或：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>current directory/
-<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>└── sampled.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>current directory/
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>└── sampled.xyz
 </code></pre></div>
 <p>运行后脚本会创建：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>current directory/
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>├── struct_fp/
-<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>│   ├── POSCAR_1.vasp
-<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>│   ├── POSCAR_2.vasp
-<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>│   └── ...
-<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>├── fp/
-<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>├── &lt;prefix&gt;_1/
-<a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a>├── &lt;prefix&gt;_2/
-<a id="__codelineno-5-9" name="__codelineno-5-9" href="#__codelineno-5-9"></a>└── presub.sh
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>current directory/
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>├── struct_fp/
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>│   ├── POSCAR_1.vasp
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>│   ├── POSCAR_2.vasp
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a>│   └── ...
+<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>├── fp/
+<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a>├── &lt;prefix&gt;_1/
+<a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a>├── &lt;prefix&gt;_2/
+<a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a>└── presub.sh
 </code></pre></div>
 <p><code>fp/</code> 是脚本自动创建的。脚本结束后，需要用户把 <code>INCAR</code>、<code>POTCAR</code>、<code>KPOINTS</code> 放到 <code>fp/</code> 中，计算目录会链接这里的文件。</p>
 <p>运行过程中输入的 <code>prefix</code> 会作为计算文件夹名前缀。后续使用 <code>out2xyz</code> 提取结果时，文件夹名会作为 <code>config_type</code> 写入 extxyz，便于之后检查结构来源。</p>
 <h3 id="cp2k">CP2K</h3>
 <p>CP2K 可以从交互菜单进入，也可以直接命令行调用：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh
-<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="c1"># 选择 3 -&gt; 301 -&gt; CP2K</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="c1"># 选择 3 -&gt; 301 -&gt; CP2K</span>
 </code></pre></div>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>python<span class="w"> </span>Scripts/workflow/scf_batch_pretreatment_cp2k.py<span class="w"> </span>train.xyz<span class="w"> </span>template.inp<span class="w"> </span>calc
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>python<span class="w"> </span>Scripts/workflow/scf_batch_pretreatment_cp2k.py<span class="w"> </span>train.xyz<span class="w"> </span>template.inp<span class="w"> </span>calc
 </code></pre></div>
 <p>交互模式会要求输入：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;
 </code></pre></div>
 <p>示例：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>dump.xyz template.inp H2O
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>dump.xyz template.inp H2O
 </code></pre></div>
 <p>CP2K 模板应设置为从 <code>pos.xyz</code> 读取坐标。参考模板在：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>Scripts/workflow/cp2k_template.inp
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>Scripts/workflow/cp2k_template.inp
 </code></pre></div>
 <p>脚本会为每个结构生成 <code>&lt;prefix&gt;_&lt;index&gt;/</code> 目录，并写入 <code>input.inp</code> 和 <code>pos.xyz</code>。</p>
 <h2 id="md">MD 采样预处理</h2>
 <h3 id="gpumd">GPUMD</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh
-<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="c1"># 选择 3 -&gt; 302</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a><span class="c1"># 选择 3 -&gt; 302</span>
 </code></pre></div>
 <p>运行前，把 <code>.vasp</code> 文件或一个 extxyz 文件放在当前目录。检测顺序与 VASP SCF 预处理一致：优先处理 <code>.vasp</code>；如果没有 <code>.vasp</code> 且存在多个 <code>.xyz</code>，会让用户选择一个。</p>
 <p>运行前典型目录：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>current directory/
-<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>├── POSCAR_1.vasp
-<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a>└── POSCAR_2.vasp
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>current directory/
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>├── POSCAR_1.vasp
+<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>└── POSCAR_2.vasp
 </code></pre></div>
 <p>或：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>current directory/
-<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>└── dump.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>current directory/
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>└── dump.xyz
 </code></pre></div>
 <p>运行后脚本会创建：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>current directory/
-<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>├── struct_md/
-<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a>│   ├── model_1.xyz
-<a id="__codelineno-14-4" name="__codelineno-14-4" href="#__codelineno-14-4"></a>│   ├── model_2.xyz
-<a id="__codelineno-14-5" name="__codelineno-14-5" href="#__codelineno-14-5"></a>│   └── ...
-<a id="__codelineno-14-6" name="__codelineno-14-6" href="#__codelineno-14-6"></a>├── md/
-<a id="__codelineno-14-7" name="__codelineno-14-7" href="#__codelineno-14-7"></a>├── sample_1/
-<a id="__codelineno-14-8" name="__codelineno-14-8" href="#__codelineno-14-8"></a>├── sample_2/
-<a id="__codelineno-14-9" name="__codelineno-14-9" href="#__codelineno-14-9"></a>└── presub.sh
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>current directory/
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>├── struct_md/
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a>│   ├── model_1.xyz
+<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a>│   ├── model_2.xyz
+<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a>│   └── ...
+<a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a>├── md/
+<a id="__codelineno-15-7" name="__codelineno-15-7" href="#__codelineno-15-7"></a>├── sample_1/
+<a id="__codelineno-15-8" name="__codelineno-15-8" href="#__codelineno-15-8"></a>├── sample_2/
+<a id="__codelineno-15-9" name="__codelineno-15-9" href="#__codelineno-15-9"></a>└── presub.sh
 </code></pre></div>
 <p><code>md/</code> 是脚本自动创建的。脚本结束后，需要把 <code>nep.txt</code> 和 <code>run_*.in</code> 放入 <code>md/</code>。例如 <code>run_1.in</code> 会链接到 <code>sample_1/run.in</code>，<code>run_2.in</code> 会链接到 <code>sample_2/run.in</code>。</p>
 <h3 id="lammps">LAMMPS</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh
-<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="c1"># 选择 3 -&gt; 303</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a><span class="c1"># 选择 3 -&gt; 303</span>
 </code></pre></div>
 <p>运行前，把 <code>.vasp</code> 文件或一个 extxyz 文件放在当前目录；两种格式同时存在时优先处理 <code>.vasp</code>。</p>
 <p>运行后脚本会创建：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>current directory/
-<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>├── struct_md/
-<a id="__codelineno-16-3" name="__codelineno-16-3" href="#__codelineno-16-3"></a>│   ├── lammps_1.data
-<a id="__codelineno-16-4" name="__codelineno-16-4" href="#__codelineno-16-4"></a>│   ├── lammps_2.data
-<a id="__codelineno-16-5" name="__codelineno-16-5" href="#__codelineno-16-5"></a>│   └── ...
-<a id="__codelineno-16-6" name="__codelineno-16-6" href="#__codelineno-16-6"></a>├── md/
-<a id="__codelineno-16-7" name="__codelineno-16-7" href="#__codelineno-16-7"></a>├── sample_1/
-<a id="__codelineno-16-8" name="__codelineno-16-8" href="#__codelineno-16-8"></a>├── sample_2/
-<a id="__codelineno-16-9" name="__codelineno-16-9" href="#__codelineno-16-9"></a>└── presub.sh
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>current directory/
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>├── struct_md/
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>│   ├── lammps_1.data
+<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a>│   ├── lammps_2.data
+<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a>│   └── ...
+<a id="__codelineno-17-6" name="__codelineno-17-6" href="#__codelineno-17-6"></a>├── md/
+<a id="__codelineno-17-7" name="__codelineno-17-7" href="#__codelineno-17-7"></a>├── sample_1/
+<a id="__codelineno-17-8" name="__codelineno-17-8" href="#__codelineno-17-8"></a>├── sample_2/
+<a id="__codelineno-17-9" name="__codelineno-17-9" href="#__codelineno-17-9"></a>└── presub.sh
 </code></pre></div>
 <p>脚本结束后，需要把 <code>lmprun.in</code> 和 <code>nep.txt</code> 放到 <code>md/</code> 中。</p>
 <h2 id="_2">主动学习式流程</h2>
@@ -1617,7 +1651,17 @@ <h2 id="_2">主动学习式流程</h2>
 <li>重新训练 NEP。</li>
 </ol>
 <p>更完整的开发版主动学习脚本说明见 <a href="%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html">主动学习</a>。</p>
-<h2 id="_3">使用建议</h2>
+<h2 id="_3">基于模板的温度系列</h2>
+<p>对于简单的温度系列模拟，使用 shell 循环即可：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a><span class="k">for</span><span class="w"> </span>temp<span class="w"> </span><span class="k">in</span><span class="w"> </span><span class="m">300</span><span class="w"> </span><span class="m">500</span><span class="w"> </span><span class="m">700</span><span class="w"> </span><span class="m">900</span><span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a><span class="w">    </span>mkdir<span class="w"> </span>-p<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K&quot;</span>
+<a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a><span class="w">    </span>cp<span class="w"> </span>model.xyz<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/&quot;</span>
+<a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a><span class="w">    </span>cp<span class="w"> </span>nep.txt<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/&quot;</span>
+<a id="__codelineno-18-5" name="__codelineno-18-5" href="#__codelineno-18-5"></a><span class="w">    </span>sed<span class="w"> </span><span class="s2">&quot;s/TEMPERATURE/</span><span class="nv">$temp</span><span class="s2">/g&quot;</span><span class="w"> </span>run_template.in<span class="w"> </span>&gt;<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">temp</span><span class="si">}</span><span class="s2">K/run.in&quot;</span>
+<a id="__codelineno-18-6" name="__codelineno-18-6" href="#__codelineno-18-6"></a><span class="k">done</span>
+</code></pre></div>
+<p>然后根据你的集群系统提交生成的文件夹。</p>
+<h2 id="_4">使用建议</h2>
 <ul>
 <li>工作流脚本和集群环境强相关，正式批量提交前先用少量结构测试。</li>
 <li>模板文件如 <code>INCAR</code>、<code>KPOINTS</code>、<code>POTCAR</code>、<code>run.in</code> 应仔细检查。</li>
diff --git "a/docs/htmls/zh/\345\277\253\351\200\237\345\205\245\351\227\250.html" "b/docs/htmls/zh/\345\277\253\351\200\237\345\205\245\351\227\250.html"
index b5c441d..2bacb2e 100644
--- "a/docs/htmls/zh/\345\277\253\351\200\237\345\205\245\351\227\250.html"
+++ "b/docs/htmls/zh/\345\277\253\351\200\237\345\205\245\351\227\250.html"
@@ -143,7 +143,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#1-python" class="md-skip">
+        <a href="#_1" class="md-skip">
           Skip to content
         </a>
       
@@ -879,10 +879,10 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#1-python" class="md-nav__link">
+  <a href="#_1" class="md-nav__link">
     <span class="md-ellipsis">
       
-        1. 准备 Python 环境
+        功能简介
       
     </span>
   </a>
@@ -890,33 +890,33 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#2-gpumdkit" class="md-nav__link">
+  <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
-        2. 安装 GPUMDkit
+        准备工作
       
     </span>
   </a>
   
-</li>
-      
-        <li class="md-nav__item">
-  <a href="#3" class="md-nav__link">
+    <nav class="md-nav" aria-label="准备工作">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#1-python" class="md-nav__link">
     <span class="md-ellipsis">
       
-        3. 使用方式
+        1. 准备 Python 环境
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="3. 使用方式">
-      <ul class="md-nav__list">
+</li>
         
           <li class="md-nav__item">
-  <a href="#_1" class="md-nav__link">
+  <a href="#2-gpumdkit" class="md-nav__link">
     <span class="md-ellipsis">
       
-        交互模式
+        2. 安装 GPUMDkit
       
     </span>
   </a>
@@ -924,10 +924,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_2" class="md-nav__link">
+  <a href="#3" class="md-nav__link">
     <span class="md-ellipsis">
       
-        命令行模式
+        3. 验证安装
       
     </span>
   </a>
@@ -940,15 +940,37 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#4" class="md-nav__link">
+  <a href="#_3" class="md-nav__link">
     <span class="md-ellipsis">
       
-        4. 实际例子
+        交互模式
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        命令行模式
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        常见示例
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="4. 实际例子">
+    <nav class="md-nav" aria-label="常见示例">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -996,7 +1018,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
+  <a href="#_6" class="md-nav__link">
     <span class="md-ellipsis">
       
         绘制热力学量
@@ -1023,10 +1045,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#5" class="md-nav__link">
+  <a href="#_7" class="md-nav__link">
     <span class="md-ellipsis">
       
-        5. 获取帮助
+        说明
       
     </span>
   </a>
@@ -1382,10 +1404,10 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#1-python" class="md-nav__link">
+  <a href="#_1" class="md-nav__link">
     <span class="md-ellipsis">
       
-        1. 准备 Python 环境
+        功能简介
       
     </span>
   </a>
@@ -1393,33 +1415,33 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#2-gpumdkit" class="md-nav__link">
+  <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
-        2. 安装 GPUMDkit
+        准备工作
       
     </span>
   </a>
   
-</li>
-      
-        <li class="md-nav__item">
-  <a href="#3" class="md-nav__link">
+    <nav class="md-nav" aria-label="准备工作">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#1-python" class="md-nav__link">
     <span class="md-ellipsis">
       
-        3. 使用方式
+        1. 准备 Python 环境
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="3. 使用方式">
-      <ul class="md-nav__list">
+</li>
         
           <li class="md-nav__item">
-  <a href="#_1" class="md-nav__link">
+  <a href="#2-gpumdkit" class="md-nav__link">
     <span class="md-ellipsis">
       
-        交互模式
+        2. 安装 GPUMDkit
       
     </span>
   </a>
@@ -1427,10 +1449,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_2" class="md-nav__link">
+  <a href="#3" class="md-nav__link">
     <span class="md-ellipsis">
       
-        命令行模式
+        3. 验证安装
       
     </span>
   </a>
@@ -1443,15 +1465,37 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#4" class="md-nav__link">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        交互模式
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        命令行模式
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
     <span class="md-ellipsis">
       
-        4. 实际例子
+        常见示例
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="4. 实际例子">
+    <nav class="md-nav" aria-label="常见示例">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -1499,7 +1543,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
+  <a href="#_6" class="md-nav__link">
     <span class="md-ellipsis">
       
         绘制热力学量
@@ -1526,10 +1570,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#5" class="md-nav__link">
+  <a href="#_7" class="md-nav__link">
     <span class="md-ellipsis">
       
-        5. 获取帮助
+        说明
       
     </span>
   </a>
@@ -1558,11 +1602,13 @@
 
 <div align="center">
   <h1>🚀 快速入门</h1>
-  <p style="text-align: justify;">本页介绍 GPUMDkit 的基本安装方式和几个常用命令。GPUMDkit 既可以通过交互菜单使用，也可以直接通过命令行选项调用。</p>
+  <p style="text-align: justify;">本页帮助你安装 GPUMDkit 并运行第一个命令。你可以通过交互菜单或直接使用命令行选项来使用 GPUMDkit。</p>
 </div>
 
-<h2 id="1-python">1. 准备 Python 环境</h2>
-<p>可以使用干净的 conda 环境：</p>
+<h2 id="_1">功能简介</h2>
+<p>GPUMDkit 为计算材料科学中的常见任务提供统一入口——格式转换、结构分析、性质计算和可视化——无需编写自定义脚本。</p>
+<h2 id="_2">准备工作</h2>
+<h3 id="1-python">1. 准备 Python 环境</h3>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>gpumdkit<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12
 <a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>gpumdkit
 </code></pre></div>
@@ -1570,158 +1616,122 @@ <h2 id="1-python">1. 准备 Python 环境</h2>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>pip<span class="w"> </span>install<span class="w"> </span>neptrain<span class="w"> </span>dpdata<span class="w"> </span>calorine
 </code></pre></div>
 <p>其他 Python 依赖由对应脚本在运行时导入。如果缺少某个包，使用对应功能时 Python 会给出提示。</p>
-<h2 id="2-gpumdkit">2. 安装 GPUMDkit</h2>
-<p>克隆仓库：</p>
+<h3 id="2-gpumdkit">2. 安装 GPUMDkit</h3>
+<p>克隆仓库并运行安装脚本：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
 <a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
-</code></pre></div>
-<p>运行安装脚本：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="nb">source</span><span class="w"> </span>./install.sh
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a><span class="nb">source</span><span class="w"> </span>./install.sh
 </code></pre></div>
 <p>安装脚本会写入 <code>GPUMDkit_path</code> 和 <code>PATH</code> 设置，并在当前 shell 中加载。默认写入 <code>~/.bashrc</code>；如果当前 shell 是 zsh，则写入 <code>~/.zshrc</code>。如果检测到已有 GPUMDkit 路径，安装脚本会打印旧路径并询问是否替换；修改 rc 文件前会先创建备份。</p>
 <p>典型安装输出：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>======================================================
-<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>  GPUMDkit Installation
-<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>======================================================
-<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a> [1/4] Detecting GPUMDkit directory...
-<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>       /path/to/GPUMDkit
-<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a> [2/4] Detecting shell configuration...
-<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a>       Target: /Users/you/.bashrc
-<a id="__codelineno-4-8" name="__codelineno-4-8" href="#__codelineno-4-8"></a>       Adding environment variables to /Users/you/.bashrc
-<a id="__codelineno-4-9" name="__codelineno-4-9" href="#__codelineno-4-9"></a>       Success: Environment variables added.
-<a id="__codelineno-4-10" name="__codelineno-4-10" href="#__codelineno-4-10"></a> [3/4] Setting executable permissions...
-<a id="__codelineno-4-11" name="__codelineno-4-11" href="#__codelineno-4-11"></a>       Added executable permission to gpumdkit.sh
-<a id="__codelineno-4-12" name="__codelineno-4-12" href="#__codelineno-4-12"></a> [4/4] Loading environment...
-<a id="__codelineno-4-13" name="__codelineno-4-13" href="#__codelineno-4-13"></a>
-<a id="__codelineno-4-14" name="__codelineno-4-14" href="#__codelineno-4-14"></a>======================================================
-<a id="__codelineno-4-15" name="__codelineno-4-15" href="#__codelineno-4-15"></a>  Installation Complete!  GPUMDkit is ready to use.
-<a id="__codelineno-4-16" name="__codelineno-4-16" href="#__codelineno-4-16"></a>======================================================
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>======================================================
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>  GPUMDkit Installation
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>======================================================
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a> [1/4] Detecting GPUMDkit directory...
+<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>       /path/to/GPUMDkit
+<a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a> [2/4] Detecting shell configuration...
+<a id="__codelineno-3-7" name="__codelineno-3-7" href="#__codelineno-3-7"></a>       Target: /Users/you/.bashrc
+<a id="__codelineno-3-8" name="__codelineno-3-8" href="#__codelineno-3-8"></a>       Adding environment variables to /Users/you/.bashrc
+<a id="__codelineno-3-9" name="__codelineno-3-9" href="#__codelineno-3-9"></a>       Success: Environment variables added.
+<a id="__codelineno-3-10" name="__codelineno-3-10" href="#__codelineno-3-10"></a> [3/4] Setting executable permissions...
+<a id="__codelineno-3-11" name="__codelineno-3-11" href="#__codelineno-3-11"></a>       Added executable permission to gpumdkit.sh
+<a id="__codelineno-3-12" name="__codelineno-3-12" href="#__codelineno-3-12"></a> [4/4] Loading environment...
+<a id="__codelineno-3-13" name="__codelineno-3-13" href="#__codelineno-3-13"></a>
+<a id="__codelineno-3-14" name="__codelineno-3-14" href="#__codelineno-3-14"></a>======================================================
+<a id="__codelineno-3-15" name="__codelineno-3-15" href="#__codelineno-3-15"></a>  Installation Complete!  GPUMDkit is ready to use.
+<a id="__codelineno-3-16" name="__codelineno-3-16" href="#__codelineno-3-16"></a>======================================================
 </code></pre></div>
 <p>如果之前已经安装过 GPUMDkit，可能会看到：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>Existing GPUMDkit configuration found.
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>Existing path(s):
-<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>  - /old/path/to/GPUMDkit
-<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>New path:
-<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>  - /new/path/to/GPUMDkit
-<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>
-<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>Replace the existing GPUMDkit configuration with the new path? [y/N]:
-</code></pre></div>
-<p>检查命令：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-h
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>Existing GPUMDkit configuration found.
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>Existing path(s):
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>  - /old/path/to/GPUMDkit
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a>New path:
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>  - /new/path/to/GPUMDkit
+<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a>
+<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a>Replace the existing GPUMDkit configuration with the new path? [y/N]:
 </code></pre></div>
-<p>帮助表：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
-<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>|                                          MAIN FUNCTIONS                                               |
-<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a>| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |
-<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a>| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |
-<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
-<a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a>|                                         FORMAT CONVERSION                                             |
-<a id="__codelineno-7-11" name="__codelineno-7-11" href="#__codelineno-7-11"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a>| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |
-<a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a>| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |
-<a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a>| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |
-<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a>| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |
-<a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a>| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |
-<a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a>| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |
-<a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a>| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
-<a id="__codelineno-7-19" name="__codelineno-7-19" href="#__codelineno-7-19"></a>| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
-<a id="__codelineno-7-20" name="__codelineno-7-20" href="#__codelineno-7-20"></a>| -frame_range  Extract frames by range         |                                                       |
-<a id="__codelineno-7-21" name="__codelineno-7-21" href="#__codelineno-7-21"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-22" name="__codelineno-7-22" href="#__codelineno-7-22"></a>|                                            ANALYSIS                                                   |
-<a id="__codelineno-7-23" name="__codelineno-7-23" href="#__codelineno-7-23"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-24" name="__codelineno-7-24" href="#__codelineno-7-24"></a>| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
-<a id="__codelineno-7-25" name="__codelineno-7-25" href="#__codelineno-7-25"></a>| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
-<a id="__codelineno-7-26" name="__codelineno-7-26" href="#__codelineno-7-26"></a>| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
-<a id="__codelineno-7-27" name="__codelineno-7-27" href="#__codelineno-7-27"></a>| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-<a id="__codelineno-7-28" name="__codelineno-7-28" href="#__codelineno-7-28"></a>| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-<a id="__codelineno-7-29" name="__codelineno-7-29" href="#__codelineno-7-29"></a>| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
-<a id="__codelineno-7-30" name="__codelineno-7-30" href="#__codelineno-7-30"></a>+-------------------------------------------------------------------------------------------------------+
-<a id="__codelineno-7-31" name="__codelineno-7-31" href="#__codelineno-7-31"></a>| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |
-<a id="__codelineno-7-32" name="__codelineno-7-32" href="#__codelineno-7-32"></a>+-------------------------------------------------------------------------------------------------------+
+<h3 id="3">3. 验证安装</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-h
 </code></pre></div>
-<h2 id="3">3. 使用方式</h2>
-<h3 id="_1">交互模式</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh
+<p>此命令会打印帮助表，列出所有可用选项。</p>
+<h2 id="_3">交互模式</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh
 </code></pre></div>
-<p>主菜单：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>           ____ ____  _   _ __  __ ____  _    _ _
-<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
-<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>         | |  _| |_) | | | | |\/| | | | | |/ / | __|
-<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a>         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_
-<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
-<a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a>
-<a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a>          GPUMDkit Version 1.5.6 (dev) (2026-06-17)
-<a id="__codelineno-9-8" name="__codelineno-9-8" href="#__codelineno-9-8"></a>    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
-<a id="__codelineno-9-9" name="__codelineno-9-9" href="#__codelineno-9-9"></a> Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA
-<a id="__codelineno-9-10" name="__codelineno-9-10" href="#__codelineno-9-10"></a>
-<a id="__codelineno-9-11" name="__codelineno-9-11" href="#__codelineno-9-11"></a> ---------------------- GPUMD ------------------------
-<a id="__codelineno-9-12" name="__codelineno-9-12" href="#__codelineno-9-12"></a> 1) Format Conversion          2) Sample Structures
-<a id="__codelineno-9-13" name="__codelineno-9-13" href="#__codelineno-9-13"></a> 3) Workflow                   4) Calculators
-<a id="__codelineno-9-14" name="__codelineno-9-14" href="#__codelineno-9-14"></a> 5) Analyzer                   6) Visualization
-<a id="__codelineno-9-15" name="__codelineno-9-15" href="#__codelineno-9-15"></a> 7) Utilities                  8) Developing...
-<a id="__codelineno-9-16" name="__codelineno-9-16" href="#__codelineno-9-16"></a> 0) Exit
-<a id="__codelineno-9-17" name="__codelineno-9-17" href="#__codelineno-9-17"></a> ------------&gt;&gt;
-<a id="__codelineno-9-18" name="__codelineno-9-18" href="#__codelineno-9-18"></a> Input the function number:
+<p>打开主菜单：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>           ____ ____  _   _ __  __ ____  _    _ _
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>         | |  _| |_) | | | | |\/| | | | | |/ / | __|
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
+<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a>
+<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a>          GPUMDkit Version 1.5.6 (dev) (2026-06-17)
+<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+<a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a> Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA
+<a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a>
+<a id="__codelineno-7-11" name="__codelineno-7-11" href="#__codelineno-7-11"></a> ---------------------- GPUMD ------------------------
+<a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a> 1) Format Conversion          2) Sample Structures
+<a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a> 3) Workflow                   4) Calculators
+<a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a> 5) Analyzer                   6) Visualization
+<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a> 7) Utilities                  8) Developing...
+<a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a> 0) Exit
+<a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a> ------------&gt;&gt;
+<a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a> Input the function number:
 </code></pre></div>
-<h3 id="_2">命令行模式</h3>
+<p>按数字选择模块。每个模块提供包含具体功能的子菜单。</p>
+<h2 id="_4">命令行模式</h2>
 <p>直接命令使用固定的位置参数：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
-<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
-<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-&lt;选项&gt;<span class="w"> </span><span class="o">[</span>参数...<span class="o">]</span>
 </code></pre></div>
-<p>例如：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<p>示例：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>trajectory.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
 </code></pre></div>
-<p>表示读取 <code>POSCAR</code>，写出 <code>model.xyz</code>。</p>
-<h2 id="4">4. 实际例子</h2>
+<p>第一个示例读取 <code>POSCAR</code>，写出 <code>model.xyz</code>。</p>
+<h2 id="_5">常见示例</h2>
 <h3 id="poscar-extxyz">POSCAR 转 extxyz</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
 </code></pre></div>
 <h3 id="gpumd-group">添加 GPUMD group 标签</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
 </code></pre></div>
 <p>group 标签用于一些需要原子分组的 GPUMD 相关流程和分析，例如特定元素的 MSD 或扩散性质计算。</p>
 <h3 id="nep">绘制 NEP 训练结果</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/train.png" alt="NEP training results" width="72%" />
 </div>
 
 <h3 id="nep_1">绘制 NEP 测试集结果</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/prediction.png" alt="NEP test results" width="72%" />
 </div>
 
-<h3 id="_3">绘制热力学量</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+<h3 id="_6">绘制热力学量</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/thermo.png" alt="Thermo plot" width="72%" />
 </div>
 
 <h3 id="msd">绘制 MSD 和自扩散系数</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
-<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
   <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
 </div>
 
-<h2 id="5">5. 获取帮助</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-h
-<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>-h
-<a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>-h
-<a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train<span class="w"> </span>-h
-<a id="__codelineno-18-5" name="__codelineno-18-5" href="#__codelineno-18-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>-h
-</code></pre></div>
+<h2 id="_7">说明</h2>
+<ul>
+<li>使用 <code>gpumdkit.sh -h</code> 查看所有可用选项。</li>
+<li>使用 <code>gpumdkit.sh -&lt;选项&gt; -h</code> 获取特定选项的帮助（例如 <code>gpumdkit.sh -plt train -h</code>）。</li>
+<li>各模块的详细用法请参见<a href="index.html">首页</a>中链接的对应教程页面。</li>
+</ul>
 
 
 
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+        依赖
+      
+    </span>
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+    <span class="md-ellipsis">
+      
+        依赖
+      
+    </span>
+  </a>
+  
+</li>
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+        <li class="md-nav__item">
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           <li class="md-nav__item">
-  <a href="#_16" class="md-nav__link">
+  <a href="#_17" class="md-nav__link">
     <span class="md-ellipsis">
       
         参数（完整）
@@ -1955,7 +1977,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_17" class="md-nav__link">
+  <a href="#_18" class="md-nav__link">
     <span class="md-ellipsis">
       
         输出文件
@@ -1982,7 +2004,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_18" class="md-nav__link">
+  <a href="#_19" class="md-nav__link">
     <span class="md-ellipsis">
       
         输出文件一览
@@ -1993,7 +2015,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_19" class="md-nav__link">
+  <a href="#_20" class="md-nav__link">
     <span class="md-ellipsis">
       
         真实案例
@@ -2127,7 +2149,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_20" class="md-nav__link">
+  <a href="#_21" class="md-nav__link">
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         其他体系
@@ -2150,7 +2172,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_21" class="md-nav__link">
+  <a href="#_22" class="md-nav__link">
     <span class="md-ellipsis">
       
         其他铁电材料家族
@@ -2202,32 +2224,105 @@ <h1>🧲 极性材料分析</h1>
 <li><code>oct-tilt</code> 用于八面体环境分析，需要每个中心原子周围有 6 个近邻。</li>
 <li><code>pol-abo3</code> 专用于 <code>ABO3</code> 体系的极化分析。</li>
 </ul>
-<h2 id="_1">依赖</h2>
+<h2 id="_1">概览</h2>
+<table>
+<thead>
+<tr>
+<th>步骤</th>
+<th>CLI 命令</th>
+<th>主要输入</th>
+<th>输出</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>构建近邻列表</td>
+<td><code>gpumdkit.sh -calc nlist ...</code></td>
+<td><code>model.xyz</code></td>
+<td><code>nl-*.dat</code></td>
+</tr>
+<tr>
+<td>计算位移</td>
+<td><code>gpumdkit.sh -calc disp ...</code></td>
+<td>轨迹 + <code>nl-*.dat</code></td>
+<td><code>displacements.dat</code></td>
+</tr>
+<tr>
+<td>平均轨迹结构</td>
+<td><code>gpumdkit.sh -calc avg-struct ...</code></td>
+<td>轨迹</td>
+<td>平均结构 extxyz</td>
+</tr>
+<tr>
+<td>八面体倾斜</td>
+<td><code>gpumdkit.sh -calc oct-tilt ...</code></td>
+<td>轨迹 + B-O 近邻列表</td>
+<td>倾斜角数据表</td>
+</tr>
+<tr>
+<td>ABO3 极化</td>
+<td><code>gpumdkit.sh -calc pol-abo3 ...</code></td>
+<td>轨迹 + 近邻列表</td>
+<td>极化数据表</td>
+</tr>
+<tr>
+<td>plane-grid 绘图</td>
+<td><code>gpumdkit.sh -plt plane-grid ...</code></td>
+<td>结构 + 位移数据</td>
+<td>平面剖面图</td>
+</tr>
+</tbody>
+</table>
+<h2 id="_2">依赖</h2>
 <p>这些脚本需要 <code>ferrodispcalc</code>：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
 </code></pre></div>
-<h2 id="_2">交互模式入口</h2>
+<h2 id="_3">交互模式入口</h2>
 <p>选项 <code>406-410</code> 是本教程中的核心功能。下面各节会说明每个功能的用途和运行方式。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="c1"># 选择 4) Calculators</span>
+</code></pre></div>
+<p>计算器菜单如下：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>|                     CALCULATOR TOOLS                     |
+<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>| 401) Calc ionic conductivity                             |
+<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>| 402) Calc properties by nep                              |
+<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>| 403) Calc descriptors of specific elements               |
+<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>| 404) Calc density of atomistic states (DOAS)             |
+<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>| 405) Calc nudged elastic band (NEB) by nep               |
+<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>| 406) Build neighbor list                                 |
+<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a>| 407) Calc displacement from trajectory                   |
+<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a>| 408) Calc averaged structure                             |
+<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a>| 409) Calc octahedral tilt                                |
+<a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a>| 410) Calc polarization for ABO3                          |
+<a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a>| 411) Minimize structure by nep                           |
+<a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a>| 412) Calc mean square displacement (MSD) from trajectory |
+<a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-17" name="__codelineno-2-17" href="#__codelineno-2-17"></a>| 000) Return to the main menu                             |
+<a id="__codelineno-2-18" name="__codelineno-2-18" href="#__codelineno-2-18"></a>+----------------------------------------------------------+
+<a id="__codelineno-2-19" name="__codelineno-2-19" href="#__codelineno-2-19"></a>Input the function number:
+</code></pre></div>
 <p>完整参数说明可以通过以下命令查看：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-h
-<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-h
-<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-h
-<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-h
-<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-h
-<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-h
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-h
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-h
+<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-h
+<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-h
+<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-h
+<a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-h
 </code></pre></div>
 <h2 id="406-calc_neighbor_listpy">406) 构建近邻列表 (<code>calc_neighbor_list.py</code>)</h2>
 <p>为指定中心元素和近邻元素构建近邻列表。</p>
 <p>使用场景：
 这通常是运行 <code>disp</code>、<code>oct-tilt</code> 和 <code>pol-abo3</code> 之前的第一步，因为这些脚本会读取 <code>nl-*.dat</code> 近邻文件。</p>
-<h3 id="_3">用法</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="c1"># 示例 1：为八面体分析构建 Ti-O 最近 6 个近邻</span>
-<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
-<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
-<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="c1"># 示例 2：为 A 位中心分析构建 Pb/Sr-O 最近 12 个近邻</span>
-<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
+<h3 id="_4">用法</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="c1"># 示例 1：为八面体分析构建 Ti-O 最近 6 个近邻</span>
+<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>
+<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="c1"># 示例 2：为 A 位中心分析构建 Pb/Sr-O 最近 12 个近邻</span>
+<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
 </code></pre></div>
-<h3 id="_4">参数（完整）</h3>
+<h3 id="_5">参数（完整）</h3>
 <ul>
 <li><code>-i, --input</code>：
   输入结构文件。默认值：<code>model.xyz</code>。</li>
@@ -2246,21 +2341,21 @@ <h3 id="_4">参数（完整）</h3>
 <li><code>-o, --output</code>：
   输出文件路径。默认值：<code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>。</li>
 </ul>
-<h3 id="_5">输出文件</h3>
+<h3 id="_6">输出文件</h3>
 <ul>
 <li>主要输出：近邻列表文本文件，例如 <code>nl-Ti-O.dat</code>。</li>
 <li>文件是一个二维整数数组，形状为 <code>(n_center, neighbor_num + 1)</code>。每一行对应一个中心原子：第一列是中心原子编号，后续列是近邻原子编号，所有编号均为 1-based。</li>
 </ul>
 <h2 id="407-calc_displacementpy">407) 从轨迹计算位移 (<code>calc_displacement.py</code>)</h2>
 <p>根据轨迹或模型结构以及近邻列表，计算局域位移矢量。</p>
-<h3 id="_6">用法</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># 示例 1：从 model.xyz 计算单帧位移</span>
-<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>disp_model.dat
-<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>
-<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="c1"># 示例 2：使用 movie.xyz 的最后 20% 帧</span>
-<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+<h3 id="_7">用法</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="c1"># 示例 1：从 model.xyz 计算单帧位移</span>
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>disp_model.dat
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>
+<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="c1"># 示例 2：使用 movie.xyz 的最后 20% 帧</span>
+<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>displacements.dat
 </code></pre></div>
-<h3 id="_7">参数（完整）</h3>
+<h3 id="_8">参数（完整）</h3>
 <ul>
 <li><code>-i, --input</code>：
   输入 xyz 文件。默认值：<code>model.xyz</code>。</li>
@@ -2278,9 +2373,9 @@ <h3 id="_7">参数（完整）</h3>
   选择末尾部分帧。
   整数表示最后 <code>N</code> 帧；
   <code>0 &lt; value &lt; 1</code> 表示最后一部分比例的帧。</li>
-<li><code>--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
+<li><code>-l/--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
 </ul>
-<h3 id="_8">输出文件</h3>
+<h3 id="_9">输出文件</h3>
 <ul>
 <li>主要输出：<code>displacements.dat</code>，或你指定的输出文件名。</li>
 <li>保存的文本文件是二维数组：对于单帧输入，形状为 <code>(n_center, 3)</code>；对于多帧输入，形状为 <code>(n_selected_frame * n_center, 3)</code>，按帧优先顺序排列。三列分别为 <code>dx</code>、<code>dy</code> 和 <code>dz</code> 位移分量，单位为 Angstrom。</li>
@@ -2288,14 +2383,14 @@ <h3 id="_8">输出文件</h3>
 <h2 id="408-calc_averaged_structurepy">408) 计算平均结构 (<code>calc_averaged_structure.py</code>)</h2>
 <p>从选定轨迹帧生成一个平均结构。
 通常可在体系平衡后使用：对于接近平衡的固体，可以对目标温度下的一段轨迹取平均，并分析该代表性结构，而不是逐帧处理每个 snapshot。</p>
-<h3 id="_9">用法</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="c1"># 示例 1：平均所有帧</span>
-<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
-<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>
-<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="c1"># 示例 2：平均选定帧范围 (100:500:2)</span>
-<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-s<span class="w"> </span><span class="m">100</span><span class="w"> </span>-t<span class="w"> </span><span class="m">500</span><span class="w"> </span>-p<span class="w"> </span><span class="m">2</span><span class="w"> </span>-o<span class="w"> </span>avg_slice.xyz
+<h3 id="_10">用法</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="c1"># 示例 1：平均所有帧</span>
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="c1"># 示例 2：平均选定帧范围 (100:500:2)</span>
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-s<span class="w"> </span><span class="m">100</span><span class="w"> </span>-t<span class="w"> </span><span class="m">500</span><span class="w"> </span>-p<span class="w"> </span><span class="m">2</span><span class="w"> </span>-o<span class="w"> </span>avg_slice.xyz
 </code></pre></div>
-<h3 id="_10">参数（完整）</h3>
+<h3 id="_11">参数（完整）</h3>
 <ul>
 <li><code>-i, --input</code>：
   输入轨迹文件。默认值：<code>movie.xyz</code>。</li>
@@ -2309,9 +2404,9 @@ <h3 id="_10">参数（完整）</h3>
   切片步长。默认值：<code>1</code>。</li>
 <li><code>-l, --last</code>：
   选择末尾帧，可以是最后 <code>N</code> 帧或最后一部分比例的帧。</li>
-<li><code>--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
+<li><code>-l/--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
 </ul>
-<h3 id="_11">输出文件</h3>
+<h3 id="_12">输出文件</h3>
 <ul>
 <li>主要输出：单帧平均结构 extxyz 文件。</li>
 <li>位置平均会相对于所选第一帧进行 MIC/PBC 修正。</li>
@@ -2319,14 +2414,14 @@ <h3 id="_11">输出文件</h3>
 <h2 id="409-calc_oct_tiltpy">409) 计算八面体倾转 (<code>calc_oct_tilt.py</code>)</h2>
 <p>根据 B-O 近邻列表计算八面体倾转角。
 该功能常用于分析 <code>ABO3</code> 体系中的八面体转动模式，例如 <code>SrTiO3</code> 和 <code>PbZrO3</code>。</p>
-<h3 id="_12">用法</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="c1"># 示例 1：从单帧结构计算 TiO6 八面体倾转</span>
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>oct_tilt_model.dat
-<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>
-<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="c1"># 示例 2：从轨迹最后 20% 帧计算 TiO6 八面体倾转</span>
-<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>octahedral_tilt.dat
+<h3 id="_13">用法</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># 示例 1：从单帧结构计算 TiO6 八面体倾转</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-o<span class="w"> </span>oct_tilt_model.dat
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="c1"># 示例 2：从轨迹最后 20% 帧计算 TiO6 八面体倾转</span>
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>octahedral_tilt.dat
 </code></pre></div>
-<h3 id="_13">参数（完整）</h3>
+<h3 id="_14">参数（完整）</h3>
 <ul>
 <li><code>-i, --input</code>：
   输入 xyz 文件。默认值：<code>model.xyz</code>。</li>
@@ -2342,25 +2437,25 @@ <h3 id="_13">参数（完整）</h3>
   切片步长。默认值：<code>1</code>。</li>
 <li><code>-l, --last</code>：
   选择末尾帧，可以是最后 <code>N</code> 帧或最后一部分比例的帧。</li>
-<li><code>--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
+<li><code>-l/--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
 </ul>
-<h3 id="_14">输出文件</h3>
+<h3 id="_15">输出文件</h3>
 <ul>
 <li>主要输出：<code>octahedral_tilt.dat</code>，或自定义输出文件名。</li>
 <li>保存的文本文件是三列二维数组，分别为 <code>theta_x</code>、<code>theta_y</code>、<code>theta_z</code>，单位为 degree。对于单帧输入，形状为 <code>(n_center, 3)</code>；对于多帧输入，形状为 <code>(n_selected_frame * n_center, 3)</code>。</li>
 </ul>
 <h2 id="410-abo3-calc_polarization_abo3py">410) 计算 ABO3 体系极化 (<code>calc_polarization_abo3.py</code>)</h2>
 <p>计算 <code>ABO3</code> 体系的局域极化矢量。</p>
-<h3 id="_15">用法</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="c1"># 示例 1：单帧 ABO3 极化</span>
-<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
-<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Sr</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-o<span class="w"> </span>polarization_model.dat
-<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>
-<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="c1"># 示例 2：选定轨迹帧范围上的极化</span>
-<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
-<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-s<span class="w"> </span><span class="m">200</span><span class="w"> </span>-t<span class="w"> </span><span class="m">600</span><span class="w"> </span>-p<span class="w"> </span><span class="m">5</span><span class="w"> </span>-o<span class="w"> </span>polarization_slice.dat
+<h3 id="_16">用法</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="c1"># 示例 1：单帧 ABO3 极化</span>
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Sr</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-o<span class="w"> </span>polarization_model.dat
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>
+<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a><span class="c1"># 示例 2：选定轨迹帧范围上的极化</span>
+<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-s<span class="w"> </span><span class="m">200</span><span class="w"> </span>-t<span class="w"> </span><span class="m">600</span><span class="w"> </span>-p<span class="w"> </span><span class="m">5</span><span class="w"> </span>-o<span class="w"> </span>polarization_slice.dat
 </code></pre></div>
-<h3 id="_16">参数（完整）</h3>
+<h3 id="_17">参数（完整）</h3>
 <ul>
 <li><code>-i, --input</code>：
   输入 xyz 文件。默认值：<code>model.xyz</code>。</li>
@@ -2381,25 +2476,25 @@ <h3 id="_16">参数（完整）</h3>
   切片步长。默认值：<code>1</code>。</li>
 <li><code>-l, --last</code>：
   选择末尾帧，可以是最后 <code>N</code> 帧或最后一部分比例的帧。</li>
-<li><code>--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
+<li><code>-l/--last</code> 与 <code>-s/-t/-p</code> 互斥。</li>
 </ul>
 <p>重要检查：</p>
 <ul>
 <li><code>--bec</code> 必须包含输入结构中的所有元素种类。</li>
 <li><code>--nl-ba</code> 和 <code>--nl-bo</code> 中的中心原子编号必须匹配。</li>
 </ul>
-<h3 id="_17">输出文件</h3>
+<h3 id="_18">输出文件</h3>
 <ul>
 <li>主要输出：<code>polarization.dat</code>，或自定义输出文件名。</li>
 <li>保存的文本文件是三列二维数组，分别为 <code>Px</code>、<code>Py</code>、<code>Pz</code>，单位为 <code>C/m^2</code>。对于单帧输入，形状为 <code>(n_center, 3)</code>；对于多帧输入，形状为 <code>(n_selected_frame * n_center, 3)</code>，按帧优先顺序排列。如果总 Born 电荷不平衡，脚本会打印 warning。</li>
 </ul>
 <h3 id="plane-grid-plt_plane_gridpy">Plane-grid 可视化 (<code>plt_plane_grid.py</code>)</h3>
 <p>你可以可视化 <code>displacements.dat</code> 或 <code>polarization.dat</code>：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># 示例 1：Ti 位点上的位移图，选择第一个 XY 层</span>
-<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span>
-<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>
-<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="c1"># 示例 2：Pb 位点上的极化图，选择 XZ 和 YZ 层</span>
-<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>polarization.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span>--select-yz<span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">4</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="c1"># 示例 1：Ti 位点上的位移图，选择第一个 XY 层</span>
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span>
+<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>
+<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a><span class="c1"># 示例 2：Pb 位点上的极化图，选择 XZ 和 YZ 层</span>
+<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-d<span class="w"> </span>polarization.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span>--select-yz<span class="w"> </span><span class="m">3</span><span class="w"> </span><span class="m">4</span>
 </code></pre></div>
 <p>参数（完整）：</p>
 <ul>
@@ -2430,10 +2525,10 @@ <h3 id="plane-grid-plt_plane_gridpy">Plane-grid 可视化 (<code>plt_plane_grid.
 <li>图片保存为 <code>XY_*.png</code>、<code>XZ_*.png</code>、<code>YZ_*.png</code>。</li>
 </ul>
 <div align="center">
-    <img src="../Gallery/PTO_STO_superlattice.png" alt="PTO_STO" width="65%" />
+    <img src="../../Gallery/PTO_STO_superlattice.png" alt="PTO_STO" width="65%" />
 </div>
 
-<h2 id="_18">输出文件一览</h2>
+<h2 id="_19">输出文件一览</h2>
 <table>
 <thead>
 <tr>
@@ -2475,95 +2570,95 @@ <h2 id="_18">输出文件一览</h2>
 </tr>
 </tbody>
 </table>
-<h2 id="_19">真实案例</h2>
+<h2 id="_20">真实案例</h2>
 <h3 id="pbtio3-">PbTiO3 的温度驱动铁电-顺电相变</h3>
 <p>假设所有文件都位于当前目录 <code>./</code>：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>./
-<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>├── model.xyz
-<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>├── 300K.xyz
-<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>├── 350K.xyz
-<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a>├── 400K.xyz
-<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>├── ...
-<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a>└── 800K.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>./
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>├── model.xyz
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>├── 300K.xyz
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a>├── 350K.xyz
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>├── 400K.xyz
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>├── ...
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a>└── 800K.xyz
 </code></pre></div>
 <p><code>model.xyz</code> 是用于进行 MD 模拟的初始结构。每个 <code>TEMP K.xyz</code> 是对应温度下的轨迹。</p>
 <h4 id="1">第 1 步：从每条轨迹的后半段得到平均结构</h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
-<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
-<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span>
-<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a><span class="k">done</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span>
+<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a><span class="k">done</span>
 </code></pre></div>
 <p>这会写出 <code>300K-avg.xyz</code>、<code>350K-avg.xyz</code>、...、<code>800K-avg.xyz</code>。</p>
 <h4 id="2-modelxyz">第 2 步：基于 <code>model.xyz</code> 构建近邻列表</h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="c1"># B-O list: for each Ti, find the nearest 6 O atoms</span>
-<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
-<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>
-<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="c1"># A-O list: for each Pb, find the nearest 12 O atoms</span>
-<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Pb-O.dat
-<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>
-<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a><span class="c1"># B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms</span>
-<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">5</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">8</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>Pb<span class="w"> </span>-o<span class="w"> </span>nl-Ti-Pb.dat
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="c1"># B-O list: for each Ti, find the nearest 6 O atoms</span>
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a>
+<a id="__codelineno-12-4" name="__codelineno-12-4" href="#__codelineno-12-4"></a><span class="c1"># A-O list: for each Pb, find the nearest 12 O atoms</span>
+<a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Pb-O.dat
+<a id="__codelineno-12-6" name="__codelineno-12-6" href="#__codelineno-12-6"></a>
+<a id="__codelineno-12-7" name="__codelineno-12-7" href="#__codelineno-12-7"></a><span class="c1"># B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms</span>
+<a id="__codelineno-12-8" name="__codelineno-12-8" href="#__codelineno-12-8"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">5</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">8</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>Pb<span class="w"> </span>-o<span class="w"> </span>nl-Ti-Pb.dat
 </code></pre></div>
 <h4 id="3">第 3 步：为每个温度计算位移和极化</h4>
 <p>这里使用 Born 有效电荷（BEC），不是名义离子电荷。对于本例中的 PbTiO3：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="n">PTO</span> <span class="o">=</span> <span class="p">{</span>
-<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>    <span class="s1">&#39;Pb&#39;</span><span class="p">:</span> <span class="mf">3.44</span><span class="p">,</span>
-<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>    <span class="s1">&#39;Ti&#39;</span><span class="p">:</span> <span class="mf">5.18</span><span class="p">,</span>
-<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a>    <span class="s1">&#39;O&#39;</span><span class="p">:</span> <span class="o">-</span><span class="p">(</span><span class="mf">3.44</span> <span class="o">+</span> <span class="mf">5.18</span><span class="p">)</span> <span class="o">/</span> <span class="mi">3</span>
-<a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="p">}</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="n">PTO</span> <span class="o">=</span> <span class="p">{</span>
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>    <span class="s1">&#39;Pb&#39;</span><span class="p">:</span> <span class="mf">3.44</span><span class="p">,</span>
+<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>    <span class="s1">&#39;Ti&#39;</span><span class="p">:</span> <span class="mf">5.18</span><span class="p">,</span>
+<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a>    <span class="s1">&#39;O&#39;</span><span class="p">:</span> <span class="o">-</span><span class="p">(</span><span class="mf">3.44</span> <span class="o">+</span> <span class="mf">5.18</span><span class="p">)</span> <span class="o">/</span> <span class="mi">3</span>
+<a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a><span class="p">}</span>
 </code></pre></div>
 <p>你可以从自己的 DFPT 计算或文献中获得 BEC。因此，可以使用以下命令计算局域位移和极化：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
-<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
-<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span>
-<a id="__codelineno-12-4" name="__codelineno-12-4" href="#__codelineno-12-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
-<a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a><span class="w">    </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">3</span>.44<span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">5</span>.18<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.8733333333<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span>
-<a id="__codelineno-12-6" name="__codelineno-12-6" href="#__codelineno-12-6"></a><span class="k">done</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span>
+<a id="__codelineno-14-4" name="__codelineno-14-4" href="#__codelineno-14-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$f</span><span class="s2">&quot;</span><span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
+<a id="__codelineno-14-5" name="__codelineno-14-5" href="#__codelineno-14-5"></a><span class="w">    </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">3</span>.44<span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">5</span>.18<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.8733333333<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span>
+<a id="__codelineno-14-6" name="__codelineno-14-6" href="#__codelineno-14-6"></a><span class="k">done</span>
 </code></pre></div>
 <h4 id="4">第 4 步：绘制实空间位移和极化图</h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
-<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
-<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp&quot;</span>
-<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol&quot;</span>
-<a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a><span class="k">done</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a><span class="k">for</span><span class="w"> </span>f<span class="w"> </span><span class="k">in</span><span class="w"> </span>*K.xyz<span class="p">;</span><span class="w"> </span><span class="k">do</span>
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="w">  </span><span class="nv">tag</span><span class="o">=</span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">f</span><span class="p">%.xyz</span><span class="si">}</span><span class="s2">&quot;</span>
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-disp&quot;</span>
+<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a><span class="w">  </span>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-avg.xyz&quot;</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol.dat&quot;</span><span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xz<span class="w"> </span><span class="m">1</span><span class="w"> </span>-o<span class="w"> </span><span class="s2">&quot;plot-</span><span class="si">${</span><span class="nv">tag</span><span class="si">}</span><span class="s2">-pol&quot;</span>
+<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a><span class="k">done</span>
 </code></pre></div>
 <h4 id="5-">第 5 步：构建温度-序参量曲线</h4>
 <p>结合每个温度平均结构的晶格信息和极化文件（<code>XX-pol.dat</code>）进行分析，可以得到如下图：</p>
 <div align="center">
-    <img src="../Gallery/PTO-temp.png" alt="PTO-temp" width="65%" />
+    <img src="../../Gallery/PTO-temp.png" alt="PTO-temp" width="65%" />
 </div>
 
 <p>该趋势显示在约 <code>600 K</code> 附近发生明显相变，此时极化消失。</p>
 <h3 id="pbtio3srtio3">PbTiO3/SrTiO3 超晶格中的拓扑结构</h3>
 <p>假设 <code>movie.xyz</code> 是当前目录下 PbTiO3/SrTiO3 超晶格的轨迹。</p>
 <h4 id="1-25">第 1 步：使用最后 25% 帧构建平均结构</h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>model-avg.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>model-avg.xyz
 </code></pre></div>
 <h4 id="2-ti">第 2 步：构建 Ti 近邻列表</h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
 </code></pre></div>
 <h4 id="3-plane-grid">第 3 步：绘制 plane-grid 图</h4>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>disp-last25.dat
-<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-d<span class="w"> </span>disp-last25.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span>-o<span class="w"> </span>plot-topology
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span>-o<span class="w"> </span>disp-last25.dat
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>model-avg.xyz<span class="w"> </span>-d<span class="w"> </span>disp-last25.dat<span class="w"> </span>-e<span class="w"> </span>Ti<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span>-o<span class="w"> </span>plot-topology
 </code></pre></div>
 <div align="center">
-    <img src="../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
+    <img src="../../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
 </div>
 
-<p>这会得到与前面展示相似的图。在 PTO 区域可以看到类似涡旋的极化图样，而 STO 区域的极化接近于零。通过分析涡旋核附近极化的变化，可以估计局域介电响应，但这超出了本教程范围。</p>
-<p>注意：该图使用的 colormap 与 GPUMDkit 默认绘图风格不同。默认输出不会与图中完全一致，但可以通过少量修改绘图脚本获得这种风格。</p>
-<h3 id="_20">其他体系</h3>
+<p>这会得到与前面展示相似的图。在 PTO 区域可以看到类似涡旋的极化图样，而 STO 区域的极化接近于零。</p>
+<p>注意：示例图使用了自定义 colormap。GPUMDkit 默认输出使用不同风格，可通过修改绘图脚本进行调整。</p>
+<h3 id="_21">其他体系</h3>
 <h4 id="-">有机-无机杂化铁电体</h4>
 <p>在许多有机-无机铁电体中，极化与各向异性的分子单元密切相关。跟踪分子取向的一种实用方法是使用键矢量。</p>
 <p>对于 TMCM-CdCl3，可以使用 TMCM 分子中的 C-Cl 键方向作为取向代理，并据此估计极化态：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a><span class="c1"># Find the nearest Cl around each C (tune cutoff if needed)</span>
-<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">3</span><span class="w"> </span>-n<span class="w"> </span><span class="m">1</span><span class="w"> </span>-C<span class="w"> </span>C<span class="w"> </span>-E<span class="w"> </span>Cl<span class="w"> </span>-o<span class="w"> </span>nl-C-Cl.dat
-<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>
-<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a><span class="c1"># Compute C-Cl bond vectors from the trajectory</span>
-<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-C-Cl.dat<span class="w"> </span>-o<span class="w"> </span>ccl_vectors.dat
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a><span class="c1"># Find the nearest Cl around each C (tune cutoff if needed)</span>
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">3</span><span class="w"> </span>-n<span class="w"> </span><span class="m">1</span><span class="w"> </span>-C<span class="w"> </span>C<span class="w"> </span>-E<span class="w"> </span>Cl<span class="w"> </span>-o<span class="w"> </span>nl-C-Cl.dat
+<a id="__codelineno-19-3" name="__codelineno-19-3" href="#__codelineno-19-3"></a>
+<a id="__codelineno-19-4" name="__codelineno-19-4" href="#__codelineno-19-4"></a><span class="c1"># Compute C-Cl bond vectors from the trajectory</span>
+<a id="__codelineno-19-5" name="__codelineno-19-5" href="#__codelineno-19-5"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-C-Cl.dat<span class="w"> </span>-o<span class="w"> </span>ccl_vectors.dat
 </code></pre></div>
 <p>随后可以把 <code>ccl_vectors.dat</code> 作为取向序参量进行分析。更多细节可参考：Phys. Rev. Lett. 136, 016801。</p>
-<h4 id="_21">其他铁电材料家族</h4>
+<h4 id="_22">其他铁电材料家族</h4>
 <p>除 <code>ABO3</code> 外，<code>ferrodispcalc</code> 也可以适配许多铁电体系，包括氮化物、氧化铪基化合物、有机-无机杂化体系以及部分二维铁电材料。</p>
 
 
diff --git "a/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html" "b/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html"
index 6836600..e1819d1 100644
--- "a/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html"
+++ "b/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html"
@@ -938,7 +938,7 @@
   <a href="#_1" class="md-nav__link">
     <span class="md-ellipsis">
       
-        支持的格式
+        功能简介
       
     </span>
   </a>
@@ -947,6 +947,28 @@
       
         <li class="md-nav__item">
   <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        准备工作
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        支持的格式
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
         交互模式
@@ -958,7 +980,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
+  <a href="#_5" class="md-nav__link">
     <span class="md-ellipsis">
       
         每个入口的作用
@@ -974,7 +996,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
+  <a href="#_6" class="md-nav__link">
     <span class="md-ellipsis">
       
         快速命令表
@@ -985,7 +1007,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
+  <a href="#_7" class="md-nav__link">
     <span class="md-ellipsis">
       
         常见例子
@@ -1024,7 +1046,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
+  <a href="#_8" class="md-nav__link">
     <span class="md-ellipsis">
       
         常用脚本说明
@@ -1080,7 +1102,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
+  <a href="#_9" class="md-nav__link">
     <span class="md-ellipsis">
       
         添加权重
@@ -1091,7 +1113,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_8" class="md-nav__link">
+  <a href="#_10" class="md-nav__link">
     <span class="md-ellipsis">
       
         扩胞
@@ -1099,6 +1121,50 @@
     </span>
   </a>
   
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_11" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        提取单帧
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        拆分多帧 extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#mtp" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MTP 转换
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#abacus" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        ABACUS 转换
+      
+    </span>
+  </a>
+  
 </li>
         
       </ul>
@@ -1107,7 +1173,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_9" class="md-nav__link">
+  <a href="#_12" class="md-nav__link">
     <span class="md-ellipsis">
       
         常见问题
@@ -1118,7 +1184,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_10" class="md-nav__link">
+  <a href="#_13" class="md-nav__link">
     <span class="md-ellipsis">
       
         说明
@@ -1424,7 +1490,7 @@
   <a href="#_1" class="md-nav__link">
     <span class="md-ellipsis">
       
-        支持的格式
+        功能简介
       
     </span>
   </a>
@@ -1433,6 +1499,28 @@
       
         <li class="md-nav__item">
   <a href="#_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        准备工作
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        支持的格式
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
         交互模式
@@ -1444,7 +1532,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
+  <a href="#_5" class="md-nav__link">
     <span class="md-ellipsis">
       
         每个入口的作用
@@ -1460,7 +1548,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
+  <a href="#_6" class="md-nav__link">
     <span class="md-ellipsis">
       
         快速命令表
@@ -1471,7 +1559,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
+  <a href="#_7" class="md-nav__link">
     <span class="md-ellipsis">
       
         常见例子
@@ -1510,7 +1598,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
+  <a href="#_8" class="md-nav__link">
     <span class="md-ellipsis">
       
         常用脚本说明
@@ -1566,7 +1654,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
+  <a href="#_9" class="md-nav__link">
     <span class="md-ellipsis">
       
         添加权重
@@ -1577,7 +1665,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_8" class="md-nav__link">
+  <a href="#_10" class="md-nav__link">
     <span class="md-ellipsis">
       
         扩胞
@@ -1585,6 +1673,50 @@
     </span>
   </a>
   
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#_11" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        提取单帧
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#extxyz" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        拆分多帧 extxyz
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#mtp" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        MTP 转换
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#abacus" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        ABACUS 转换
+      
+    </span>
+  </a>
+  
 </li>
         
       </ul>
@@ -1593,7 +1725,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_9" class="md-nav__link">
+  <a href="#_12" class="md-nav__link">
     <span class="md-ellipsis">
       
         常见问题
@@ -1604,7 +1736,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_10" class="md-nav__link">
+  <a href="#_13" class="md-nav__link">
     <span class="md-ellipsis">
       
         说明
@@ -1639,8 +1771,12 @@ <h1>🔄 格式转换</h1>
   <p style="text-align: justify;">格式转换模块用于在常见原子模拟文件格式之间转换，同时提供 group 标签、权重、帧提取等元数据处理功能。</p>
 </div>
 
+<h2 id="_1">功能简介</h2>
+<p>本模块在计算材料科学中常用的结构和轨迹文件格式之间进行转换。支持 VASP、LAMMPS、CP2K、ABACUS、CIF、ASE 轨迹和 extxyz 格式。还提供添加 group 标签、权重、提取帧和扩胞等工具。</p>
+<h2 id="_2">准备工作</h2>
 <p><strong>脚本位置：</strong> <code>Scripts/format_conversion/</code></p>
-<h2 id="_1">支持的格式</h2>
+<p>确保已安装 GPUMDkit。安装说明请参见<a href="%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html">快速入门</a>。</p>
+<h2 id="_3">支持的格式</h2>
 <ul>
 <li><strong>VASP</strong>：<code>POSCAR</code>、<code>CONTCAR</code>、<code>OUTCAR</code>、<code>XDATCAR</code></li>
 <li><strong>LAMMPS</strong>：data 文件和 dump 轨迹</li>
@@ -1650,7 +1786,7 @@ <h2 id="_1">支持的格式</h2>
 <li><strong>ASE trajectory</strong>：<code>.traj</code></li>
 <li><strong>extxyz</strong>：GPUMD 和 NEP 常用的结构格式</li>
 </ul>
-<h2 id="_2">交互模式</h2>
+<h2 id="_4">交互模式</h2>
 <p>打开 GPUMDkit：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh
 </code></pre></div>
@@ -1676,7 +1812,7 @@ <h2 id="_2">交互模式</h2>
 <a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a>+-------------------------------------------------------------+
 <a id="__codelineno-2-17" name="__codelineno-2-17" href="#__codelineno-2-17"></a>Input the function number or converter keyword:
 </code></pre></div>
-<h3 id="_3">每个入口的作用</h3>
+<h3 id="_5">每个入口的作用</h3>
 <table>
 <thead>
 <tr>
@@ -1778,7 +1914,7 @@ <h3 id="_3">每个入口的作用</h3>
 </tr>
 </tbody>
 </table>
-<h2 id="_4">快速命令表</h2>
+<h2 id="_6">快速命令表</h2>
 <table>
 <thead>
 <tr>
@@ -1838,17 +1974,23 @@ <h2 id="_4">快速命令表</h2>
 <td>extxyz</td>
 <td><code>gpumdkit.sh -traj2exyz input.traj output.xyz</code></td>
 </tr>
+<tr>
+<td>extxyz</td>
+<td>clean extxyz</td>
+<td><code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code></td>
+</tr>
 </tbody>
 </table>
-<h2 id="_5">常见例子</h2>
+<h2 id="_7">常见例子</h2>
 <h3 id="vasp">转换 VASP 结果</h3>
-<p>如果每个计算目录下都有 <code>OUTCAR</code>：</p>
+<p><strong>功能：</strong> 在目录中搜索 VASP OUTCAR 文件，并将它们转换为单个 extxyz 文件，用于 NEP 训练或分析。</p>
+<p><strong>命令行模式：</strong></p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-out2xyz<span class="w"> </span>./vasp_results/
 </code></pre></div>
 <p>也可以使用 Python 版本：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-out2exyz<span class="w"> </span>./vasp_results/
 </code></pre></div>
-<p>在交互模式中选择 <code>101</code>，会看到：</p>
+<p><strong>交互模式：</strong> 在格式转换菜单中选择 <code>101</code>，会看到：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>&gt;-------------------------------------------------&lt;
 <a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>| Calling the script in Scripts/format_conversion |
 <a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>| Script: out2xyz.sh                              |
@@ -1858,12 +2000,14 @@ <h3 id="vasp">转换 VASP 结果</h3>
 <a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>Example: ./
 <a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a>------------&gt;&gt;
 </code></pre></div>
+<p><strong>输出：</strong> 包含转换后结构的 extxyz 文件，可用于 NEP 训练或进一步分析。</p>
 <h3 id="group">添加 group 标签</h3>
-<p>一些 GPUMD 相关流程会使用 group 标签进行原子分组，例如特定元素的 MSD 或扩散性质计算。</p>
+<p><strong>功能：</strong> 为结构文件添加原子 group 标签。一些 GPUMD 相关流程需要 group 标签，例如特定元素的 MSD 或扩散性质计算。</p>
+<p><strong>命令行模式：</strong></p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
 </code></pre></div>
 <p>该命令读取输入结构，并写出带 group 信息的 extxyz 文件。</p>
-<p>在交互模式中选择 <code>106</code>，会看到：</p>
+<p><strong>交互模式：</strong> 在格式转换菜单中选择 <code>106</code>，会看到：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>&gt;-------------------------------------------------&lt;
 <a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>| Calling the script in Scripts/format_conversion |
 <a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>| Script: add_groups.py                           |
@@ -1873,7 +2017,8 @@ <h3 id="group">添加 group 标签</h3>
 <a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a>Example: POSCAR Li Y Cl
 <a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>------------&gt;&gt;
 </code></pre></div>
-<h2 id="_6">常用脚本说明</h2>
+<p><strong>输出：</strong> 添加了 group 标签的 extxyz 文件。</p>
+<h2 id="_8">常用脚本说明</h2>
 <h3 id="poscar-extxyz">POSCAR 转 extxyz</h3>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
 </code></pre></div>
@@ -1906,16 +2051,43 @@ <h3 id="cif">CIF 转换</h3>
 <a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>gpumdkit.sh<span class="w"> </span>-cif2exyz<span class="w"> </span>input.cif<span class="w"> </span>model.xyz
 </code></pre></div>
 <p>如果后续需要 VASP 计算，使用 <code>-cif2pos</code>；如果后续要进入 GPUMDkit 分析，使用 <code>-cif2exyz</code>。</p>
-<h3 id="_7">添加权重</h3>
+<h3 id="_9">添加权重</h3>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-addweight<span class="w"> </span>train.xyz<span class="w"> </span>train_weighted.xyz<span class="w"> </span><span class="m">5</span>
 </code></pre></div>
 <p>用于给训练集结构添加或修改权重。</p>
-<h3 id="_8">扩胞</h3>
+<h3 id="_10">扩胞</h3>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-replicate<span class="w"> </span>POSCAR<span class="w"> </span>supercell.vasp<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">2</span>
 <a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-replicate<span class="w"> </span>POSCAR<span class="w"> </span>supercell.vasp<span class="w"> </span><span class="m">256</span>
 </code></pre></div>
 <p>第一种按晶胞倍数扩胞，第二种按目标原子数自动选择扩胞方式。</p>
-<h2 id="_9">常见问题</h2>
+<h3 id="_11">提取单帧</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-get_frame<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">1000</span>
+</code></pre></div>
+<p>从 extxyz 轨迹中提取第 <code>1000</code> 帧（索引从 0 开始）。</p>
+<h3 id="extxyz">拆分多帧 extxyz</h3>
+<p><code>split_single_xyz.py</code> 将多帧 extxyz 文件拆分为单帧文件。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>python<span class="w"> </span>Scripts/format_conversion/split_single_xyz.py<span class="w"> </span>dump.xyz
+</code></pre></div>
+<p>生成 <code>model_0.xyz</code>、<code>model_1.xyz</code>、... 等单帧文件。</p>
+<h3 id="mtp">MTP 转换</h3>
+<p>将 MTP <code>.cfg</code> 格式转换为 extxyz：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w">    </span><span class="c1"># 选择：1) 格式转换 → 102</span>
+</code></pre></div>
+<p>交互提示：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;
+<a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a>Example: train.cfg Pd Ag
+<a id="__codelineno-20-3" name="__codelineno-20-3" href="#__codelineno-20-3"></a>------------&gt;&gt;
+</code></pre></div>
+<h3 id="abacus">ABACUS 转换</h3>
+<p>将 ABACUS 输出转换为 extxyz：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w">    </span><span class="c1"># 选择：1) 格式转换 → 104</span>
+</code></pre></div>
+<p>菜单提供两个选项：</p>
+<ol>
+<li>SCF 输出（<code>running_scf.log</code>）</li>
+<li>MD 输出（<code>running_md.log</code>）</li>
+</ol>
+<h2 id="_12">常见问题</h2>
 <table>
 <thead>
 <tr>
@@ -1938,7 +2110,7 @@ <h2 id="_9">常见问题</h2>
 </tr>
 </tbody>
 </table>
-<h2 id="_10">说明</h2>
+<h2 id="_13">说明</h2>
 <p>如果某个转换脚本缺少所需 Python 包，运行该功能时 Python 会给出相应提示。</p>
 
 
diff --git "a/docs/htmls/zh/\347\273\223\346\236\204\351\207\207\346\240\267.html" "b/docs/htmls/zh/\347\273\223\346\236\204\351\207\207\346\240\267.html"
index 9b42df7..7fd034e 100644
--- "a/docs/htmls/zh/\347\273\223\346\236\204\351\207\207\346\240\267.html"
+++ "b/docs/htmls/zh/\347\273\223\346\236\204\351\207\207\346\240\267.html"
@@ -1004,6 +1004,45 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="PyNEP 旧入口">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#pynep_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        串行 PyNEP
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#pynep_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        并行 PyNEP
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gpumdkit" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        GPUMDkit 入口
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1032,7 +1071,7 @@
   <a href="#_5" class="md-nav__link">
     <span class="md-ellipsis">
       
-        示例命令
+        帧范围提取
       
     </span>
   </a>
@@ -1041,6 +1080,17 @@
       
         <li class="md-nav__item">
   <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例命令
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
     <span class="md-ellipsis">
       
         常见问题
@@ -1356,6 +1406,45 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="PyNEP 旧入口">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#pynep_1" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        串行 PyNEP
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#pynep_2" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        并行 PyNEP
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gpumdkit" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        GPUMDkit 入口
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1384,7 +1473,7 @@
   <a href="#_5" class="md-nav__link">
     <span class="md-ellipsis">
       
-        示例命令
+        帧范围提取
       
     </span>
   </a>
@@ -1393,6 +1482,17 @@
       
         <li class="md-nav__item">
   <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        示例命令
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
     <span class="md-ellipsis">
       
         常见问题
@@ -1578,7 +1678,7 @@ <h2 id="neptrain-fps">NepTrain FPS</h2>
 </code></pre></div>
 <p>该功能需要 <code>NepTrain</code>，运行时会提示相关引用。</p>
 <h2 id="pynep">PyNEP 旧入口</h2>
-<p>PyNEP FPS 仍然保留兼容，但只通过 <code>-pynep</code> 入口调用：</p>
+<p>PyNEP FPS 仍然保留兼容，但只通过 <code>-pynep</code> 入口调用。</p>
 <p>如果在交互菜单中选择 <code>202</code>，会看到：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>+-------------------------------------------------+
 <a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>| Function 202 is no longer supported here.       |
@@ -1588,20 +1688,28 @@ <h2 id="pynep">PyNEP 旧入口</h2>
 <a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a>|                 gpumdkit.sh -pynep              |
 <a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a>+-------------------------------------------------+
 </code></pre></div>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pynep
+<h3 id="pynep_1">串行 PyNEP</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>python<span class="w"> </span>Scripts/sample_structures/pynep_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
+</code></pre></div>
+<h3 id="pynep_2">并行 PyNEP</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>python<span class="w"> </span>Scripts/sample_structures/parallel_pynep_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt<span class="w"> </span><span class="m">8</span>
+</code></pre></div>
+<p>最后一个参数是 CPU 线程数。</p>
+<h3 id="gpumdkit">GPUMDkit 入口</h3>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-pynep
 </code></pre></div>
 <p>随后输入：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>dump.xyz train.xyz nep.txt 8
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>dump.xyz train.xyz nep.txt 8
 </code></pre></div>
 <p>这个入口需要 <code>pynep</code>。</p>
 <h2 id="_3">结构扰动</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>python<span class="w"> </span>Scripts/sample_structures/perturb_structure.py<span class="w"> </span>POSCAR<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">0</span>.03<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>uniform
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>python<span class="w"> </span>Scripts/sample_structures/perturb_structure.py<span class="w"> </span>POSCAR<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">0</span>.03<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>uniform
 </code></pre></div>
 <p>交互模式选择 <code>204</code>，会看到：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;
-<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>The default parameters for perturb are 20 0.03 0.2 uniform
-<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>Example: POSCAR 20 0.03 0.2 uniform
-<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a>------------&gt;&gt;
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>The default parameters for perturb are 20 0.03 0.2 uniform
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a>Example: POSCAR 20 0.03 0.2 uniform
+<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a>------------&gt;&gt;
 </code></pre></div>
 <p>参数含义：</p>
 <table>
@@ -1638,18 +1746,18 @@ <h2 id="_3">结构扰动</h2>
 <ul>
 <li><code>POSCAR_01.vasp</code>、<code>POSCAR_02.vasp</code> 等</li>
 </ul>
-<p>该功能需要 <code>dpdata</code>。</p>
+<p>该功能需要 <code>dpdata</code>。使用此功能时建议引用 dpdata 包。</p>
 <h2 id="_4">最大力偏差结构选择</h2>
 <p>该功能需要配合 GPUMD 的 <code>active</code> 命令使用。<code>active</code> 通过委员会评审机制，让多条势函数对同一结构进行预测，并记录每个结构的最大力偏差。<code>select_max_modev.py</code> 会从 <code>active.out</code> 和 <code>active.xyz</code> 中选择力偏差较大的结构，写入 <code>selected.xyz</code>。</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>python<span class="w"> </span>Scripts/sample_structures/select_max_modev.py<span class="w"> </span><span class="m">200</span><span class="w"> </span><span class="m">0</span>.15
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>python<span class="w"> </span>Scripts/sample_structures/select_max_modev.py<span class="w"> </span><span class="m">200</span><span class="w"> </span><span class="m">0</span>.15
 </code></pre></div>
 <p>交互模式选择 <code>205</code>，会看到：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>+----------------------------------------------------+
-<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>| Select max force deviation structs from active.xyz |
-<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a>|     generated by the active command in gpumd.      |
-<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a>+----------------------------------------------------+
-<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a>Input &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)
-<a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a>------------&gt;&gt;
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>+----------------------------------------------------+
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>| Select max force deviation structs from active.xyz |
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>|     generated by the active command in gpumd.      |
+<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a>+----------------------------------------------------+
+<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a>Input &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)
+<a id="__codelineno-17-6" name="__codelineno-17-6" href="#__codelineno-17-6"></a>------------&gt;&gt;
 </code></pre></div>
 <p>需要当前目录下有：</p>
 <ul>
@@ -1660,12 +1768,17 @@ <h2 id="_4">最大力偏差结构选择</h2>
 <ul>
 <li><code>selected.xyz</code></li>
 </ul>
-<h2 id="_5">示例命令</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
-<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
-<a id="__codelineno-16-3" name="__codelineno-16-3" href="#__codelineno-16-3"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
+<h2 id="_5">帧范围提取</h2>
+<p>提取轨迹的一部分帧：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>python<span class="w"> </span>Scripts/sample_structures/frame_range.py<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span>.8
+</code></pre></div>
+<p>这会写入轨迹 0% 到 80% 的帧。</p>
+<h2 id="_6">示例命令</h2>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
+<a id="__codelineno-19-3" name="__codelineno-19-3" href="#__codelineno-19-3"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
 </code></pre></div>
-<h2 id="_6">常见问题</h2>
+<h2 id="_7">常见问题</h2>
 <table>
 <thead>
 <tr>
diff --git "a/docs/htmls/zh/\347\273\230\345\233\276\350\204\232\346\234\254.html" "b/docs/htmls/zh/\347\273\230\345\233\276\350\204\232\346\234\254.html"
index 7089eac..12209da 100644
--- "a/docs/htmls/zh/\347\273\230\345\233\276\350\204\232\346\234\254.html"
+++ "b/docs/htmls/zh/\347\273\230\345\233\276\350\204\232\346\234\254.html"
@@ -1098,10 +1098,126 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
+  <a href="#plt_trainpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_train.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_predictionpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_prediction.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_train_testpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_train_test.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_parity_densitypy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_parity_density.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_force_errorspy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_force_errors.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_learning_ratepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_learning_rate.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_nep_restartpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_nep_restart.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_chargepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_charge.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_born_chargepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_born_charge.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
   <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
-        训练结果
+        热力学量
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="热力学量">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_thermopy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_thermo.py
       
     </span>
   </a>
@@ -1109,10 +1225,38 @@
 </li>
         
           <li class="md-nav__item">
+  <a href="#plt_thermo2py-plt_thermo3py" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_thermo2.py &amp; plt_thermo3.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
   <a href="#_3" class="md-nav__link">
     <span class="md-ellipsis">
       
-        预测结果
+        扩散和离子输运
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="扩散和离子输运">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_msdpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_msd.py
       
     </span>
   </a>
@@ -1120,10 +1264,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
+  <a href="#plt_msd_allpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        训练/测试集对比
+        plt_msd_all.py
       
     </span>
   </a>
@@ -1131,10 +1275,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#parity-plot" class="md-nav__link">
+  <a href="#plt_msd_convergence_checkpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        密度 parity plot
+        plt_msd_convergence_check.py
       
     </span>
   </a>
@@ -1142,10 +1286,21 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
+  <a href="#plt_sdcpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_sdc.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_arrhenius_dpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        力误差分析
+        plt_arrhenius_d.py
       
     </span>
   </a>
@@ -1153,10 +1308,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#born" class="md-nav__link">
+  <a href="#plt_arrhenius_sigmapy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        电荷和 Born 有效电荷
+        plt_arrhenius_sigma.py
       
     </span>
   </a>
@@ -1169,22 +1324,22 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#md" class="md-nav__link">
+  <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
-        MD 和结构分析绘图
+        热输运
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="MD 和结构分析绘图">
+    <nav class="md-nav" aria-label="热输运">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
+  <a href="#plt_emdpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        热力学量
+        plt_emd.py
       
     </span>
   </a>
@@ -1192,10 +1347,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#rdf" class="md-nav__link">
+  <a href="#plt_nemdpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        RDF
+        plt_nemd.py
       
     </span>
   </a>
@@ -1203,10 +1358,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#vac-pdos" class="md-nav__link">
+  <a href="#plt_hnemdpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        VAC 和 PDOS
+        plt_hnemd.py
       
     </span>
   </a>
@@ -1219,25 +1374,103 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
+  <a href="#_5" class="md-nav__link">
     <span class="md-ellipsis">
       
-        扩散和离子输运
+        结构分析
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="结构分析">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_rdfpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_rdf.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_rdf_pmfpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_rdf_pmf.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_vacpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_vac.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_cohesivepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_cohesive.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_net_forcepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_net_force.py
       
     </span>
   </a>
   
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
-  <a href="#_8" class="md-nav__link">
+  <a href="#_6" class="md-nav__link">
     <span class="md-ellipsis">
       
-        热输运
+        声子
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="声子">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_pdospy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_pdos.py
       
     </span>
   </a>
   
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1253,10 +1486,10 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_9" class="md-nav__link">
+  <a href="#plt_descriptorspy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        描述符可视化
+        plt_descriptors.py
       
     </span>
   </a>
@@ -1264,10 +1497,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#dimer_1" class="md-nav__link">
+  <a href="#plt_descriptors_comparepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Dimer 曲线
+        plt_descriptors_compare.py
       
     </span>
   </a>
@@ -1275,10 +1508,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#doas" class="md-nav__link">
+  <a href="#plt_dimerpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        DOAS
+        plt_dimer.py
       
     </span>
   </a>
@@ -1286,10 +1519,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#net-force" class="md-nav__link">
+  <a href="#plt_doaspy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Net force
+        plt_doas.py
       
     </span>
   </a>
@@ -1302,10 +1535,21 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_10" class="md-nav__link">
+  <a href="#plane-grid" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        极性材料的 Plane-Grid 绘图
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
     <span class="md-ellipsis">
       
-        快速表
+        快速参考表
       
     </span>
   </a>
@@ -1488,10 +1732,10 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_2" class="md-nav__link">
+  <a href="#plt_trainpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        训练结果
+        plt_train.py
       
     </span>
   </a>
@@ -1499,10 +1743,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
+  <a href="#plt_predictionpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        预测结果
+        plt_prediction.py
       
     </span>
   </a>
@@ -1510,10 +1754,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
+  <a href="#plt_train_testpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        训练/测试集对比
+        plt_train_test.py
       
     </span>
   </a>
@@ -1521,10 +1765,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#parity-plot" class="md-nav__link">
+  <a href="#plt_parity_densitypy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        密度 parity plot
+        plt_parity_density.py
       
     </span>
   </a>
@@ -1532,10 +1776,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
+  <a href="#plt_force_errorspy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        力误差分析
+        plt_force_errors.py
       
     </span>
   </a>
@@ -1543,38 +1787,21 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#born" class="md-nav__link">
+  <a href="#plt_learning_ratepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        电荷和 Born 有效电荷
+        plt_learning_rate.py
       
     </span>
   </a>
   
 </li>
         
-      </ul>
-    </nav>
-  
-</li>
-      
-        <li class="md-nav__item">
-  <a href="#md" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        MD 和结构分析绘图
-      
-    </span>
-  </a>
-  
-    <nav class="md-nav" aria-label="MD 和结构分析绘图">
-      <ul class="md-nav__list">
-        
           <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
+  <a href="#plt_nep_restartpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        热力学量
+        plt_nep_restart.py
       
     </span>
   </a>
@@ -1582,10 +1809,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#rdf" class="md-nav__link">
+  <a href="#plt_chargepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        RDF
+        plt_charge.py
       
     </span>
   </a>
@@ -1593,10 +1820,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#vac-pdos" class="md-nav__link">
+  <a href="#plt_born_chargepy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        VAC 和 PDOS
+        plt_born_charge.py
       
     </span>
   </a>
@@ -1609,44 +1836,61 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
+  <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
-        扩散和离子输运
+        热力学量
       
     </span>
   </a>
   
-</li>
-      
-        <li class="md-nav__item">
-  <a href="#_8" class="md-nav__link">
+    <nav class="md-nav" aria-label="热力学量">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_thermopy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        热输运
+        plt_thermo.py
       
     </span>
   </a>
   
 </li>
-      
-        <li class="md-nav__item">
-  <a href="#dimer" class="md-nav__link">
+        
+          <li class="md-nav__item">
+  <a href="#plt_thermo2py-plt_thermo3py" class="md-nav__link">
     <span class="md-ellipsis">
       
-        描述符、Dimer 和其他分析
+        plt_thermo2.py &amp; plt_thermo3.py
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="描述符、Dimer 和其他分析">
-      <ul class="md-nav__list">
+</li>
         
-          <li class="md-nav__item">
-  <a href="#_9" class="md-nav__link">
-    <span class="md-ellipsis">
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        扩散和离子输运
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="扩散和离子输运">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_msdpy" class="md-nav__link">
+    <span class="md-ellipsis">
       
-        描述符可视化
+        plt_msd.py
       
     </span>
   </a>
@@ -1654,10 +1898,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#dimer_1" class="md-nav__link">
+  <a href="#plt_msd_allpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Dimer 曲线
+        plt_msd_all.py
       
     </span>
   </a>
@@ -1665,10 +1909,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#doas" class="md-nav__link">
+  <a href="#plt_msd_convergence_checkpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        DOAS
+        plt_msd_convergence_check.py
       
     </span>
   </a>
@@ -1676,10 +1920,32 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#net-force" class="md-nav__link">
+  <a href="#plt_sdcpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Net force
+        plt_sdc.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_arrhenius_dpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_arrhenius_d.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_arrhenius_sigmapy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_arrhenius_sigma.py
       
     </span>
   </a>
@@ -1692,10 +1958,232 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_10" class="md-nav__link">
+  <a href="#_4" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        热输运
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="热输运">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_emdpy" class="md-nav__link">
     <span class="md-ellipsis">
       
-        快速表
+        plt_emd.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_nemdpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_nemd.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_hnemdpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_hnemd.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_5" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        结构分析
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="结构分析">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_rdfpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_rdf.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_rdf_pmfpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_rdf_pmf.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_vacpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_vac.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_cohesivepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_cohesive.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_net_forcepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_net_force.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_6" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        声子
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="声子">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_pdospy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_pdos.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#dimer" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        描述符、Dimer 和其他分析
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="描述符、Dimer 和其他分析">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#plt_descriptorspy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_descriptors.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_descriptors_comparepy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_descriptors_compare.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_dimerpy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_dimer.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#plt_doaspy" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        plt_doas.py
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#plane-grid" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        极性材料的 Plane-Grid 绘图
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#_7" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        快速参考表
       
     </span>
   </a>
@@ -1724,159 +2212,452 @@
 
 <div align="center">
   <h1>📊 绘图脚本</h1>
-  <p style="text-align: justify;">绘图模块用于可视化 GPUMD、NEP 和 GPUMDkit 计算器产生的数据。</p>
+  <p style="text-align: justify;">绘图模块包含一系列 Python 脚本，用于可视化 GPUMD、NEP 和 GPUMDkit 计算器产生的数据。所有图表均可交互显示或保存为高分辨率 PNG 文件。</p>
 </div>
 
 <p><strong>脚本位置：</strong> <code>Scripts/plt_scripts/</code></p>
 <h2 id="_1">快速入口</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-plt
-<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;
-<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>save
-<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>-h
+<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w">              </span><span class="c1"># 显示所有绘图选项</span>
+<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w">       </span><span class="c1"># 生成指定图表</span>
+<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>save<span class="w">  </span><span class="c1"># 保存为 PNG</span>
+<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span>-h<span class="w">    </span><span class="c1"># 显示特定图表的帮助</span>
 </code></pre></div>
+<p>运行 <code>gpumdkit.sh -plt</code> 会显示绘图命令菜单：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |
+<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |
+<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>|                                    NEP Training &amp; Evaluation                                  |
+<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a>|  train          - NEP training results           prediction     - NEP prediction results      |
+<a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a>|  train_test     - NEP train and test results     parity_density - Parity density plot         |
+<a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a>|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |
+<a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a>|  charge         - Charge distribution            born_charge    - Born effective charges      |
+<a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a>|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |
+<a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a>|  des            - Descriptors                    lr             - Learning rate for gnep      |
+<a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a>|                                     Diffusion &amp; Transport                                     |
+<a id="__codelineno-1-16" name="__codelineno-1-16" href="#__codelineno-1-16"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-17" name="__codelineno-1-17" href="#__codelineno-1-17"></a>|  msd            - Mean square displacement       msd_conv       - MSD convergence             |
+<a id="__codelineno-1-18" name="__codelineno-1-18" href="#__codelineno-1-18"></a>|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |
+<a id="__codelineno-1-19" name="__codelineno-1-19" href="#__codelineno-1-19"></a>|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|
+<a id="__codelineno-1-20" name="__codelineno-1-20" href="#__codelineno-1-20"></a>|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |
+<a id="__codelineno-1-21" name="__codelineno-1-21" href="#__codelineno-1-21"></a>|  D_xyz          - Directional Arrhenius D                                                     |
+<a id="__codelineno-1-22" name="__codelineno-1-22" href="#__codelineno-1-22"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-23" name="__codelineno-1-23" href="#__codelineno-1-23"></a>|                                    MD &amp; Structural Analysis                                   |
+<a id="__codelineno-1-24" name="__codelineno-1-24" href="#__codelineno-1-24"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-25" name="__codelineno-1-25" href="#__codelineno-1-25"></a>|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |
+<a id="__codelineno-1-26" name="__codelineno-1-26" href="#__codelineno-1-26"></a>|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
+<a id="__codelineno-1-27" name="__codelineno-1-27" href="#__codelineno-1-27"></a>|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
+<a id="__codelineno-1-28" name="__codelineno-1-28" href="#__codelineno-1-28"></a>|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
+<a id="__codelineno-1-29" name="__codelineno-1-29" href="#__codelineno-1-29"></a>|  doas           - Density of atomistic states                                                 |
+<a id="__codelineno-1-30" name="__codelineno-1-30" href="#__codelineno-1-30"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-31" name="__codelineno-1-31" href="#__codelineno-1-31"></a>|                                        Heat Transport                                         |
+<a id="__codelineno-1-32" name="__codelineno-1-32" href="#__codelineno-1-32"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-33" name="__codelineno-1-33" href="#__codelineno-1-33"></a>|  emd            - EMD results                    nemd           - NEMD results                |
+<a id="__codelineno-1-34" name="__codelineno-1-34" href="#__codelineno-1-34"></a>|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |
+<a id="__codelineno-1-35" name="__codelineno-1-35" href="#__codelineno-1-35"></a>+-----------------------------------------------------------------------------------------------+
+</code></pre></div>
+<hr />
 <h2 id="nep">NEP 训练与预测</h2>
-<h3 id="_2">训练结果</h3>
-<p>读取 <code>loss.out</code>、<code>energy_train.out</code>、<code>force_train.out</code>、<code>virial_train.out</code>，绘制 loss 和能量/力/virial 的 parity plot。</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<h3 id="plt_trainpy">plt_train.py</h3>
+<p>可视化 NEP 训练过程，包括 loss 曲线、RMSE 演化，以及能量/力/virial 的 DFT vs NEP parity plot。</p>
+<p><strong>输入文件：</strong> <code>loss.out</code>、<code>energy_train.out</code>、<code>force_train.out</code>、<code>virial_train.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/train.png" alt="NEP training results" width="75%" />
 </div>
 
-<h3 id="_3">预测结果</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>prediction
-<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
+<hr />
+<h3 id="plt_predictionpy">plt_prediction.py</h3>
+<p>可视化测试集上的 NEP 预测结果。</p>
+<p><strong>输入文件：</strong> <code>energy_test.out</code>、<code>force_test.out</code>、<code>virial_test.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>prediction
+<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span><span class="w">         </span><span class="c1"># 替代命令</span>
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/prediction.png" alt="NEP prediction results" width="75%" />
 </div>
 
-<h3 id="_4">训练/测试集对比</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train_test
+<hr />
+<h3 id="plt_train_testpy">plt_train_test.py</h3>
+<p>将训练集和测试集的 parity plot 合并显示。</p>
+<p><strong>输入文件：</strong> <code>energy_train.out</code>、<code>force_train.out</code>、<code>virial_train.out</code>、<code>energy_test.out</code>、<code>force_test.out</code>、<code>virial_test.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train_test
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/train_test.png" alt="NEP train and test comparison" width="75%" />
 </div>
 
-<h3 id="parity-plot">密度 parity plot</h3>
-<p>大数据集散点太密时，密度图更容易观察误差分布：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>parity_density
+<hr />
+<h3 id="plt_parity_densitypy">plt_parity_density.py</h3>
+<p>生成基于密度的 parity plot，适用于大数据集（散点图过于密集时更易阅读）。</p>
+<p><strong>输入文件：</strong> <code>energy_train.out</code>、<code>force_train.out</code>、<code>virial_train.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>parity_density
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/parity_plot_density.png" alt="Parity density plot" width="70%" />
 </div>
 
-<h3 id="_5">力误差分析</h3>
-<p><code>plt_force_errors.py</code> 参考 <a href="https://doi.org/10.1038/s41524-023-01123-3">Liu et al.</a> 的方式分析力大小误差和角度误差。</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>force_errors
+<hr />
+<h3 id="plt_force_errorspy">plt_force_errors.py</h3>
+<p>参考 <a href="https://doi.org/10.1038/s41524-023-01123-3">Liu et al.</a> 的方法绘制力误差评估指标。</p>
+<p><strong>输入文件：</strong> <code>force_train.out</code></p>
+<p><strong>显示指标：</strong>
+- 力大小误差 (delta_F)
+- 力角度误差 (delta_theta)
+- 误差分布</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>force_errors
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/force_errors.png" alt="Force error analysis" width="70%" />
 </div>
 
-<h3 id="born">电荷和 Born 有效电荷</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>charge
-<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>born_charge
-<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>bec
+<hr />
+<h3 id="plt_learning_ratepy">plt_learning_rate.py</h3>
+<p>可视化 <code>gnep</code> 训练过程中的学习率变化。</p>
+<p><strong>输入文件：</strong> <code>loss.out</code></p>
+<p><strong>注意：</strong> 仅适用于 <code>gnep</code> 训练过程。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>lr
+</code></pre></div>
+<hr />
+<h3 id="plt_nep_restartpy">plt_nep_restart.py</h3>
+<p>可视化 <code>nep.restart</code> 文件中存储的参数。</p>
+<p><strong>输入文件：</strong> <code>nep.restart</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>restart
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/nep_restart.png" alt="NEP restart parameters" width="60%" />
+</div>
+
+<hr />
+<h3 id="plt_chargepy">plt_charge.py</h3>
+<p>绘制 <code>qNEP</code> 模型的电荷分布。</p>
+<p><strong>输入文件：</strong> <code>charge_train.out</code></p>
+<p><strong>重要提示：</strong> 确保训练集和电荷输出的原子排序一致。建议使用全 batch 训练或先运行预测步骤。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>charge
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/charge.png" alt="Charge distribution" width="45%" />
+</div>
+
+<hr />
+<h3 id="plt_born_chargepy">plt_born_charge.py</h3>
+<p>为训练集和测试集创建 Born 有效电荷 (BEC) 的 parity plot。全零参考 BEC 的结构会被过滤。</p>
+<p><strong>输入文件：</strong> <code>bec_train.out</code>、<code>bec_test.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>born_charge
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>bec<span class="w">          </span><span class="c1"># 替代命令</span>
+</code></pre></div>
+<div align="center">
   <img src="../../Gallery/born_charge.png" alt="Born effective charge parity plot" width="45%" />
 </div>
 
-<h2 id="md">MD 和结构分析绘图</h2>
-<h3 id="_6">热力学量</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
-<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo2
-<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo3
+<hr />
+<h2 id="_2">热力学量</h2>
+<h3 id="plt_thermopy">plt_thermo.py</h3>
+<p>综合可视化热力学性质的主脚本。</p>
+<p><strong>输入文件：</strong> <code>thermo.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/thermo.png" alt="Thermo plot" width="75%" />
 </div>
 
-<h3 id="rdf">RDF</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf
-<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf<span class="w"> </span>&lt;column&gt;
+<hr />
+<h3 id="plt_thermo2py-plt_thermo3py">plt_thermo2.py &amp; plt_thermo3.py</h3>
+<p>不同风格的热力学量可视化。</p>
+<p><strong>输入文件：</strong> <code>thermo.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo2
+<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo3
+</code></pre></div>
+<hr />
+<h2 id="_3">扩散和离子输运</h2>
+<h3 id="plt_msdpy">plt_msd.py</h3>
+<p>绘制各方向的均方位移 (MSD)。</p>
+<p><strong>输入文件：</strong> <code>msd.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
 </code></pre></div>
 <div align="center">
-  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
-  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
+  <img src="../../Gallery/msd.png" alt="Mean square displacement" width="48%" />
 </div>
 
-<h3 id="vac-pdos">VAC 和 PDOS</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos
-<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos<span class="w"> </span>save
+<hr />
+<h3 id="plt_msd_allpy">plt_msd_all.py</h3>
+<p>当 GPUMD 中使用 <code>all_groups</code> 时，分别绘制每种原子的 MSD。</p>
+<p><strong>输入文件：</strong> <code>msd.out</code>（需要使用 <code>all_groups</code> 选项计算）</p>
+<p><strong>要求：</strong> <code>run.in</code> 中的 <code>compute_msd</code> 命令必须使用 <code>all_groups</code>。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd_all<span class="w"> </span>msd.out<span class="w"> </span>Li<span class="w"> </span>P<span class="w"> </span>S
 </code></pre></div>
-<p>输入文件通常包括 <code>model.xyz</code>、<code>run.in</code>、<code>dos.out</code>、<code>mvac.out</code>。</p>
 <div align="center">
-  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
-  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
+  <img src="../../Gallery/msd_all.png" alt="MSD for all species" width="48%" />
 </div>
 
-<h2 id="_7">扩散和离子输运</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
-<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
-<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd_conv
-<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_d
-<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_sigma
+<hr />
+<h3 id="plt_msd_convergence_checkpy">plt_msd_convergence_check.py</h3>
+<p>检查不同时间窗口下 MSD 计算的收敛性。</p>
+<p><strong>输入文件：</strong> <code>msd_step*.out</code>（需要在 <code>compute_msd</code> 中使用 <code>save_every</code> 选项）</p>
+<p><strong>要求：</strong> 在 <code>compute_msd</code> 命令中使用 <code>save_every</code>。</p>
+<p><strong>用途：</strong> 验证 MSD 是否已充分收敛以准确计算扩散系数。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd_conv
 </code></pre></div>
 <div align="center">
-  <img src="../../Gallery/msd.png" alt="Mean square displacement" width="45%" />
-  <img src="../../Gallery/sdc.png" alt="Self-diffusion coefficient" width="45%" />
+  <img src="../../Gallery/msd_convergence.png" alt="MSD convergence" width="48%" />
 </div>
 
-<p>Arrhenius 图：</p>
+<hr />
+<h3 id="plt_sdcpy">plt_sdc.py</h3>
+<p>绘制自扩散系数 (SDC) 随时间的变化。</p>
+<p><strong>输入文件：</strong> <code>msd.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+</code></pre></div>
 <div align="center">
-  <img src="../../Gallery/Arrhenius_D.png" alt="Arrhenius diffusivity" width="55%" />
-  <img src="../../Gallery/Arrhenius_sigma.png" alt="Arrhenius ionic conductivity" width="55%" />
+  <img src="../../Gallery/sdc.png" alt="Self-diffusion coefficient" width="48%" />
 </div>
 
-<h2 id="_8">热输运</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>emd<span class="w"> </span>x
-<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>nemd<span class="w"> </span><span class="o">[</span>real_length<span class="o">]</span><span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
-<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>hnemd<span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
+<hr />
+<h3 id="plt_arrhenius_dpy">plt_arrhenius_d.py</h3>
+<p>创建 Arrhenius 扩散系数图（log10 D vs 1000/T）。</p>
+<p><strong>输入文件：</strong> <code>*K/msd.out</code>（每个温度子目录下的 <code>msd.out</code>）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_d
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>D<span class="w">             </span><span class="c1"># 替代命令</span>
+</code></pre></div>
+<p><strong>输出示例：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>T: 300K, D_total: 1.001e-07 cm2/s
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>T: 350K, D_total: 4.184e-07 cm2/s
+<a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a>T: 400K, D_total: 1.027e-06 cm2/s
+<a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a>Ea: 0.230 eV
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/Arrhenius_D.png" alt="Arrhenius diffusivity" width="58%" />
+</div>
+
+<hr />
+<h3 id="plt_arrhenius_sigmapy">plt_arrhenius_sigma.py</h3>
+<p>创建 Arrhenius 离子电导率图（ln(σ·T) vs 1000/T）。</p>
+<p><strong>输入文件：</strong> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code>（每个温度子目录）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>arrhenius_sigma
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sigma<span class="w">         </span><span class="c1"># 替代命令</span>
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/Arrhenius_sigma.png" alt="Arrhenius ionic conductivity" width="58%" />
+</div>
+
+<hr />
+<h2 id="_4">热输运</h2>
+<h3 id="plt_emdpy">plt_emd.py</h3>
+<p>分析并绘制平衡分子动力学 (EMD) 热导率。</p>
+<p><strong>输入文件：</strong> GPUMD 的 EMD 输出文件</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>emd<span class="w"> </span>x<span class="w">        </span><span class="c1"># x 方向</span>
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/emd.png" alt="EMD thermal conductivity" width="70%" />
+</div>
+
+<hr />
+<h3 id="plt_nemdpy">plt_nemd.py</h3>
+<p>可视化非平衡分子动力学 (NEMD) 热输运性质。</p>
+<p><strong>输入文件：</strong> GPUMD 的 NEMD 输出文件</p>
+<p><strong>参数说明：</strong></p>
+<table>
+<thead>
+<tr>
+<th>参数</th>
+<th>说明</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>real_length</code></td>
+<td>传热区实际长度（nm），设为 <code>Auto</code> 可自动计算</td>
+</tr>
+<tr>
+<td><code>scale_eff_size</code></td>
+<td>有效截面积缩放因子（默认：1）。三维体相用 1；含真空层的低维体系用 S_box / S_eff</td>
+</tr>
+<tr>
+<td><code>cutoff_freq</code></td>
+<td>SHC 计算的截止频率（THz，默认：60）</td>
+</tr>
+<tr>
+<td><code>save</code></td>
+<td>可选，保存图片为 <code>nemd.png</code></td>
+</tr>
+</tbody>
+</table>
+<p><strong>注意：</strong> 如果没有 SHC 数据，使用 <code>save</code> 时请将 <code>scale_eff_size</code> 和 <code>cutoff_freq</code> 设为任意占位数字。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>nemd<span class="w"> </span><span class="o">[</span>real_length<span class="o">]</span><span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
+</code></pre></div>
+<div align="center">
   <img src="../../Gallery/nemd.png" alt="NEMD results" width="70%" />
+</div>
+
+<hr />
+<h3 id="plt_hnemdpy">plt_hnemd.py</h3>
+<p>绘制非均匀非平衡分子动力学 (HNEMD) 结果。</p>
+<p><strong>输入文件：</strong> GPUMD 的 HNEMD 输出文件</p>
+<p><strong>参数说明：</strong></p>
+<table>
+<thead>
+<tr>
+<th>参数</th>
+<th>说明</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>scale_eff_size</code></td>
+<td>有效截面积缩放因子（默认：1）</td>
+</tr>
+<tr>
+<td><code>cutoff_freq</code></td>
+<td>SHC 计算的截止频率（THz，默认：60）</td>
+</tr>
+<tr>
+<td><code>save</code></td>
+<td>可选，保存图片为 <code>hnemd.png</code></td>
+</tr>
+</tbody>
+</table>
+<p><strong>注意：</strong> 如果没有 SHC 数据，使用 <code>save</code> 时请将 <code>scale_eff_size</code> 和 <code>cutoff_freq</code> 设为任意占位数字。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>hnemd<span class="w"> </span><span class="o">[</span>scale_eff_size<span class="o">]</span><span class="w"> </span><span class="o">[</span>cutoff_freq<span class="o">]</span><span class="w"> </span><span class="o">[</span>save<span class="o">]</span>
+</code></pre></div>
+<div align="center">
   <img src="../../Gallery/hnemd.png" alt="HNEMD results" width="70%" />
 </div>
 
+<hr />
+<h2 id="_5">结构分析</h2>
+<h3 id="plt_rdfpy">plt_rdf.py</h3>
+<p>绘制径向分布函数 (RDF)，展示原子对关联。</p>
+<p><strong>输入文件：</strong> <code>rdf.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-23-1" name="__codelineno-23-1" href="#__codelineno-23-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf<span class="w">               </span><span class="c1"># 显示所有 RDF 对</span>
+<a id="__codelineno-23-2" name="__codelineno-23-2" href="#__codelineno-23-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf<span class="w"> </span>&lt;column&gt;<span class="w">      </span><span class="c1"># 显示特定对</span>
+</code></pre></div>
+<p><strong>完整 RDF 输出：</strong></p>
+<div align="center">
+  <img src="../../Gallery/rdf1.png" alt="Complete RDF" width="90%" />
+</div>
+
+<p><strong>单对 RDF：</strong></p>
+<div align="center">
+  <img src="../../Gallery/rdf2.png" alt="Single RDF" width="55%" />
+</div>
+
+<hr />
+<h3 id="plt_rdf_pmfpy">plt_rdf_pmf.py</h3>
+<p>绘制 RDF 与平均力势 (PMF) 的组合图。</p>
+<p><strong>输入文件：</strong> <code>rdf.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-24-1" name="__codelineno-24-1" href="#__codelineno-24-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf_pmf
+</code></pre></div>
+<hr />
+<h3 id="plt_vacpy">plt_vac.py</h3>
+<p>绘制速度自相关函数 (VAC)。可用于分析声子性质和原子动力学。</p>
+<p><strong>输入文件：</strong> <code>sdc.out</code>（绘图脚本会从该文件中读取 VAC 相关列）</p>
+<p><strong>输出：</strong> 交互式图表或 <code>vac.png</code>（使用 <code>save</code> 选项时）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-25-1" name="__codelineno-25-1" href="#__codelineno-25-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>vac
+</code></pre></div>
+<hr />
+<h3 id="plt_cohesivepy">plt_cohesive.py</h3>
+<p>从 <code>cohesive.out</code> 绘制内聚能曲线。可用于分析晶格稳定性和平衡晶格常数。</p>
+<p><strong>输入文件：</strong> <code>cohesive.out</code>（各向同性缩放因子 vs 内聚能）</p>
+<p><strong>输出：</strong> 交互式图表或 <code>cohesive.png</code>（使用 <code>save</code> 选项时）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-26-1" name="__codelineno-26-1" href="#__codelineno-26-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>cohesive
+</code></pre></div>
+<hr />
+<h3 id="plt_net_forcepy">plt_net_force.py</h3>
+<p>绘制结构上的净力分布，可用于识别问题构型。</p>
+<p><strong>输入文件：</strong> <code>train.xyz</code>（extxyz 格式）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-27-1" name="__codelineno-27-1" href="#__codelineno-27-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>net_force<span class="w"> </span>train.xyz
+</code></pre></div>
+<p><strong>参考文献：</strong> <a href="https://arxiv.org/abs/2510.19774">arXiv:2510.19774</a></p>
+<div align="center">
+  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
+</div>
+
+<hr />
+<h2 id="_6">声子</h2>
+<h3 id="plt_pdospy">plt_pdos.py</h3>
+<p>计算并绘制归一化的速度自相关函数 (VAC)、声子态密度 (PDOS) 和热容 (Cv)。</p>
+<p><strong>输入文件：</strong> <code>model.xyz</code>、<code>run.in</code>、<code>dos.out</code>、<code>mvac.out</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-28-1" name="__codelineno-28-1" href="#__codelineno-28-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos
+<a id="__codelineno-28-2" name="__codelineno-28-2" href="#__codelineno-28-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>pdos<span class="w"> </span>save
+</code></pre></div>
+<div align="center">
+  <img src="../../Gallery/vac_pdos.png" alt="VAC and PDOS" width="70%" />
+</div>
+
+<p>热容输出：</p>
+<div align="center">
+  <img src="../../Gallery/heat_capacity.png" alt="Heat capacity" width="50%" />
+</div>
+
+<hr />
 <h2 id="dimer">描述符、Dimer 和其他分析</h2>
-<h3 id="_9">描述符可视化</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
-<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
-<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
+<h3 id="plt_descriptorspy">plt_descriptors.py</h3>
+<p>使用降维方法（PCA 或 UMAP）可视化高维 NEP 描述符。</p>
+<p><strong>输入文件：</strong> <code>descriptors.npy</code>（由 <code>gpumdkit.sh -calc des</code> 生成）</p>
+<p><strong>方法：</strong>
+- <code>pca</code> — 主成分分析
+- <code>umap</code> — 统一流形逼近与投影</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-29-1" name="__codelineno-29-1" href="#__codelineno-29-1"></a><span class="c1"># 先计算描述符</span>
+<a id="__codelineno-29-2" name="__codelineno-29-2" href="#__codelineno-29-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
+<a id="__codelineno-29-3" name="__codelineno-29-3" href="#__codelineno-29-3"></a>
+<a id="__codelineno-29-4" name="__codelineno-29-4" href="#__codelineno-29-4"></a><span class="c1"># 再可视化</span>
+<a id="__codelineno-29-5" name="__codelineno-29-5" href="#__codelineno-29-5"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
+<a id="__codelineno-29-6" name="__codelineno-29-6" href="#__codelineno-29-6"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/des_umap.png" alt="UMAP descriptor visualization" width="52%" />
 </div>
 
-<h3 id="dimer_1">Dimer 曲线</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span>nep.txt
+<hr />
+<h3 id="plt_descriptors_comparepy">plt_descriptors_compare.py</h3>
+<p>比较多个训练集或模型的描述符。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-30-1" name="__codelineno-30-1" href="#__codelineno-30-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des_compare
+</code></pre></div>
+<hr />
+<h3 id="plt_dimerpy">plt_dimer.py</h3>
+<p>绘制二聚体相互作用曲线。将两个原子放入立方盒子（30 Å），使用 NEP 模型计算势能和力随距离的变化。</p>
+<p><strong>输入文件：</strong> <code>nep.txt</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-31-1" name="__codelineno-31-1" href="#__codelineno-31-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>&lt;element1&gt;<span class="w"> </span>&lt;element2&gt;<span class="w"> </span>&lt;nep_model&gt;
+<a id="__codelineno-31-2" name="__codelineno-31-2" href="#__codelineno-31-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span>nep.txt
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/dimer_nep.png" alt="Dimer NEP curve" width="45%" />
   <img src="../../Gallery/dimer.png" alt="Dimer comparison" width="45%" />
 </div>
 
-<p><strong>Reference:</strong> <a href="https://doi.org/10.1021/acs.jcim.5c02335">J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</a></p>
-<h3 id="doas">DOAS</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
+<p><strong>参考文献：</strong> <a href="https://doi.org/10.1021/acs.jcim.5c02335">J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</a></p>
+<hr />
+<h3 id="plt_doaspy">plt_doas.py</h3>
+<p>绘制 <a href="https://doi.org/10.1002/anie.202215544">Wang et al.</a> 提出的原子态密度 (DOAS)。</p>
+<p><strong>输入文件：</strong> <code>doas.out</code>（由 <code>gpumdkit.sh -calc doas</code> 计算）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-32-1" name="__codelineno-32-1" href="#__codelineno-32-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>&lt;doas.out&gt;<span class="w"> </span>&lt;species&gt;
+<a id="__codelineno-32-2" name="__codelineno-32-2" href="#__codelineno-32-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
 </div>
 
-<h3 id="net-force">Net force</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>net_force<span class="w"> </span>train.xyz
+<hr />
+<h2 id="plane-grid">极性材料的 Plane-Grid 绘图</h2>
+<p>此工作流将位移或极化数据映射到网格上，并绘制选定平面的轮廓。详细用法和实际案例请参见 <strong><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></strong>。</p>
+<p><strong>依赖：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-33-1" name="__codelineno-33-1" href="#__codelineno-33-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
 </code></pre></div>
-<p><strong>Reference:</strong> <a href="https://arxiv.org/abs/2510.19774">arXiv:2510.19774</a></p>
-<div align="center">
-  <img src="../../Gallery/net_force_distribution.png" alt="Net force distribution" width="58%" />
-</div>
-
-<h2 id="_10">快速表</h2>
+<p><strong>典型前置步骤：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-34-1" name="__codelineno-34-1" href="#__codelineno-34-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span><span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
+<a id="__codelineno-34-2" name="__codelineno-34-2" href="#__codelineno-34-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Pb_Sr-O.dat<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+<a id="__codelineno-34-3" name="__codelineno-34-3" href="#__codelineno-34-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+</code></pre></div>
+<p><strong>使用方法：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-35-1" name="__codelineno-35-1" href="#__codelineno-35-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr
+<a id="__codelineno-35-2" name="__codelineno-35-2" href="#__codelineno-35-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span>
+</code></pre></div>
+<hr />
+<h2 id="_7">快速参考表</h2>
 <table>
 <thead>
 <tr>
@@ -1892,11 +2673,46 @@ <h2 id="_10">快速表</h2>
 <td>NEP 训练结果</td>
 </tr>
 <tr>
-<td><code>prediction</code></td>
+<td><code>prediction</code> / <code>test</code></td>
 <td><code>*_test.out</code></td>
 <td>NEP 预测结果</td>
 </tr>
 <tr>
+<td><code>train_test</code></td>
+<td><code>*_train.out</code>, <code>*_test.out</code></td>
+<td>合并 parity plot</td>
+</tr>
+<tr>
+<td><code>parity_density</code></td>
+<td><code>*_train.out</code></td>
+<td>密度 parity plot</td>
+</tr>
+<tr>
+<td><code>force_errors</code></td>
+<td><code>force_train.out</code></td>
+<td>力误差指标</td>
+</tr>
+<tr>
+<td><code>lr</code></td>
+<td><code>loss.out</code> (gnep)</td>
+<td>学习率</td>
+</tr>
+<tr>
+<td><code>restart</code></td>
+<td><code>nep.restart</code></td>
+<td>重启文件参数</td>
+</tr>
+<tr>
+<td><code>charge</code></td>
+<td><code>charge_train.out</code></td>
+<td>电荷分布</td>
+</tr>
+<tr>
+<td><code>born_charge</code> / <code>bec</code></td>
+<td><code>bec_train.out</code>, <code>bec_test.out</code></td>
+<td>Born 有效电荷</td>
+</tr>
+<tr>
 <td><code>thermo</code></td>
 <td><code>thermo.out</code></td>
 <td>热力学量</td>
@@ -1907,29 +2723,64 @@ <h2 id="_10">快速表</h2>
 <td>均方位移</td>
 </tr>
 <tr>
+<td><code>msd_all</code></td>
+<td><code>msd.out</code> (all_groups)</td>
+<td>全组分 MSD</td>
+</tr>
+<tr>
+<td><code>msd_conv</code></td>
+<td><code>msd_step*.out</code></td>
+<td>MSD 收敛性检查</td>
+</tr>
+<tr>
 <td><code>sdc</code></td>
 <td><code>msd.out</code></td>
 <td>自扩散系数</td>
 </tr>
 <tr>
+<td><code>arrhenius_d</code> / <code>D</code></td>
+<td><code>*K/msd.out</code></td>
+<td>Arrhenius 扩散系数</td>
+</tr>
+<tr>
+<td><code>arrhenius_sigma</code> / <code>sigma</code></td>
+<td><code>*K/{model.xyz, run.in, thermo.out, msd.out}</code></td>
+<td>Arrhenius 离子电导率</td>
+</tr>
+<tr>
 <td><code>rdf</code></td>
 <td><code>rdf.out</code></td>
 <td>径向分布函数</td>
 </tr>
 <tr>
-<td><code>pdos</code></td>
-<td><code>dos.out</code>, <code>mvac.out</code></td>
-<td>VAC 和 PDOS</td>
+<td><code>rdf_pmf</code></td>
+<td><code>rdf.out</code></td>
+<td>RDF + 平均力势</td>
+</tr>
+<tr>
+<td><code>vac</code></td>
+<td><code>sdc.out</code></td>
+<td>速度自相关</td>
+</tr>
+<tr>
+<td><code>cohesive</code></td>
+<td><code>cohesive.out</code></td>
+<td>内聚能曲线</td>
+</tr>
+<tr>
+<td><code>net_force</code></td>
+<td><code>train.xyz</code></td>
+<td>净力分布</td>
 </tr>
 <tr>
-<td><code>emd</code>/<code>nemd</code>/<code>hnemd</code></td>
-<td>热输运输出</td>
-<td>热导率分析</td>
+<td><code>doas</code></td>
+<td><code>doas.out</code></td>
+<td>原子态密度</td>
 </tr>
 <tr>
 <td><code>des</code></td>
 <td><code>descriptors.npy</code></td>
-<td>描述符降维</td>
+<td>描述符 PCA/UMAP</td>
 </tr>
 <tr>
 <td><code>dimer</code></td>
@@ -1937,9 +2788,29 @@ <h2 id="_10">快速表</h2>
 <td>二聚体能量/力曲线</td>
 </tr>
 <tr>
-<td><code>doas</code></td>
-<td><code>doas.out</code></td>
-<td>原子态密度</td>
+<td><code>pdos</code></td>
+<td><code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></td>
+<td>VAC 和 PDOS</td>
+</tr>
+<tr>
+<td><code>emd</code></td>
+<td>EMD 输出</td>
+<td>EMD 热导率</td>
+</tr>
+<tr>
+<td><code>nemd</code></td>
+<td>NEMD 输出</td>
+<td>NEMD 热输运</td>
+</tr>
+<tr>
+<td><code>hnemd</code></td>
+<td>HNEMD 输出</td>
+<td>HNEMD 热输运</td>
+</tr>
+<tr>
+<td><code>viscosity</code></td>
+<td>粘度输出</td>
+<td>粘度</td>
 </tr>
 </tbody>
 </table>
diff --git "a/docs/htmls/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.html" "b/docs/htmls/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.html"
index fea5054..467d935 100644
--- "a/docs/htmls/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.html"
+++ "b/docs/htmls/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.html"
@@ -1096,75 +1096,25 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        铁电和极性材料工具
-      
-    </span>
-  </a>
-  
-    <nav class="md-nav" aria-label="铁电和极性材料工具">
-      <ul class="md-nav__list">
-        
-          <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        邻居列表
-      
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
+  <a href="#ovito-rdf" class="md-nav__link">
     <span class="md-ellipsis">
       
-        位移
+        使用 OVITO 计算 RDF
       
     </span>
   </a>
   
 </li>
-        
-          <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        平均结构
       
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        八面体倾转
-      
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#abo3" class="md-nav__link">
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
     <span class="md-ellipsis">
       
-        ABO3 局域极化
+        铁电和极性材料工具
       
     </span>
   </a>
   
-</li>
-        
-      </ul>
-    </nav>
-  
 </li>
       
     </ul>
@@ -1453,75 +1403,25 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        铁电和极性材料工具
-      
-    </span>
-  </a>
-  
-    <nav class="md-nav" aria-label="铁电和极性材料工具">
-      <ul class="md-nav__list">
-        
-          <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
+  <a href="#ovito-rdf" class="md-nav__link">
     <span class="md-ellipsis">
       
-        邻居列表
+        使用 OVITO 计算 RDF
       
     </span>
   </a>
   
 </li>
-        
-          <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        位移
       
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        平均结构
-      
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        八面体倾转
-      
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#abo3" class="md-nav__link">
+        <li class="md-nav__item">
+  <a href="#_3" class="md-nav__link">
     <span class="md-ellipsis">
       
-        ABO3 局域极化
+        铁电和极性材料工具
       
     </span>
   </a>
   
-</li>
-        
-      </ul>
-    </nav>
-  
 </li>
       
     </ul>
@@ -1597,28 +1497,28 @@ <h2 id="_1">功能概览</h2>
 </tr>
 <tr>
 <td>邻居列表</td>
-<td><code>gpumdkit.sh -calc nlist [args...]</code></td>
-<td>结构</td>
+<td><code>gpumdkit.sh -calc nlist ...</code></td>
+<td>参见 <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
 </tr>
 <tr>
 <td>位移</td>
-<td><code>gpumdkit.sh -calc disp [args...]</code></td>
-<td>轨迹 + 邻居列表</td>
+<td><code>gpumdkit.sh -calc disp ...</code></td>
+<td>参见 <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
 </tr>
 <tr>
 <td>平均结构</td>
-<td><code>gpumdkit.sh -calc avg-struct [args...]</code></td>
-<td>轨迹</td>
+<td><code>gpumdkit.sh -calc avg-struct ...</code></td>
+<td>参见 <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
 </tr>
 <tr>
 <td>八面体倾转</td>
-<td><code>gpumdkit.sh -calc oct-tilt [args...]</code></td>
-<td>轨迹 + B-O 邻居列表</td>
+<td><code>gpumdkit.sh -calc oct-tilt ...</code></td>
+<td>参见 <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
 </tr>
 <tr>
 <td>ABO3 极化</td>
-<td><code>gpumdkit.sh -calc pol-abo3 [args...]</code></td>
-<td>轨迹 + 邻居列表</td>
+<td><code>gpumdkit.sh -calc pol-abo3 ...</code></td>
+<td>参见 <a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
 </tr>
 </tbody>
 </table>
@@ -1765,11 +1665,18 @@ <h2 id="msd">从轨迹计算 MSD</h2>
 </div>
 
 <h2 id="nep">NEP 预测性质</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nep<span class="w"> </span>structures.xyz<span class="w"> </span>predictions.xyz<span class="w"> </span>nep.txt
+<p><code>calc_properties_with_nep.py</code> 使用训练好的 NEP 模型计算能量、力和应力。</p>
+<p><strong>依赖：</strong> <code>calorine</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>pip<span class="w"> </span>install<span class="w"> </span>calorine
+</code></pre></div>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nep<span class="w"> </span>structures.xyz<span class="w"> </span>predictions.xyz<span class="w"> </span>nep.txt
+</code></pre></div>
+<p>使用此功能可以用训练好的 NEP 模型进行预测。建议在使用前先验证模型在目标结构上的预测质量。</p>
+<p><strong>提示：</strong> 预测前可以清理 extxyz 元数据：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-clean_xyz<span class="w"> </span>train.xyz<span class="w"> </span>clean_train.xyz
 </code></pre></div>
-<p>该功能使用训练好的 NEP 模型计算能量、力和应力。只有当你确认模型质量可靠，并明确希望使用 NEP 作为替代计算器时，才建议使用它。</p>
 <h2 id="nep_1">NEP 描述符</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
 </code></pre></div>
 <p>用途包括：</p>
 <ul>
@@ -1778,8 +1685,8 @@ <h2 id="nep_1">NEP 描述符</h2>
 <li>判断新数据是否扩展了描述符空间。</li>
 </ul>
 <p>绘图：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
-<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
+<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/des_umap.png" alt="Descriptor UMAP" width="52%" />
@@ -1787,8 +1694,8 @@ <h2 id="nep_1">NEP 描述符</h2>
 
 <h2 id="doas">DOAS</h2>
 <p><code>calc_doas.py</code> 用于计算 <a href="https://doi.org/10.1002/anie.202215544">Wang et al.</a> 提出的 density of atomistic states。</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>doas<span class="w"> </span>structures.xyz<span class="w"> </span>nep.txt<span class="w"> </span>doas.out
-<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>doas<span class="w"> </span>structures.xyz<span class="w"> </span>nep.txt<span class="w"> </span>doas.out
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
 </code></pre></div>
 <p>脚本会：</p>
 <ol>
@@ -1804,38 +1711,60 @@ <h2 id="doas">DOAS</h2>
 
 <h2 id="neb">NEB 和结构优化</h2>
 <p>NEB：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>neb<span class="w"> </span>initial.xyz<span class="w"> </span>final.xyz<span class="w"> </span><span class="m">9</span><span class="w"> </span>nep.txt
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>neb<span class="w"> </span>initial.xyz<span class="w"> </span>final.xyz<span class="w"> </span><span class="m">9</span><span class="w"> </span>nep.txt
 </code></pre></div>
-<p>结构优化：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>minimize<span class="w"> </span>POSCAR<span class="w"> </span>nep.txt<span class="w"> </span><span class="m">0</span>.01<span class="w"> </span><span class="m">1000</span>
+<p>结构优化（通过 <code>calorine</code>）：</p>
+<p><strong>依赖：</strong> <code>calorine</code></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>pip<span class="w"> </span>install<span class="w"> </span>calorine
+</code></pre></div>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>minimize<span class="w"> </span>POSCAR<span class="w"> </span>nep.txt<span class="w"> </span><span class="m">0</span>.01<span class="w"> </span><span class="m">1000</span>
 </code></pre></div>
 <p>输出包括：</p>
 <ul>
 <li><code>minimize.xyz</code></li>
 <li><code>minimize.log</code></li>
 </ul>
-<h2 id="_3">铁电和极性材料工具</h2>
-<p>这些工具需要 <code>ferrodispcalc</code>：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
-</code></pre></div>
-<p><code>ferrodispcalc</code> 目前没有需要额外引用的论文。</p>
-<h3 id="_4">邻居列表</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span>.0<span class="w"> </span>-n<span class="w"> </span><span class="m">6</span><span class="w"> </span>-C<span class="w"> </span>Ti<span class="w"> </span>-E<span class="w"> </span>O<span class="w"> </span>-o<span class="w"> </span>nl-Ti-O.dat
+<h2 id="ovito-rdf">使用 OVITO 计算 RDF</h2>
+<p><code>rdf_calculator_ovito.py</code> 使用 OVITO 的分析工具计算径向分布函数。</p>
+<p><strong>依赖：</strong> OVITO</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>pip<span class="w"> </span>install<span class="w"> </span>ovito
 </code></pre></div>
-<h3 id="_5">位移</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+<p><strong>输入文件：</strong> 结构文件（单帧或轨迹）</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>python<span class="w"> </span>Scripts/calculators/rdf_calculator_ovito.py<span class="w"> </span>trajectory.xyz<span class="w"> </span><span class="m">6</span>.0<span class="w"> </span><span class="m">400</span>
 </code></pre></div>
-<h3 id="_6">平均结构</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
-</code></pre></div>
-<h3 id="_7">八面体倾转</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>oct-tilt<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>octahedral_tilt.dat
+<p><strong>参数：</strong></p>
+<table>
+<thead>
+<tr>
+<th>参数</th>
+<th>含义</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>trajectory.xyz</code></td>
+<td>输入结构文件</td>
+</tr>
+<tr>
+<td><code>6.0</code></td>
+<td>RDF 计算的最大距离（Å）</td>
+</tr>
+<tr>
+<td><code>400</code></td>
+<td>直方图的分箱数</td>
+</tr>
+</tbody>
+</table>
+<p><strong>可视化：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf
 </code></pre></div>
-<h3 id="abo3">ABO3 局域极化</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>pol-abo3<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>--nl-ba<span class="w"> </span>nl-Ti-Pb.dat<span class="w"> </span>--nl-bo<span class="w"> </span>nl-Ti-O.dat<span class="w"> </span><span class="se">\</span>
-<a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a><span class="w">  </span>--bec<span class="w"> </span><span class="nv">Pb</span><span class="o">=</span><span class="m">2</span><span class="w"> </span><span class="nv">Ti</span><span class="o">=</span><span class="m">4</span>.0<span class="w"> </span><span class="nv">O</span><span class="o">=</span>-2.0<span class="w"> </span>-o<span class="w"> </span>polarization.dat
+<p><strong>注意：</strong> 建议优先使用 GPUMD 中的 <code>compute_rdf</code> 命令。</p>
+<h2 id="_3">铁电和极性材料工具</h2>
+<p>选项 <code>406–410</code> 涵盖钙钛矿和极性材料分析：近邻列表、局域位移、平均结构、八面体倾转和 ABO3 极化。这些工具基于 <code>ferrodispcalc</code>。</p>
+<p><strong>依赖：</strong></p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
 </code></pre></div>
-<p><code>--bec</code> 应根据你的体系或参考数据设置。</p>
+<p>完整参数列表和真实工作流案例（PbTiO3 相变、PTO/STO 超晶格拓扑等）请参见 <strong><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></strong>。</p>
 
 
 
diff --git "a/docs/htmls/zh/\350\264\241\347\214\256\346\214\207\345\215\227.html" "b/docs/htmls/zh/\350\264\241\347\214\256\346\214\207\345\215\227.html"
index 59bc61b..44bf15f 100644
--- "a/docs/htmls/zh/\350\264\241\347\214\256\346\214\207\345\215\227.html"
+++ "b/docs/htmls/zh/\350\264\241\347\214\256\346\214\207\345\215\227.html"
@@ -1199,12 +1199,12 @@
   <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
-        开发限制和指南
+        开发规范与准则
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="开发限制和指南">
+    <nav class="md-nav" aria-label="开发规范与准则">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -1222,7 +1222,7 @@
   <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
-        模块化和可复用性
+        模块化与可复用性
       
     </span>
   </a>
@@ -1257,10 +1257,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#bug" class="md-nav__link">
+  <a href="#_7" class="md-nav__link">
     <span class="md-ellipsis">
       
-        报告 Bug
+        报告问题
       
     </span>
   </a>
@@ -1268,10 +1268,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
+  <a href="#_8" class="md-nav__link">
     <span class="md-ellipsis">
       
-        提出功能建议
+        功能建议
       
     </span>
   </a>
@@ -1279,7 +1279,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_8" class="md-nav__link">
+  <a href="#_9" class="md-nav__link">
     <span class="md-ellipsis">
       
         贡献代码
@@ -1302,7 +1302,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_9" class="md-nav__link">
+  <a href="#_10" class="md-nav__link">
     <span class="md-ellipsis">
       
         创建功能分支
@@ -1313,7 +1313,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_10" class="md-nav__link">
+  <a href="#_11" class="md-nav__link">
     <span class="md-ellipsis">
       
         进行修改
@@ -1325,7 +1325,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_11" class="md-nav__link">
+  <a href="#_12" class="md-nav__link">
     <span class="md-ellipsis">
       
         交互模式贡献
@@ -1336,7 +1336,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_12" class="md-nav__link">
+  <a href="#_13" class="md-nav__link">
     <span class="md-ellipsis">
       
         命令行模式贡献
@@ -1363,10 +1363,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_13" class="md-nav__link">
+  <a href="#_14" class="md-nav__link">
     <span class="md-ellipsis">
       
-        代码风格和最佳实践
+        代码风格与最佳实践
       
     </span>
   </a>
@@ -1374,7 +1374,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_14" class="md-nav__link">
+  <a href="#_15" class="md-nav__link">
     <span class="md-ellipsis">
       
         测试你的修改
@@ -1385,7 +1385,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_15" class="md-nav__link">
+  <a href="#_16" class="md-nav__link">
     <span class="md-ellipsis">
       
         提交信息
@@ -1399,7 +1399,7 @@
   <a href="#pull-request" class="md-nav__link">
     <span class="md-ellipsis">
       
-        推送并打开 Pull Request
+        推送并创建 Pull Request
       
     </span>
   </a>
@@ -1412,7 +1412,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_16" class="md-nav__link">
+  <a href="#_17" class="md-nav__link">
     <span class="md-ellipsis">
       
         有问题或需要帮助？
@@ -1477,12 +1477,12 @@
   <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
-        开发限制和指南
+        开发规范与准则
       
     </span>
   </a>
   
-    <nav class="md-nav" aria-label="开发限制和指南">
+    <nav class="md-nav" aria-label="开发规范与准则">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -1500,7 +1500,7 @@
   <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
-        模块化和可复用性
+        模块化与可复用性
       
     </span>
   </a>
@@ -1535,10 +1535,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#bug" class="md-nav__link">
+  <a href="#_7" class="md-nav__link">
     <span class="md-ellipsis">
       
-        报告 Bug
+        报告问题
       
     </span>
   </a>
@@ -1546,10 +1546,10 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
+  <a href="#_8" class="md-nav__link">
     <span class="md-ellipsis">
       
-        提出功能建议
+        功能建议
       
     </span>
   </a>
@@ -1557,7 +1557,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_8" class="md-nav__link">
+  <a href="#_9" class="md-nav__link">
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         贡献代码
@@ -1580,7 +1580,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_9" class="md-nav__link">
+  <a href="#_10" class="md-nav__link">
     <span class="md-ellipsis">
       
         创建功能分支
@@ -1591,7 +1591,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_10" class="md-nav__link">
+  <a href="#_11" class="md-nav__link">
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         进行修改
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       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_11" class="md-nav__link">
+  <a href="#_12" class="md-nav__link">
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         交互模式贡献
@@ -1614,7 +1614,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_12" class="md-nav__link">
+  <a href="#_13" class="md-nav__link">
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         命令行模式贡献
@@ -1641,10 +1641,10 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_13" class="md-nav__link">
+  <a href="#_14" class="md-nav__link">
     <span class="md-ellipsis">
       
-        代码风格和最佳实践
+        代码风格与最佳实践
       
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   </a>
@@ -1652,7 +1652,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_14" class="md-nav__link">
+  <a href="#_15" class="md-nav__link">
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         测试你的修改
@@ -1663,7 +1663,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_15" class="md-nav__link">
+  <a href="#_16" class="md-nav__link">
     <span class="md-ellipsis">
       
         提交信息
@@ -1677,7 +1677,7 @@
   <a href="#pull-request" class="md-nav__link">
     <span class="md-ellipsis">
       
-        推送并打开 Pull Request
+        推送并创建 Pull Request
       
     </span>
   </a>
@@ -1690,7 +1690,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_16" class="md-nav__link">
+  <a href="#_17" class="md-nav__link">
     <span class="md-ellipsis">
       
         有问题或需要帮助？
@@ -1721,186 +1721,200 @@
 
 
 <div align="center">
-  <h1>🤝 贡献指南</h1>
-  <p style="text-align: justify;">感谢你有兴趣为 <strong>GPUMDkit</strong> 做贡献。我们非常感谢你愿意花时间和精力帮助改进这个工具包。</p>
+  <h1>🤝 为 GPUMDkit 贡献代码</h1>
+  <p style="text-align: justify;">感谢你有兴趣为 <strong>GPUMDkit</strong> 做出贡献！我们感谢你为改善这个工具包所付出的时间和努力。</p>
 </div>
 
-<p><code>GPUMDkit</code> 是一个开源软件包。无论是修复 bug、添加新功能、改进文档，还是提出使用建议，我们都欢迎社区贡献。</p>
+<p align="center">
+  <a href="../en/contributing_to_gpumdkit.md">English</a>
+  &nbsp;·&nbsp;
+  <strong>简体中文</strong>
+</p>
+
+<p><code>GPUMDkit</code> 是一个开源项目，我们欢迎社区的各种贡献，无论是修复 bug、添加新功能、改进文档还是提出建议。</p>
+<blockquote>
+<p><strong>注意</strong>：本文档的权威版本位于仓库根目录的 <a href="https://github.com/zhyan0603/GPUMDkit/blob/main/CONTRIBUTING.md"><code>CONTRIBUTING.md</code></a>。本教程页面同步其内容。中文版请参见 <a href="https://github.com/zhyan0603/GPUMDkit/blob/main/docs/CONTRIBUTING_zh-CN.md"><code>docs/CONTRIBUTING_zh-CN.md</code></a>。</p>
+</blockquote>
 <hr />
 <h2 id="_1">目录</h2>
 <ul>
-<li>开发限制和指南</li>
-<li>报告 Bug</li>
-<li>提出功能建议</li>
-<li>贡献代码</li>
-<li>Fork 并克隆仓库</li>
-<li>创建功能分支</li>
-<li>进行修改</li>
-<li>交互模式贡献</li>
-<li>命令行模式贡献</li>
-<li>更新 Tab 补全</li>
-<li>代码风格和最佳实践</li>
-<li>测试你的修改</li>
-<li>提交信息</li>
-<li>推送并打开 Pull Request</li>
+<li><a href="#开发规范与准则">开发规范与准则</a></li>
+<li><a href="#报告问题">报告问题</a></li>
+<li><a href="#功能建议">功能建议</a></li>
+<li><a href="#贡献代码">贡献代码</a></li>
+<li><a href="#fork-并克隆仓库">Fork 并克隆仓库</a></li>
+<li><a href="#创建功能分支">创建功能分支</a></li>
+<li><a href="#进行修改">进行修改</a><ul>
+<li><a href="#交互模式贡献">交互模式贡献</a></li>
+<li><a href="#命令行模式贡献">命令行模式贡献</a></li>
+<li><a href="#更新-tab-补全">更新 Tab 补全</a></li>
+</ul>
+</li>
+<li><a href="#代码风格与最佳实践">代码风格与最佳实践</a></li>
+<li><a href="#测试你的修改">测试你的修改</a></li>
+<li><a href="#提交信息">提交信息</a></li>
+<li><a href="#推送并创建-pull-request">推送并创建 Pull Request</a></li>
 </ul>
 <hr />
-<h2 id="_2">开发限制和指南</h2>
-<p>为了保持项目代码质量和一致性，请遵守以下指南。</p>
+<h2 id="_2">开发规范与准则</h2>
+<p>为保持代码质量和项目一致性，请遵循以下准则：</p>
 <h3 id="_3">语言要求</h3>
 <ul>
-<li><strong>所有代码应使用英文编写</strong>：包括变量名、函数名、注释、docstring、提交信息和文档。</li>
-<li>我们理解贡献者可能来自不同背景，但使用英文可以让代码库对更广泛的用户保持可读和可维护。</li>
+<li><strong>所有代码应使用英文编写</strong>：包括变量名、函数名、注释、文档字符串、提交信息和文档。</li>
+<li>虽然我们理解贡献者来自不同背景，但使用英文能确保代码库对最广泛的用户群体可访问。</li>
 </ul>
-<h3 id="_4">模块化和可复用性</h3>
+<h3 id="_4">模块化与可复用性</h3>
 <ul>
-<li><strong>编写模块化、可复用的代码</strong>：函数和脚本应尽量具有灵活性。</li>
-<li><strong>优先通过参数传递信息，避免硬编码</strong>：使用函数参数、命令行参数或配置文件，而不是把数值直接写死。不过，某些文件名是 GPUMD 和 NEP 程序固定要求的，例如 <code>train.xyz</code>、<code>thermo.out</code>，这类情况可以按需要保留固定文件名。</li>
-<li><strong>示例</strong>：</li>
-</ul>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="c1"># Good: accepts parameters</span>
+<li><strong>编写模块化和可复用的代码</strong>：函数和脚本的设计应具有灵活性。</li>
+<li><strong>优先传递参数而非硬编码值</strong>：使用函数参数、命令行参数或配置文件来替代硬编码值。但某些文件名由 GPUMD 和 NEP 程序固定要求（如 <code>train.xyz</code>、<code>thermo.out</code>），这些可以按需硬编码。</li>
+<li><strong>示例</strong>：
+  <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="c1"># 好的做法：接受参数</span>
 <a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="k">function</span><span class="w"> </span>convert_file<span class="o">()</span><span class="w"> </span><span class="o">{</span>
 <a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="w">    </span><span class="nb">local</span><span class="w"> </span><span class="nv">input_file</span><span class="o">=</span><span class="nv">$1</span>
 <a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a><span class="w">    </span><span class="nb">local</span><span class="w"> </span><span class="nv">output_file</span><span class="o">=</span><span class="nv">$2</span>
-<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a><span class="w">    </span><span class="c1"># processing logic</span>
+<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a><span class="w">    </span><span class="c1"># 处理逻辑</span>
 <a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a><span class="o">}</span>
 <a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a>
-<a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a><span class="c1"># Avoid: hardcoded values (unless required by GPUMD/NEP)</span>
+<a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a><span class="c1"># 避免：硬编码值（除非 GPUMD/NEP 要求）</span>
 <a id="__codelineno-0-9" name="__codelineno-0-9" href="#__codelineno-0-9"></a><span class="k">function</span><span class="w"> </span>convert_file<span class="o">()</span><span class="w"> </span><span class="o">{</span>
 <a id="__codelineno-0-10" name="__codelineno-0-10" href="#__codelineno-0-10"></a><span class="w">    </span><span class="nb">local</span><span class="w"> </span><span class="nv">input_file</span><span class="o">=</span><span class="s2">&quot;hardcoded_input.xyz&quot;</span>
-<a id="__codelineno-0-11" name="__codelineno-0-11" href="#__codelineno-0-11"></a><span class="w">    </span><span class="c1"># processing logic</span>
+<a id="__codelineno-0-11" name="__codelineno-0-11" href="#__codelineno-0-11"></a><span class="w">    </span><span class="c1"># 处理逻辑</span>
 <a id="__codelineno-0-12" name="__codelineno-0-12" href="#__codelineno-0-12"></a><span class="o">}</span>
-</code></pre></div>
+</code></pre></div></li>
+</ul>
 <h3 id="_5">代码风格</h3>
 <ul>
 <li>编写清晰、易于他人维护和修改的代码。</li>
-<li>使用有意义的变量名和函数名。</li>
-<li>在必要时添加注释，解释复杂逻辑。</li>
+<li>使用有意义的变量和函数名。</li>
+<li>在必要处添加注释以解释复杂逻辑。</li>
 </ul>
 <h3 id="_6">文档</h3>
 <ul>
-<li>确保帮助信息（例如 <code>-h</code> 参数）清晰、准确。</li>
-<li><code>docs/</code> 目录中的文档通常由维护者更新，因此一般不需要贡献者直接修改。</li>
+<li>确保帮助信息（如 <code>-h</code> 标志）清晰准确。</li>
+<li>教程文档位于 <code>docs/tutorials/en/</code>（英文）和 <code>docs/tutorials/zh/</code>（中文）。如果你添加了新功能，请考虑更新相关教程页面。</li>
+<li>编辑教程 Markdown 文件后，使用 <code>mkdocs build -f docs/mkdocs.yml</code> 重新构建 HTML。</li>
 </ul>
 <hr />
-<h2 id="bug">报告 Bug</h2>
-<p>如果你遇到 bug，请通过 GitHub Issues 帮助我们定位和修复：</p>
+<h2 id="_7">报告问题</h2>
+<p>如果你遇到 bug，请通过 GitHub Issues 帮助我们修复：</p>
 <ol>
-<li><strong>先搜索已有 issue</strong>，确认这个 bug 是否已经被报告过。</li>
-<li><strong>如果还没有报告，请创建新 issue</strong>：<a href="https://github.com/zhyan0603/GPUMDkit/issues/new">Create an Issue</a></li>
-<li><strong>详细描述问题</strong>，如果可以，请提供测试文件。</li>
+<li><strong>搜索现有 issues</strong> 查看该 bug 是否已被报告。</li>
+<li><strong>创建新 issue</strong>（如果尚未被报告）：<a href="https://github.com/zhyan0603/GPUMDkit/issues/new">创建 Issue</a></li>
+<li><strong>详细描述问题</strong>，如果可能请提供测试文件。</li>
 </ol>
-<p>你也可以通过以下方式联系我们：</p>
-<ul>
-<li><strong>QQ 群</strong>：825696376</li>
-<li><strong>Email</strong>：yanzihan@westlake.edu.cn</li>
-<li><strong>脚本开发者</strong>：联系脚本文件头部列出的开发者</li>
-</ul>
+<p>你也可以通过以下方式联系我们：
+- <strong>QQ 群</strong>：825696376
+- <strong>邮箱</strong>：yanzihan@westlake.edu.cn
+- <strong>脚本开发者</strong>：联系脚本头部列出的开发者</p>
 <hr />
-<h2 id="_7">提出功能建议</h2>
-<p>我们欢迎新的功能建议。提出新功能时，可以按以下方式进行：</p>
+<h2 id="_8">功能建议</h2>
+<p>我们欢迎功能建议！提出新功能：</p>
 <ol>
-<li><strong>先搜索已有 issue</strong>，确认是否已经有人提出过类似建议。</li>
-<li><strong>创建新的功能请求</strong>：<a href="https://github.com/zhyan0603/GPUMDkit/issues/new">Create a Feature Request</a>，并提及 @zhyan0603。</li>
-<li><strong>清楚描述你的需求</strong>，并说明它为什么有用。</li>
+<li><strong>搜索现有 issues</strong> 查看是否已有人提出。</li>
+<li><strong>创建新功能请求</strong>：<a href="https://github.com/zhyan0603/GPUMDkit/issues/new">创建功能请求</a> 并 mention @zhyan0603</li>
+<li><strong>清楚描述你的需求</strong> 并解释其用途。</li>
 </ol>
 <hr />
-<h2 id="_8">贡献代码</h2>
+<h2 id="_9">贡献代码</h2>
 <h3 id="fork">Fork 并克隆仓库</h3>
 <ol>
 <li>
-<p>在 GitHub 的 <a href="https://github.com/zhyan0603/GPUMDkit">GPUMDkit 仓库页面</a>右上角点击 "Fork"，将仓库 fork 到自己的账号下。</p>
+<p>在 GitHub 上 <strong>Fork 仓库</strong>，点击 <a href="https://github.com/zhyan0603/GPUMDkit">仓库页面</a> 右上角的 "Fork" 按钮。</p>
 </li>
 <li>
-<p>将你的 fork 克隆到本地：</p>
+<p><strong>克隆你的 fork</strong> 到本地：</p>
 </li>
 </ol>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/YOUR_USERNAME/GPUMDkit.git
 <a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="nb">cd</span><span class="w"> </span>GPUMDkit
 </code></pre></div>
 <ol>
-<li>设置 upstream remote，方便和主仓库保持同步：</li>
+<li><strong>设置 upstream remote</strong> 以保持 fork 同步：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>git<span class="w"> </span>remote<span class="w"> </span>add<span class="w"> </span>upstream<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
+</code></pre></div></li>
 </ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>git<span class="w"> </span>remote<span class="w"> </span>add<span class="w"> </span>upstream<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
-</code></pre></div>
-<h3 id="_9">创建功能分支</h3>
-<p>为你的修改创建一个新分支：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># Create and checkout a new branch from main</span>
+<h3 id="_10">创建功能分支</h3>
+<p>为你的修改创建新分支：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># 从 main 创建并切换到新分支</span>
 <a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>git<span class="w"> </span>checkout<span class="w"> </span>-b<span class="w"> </span>your-branch-name
 </code></pre></div>
-<p>分支名可以按你的习惯命名。</p>
-<h3 id="_10">进行修改</h3>
-<p><code>GPUMDkit</code> 的结构包括：</p>
-<ul>
-<li><strong><code>gpumdkit.sh</code></strong>：主入口 Bash 脚本，负责交互菜单模式和命令行模式。</li>
-<li><strong><code>Scripts/</code></strong>：按功能分类组织的 Python 工具脚本。</li>
-<li><code>plt_scripts/</code>：绘图脚本</li>
-<li><code>calculators/</code>：计算工具</li>
-<li><code>format_conversion/</code>：格式转换工具</li>
-<li><code>workflow/</code>：工作流自动化</li>
-<li><code>sample_structures/</code>：结构采样工具</li>
-<li><code>analyzer/</code>：分析工具</li>
-<li><code>utils/</code>：实用函数，包括用于 Tab 补全的 <code>completion.sh</code></li>
-<li><strong><code>src/</code></strong>：包含交互模式菜单函数的 Shell 脚本。</li>
-<li><code>f1_format_conversions.sh</code></li>
-<li><code>f2_sample_structures.sh</code></li>
-<li><code>f3_workflows.sh</code></li>
-<li><code>f4_calculators.sh</code></li>
-<li><code>f5_analyzers.sh</code></li>
-<li><code>f6_plots.sh</code></li>
-<li><code>f7_utilities.sh</code></li>
-<li><strong><code>docs/</code></strong>：文档文件。</li>
-</ul>
-<h4 id="_11">交互模式贡献</h4>
-<p>如果要添加一个可通过交互菜单访问的新功能：</p>
+<p>分支名称随意。</p>
+<h3 id="_11">进行修改</h3>
+<p><code>GPUMDkit</code> 的结构包括：
+- <strong><code>gpumdkit.sh</code></strong>：主入口（Bash 脚本），处理交互菜单模式和命令行模式
+- <strong><code>install.sh</code></strong>：安装脚本，设置环境变量和 shell 配置
+- <strong><code>Scripts/</code></strong>：按功能组织的 Python 和 Bash 实现脚本
+  - <code>plt_scripts/</code>：绘图脚本
+  - <code>calculators/</code>：计算工具
+  - <code>format_conversion/</code>：格式转换工具
+  - <code>workflow/</code>：工作流自动化
+  - <code>sample_structures/</code>：结构采样工具
+  - <code>analyzer/</code>：分析工具
+  - <code>utils/</code>：实用函数（包括 <code>completion.sh</code> Tab 补全）
+- <strong><code>src/</code></strong>：交互模式菜单函数的 Shell 脚本
+  - <code>f1_format_conversions.sh</code>
+  - <code>f2_sample_structures.sh</code>
+  - <code>f3_workflows.sh</code>
+  - <code>f4_calculators.sh</code>
+  - <code>f5_analyzers.sh</code>
+  - <code>f6_plots.sh</code>
+  - <code>f7_utilities.sh</code>
+- <strong><code>skills/</code></strong>：AI agent 技能定义（用于 opencode/Claude Code 集成的 SKILL.md 文件）
+- <strong><code>docs/</code></strong>：文档文件
+  - <code>tutorials/en/</code> 和 <code>tutorials/zh/</code>：双语教程页面
+  - <code>mkdocs.yml</code>：构建教程 HTML 的 MkDocs 配置
+  - <code>command_reference.tsv</code>：机器可读的命令参考
+  - <code>htmls/</code>：MkDocs 生成的 HTML 输出</p>
+<h4 id="_12">交互模式贡献</h4>
+<p>要添加通过交互菜单访问的新功能：</p>
 <ol>
-<li><strong>在合适的 <code>Scripts/</code> 子目录中创建实现脚本</strong>：</li>
+<li><strong>在相应的 <code>Scripts/</code> 子目录中创建实现脚本</strong>：</li>
 </ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="c1"># Example: Add a new format conversion script</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="c1"># 示例：添加新的格式转换脚本</span>
 <a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>touch<span class="w"> </span>Scripts/format_conversion/new_converter.py
 </code></pre></div>
 <ol>
 <li>
-<p><strong>实现你的功能</strong>，并遵循模块化指南：接受参数，避免不必要的硬编码。</p>
+<p><strong>实现你的功能</strong>，遵循模块化准则（接受参数，避免硬编码）。</p>
 </li>
 <li>
-<p><strong>在对应的 <code>src/</code> 文件中添加包装函数</strong>：</p>
+<p><strong>在相应的 <code>src/</code> 文件中添加包装函数</strong>：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="c1"># 示例：编辑 src/f1_format_conversions.sh</span>
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>vim<span class="w"> </span>src/f1_format_conversions.sh
+</code></pre></div></p>
 </li>
 </ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="c1"># Example: Edit src/f1_format_conversions.sh</span>
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>vim<span class="w"> </span>src/f1_format_conversions.sh
-</code></pre></div>
-<p>添加一个新函数：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="k">function</span><span class="w"> </span>f106_new_converter<span class="o">(){</span>
+<p>添加新函数：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="k">function</span><span class="w"> </span>f111_new_converter<span class="o">(){</span>
 <a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
 <a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Calling the script in Scripts/format_conversion |&quot;</span>
 <a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Script: new_converter.py                        |&quot;</span>
 <a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Developer: Your Name (your@email.com)           |&quot;</span>
 <a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
-<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Input the required parameters:&quot;</span>
+<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Input &lt;required_param1&gt; &lt;required_param2&gt;&quot;</span>
 <a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Example: input.xyz output.lmp&quot;</span>
 <a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ------------&gt;&gt;&quot;</span>
-<a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a><span class="nb">read</span><span class="w"> </span>-p<span class="w"> </span><span class="s2">&quot; &quot;</span><span class="w"> </span>converter_params
+<a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a><span class="nb">read</span><span class="w"> </span>-r<span class="w"> </span>-a<span class="w"> </span>converter_args
 <a id="__codelineno-6-11" name="__codelineno-6-11" href="#__codelineno-6-11"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ---------------------------------------------------&quot;</span>
-<a id="__codelineno-6-12" name="__codelineno-6-12" href="#__codelineno-6-12"></a>python<span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/Scripts/format_conversion/new_converter.py<span class="w"> </span><span class="si">${</span><span class="nv">converter_params</span><span class="si">}</span>
+<a id="__codelineno-6-12" name="__codelineno-6-12" href="#__codelineno-6-12"></a>python<span class="w"> </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span>/Scripts/format_conversion/new_converter.py<span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">converter_args</span><span class="p">[@]</span><span class="si">}</span><span class="s2">&quot;</span>
 <a id="__codelineno-6-13" name="__codelineno-6-13" href="#__codelineno-6-13"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Code path: </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span><span class="s2">/Scripts/format_conversion/new_converter.py&quot;</span>
 <a id="__codelineno-6-14" name="__codelineno-6-14" href="#__codelineno-6-14"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; ---------------------------------------------------&quot;</span>
 <a id="__codelineno-6-15" name="__codelineno-6-15" href="#__codelineno-6-15"></a><span class="o">}</span>
-</code></pre></div>
+</code></pre></div></p>
 <ol>
-<li><strong>更新 <code>gpumdkit.sh</code> 中的菜单显示</strong>：</li>
-</ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># Find the menu() function and update it if needed</span>
-<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="c1"># Find the array_choice array and add your new choice number</span>
+<li>
+<p><strong>在 <code>gpumdkit.sh</code> 中更新菜单显示</strong>：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># 找到 menu() 函数并按需更新</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="c1"># 找到 array_choice 数组并添加你的新选择编号</span>
 <a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="nv">array_choice</span><span class="o">=(</span>
-<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="w">    </span><span class="s2">&quot;0&quot;</span><span class="w"> </span><span class="s2">&quot;1&quot;</span><span class="w"> </span><span class="s2">&quot;101&quot;</span><span class="w"> </span><span class="s2">&quot;102&quot;</span><span class="w"> </span><span class="s2">&quot;103&quot;</span><span class="w"> </span><span class="s2">&quot;104&quot;</span><span class="w"> </span><span class="s2">&quot;105&quot;</span><span class="w"> </span><span class="s2">&quot;106&quot;</span><span class="w">  </span><span class="c1"># Added &quot;106&quot;</span>
-<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a><span class="w">    </span><span class="c1"># ... rest of choices</span>
+<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="w">    </span><span class="s2">&quot;0&quot;</span><span class="w"> </span><span class="s2">&quot;1&quot;</span><span class="w"> </span><span class="s2">&quot;101&quot;</span><span class="w"> </span><span class="s2">&quot;102&quot;</span><span class="w"> </span><span class="s2">&quot;103&quot;</span><span class="w"> </span><span class="s2">&quot;104&quot;</span><span class="w"> </span><span class="s2">&quot;105&quot;</span><span class="w"> </span><span class="s2">&quot;106&quot;</span><span class="w"> </span><span class="s2">&quot;107&quot;</span><span class="w"> </span><span class="s2">&quot;108&quot;</span><span class="w"> </span><span class="s2">&quot;109&quot;</span><span class="w"> </span><span class="s2">&quot;110&quot;</span><span class="w"> </span><span class="s2">&quot;111&quot;</span><span class="w">  </span><span class="c1"># 添加 &quot;111&quot;</span>
+<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a><span class="w">    </span><span class="c1"># ... 其余选择</span>
 <a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a><span class="o">)</span>
-</code></pre></div>
-<ol>
-<li><strong>在 <code>gpumdkit.sh</code> 中添加 case 分支</strong>：</li>
-</ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="c1"># In the main() function, find the appropriate case statement</span>
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>在 <code>gpumdkit.sh</code> 中添加 case 语句</strong>：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="c1"># 在 main() 函数中找到相应的 case 语句</span>
 <a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a><span class="k">case</span><span class="w"> </span><span class="s2">&quot;</span><span class="si">${</span><span class="nv">choice</span><span class="p">:</span><span class="nv">0</span><span class="p">:</span><span class="nv">1</span><span class="si">}</span><span class="s2">&quot;</span><span class="w"> </span><span class="k">in</span>
 <a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a><span class="w">    </span><span class="c1"># ...</span>
 <a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="w">    </span><span class="s2">&quot;1&quot;</span><span class="o">)</span>
@@ -1908,199 +1922,236 @@ <h4 id="_11">交互模式贡献</h4>
 <a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a><span class="w">        </span><span class="k">case</span><span class="w"> </span><span class="nv">$choice</span><span class="w"> </span><span class="k">in</span>
 <a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="w">            </span><span class="s2">&quot;1&quot;</span><span class="o">)</span><span class="w"> </span>f1_format_conversion<span class="w"> </span><span class="p">;;</span>
 <a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a><span class="w">            </span><span class="s2">&quot;101&quot;</span><span class="o">)</span><span class="w"> </span>f101_out2xyz<span class="w"> </span><span class="p">;;</span>
-<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a><span class="w">            </span><span class="c1"># ... existing cases ...</span>
-<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a><span class="w">            </span><span class="s2">&quot;106&quot;</span><span class="o">)</span><span class="w"> </span>f106_new_converter<span class="w"> </span><span class="p">;;</span><span class="w">  </span><span class="c1"># Add your case</span>
+<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a><span class="w">            </span><span class="c1"># ... 现有 case ...</span>
+<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a><span class="w">            </span><span class="s2">&quot;111&quot;</span><span class="o">)</span><span class="w"> </span>f111_new_converter<span class="w"> </span><span class="p">;;</span><span class="w">  </span><span class="c1"># 添加你的 case</span>
 <a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a><span class="w">        </span><span class="k">esac</span><span class="w"> </span><span class="p">;;</span>
 <a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></a><span class="w">    </span><span class="c1"># ...</span>
 <a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a><span class="k">esac</span>
-</code></pre></div>
-<h4 id="_12">命令行模式贡献</h4>
-<p>如果要添加新的命令行 flag 或子命令：</p>
-<ol>
-<li><strong>在合适的 <code>Scripts/</code> 子目录中创建实现脚本</strong>：</li>
+</code></pre></div></p>
+</li>
 </ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="c1"># Example: Add a new analyzer script</span>
-<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>touch<span class="w"> </span>Scripts/analyzer/analyze_bonds.py
-</code></pre></div>
+<h4 id="_13">命令行模式贡献</h4>
+<p>要添加新的命令行标志或子命令：</p>
 <ol>
-<li><strong>实现功能，并明确参数要求</strong>：</li>
-</ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="c1"># Example: Scripts/analyzer/analyze_bonds.py</span>
+<li>
+<p><strong>在相应的 <code>Scripts/</code> 子目录中创建实现脚本</strong>：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="c1"># 示例：添加新的分析器脚本</span>
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>touch<span class="w"> </span>Scripts/analyzer/analyze_bonds.py
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>实现你的功能</strong>，明确参数要求：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="c1"># 示例：Scripts/analyzer/analyze_bonds.py</span>
 <a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a><span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
 <a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>
-<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="k">def</span><span class="w"> </span><span class="nf">main</span><span class="p">():</span>
-<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">3</span><span class="p">:</span>
-<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;&quot;</span><span class="p">)</span>
-<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a>        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0&quot;</span><span class="p">)</span>
-<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>        <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
-<a id="__codelineno-10-9" name="__codelineno-10-9" href="#__codelineno-10-9"></a>
-<a id="__codelineno-10-10" name="__codelineno-10-10" href="#__codelineno-10-10"></a>    <span class="n">input_file</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-<a id="__codelineno-10-11" name="__codelineno-10-11" href="#__codelineno-10-11"></a>    <span class="n">cutoff</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
-<a id="__codelineno-10-12" name="__codelineno-10-12" href="#__codelineno-10-12"></a>
-<a id="__codelineno-10-13" name="__codelineno-10-13" href="#__codelineno-10-13"></a>    <span class="c1"># Your implementation here</span>
-<a id="__codelineno-10-14" name="__codelineno-10-14" href="#__codelineno-10-14"></a>
-<a id="__codelineno-10-15" name="__codelineno-10-15" href="#__codelineno-10-15"></a><span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
-<a id="__codelineno-10-16" name="__codelineno-10-16" href="#__codelineno-10-16"></a>    <span class="n">main</span><span class="p">()</span>
-</code></pre></div>
-<ol>
-<li><strong>在 <code>gpumdkit.sh</code> 中添加命令行 flag 处理逻辑</strong>：</li>
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">3</span><span class="p">:</span>
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a>    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;&quot;</span><span class="p">)</span>
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a>    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0&quot;</span><span class="p">)</span>
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a>    <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
+<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a>
+<a id="__codelineno-10-9" name="__codelineno-10-9" href="#__codelineno-10-9"></a><span class="n">input_file</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<a id="__codelineno-10-10" name="__codelineno-10-10" href="#__codelineno-10-10"></a><span class="n">cutoff</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+<a id="__codelineno-10-11" name="__codelineno-10-11" href="#__codelineno-10-11"></a>
+<a id="__codelineno-10-12" name="__codelineno-10-12" href="#__codelineno-10-12"></a><span class="c1"># 你的实现</span>
+</code></pre></div></p>
+</li>
 </ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="c1"># Find the command-line parsing section (after line ~167)</span>
-<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="c1"># Add your new flag in the appropriate location</span>
+<blockquote>
+<p><strong>注意</strong>：GPUMDkit Python 脚本设计为直接运行（不作为模块导入）。
+如果你愿意，可以使用 <code>main()</code> 函数配合 <code>if __name__ == "__main__":</code> 保护，
+但这不是必需的。大多数现有脚本在模块级别执行。</p>
+</blockquote>
+<ol>
+<li>
+<p><strong>在 <code>gpumdkit.sh</code> 中添加命令行标志处理</strong>：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="c1"># 找到命令行解析部分（大的 &quot;case $1 in&quot; 块）</span>
+<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="c1"># 在适当位置添加你的新标志</span>
 <a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>
 <a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a><span class="k">case</span><span class="w"> </span><span class="nv">$1</span><span class="w"> </span><span class="k">in</span>
-<a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="w">    </span><span class="c1"># ... existing cases ...</span>
+<a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="w">    </span><span class="c1"># ... 现有 case ...</span>
 <a id="__codelineno-11-6" name="__codelineno-11-6" href="#__codelineno-11-6"></a><span class="w">    </span>-analyze_bonds<span class="o">)</span>
-<a id="__codelineno-11-7" name="__codelineno-11-7" href="#__codelineno-11-7"></a><span class="w">        </span><span class="k">if</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$3</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span>
-<a id="__codelineno-11-8" name="__codelineno-11-8" href="#__codelineno-11-8"></a><span class="w">            </span>python<span class="w"> </span><span class="si">${</span><span class="nv">analyzer_path</span><span class="si">}</span>/analyze_bonds.py<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$3</span><span class="s2">&quot;</span>
+<a id="__codelineno-11-7" name="__codelineno-11-7" href="#__codelineno-11-7"></a><span class="w">        </span><span class="k">if</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="o">[</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$2</span><span class="s2">&quot;</span><span class="w"> </span>!<span class="o">=</span><span class="w"> </span><span class="s2">&quot;-h&quot;</span><span class="w"> </span><span class="o">]</span><span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span>-z<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$3</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span>
+<a id="__codelineno-11-8" name="__codelineno-11-8" href="#__codelineno-11-8"></a><span class="w">            </span>python<span class="w"> </span><span class="si">${</span><span class="nv">analyzer_path</span><span class="si">}</span>/analyze_bonds.py<span class="w"> </span><span class="nv">$2</span><span class="w"> </span><span class="nv">$3</span>
 <a id="__codelineno-11-9" name="__codelineno-11-9" href="#__codelineno-11-9"></a><span class="w">        </span><span class="k">else</span>
 <a id="__codelineno-11-10" name="__codelineno-11-10" href="#__codelineno-11-10"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;&quot;</span>
 <a id="__codelineno-11-11" name="__codelineno-11-11" href="#__codelineno-11-11"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0&quot;</span>
 <a id="__codelineno-11-12" name="__codelineno-11-12" href="#__codelineno-11-12"></a><span class="w">            </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; Code path: </span><span class="si">${</span><span class="nv">analyzer_path</span><span class="si">}</span><span class="s2">/analyze_bonds.py&quot;</span>
-<a id="__codelineno-11-13" name="__codelineno-11-13" href="#__codelineno-11-13"></a><span class="w">            </span><span class="nb">exit</span><span class="w"> </span><span class="m">1</span>
-<a id="__codelineno-11-14" name="__codelineno-11-14" href="#__codelineno-11-14"></a><span class="w">        </span><span class="k">fi</span><span class="w"> </span><span class="p">;;</span>
-<a id="__codelineno-11-15" name="__codelineno-11-15" href="#__codelineno-11-15"></a><span class="w">    </span><span class="c1"># ... rest of cases ...</span>
-<a id="__codelineno-11-16" name="__codelineno-11-16" href="#__codelineno-11-16"></a><span class="k">esac</span>
-</code></pre></div>
-<ol>
-<li><strong>更新 <code>gpumdkit.sh</code> 中的帮助信息</strong>：</li>
-</ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="c1"># Find the help_info_table() function and add your command</span>
+<a id="__codelineno-11-13" name="__codelineno-11-13" href="#__codelineno-11-13"></a><span class="w">        </span><span class="k">fi</span><span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-11-14" name="__codelineno-11-14" href="#__codelineno-11-14"></a><span class="w">    </span><span class="c1"># ... 其余 case ...</span>
+<a id="__codelineno-11-15" name="__codelineno-11-15" href="#__codelineno-11-15"></a><span class="k">esac</span>
+</code></pre></div></p>
+</li>
+<li>
+<p><strong>在 <code>gpumdkit.sh</code> 中更新帮助信息</strong>：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="c1"># 找到 help_info_table() 函数并添加你的命令</span>
 <a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a><span class="k">function</span><span class="w"> </span>help_info_table<span class="o">(){</span>
 <a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;+====================================== Analysis ===============================================+&quot;</span>
 <a id="__codelineno-12-4" name="__codelineno-12-4" href="#__codelineno-12-4"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |&quot;</span>
-<a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a><span class="w">    </span><span class="c1"># ... rest of help table ...</span>
+<a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a><span class="w">    </span><span class="c1"># ... 其余帮助表 ...</span>
 <a id="__codelineno-12-6" name="__codelineno-12-6" href="#__codelineno-12-6"></a><span class="o">}</span>
-</code></pre></div>
+</code></pre></div></p>
+</li>
+</ol>
 <h4 id="tab">更新 Tab 补全</h4>
-<p>添加新的命令行 flag 时，请更新 Tab 补全脚本：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="c1"># Edit Scripts/utils/completion.sh</span>
+<p>添加新的命令行标志时，更新 Tab 补全脚本：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="c1"># 编辑 Scripts/utils/completion.sh</span>
 <a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>vim<span class="w"> </span>Scripts/utils/completion.sh
 </code></pre></div>
-<p>将新的 flag 加入 <code>opts</code> 变量：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a><span class="c1"># Find the line with local opts=...</span>
-<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a><span class="nb">local</span><span class="w"> </span><span class="nv">opts</span><span class="o">=</span><span class="s2">&quot;-h -update -U -help -clean -time -plt -calc -analyze_bonds -range -out2xyz ...&quot;</span>
-<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a><span class="c1">#                                                      ^^^^^^^^^^^^^^ Add your flag here</span>
-</code></pre></div>
-<p>如果这个 flag 接受二级选项，例如 <code>-plt</code> 或 <code>-calc</code>，也需要为它添加对应的 <code>case</code> 分支：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a><span class="k">case</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$prev</span><span class="s2">&quot;</span><span class="w"> </span><span class="k">in</span>
-<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="w">    </span><span class="c1"># ... existing cases ...</span>
-<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a><span class="w">    </span>-analyze_bonds<span class="o">)</span>
-<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a><span class="w">        </span><span class="nv">COMPREPLY</span><span class="o">=(</span><span class="k">$(</span><span class="nb">compgen</span><span class="w"> </span>-f<span class="w"> </span>--<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$cur</span><span class="s2">&quot;</span><span class="k">)</span><span class="o">)</span><span class="w">  </span><span class="c1"># Complete with filenames</span>
-<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a><span class="w">        </span><span class="p">;;</span>
-<a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a><span class="w">    </span><span class="c1"># ... rest of cases ...</span>
-<a id="__codelineno-15-7" name="__codelineno-15-7" href="#__codelineno-15-7"></a><span class="k">esac</span>
-</code></pre></div>
-<h3 id="_13">代码风格和最佳实践</h3>
+<p>将你的新标志添加到 <code>opts</code> 变量：
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a><span class="c1"># 找到 local opts=... 行</span>
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a><span class="nb">local</span><span class="w"> </span><span class="nv">opts</span><span class="o">=</span><span class="s2">&quot;-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...&quot;</span>
+<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a><span class="c1">#                                                        在此添加你的标志</span>
+</code></pre></div></p>
+<p>如果你的标志需要文件参数，将其添加到现有的文件补全 case 中：
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a><span class="c1"># 找到需要文件参数的 case 并用 | 添加你的标志</span>
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>-out2xyz<span class="p">|</span>-out2exyz<span class="p">|</span>-...<span class="p">|</span>-your_new_flag<span class="o">)</span>
+<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a><span class="w">    </span><span class="nv">COMPREPLY</span><span class="o">=(</span><span class="k">$(</span><span class="nb">compgen</span><span class="w"> </span>-f<span class="w"> </span>--<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$cur</span><span class="s2">&quot;</span><span class="k">)</span><span class="o">)</span><span class="w"> </span><span class="p">;;</span>
+</code></pre></div></p>
+<p>如果你的标志接受二级选项（如 <code>-plt</code> 或 <code>-calc</code>），添加新 case：
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a><span class="k">case</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$prev</span><span class="s2">&quot;</span><span class="w"> </span><span class="k">in</span>
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a><span class="w">    </span><span class="c1"># ... 现有 case ...</span>
+<a id="__codelineno-16-3" name="__codelineno-16-3" href="#__codelineno-16-3"></a><span class="w">    </span>-your_new_flag<span class="o">)</span>
+<a id="__codelineno-16-4" name="__codelineno-16-4" href="#__codelineno-16-4"></a><span class="w">        </span><span class="nv">COMPREPLY</span><span class="o">=(</span><span class="k">$(</span><span class="nb">compgen</span><span class="w"> </span>-W<span class="w"> </span><span class="s2">&quot;option1 option2 option3&quot;</span><span class="w"> </span>--<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$cur</span><span class="s2">&quot;</span><span class="k">)</span><span class="o">)</span><span class="w"> </span><span class="p">;;</span>
+<a id="__codelineno-16-5" name="__codelineno-16-5" href="#__codelineno-16-5"></a><span class="w">    </span><span class="c1"># ... 其余 case ...</span>
+<a id="__codelineno-16-6" name="__codelineno-16-6" href="#__codelineno-16-6"></a><span class="k">esac</span>
+</code></pre></div></p>
+<h3 id="_14">代码风格与最佳实践</h3>
 <ul>
 <li><strong>Shell 脚本</strong>：</li>
-<li>使用 <code>${variable}</code> 进行变量展开。</li>
+<li>使用 <code>${variable}</code> 进行变量展开</li>
+<li>使用 <code>[ ! -z "$var" ]</code> 进行非空检查（项目约定）</li>
+<li>交互函数应遵循 banner 格式：
+    <div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
+<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Calling the script in Scripts/&lt;category&gt;        |&quot;</span>
+<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Script: &lt;script_name&gt;.py                        |&quot;</span>
+<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; | Developer: &lt;Name&gt; (&lt;email&gt;)                     |&quot;</span>
+<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot; &gt;-------------------------------------------------&lt;&quot;</span>
+</code></pre></div></li>
+<li>使用 <code>read -r -a varname</code> 读取多词输入，然后用 <code>"${varname[@]}"</code> 传递</li>
 <li>
-<p>编写清晰、易维护的代码。</p>
+<p><code>src/</code> 中的 Shell 脚本应以文件头注释块开始：
+    <div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a><span class="c1"># ============================================================</span>
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a><span class="c1"># GPUMDkit &lt;module name&gt; module</span>
+<a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a><span class="c1"># Repository: https://github.com/zhyan0603/GPUMDkit</span>
+<a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a><span class="c1"># Author: &lt;Name&gt; (&lt;email&gt;)</span>
+<a id="__codelineno-18-5" name="__codelineno-18-5" href="#__codelineno-18-5"></a><span class="c1"># ============================================================</span>
+</code></pre></div></p>
 </li>
 <li>
 <p><strong>Python 脚本</strong>：</p>
 </li>
-<li>编写清晰、可维护的代码。</li>
-<li>使用有意义的变量名。</li>
+<li>编写清晰、可维护的代码</li>
+<li>使用有意义的变量名</li>
+<li>使用 <code>sys.argv</code> 进行参数解析（与大多数现有脚本一致）</li>
+<li>提供清晰的使用信息：<code>print("Usage: ...")</code> 和 <code>print("Example: ...")</code></li>
+<li>如果你的脚本使用重型/特殊包（<code>NepTrain</code>、<code>calorine</code>、<code>dpdata</code>），请添加
+    <code>print_dependency_notice()</code> 函数以通知用户引用建议</li>
 </ul>
-<h3 id="_14">测试你的修改</h3>
-<p>提交贡献前，请进行测试：</p>
-<ol>
-<li><strong>测试交互模式</strong>（如果适用）：</li>
-</ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh
-<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a><span class="c1"># Navigate to your new feature and test it thoroughly</span>
-</code></pre></div>
-<ol>
-<li><strong>测试命令行模式</strong>（如果适用）：</li>
-</ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span><span class="o">[</span>arguments<span class="o">]</span>
-<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span>-h<span class="w">  </span><span class="c1"># Test help message</span>
-</code></pre></div>
-<ol>
-<li><strong>测试 Tab 补全</strong>（如果修改了 <code>completion.sh</code>）：</li>
-</ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a><span class="nb">source</span><span class="w"> </span>Scripts/utils/completion.sh
-<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>gpumdkit.sh<span class="w"> </span>-&lt;TAB&gt;<span class="w">  </span><span class="c1"># Should show your new flag</span>
+<h3 id="_15">测试你的修改</h3>
+<p>提交贡献前，运行相关验证命令：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a><span class="c1"># Shell 语法检查（始终运行）</span>
+<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>bash<span class="w"> </span>-n<span class="w"> </span>gpumdkit.sh
+<a id="__codelineno-19-3" name="__codelineno-19-3" href="#__codelineno-19-3"></a>find<span class="w"> </span>src<span class="w"> </span>Scripts<span class="w"> </span>-name<span class="w"> </span><span class="s1">&#39;*.sh&#39;</span><span class="w"> </span>-exec<span class="w"> </span>bash<span class="w"> </span>-n<span class="w"> </span><span class="o">{}</span><span class="w"> </span>+
+<a id="__codelineno-19-4" name="__codelineno-19-4" href="#__codelineno-19-4"></a>
+<a id="__codelineno-19-5" name="__codelineno-19-5" href="#__codelineno-19-5"></a><span class="c1"># Python 语法检查（针对修改的 Python 文件）</span>
+<a id="__codelineno-19-6" name="__codelineno-19-6" href="#__codelineno-19-6"></a>python3<span class="w"> </span>-m<span class="w"> </span>py_compile<span class="w"> </span>path/to/modified_script.py
+<a id="__codelineno-19-7" name="__codelineno-19-7" href="#__codelineno-19-7"></a>
+<a id="__codelineno-19-8" name="__codelineno-19-8" href="#__codelineno-19-8"></a><span class="c1"># MkDocs 构建（如果修改了文档）</span>
+<a id="__codelineno-19-9" name="__codelineno-19-9" href="#__codelineno-19-9"></a>mkdocs<span class="w"> </span>build<span class="w"> </span>-f<span class="w"> </span>docs/mkdocs.yml
+<a id="__codelineno-19-10" name="__codelineno-19-10" href="#__codelineno-19-10"></a>
+<a id="__codelineno-19-11" name="__codelineno-19-11" href="#__codelineno-19-11"></a><span class="c1"># 检查尾随空格问题</span>
+<a id="__codelineno-19-12" name="__codelineno-19-12" href="#__codelineno-19-12"></a>git<span class="w"> </span>diff<span class="w"> </span>--check
 </code></pre></div>
+<p>然后测试功能：</p>
 <ol>
 <li>
-<p><strong>使用不同输入测试</strong>：</p>
+<p><strong>测试交互模式</strong>（如适用）：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh
+<a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a><span class="c1"># 导航到你的新功能并充分测试</span>
+</code></pre></div></p>
 </li>
 <li>
-<p>测试常规输入。</p>
+<p><strong>测试命令行模式</strong>（如适用）：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span><span class="o">[</span>arguments<span class="o">]</span>
+<a id="__codelineno-21-2" name="__codelineno-21-2" href="#__codelineno-21-2"></a>gpumdkit.sh<span class="w"> </span>-your_new_flag<span class="w"> </span>-h<span class="w">  </span><span class="c1"># 测试帮助信息</span>
+</code></pre></div></p>
 </li>
-<li>测试边界情况，例如空文件、大文件等。</li>
 <li>
-<p>测试错误处理，例如缺少文件、参数无效等。</p>
+<p><strong>测试 Tab 补全</strong>（如果你修改了 <code>completion.sh</code>）：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a><span class="nb">source</span><span class="w"> </span>Scripts/utils/completion.sh
+<a id="__codelineno-22-2" name="__codelineno-22-2" href="#__codelineno-22-2"></a>gpumdkit.sh<span class="w"> </span>-&lt;TAB&gt;<span class="w">  </span><span class="c1"># 应显示你的新标志</span>
+</code></pre></div></p>
 </li>
 <li>
-<p><strong>确认没有回归问题</strong>：确保已有功能仍然可以正常工作。</p>
+<p><strong>用各种输入测试</strong>：</p>
+</li>
+<li>用典型输入测试</li>
+<li>用边缘情况测试（空文件、大文件等）</li>
+<li>
+<p>测试错误处理（缺少文件、无效参数）</p>
+</li>
+<li>
+<p><strong>验证无回归</strong>：确保现有功能仍然正常工作。</p>
 </li>
 </ol>
-<h3 id="_15">提交信息</h3>
-<p>提交信息应清楚、具体，说明你修改了什么。不要求严格格式，但需要让他人能够理解。</p>
-<h3 id="pull-request">推送并打开 Pull Request</h3>
-<ol>
-<li><strong>提交你的修改</strong>：</li>
-</ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>git<span class="w"> </span>add<span class="w"> </span>.
-<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>git<span class="w"> </span>commit<span class="w"> </span>-m<span class="w"> </span><span class="s2">&quot;your descriptive message&quot;</span>
-</code></pre></div>
-<ol>
-<li><strong>让你的分支与 upstream <code>main</code> 分支保持同步</strong>：</li>
-</ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>git<span class="w"> </span>fetch<span class="w"> </span>upstream
-<a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a>git<span class="w"> </span>rebase<span class="w"> </span>upstream/main
-</code></pre></div>
-<ol>
-<li><strong>将分支推送到你的 fork</strong>：</li>
-</ol>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>git<span class="w"> </span>push<span class="w"> </span>origin<span class="w"> </span>your-branch-name
-</code></pre></div>
+<h3 id="_16">提交信息</h3>
+<p>编写清晰、描述性的提交信息来解释你做了什么更改。没有严格的格式要求——只要确保你的信息是可理解的。</p>
+<h3 id="pull-request">推送并创建 Pull Request</h3>
 <ol>
 <li>
-<p><strong>打开 Pull Request</strong>：</p>
+<p><strong>提交你的修改</strong>：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-23-1" name="__codelineno-23-1" href="#__codelineno-23-1"></a>git<span class="w"> </span>add<span class="w"> </span>.
+<a id="__codelineno-23-2" name="__codelineno-23-2" href="#__codelineno-23-2"></a>git<span class="w"> </span>commit<span class="w"> </span>-m<span class="w"> </span><span class="s2">&quot;你的描述性信息&quot;</span>
+</code></pre></div></p>
 </li>
 <li>
-<p>进入 <a href="https://github.com/zhyan0603/GPUMDkit">GPUMDkit repository</a>。</p>
+<p><strong>保持你的分支与最新的 <code>dev</code> 分支同步</strong>：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-24-1" name="__codelineno-24-1" href="#__codelineno-24-1"></a>git<span class="w"> </span>fetch<span class="w"> </span>origin
+<a id="__codelineno-24-2" name="__codelineno-24-2" href="#__codelineno-24-2"></a>git<span class="w"> </span>rebase<span class="w"> </span>origin/dev
+</code></pre></div></p>
 </li>
-<li>点击 "Pull Requests" -&gt; "New Pull Request"。</li>
-<li>将 base branch 设置为 <code>dev</code>，用于代码审查。</li>
-<li>将 compare branch 设置为你的功能分支。</li>
 <li>
-<p>填写 PR 描述，包括：</p>
-<ul>
-<li><strong>Title</strong>：简要描述修改内容。</li>
-<li><strong>Description</strong>：详细说明修改了什么以及为什么修改。</li>
-<li><strong>Testing</strong>：说明你如何测试这些修改。</li>
-</ul>
+<p><strong>推送你的分支</strong>到你的 fork：
+   <div class="highlight"><pre><span></span><code><a id="__codelineno-25-1" name="__codelineno-25-1" href="#__codelineno-25-1"></a>git<span class="w"> </span>push<span class="w"> </span>origin<span class="w"> </span>your-branch-name
+</code></pre></div></p>
 </li>
 <li>
-<p><strong>回应审查意见</strong>：</p>
+<p><strong>创建 Pull Request</strong>：</p>
+</li>
+<li>前往 <a href="https://github.com/zhyan0603/GPUMDkit">GPUMDkit 仓库</a></li>
+<li>点击 "Pull Requests" → "New Pull Request"</li>
+<li>设置目标分支为 <code>dev</code> 进行代码审查</li>
+<li>设置比较分支为你的功能分支</li>
+<li>
+<p>填写 PR 描述：</p>
+<ul>
+<li><strong>标题</strong>：简要描述更改</li>
+<li><strong>描述</strong>：详细解释更改内容和原因</li>
+<li><strong>测试</strong>：描述你如何测试这些更改</li>
+</ul>
 </li>
 <li>
-<p>接受建议和建设性意见。</p>
+<p><strong>回应审查反馈</strong>：</p>
 </li>
-<li>及时完成要求的修改。</li>
+<li>对建议和建设性批评保持开放</li>
+<li>及时进行请求的修改</li>
 <li>
-<p>将额外提交推送到你的分支，它们会自动显示在 PR 中。</p>
+<p>推送额外提交到你的分支（它们会自动出现在 PR 中）</p>
 </li>
 <li>
-<p><strong>审查通过后</strong>：维护者会合并你的 PR。</p>
+<p><strong>批准后</strong>：维护者将合并你的 PR。</p>
 </li>
 </ol>
 <hr />
-<h2 id="_16">有问题或需要帮助？</h2>
-<p>如果你对贡献流程有疑问，或需要帮助：</p>
+<h2 id="_17">有问题或需要帮助？</h2>
+<p>如果你对贡献有疑问或需要帮助：</p>
 <ul>
-<li><strong>打开讨论</strong>：一般问题可以使用 <a href="https://github.com/zhyan0603/GPUMDkit/discussions">GitHub Discussions</a>。</li>
-<li><strong>在 issue 中提问</strong>：与具体问题相关的内容可以在对应 issue 下评论。</li>
-<li><strong>联系维护者</strong>：联系 README 中列出的核心开发者。</li>
+<li><strong>发起讨论</strong>：使用 <a href="https://github.com/zhyan0603/GPUMDkit/discussions">GitHub Discussions</a> 提出一般性问题</li>
+<li><strong>在 issue 中提问</strong>：在相关 issue 中评论以获取具体问题的帮助</li>
+<li><strong>联系维护者</strong>：联系 README 中列出的核心开发者</li>
 </ul>
 <hr />
-<p>再次感谢你为 <code>GPUMDkit</code> 做贡献。你的工作会帮助整个 GPUMD 和 NEP 社区更好地使用这个工具包。</p>
+<p>再次感谢你为 <code>GPUMDkit</code> 做出贡献！你的努力帮助这个工具包为整个 GPUMD 和 NEP 社区变得更好。</p>
 
 
 
diff --git a/docs/script.js b/docs/script.js
index 5be0d05..a1b0eec 100644
--- a/docs/script.js
+++ b/docs/script.js
@@ -83,8 +83,8 @@ const helpContentText = ` +-----------------------------------------------------
 | -chem_species Analyze chemical species        | -cbc               Charge balance check               |
 | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
+| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
+| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
 +-------------------------------------------------------------------------------------------------------+
 | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
 +-------------------------------------------------------------------------------------------------------+`;
diff --git a/docs/tutorials/en/analyzer_scripts.md b/docs/tutorials/en/analyzer_scripts.md
index d358b1f..40b057d 100644
--- a/docs/tutorials/en/analyzer_scripts.md
+++ b/docs/tutorials/en/analyzer_scripts.md
@@ -3,7 +3,15 @@
   <p style="text-align: justify;">Analyzer scripts provide structure statistics, distance checks, filters, composition analysis, outlier detection, and time estimation for extxyz datasets.</p>
 </div>
 
-**Script Location:** `Scripts/analyzer/`
+## What it does
+
+This module helps you inspect, filter, and validate structure datasets. You can check composition, analyze property ranges, detect short contacts, filter structures by various criteria, find outliers in NEP training data, and estimate remaining simulation time.
+
+## Before you start
+
+**Script location:** `Scripts/analyzer/`
+
+Make sure GPUMDkit is installed. See [Quick Start](quick_start.md) for installation instructions.
 
 ## Overview
 
@@ -20,6 +28,7 @@
 | Property filter | `gpumdkit.sh -filter_value train.xyz force 20` | Filter by energy/force/virial threshold |
 | Pair-distance range | `gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0` | Extract structures by pair distance |
 | Outlier detection | Menu 502 | Find high-RMSE structures in training set |
+| Probability density | `gpumdkit.sh -pda <ref> <traj> <element> <interval>` | 3D probability density for diffusion channels |
 | GPUMD time | `gpumdkit.sh -time gpumd` | Estimate remaining GPUMD run time |
 | NEP time | `gpumdkit.sh -time nep` | Estimate remaining NEP training time |
 
@@ -61,12 +70,16 @@ Most analyzer functions also have direct CLI shortcuts, which are listed in the
 
 `analyze_composition.py` analyzes the composition of your extxyz file and lets you export subsets.
 
-**Input file:** `train.xyz` (extxyz format)
+**What it does:** Groups structures by chemical composition and shows how many structures belong to each composition. You can export subsets by composition.
+
+**CLI mode:**
 
 ```bash
 gpumdkit.sh -analyze_comp train.xyz
 ```
 
+**Interactive mode:** Choose `501` from the analyzer menu.
+
 **Output example:**
 
 ```text
@@ -128,12 +141,16 @@ With `hist` option:
 
 `get_min_dist.py` calculates minimum interatomic distances without considering periodic boundary conditions. Fast but may be inaccurate for periodic systems.
 
-**Input file:** `dump.xyz` (extxyz format)
+**What it does:** Reports the minimum distance between each pair of elements in every frame, ignoring periodic boundary conditions.
+
+**CLI mode:**
 
 ```bash
 gpumdkit.sh -min_dist dump.xyz
 ```
 
+**Interactive mode:** Choose `507` from the analyzer menu.
+
 **Output example:**
 
 ```text
@@ -152,16 +169,22 @@ Minimum interatomic distances:
 Overall min_distance: 1.587 Å
 ```
 
+**Notes:** Use this for a quick check. For periodic systems, prefer `-min_dist_pbc` for accurate results.
+
 ### With PBC (Accurate)
 
 `get_min_dist_pbc.py` calculates minimum interatomic distances considering periodic boundary conditions.
 
-**Input file:** `dump.xyz` (extxyz format)
+**What it does:** Reports the minimum distance between each pair of elements, accounting for periodic boundary conditions.
+
+**CLI mode:**
 
 ```bash
 gpumdkit.sh -min_dist_pbc dump.xyz
 ```
 
+**Interactive mode:** Choose `507` from the analyzer menu and answer `y` when asked whether to consider PBC.
+
 **Output example:**
 
 ```text
@@ -338,11 +361,29 @@ gpumdkit.sh -time nep
 
 **Input files:** Reference structure (POSCAR), trajectory file (extxyz)
 
+**CLI mode:**
+
 ```bash
 gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25
 ```
 
-**Output:** `probability_density_0.25.vasp` — probability density grid for visualization with VESTA or similar tools.
+**Arguments:**
+
+| Argument | Meaning |
+|----------|---------|
+| `LLZO.vasp` | Reference structure (POSCAR format) |
+| `dump.xyz` | Trajectory file (extxyz format) |
+| `Li` | Target mobile species |
+| `0.25` | Grid interval for the probability density (Å) |
+
+**Output:** `probability_density_0.25.vasp` — probability density grid in VASP format for visualization with VESTA or similar tools.
+
+**Visualization suggestions:**
+
+1. Open `probability_density_0.25.vasp` in VESTA
+2. Use "Edit → Data → Volumetric Data" to adjust isosurface levels
+3. Color the probability density by value to highlight preferred diffusion pathways
+4. Overlay with the crystal structure for context
 
 ---
 
diff --git a/docs/tutorials/en/calculator_scripts.md b/docs/tutorials/en/calculator_scripts.md
index 1a261f6..5763b48 100644
--- a/docs/tutorials/en/calculator_scripts.md
+++ b/docs/tutorials/en/calculator_scripts.md
@@ -16,11 +16,11 @@
 | DOAS | `gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>` | extxyz + NEP model |
 | NEB | `gpumdkit.sh -calc neb <initial.xyz> <final.xyz> <n_images> <nep.txt>` | initial/final structures |
 | Minimization | `gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]` | structure + NEP model |
-| Neighbor list | `gpumdkit.sh -calc nlist [args...]` | structure |
-| Displacement | `gpumdkit.sh -calc disp [args...]` | trajectory + neighbor list |
-| Average structure | `gpumdkit.sh -calc avg-struct [args...]` | trajectory |
-| Octahedral tilt | `gpumdkit.sh -calc oct-tilt [args...]` | trajectory + B-O neighbor list |
-| ABO3 polarization | `gpumdkit.sh -calc pol-abo3 [args...]` | trajectory + neighbor lists |
+| Neighbor list | `gpumdkit.sh -calc nlist ...` | see [Polar Material Analysis](polar_material_analysis.md) |
+| Displacement | `gpumdkit.sh -calc disp ...` | see [Polar Material Analysis](polar_material_analysis.md) |
+| Average structure | `gpumdkit.sh -calc avg-struct ...` | see [Polar Material Analysis](polar_material_analysis.md) |
+| Octahedral tilt | `gpumdkit.sh -calc oct-tilt ...` | see [Polar Material Analysis](polar_material_analysis.md) |
+| ABO3 polarization | `gpumdkit.sh -calc pol-abo3 ...` | see [Polar Material Analysis](polar_material_analysis.md) |
 
 For a full command list:
 
@@ -194,7 +194,7 @@ pip install calorine
 gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
 ```
 
-This function is useful when you intentionally want to use a trained NEP model as a surrogate calculator. It should not be treated as a replacement for DFT unless the model quality has been carefully validated.
+Use this function to run predictions with a trained NEP model. For best results, validate model quality on your target structures before relying on the output.
 
 **Tip:** Before prediction, you may want to clean the extxyz metadata:
 
@@ -244,7 +244,7 @@ The script:
 4. groups atomic energies by element;
 5. writes the grouped values to the output file.
 
-For very large systems, doing minimization and atomistic-energy extraction directly in GPUMD may be more efficient.
+For very large systems, running minimization and atomistic-energy extraction directly in GPUMD can be more efficient.
 
 <div align="center">
   <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
@@ -327,51 +327,12 @@ gpumdkit.sh -plt rdf
 
 ## Ferroelectric and Polar Material Tools
 
-The following tools are useful for perovskite and polar-material analysis. They require `ferrodispcalc`:
+Options `406–410` cover perovskite and polar-material analysis: neighbor lists, local displacements, averaged structures, octahedral tilt, and ABO3 polarization. These tools are built on `ferrodispcalc`.
 
-```bash
-pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
-```
-
-`ferrodispcalc` currently has no associated paper to cite.
-
-### Build Neighbor Lists
-
-```bash
-gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat
-```
-
-This creates a neighbor-list file where each row stores one center atom and its nearest neighbor atoms.
-
-### Calculate Displacements
-
-```bash
-gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat
-```
-
-Use `-l 0.2` to analyze the last 20% of frames. Use `-s`, `-t`, and `-p` if you want an explicit slice.
-
-### Average a Structure
-
-```bash
-gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz
-```
-
-This is useful before displacement or polarization analysis when a representative averaged structure is needed.
-
-### Octahedral Tilt
+**Dependency:**
 
 ```bash
-gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat
-```
-
-The neighbor list should usually contain six B-O neighbors for each B-site center in an `ABO3`-like structure.
-
-### ABO3 Polarization
-
-```bash
-gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \
-  --bec Pb=2 Ti=4.0 O=-2.0 -o polarization.dat
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
 ```
 
-The `--bec` values should be chosen according to your model or reference data. The tool is designed for `ABO3`-type local polarization analysis.
+For complete argument lists, real-world workflow examples (PbTiO3 phase transition, PTO/STO superlattice topology, etc.), see **[Polar Material Analysis](polar_material_analysis.md)**.
diff --git a/docs/tutorials/en/command_reference.md b/docs/tutorials/en/command_reference.md
index f4aa1ea..fa22bed 100644
--- a/docs/tutorials/en/command_reference.md
+++ b/docs/tutorials/en/command_reference.md
@@ -35,8 +35,8 @@ The source table is maintained in `docs/command_reference.tsv`.
 | -chem_species Analyze chemical species        | -cbc               Charge balance check               |
 | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
+| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
+| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
 +-------------------------------------------------------------------------------------------------------+
 | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
 +-------------------------------------------------------------------------------------------------------+
diff --git a/docs/tutorials/en/format_conversion.md b/docs/tutorials/en/format_conversion.md
index 9995b98..f912c48 100644
--- a/docs/tutorials/en/format_conversion.md
+++ b/docs/tutorials/en/format_conversion.md
@@ -3,9 +3,17 @@
   <p style="text-align: justify;">GPUMDkit contains utilities for converting common atomistic simulation formats, with extra handling for metadata such as group labels, weights, and frame extraction.</p>
 </div>
 
-**Script Location:** `Scripts/format_conversion/`
+## What it does
 
-## Overview
+This module converts structure and trajectory files between common formats used in computational materials science. It supports VASP, LAMMPS, CP2K, ABACUS, CIF, ASE trajectories, and extxyz. It also provides tools for adding group labels, weights, extracting frames, and replicating structures.
+
+## Before you start
+
+**Script location:** `Scripts/format_conversion/`
+
+Make sure GPUMDkit is installed. See [Quick Start](quick_start.md) for installation instructions.
+
+## Supported formats
 
 The format conversion module covers:
 
@@ -96,19 +104,21 @@ Input the function number or converter keyword:
 
 ### Convert VASP calculations to extxyz
 
-If each calculation directory contains an `OUTCAR`, run:
+**What it does:** Searches a directory for VASP OUTCAR files and converts them into a single extxyz file for NEP training or analysis.
+
+**CLI mode:**
 
 ```bash
 gpumdkit.sh -out2xyz ./vasp_results/
 ```
 
-The shell version searches the target directory and converts VASP results into an extxyz file suitable for later analysis. If you prefer the Python implementation:
+The shell version searches the target directory and converts VASP results into an extxyz file. If you prefer the Python implementation:
 
 ```bash
 gpumdkit.sh -out2exyz ./vasp_results/
 ```
 
-From interactive mode, choose `101`. You will see:
+**Interactive mode:** Choose `101` from the format conversion menu. You will see:
 
 ```text
 >-------------------------------------------------<
@@ -121,9 +131,13 @@ Example: ./
 ------------>>
 ```
 
+**Output:** An extxyz file containing the converted structures, suitable for NEP training or further analysis.
+
 ### Add group labels
 
-Some GPUMD-related workflows use group labels for atom grouping, for example in species-specific MSD or diffusion calculations.
+**What it does:** Adds atom group labels to a structure file. Group labels are required by some GPUMD-related workflows, such as species-specific MSD or diffusion calculations.
+
+**CLI mode:**
 
 ```bash
 gpumdkit.sh -addgroup POSCAR Li Y Cl
@@ -131,7 +145,7 @@ gpumdkit.sh -addgroup POSCAR Li Y Cl
 
 This command reads the input structure and writes an extxyz file with group information.
 
-From interactive mode, choose `106`. You will see:
+**Interactive mode:** Choose `106` from the format conversion menu. You will see:
 
 ```text
 >-------------------------------------------------<
@@ -144,6 +158,8 @@ Example: POSCAR Li Y Cl
 ------------>>
 ```
 
+**Output:** An extxyz file with group labels added.
+
 ## Script Details
 
 ### POSCAR to extxyz
diff --git a/docs/tutorials/en/index.md b/docs/tutorials/en/index.md
index a6333ce..03dc970 100644
--- a/docs/tutorials/en/index.md
+++ b/docs/tutorials/en/index.md
@@ -3,18 +3,25 @@
   <p style="text-align: justify;">Welcome to <strong>GPUMDkit</strong>, a command-line toolkit for GPUMD and NEP.</p>
 </div>
 
-## What is GPUMDkit?
+## What it does
 
-GPUMDkit streamlines common tasks in computational materials science:
+GPUMDkit helps you perform common tasks in computational materials science without writing custom scripts. It supports format conversion, structure analysis, property calculation, visualization, and batch workflows — all from one command-line tool.
 
-- **Format Conversion**: Convert between VASP, LAMMPS, CP2K, ABACUS, CIF, and extxyz formats
-- **Visualization**: Plotting tools for NEP training, MD simulations, and analysis
-- **Calculators**: Compute ionic conductivity, descriptors, MSD, NEB, and more
-- **Analyzers**: Structure validation, filtering, composition analysis
-- **Workflows**: Batch processing for DFT and MD simulations
-- **Sampling**: Structure selection using uniform, random, or FPS methods
+## Common Tasks
 
-## Quick Start
+| I want to... | Tutorial |
+|--------------|----------|
+| Install GPUMDkit and run my first command | [Quick Start](quick_start.md) |
+| Convert VASP, LAMMPS, CP2K, or CIF files to extxyz | [Format Conversion](format_conversion.md) |
+| Check structure distances, filter datasets, or find outliers | [Analyzer Scripts](analyzer_scripts.md) |
+| Calculate MSD, ionic conductivity, or descriptors | [Calculator Scripts](calculator_scripts.md) |
+| Analyze polar materials, ferroelectrics, or ABO3 systems | [Polar Material Analysis](polar_material_analysis.md) |
+| Plot NEP training results or thermodynamic data | [Plot Scripts](plot_scripts.md) |
+| Run batch DFT or MD simulations | [Workflow Scripts](workflow_scripts.md) |
+| Select representative structures from a dataset | [Structure Sampling](structure_sampling.md) |
+| Add my own shortcuts to GPUMDkit | [Custom Commands](custom_commands.md) |
+
+## Before you start
 
 ### Installation
 
@@ -32,57 +39,30 @@ conda activate gpumdkit
 pip install neptrain dpdata calorine
 ```
 
-### Usage
+## Interactive mode
 
 ```bash
-# Interactive mode
 gpumdkit.sh
-
-# Command-line mode
-gpumdkit.sh -<option> [args...]
-
-# Get help
-gpumdkit.sh -h
 ```
 
-## Tutorials
+This opens a menu where you can select modules by number.
 
-| Tutorial | Description |
-|----------|-------------|
-| [Quick Start](quick_start.md) | Installation and first steps |
-| [Command Reference](command_reference.md) | One-page CLI and menu reference |
-| [Format Conversion](format_conversion.md) | Convert between file formats |
-| [Calculator Scripts](calculator_scripts.md) | Compute material properties |
-| [Analyzer Scripts](analyzer_scripts.md) | Structure analysis and validation |
-| [Plot Scripts](plot_scripts.md) | Plotting and visualization |
-| [Workflow Scripts](workflow_scripts.md) | Batch processing and automation |
-| [Structure Sampling](structure_sampling.md) | Structure selection methods |
-| [Custom Commands](custom_commands.md) | User-defined GPUMDkit shortcuts |
-| [Active Learning Workflow](active_learning_workflow.md) | Batch active-learning workflow notes |
-| [Polar Material Analysis](polar_material_analysis.md) | Ferroelectric and polarization tools |
-| [Contributing to GPUMDkit](contributing_to_gpumdkit.md) | Development notes |
-
-## Example: Convert VASP OUTCARs
+## CLI mode
 
 ```bash
-gpumdkit.sh -out2xyz ./vasp_results/
+gpumdkit.sh -<option> [args...]
 ```
 
-## Example: Plot NEP Results
+For example:
 
 ```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
 gpumdkit.sh -plt train
-gpumdkit.sh -plt prediction
-```
-
-## Example: Ionic Conductivity
-
-```bash
 gpumdkit.sh -calc msd trajectory.xyz Li 10
-gpumdkit.sh -calc ionic-cond Li 1
-gpumdkit.sh -plt msd
 ```
 
+Use `gpumdkit.sh -h` to see all available options.
+
 ## Module Overview
 
 | Module | Menu | CLI | Description |
@@ -95,6 +75,23 @@ gpumdkit.sh -plt msd
 | Visualization | 6 | `-plt <type>` | Plotting tools |
 | Utilities | 7 | `-time`, `-clean` | Utility functions |
 
+## All Tutorials
+
+| Tutorial | Description |
+|----------|-------------|
+| [Quick Start](quick_start.md) | Installation and first steps |
+| [Command Reference](command_reference.md) | One-page CLI and menu reference |
+| [Format Conversion](format_conversion.md) | Convert between file formats |
+| [Calculator Scripts](calculator_scripts.md) | Compute material properties |
+| [Analyzer Scripts](analyzer_scripts.md) | Structure analysis and validation |
+| [Plot Scripts](plot_scripts.md) | Plotting and visualization |
+| [Workflow Scripts](workflow_scripts.md) | Batch processing and automation |
+| [Structure Sampling](structure_sampling.md) | Structure selection methods |
+| [Custom Commands](custom_commands.md) | User-defined GPUMDkit shortcuts |
+| [Active Learning Workflow](active_learning_workflow.md) | Batch active-learning workflow notes |
+| [Polar Material Analysis](polar_material_analysis.md) | Ferroelectric and polarization tools |
+| [Contributing to GPUMDkit](contributing_to_gpumdkit.md) | Development notes |
+
 ## Links
 
 - GitHub: https://github.com/zhyan0603/GPUMDkit
diff --git a/docs/tutorials/en/plot_scripts.md b/docs/tutorials/en/plot_scripts.md
index 9315480..73a4933 100644
--- a/docs/tutorials/en/plot_scripts.md
+++ b/docs/tutorials/en/plot_scripts.md
@@ -467,9 +467,11 @@ gpumdkit.sh -plt rdf_pmf
 
 ### plt_vac.py
 
-Plots velocity autocorrelation function.
+Plots velocity autocorrelation function (VAC). Useful for analyzing phonon properties and atomic dynamics.
 
-**Input File:** `vac.out`
+**Input File:** `sdc.out` (the VAC columns are read from this file by the plotting script)
+
+**Output:** Interactive plot or `vac.png` (with `save` option)
 
 ```bash
 gpumdkit.sh -plt vac
@@ -479,7 +481,11 @@ gpumdkit.sh -plt vac
 
 ### plt_cohesive.py
 
-Plots cohesive energy curve.
+Plots cohesive energy curve from `cohesive.out`. Useful for analyzing lattice stability and equilibrium lattice constants.
+
+**Input File:** `cohesive.out` (isotropic scaling factor vs cohesive energy)
+
+**Output:** Interactive plot or `cohesive.png` (with `save` option)
 
 ```bash
 gpumdkit.sh -plt cohesive
@@ -606,7 +612,7 @@ gpumdkit.sh -plt doas doas.out Li
 
 ## Plane-Grid Plot for Polar Materials
 
-This workflow maps displacement or polarization data onto a grid and plots selected plane profiles.
+This workflow maps displacement or polarization data onto a grid and plots selected plane profiles. For detailed usage and real-world examples, see **[Polar Material Analysis](polar_material_analysis.md)**.
 
 **Dependency:**
 
@@ -653,8 +659,8 @@ gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb
 | `arrhenius_sigma` / `sigma` | `*K/{model.xyz, run.in, thermo.out, msd.out}` | Arrhenius ionic conductivity |
 | `rdf` | `rdf.out` | Radial distribution function |
 | `rdf_pmf` | `rdf.out` | RDF + potential of mean force |
-| `vac` | `vac.out` | Velocity autocorrelation |
-| `cohesive` | — | Cohesive energy curve |
+| `vac` | `sdc.out` | Velocity autocorrelation |
+| `cohesive` | `cohesive.out` | Cohesive energy curve |
 | `net_force` | `train.xyz` | Net force distribution |
 | `doas` | `doas.out` | Density of atomistic states |
 | `des` | `descriptors.npy` | Descriptor PCA/UMAP |
diff --git a/docs/tutorials/en/polar_material_analysis.md b/docs/tutorials/en/polar_material_analysis.md
index 207c60e..536d557 100644
--- a/docs/tutorials/en/polar_material_analysis.md
+++ b/docs/tutorials/en/polar_material_analysis.md
@@ -444,9 +444,9 @@ gpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-x
     <img src="../../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
 </div>
 
-This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero. By analyzing how polarization varies around the vortex core, you can estimate the local dielectric response, but that is beyond the scope of this tutorial.
+This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero.
 
-Note: this figure uses a different colormap from the default GPUMDkit plotting style. The default output does not look exactly the same, but you can get this style with small plotting-script changes.
+Note: the example figure uses a custom colormap. The default GPUMDkit output uses a different style, which can be adjusted by editing the plotting script.
 
 ### Other Systems
 
diff --git a/docs/tutorials/en/quick_start.md b/docs/tutorials/en/quick_start.md
index ad1dd16..de72e2a 100644
--- a/docs/tutorials/en/quick_start.md
+++ b/docs/tutorials/en/quick_start.md
@@ -1,18 +1,22 @@
 <div align="center">
   <h1>🚀 Quick Start</h1>
-  <p style="text-align: justify;">This page introduces the basic installation and several common commands. GPUMDkit can be used through the interactive menu or by direct command-line options.</p>
+  <p style="text-align: justify;">This page helps you install GPUMDkit and run your first commands. You can use GPUMDkit through an interactive menu or direct command-line options.</p>
 </div>
 
-## 1. Prepare a Python Environment
+## What it does
 
-You can use a clean conda environment:
+GPUMDkit provides a single entry point for common tasks in computational materials science — format conversion, structure analysis, property calculation, and visualization — without writing custom scripts.
+
+## Before you start
+
+### 1. Prepare a Python environment
 
 ```bash
 conda create -n gpumdkit python=3.12
 conda activate gpumdkit
 ```
 
-Some optional functions use additional packages:
+Some optional functions require additional packages:
 
 ```bash
 pip install neptrain dpdata calorine
@@ -20,18 +24,13 @@ pip install neptrain dpdata calorine
 
 Other Python dependencies are loaded by the corresponding scripts. If a package is missing, Python will report it when that function is used.
 
-## 2. Install GPUMDkit
+### 2. Install GPUMDkit
 
-Clone the repository:
+Clone the repository and run the installer:
 
 ```bash
 git clone https://github.com/zhyan0603/GPUMDkit.git
 cd GPUMDkit
-```
-
-Run the installer:
-
-```bash
 source ./install.sh
 ```
 
@@ -70,58 +69,21 @@ New path:
 Replace the existing GPUMDkit configuration with the new path? [y/N]:
 ```
 
-Check the command:
+### 3. Verify the installation
 
 ```bash
 gpumdkit.sh -h
 ```
 
-The help table:
+This prints a help table listing all available options.
 
-```text
-+-------------------------------------------------------------------------------------------------------+
-|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
-+-------------------------------------------------------------------------------------------------------+
-|                                          MAIN FUNCTIONS                                               |
-+-------------------------------------------------------------------------------------------------------+
-| -h            Show this help table            | -plt <type>        Plot and visualization tools       |
-| -calc <type>  Calculator tools                | -time <gpumd|nep>  Time-consuming analyzer            |
-| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
-+-------------------------------------------------------------------------------------------------------+
-|                                         FORMAT CONVERSION                                             |
-+-------------------------------------------------------------------------------------------------------+
-| -out2xyz      OUTCAR -> extxyz (shell)        | -out2exyz          OUTCAR -> extxyz (python)          |
-| -cp2k2xyz     CP2K log -> xyz                 | -xdat2exyz         XDATCAR -> extxyz                  |
-| -cif2pos      cif -> POSCAR                   | -cif2exyz          cif -> extxyz                      |
-| -pos2exyz     POSCAR -> extxyz                | -exyz2pos          extxyz -> POSCAR                   |
-| -pos2lmp      POSCAR -> LAMMPS data           | -lmp2exyz          LAMMPS dump -> extxyz              |
-| -traj2exyz    ASE traj -> extxyz              | -replicate         Replicate structure                |
-| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
-| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
-| -frame_range  Extract frames by range         |                                                       |
-+-------------------------------------------------------------------------------------------------------+
-|                                            ANALYSIS                                                   |
-+-------------------------------------------------------------------------------------------------------+
-| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
-| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
-| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
-| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
-| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
-+-------------------------------------------------------------------------------------------------------+
-| Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
-+-------------------------------------------------------------------------------------------------------+
-```
-
-## 3. Usage Modes
-
-### Interactive Mode
+## Interactive mode
 
 ```bash
 gpumdkit.sh
 ```
 
-Main menu:
+This opens the main menu:
 
 ```text
            ____ ____  _   _ __  __ ____  _    _ _
@@ -144,41 +106,43 @@ Main menu:
  Input the function number:
 ```
 
-### Command-Line Mode
+Select a module by number. Each module provides sub-menus with specific functions.
+
+## CLI mode
 
 Direct commands use fixed positional arguments:
 
 ```bash
-gpumdkit.sh -pos2exyz POSCAR model.xyz
-gpumdkit.sh -plt train
-gpumdkit.sh -plt thermo
+gpumdkit.sh -<option> [args...]
 ```
 
-For example:
+Examples:
 
 ```bash
 gpumdkit.sh -pos2exyz POSCAR model.xyz
+gpumdkit.sh -plt train
+gpumdkit.sh -calc msd trajectory.xyz Li 10
 ```
 
-means reading `POSCAR` and writing `model.xyz`.
+The first example reads `POSCAR` and writes `model.xyz`.
 
-## 4. Practical Examples
+## Common examples
 
-### Convert POSCAR to extxyz
+### Convert a POSCAR to extxyz
 
 ```bash
 gpumdkit.sh -pos2exyz POSCAR model.xyz
 ```
 
-### Add GPUMD Group Labels
+### Add GPUMD group labels
 
 ```bash
 gpumdkit.sh -addgroup POSCAR Li Y Cl
 ```
 
-Group labels are used by some GPUMD-related workflows and analyses that need atom grouping, such as species-specific MSD or diffusion calculations.
+Group labels are used by some GPUMD-related workflows that need atom grouping, such as species-specific MSD or diffusion calculations.
 
-### Plot NEP Training Results
+### Plot NEP training results
 
 ```bash
 gpumdkit.sh -plt train
@@ -188,7 +152,7 @@ gpumdkit.sh -plt train
   <img src="../../Gallery/train.png" alt="NEP training results" width="72%" />
 </div>
 
-### Plot NEP Test Results
+### Plot NEP test results
 
 ```bash
 gpumdkit.sh -plt test
@@ -198,7 +162,7 @@ gpumdkit.sh -plt test
   <img src="../../Gallery/prediction.png" alt="NEP test results" width="72%" />
 </div>
 
-### Plot Thermodynamic Data
+### Plot thermodynamic data
 
 ```bash
 gpumdkit.sh -plt thermo
@@ -208,7 +172,7 @@ gpumdkit.sh -plt thermo
   <img src="../../Gallery/thermo.png" alt="Thermo plot" width="72%" />
 </div>
 
-### Plot MSD and Self-Diffusion Coefficient
+### Plot MSD and self-diffusion coefficient
 
 ```bash
 gpumdkit.sh -plt msd
@@ -220,12 +184,8 @@ gpumdkit.sh -plt sdc
   <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
 </div>
 
-## 5. Help
+## Notes
 
-```bash
-gpumdkit.sh -h
-gpumdkit.sh -plt -h
-gpumdkit.sh -calc -h
-gpumdkit.sh -plt train -h
-gpumdkit.sh -calc msd -h
-```
+- Use `gpumdkit.sh -h` to see all available options.
+- Use `gpumdkit.sh -<option> -h` to get help for a specific option (e.g., `gpumdkit.sh -plt train -h`).
+- For detailed usage of each module, see the corresponding tutorial pages linked in the [index](index.md).
diff --git a/docs/tutorials/zh/index.md b/docs/tutorials/zh/index.md
index 9027e2b..ba71e98 100644
--- a/docs/tutorials/zh/index.md
+++ b/docs/tutorials/zh/index.md
@@ -3,18 +3,25 @@
   <p style="text-align: justify;">欢迎使用 <strong>GPUMDkit</strong>，这是一个面向 GPUMD 和 NEP 的命令行工具包。</p>
 </div>
 
-## 什么是 GPUMDkit？
+## 功能简介
 
-GPUMDkit 简化了计算材料科学中的常见任务：
+GPUMDkit 帮助你在计算材料科学研究中完成常见任务，无需编写自定义脚本。它支持格式转换、结构分析、性质计算、可视化和批量工作流——全部通过一个命令行工具完成。
 
-- **格式转换**：在 VASP、LAMMPS、CP2K、ABACUS、CIF 和 extxyz 格式之间转换
-- **可视化**：用于 NEP 训练、MD 模拟和分析的绘图工具
-- **计算器**：计算离子电导率、描述符、MSD、NEB 等
-- **分析工具**：结构验证、过滤、成分分析
-- **工作流**：DFT 和 MD 模拟的批处理
-- **结构采样**：使用均匀、随机或 FPS 方法选择结构
+## 常见任务
 
-## 快速开始
+| 我想要... | 教程 |
+|-----------|------|
+| 安装 GPUMDkit 并运行第一个命令 | [快速入门](快速入门.md) |
+| 将 VASP、LAMMPS、CP2K 或 CIF 文件转换为 extxyz | [格式转换](格式转换.md) |
+| 检查结构距离、过滤数据集或查找异常值 | [分析工具](分析工具.md) |
+| 计算 MSD、离子电导率或描述符 | [计算器脚本](计算器脚本.md) |
+| 分析极性材料、铁电体或 ABO3 体系 | [极性材料分析](极性材料分析.md) |
+| 绘制 NEP 训练结果或热力学数据 | [绘图脚本](绘图脚本.md) |
+| 运行批量 DFT 或 MD 模拟 | [工作流脚本](工作流脚本.md) |
+| 从数据集中选择代表性结构 | [结构采样](结构采样.md) |
+| 添加自己的 GPUMDkit 快捷命令 | [自定义命令](自定义命令.md) |
+
+## 准备工作
 
 ### 安装
 
@@ -32,57 +39,30 @@ conda activate gpumdkit
 pip install neptrain dpdata calorine
 ```
 
-### 使用方法
+## 交互模式
 
 ```bash
-# 交互模式
 gpumdkit.sh
-
-# 命令行模式
-gpumdkit.sh -<选项> [参数...]
-
-# 获取帮助
-gpumdkit.sh -h
 ```
 
-## 教程列表
+打开菜单后，按数字选择模块。
 
-| 教程 | 描述 |
-|------|------|
-| [快速入门](快速入门.md) | 安装和第一步 |
-| [命令参考](命令参考.md) | 常用 CLI 和菜单入口速查 |
-| [格式转换](格式转换.md) | 在文件格式之间转换 |
-| [计算器脚本](计算器脚本.md) | 计算材料属性 |
-| [分析工具](分析工具.md) | 结构分析和验证 |
-| [绘图脚本](绘图脚本.md) | 绘图和可视化 |
-| [工作流脚本](工作流脚本.md) | 批处理和自动化 |
-| [结构采样](结构采样.md) | 结构选择方法 |
-| [自定义命令](自定义命令.md) | 用户自定义 GPUMDkit 快捷命令 |
-| [主动学习工作流](主动学习工作流.md) | 批量主动学习流程说明 |
-| [极性材料分析](极性材料分析.md) | 铁电和极化相关工具 |
-| [贡献指南](贡献指南.md) | 开发和贡献说明 |
-
-## 示例：转换 VASP OUTCAR
+## 命令行模式
 
 ```bash
-gpumdkit.sh -out2xyz ./vasp_results/
+gpumdkit.sh -<选项> [参数...]
 ```
 
-## 示例：绘制 NEP 结果
+例如：
 
 ```bash
+gpumdkit.sh -pos2exyz POSCAR model.xyz
 gpumdkit.sh -plt train
-gpumdkit.sh -plt prediction
-```
-
-## 示例：离子电导率
-
-```bash
 gpumdkit.sh -calc msd trajectory.xyz Li 10
-gpumdkit.sh -calc ionic-cond Li 1
-gpumdkit.sh -plt msd
 ```
 
+使用 `gpumdkit.sh -h` 查看所有可用选项。
+
 ## 模块概览
 
 | 模块 | 菜单 | CLI | 描述 |
@@ -95,6 +75,23 @@ gpumdkit.sh -plt msd
 | 可视化 | 6 | `-plt <类型>` | 绘图工具 |
 | 实用工具 | 7 | `-time`, `-clean` | 实用功能 |
 
+## 全部教程
+
+| 教程 | 描述 |
+|------|------|
+| [快速入门](快速入门.md) | 安装和第一步 |
+| [命令参考](命令参考.md) | 常用 CLI 和菜单入口速查 |
+| [格式转换](格式转换.md) | 在文件格式之间转换 |
+| [计算器脚本](计算器脚本.md) | 计算材料属性 |
+| [分析工具](分析工具.md) | 结构分析和验证 |
+| [绘图脚本](绘图脚本.md) | 绘图和可视化 |
+| [工作流脚本](工作流脚本.md) | 批处理和自动化 |
+| [结构采样](结构采样.md) | 结构选择方法 |
+| [自定义命令](自定义命令.md) | 用户自定义 GPUMDkit 快捷命令 |
+| [主动学习工作流](主动学习工作流.md) | 批量主动学习流程说明 |
+| [极性材料分析](极性材料分析.md) | 铁电和极化相关工具 |
+| [贡献指南](贡献指南.md) | 开发和贡献说明 |
+
 ## 链接
 
 - GitHub: https://github.com/zhyan0603/GPUMDkit
diff --git "a/docs/tutorials/zh/\345\210\206\346\236\220\345\267\245\345\205\267.md" "b/docs/tutorials/zh/\345\210\206\346\236\220\345\267\245\345\205\267.md"
index dbaf464..7453513 100644
--- "a/docs/tutorials/zh/\345\210\206\346\236\220\345\267\245\345\205\267.md"
+++ "b/docs/tutorials/zh/\345\210\206\346\236\220\345\267\245\345\205\267.md"
@@ -3,8 +3,16 @@
   <p style="text-align: justify;">分析脚本为 extxyz 数据集提供结构统计、距离检查、过滤、成分分析、异常检测和时间估算功能。</p>
 </div>
 
+## 功能简介
+
+本模块帮助你检查、过滤和验证结构数据集。可以检查成分、分析性质范围、检测短距离接触、按各种条件过滤结构、查找 NEP 训练数据中的异常值，以及估算剩余模拟时间。
+
+## 准备工作
+
 **脚本位置：** `Scripts/analyzer/`
 
+确保已安装 GPUMDkit。安装说明请参见[快速入门](快速入门.md)。
+
 ## 概览
 
 | 任务 | 命令 | 用途 |
@@ -20,6 +28,7 @@
 | 性质过滤 | `gpumdkit.sh -filter_value train.xyz force 20` | 按能量/力/virial 阈值过滤 |
 | 对距离范围 | `gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0` | 按对距离提取结构 |
 | 异常检测 | 菜单 502 | 查找训练集中高 RMSE 的结构 |
+| 概率密度 | `gpumdkit.sh -pda <参考结构> <轨迹> <元素> <网格间距>` | 3D 概率密度分析扩散通道 |
 | GPUMD 时间 | `gpumdkit.sh -time gpumd` | 估算 GPUMD 剩余运行时间 |
 | NEP 时间 | `gpumdkit.sh -time nep` | 估算 NEP 剩余训练时间 |
 
@@ -61,12 +70,16 @@ Input the function number:
 
 `analyze_composition.py` 分析 extxyz 文件的成分，并允许导出子集。
 
-**输入文件：** `train.xyz`（extxyz 格式）
+**功能：** 按化学成分对结构分组，并显示每种成分的结构数量。可以按成分导出子集。
+
+**命令行模式：**
 
 ```bash
 gpumdkit.sh -analyze_comp train.xyz
 ```
 
+**交互模式：** 在分析工具菜单中选择 `501`。
+
 **输出示例：**
 
 ```text
@@ -128,12 +141,16 @@ Force range: 0.03210566767721861 to 9.230115912468435
 
 `get_min_dist.py` 计算不考虑周期性边界条件的最短原子间距。速度快，但对周期性体系可能不准确。
 
-**输入文件：** `dump.xyz`（extxyz 格式）
+**功能：** 报告每帧中每对元素之间的最短距离，忽略周期性边界条件。
+
+**命令行模式：**
 
 ```bash
 gpumdkit.sh -min_dist dump.xyz
 ```
 
+**交互模式：** 在分析工具菜单中选择 `507`。
+
 **输出示例：**
 
 ```text
@@ -152,16 +169,22 @@ Minimum interatomic distances:
 Overall min_distance: 1.587 Å
 ```
 
+**说明：** 用于快速检查。对于周期性体系，建议使用 `-min_dist_pbc` 获得准确结果。
+
 ### 含 PBC（准确）
 
 `get_min_dist_pbc.py` 计算考虑周期性边界条件的最短原子间距。
 
-**输入文件：** `dump.xyz`（extxyz 格式）
+**功能：** 报告每对元素之间的最短距离，考虑周期性边界条件。
+
+**命令行模式：**
 
 ```bash
 gpumdkit.sh -min_dist_pbc dump.xyz
 ```
 
+**交互模式：** 在分析工具菜单中选择 `507`，当提示是否考虑 PBC 时输入 `y`。
+
 **输出示例：**
 
 ```text
@@ -338,11 +361,29 @@ gpumdkit.sh -time nep
 
 **输入文件：** 参考结构（POSCAR）、轨迹文件（extxyz）
 
+**命令行模式：**
+
 ```bash
 gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25
 ```
 
-**输出：** `probability_density_0.25.vasp` — 概率密度网格，可用 VESTA 等工具可视化。
+**参数说明：**
+
+| 参数 | 含义 |
+|------|------|
+| `LLZO.vasp` | 参考结构（POSCAR 格式） |
+| `dump.xyz` | 轨迹文件（extxyz 格式） |
+| `Li` | 目标移动离子 |
+| `0.25` | 概率密度网格间距（Å） |
+
+**输出：** `probability_density_0.25.vasp` — VASP 格式的概率密度网格，可用 VESTA 等工具可视化。
+
+**可视化建议：**
+
+1. 在 VESTA 中打开 `probability_density_0.25.vasp`
+2. 使用 "Edit → Data → Volumetric Data" 调整等值面级别
+3. 按数值对概率密度着色，以突出优选扩散路径
+4. 叠加晶体结构作为参考
 
 ---
 
diff --git "a/docs/tutorials/zh/\345\221\275\344\273\244\345\217\202\350\200\203.md" "b/docs/tutorials/zh/\345\221\275\344\273\244\345\217\202\350\200\203.md"
index 2a7a845..22d5d53 100644
--- "a/docs/tutorials/zh/\345\221\275\344\273\244\345\217\202\350\200\203.md"
+++ "b/docs/tutorials/zh/\345\221\275\344\273\244\345\217\202\350\200\203.md"
@@ -35,8 +35,8 @@
 | -chem_species Analyze chemical species        | -cbc               Charge balance check               |
 | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-| -pda          Probability density analysis    | -hbond             Hydrogen-bond analysis             |
-| -pynep        Deprecated PyNEP sampling       | -filter_box        Filter by box-edge length          |
+| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
+| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
 +-------------------------------------------------------------------------------------------------------+
 | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
 +-------------------------------------------------------------------------------------------------------+
diff --git "a/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md" "b/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md"
index d326281..854491d 100644
--- "a/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md"
+++ "b/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md"
@@ -1,11 +1,15 @@
 <div align="center">
   <h1>🚀 快速入门</h1>
-  <p style="text-align: justify;">本页介绍 GPUMDkit 的基本安装方式和几个常用命令。GPUMDkit 既可以通过交互菜单使用，也可以直接通过命令行选项调用。</p>
+  <p style="text-align: justify;">本页帮助你安装 GPUMDkit 并运行第一个命令。你可以通过交互菜单或直接使用命令行选项来使用 GPUMDkit。</p>
 </div>
 
-## 1. 准备 Python 环境
+## 功能简介
 
-可以使用干净的 conda 环境：
+GPUMDkit 为计算材料科学中的常见任务提供统一入口——格式转换、结构分析、性质计算和可视化——无需编写自定义脚本。
+
+## 准备工作
+
+### 1. 准备 Python 环境
 
 ```bash
 conda create -n gpumdkit python=3.12
@@ -20,18 +24,13 @@ pip install neptrain dpdata calorine
 
 其他 Python 依赖由对应脚本在运行时导入。如果缺少某个包，使用对应功能时 Python 会给出提示。
 
-## 2. 安装 GPUMDkit
+### 2. 安装 GPUMDkit
 
-克隆仓库：
+克隆仓库并运行安装脚本：
 
 ```bash
 git clone https://github.com/zhyan0603/GPUMDkit.git
 cd GPUMDkit
-```
-
-运行安装脚本：
-
-```bash
 source ./install.sh
 ```
 
@@ -70,58 +69,21 @@ New path:
 Replace the existing GPUMDkit configuration with the new path? [y/N]:
 ```
 
-检查命令：
+### 3. 验证安装
 
 ```bash
 gpumdkit.sh -h
 ```
 
-帮助表：
+此命令会打印帮助表，列出所有可用选项。
 
-```text
-+-------------------------------------------------------------------------------------------------------+
-|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
-+-------------------------------------------------------------------------------------------------------+
-|                                          MAIN FUNCTIONS                                               |
-+-------------------------------------------------------------------------------------------------------+
-| -h            Show this help table            | -plt <type>        Plot and visualization tools       |
-| -calc <type>  Calculator tools                | -time <gpumd|nep>  Time-consuming analyzer            |
-| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
-+-------------------------------------------------------------------------------------------------------+
-|                                         FORMAT CONVERSION                                             |
-+-------------------------------------------------------------------------------------------------------+
-| -out2xyz      OUTCAR -> extxyz (shell)        | -out2exyz          OUTCAR -> extxyz (python)          |
-| -cp2k2xyz     CP2K log -> xyz                 | -xdat2exyz         XDATCAR -> extxyz                  |
-| -cif2pos      cif -> POSCAR                   | -cif2exyz          cif -> extxyz                      |
-| -pos2exyz     POSCAR -> extxyz                | -exyz2pos          extxyz -> POSCAR                   |
-| -pos2lmp      POSCAR -> LAMMPS data           | -lmp2exyz          LAMMPS dump -> extxyz              |
-| -traj2exyz    ASE traj -> extxyz              | -replicate         Replicate structure                |
-| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
-| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
-| -frame_range  Extract frames by range         |                                                       |
-+-------------------------------------------------------------------------------------------------------+
-|                                            ANALYSIS                                                   |
-+-------------------------------------------------------------------------------------------------------+
-| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
-| -chem_species Analyze chemical species        | -cbc               Charge balance check               |
-| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
-| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
-| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
-| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
-+-------------------------------------------------------------------------------------------------------+
-| Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
-+-------------------------------------------------------------------------------------------------------+
-```
-
-## 3. 使用方式
-
-### 交互模式
+## 交互模式
 
 ```bash
 gpumdkit.sh
 ```
 
-主菜单：
+打开主菜单：
 
 ```text
            ____ ____  _   _ __  __ ____  _    _ _
@@ -144,25 +106,27 @@ gpumdkit.sh
  Input the function number:
 ```
 
-### 命令行模式
+按数字选择模块。每个模块提供包含具体功能的子菜单。
+
+## 命令行模式
 
 直接命令使用固定的位置参数：
 
 ```bash
-gpumdkit.sh -pos2exyz POSCAR model.xyz
-gpumdkit.sh -plt train
-gpumdkit.sh -plt thermo
+gpumdkit.sh -<选项> [参数...]
 ```
 
-例如：
+示例：
 
 ```bash
 gpumdkit.sh -pos2exyz POSCAR model.xyz
+gpumdkit.sh -plt train
+gpumdkit.sh -calc msd trajectory.xyz Li 10
 ```
 
-表示读取 `POSCAR`，写出 `model.xyz`。
+第一个示例读取 `POSCAR`，写出 `model.xyz`。
 
-## 4. 实际例子
+## 常见示例
 
 ### POSCAR 转 extxyz
 
@@ -220,12 +184,8 @@ gpumdkit.sh -plt sdc
   <img src="../../Gallery/sdc.png" alt="SDC plot" width="45%" />
 </div>
 
-## 5. 获取帮助
+## 说明
 
-```bash
-gpumdkit.sh -h
-gpumdkit.sh -plt -h
-gpumdkit.sh -calc -h
-gpumdkit.sh -plt train -h
-gpumdkit.sh -calc msd -h
-```
+- 使用 `gpumdkit.sh -h` 查看所有可用选项。
+- 使用 `gpumdkit.sh -<选项> -h` 获取特定选项的帮助（例如 `gpumdkit.sh -plt train -h`）。
+- 各模块的详细用法请参见[首页](index.md)中链接的对应教程页面。
diff --git "a/docs/tutorials/zh/\346\236\201\346\200\247\346\235\220\346\226\231\345\210\206\346\236\220.md" "b/docs/tutorials/zh/\346\236\201\346\200\247\346\235\220\346\226\231\345\210\206\346\236\220.md"
index 619892d..5999e55 100644
--- "a/docs/tutorials/zh/\346\236\201\346\200\247\346\235\220\346\226\231\345\210\206\346\236\220.md"
+++ "b/docs/tutorials/zh/\346\236\201\346\200\247\346\235\220\346\226\231\345\210\206\346\236\220.md"
@@ -444,9 +444,9 @@ gpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-x
     <img src="../../Gallery/PTO-STO.png" alt="PTO_STO" width="65%" />
 </div>
 
-这会得到与前面展示相似的图。在 PTO 区域可以看到类似涡旋的极化图样，而 STO 区域的极化接近于零。通过分析涡旋核附近极化的变化，可以估计局域介电响应，但这超出了本教程范围。
+这会得到与前面展示相似的图。在 PTO 区域可以看到类似涡旋的极化图样，而 STO 区域的极化接近于零。
 
-注意：该图使用的 colormap 与 GPUMDkit 默认绘图风格不同。默认输出不会与图中完全一致，但可以通过少量修改绘图脚本获得这种风格。
+注意：示例图使用了自定义 colormap。GPUMDkit 默认输出使用不同风格，可通过修改绘图脚本进行调整。
 
 ### 其他体系
 
diff --git "a/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md" "b/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
index 29b61b8..d69fcf8 100644
--- "a/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
+++ "b/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
@@ -3,8 +3,16 @@
   <p style="text-align: justify;">格式转换模块用于在常见原子模拟文件格式之间转换，同时提供 group 标签、权重、帧提取等元数据处理功能。</p>
 </div>
 
+## 功能简介
+
+本模块在计算材料科学中常用的结构和轨迹文件格式之间进行转换。支持 VASP、LAMMPS、CP2K、ABACUS、CIF、ASE 轨迹和 extxyz 格式。还提供添加 group 标签、权重、提取帧和扩胞等工具。
+
+## 准备工作
+
 **脚本位置：** `Scripts/format_conversion/`
 
+确保已安装 GPUMDkit。安装说明请参见[快速入门](快速入门.md)。
+
 ## 支持的格式
 
 - **VASP**：`POSCAR`、`CONTCAR`、`OUTCAR`、`XDATCAR`
@@ -94,7 +102,9 @@ Input the function number or converter keyword:
 
 ### 转换 VASP 结果
 
-如果每个计算目录下都有 `OUTCAR`：
+**功能：** 在目录中搜索 VASP OUTCAR 文件，并将它们转换为单个 extxyz 文件，用于 NEP 训练或分析。
+
+**命令行模式：**
 
 ```bash
 gpumdkit.sh -out2xyz ./vasp_results/
@@ -106,7 +116,7 @@ gpumdkit.sh -out2xyz ./vasp_results/
 gpumdkit.sh -out2exyz ./vasp_results/
 ```
 
-在交互模式中选择 `101`，会看到：
+**交互模式：** 在格式转换菜单中选择 `101`，会看到：
 
 ```text
 >-------------------------------------------------<
@@ -119,9 +129,13 @@ Example: ./
 ------------>>
 ```
 
+**输出：** 包含转换后结构的 extxyz 文件，可用于 NEP 训练或进一步分析。
+
 ### 添加 group 标签
 
-一些 GPUMD 相关流程会使用 group 标签进行原子分组，例如特定元素的 MSD 或扩散性质计算。
+**功能：** 为结构文件添加原子 group 标签。一些 GPUMD 相关流程需要 group 标签，例如特定元素的 MSD 或扩散性质计算。
+
+**命令行模式：**
 
 ```bash
 gpumdkit.sh -addgroup POSCAR Li Y Cl
@@ -129,7 +143,7 @@ gpumdkit.sh -addgroup POSCAR Li Y Cl
 
 该命令读取输入结构，并写出带 group 信息的 extxyz 文件。
 
-在交互模式中选择 `106`，会看到：
+**交互模式：** 在格式转换菜单中选择 `106`，会看到：
 
 ```text
 >-------------------------------------------------<
@@ -142,6 +156,8 @@ Example: POSCAR Li Y Cl
 ------------>>
 ```
 
+**输出：** 添加了 group 标签的 extxyz 文件。
+
 ## 常用脚本说明
 
 ### POSCAR 转 extxyz
diff --git "a/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md" "b/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md"
index 6bcca6f..da213f4 100644
--- "a/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md"
+++ "b/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md"
@@ -467,9 +467,11 @@ gpumdkit.sh -plt rdf_pmf
 
 ### plt_vac.py
 
-绘制速度自相关函数。
+绘制速度自相关函数 (VAC)。可用于分析声子性质和原子动力学。
 
-**输入文件：** `vac.out`
+**输入文件：** `sdc.out`（绘图脚本会从该文件中读取 VAC 相关列）
+
+**输出：** 交互式图表或 `vac.png`（使用 `save` 选项时）
 
 ```bash
 gpumdkit.sh -plt vac
@@ -479,7 +481,11 @@ gpumdkit.sh -plt vac
 
 ### plt_cohesive.py
 
-绘制内聚能曲线。
+从 `cohesive.out` 绘制内聚能曲线。可用于分析晶格稳定性和平衡晶格常数。
+
+**输入文件：** `cohesive.out`（各向同性缩放因子 vs 内聚能）
+
+**输出：** 交互式图表或 `cohesive.png`（使用 `save` 选项时）
 
 ```bash
 gpumdkit.sh -plt cohesive
@@ -606,7 +612,7 @@ gpumdkit.sh -plt doas doas.out Li
 
 ## 极性材料的 Plane-Grid 绘图
 
-此工作流将位移或极化数据映射到网格上，并绘制选定平面的轮廓。
+此工作流将位移或极化数据映射到网格上，并绘制选定平面的轮廓。详细用法和实际案例请参见 **[极性材料分析](极性材料分析.md)**。
 
 **依赖：**
 
@@ -653,8 +659,8 @@ gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb
 | `arrhenius_sigma` / `sigma` | `*K/{model.xyz, run.in, thermo.out, msd.out}` | Arrhenius 离子电导率 |
 | `rdf` | `rdf.out` | 径向分布函数 |
 | `rdf_pmf` | `rdf.out` | RDF + 平均力势 |
-| `vac` | `vac.out` | 速度自相关 |
-| `cohesive` | — | 内聚能曲线 |
+| `vac` | `sdc.out` | 速度自相关 |
+| `cohesive` | `cohesive.out` | 内聚能曲线 |
 | `net_force` | `train.xyz` | 净力分布 |
 | `doas` | `doas.out` | 原子态密度 |
 | `des` | `descriptors.npy` | 描述符 PCA/UMAP |
diff --git "a/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md" "b/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md"
index ec58b1a..c8889b5 100644
--- "a/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md"
+++ "b/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md"
@@ -16,11 +16,11 @@
 | DOAS | `gpumdkit.sh -calc doas <input.xyz> <nep.txt> <output.txt>` | extxyz + NEP 模型 |
 | NEB | `gpumdkit.sh -calc neb <initial.xyz> <final.xyz> <n_images> <nep.txt>` | 初末态结构 |
 | 结构优化 | `gpumdkit.sh -calc minimize <structure> <nep.txt> [fmax] [max_steps]` | 结构 + NEP 模型 |
-| 邻居列表 | `gpumdkit.sh -calc nlist [args...]` | 结构 |
-| 位移 | `gpumdkit.sh -calc disp [args...]` | 轨迹 + 邻居列表 |
-| 平均结构 | `gpumdkit.sh -calc avg-struct [args...]` | 轨迹 |
-| 八面体倾转 | `gpumdkit.sh -calc oct-tilt [args...]` | 轨迹 + B-O 邻居列表 |
-| ABO3 极化 | `gpumdkit.sh -calc pol-abo3 [args...]` | 轨迹 + 邻居列表 |
+| 邻居列表 | `gpumdkit.sh -calc nlist ...` | 参见 [极性材料分析](极性材料分析.md) |
+| 位移 | `gpumdkit.sh -calc disp ...` | 参见 [极性材料分析](极性材料分析.md) |
+| 平均结构 | `gpumdkit.sh -calc avg-struct ...` | 参见 [极性材料分析](极性材料分析.md) |
+| 八面体倾转 | `gpumdkit.sh -calc oct-tilt ...` | 参见 [极性材料分析](极性材料分析.md) |
+| ABO3 极化 | `gpumdkit.sh -calc pol-abo3 ...` | 参见 [极性材料分析](极性材料分析.md) |
 
 查看完整帮助：
 
@@ -170,7 +170,7 @@ pip install calorine
 gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
 ```
 
-只有当你确认模型质量可靠，并明确希望使用 NEP 作为替代计算器时，才建议使用它。
+使用此功能可以用训练好的 NEP 模型进行预测。建议在使用前先验证模型在目标结构上的预测质量。
 
 **提示：** 预测前可以清理 extxyz 元数据：
 
@@ -281,43 +281,12 @@ gpumdkit.sh -plt rdf
 
 ## 铁电和极性材料工具
 
-这些工具需要 `ferrodispcalc`：
+选项 `406–410` 涵盖钙钛矿和极性材料分析：近邻列表、局域位移、平均结构、八面体倾转和 ABO3 极化。这些工具基于 `ferrodispcalc`。
 
-```bash
-pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
-```
-
-`ferrodispcalc` 目前没有需要额外引用的论文。
-
-### 邻居列表
-
-```bash
-gpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat
-```
-
-### 位移
-
-```bash
-gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat
-```
-
-### 平均结构
-
-```bash
-gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz
-```
-
-### 八面体倾转
+**依赖：**
 
 ```bash
-gpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat
-```
-
-### ABO3 局域极化
-
-```bash
-gpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \
-  --bec Pb=2 Ti=4.0 O=-2.0 -o polarization.dat
+pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
 ```
 
-`--bec` 应根据你的体系或参考数据设置。
+完整参数列表和真实工作流案例（PbTiO3 相变、PTO/STO 超晶格拓扑等）请参见 **[极性材料分析](极性材料分析.md)**。
diff --git a/gpumdkit.sh b/gpumdkit.sh
index 62ffa96..dfc744b 100755
--- a/gpumdkit.sh
+++ b/gpumdkit.sh
@@ -470,11 +470,6 @@ if [ ! -z "$1" ]; then
         -pda)
             run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${analyzer_path}/probability_density_analysis.py" "${@:2}" ;;
 
-        -hbond)
-            echo " Calling script by Zherui CHEN "
-            python ${GPUMD_path}/tools/Analysis_and_Processing/hydrogen_bond_analysis/Hydrogen-bond-analysis.py ${@:2}
-            echo " Code path: ${GPUMD_path}/tools/Analysis_and_Processing/hydrogen_bond_analysis/Hydrogen-bond-analysis.py" ;;
-
         *)
             # echo " Unknown option: $1 "; help_info_table; exit 1 ;;
             alias_key="${1#-}"
diff --git a/src/f1_format_conversions.sh b/src/f1_format_conversions.sh
index 3d25608..984d9d7 100644
--- a/src/f1_format_conversions.sh
+++ b/src/f1_format_conversions.sh
@@ -187,7 +187,7 @@ echo " | Calling the script in Scripts/format_conversion |"
 echo " | Script: get_frame.py                            |"
 echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
 echo " >-------------------------------------------------<"
-echo " Input <input.xyz> <frame_index>"
+echo " Input <input.xyz> <frame_number>"
 echo " Example: train.xyz 1"
 echo " ------------>>"
 read -r -a getframe_args
diff --git a/src/f4_calculators.sh b/src/f4_calculators.sh
index 52cd239..930a36c 100644
--- a/src/f4_calculators.sh
+++ b/src/f4_calculators.sh
@@ -178,7 +178,7 @@ echo " ---------------------------------------------------"
 function f411_minimize_structure_by_nep(){
 echo " >-------------------------------------------------<"
 echo " | This function calls the script in calculators   |"
-echo " | Script: minimize_structure_by_nep.py            |"
+echo " | Script: calc_minimize.py                         |"
 echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
 echo " >-------------------------------------------------<"
 echo " Input <structure_file> <nep.txt> [fmax=0.01] [max_steps=1000]"

From 2f186ee825f477e2503ef0b6cc56ee6d70535715 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Wed, 1 Jul 2026 12:53:27 +0800
Subject: [PATCH 14/24] update

---
 README.md                                     |   2 +-
 Scripts/analyzer/find_outliers.py             |  64 +++++++--
 Scripts/format_conversion/exyz2lmp.py         |  29 +++-
 .../neptrain_select_structs.py                |  51 +++++--
 .../parallel_pynep_select_structs.py          |  50 +++++--
 .../sample_structures/perturb_structure.py    |  56 +++++++-
 .../sample_structures/sample_structures.py    |  14 +-
 Scripts/sample_structures/select_max_modev.py |  46 ++++++-
 docs/README_zh-CN.md                          |   2 +-
 docs/htmls/en/calculator_scripts.html         |  56 +++++++-
 docs/htmls/en/format_conversion.html          |  19 +++
 docs/htmls/en/index.html                      |   2 +-
 docs/htmls/en/structure_sampling.html         |  15 +-
 docs/htmls/search/search_index.json           |   2 +-
 docs/htmls/sitemap.xml                        |  54 ++++----
 docs/htmls/sitemap.xml.gz                     | Bin 615 -> 614 bytes
 docs/htmls/zh/index.html                      |   2 +-
 ...\345\274\217\350\275\254\346\215\242.html" |  19 +++
 ...\346\236\204\351\207\207\346\240\267.html" |  13 +-
 ...\345\231\250\350\204\232\346\234\254.html" | 128 ++++++++++++++----
 docs/tutorials/en/calculator_scripts.md       |  24 +++-
 docs/tutorials/en/format_conversion.md        |  40 +++---
 docs/tutorials/en/index.md                    |   2 +-
 docs/tutorials/en/structure_sampling.md       |  15 +-
 docs/tutorials/zh/index.md                    |   2 +-
 ...74\345\274\217\350\275\254\346\215\242.md" |  40 +++---
 ...23\346\236\204\351\207\207\346\240\267.md" |  15 +-
 ...27\345\231\250\350\204\232\346\234\254.md" |  57 +++++++-
 gpumdkit.sh                                   |  14 +-
 skills/gpumdkit-analyzers/SKILL.md            |  17 +--
 skills/gpumdkit-sampling/SKILL.md             |   7 +-
 src/f1_format_conversions.sh                  |  12 +-
 src/f2_sample_structures.sh                   |   4 +-
 src/f3_workflows.sh                           |  17 ++-
 src/f4_calculators.sh                         |  28 ++--
 src/f5_analyzers.sh                           |  27 ++--
 src/f7_utilities.sh                           |   6 +-
 37 files changed, 710 insertions(+), 241 deletions(-)

diff --git a/README.md b/README.md
index 65074f1..1ad6b62 100644
--- a/README.md
+++ b/README.md
@@ -159,7 +159,7 @@ the help information:
 | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
 | -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
-| -pynep        Deprecated PyNEP sampling       |                                                       |
+| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
 +-------------------------------------------------------------------------------------------------------+
 | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
 +-------------------------------------------------------------------------------------------------------+
diff --git a/Scripts/analyzer/find_outliers.py b/Scripts/analyzer/find_outliers.py
index 0dcc9e9..a234023 100644
--- a/Scripts/analyzer/find_outliers.py
+++ b/Scripts/analyzer/find_outliers.py
@@ -10,7 +10,9 @@
 Purpose:    Find outlier structures in NEP training data based on RMSE
             thresholds for energy, force, and stress. Selected outliers
             are saved to selected.xyz, and the remaining to remained.xyz.
-Usage:      python find_outliers.py [energy_thresh_meV force_thresh_meV stress_thresh_GPa]
+Usage:      gpumdkit.sh
+            choose 502) Find outliers of extxyz
+            python find_outliers.py [energy_thresh_meV force_thresh_meV stress_thresh_GPa]
 Arguments:
   energy_thresh_meV  (optional) Energy RMSE threshold in meV/atom
   force_thresh_meV   (optional) Force RMSE threshold in meV/Angstrom
@@ -31,8 +33,53 @@
 
 import sys
 import os
-import matplotlib.pyplot as plt
-import numpy as np
+
+
+def print_usage():
+    print(" Usage: gpumdkit.sh")
+    print("        choose 502) Find outliers of extxyz")
+    print("    or: python find_outliers.py [energy_thresh_meV force_thresh_meV stress_thresh_GPa]")
+    print("")
+    print(" Arguments:")
+    print("   energy_thresh_meV  Optional energy RMSE threshold in meV/atom")
+    print("   force_thresh_meV   Optional force RMSE threshold in meV/Angstrom")
+    print("   stress_thresh_GPa  Optional stress RMSE threshold in GPa")
+    print("")
+    print(" Input files:")
+    print("   train.xyz")
+    print("   energy_train.out")
+    print("   force_train.out")
+    print("   stress_train.out")
+    print("")
+    print(" Output:")
+    print("   selected.xyz")
+    print("   remained.xyz")
+    print("   selected_remained.png")
+    print("")
+    print(" Example: in interactive mode, choose 502 and enter thresholds when prompted")
+    print("          python find_outliers.py 20 100 1.0")
+    print("")
+
+
+args = sys.argv[1:]
+if args and args[0] in ("-h", "--help"):
+    print_usage()
+    sys.exit(0)
+if args and len(args) < 3:
+    print_usage()
+    sys.exit(1)
+
+energy_thresh = force_thresh = stress_thresh = None
+if len(args) >= 3:
+    try:
+        energy_thresh = float(args[0]) / 1000  # Convert meV/atom to eV/atom
+        force_thresh = float(args[1]) / 1000   # Convert meV/Angstrom to eV/Angstrom
+        stress_thresh = float(args[2])         # GPa, no conversion needed
+    except ValueError:
+        print(" Error: thresholds must be numbers.")
+        print("")
+        print_usage()
+        sys.exit(1)
 
 # Function to parse xyz file and get natoms list and frames
 def parse_xyz(filename):
@@ -113,6 +160,9 @@ def select_outliers(rmse_func, err_func, thresh, n_struct):
         print(f"  train.xyz, energy_train.out, force_train.out, stress_train.out")
         sys.exit(1)
 
+import matplotlib.pyplot as plt
+import numpy as np
+
 energy_train = np.loadtxt('energy_train.out')
 force_train = np.loadtxt('force_train.out')
 stress_train = np.loadtxt('stress_train.out')
@@ -143,13 +193,7 @@ def select_outliers(rmse_func, err_func, thresh, n_struct):
 n_struct = len(natoms_list)
 cum = np.cumsum([0] + natoms_list)
 
-# Input RMSE thresholds (in meV for energy and force, GPa for stress)
-if len(sys.argv) >= 4:
-    # Use command-line arguments if provided (in order: energy, force, stress)
-    energy_thresh = float(sys.argv[1]) / 1000  # Convert meV/atom to eV/atom
-    force_thresh = float(sys.argv[2]) / 1000   # Convert meV/Å to eV/Å
-    stress_thresh = float(sys.argv[3])         # GPa, no conversion needed
-else:
+if energy_thresh is None:
     # Prompt for manual input if command-line arguments are not provided
     energy_thresh = float(input(" Enter energy RMSE threshold (meV/atom): ")) / 1000  # Convert to eV/atom
     force_thresh = float(input(" Enter force RMSE threshold (meV/Å): ")) / 1000      # Convert to eV/Å
diff --git a/Scripts/format_conversion/exyz2lmp.py b/Scripts/format_conversion/exyz2lmp.py
index 630fc5f..97b9644 100644
--- a/Scripts/format_conversion/exyz2lmp.py
+++ b/Scripts/format_conversion/exyz2lmp.py
@@ -21,9 +21,25 @@
 """
 
 import sys
-from ase.io import read, write
+
+
+def print_usage():
+    print(" Usage: python exyz2lmp.py <extxyz_file> <lammps_data_file>")
+    print("")
+    print(" Arguments:")
+    print("   extxyz_file       Input extxyz file")
+    print("   lammps_data_file  Output LAMMPS data file")
+    print("")
+    print(" Output:")
+    print("   <lammps_data_file>")
+    print("")
+    print(" Example: python exyz2lmp.py model.xyz data.lammps")
+    print("")
+
 
 def convert_extxyz_to_lammps_data(extxyz_file, lammps_data_file):
+    from ase.io import read
+
     # Read the EXTXYZ file
     atoms = read(extxyz_file, format='extxyz')
     
@@ -69,11 +85,12 @@ def convert_extxyz_to_lammps_data(extxyz_file, lammps_data_file):
 #   print(f"Conversion complete! {extxyz_file} has been converted to {lammps_data_file}")
 
 if __name__ == '__main__':
-    if len(sys.argv) != 3:
-        print(" Usage: python exyz2lmp.py <extxyz_file> <lammps_data_file>")
-        sys.exit(1)
+    args = sys.argv[1:]
+    if len(args) != 2 or args[0] in ("-h", "--help"):
+        print_usage()
+        sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
     
-    extxyz_file = sys.argv[1]
-    lammps_data_file = sys.argv[2]
+    extxyz_file = args[0]
+    lammps_data_file = args[1]
     
     convert_extxyz_to_lammps_data(extxyz_file, lammps_data_file)
diff --git a/Scripts/sample_structures/neptrain_select_structs.py b/Scripts/sample_structures/neptrain_select_structs.py
index 4926aa3..4ced0c9 100644
--- a/Scripts/sample_structures/neptrain_select_structs.py
+++ b/Scripts/sample_structures/neptrain_select_structs.py
@@ -10,7 +10,9 @@
 Purpose:    Select diverse structures from a sampledata set using
             farthest-point sampling on NepTrain descriptors, relative to
             an existing training set.
-Usage:      python neptrain_select_structs.py <sampledata_file> <traindata_file> <nep_model_file>
+Usage:      gpumdkit.sh
+            choose 203) FPS sampling by NepTrain
+            python neptrain_select_structs.py <sampledata_file> <traindata_file> <nep_model_file>
 Arguments:
   sampledata_file  Extxyz file with candidate structures
   traindata_file   Extxyz file with existing training structures
@@ -25,12 +27,6 @@
 """
 
 import sys
-import numpy as np
-from ase.io import read, write
-import matplotlib.pyplot as plt
-from sklearn.decomposition import PCA
-from NepTrain.core.nep import *
-from scipy.spatial.distance import cdist
 
 
 def print_dependency_notice():
@@ -40,6 +36,26 @@ def print_dependency_notice():
     print(" https://doi.org/10.1016/j.cpc.2025.109859")
 
 
+def print_usage():
+    print(" Usage: gpumdkit.sh")
+    print("        choose 203) FPS sampling by NepTrain")
+    print("    or: python neptrain_select_structs.py <sampledata_file> <traindata_file> <nep_model_file>")
+    print("")
+    print(" Arguments:")
+    print("   sampledata_file  Extxyz file with candidate structures")
+    print("   traindata_file   Extxyz file with existing training structures")
+    print("   nep_model_file   NEP model file (e.g., nep.txt)")
+    print("")
+    print(" Output:")
+    print("   selected.xyz")
+    print("   select.png")
+    print("   pca_sample.txt, pca_train.txt, pca_selected.txt")
+    print("")
+    print(" Example: in interactive mode, enter: dump.xyz train.xyz nep.txt")
+    print("          python neptrain_select_structs.py dump.xyz train.xyz nep.txt")
+    print("")
+
+
 def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, length=50, fill='█'):
     percent = ("{0:." + str(decimals) + "f}").format(100 * (iteration / float(total)))
     filled_length = int(length * iteration // total)
@@ -94,14 +110,25 @@ def FarthestPointSample(new_data, now_data=[], min_distance=None, min_select=1,
     return to_add
 
 
-# Check command line arguments
-if len(sys.argv) < 4:
-    print(" Usage: python neptrain_select_structs.py <sampledata_file> <traindata_file> <nep_model_file>")
-    print(" Example: python neptrain_select_structs.py dump.xyz train.xyz nep.txt")
-    sys.exit(1)
+args = sys.argv[1:]
+if len(args) != 3 or args[0] in ("-h", "--help"):
+    print_usage()
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
 
 print_dependency_notice()
 
+try:
+    import numpy as np
+    from ase.io import read, write
+    import matplotlib.pyplot as plt
+    from sklearn.decomposition import PCA
+    from NepTrain.core.nep import Nep3Calculator
+    from scipy.spatial.distance import cdist
+except ImportError:
+    print(" Error: required Python dependencies are not installed or cannot be imported.")
+    print(" Please install NepTrain and the scientific Python stack before using this function.")
+    sys.exit(1)
+
 # Load data
 sampledata = read(sys.argv[1], ':')
 traindata = read(sys.argv[2], ':')
diff --git a/Scripts/sample_structures/parallel_pynep_select_structs.py b/Scripts/sample_structures/parallel_pynep_select_structs.py
index 4ada447..6f27af3 100644
--- a/Scripts/sample_structures/parallel_pynep_select_structs.py
+++ b/Scripts/sample_structures/parallel_pynep_select_structs.py
@@ -10,7 +10,8 @@
 Purpose:    Parallelized version of pynep_select_structs.py. Select diverse
             structures using farthest-point sampling on pynep descriptors
             with multi-processing for descriptor computation and I/O.
-Usage:      python parallel_pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file> <threads>
+Usage:      gpumdkit.sh -pynep
+            python parallel_pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file> <threads>
 Arguments:
   sampledata_file  Extxyz file with candidate structures
   traindata_file   Extxyz file with existing training structures
@@ -25,16 +26,9 @@
 """
 
 import sys
-import numpy as np
-from ase.io import read, write
-import matplotlib.pyplot as plt
-from sklearn.decomposition import PCA
-from pynep.calculate import NEP
-from pynep.select import FarthestPointSample
 from concurrent.futures import ProcessPoolExecutor, as_completed
 import multiprocessing
 import argparse
-import time
 import os
 
 
@@ -43,6 +37,25 @@ def print_dependency_notice():
     print(" This PyNEP sampling entry is deprecated. We recommend using NepTrain sampling instead.")
 
 
+def print_usage():
+    print(" Usage: gpumdkit.sh -pynep")
+    print("    or: python parallel_pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file> <threads>")
+    print("")
+    print(" Arguments:")
+    print("   sampledata_file  Extxyz file with candidate structures")
+    print("   traindata_file   Extxyz file with existing training structures")
+    print("   nep_model_file   NEP model file (e.g., nep.txt)")
+    print("   threads          Number of parallel workers")
+    print("")
+    print(" Output:")
+    print("   selected.xyz     Selected diverse structures")
+    print("   select.png       PCA visualization of descriptor space")
+    print("")
+    print(" Example: gpumdkit.sh -pynep")
+    print("          dump.xyz train.xyz nep.txt 8")
+    print("")
+
+
 def get_num_frames(file_path):
     count = 0
     with open(file_path, 'r') as f:
@@ -124,11 +137,10 @@ def calculate_descriptors(data, desc_type, max_workers=None):
     
     return np.array(results)
 
-# Check command line arguments
-if len(sys.argv) < 4:
-    print(" Usage: python parallel_pynep_select_structs.py <sampledata_file> <traindata_file> <nep_model_file> <threads>")
-    print(" Example: python parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8")
-    sys.exit(1)
+args_in = sys.argv[1:]
+if len(args_in) != 4 or args_in[0] in ("-h", "--help"):
+    print_usage()
+    sys.exit(0 if args_in and args_in[0] in ("-h", "--help") else 1)
 
 # Parse command-line arguments
 parser = argparse.ArgumentParser(description='Select structures using NEP descriptors.')
@@ -140,6 +152,18 @@ def calculate_descriptors(data, desc_type, max_workers=None):
 
 print_dependency_notice()
 
+try:
+    import numpy as np
+    from ase.io import read, write
+    import matplotlib.pyplot as plt
+    from sklearn.decomposition import PCA
+    from pynep.calculate import NEP
+    from pynep.select import FarthestPointSample
+except ImportError:
+    print(" Error: required Python dependencies are not installed or cannot be imported.")
+    print(" Please install pynep and the scientific Python stack, or use function 203) NepTrain sampling instead.")
+    sys.exit(1)
+
 # Function to load data from file
 def load_data(file_path):
     return read(file_path, ':')
diff --git a/Scripts/sample_structures/perturb_structure.py b/Scripts/sample_structures/perturb_structure.py
index e4a0d46..69a0252 100644
--- a/Scripts/sample_structures/perturb_structure.py
+++ b/Scripts/sample_structures/perturb_structure.py
@@ -10,7 +10,9 @@
 Purpose:    Generate perturbed structures from a POSCAR/CONTCAR file using
             dpdata. Supports cell and atom perturbations with different
             perturbation styles (normal, uniform, const).
-Usage:      python perturb_structure.py <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>
+Usage:      gpumdkit.sh
+            choose 204) Perturb structure
+            python perturb_structure.py <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>
 Arguments:
   input.vasp           Input POSCAR/CONTCAR file
   pert_num             Number of perturbed structures to generate
@@ -26,7 +28,6 @@
 
 import argparse
 import sys
-import dpdata
 
 
 def print_dependency_notice():
@@ -34,9 +35,40 @@ def print_dependency_notice():
     print(" If you use this function, we recommend citing dpdata according to its official documentation.")
 
 
+def print_usage():
+    print(" Usage: gpumdkit.sh")
+    print("        choose 204) Perturb structure")
+    print("    or: python perturb_structure.py <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>")
+    print("")
+    print(" Arguments:")
+    print("   input.vasp           Input POSCAR/CONTCAR file")
+    print("   pert_num             Number of perturbed structures to generate")
+    print("   cell_pert_fraction   Fraction of cell perturbation")
+    print("   atom_pert_distance   Distance of atom perturbation (Angstrom)")
+    print("   atom_pert_style      Style: normal, uniform, or const")
+    print("")
+    print(" Output:")
+    print("   POSCAR_*.vasp")
+    print("")
+    print(" Example: in interactive mode, enter: POSCAR 20 0.03 0.2 uniform")
+    print("          python perturb_structure.py POSCAR 20 0.03 0.2 uniform")
+    print("")
+
+
 def parse_args():
     parser = argparse.ArgumentParser(
-             description="Usage: python perturb_structure.py <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>")
+             formatter_class=argparse.RawDescriptionHelpFormatter,
+             description="""Generate perturbed structures from a POSCAR/CONTCAR file.
+
+Usage:
+  gpumdkit.sh
+  choose 204) Perturb structure
+  python perturb_structure.py <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <atom_pert_style>
+
+Example:
+  in interactive mode, enter: POSCAR 20 0.03 0.2 uniform
+  python perturb_structure.py POSCAR 20 0.03 0.2 uniform
+""")
     parser.add_argument('input_file', help='The path to POSCAR/CONTCAR file')
     parser.add_argument('pert_num', type=int, default=20, help='The perturbation number')
     parser.add_argument('cell_pert_fraction', type=float, default=0.03, help='The fraction of cell perturbation')
@@ -45,16 +77,30 @@ def parse_args():
     return parser.parse_args()
 
 def main():
+    args_in = sys.argv[1:]
+    if len(args_in) != 5 and not (args_in and args_in[0] in ("-h", "--help")):
+        print_usage()
+        sys.exit(1)
+
     try:
         args = parse_args()
-    except SystemExit:
+    except SystemExit as exc:
+        if exc.code == 0:
+            sys.exit(0)
         print(f"Default values: pert_num=20, cell_pert_fraction=0.03, atom_pert_distance=0.2, atom_pert_style=uniform")
         print("atom_pert_style options: 'normal', 'uniform', 'const'")
         print("dpdata documentation: https://docs.deepmodeling.com/projects/dpdata/en/master/index.html \n")
-        sys.exit(1)
+        sys.exit(exc.code)
 
     print_dependency_notice()
 
+    try:
+        import dpdata
+    except ImportError:
+        print(" Error: dpdata is not installed or cannot be imported.")
+        print(" Please install dpdata before using this function.")
+        sys.exit(1)
+
     # Read the POSCAR file and perform perturbation
     system = dpdata.System(args.input_file, fmt='vasp/poscar')
     perturbed_systems = system.perturb(pert_num=args.pert_num,
diff --git a/Scripts/sample_structures/sample_structures.py b/Scripts/sample_structures/sample_structures.py
index a208794..0b9c08c 100644
--- a/Scripts/sample_structures/sample_structures.py
+++ b/Scripts/sample_structures/sample_structures.py
@@ -9,7 +9,9 @@
 Category:   Sample Structure Scripts
 Purpose:    Uniformly or randomly sample a specified number of frames from
             an extxyz trajectory, with an option to skip initial frames.
-Usage:      python sample_structures.py <extxyz_file> <method> <num_samples> [skip_initial]
+Usage:      gpumdkit.sh
+            choose 201) Sample structures from extxyz
+            python sample_structures.py <extxyz_file> <method> <num_samples> [skip_initial]
 Arguments:
   extxyz_file  Input extxyz trajectory file
   method       Sampling method: uniform or random
@@ -46,7 +48,13 @@ def parse_args():
     Modified by:
         Dr. Huan Wang <huan.wang@whut.edu.cn>
     Usage:
-        python sample_structures.py <extxyz_file> <sampling_method> <num_samples> [skip_initial])
+        gpumdkit.sh
+        choose 201) Sample structures from extxyz
+        python sample_structures.py <extxyz_file> <sampling_method> <num_samples> [skip_initial]
+
+    Example:
+        in interactive mode, enter: dump.xyz uniform 50
+        python sample_structures.py dump.xyz random 100 500
     """))
     parser.add_argument('extxyz_file', 
                         type=Path, 
@@ -112,4 +120,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()
diff --git a/Scripts/sample_structures/select_max_modev.py b/Scripts/sample_structures/select_max_modev.py
index 9892286..7753db7 100644
--- a/Scripts/sample_structures/select_max_modev.py
+++ b/Scripts/sample_structures/select_max_modev.py
@@ -9,7 +9,9 @@
 Category:   Sample Structure Scripts
 Purpose:    Extract the top N structures with the highest max force
             deviation from active learning output (active.out + active.xyz).
-Usage:      python select_max_modev.py <top_n> <min_deviation>
+Usage:      gpumdkit.sh
+            choose 205) Select max force deviation structs
+            python select_max_modev.py <top_n> <min_deviation>
 Arguments:
   top_n          Number of top structures to extract
   min_deviation  Minimum force deviation threshold for filtering
@@ -27,15 +29,48 @@
 import numpy as np
 from ase.io import read, write
 
+
+def print_usage():
+    print(" Usage: gpumdkit.sh")
+    print("        choose 205) Select max force deviation structs")
+    print("    or: python select_max_modev.py <top_n> <min_deviation>")
+    print("")
+    print(" Arguments:")
+    print("   top_n          Number of top structures to extract")
+    print("   min_deviation  Minimum force deviation threshold for filtering")
+    print("")
+    print(" Input files:")
+    print("   active.out     Max force deviation per structure")
+    print("   active.xyz     Corresponding structures in extxyz format")
+    print("")
+    print(" Output:")
+    print("   selected.xyz")
+    print("")
+    print(" Example: in interactive mode, enter: 200 0.15")
+    print("          python select_max_modev.py 200 0.15")
+    print("")
+
+
+args = sys.argv[1:]
+if len(args) != 2 or args[0] in ("-h", "--help"):
+    print_usage()
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+try:
+    top_n = int(args[0])
+    min_deviation = float(args[1])
+except ValueError:
+    print(" Error: <top_n> must be an integer and <min_deviation> must be a number.")
+    print("")
+    print_usage()
+    sys.exit(1)
+
 # Define file paths
 input_file = 'active.out'  # Input file for max force deviation
 #output_file = 'filtered_max_force_deviations.txt'  # Output file for filtered max force deviations
 xyz_file = 'active.xyz'  # Input .extxyz file
 output_xyz_file = 'selected.xyz'  # Output file for extracted structures
 
-# Number of top structures to extract
-top_n = int(sys.argv[1])  # Specify the number of top structures to extract (e.g., top 100)
-
 # Lists to store filtered max force deviations and corresponding indices
 filtered_deviations = []
 filtered_indices = []
@@ -48,7 +83,7 @@
         time, max_force_deviation = line.split()
         max_force_deviation = float(max_force_deviation)
 
-        if max_force_deviation > float(sys.argv[2]):
+        if max_force_deviation > min_deviation:
             filtered_deviations.append(max_force_deviation)
             filtered_indices.append(idx)  # Store the index in the original file
 
@@ -82,4 +117,3 @@ def extract_xyz_structures(xyz_file, indices, output_xyz_file):
 
 # Extract the top N structures and save them to the output .xyz file
 extract_xyz_structures(xyz_file, top_indices_in_filtered, output_xyz_file)
-
diff --git a/docs/README_zh-CN.md b/docs/README_zh-CN.md
index daad7f7..9de2a48 100644
--- a/docs/README_zh-CN.md
+++ b/docs/README_zh-CN.md
@@ -160,7 +160,7 @@ gpumdkit.sh -h
 | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
 | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
 | -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
-| -pynep        Deprecated PyNEP sampling       |                                                       |
+| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
 +-------------------------------------------------------------------------------------------------------+
 | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
 +-------------------------------------------------------------------------------------------------------+
diff --git a/docs/htmls/en/calculator_scripts.html b/docs/htmls/en/calculator_scripts.html
index 3e5a28b..65a8b2f 100644
--- a/docs/htmls/en/calculator_scripts.html
+++ b/docs/htmls/en/calculator_scripts.html
@@ -1551,6 +1551,13 @@ <h1>🧮 Calculator Scripts</h1>
 
 <p><strong>Script Location:</strong> <code>Scripts/calculators/</code></p>
 <h2 id="overview">Overview</h2>
+<p>The calculator module can be read as three groups:</p>
+<ul>
+<li><strong>Trajectory properties:</strong> compute time-dependent quantities such as MSD and ionic conductivity from GPUMD or extxyz trajectories;</li>
+<li><strong>NEP-assisted calculations:</strong> use a NEP model to predict energies/forces/stresses, extract descriptors, calculate DOAS, run NEB, or minimize structures;</li>
+<li><strong>Polar-material analysis:</strong> build neighbor lists and calculate local displacement, averaged structures, octahedral tilt, and local polarization for perovskite or polar systems.</li>
+</ul>
+<p>If you are not sure about the required arguments, start from the interactive menu to see the prompt. If the arguments are already clear, use <code>gpumdkit.sh -calc ...</code> directly.</p>
 <table>
 <thead>
 <tr>
@@ -1914,11 +1921,54 @@ <h2 id="rdf-calculation-with-ovito">RDF Calculation with OVITO</h2>
 <p><strong>Note:</strong> It is recommended to use the <code>compute_rdf</code> command directly in GPUMD when possible.</p>
 <hr />
 <h2 id="ferroelectric-and-polar-material-tools">Ferroelectric and Polar Material Tools</h2>
-<p>Options <code>406–410</code> cover perovskite and polar-material analysis: neighbor lists, local displacements, averaged structures, octahedral tilt, and ABO3 polarization. These tools are built on <code>ferrodispcalc</code>.</p>
-<p><strong>Dependency:</strong></p>
+<p>Options <code>406–410</code> are for perovskite and polar-material analysis. They are commonly used to extract local structural information from MD trajectories before analyzing phase transitions, domain patterns, or polarization textures.</p>
+<p>This page only gives a quick index for these scripts because they are usually used together. For full workflows and argument details, see <strong><a href="polar_material_analysis.html">Polar Material Analysis</a></strong>.</p>
+<table>
+<thead>
+<tr>
+<th>Menu</th>
+<th>CLI subcommand</th>
+<th>Purpose</th>
+<th>Details</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>406</code></td>
+<td><code>gpumdkit.sh -calc nlist ...</code></td>
+<td>Build neighbor lists between selected center and neighbor atoms</td>
+<td><a href="polar_material_analysis.html">Polar Material Analysis</a></td>
+</tr>
+<tr>
+<td><code>407</code></td>
+<td><code>gpumdkit.sh -calc disp ...</code></td>
+<td>Calculate local displacement from a trajectory and neighbor list</td>
+<td><a href="polar_material_analysis.html">Polar Material Analysis</a></td>
+</tr>
+<tr>
+<td><code>408</code></td>
+<td><code>gpumdkit.sh -calc avg-struct ...</code></td>
+<td>Calculate an averaged structure from a trajectory</td>
+<td><a href="polar_material_analysis.html">Polar Material Analysis</a></td>
+</tr>
+<tr>
+<td><code>409</code></td>
+<td><code>gpumdkit.sh -calc oct-tilt ...</code></td>
+<td>Calculate octahedral tilt angles</td>
+<td><a href="polar_material_analysis.html">Polar Material Analysis</a></td>
+</tr>
+<tr>
+<td><code>410</code></td>
+<td><code>gpumdkit.sh -calc pol-abo3 ...</code></td>
+<td>Estimate local ABO3 polarization from Born effective charges</td>
+<td><a href="polar_material_analysis.html">Polar Material Analysis</a></td>
+</tr>
+</tbody>
+</table>
+<p>Some scripts require <code>ferrodispcalc</code>:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
 </code></pre></div>
-<p>For complete argument lists, real-world workflow examples (PbTiO3 phase transition, PTO/STO superlattice topology, etc.), see <strong><a href="polar_material_analysis.html">Polar Material Analysis</a></strong>.</p>
+<p>A typical sequence is to build neighbor lists with <code>nlist</code>, then reuse those lists for displacement, tilt, or polarization calculations. For averaged structures, you can start directly from the trajectory and use the length tolerance to control which frames are included.</p>
 
 
 
diff --git a/docs/htmls/en/format_conversion.html b/docs/htmls/en/format_conversion.html
index cf278a4..ff8058f 100644
--- a/docs/htmls/en/format_conversion.html
+++ b/docs/htmls/en/format_conversion.html
@@ -1818,6 +1818,7 @@ <h3 id="what-each-entry-does">What Each Entry Does</h3>
 <thead>
 <tr>
 <th>Entry</th>
+<th>Called script</th>
 <th>Function</th>
 <th>When to Use</th>
 </tr>
@@ -1825,91 +1826,109 @@ <h3 id="what-each-entry-does">What Each Entry Does</h3>
 <tbody>
 <tr>
 <td><code>101</code></td>
+<td><code>out2xyz.sh</code></td>
 <td>VASP OUTCAR to extxyz, shell version</td>
 <td>convert VASP calculation directories</td>
 </tr>
 <tr>
 <td><code>102</code></td>
+<td><code>mtp2xyz.py</code></td>
 <td>MTP cfg to extxyz</td>
 <td>convert MTP training data</td>
 </tr>
 <tr>
 <td><code>103</code></td>
+<td><code>cp2k_log2xyz.py</code> / <code>cp2k2xyz.py</code></td>
 <td>CP2K to extxyz</td>
 <td>choose CP2K log/inp route or pos/frc/cell route</td>
 </tr>
 <tr>
 <td><code>104</code></td>
+<td><code>abacus2xyz_scf.sh</code> / <code>abacus2xyz_md.sh</code></td>
 <td>ABACUS to extxyz</td>
 <td>convert ABACUS SCF or MD output</td>
 </tr>
 <tr>
 <td><code>105</code></td>
+<td><code>exyz2pos.py</code></td>
 <td>extxyz to POSCAR</td>
 <td>write each extxyz frame as a POSCAR-style file</td>
 </tr>
 <tr>
 <td><code>106</code></td>
+<td><code>add_groups.py</code></td>
 <td>add group labels</td>
 <td>add atom group labels for GPUMD-related workflows</td>
 </tr>
 <tr>
 <td><code>107</code></td>
+<td><code>add_weight.py</code></td>
 <td>add weights</td>
 <td>assign training weights in extxyz</td>
 </tr>
 <tr>
 <td><code>108</code></td>
+<td><code>get_frame.py</code></td>
 <td>extract frame</td>
 <td>export one frame from an extxyz trajectory</td>
 </tr>
 <tr>
 <td><code>109</code></td>
+<td><code>clean_xyz.py</code></td>
 <td>clean XYZ info</td>
 <td>remove extra extxyz properties</td>
 </tr>
 <tr>
 <td><code>110</code></td>
+<td><code>replicate.py</code></td>
 <td>replicate structure</td>
 <td>build supercells by factors or target atom count</td>
 </tr>
 <tr>
 <td><code>out2exyz</code></td>
+<td><code>out2exyz.py</code></td>
 <td>OUTCAR to extxyz, Python version</td>
 <td>alternative VASP OUTCAR converter</td>
 </tr>
 <tr>
 <td><code>pos2exyz</code></td>
+<td><code>pos2exyz.py</code></td>
 <td>POSCAR to extxyz</td>
 <td>convert a single structure</td>
 </tr>
 <tr>
 <td><code>cif2pos</code></td>
+<td><code>cif2pos.py</code></td>
 <td>CIF to POSCAR</td>
 <td>prepare VASP input from CIF</td>
 </tr>
 <tr>
 <td><code>cif2exyz</code></td>
+<td><code>cif2exyz.py</code></td>
 <td>CIF to extxyz</td>
 <td>prepare GPUMDkit input from CIF</td>
 </tr>
 <tr>
 <td><code>xdat2exyz</code></td>
+<td><code>xdatcar2exyz.py</code></td>
 <td>XDATCAR to extxyz</td>
 <td>convert VASP MD trajectory</td>
 </tr>
 <tr>
 <td><code>pos2lmp</code></td>
+<td><code>pos2lmp.py</code></td>
 <td>POSCAR to LAMMPS data</td>
 <td>prepare LAMMPS input</td>
 </tr>
 <tr>
 <td><code>lmp2exyz</code></td>
+<td><code>lmp2exyz.py</code></td>
 <td>LAMMPS dump to extxyz</td>
 <td>convert LAMMPS trajectory</td>
 </tr>
 <tr>
 <td><code>traj2exyz</code></td>
+<td><code>traj2exyz.py</code></td>
 <td>ASE traj to extxyz</td>
 <td>convert ASE trajectory</td>
 </tr>
diff --git a/docs/htmls/en/index.html b/docs/htmls/en/index.html
index b8c871b..5daa56a 100644
--- a/docs/htmls/en/index.html
+++ b/docs/htmls/en/index.html
@@ -1576,7 +1576,7 @@ <h2 id="module-overview">Module Overview</h2>
 <tr>
 <td>Sample Structures</td>
 <td>2</td>
-<td><code>-neptrain</code>, interactive menu</td>
+<td>interactive menu, <code>-frame_range</code>, <code>-pynep</code> (deprecated)</td>
 <td>Structure sampling</td>
 </tr>
 <tr>
diff --git a/docs/htmls/en/structure_sampling.html b/docs/htmls/en/structure_sampling.html
index 43b3ec7..c3967b6 100644
--- a/docs/htmls/en/structure_sampling.html
+++ b/docs/htmls/en/structure_sampling.html
@@ -1632,7 +1632,7 @@ <h2 id="uniform-and-random-sampling">Uniform and Random Sampling</h2>
 <li><code>sampled_structures.xyz</code></li>
 </ul>
 <h2 id="farthest-point-sampling-with-neptrain">Farthest Point Sampling with NepTrain</h2>
-<p>This entry uses NepTrain descriptors for FPS.</p>
+<p>This entry uses NepTrain descriptors for FPS. Choose <code>203</code> in interactive mode, or run the script directly:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
 </code></pre></div>
 <p>From interactive mode, choose <code>203</code>. You will see:</p>
@@ -1709,7 +1709,7 @@ <h3 id="gpumdkit-entry">GPUMDkit Entry</h3>
 </code></pre></div>
 <p>This entry requires <code>pynep</code> and is kept for compatibility.</p>
 <h2 id="structure-perturbation">Structure Perturbation</h2>
-<p>Use perturbation when you want to generate initial structures around a known configuration.</p>
+<p>Use perturbation when you want to generate initial structures around a known configuration. Choose <code>204</code> in interactive mode, or run the script directly:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>python<span class="w"> </span>Scripts/sample_structures/perturb_structure.py<span class="w"> </span>POSCAR<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">0</span>.03<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>uniform
 </code></pre></div>
 <p>From interactive mode, choose <code>204</code>. You will see:</p>
@@ -1756,6 +1756,7 @@ <h2 id="structure-perturbation">Structure Perturbation</h2>
 <p>This function requires <code>dpdata</code>. If you use this function, we recommend citing the dpdata package.</p>
 <h2 id="force-deviation-selection">Force-Deviation Selection</h2>
 <p>Use this together with the GPUMD <code>active</code> command. The <code>active</code> command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. <code>select_max_modev.py</code> selects structures with large force deviations from <code>active.out</code> and <code>active.xyz</code>, then writes them to <code>selected.xyz</code>.</p>
+<p>Choose <code>205</code> in interactive mode, or run the script directly:</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>python<span class="w"> </span>Scripts/sample_structures/select_max_modev.py<span class="w"> </span><span class="m">200</span><span class="w"> </span><span class="m">0</span>.15
 </code></pre></div>
 <p>From interactive mode, choose <code>205</code>. You will see:</p>
@@ -1795,16 +1796,18 @@ <h2 id="force-deviation-selection">Force-Deviation Selection</h2>
 <li><code>selected.xyz</code></li>
 </ul>
 <h2 id="frame-range-extraction">Frame Range Extraction</h2>
-<p>Use this to extract a fraction of a trajectory:</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>python<span class="w"> </span>Scripts/sample_structures/frame_range.py<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span>.8
+<p><code>frame_range.py</code> is an independent CLI tool and is not part of the interactive sampling menu <code>201–205</code>. Use it when you want to keep only a fraction of a trajectory before sampling, for example after equilibration.</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-frame_range<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span>.8
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>python<span class="w"> </span>Scripts/sample_structures/frame_range.py<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span>.8
 </code></pre></div>
-<p>This writes frames from 0% to 80% of the trajectory.</p>
+<p>This writes frames from 0% to 80% of the trajectory. The range arguments are trajectory fractions from <code>0</code> to <code>1</code>.</p>
 <h2 id="example-commands">Example Commands</h2>
-<p>An example sequence using several sampling-related tools:</p>
+<p>An example preprocessing-and-sampling sequence is shown below. The first two commands are analyzer tools; the final step is structure sampling.</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
 <a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
 <a id="__codelineno-19-3" name="__codelineno-19-3" href="#__codelineno-19-3"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
 </code></pre></div>
+<p>The final step can also be run from interactive mode by choosing <code>2) Sample Structures -&gt; 203</code>.</p>
 <h2 id="common-mistakes">Common Mistakes</h2>
 <table>
 <thead>
diff --git a/docs/htmls/search/search_index.json b/docs/htmls/search/search_index.json
index e731dbe..0d1ff60 100644
--- a/docs/htmls/search/search_index.json
+++ b/docs/htmls/search/search_index.json
@@ -1 +1 @@
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The typical workflow includes:</p> Step Action Purpose 1 Run MD simulations Generate candidate structures with current NEP model 2 Filter structures Remove unphysical configurations (short distances, large boxes) 3 Sample structures Select diverse or uncertain structures for DFT 4 Run SCF calculations Compute DFT reference energies/forces 5 NEP prediction Check model accuracy on new structures <p>Unlike menu-driven modules, this workflow is a shell script that you customize and run directly:</p> <pre><code>bash Scripts/workflow/workflow_active_learning_dev.sh\n</code></pre> <p>The sections below explain the main blocks in the script and what each part does.</p>"},{"location":"en/active_learning_workflow.html#1-slurm-directives","title":"1. SLURM Directives","text":"<pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>The SLURM directives are used to define how the job will be submitted to the cluster:</p> <ul> <li><code>#SBATCH -p</code> defines the partition, in this case, it's <code>intel-sc3</code> and <code>intel-sc3-32c</code>.</li> <li><code>#SBATCH -q</code> specifies the queue, in this case, <code>huge</code>.</li> <li><code>#SBATCH -N</code> allocates 1 node for the job.</li> <li><code>#SBATCH -J</code> names the job <code>workflow</code>.</li> <li><code>#SBATCH -o</code> defines the output log file as <code>workflow.log</code>.</li> <li><code>--ntasks-per-node=1</code> specifies that only one task should run per node.</li> </ul> <p>NOTE: If your machine does not have the SLURM environment, you can also run the script directly from the command line. For example:</p> <pre><code>nohup bash workflow_active_learning_dev.sh &amp;&gt;workflow.log &amp;\n</code></pre>"},{"location":"en/active_learning_workflow.html#2-basic-setup","title":"2. Basic Setup","text":"<pre><code>cd $SLURM_SUBMIT_DIR \n</code></pre> <p>Ensure the working directory is correct, and that all necessary files are present for the job.</p> <pre><code>source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  # Load the submit template\npython_pynep=python  # Python executable for the deprecated pynep branch if needed\n</code></pre> <ul> <li><code>GPUMDkit_path</code> is the environment variable that stores the path for the <code>GPUMDkit</code> .</li> <li><code>python_pynep</code> points to the Python environment used for the deprecated <code>pynep</code>-related branch if needed.</li> </ul>"},{"location":"en/active_learning_workflow.html#3-variable-definitions","title":"3. Variable Definitions","text":"<pre><code>work_dir=${PWD}  # Set the working directory\nprefix_name=LiF_iter01  # Prefix for calculations\nmin_dist=1.4  # Minimum atom distance\nbox_limit=13  # Simulation box limit\nmax_fp_num=50  # Maximum number of single point calculations\nsample_method=pynep  # Sampling method (options: uniform, random, pynep)\npynep_sample_dist=0.01  # Sampling distance for pynep\n</code></pre> <p>You can customize:</p> <ul> <li><code>prefix_name</code> to reflect the name of your current work.</li> <li><code>min_dist</code>, <code>box_limit</code>, and <code>max_fp_num</code> based on your own system.</li> <li><code>sample_method</code> (choose between <code>uniform</code>, <code>random</code>, or <code>pynep</code>).</li> <li><code>pynep_sample_dist</code> is the sampling distance for <code>pynep</code>.</li> </ul>"},{"location":"en/active_learning_workflow.html#4-check-required-files","title":"4. Check Required Files","text":"<pre><code>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ -f run.in ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then\n    # Check for the required files before proceeding.\nelse\n    echo \"Please put nep.in nep.txt train.xyz run.in INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.\"\n    exit 1\nfi\n</code></pre> <p>Make sure the necessary files (<code>nep.txt</code>, <code>nep.in</code>, <code>train.xyz</code>, <code>run.in</code>, <code>INCAR</code>, <code>POTCAR</code>, <code>KPOINTS</code>) are available in the working directory. If any of these are missing, the script will terminate. <code>train.xyz</code> and <code>nep.txt</code> are used for <code>pynep</code> sampling, and <code>run.in</code> is the simulation parameters of MD in the current iteration.</p>"},{"location":"en/active_learning_workflow.html#5-file-organization","title":"5. File Organization","text":"<pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <p>The script organizes the working files into two folders:</p> <ul> <li><code>00.modev</code>: For molecular dynamics simulation.</li> <li><code>common</code>: For shared resources such as <code>nep.txt</code>, <code>run.in</code>, and the structure files, etc.</li> </ul>"},{"location":"en/active_learning_workflow.html#6-molecular-dynamics-simulation-submission","title":"6. Molecular Dynamics Simulation Submission","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>After preparing the input files, the script submits an array of molecular dynamics (MD) tasks using <code>submit_gpumd_array</code>.</p>"},{"location":"en/active_learning_workflow.html#7-monitoring-task-completion","title":"7. Monitoring Task Completion","text":"<pre><code>while true; do\n    logs=$(find \"${work_dir}/00.modev/\" -type f -name log -path \"*/sample_*/log\")\n    finished_tasks_md=$(grep \"Finished running GPUMD.\" $logs | wc -l)\n    error_tasks_md=$(grep \"Error\" $logs | wc -l)\n\n    if [ \"$error_tasks_md\" -ne 0 ]; then\n        echo \"Error: MD simulation encountered an error.\"\n        exit 1\n    fi\n    if [ $finished_tasks_md -eq $sample_struct_num ]; then\n        break\n    fi\n    sleep 30\ndone\n</code></pre> <p>The script continuously checks whether all MD tasks have finished by searching for a <code>Finished running GPUMD.</code> message in the logs. If an error is encountered, the script terminates.</p>"},{"location":"en/active_learning_workflow.html#8-analysis-and-filtering","title":"8. Analysis and Filtering","text":"<pre><code>mkdir ${work_dir}/01.select\n...\n</code></pre> <p>In the <code>01.select</code> folder, all structures in the trajectory file <code>dump.xyz</code> during the MD process will be analyzed and filtered to avoid the generation of non-physical structures as much as possible. Specifically, the <code>get_min_dist.py</code>, <code>filter_structures_by_distance.py</code> and <code>filter_exyz_by_box.py</code> scripts will be employed to check whether there are situations where the distance between atoms is too close or the simulated box exceeds the limit value, and such structures will be filtered out.</p>"},{"location":"en/active_learning_workflow.html#9-sampling-methods","title":"9. Sampling Methods","text":"<pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <p>The script supports three sampling methods: <code>uniform</code>, <code>random</code>, and <code>pynep</code>. It selects structures according to the chosen method and checks if the number exceeds <code>max_fp_num</code>, ensuring the final structure count is within limits.</p>"},{"location":"en/active_learning_workflow.html#10-scf-calculations","title":"10. SCF Calculations","text":"<pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>After sampling, SCF calculations are submitted using <code>submit_vasp_array</code>. The process is similar to the MD submission, but for SCF calculations.</p>"},{"location":"en/active_learning_workflow.html#11-prediction-step","title":"11. Prediction Step","text":"<pre><code>submit_nep_prediction\n</code></pre> <p>The final step involves submitting the NEP prediction task to check the accuracy of the NEP model. </p> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/analyzer_scripts.html","title":"Analyzer Scripts","text":"\ud83d\udd0d Analyzer Scripts <p>Analyzer scripts provide structure statistics, distance checks, filters, composition analysis, outlier detection, and time estimation for extxyz datasets.</p>"},{"location":"en/analyzer_scripts.html#what-it-does","title":"What it does","text":"<p>This module helps you inspect, filter, and validate structure datasets. You can check composition, analyze property ranges, detect short contacts, filter structures by various criteria, find outliers in NEP training data, and estimate remaining simulation time.</p>"},{"location":"en/analyzer_scripts.html#before-you-start","title":"Before you start","text":"<p>Script location: <code>Scripts/analyzer/</code></p> <p>Make sure GPUMDkit is installed. See Quick Start for installation instructions.</p>"},{"location":"en/analyzer_scripts.html#overview","title":"Overview","text":"Task Command Purpose Composition <code>gpumdkit.sh -analyze_comp train.xyz</code> Group structures by chemical composition Chemical species <code>gpumdkit.sh -chem_species train.xyz</code> List species in a file Property range <code>gpumdkit.sh -range train.xyz force</code> Inspect energy/force/virial range Minimum distance <code>gpumdkit.sh -min_dist dump.xyz</code> Fast distance check without PBC Minimum distance with PBC <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> Accurate distance check with PBC Charge balance <code>gpumdkit.sh -cbc train.xyz</code> Oxidation-state balance check Distance filter <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> Remove structures with short contacts Box filter <code>gpumdkit.sh -filter_box dump.xyz 13</code> Remove structures with too-large box edges Property filter <code>gpumdkit.sh -filter_value train.xyz force 20</code> Filter by energy/force/virial threshold Pair-distance range <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> Extract structures by pair distance Outlier detection Menu 502 Find high-RMSE structures in training set Probability density <code>gpumdkit.sh -pda &lt;ref&gt; &lt;traj&gt; &lt;element&gt; &lt;interval&gt;</code> 3D probability density for diffusion channels GPUMD time <code>gpumdkit.sh -time gpumd</code> Estimate remaining GPUMD run time NEP time <code>gpumdkit.sh -time nep</code> Estimate remaining NEP training time"},{"location":"en/analyzer_scripts.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit and choose <code>5) Analyzer</code>:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>The analyzer menu is:</p> <pre><code>+------------------------------------------------------+\n|                    ANALYZER TOOLS                    |\n+------------------------------------------------------+\n| 501) Analyze composition of extxyz                   |\n| 502) Find outliers of extxyz                         |\n| 503) Analyze chemical species of extxyz              |\n| 504) Check charge balance of extxyz                  |\n| 505) Analyze energy/force/virial range               |\n| 506) Filter structures by minimum distance           |\n| 507) Get minimum interatomic distance                |\n| 508) Probability density analysis                    |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Most analyzer functions also have direct CLI shortcuts, which are listed in the overview table and in the sections below.</p>"},{"location":"en/analyzer_scripts.html#composition-analysis","title":"Composition Analysis","text":"<p><code>analyze_composition.py</code> analyzes the composition of your extxyz file and lets you export subsets.</p> <p>What it does: Groups structures by chemical composition and shows how many structures belong to each composition. You can export subsets by composition.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>Interactive mode: Choose <code>501</code> from the analyzer menu.</p> <p>Output example:</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>This is useful when <code>train.xyz</code> contains structures from different systems or different cell sizes. You can export a subset by composition from the interactive prompt.</p>"},{"location":"en/analyzer_scripts.html#chemical-species","title":"Chemical Species","text":"<p><code>analyze_chem_species.py</code> lists all unique chemical species in an extxyz file.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -chem_species train.xyz\n</code></pre>"},{"location":"en/analyzer_scripts.html#property-range-analysis","title":"Property Range Analysis","text":"<p><code>energy_force_virial_analyzer.py</code> calculates and visualizes the range of properties from an extxyz file.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <p>Supported properties: <code>energy</code>, <code>force</code>, <code>virial</code></p> <pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist    # Show histogram\n</code></pre> <p>Output example:</p> <pre><code>Force range: 0.03210566767721861 to 9.230115912468435\n</code></pre> <p>With <code>hist</code> option:</p>"},{"location":"en/analyzer_scripts.html#minimum-distance-checks","title":"Minimum Distance Checks","text":""},{"location":"en/analyzer_scripts.html#without-pbc-fast","title":"Without PBC (Fast)","text":"<p><code>get_min_dist.py</code> calculates minimum interatomic distances without considering periodic boundary conditions. Fast but may be inaccurate for periodic systems.</p> <p>What it does: Reports the minimum distance between each pair of elements in every frame, ignoring periodic boundary conditions.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>Interactive mode: Choose <code>507</code> from the analyzer menu.</p> <p>Output example:</p> <pre><code>+---------------------------+\n|   PBC ignored for speed   |\n| use -min_dist_pbc for PBC |\n+---------------------------+\nMinimum interatomic distances:\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.480     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre> <p>Notes: Use this for a quick check. For periodic systems, prefer <code>-min_dist_pbc</code> for accurate results.</p>"},{"location":"en/analyzer_scripts.html#with-pbc-accurate","title":"With PBC (Accurate)","text":"<p><code>get_min_dist_pbc.py</code> calculates minimum interatomic distances considering periodic boundary conditions.</p> <p>What it does: Reports the minimum distance between each pair of elements, accounting for periodic boundary conditions.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>Interactive mode: Choose <code>507</code> from the analyzer menu and answer <code>y</code> when asked whether to consider PBC.</p> <p>Output example:</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre>"},{"location":"en/analyzer_scripts.html#filtering-structures","title":"Filtering Structures","text":""},{"location":"en/analyzer_scripts.html#filter-by-minimum-distance","title":"Filter by Minimum Distance","text":"<p><code>filter_structures_by_distance_pbc.py</code> removes structures with any interatomic distance below a threshold.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>This removes structures with any interatomic distance below <code>1.0 \u00c5</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-box-size","title":"Filter by Box Size","text":"<p><code>filter_exyz_by_box.py</code> filters structures by box-edge length.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>This keeps structures where all box edges are below <code>13 \u00c5</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-property-value","title":"Filter by Property Value","text":"<p><code>filter_exyz_by_value.py</code> filters structures by energy, force, or virial threshold.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <p>Supported properties: <code>energy</code>, <code>force</code>, <code>virial</code></p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre> <p>This filters out structures with force components exceeding <code>20 eV/\u00c5</code> (or energy exceeding <code>5 eV/atom</code>).</p>"},{"location":"en/analyzer_scripts.html#filter-by-pair-distance-range","title":"Filter by Pair-Distance Range","text":"<p><code>filter_dist_range.py</code> extracts structures where a specific element-pair distance falls within a given range.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>This extracts structures where the Li-Li minimum distance is between <code>1.8 \u00c5</code> and <code>2.0 \u00c5</code>. Output: <code>filtered_Li_Li_1.8_2.0.xyz</code>.</p>"},{"location":"en/analyzer_scripts.html#charge-balance-check","title":"Charge Balance Check","text":"<p><code>charge_balance_check.py</code> checks the oxidation-state balance of structures.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>Output files:</p> <ul> <li><code>balanced.xyz</code> \u2014 structures with balanced charges</li> <li><code>unbalanced.xyz</code> \u2014 structures with unbalanced charges</li> <li><code>indices.txt</code> \u2014 indices of balanced structures</li> </ul> <p>This is intended for systems where common oxidation states are meaningful.</p>"},{"location":"en/analyzer_scripts.html#outlier-detection","title":"Outlier Detection","text":"<p><code>find_outliers.py</code> finds outlier structures in NEP training data based on RMSE thresholds for energy, force, and stress.</p> <p>Input files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>stress_train.out</code>, <code>train.xyz</code></p> <p>These files are generated during NEP training. The script compares DFT vs NEP predictions and identifies structures with large errors.</p> <pre><code># Interactive mode\ngpumdkit.sh    # Select: 5) Analyzer \u2192 502) Find outliers of extxyz\n</code></pre> <p>Interactive prompts:</p> <pre><code>Enter energy RMSE threshold (meV/atom): 1\nEnter force RMSE threshold (meV/\u00c5): 60\nEnter stress RMSE threshold (GPa): 0.03\n</code></pre> <p>Output files:</p> <ul> <li><code>selected.xyz</code> \u2014 structures exceeding the RMSE thresholds (outliers)</li> <li><code>remained.xyz</code> \u2014 structures within the thresholds</li> <li><code>selected_remained.png</code> \u2014 comparison plot</li> </ul> <p>Use case: After NEP training, use this to identify problematic structures that contribute most to the error. Remove or improve these structures to enhance the training set.</p>"},{"location":"en/analyzer_scripts.html#time-estimation","title":"Time Estimation","text":""},{"location":"en/analyzer_scripts.html#gpumd-remaining-time","title":"GPUMD Remaining Time","text":"<p><code>time_consuming_gpumd.sh</code> estimates the remaining time for a GPUMD simulation.</p> <p>Input files: <code>run.in</code>, <code>thermo.out</code> (in the current GPUMD working directory)</p> <pre><code>gpumdkit.sh -time gpumd\n</code></pre> <p>Output example:</p> <pre><code>----------------- System Information ----------------\ntotal frames: 1050000\n-----------------------------------------------------\nCurrent Frame  Speed (steps/s)   Total Time       Time Left       Estimated End\n-------------   -------------   -------------   -------------   -----------------\n    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04\n    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56\n</code></pre>"},{"location":"en/analyzer_scripts.html#nep-remaining-time","title":"NEP Remaining Time","text":"<p><code>time_consuming_nep.sh</code> estimates the remaining time for NEP training.</p> <p>Input files: <code>loss.out</code> (in the current NEP working directory)</p> <pre><code>gpumdkit.sh -time nep\n</code></pre> <p>Output example:</p> <pre><code>+-----------------+-----------+-----------------+---------------------+\n|       Step      | Time Diff |    Time Left    |    Finish Time      |\n+-----------------+-----------+-----------------+---------------------+\n| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |\n| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |\n| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |\n+-----------------+-----------+-----------------+---------------------+\n</code></pre>"},{"location":"en/analyzer_scripts.html#probability-density-analysis","title":"Probability Density Analysis","text":"<p><code>probability_density_analysis.py</code> calculates 3D probability density of mobile ions for diffusion channel analysis.</p> <p>Input files: Reference structure (POSCAR), trajectory file (extxyz)</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n</code></pre> <p>Arguments:</p> Argument Meaning <code>LLZO.vasp</code> Reference structure (POSCAR format) <code>dump.xyz</code> Trajectory file (extxyz format) <code>Li</code> Target mobile species <code>0.25</code> Grid interval for the probability density (\u00c5) <p>Output: <code>probability_density_0.25.vasp</code> \u2014 probability density grid in VASP format for visualization with VESTA or similar tools.</p> <p>Visualization suggestions:</p> <ol> <li>Open <code>probability_density_0.25.vasp</code> in VESTA</li> <li>Use \"Edit \u2192 Data \u2192 Volumetric Data\" to adjust isosurface levels</li> <li>Color the probability density by value to highlight preferred diffusion pathways</li> <li>Overlay with the crystal structure for context</li> </ol>"},{"location":"en/analyzer_scripts.html#example-workflows","title":"Example Workflows","text":""},{"location":"en/analyzer_scripts.html#structure-quality-check","title":"Structure Quality Check","text":"<pre><code># 1. Check composition\ngpumdkit.sh -analyze_comp train.xyz\n\n# 2. Check energy/force range\ngpumdkit.sh -range train.xyz force hist\n\n# 3. Check minimum distances\ngpumdkit.sh -min_dist_pbc train.xyz\n\n# 4. Find outliers (after NEP training)\n# Interactive: 5) Analyzer \u2192 502\n</code></pre>"},{"location":"en/analyzer_scripts.html#structure-filtering-pipeline","title":"Structure Filtering Pipeline","text":"<pre><code># 1. Filter by minimum distance\ngpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n\n# 2. Filter by box size\ngpumdkit.sh -filter_box filtered_dist_pbc.xyz 13\n\n# 3. Filter by force threshold\ngpumdkit.sh -filter_value filtered_box.xyz force 20\n</code></pre>"},{"location":"en/analyzer_scripts.html#diffusion-channel-analysis","title":"Diffusion Channel Analysis","text":"<pre><code># 1. Calculate probability density\ngpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n\n# 2. Visualize with VESTA\n# Open probability_density_0.25.vasp\n</code></pre>"},{"location":"en/calculator_scripts.html","title":"Calculator Scripts","text":"\ud83e\uddee Calculator Scripts <p>The calculator module contains scripts for computing properties from MD trajectories, NEP models, and structure files.</p> <p>Script Location: <code>Scripts/calculators/</code></p>"},{"location":"en/calculator_scripts.html#overview","title":"Overview","text":"Task Command Main Input Ionic conductivity <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>, <code>thermo.out</code>, <code>model.xyz</code> MSD from trajectory <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz trajectory NEP prediction <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP model NEP descriptors <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP model DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP model NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> initial/final structures Minimization <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> structure + NEP model Neighbor list <code>gpumdkit.sh -calc nlist ...</code> see Polar Material Analysis Displacement <code>gpumdkit.sh -calc disp ...</code> see Polar Material Analysis Average structure <code>gpumdkit.sh -calc avg-struct ...</code> see Polar Material Analysis Octahedral tilt <code>gpumdkit.sh -calc oct-tilt ...</code> see Polar Material Analysis ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 ...</code> see Polar Material Analysis <p>For a full command list:</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>The command-line help table looks like:</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>In interactive mode, choose <code>4) Calculators</code>. The menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"en/calculator_scripts.html#ionic-conductivity","title":"Ionic Conductivity","text":"<p><code>calc_ion_conductivity.py</code> calculates ionic diffusivity and conductivity from <code>msd.out</code>.</p>"},{"location":"en/calculator_scripts.html#required-and-optional-files","title":"Required and Optional Files","text":"File Role <code>msd.out</code> Required MSD data <code>thermo.out</code> Optional, used for automatic temperature detection <code>model.xyz</code> Optional, used for volume and ion-count detection <code>run.in</code> Optional, used to detect replication"},{"location":"en/calculator_scripts.html#usage","title":"Usage","text":"<pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>From interactive mode, choose <code>401</code>. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>If automatic files are missing, the script will ask for temperature, volume, and ion count interactively.</p> <p>Interactive prompts in manual mode look like:</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre>"},{"location":"en/calculator_scripts.html#example-output","title":"Example Output","text":"<pre><code>Diffusivity (D):\n  D_x: 4.153e-07 cm^2/s\n  D_y: 4.174e-07 cm^2/s\n  D_z: 2.610e-07 cm^2/s\n  D_total: 3.646e-07 cm^2/s\n------------------------------\nIonic Conductivity:\n  Sigma_x: 2.576e-02 mS/cm\n  Sigma_y: 2.589e-02 mS/cm\n  Sigma_z: 1.619e-02 mS/cm\n  Sigma_total: 2.261e-02 mS/cm\n</code></pre>"},{"location":"en/calculator_scripts.html#mean-square-displacement","title":"Mean Square Displacement","text":"<p><code>calc_msd.py</code> computes MSD directly from an extxyz trajectory.</p> <pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>From interactive mode, choose <code>412</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>Li</code> target mobile species <code>10</code> time interval between frames, in fs <code>5000</code> optional maximum correlation steps <p>Output:</p> <ul> <li><code>msd.out</code></li> </ul> <p>The beginning of <code>msd.out</code> is a text table with time and MSD columns. After generating it, use the plot commands below.</p> <p>You can then plot:</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-property-prediction","title":"NEP Property Prediction","text":"<p><code>calc_properties_with_nep.py</code> calculates energy, force, and stress for structures using a NEP model.</p> <p>Dependency: <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>Use this function to run predictions with a trained NEP model. For best results, validate model quality on your target structures before relying on the output.</p> <p>Tip: Before prediction, you may want to clean the extxyz metadata:</p> <pre><code>gpumdkit.sh -clean_xyz train.xyz clean_train.xyz\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-descriptors","title":"NEP Descriptors","text":"<p><code>calc_descriptors.py</code> extracts NEP descriptors for a selected element.</p> <pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>Use cases:</p> <ul> <li>visualize chemical environments with PCA/UMAP;</li> <li>compare training and candidate structures;</li> <li>inspect whether new data expands descriptor space.</li> </ul> <p>Plot descriptors with:</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/calculator_scripts.html#density-of-atomistic-states","title":"Density of Atomistic States","text":"<p><code>calc_doas.py</code> calculates density of atomistic states (DOAS), following the idea proposed by Wang et al..</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>The script:</p> <ol> <li>reads all structures;</li> <li>relaxes each structure with a NEP calculator;</li> <li>extracts per-atom energies;</li> <li>groups atomic energies by element;</li> <li>writes the grouped values to the output file.</li> </ol> <p>For very large systems, running minimization and atomistic-energy extraction directly in GPUMD can be more efficient.</p>"},{"location":"en/calculator_scripts.html#neb-with-a-nep-model","title":"NEB with a NEP Model","text":"<pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>This runs a NEB calculation with <code>9</code> intermediate images. During execution, the script asks how atoms should be fixed:</p> <ul> <li><code>none</code>: no atoms fixed;</li> <li><code>index</code>: fix atoms by index;</li> <li><code>element</code>: fix all atoms of one element;</li> <li><code>position</code>: fix atoms inside a coordinate range.</li> </ul>"},{"location":"en/calculator_scripts.html#structure-minimization","title":"Structure Minimization","text":"<p><code>calc_minimize.py</code> minimizes a structure using a NEP model through <code>calorine</code>.</p> <p>Dependency: <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input structure, POSCAR/CONTCAR or extxyz <code>nep.txt</code> NEP model <code>0.01</code> optional force convergence threshold in eV/Ang <code>1000</code> optional maximum optimization steps <p>Output:</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"en/calculator_scripts.html#rdf-calculation-with-ovito","title":"RDF Calculation with OVITO","text":"<p><code>rdf_calculator_ovito.py</code> calculates radial distribution function using OVITO's analysis tools.</p> <p>Dependency: OVITO</p> <pre><code>pip install ovito\n</code></pre> <p>Input file: Structure file (single frame or trajectory)</p> <pre><code>python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400\n</code></pre> <p>Parameters:</p> Argument Meaning <code>trajectory.xyz</code> Input structure file <code>6.0</code> Maximum distance for RDF calculation (\u00c5) <code>400</code> Number of histogram bins <p>Visualization:</p> <pre><code>gpumdkit.sh -plt rdf\n</code></pre> <p>Note: It is recommended to use the <code>compute_rdf</code> command directly in GPUMD when possible.</p>"},{"location":"en/calculator_scripts.html#ferroelectric-and-polar-material-tools","title":"Ferroelectric and Polar Material Tools","text":"<p>Options <code>406\u2013410</code> cover perovskite and polar-material analysis: neighbor lists, local displacements, averaged structures, octahedral tilt, and ABO3 polarization. These tools are built on <code>ferrodispcalc</code>.</p> <p>Dependency:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>For complete argument lists, real-world workflow examples (PbTiO3 phase transition, PTO/STO superlattice topology, etc.), see Polar Material Analysis.</p>"},{"location":"en/command_reference.html","title":"Command Reference","text":"\ud83d\udccb Command Reference <p>This page lists the stable GPUMDkit command-line shortcuts. Interactive mode is available for workflows with many choices.</p> <p>The source table is maintained in <code>docs/command_reference.tsv</code>.</p>"},{"location":"en/command_reference.html#gpumdkitsh-h-output","title":"<code>gpumdkit.sh -h</code> Output","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |\n| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/command_reference.html#main","title":"Main","text":"Command Syntax Description <code>-h</code> <code>gpumdkit.sh -h</code> Show general help <code>-update</code> <code>gpumdkit.sh -update</code> Update GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> Clean extra files in the current directory"},{"location":"en/command_reference.html#format-conversion","title":"Format Conversion","text":"Command Syntax Description <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR to extxyz, shell version <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR to extxyz, Python version <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K output to xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR to extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF to POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF to extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR to extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz frames to POSCAR files <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR to LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump to extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory to extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> Replicate by cell factors <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> Replicate toward a target atom count <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> Add GPUMD group labels <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> Add structure weights <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> Extract one frame <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> Remove extra extxyz properties <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> Extract frames by fractional range"},{"location":"en/command_reference.html#calculators","title":"Calculators","text":"Command Syntax Description <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> Ionic conductivity <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP property prediction <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP descriptors <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> Density of atomistic states <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> NEB with a NEP model <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> Structure minimization <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> MSD from trajectory <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> Neighbor lists <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> Displacements <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> Averaged structure <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> Octahedral tilt <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 local polarization"},{"location":"en/command_reference.html#analyzers","title":"Analyzers","text":"Command Syntax Description <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> Property range analysis <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> Composition analysis <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> Chemical species list <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> Charge-balance check <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> Minimum distance without PBC <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> Minimum distance with PBC <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> Distance filtering <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> PBC-aware distance filtering <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> Box-edge filtering <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> Property threshold filtering <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> Element-pair distance range filtering <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> Probability density analysis"},{"location":"en/command_reference.html#visualization","title":"Visualization","text":"<p>Use:</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>Common types include <code>train</code>, <code>prediction</code>, <code>thermo</code>, <code>msd</code>, <code>sdc</code>, <code>rdf</code>, <code>emd</code>, <code>nemd</code>, <code>hnemd</code>, <code>pdos</code>, and <code>plane-grid</code>.</p>"},{"location":"en/command_reference.html#utilities","title":"Utilities","text":"Command Syntax Description <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> Monitor GPUMD or NEP progress <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> Modify NEP models interactively <code>-pynep</code> <code>gpumdkit.sh -pynep</code> Deprecated PyNEP FPS sampling"},{"location":"en/contributing_to_gpumdkit.html","title":"Contributing to GPUMDkit","text":"\ud83e\udd1d Contributing to GPUMDkit <p>Thank you for your interest in contributing to GPUMDkit! We appreciate your time and effort in helping improve this toolkit.</p> <p> English   \u00a0\u00b7\u00a0   \u7b80\u4f53\u4e2d\u6587 </p> <p><code>GPUMDkit</code> is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.</p> <p>Note: The authoritative version of this document is <code>CONTRIBUTING.md</code> in the repository root. This tutorial page mirrors its content.</p>"},{"location":"en/contributing_to_gpumdkit.html#table-of-contents","title":"Table of Contents","text":"<ul> <li>Development Restrictions and Guidelines</li> <li>Reporting Bugs</li> <li>Suggesting Features</li> <li>Contributing Code</li> <li>Fork and Clone the Repository</li> <li>Create a Feature Branch</li> <li>Making Changes<ul> <li>Interactive Mode Contributions</li> <li>Command-Line Mode Contributions</li> <li>Updating Tab Completion</li> </ul> </li> <li>Code Style and Best Practices</li> <li>Testing Your Changes</li> <li>Commit Messages</li> <li>Push and Open a Pull Request</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#development-restrictions-and-guidelines","title":"Development Restrictions and Guidelines","text":"<p>To maintain code quality and consistency across the project, please adhere to these guidelines:</p>"},{"location":"en/contributing_to_gpumdkit.html#language-requirements","title":"Language Requirements","text":"<ul> <li>All code should be written in English: This includes variable names, function names, comments, docstrings, commit messages, and documentation.</li> <li>While we understand that contributors come from diverse backgrounds, using English ensures that the codebase is accessible to the widest possible audience.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#modularity-and-reusability","title":"Modularity and Reusability","text":"<ul> <li>Write modular and reusable code: Functions and scripts should be designed with flexibility in mind.</li> <li>Prefer passing parameters over hardcoding values: Use function arguments, command-line parameters, or configuration files instead of hardcoded values. However, some filenames are required to be fixed by GPUMD and NEP programs (e.g., <code>train.xyz</code>, <code>thermo.out</code>), and these can be hardcoded as needed.</li> <li>Example:    <pre><code># Good: accepts parameters\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # processing logic\n}\n\n# Avoid: hardcoded values (unless required by GPUMD/NEP)\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # processing logic\n}\n</code></pre></li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#code-style","title":"Code Style","text":"<ul> <li>Write code that is clear and easy for others to maintain and modify.</li> <li>Use meaningful variable and function names.</li> <li>Add comments where necessary to explain complex logic.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#documentation","title":"Documentation","text":"<ul> <li>Ensure that help messages (e.g., <code>-h</code> flags) are clear and accurate.</li> <li>Tutorial documentation lives in <code>docs/tutorials/en/</code> (English) and <code>docs/tutorials/zh/</code> (Chinese).   If you add a new feature, consider updating the relevant tutorial page.</li> <li>After editing tutorial markdown files, rebuild the HTML with <code>mkdocs build -f docs/mkdocs.yml</code>.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#reporting-bugs","title":"Reporting Bugs","text":"<p>If you encounter a bug, please help us fix it by reporting it through GitHub Issues:</p> <ol> <li>Search existing issues to see if the bug has already been reported.</li> <li>Open a new issue if it hasn't been reported yet: Create an Issue</li> <li>Describe the problem in detail and provide test files if possible.</li> </ol> <p>You can also reach out to us through: - QQ Group: 825696376 - Email: yanzihan@westlake.edu.cn - Script Developer: Contact the developer listed in the script header</p>"},{"location":"en/contributing_to_gpumdkit.html#suggesting-features","title":"Suggesting Features","text":"<p>We welcome feature suggestions! To propose a new feature:</p> <ol> <li>Search existing issues to see if someone has already suggested it.</li> <li>Open a new feature request: Create a Feature Request and mention @zhyan0603</li> <li>Describe what you need clearly and explain how it would be useful.</li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#contributing-code","title":"Contributing Code","text":""},{"location":"en/contributing_to_gpumdkit.html#fork-and-clone-the-repository","title":"Fork and Clone the Repository","text":"<ol> <li> <p>Fork the repository on GitHub by clicking the \"Fork\" button at the top right of the repository page.</p> </li> <li> <p>Clone your fork to your local machine:</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>Set up the upstream remote to keep your fork in sync:    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#create-a-feature-branch","title":"Create a Feature Branch","text":"<p>Create a new branch for your changes:</p> <pre><code># Create and checkout a new branch from main\ngit checkout -b your-branch-name\n</code></pre> <p>Name your branch as you prefer.</p>"},{"location":"en/contributing_to_gpumdkit.html#making-changes","title":"Making Changes","text":"<p>The structure of <code>GPUMDkit</code> consists of: - <code>gpumdkit.sh</code>: Main entry point (Bash script) handling both interactive menu mode and command-line mode - <code>install.sh</code>: Installation script that sets up environment variables and shell configuration - <code>Scripts/</code>: Python and Bash implementation scripts organized by functionality   - <code>plt_scripts/</code>: Plotting scripts   - <code>calculators/</code>: Calculation utilities   - <code>format_conversion/</code>: Format conversion tools   - <code>workflow/</code>: Workflow automation   - <code>sample_structures/</code>: Structure sampling utilities   - <code>analyzer/</code>: Analysis tools   - <code>utils/</code>: Utility functions (including <code>completion.sh</code> for tab completion) - <code>src/</code>: Shell scripts containing menu functions for interactive mode   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>skills/</code>: AI agent skill definitions (SKILL.md files for opencode/Claude Code integration) - <code>docs/</code>: Documentation files   - <code>tutorials/en/</code> and <code>tutorials/zh/</code>: Bilingual tutorial pages   - <code>mkdocs.yml</code>: MkDocs configuration for building tutorial HTML   - <code>command_reference.tsv</code>: Machine-readable command reference   - <code>htmls/</code>: Generated HTML output from MkDocs</p>"},{"location":"en/contributing_to_gpumdkit.html#interactive-mode-contributions","title":"Interactive Mode Contributions","text":"<p>To add a new feature accessible through the interactive menu:</p> <ol> <li>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:</li> </ol> <pre><code># Example: Add a new format conversion script\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>Implement your functionality following the modularity guidelines (accept parameters, avoid hardcoding).</p> </li> <li> <p>Add a wrapper function in the corresponding <code>src/</code> file:    <pre><code># Example: Edit src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>Add a new function:    <pre><code>function f111_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input &lt;required_param1&gt; &lt;required_param2&gt;\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -r -a converter_args\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py \"${converter_args[@]}\"\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>Update the menu display in <code>gpumdkit.sh</code>:    <pre><code># Find the menu() function and update it if needed\n# Find the array_choice array and add your new choice number\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\" \"107\" \"108\" \"109\" \"110\" \"111\"  # Added \"111\"\n    # ... rest of choices\n)\n</code></pre></p> </li> <li> <p>Add the case statement in <code>gpumdkit.sh</code>:    <pre><code># In the main() function, find the appropriate case statement\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n             \"101\") f101_out2xyz ;;\n             # ... existing cases ...\n             \"111\") f111_new_converter ;;  # Add your case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#command-line-mode-contributions","title":"Command-Line Mode Contributions","text":"<p>To add a new command-line flag or subcommand:</p> <ol> <li> <p>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:    <pre><code># Example: Add a new analyzer script\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>Implement your functionality with clear parameter requirements:    <pre><code># Example: Scripts/analyzer/analyze_bonds.py\nimport sys\n\nif len(sys.argv) != 3:\n    print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n    print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n    sys.exit(1)\n\ninput_file = sys.argv[1]\ncutoff = float(sys.argv[2])\n\n# Your implementation here\n</code></pre></p> </li> </ol> <p>Note: GPUMDkit Python scripts are designed to run directly (not imported as modules). You may use a <code>main()</code> function with <code>if __name__ == \"__main__\":</code> guard if you prefer, but it is not required. Most existing scripts execute at module level.</p> <ol> <li> <p>Add the command-line flag handler in <code>gpumdkit.sh</code>:    <pre><code># Find the command-line parsing section (the large \"case $1 in\" block)\n# Add your new flag in the appropriate location\n\ncase $1 in\n    # ... existing cases ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ \"$2\" != \"-h\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py $2 $3\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n        fi ;;\n    # ... rest of cases ...\nesac\n</code></pre></p> </li> <li> <p>Update the help information in <code>gpumdkit.sh</code>:    <pre><code># Find the help_info_table() function and add your command\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... rest of help table ...\n}\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#updating-tab-completion","title":"Updating Tab Completion","text":"<p>When adding new command-line flags, update the tab completion script:</p> <pre><code># Edit Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>Add your new flag to the <code>opts</code> variable: <pre><code># Find the line with local opts=...\nlocal opts=\"-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...\"\n#                                                        Add your flag here\n</code></pre></p> <p>If your flag requires file arguments, add it to the existing file-completion case: <pre><code># Find the case for file-requiring flags and add yours with |\n-out2xyz|-out2exyz|-...|-your_new_flag)\n    COMPREPLY=($(compgen -f -- \"$cur\")) ;;\n</code></pre></p> <p>If your flag accepts secondary options (like <code>-plt</code> or <code>-calc</code>), add a new case: <pre><code>case \"$prev\" in\n    # ... existing cases ...\n    -your_new_flag)\n        COMPREPLY=($(compgen -W \"option1 option2 option3\" -- \"$cur\")) ;;\n    # ... rest of cases ...\nesac\n</code></pre></p>"},{"location":"en/contributing_to_gpumdkit.html#code-style-and-best-practices","title":"Code Style and Best Practices","text":"<ul> <li>Shell Scripts:</li> <li>Use <code>${variable}</code> for variable expansion</li> <li>Use <code>[ ! -z \"$var\" ]</code> for non-empty checks (project convention)</li> <li>Interactive functions should follow the banner format:     <pre><code>echo \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/&lt;category&gt;        |\"\necho \" | Script: &lt;script_name&gt;.py                        |\"\necho \" | Developer: &lt;Name&gt; (&lt;email&gt;)                     |\"\necho \" &gt;-------------------------------------------------&lt;\"\n</code></pre></li> <li>Use <code>read -r -a varname</code> for multi-word input, then pass with <code>\"${varname[@]}\"</code></li> <li> <p>Shell scripts in <code>src/</code> should start with a file header block:     <pre><code># ============================================================\n# GPUMDkit &lt;module name&gt; module\n# Repository: https://github.com/zhyan0603/GPUMDkit\n# Author: &lt;Name&gt; (&lt;email&gt;)\n# ============================================================\n</code></pre></p> </li> <li> <p>Python Scripts:</p> </li> <li>Write clear, maintainable code</li> <li>Use meaningful variable names</li> <li>Use <code>sys.argv</code> for argument parsing (consistent with most existing scripts)</li> <li>Provide clear usage messages with <code>print(\"Usage: ...\")</code> and <code>print(\"Example: ...\")</code></li> <li>If your script uses heavy/special packages (<code>NepTrain</code>, <code>calorine</code>, <code>dpdata</code>), add a     <code>print_dependency_notice()</code> function to inform users about citation recommendations</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#testing-your-changes","title":"Testing Your Changes","text":"<p>Before submitting your contribution, run the relevant validation commands:</p> <pre><code># Shell syntax checks (always run these)\nbash -n gpumdkit.sh\nfind src Scripts -name '*.sh' -exec bash -n {} +\n\n# Python syntax checks (for modified Python files)\npython3 -m py_compile path/to/modified_script.py\n\n# MkDocs build (if you modified documentation)\nmkdocs build -f docs/mkdocs.yml\n\n# Check for trailing whitespace issues\ngit diff --check\n</code></pre> <p>Then test functionality:</p> <ol> <li> <p>Test interactive mode (if applicable):    <pre><code>gpumdkit.sh\n# Navigate to your new feature and test it thoroughly\n</code></pre></p> </li> <li> <p>Test command-line mode (if applicable):    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # Test help message\n</code></pre></p> </li> <li> <p>Test tab completion (if you modified <code>completion.sh</code>):    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # Should show your new flag\n</code></pre></p> </li> <li> <p>Test with various inputs:</p> </li> <li>Test with typical inputs</li> <li>Test with edge cases (empty files, large files, etc.)</li> <li> <p>Test error handling (missing files, invalid parameters)</p> </li> <li> <p>Verify no regressions: Ensure existing functionality still works correctly.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#commit-messages","title":"Commit Messages","text":"<p>Write clear, descriptive commit messages that explain what you changed. There are no strict format requirements - just make sure your message is understandable.</p>"},{"location":"en/contributing_to_gpumdkit.html#push-and-open-a-pull-request","title":"Push and Open a Pull Request","text":"<ol> <li> <p>Commit your changes:    <pre><code>git add .\ngit commit -m \"your descriptive message\"\n</code></pre></p> </li> <li> <p>Keep your branch updated with the latest <code>dev</code> branch:    <pre><code>git fetch origin\ngit rebase origin/dev\n</code></pre></p> </li> <li> <p>Push your branch to your fork:    <pre><code>git push origin your-branch-name\n</code></pre></p> </li> <li> <p>Open a Pull Request:</p> </li> <li>Go to the GPUMDkit repository</li> <li>Click \"Pull Requests\" \u2192 \"New Pull Request\"</li> <li>Set the base branch to <code>dev</code> for code review</li> <li>Set the compare branch to your feature branch</li> <li> <p>Fill in the PR description with:</p> <ul> <li>Title: Brief description of changes</li> <li>Description: Detailed explanation of what changed and why</li> <li>Testing: Describe how you tested the changes</li> </ul> </li> <li> <p>Respond to review feedback:</p> </li> <li>Be open to suggestions and constructive criticism</li> <li>Make requested changes promptly</li> <li> <p>Push additional commits to your branch (they'll automatically appear in the PR)</p> </li> <li> <p>After approval: A maintainer will merge your PR.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#questions-or-need-help","title":"Questions or Need Help?","text":"<p>If you have questions about contributing or need help with your contribution:</p> <ul> <li>Open a discussion: Use GitHub Discussions for general questions</li> <li>Ask in an issue: Comment on related issues for specific questions</li> <li>Contact maintainers: Reach out to the core developers listed in the README</li> </ul> <p>Thank you again for contributing to <code>GPUMDkit</code>! Your efforts help make this toolkit better for the entire GPUMD and NEP community.</p>"},{"location":"en/custom_commands.html","title":"Custom Commands","text":"\ud83d\udd27 Custom Commands <p>GPUMDkit allows users to extend the command-line interface with custom commands. Define shortcuts for frequently used scripts in your ~/.gpumdkit.in file.</p>"},{"location":"en/custom_commands.html#setup","title":"Setup","text":"<p>Create or edit <code>~/.gpumdkit.in</code>: <pre><code>vi ~/.gpumdkit.in\n</code></pre></p> <p>Define custom functions with the <code>custom_</code> prefix.</p>"},{"location":"en/custom_commands.html#examples","title":"Examples","text":""},{"location":"en/custom_commands.html#simple-greeting","title":"Simple Greeting","text":"<p>Write the following codes in your <code>~/.gpumdkit.in</code> </p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>and run <code>gpumdkit.sh -hello</code>, you will see:</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"en/custom_commands.html#command-with-required-arguments","title":"Command with Required Arguments","text":"<p>For the following function:</p> <pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>and you can add an argument, for example: <code>gpumdkit.sh -greet Zihan</code>, then you will see:</p> <pre><code>Hello, Zihan!\n</code></pre> <p>Passing arguments: Use <code>\"$@\"</code> to forward all arguments safely. Use <code>${@:1}</code> when you need to refer to arguments starting from the first one. </p>"},{"location":"en/custom_commands.html#calling-an-external-script","title":"Calling an External Script","text":"<p>If you want to call an external script like <code>gpumdkit.sh</code>.</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>and run <code>gpumdkit.sh -nepanalyse</code></p>"},{"location":"en/custom_commands.html#advanced-examples","title":"Advanced Examples","text":""},{"location":"en/custom_commands.html#batch-processing","title":"Batch Processing","text":"<p>Process multiple files: <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -batch_plot dir1 dir2 dir3</code></p>"},{"location":"en/custom_commands.html#analysis-pipeline","title":"Analysis Pipeline","text":"<p>Combine multiple operations: <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -analyze_training train.xyz</code></p>"},{"location":"en/custom_commands.html#custom-workflow","title":"Custom Workflow","text":"<p>Automate common workflow: <pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    # Convert VASP outputs\n    gpumdkit.sh -out2xyz ./\n\n    # Filter outliers\n    gpumdkit.sh -filter_value train.xyz force 30\n\n    # Check quality\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -prep_training</code></p>"},{"location":"en/custom_commands.html#tips","title":"Tips","text":"<ul> <li>Use descriptive names: <code>custom_analyze_nep_training</code> is clearer than <code>custom_ant</code></li> <li>Add help messages: Echo usage info when no arguments provided</li> <li>Error handling: Check if required files exist before processing</li> <li>Forward arguments safely: Use <code>\"$@\"</code> to preserve spaces and special characters</li> </ul> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/format_conversion.html","title":"Format Conversion","text":"\ud83d\udd04 Format Conversion <p>GPUMDkit contains utilities for converting common atomistic simulation formats, with extra handling for metadata such as group labels, weights, and frame extraction.</p>"},{"location":"en/format_conversion.html#what-it-does","title":"What it does","text":"<p>This module converts structure and trajectory files between common formats used in computational materials science. It supports VASP, LAMMPS, CP2K, ABACUS, CIF, ASE trajectories, and extxyz. It also provides tools for adding group labels, weights, extracting frames, and replicating structures.</p>"},{"location":"en/format_conversion.html#before-you-start","title":"Before you start","text":"<p>Script location: <code>Scripts/format_conversion/</code></p> <p>Make sure GPUMDkit is installed. See Quick Start for installation instructions.</p>"},{"location":"en/format_conversion.html#supported-formats","title":"Supported formats","text":"<p>The format conversion module covers:</p> <ul> <li>VASP: <code>POSCAR</code>, <code>CONTCAR</code>, <code>OUTCAR</code>, <code>XDATCAR</code></li> <li>LAMMPS: data files and dump trajectories</li> <li>CP2K: output logs, position, force, and cell files</li> <li>ABACUS: SCF/MD logs</li> <li>CIF: crystallographic structure files</li> <li>ASE trajectory: <code>.traj</code></li> <li>extxyz: a common structure format for GPUMD and NEP</li> </ul>"},{"location":"en/format_conversion.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>1) Format Conversion\n</code></pre> <p>The format conversion menu is:</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"en/format_conversion.html#what-each-entry-does","title":"What Each Entry Does","text":"Entry Function When to Use <code>101</code> VASP OUTCAR to extxyz, shell version convert VASP calculation directories <code>102</code> MTP cfg to extxyz convert MTP training data <code>103</code> CP2K to extxyz choose CP2K log/inp route or pos/frc/cell route <code>104</code> ABACUS to extxyz convert ABACUS SCF or MD output <code>105</code> extxyz to POSCAR write each extxyz frame as a POSCAR-style file <code>106</code> add group labels add atom group labels for GPUMD-related workflows <code>107</code> add weights assign training weights in extxyz <code>108</code> extract frame export one frame from an extxyz trajectory <code>109</code> clean XYZ info remove extra extxyz properties <code>110</code> replicate structure build supercells by factors or target atom count <code>out2exyz</code> OUTCAR to extxyz, Python version alternative VASP OUTCAR converter <code>pos2exyz</code> POSCAR to extxyz convert a single structure <code>cif2pos</code> CIF to POSCAR prepare VASP input from CIF <code>cif2exyz</code> CIF to extxyz prepare GPUMDkit input from CIF <code>xdat2exyz</code> XDATCAR to extxyz convert VASP MD trajectory <code>pos2lmp</code> POSCAR to LAMMPS data prepare LAMMPS input <code>lmp2exyz</code> LAMMPS dump to extxyz convert LAMMPS trajectory <code>traj2exyz</code> ASE traj to extxyz convert ASE trajectory"},{"location":"en/format_conversion.html#quick-command-reference","title":"Quick Command Reference","text":"Source Target Command OUTCAR directory extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR directory extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> extxyz POSCAR files <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"en/format_conversion.html#common-examples","title":"Common Examples","text":""},{"location":"en/format_conversion.html#convert-vasp-calculations-to-extxyz","title":"Convert VASP calculations to extxyz","text":"<p>What it does: Searches a directory for VASP OUTCAR files and converts them into a single extxyz file for NEP training or analysis.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>The shell version searches the target directory and converts VASP results into an extxyz file. If you prefer the Python implementation:</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>Interactive mode: Choose <code>101</code> from the format conversion menu. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre> <p>Output: An extxyz file containing the converted structures, suitable for NEP training or further analysis.</p>"},{"location":"en/format_conversion.html#add-group-labels","title":"Add group labels","text":"<p>What it does: Adds atom group labels to a structure file. Group labels are required by some GPUMD-related workflows, such as species-specific MSD or diffusion calculations.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>This command reads the input structure and writes an extxyz file with group information.</p> <p>Interactive mode: Choose <code>106</code> from the format conversion menu. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre> <p>Output: An extxyz file with group labels added.</p>"},{"location":"en/format_conversion.html#script-details","title":"Script Details","text":""},{"location":"en/format_conversion.html#poscar-to-extxyz","title":"POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>Use this when you have a single VASP structure and want an extxyz output.</p> <p>Interactive keyword: <code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#extxyz-to-poscar","title":"extxyz to POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>This converts all frames in an extxyz file into <code>POSCAR_*.vasp</code> files. Frame indices are 0-based in most GPUMDkit scripts, but output filenames are meant for direct inspection and batch calculations.</p> <p>Interactive entry: <code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#lammps-dump-to-extxyz","title":"LAMMPS dump to extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>The element symbols must match the LAMMPS atom type IDs. For example, if type <code>1</code> is Li, type <code>2</code> is Y, and type <code>3</code> is Cl, the order should be <code>Li Y Cl</code>.</p> <p>Interactive keyword: <code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#cif-conversion","title":"CIF conversion","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>Use <code>-cif2pos</code> if you want a VASP-style structure, and <code>-cif2exyz</code> if the next step is GPUMDkit analysis.</p>"},{"location":"en/format_conversion.html#add-weights","title":"Add weights","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>This is useful when you want some structures to have a different training weight in a NEP dataset.</p>"},{"location":"en/format_conversion.html#replicate-structures","title":"Replicate structures","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>The first form uses explicit replication factors. The second form tries to build a supercell close to a target atom count.</p>"},{"location":"en/format_conversion.html#extract-one-frame","title":"Extract one frame","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>This extracts frame index <code>1000</code> from an extxyz trajectory.</p>"},{"location":"en/format_conversion.html#split-multi-frame-extxyz","title":"Split multi-frame extxyz","text":"<p><code>split_single_xyz.py</code> splits an extxyz file into individual frames, each written to a separate file.</p> <pre><code>python Scripts/format_conversion/split_single_xyz.py dump.xyz\n</code></pre> <p>This creates <code>model_0.xyz</code>, <code>model_1.xyz</code>, ... for each frame in the trajectory.</p>"},{"location":"en/format_conversion.html#mtp-conversion","title":"MTP conversion","text":"<p>Convert MTP <code>.cfg</code> format to extxyz:</p> <pre><code>gpumdkit.sh    # Select: 1) Format Conversion \u2192 102\n</code></pre> <p>Interactive prompt:</p> <pre><code>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;\nExample: train.cfg Pd Ag\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#abacus-conversion","title":"ABACUS conversion","text":"<p>Convert ABACUS output to extxyz:</p> <pre><code>gpumdkit.sh    # Select: 1) Format Conversion \u2192 104\n</code></pre> <p>The menu offers two options:</p> <ol> <li>SCF output (<code>running_scf.log</code>)</li> <li>MD output (<code>running_md.log</code>)</li> </ol>"},{"location":"en/format_conversion.html#common-mistakes","title":"Common Mistakes","text":"Problem What to Check LAMMPS elements are wrong Check the element order passed after the dump file A trajectory has strange metadata Try <code>-clean_xyz input.xyz clean.xyz</code> A converted structure looks shifted Inspect PBC/cell information in the source file Frame extraction gives the wrong structure Remember that frame indices are 0-based"},{"location":"en/format_conversion.html#notes","title":"Notes","text":"<p>If a Python package required by a specific converter is missing, Python will report it when that converter is used.</p>"},{"location":"en/plot_scripts.html","title":"Plot Scripts","text":"\ud83d\udcca Plot Scripts <p>The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators. All plots can be displayed interactively or saved as high-resolution PNG files.</p> <p>Script Location: <code>Scripts/plt_scripts/</code></p>"},{"location":"en/plot_scripts.html#quick-access","title":"Quick Access","text":"<pre><code>gpumdkit.sh -plt              # Show all plotting options\ngpumdkit.sh -plt &lt;type&gt;       # Generate a plot\ngpumdkit.sh -plt &lt;type&gt; save  # Save plot as PNG\ngpumdkit.sh -plt &lt;type&gt; -h    # Show help for a specific plot type\n</code></pre> <p>Running <code>gpumdkit.sh -plt</code> prints the plotting command menu:</p> <pre><code>+-----------------------------------------------------------------------------------------------+\n|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |\n+-----------------------------------------------------------------------------------------------+\n|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |\n+-----------------------------------------------------------------------------------------------+\n|                                    NEP Training &amp; Evaluation                                  |\n+-----------------------------------------------------------------------------------------------+\n|  train          - NEP training results           prediction     - NEP prediction results      |\n|  train_test     - NEP train and test results     parity_density - Parity density plot         |\n|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |\n|  charge         - Charge distribution            born_charge    - Born effective charges      |\n|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |\n|  des            - Descriptors                    lr             - Learning rate for gnep      |\n+-----------------------------------------------------------------------------------------------+\n|                                     Diffusion &amp; Transport                                     |\n+-----------------------------------------------------------------------------------------------+\n|  msd            - Mean square displacement       msd_conv       - MSD convergence             |\n|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |\n|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|\n|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |\n|  D_xyz          - Directional Arrhenius D                                                     |\n+-----------------------------------------------------------------------------------------------+\n|                                    MD &amp; Structural Analysis                                   |\n+-----------------------------------------------------------------------------------------------+\n|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |\n|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |\n|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |\n|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |\n|  doas           - Density of atomistic states                                                 |\n+-----------------------------------------------------------------------------------------------+\n|                                        Heat Transport                                         |\n+-----------------------------------------------------------------------------------------------+\n|  emd            - EMD results                    nemd           - NEMD results                |\n|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |\n+-----------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/plot_scripts.html#nep-training-and-prediction","title":"NEP Training and Prediction","text":""},{"location":"en/plot_scripts.html#plt_trainpy","title":"plt_train.py","text":"<p>Visualizes NEP training progress including loss curves, RMSE evolution, and parity plots comparing DFT vs NEP predictions for energy, forces, and stresses.</p> <p>Input Files: <code>loss.out</code>, <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/plot_scripts.html#plt_predictionpy","title":"plt_prediction.py","text":"<p>Visualizes NEP prediction results on the test set.</p> <p>Input Files: <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test         # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#plt_train_testpy","title":"plt_train_test.py","text":"<p>Creates combined parity plots for both training and testing datasets.</p> <p>Input Files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code>, <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"en/plot_scripts.html#plt_parity_densitypy","title":"plt_parity_density.py","text":"<p>Generates density-based parity plots for energies, forces, and stresses. Useful for large datasets where scatter plots become unreadable.</p> <p>Input Files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"en/plot_scripts.html#plt_force_errorspy","title":"plt_force_errors.py","text":"<p>Plots force error evaluation metrics as proposed by Liu et al..</p> <p>Input File: <code>force_train.out</code></p> <p>Metrics Displayed: - Force magnitude errors (delta_F) - Force angle errors (delta_theta) - Distribution of errors</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"en/plot_scripts.html#plt_learning_ratepy","title":"plt_learning_rate.py","text":"<p>Visualizes learning rate during <code>gnep</code> training.</p> <p>Input File: <code>loss.out</code></p> <p>Note: Only for the <code>gnep</code> training process.</p> <pre><code>gpumdkit.sh -plt lr\n</code></pre>"},{"location":"en/plot_scripts.html#plt_nep_restartpy","title":"plt_nep_restart.py","text":"<p>Visualizes parameters stored in the <code>nep.restart</code> file.</p> <p>Input File: <code>nep.restart</code></p> <pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"en/plot_scripts.html#plt_chargepy","title":"plt_charge.py","text":"<p>Plots charge distribution from <code>qNEP</code> model.</p> <p>Input File: <code>charge_train.out</code></p> <p>Important: Ensure consistency between training set and charge output atom ordering. Use full batch training or run prediction step first.</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre>"},{"location":"en/plot_scripts.html#plt_born_chargepy","title":"plt_born_charge.py","text":"<p>Creates parity plots for Born effective charges (BEC) on training and testing datasets. Structures with all-zero reference BEC are filtered out.</p> <p>Input Files: <code>bec_train.out</code>, <code>bec_test.out</code></p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec          # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#thermodynamic-properties","title":"Thermodynamic Properties","text":""},{"location":"en/plot_scripts.html#plt_thermopy","title":"plt_thermo.py","text":"<p>Primary script for comprehensive thermodynamic property visualization.</p> <p>Input File: <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/plot_scripts.html#plt_thermo2py-plt_thermo3py","title":"plt_thermo2.py &amp; plt_thermo3.py","text":"<p>Alternative thermodynamic visualization with different styles.</p> <p>Input File: <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"en/plot_scripts.html#diffusion-and-ionic-transport","title":"Diffusion and Ionic Transport","text":""},{"location":"en/plot_scripts.html#plt_msdpy","title":"plt_msd.py","text":"<p>Plots mean square displacement (MSD) for all directions.</p> <p>Input File: <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"en/plot_scripts.html#plt_msd_allpy","title":"plt_msd_all.py","text":"<p>Plots MSD for all atomic species separately when using <code>all_groups</code> in GPUMD.</p> <p>Input File: <code>msd.out</code> (computed with <code>all_groups</code> option)</p> <p>Requirements: Must use <code>all_groups</code> in the <code>compute_msd</code> command in <code>run.in</code>.</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"en/plot_scripts.html#plt_msd_convergence_checkpy","title":"plt_msd_convergence_check.py","text":"<p>Checks convergence of MSD calculations across different time windows.</p> <p>Input File: <code>msd_step*.out</code> (computed with <code>save_every</code> option)</p> <p>Requirements: Use <code>save_every</code> in the <code>compute_msd</code> command.</p> <p>Purpose: Verify MSD has converged sufficiently for accurate diffusion coefficient calculation.</p> <pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"en/plot_scripts.html#plt_sdcpy","title":"plt_sdc.py","text":"<p>Plots self-diffusion coefficient (SDC) vs time.</p> <p>Input File: <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/plot_scripts.html#plt_arrhenius_dpy","title":"plt_arrhenius_d.py","text":"<p>Creates Arrhenius plot for diffusivity (log10 D vs 1000/T).</p> <p>Input Files: <code>*K/msd.out</code> files (each temperature subdirectory should contain an <code>msd.out</code>)</p> <pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D             # Alternative command\n</code></pre> <p>Output example:</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"en/plot_scripts.html#plt_arrhenius_sigmapy","title":"plt_arrhenius_sigma.py","text":"<p>Creates Arrhenius plot for ionic conductivity (ln(\u03c3\u00b7T) vs 1000/T).</p> <p>Input Files: <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> (each temperature subdirectory)</p> <pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma         # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#heat-transport","title":"Heat Transport","text":""},{"location":"en/plot_scripts.html#plt_emdpy","title":"plt_emd.py","text":"<p>Analyzes and plots thermal conductivity from equilibrium molecular dynamics (EMD).</p> <p>Input Files: EMD output files from GPUMD</p> <pre><code>gpumdkit.sh -plt emd x        # for x direction\n</code></pre>"},{"location":"en/plot_scripts.html#plt_nemdpy","title":"plt_nemd.py","text":"<p>Visualizes non-equilibrium molecular dynamics (NEMD) thermal transport properties.</p> <p>Input Files: NEMD output files from GPUMD</p> <p>Parameters:</p> Parameter Description <code>real_length</code> Real length of heat transfer zone in nm (set to <code>Auto</code> for auto-calculation) <code>scale_eff_size</code> Scale factor for effective cross-sectional area (default: 1). For 3D bulk: use 1. For low-dimensional systems with vacuum: S_box / S_eff <code>cutoff_freq</code> Cutoff frequency for SHC calculation in THz (default: 60) <code>save</code> Optional, save the plot as <code>nemd.png</code> <p>Note: If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p> <pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#plt_hnemdpy","title":"plt_hnemd.py","text":"<p>Plots homogeneous non-equilibrium molecular dynamics (HNEMD) results.</p> <p>Input Files: HNEMD output files from GPUMD</p> <p>Parameters:</p> Parameter Description <code>scale_eff_size</code> Scale factor for effective cross-sectional area (default: 1) <code>cutoff_freq</code> Cutoff frequency for SHC calculation in THz (default: 60) <code>save</code> Optional, save the plot as <code>hnemd.png</code> <p>Note: If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p> <pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#structural-analysis","title":"Structural Analysis","text":""},{"location":"en/plot_scripts.html#plt_rdfpy","title":"plt_rdf.py","text":"<p>Plots radial distribution function (RDF) showing pair correlations.</p> <p>Input File: <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf               # Plot all RDF pairs\ngpumdkit.sh -plt rdf &lt;column&gt;      # Plot specific pair\n</code></pre> <p>Full RDF output:</p> <p>Single pair RDF:</p>"},{"location":"en/plot_scripts.html#plt_rdf_pmfpy","title":"plt_rdf_pmf.py","text":"<p>Plots RDF combined with potential of mean force (PMF).</p> <p>Input File: <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf_pmf\n</code></pre>"},{"location":"en/plot_scripts.html#plt_vacpy","title":"plt_vac.py","text":"<p>Plots velocity autocorrelation function (VAC). Useful for analyzing phonon properties and atomic dynamics.</p> <p>Input File: <code>sdc.out</code> (the VAC columns are read from this file by the plotting script)</p> <p>Output: Interactive plot or <code>vac.png</code> (with <code>save</code> option)</p> <pre><code>gpumdkit.sh -plt vac\n</code></pre>"},{"location":"en/plot_scripts.html#plt_cohesivepy","title":"plt_cohesive.py","text":"<p>Plots cohesive energy curve from <code>cohesive.out</code>. Useful for analyzing lattice stability and equilibrium lattice constants.</p> <p>Input File: <code>cohesive.out</code> (isotropic scaling factor vs cohesive energy)</p> <p>Output: Interactive plot or <code>cohesive.png</code> (with <code>save</code> option)</p> <pre><code>gpumdkit.sh -plt cohesive\n</code></pre>"},{"location":"en/plot_scripts.html#plt_net_forcepy","title":"plt_net_force.py","text":"<p>Plots distribution of net forces on structures, useful for identifying problematic configurations.</p> <p>Input File: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>Reference: arXiv:2510.19774</p>"},{"location":"en/plot_scripts.html#phonons","title":"Phonons","text":""},{"location":"en/plot_scripts.html#plt_pdospy","title":"plt_pdos.py","text":"<p>Calculates and plots normalized VAC, PDOS, and Heat Capacity (Cv).</p> <p>Input Files: <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></p> <pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>Heat capacity output:</p>"},{"location":"en/plot_scripts.html#descriptor-dimer-and-extra-analysis","title":"Descriptor, Dimer, and Extra Analysis","text":""},{"location":"en/plot_scripts.html#plt_descriptorspy","title":"plt_descriptors.py","text":"<p>Visualizes high-dimensional NEP descriptors using dimensionality reduction (PCA or UMAP).</p> <p>Input File: <code>descriptors.npy</code> (generated by <code>gpumdkit.sh -calc des</code>)</p> <p>Methods: - <code>pca</code> \u2014 Principal Component Analysis - <code>umap</code> \u2014 Uniform Manifold Approximation and Projection</p> <pre><code># First generate descriptors\ngpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n\n# Then visualize\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/plot_scripts.html#plt_descriptors_comparepy","title":"plt_descriptors_compare.py","text":"<p>Compares descriptors from multiple training sets or models.</p> <pre><code>gpumdkit.sh -plt des_compare\n</code></pre>"},{"location":"en/plot_scripts.html#plt_dimerpy","title":"plt_dimer.py","text":"<p>Plots dimer interaction curves. Two atoms are placed in a cubic box (30 \u00c5) and the potential energy and force are calculated as a function of dimer distance using a NEP model.</p> <p>Input File: <code>nep.txt</code></p> <pre><code>gpumdkit.sh -plt dimer &lt;element1&gt; &lt;element2&gt; &lt;nep_model&gt;\ngpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>Reference: J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"en/plot_scripts.html#plt_doaspy","title":"plt_doas.py","text":"<p>Plots density of atomistic states (DOAS) proposed by Wang et al..</p> <p>Input File: <code>doas.out</code> (calculated by <code>gpumdkit.sh -calc doas</code>)</p> <pre><code>gpumdkit.sh -plt doas &lt;doas.out&gt; &lt;species&gt;\ngpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"en/plot_scripts.html#plane-grid-plot-for-polar-materials","title":"Plane-Grid Plot for Polar Materials","text":"<p>This workflow maps displacement or polarization data onto a grid and plots selected plane profiles. For detailed usage and real-world examples, see Polar Material Analysis.</p> <p>Dependency:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>Typical upstream steps:</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>Usage:</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre>"},{"location":"en/plot_scripts.html#quick-reference-table","title":"Quick Reference Table","text":"Command Input File(s) Description <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP training plots <code>prediction</code> / <code>test</code> <code>*_test.out</code> NEP prediction plots <code>train_test</code> <code>*_train.out</code>, <code>*_test.out</code> Combined parity plots <code>parity_density</code> <code>*_train.out</code> Density-based parity plots <code>force_errors</code> <code>force_train.out</code> Force error metrics <code>lr</code> <code>loss.out</code> (gnep) Learning rate <code>restart</code> <code>nep.restart</code> Restart file parameters <code>charge</code> <code>charge_train.out</code> Charge distribution <code>born_charge</code> / <code>bec</code> <code>bec_train.out</code>, <code>bec_test.out</code> Born effective charges <code>thermo</code> <code>thermo.out</code> Thermodynamic properties <code>msd</code> <code>msd.out</code> Mean square displacement <code>msd_all</code> <code>msd.out</code> (all_groups) MSD for all species <code>msd_conv</code> <code>msd_step*.out</code> MSD convergence check <code>sdc</code> <code>msd.out</code> Self-diffusion coefficient <code>arrhenius_d</code> / <code>D</code> <code>*K/msd.out</code> Arrhenius diffusivity <code>arrhenius_sigma</code> / <code>sigma</code> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> Arrhenius ionic conductivity <code>rdf</code> <code>rdf.out</code> Radial distribution function <code>rdf_pmf</code> <code>rdf.out</code> RDF + potential of mean force <code>vac</code> <code>sdc.out</code> Velocity autocorrelation <code>cohesive</code> <code>cohesive.out</code> Cohesive energy curve <code>net_force</code> <code>train.xyz</code> Net force distribution <code>doas</code> <code>doas.out</code> Density of atomistic states <code>des</code> <code>descriptors.npy</code> Descriptor PCA/UMAP <code>dimer</code> <code>nep.txt</code> Dimer energy/force curve <code>pdos</code> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code> VAC and PDOS <code>emd</code> EMD outputs EMD thermal conductivity <code>nemd</code> NEMD outputs NEMD thermal transport <code>hnemd</code> HNEMD outputs HNEMD thermal transport <code>viscosity</code> Viscosity outputs Viscosity"},{"location":"en/polar_material_analysis.html","title":"Polar Material Analysis","text":"\ud83e\uddf2 Polar Material Analysis <p>This tutorial covers GPUMDkit calculator options <code>406-410</code> and the <code>plane-grid</code> plotting workflow.</p> <p>Script Location: <code>Scripts/calculators/</code> and <code>Scripts/plt_scripts/</code></p> <p>This tutorial includes both general and system-specific tools:</p> <ul> <li><code>nlist</code>, <code>disp</code>, and <code>avg-struct</code> are broadly useful for structure/trajectory analysis.</li> <li><code>oct-tilt</code> is for octahedral environments (requires 6 neighbors around each center).</li> <li><code>pol-abo3</code> is specific to <code>ABO3</code> polarization analysis.</li> </ul>"},{"location":"en/polar_material_analysis.html#overview","title":"Overview","text":"Step CLI Command Main Input Output Build neighbor list <code>gpumdkit.sh -calc nlist ...</code> <code>model.xyz</code> <code>nl-*.dat</code> Calculate displacement <code>gpumdkit.sh -calc disp ...</code> trajectory + <code>nl-*.dat</code> <code>displacements.dat</code> Average trajectory <code>gpumdkit.sh -calc avg-struct ...</code> trajectory averaged extxyz Octahedral tilt <code>gpumdkit.sh -calc oct-tilt ...</code> trajectory + B-O neighbor list tilt-angle table ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 ...</code> trajectory + neighbor lists polarization table Plane-grid plot <code>gpumdkit.sh -plt plane-grid ...</code> structure + displacement data plane profile plot"},{"location":"en/polar_material_analysis.html#dependency","title":"Dependency","text":"<p>These scripts require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"en/polar_material_analysis.html#interactive-mode-entry","title":"Interactive mode entry","text":"<p>Options <code>406-410</code> are the core functions for this tutorial. The sections below explain when to use each one and how to run it.</p> <pre><code>gpumdkit.sh\n# choose 4) Calculators\n</code></pre> <p>The calculator menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre> <p>For full argument details, use:</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"en/polar_material_analysis.html#406-build-neighbor-list-calc_neighbor_listpy","title":"406) Build neighbor list (<code>calc_neighbor_list.py</code>)","text":"<p>Build neighbor lists for selected center and neighbor elements.</p> <p>When to use it: This is usually the first step before <code>disp</code>, <code>oct-tilt</code>, and <code>pol-abo3</code>, because those scripts read <code>nl-*.dat</code> neighbor files.</p>"},{"location":"en/polar_material_analysis.html#usage","title":"Usage","text":"<pre><code># Example 1: Ti-O nearest 6 neighbors for octahedral analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# Example 2: Pb/Sr-O nearest 12 neighbors for A-site centered analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input structure file. Default: <code>model.xyz</code>.</li> <li><code>-x, --index</code>:   Frame index to read from input. Default: <code>0</code>.</li> <li><code>-c, --cutoff</code> (required):   Neighbor search cutoff (Angstrom).</li> <li><code>-n, --neighbor-num</code> (required):   Number of neighbors per center.</li> <li><code>-d, --defect</code>:   Defect mode. If enabled and neighbors are insufficient, missing slots are filled with the center index.</li> <li><code>-C, --center-elements</code> (required):   Center species list.</li> <li><code>-E, --neighbor-elements</code> (required):   Neighbor species list.</li> <li><code>-o, --output</code>:   Output file path. Default: <code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file","title":"Output file","text":"<ul> <li>Main output: neighbor list text file (for example <code>nl-Ti-O.dat</code>).</li> <li>The file is a 2D integer array with shape <code>(n_center, neighbor_num + 1)</code>. Each row corresponds to one center atom: the first column is the center index, and the remaining columns are its neighbor indices (all 1-based).</li> </ul>"},{"location":"en/polar_material_analysis.html#407-calc-displacement-from-trajectory-calc_displacementpy","title":"407) Calc displacement from trajectory (<code>calc_displacement.py</code>)","text":"<p>Compute local displacement vectors from a trajectory/model and a neighbor list.</p>"},{"location":"en/polar_material_analysis.html#usage_1","title":"Usage","text":"<pre><code># Example 1: single-frame displacement from model.xyz\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# Example 2: use the last 20% frames in movie.xyz\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_1","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   Neighbor list file from <code>nlist</code>.</li> <li><code>-o, --output</code>:   Output file. Default: <code>displacements.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames.   Integer: last <code>N</code> frames.   <code>0 &lt; value &lt; 1</code>: last ratio of frames.</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_1","title":"Output file","text":"<ul> <li>Main output: <code>displacements.dat</code> (or your custom output name).</li> <li>The saved text file is a 2D array: for a single-frame input, its shape is <code>(n_center, 3)</code>; for a multi-frame input, it is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The three columns are <code>dx</code>, <code>dy</code>, and <code>dz</code> displacement components in Angstrom.</li> </ul>"},{"location":"en/polar_material_analysis.html#408-calc-averaged-structure-calc_averaged_structurepy","title":"408) Calc averaged structure (<code>calc_averaged_structure.py</code>)","text":"<p>Generate one averaged structure from selected trajectory frames. Use this after equilibration. For a solid near equilibrium, average a frame window at the target temperature and analyze that representative structure instead of processing every snapshot.</p>"},{"location":"en/polar_material_analysis.html#usage_2","title":"Usage","text":"<pre><code># Example 1: average all frames\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# Example 2: average selected frames (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_2","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input trajectory file. Default: <code>movie.xyz</code>.</li> <li><code>-o, --output</code>:   Output structure file. Default: <code>averaged_structure.xyz</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_2","title":"Output file","text":"<ul> <li>Main output: averaged single-frame extxyz file.</li> <li>Position averaging applies MIC/PBC correction relative to the first selected frame.</li> </ul>"},{"location":"en/polar_material_analysis.html#409-calc-octahedral-tilt-calc_oct_tiltpy","title":"409) Calc octahedral tilt (<code>calc_oct_tilt.py</code>)","text":"<p>Calculate octahedral tilt angles from a B-O neighbor list. This is commonly used to analyze octahedral rotation patterns in <code>ABO3</code> systems, such as <code>SrTiO3</code> and <code>PbZrO3</code>.</p>"},{"location":"en/polar_material_analysis.html#usage_3","title":"Usage","text":"<pre><code># Example 1: octahedral tilt of the TiO6 octahedra from a single frame\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# Example 2: octahedral tilt of the TiO6 octahedra from the last 20% trajectory frames\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_3","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   B-O neighbor list file.</li> <li><code>-o, --output</code>:   Output file. Default: <code>octahedral_tilt.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_3","title":"Output file","text":"<ul> <li>Main output: <code>octahedral_tilt.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>theta_x</code>, <code>theta_y</code>, <code>theta_z</code>, in degree): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#410-calc-polarization-for-abo3-calc_polarization_abo3py","title":"410) Calc polarization for ABO3 (<code>calc_polarization_abo3.py</code>)","text":"<p>Calculate local polarization vectors for <code>ABO3</code> systems.</p>"},{"location":"en/polar_material_analysis.html#usage_4","title":"Usage","text":"<pre><code># Example 1: single-frame ABO3 polarization\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# Example 2: trajectory polarization on a selected frame window\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_4","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>--nl-ba</code> (required):   B-A neighbor list.</li> <li><code>--nl-bo</code> (required):   B-O neighbor list.</li> <li><code>-o, --output</code>:   Output file. Default: <code>polarization.dat</code>.</li> <li><code>--bec</code> (required):   Born effective charge terms in <code>Element=value</code> format.   Example: <code>Pb=2.5 Ti=4.0 O=-2.0</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul> <p>Important checks:</p> <ul> <li><code>--bec</code> must include all element species in the input structure.</li> <li>Center atom indices in <code>--nl-ba</code> and <code>--nl-bo</code> must match.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_4","title":"Output file","text":"<ul> <li>Main output: <code>polarization.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>Px</code>, <code>Py</code>, <code>Pz</code>, in <code>C/m^2</code>): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The script prints a warning if the total Born charge is not balanced.</li> </ul>"},{"location":"en/polar_material_analysis.html#plane-grid-visualization-plt_plane_gridpy","title":"Plane-grid visualization (<code>plt_plane_grid.py</code>)","text":"<p>You can visualize either <code>displacements.dat</code> or <code>polarization.dat</code>:</p> <pre><code># Example 1: displacement map on Ti sites, first XY layer\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# Example 2: polarization map on Pb sites, XZ and YZ layers\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>Arguments (complete):</p> <ul> <li><code>-i, --input</code>:   Input xyz file for atomic layout and layering. Default: <code>model.xyz</code>.</li> <li><code>-d, --disp</code>:   Vector-field data file. Default: <code>displacements.dat</code>.</li> <li><code>-e, --elements</code> (required):   Center element symbols used to map vectors to lattice layers.</li> <li><code>-m, --tol</code>:   Layer tolerance for grid mapping. Default: <code>1.0</code>.</li> <li><code>-g, --target-size</code>:   Expected grid size as <code>nx ny nz</code>.</li> <li><code>-o, --save-dir</code>:   Figure output directory. Default: <code>plot</code>.</li> <li><code>-f, --frame</code>:   Frame index to visualize when vector data has multiple frames. Default: <code>0</code>.</li> <li><code>--select-xy</code>:   Selected XY layer indices.</li> <li><code>--select-xz</code>:   Selected XZ layer indices.</li> <li><code>--select-yz</code>:   Selected YZ layer indices.</li> </ul> <p>Output:</p> <ul> <li>Creates output directory if needed.</li> <li>Saves figures as <code>XY_*.png</code>, <code>XZ_*.png</code>, <code>YZ_*.png</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-files-at-a-glance","title":"Output files at a glance","text":"Script Main output What it stores <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based center index + neighbor indices <code>calc_displacement.py</code> <code>*.dat</code> Local displacement vectors (<code>dx dy dz</code>, Angstrom) <code>calc_averaged_structure.py</code> <code>*.xyz</code> One averaged structure <code>calc_oct_tilt.py</code> <code>*.dat</code> Octahedral tilt angles (<code>theta_x theta_y theta_z</code>, degree) <code>calc_polarization_abo3.py</code> <code>*.dat</code> Local polarization vectors (<code>Px Py Pz</code>, <code>C/m^2</code>) <code>plt_plane_grid.py</code> <code>plot/*.png</code> XY/XZ/YZ plane maps from vector-field data"},{"location":"en/polar_material_analysis.html#real-examples","title":"Real Examples","text":""},{"location":"en/polar_material_analysis.html#temperature-driven-ferroelectric-to-paraelectric-phase-transition-for-pbtio3","title":"Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3","text":"<p>Assume all files are in the current directory <code>./</code>:</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> is the initial structure used to run MD simulations. Each <code>TEMP K.xyz</code> is a trajectory at that temperature.</p>"},{"location":"en/polar_material_analysis.html#step-1-get-averaged-structures-from-the-last-half-of-each-trajectory","title":"Step 1: get averaged structures from the last half of each trajectory","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>This writes <code>300K-avg.xyz</code>, <code>350K-avg.xyz</code>, ..., <code>800K-avg.xyz</code>.</p>"},{"location":"en/polar_material_analysis.html#step-2-build-neighbor-lists-from-modelxyz","title":"Step 2: build neighbor lists from <code>model.xyz</code>","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-compute-displacement-and-polarization-for-each-temperature","title":"Step 3: compute displacement and polarization for each temperature","text":"<p>Use Born effective charges (BEC), not nominal ionic charges. For PbTiO3 in this example:</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>You can obtain BEC from your own DFPT calculation or from literature values. Thus use following commands to compute local displacement and polarization:</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-4-plot-displacement-and-polarization-maps-in-real-space","title":"Step 4: plot displacement and polarization maps in real space","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-5-build-a-temperature-order-parameter-curve","title":"Step 5: build a temperature-order-parameter curve","text":"<p>By analyzing the lattice of each temperature-averaged structure together with its polarization (<code>XX-pol.dat</code>), we can obtain the following figure:</p> <p>The trend shows a clear phase transition around <code>600 K</code>, where the polarization vanishes.</p>"},{"location":"en/polar_material_analysis.html#topological-structure-in-pbtio3srtio3-superlattice","title":"Topological structure in PbTiO3/SrTiO3 superlattice","text":"<p>Assume <code>movie.xyz</code> is the trajectory of the PbTiO3/SrTiO3 superlattice in the current directory.</p>"},{"location":"en/polar_material_analysis.html#step-1-build-an-averaged-structure-from-the-last-25-frames","title":"Step 1: build an averaged structure from the last 25% frames","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-2-build-the-ti-neighbor-list","title":"Step 2: build the Ti neighbor list","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-plot-the-plane-grid-map","title":"Step 3: plot the plane-grid map","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero.</p> <p>Note: the example figure uses a custom colormap. The default GPUMDkit output uses a different style, which can be adjusted by editing the plotting script.</p>"},{"location":"en/polar_material_analysis.html#other-systems","title":"Other Systems","text":""},{"location":"en/polar_material_analysis.html#organic-inorganic-hybrid-ferroelectrics","title":"Organic-inorganic hybrid ferroelectrics","text":"<p>In many organic-inorganic ferroelectrics, polarization is strongly tied to anisotropic molecular units. A practical way to track molecular orientation is to use bond vectors.</p> <p>For TMCM-CdCl3, you can use the C-Cl bond direction of the TMCM molecule as an orientation proxy, then use it to estimate the polarization state:</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p><code>ccl_vectors.dat</code> can then be analyzed as an orientation order parameter. More details could be found at: Phys. Rev. Lett. 136, 016801</p>"},{"location":"en/polar_material_analysis.html#other-ferroelectric-families","title":"Other ferroelectric families","text":"<p>Beyond <code>ABO3</code>, <code>ferrodispcalc</code> can be adapted to many ferroelectric systems, including nitrides, hafnia-based compounds, organic-inorganic hybrids, and some 2D ferroelectrics.</p>"},{"location":"en/quick_start.html","title":"Quick Start","text":"\ud83d\ude80 Quick Start <p>This page helps you install GPUMDkit and run your first commands. You can use GPUMDkit through an interactive menu or direct command-line options.</p>"},{"location":"en/quick_start.html#what-it-does","title":"What it does","text":"<p>GPUMDkit provides a single entry point for common tasks in computational materials science \u2014 format conversion, structure analysis, property calculation, and visualization \u2014 without writing custom scripts.</p>"},{"location":"en/quick_start.html#before-you-start","title":"Before you start","text":""},{"location":"en/quick_start.html#1-prepare-a-python-environment","title":"1. Prepare a Python environment","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>Some optional functions require additional packages:</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>Other Python dependencies are loaded by the corresponding scripts. If a package is missing, Python will report it when that function is used.</p>"},{"location":"en/quick_start.html#2-install-gpumdkit","title":"2. Install GPUMDkit","text":"<p>Clone the repository and run the installer:</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre> <p>The installer writes <code>GPUMDkit_path</code> and <code>PATH</code> settings to your shell configuration and loads them for the current shell. It writes to <code>~/.bashrc</code> by default; if the current shell is zsh, it writes to <code>~/.zshrc</code>. If an existing GPUMDkit path is found, the installer prints the old path and asks whether to replace it. Before changing the rc file, it creates a backup.</p> <p>Typical installation output:</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>If GPUMDkit was installed before, you may see:</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre>"},{"location":"en/quick_start.html#3-verify-the-installation","title":"3. Verify the installation","text":"<pre><code>gpumdkit.sh -h\n</code></pre> <p>This prints a help table listing all available options.</p>"},{"location":"en/quick_start.html#interactive-mode","title":"Interactive mode","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>This opens the main menu:</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre> <p>Select a module by number. Each module provides sub-menus with specific functions.</p>"},{"location":"en/quick_start.html#cli-mode","title":"CLI mode","text":"<p>Direct commands use fixed positional arguments:</p> <pre><code>gpumdkit.sh -&lt;option&gt; [args...]\n</code></pre> <p>Examples:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>The first example reads <code>POSCAR</code> and writes <code>model.xyz</code>.</p>"},{"location":"en/quick_start.html#common-examples","title":"Common examples","text":""},{"location":"en/quick_start.html#convert-a-poscar-to-extxyz","title":"Convert a POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"en/quick_start.html#add-gpumd-group-labels","title":"Add GPUMD group labels","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>Group labels are used by some GPUMD-related workflows that need atom grouping, such as species-specific MSD or diffusion calculations.</p>"},{"location":"en/quick_start.html#plot-nep-training-results","title":"Plot NEP training results","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/quick_start.html#plot-nep-test-results","title":"Plot NEP test results","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"en/quick_start.html#plot-thermodynamic-data","title":"Plot thermodynamic data","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/quick_start.html#plot-msd-and-self-diffusion-coefficient","title":"Plot MSD and self-diffusion coefficient","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/quick_start.html#notes","title":"Notes","text":"<ul> <li>Use <code>gpumdkit.sh -h</code> to see all available options.</li> <li>Use <code>gpumdkit.sh -&lt;option&gt; -h</code> to get help for a specific option (e.g., <code>gpumdkit.sh -plt train -h</code>).</li> <li>For detailed usage of each module, see the corresponding tutorial pages linked in the index.</li> </ul>"},{"location":"en/structure_sampling.html","title":"Structure Sampling","text":"\ud83d\udce6 Structure Sampling <p>Structure sampling is used to select, generate, or filter candidate configurations for NEP training and molecular dynamics workflows.</p> <p>Script Location: <code>Scripts/sample_structures/</code></p>"},{"location":"en/structure_sampling.html#interactive-mode","title":"Interactive Mode","text":"<p>Sampling tasks are usually easier to run from the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>2) Sample Structures\n</code></pre> <p>The menu is:</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Method Use Case 201 Uniform/random sampling quick frame selection from a trajectory 202 PyNEP notice prints a notice; use <code>gpumdkit.sh -pynep</code> to run PyNEP 203 NepTrain FPS descriptor-based FPS with NepTrain 204 Perturb structure generate perturbed structures from POSCAR/CONTCAR 205 Force-deviation selection select structures with high model deviation"},{"location":"en/structure_sampling.html#uniform-and-random-sampling","title":"Uniform and Random Sampling","text":"<p>From interactive mode, choose <code>201</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>Example input:</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>or:</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>uniform</code> / <code>random</code> sampling method <code>50</code> / <code>100</code> number of selected structures <code>500</code> optional number of initial frames to skip <p>Output:</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#farthest-point-sampling-with-neptrain","title":"Farthest Point Sampling with NepTrain","text":"<p>This entry uses NepTrain descriptors for FPS.</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>From interactive mode, choose <code>203</code>. You will see:</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>Inputs:</p> File Meaning <code>dump.xyz</code> candidate structures <code>train.xyz</code> existing training set <code>nep.txt</code> current NEP model used to compute descriptors <p>Outputs:</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>During execution, choose one of two selection modes:</p> <ol> <li>select until the descriptor distance is below a threshold;</li> <li>select a specified number of structures.</li> </ol> <p>The script then prints a selection prompt:</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>This function requires the <code>NepTrain</code> package. If you use this function, we recommend citing the NepTrain paper printed by the script.</p>"},{"location":"en/structure_sampling.html#deprecated-pynep-fps","title":"Deprecated PyNEP FPS","text":"<p>PyNEP FPS is kept for compatibility, but it is only exposed through the direct <code>-pynep</code> entry.</p> <p>If you choose <code>202</code> from the interactive menu, it prints:</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre>"},{"location":"en/structure_sampling.html#serial-pynep","title":"Serial PyNEP","text":"<pre><code>python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"en/structure_sampling.html#parallel-pynep","title":"Parallel PyNEP","text":"<pre><code>python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8\n</code></pre> <p>The last argument is the number of CPU threads.</p>"},{"location":"en/structure_sampling.html#gpumdkit-entry","title":"GPUMDkit Entry","text":"<pre><code>gpumdkit.sh -pynep\n</code></pre> <p>Then input:</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>This entry requires <code>pynep</code> and is kept for compatibility.</p>"},{"location":"en/structure_sampling.html#structure-perturbation","title":"Structure Perturbation","text":"<p>Use perturbation when you want to generate initial structures around a known configuration.</p> <pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>From interactive mode, choose <code>204</code>. You will see:</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input VASP structure <code>20</code> number of perturbed structures <code>0.03</code> cell perturbation fraction <code>0.2</code> atom perturbation distance in Angstrom <code>uniform</code> perturbation style: <code>normal</code>, <code>uniform</code>, or <code>const</code> <p>Output:</p> <ul> <li><code>POSCAR_01.vasp</code>, <code>POSCAR_02.vasp</code>, ...</li> </ul> <p>This function requires <code>dpdata</code>. If you use this function, we recommend citing the dpdata package.</p>"},{"location":"en/structure_sampling.html#force-deviation-selection","title":"Force-Deviation Selection","text":"<p>Use this together with the GPUMD <code>active</code> command. The <code>active</code> command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. <code>select_max_modev.py</code> selects structures with large force deviations from <code>active.out</code> and <code>active.xyz</code>, then writes them to <code>selected.xyz</code>.</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>From interactive mode, choose <code>205</code>. You will see:</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>200</code> maximum number of structures to keep <code>0.15</code> minimum force deviation threshold <p>Required files:</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>Output:</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#frame-range-extraction","title":"Frame Range Extraction","text":"<p>Use this to extract a fraction of a trajectory:</p> <pre><code>python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>This writes frames from 0% to 80% of the trajectory.</p>"},{"location":"en/structure_sampling.html#example-commands","title":"Example Commands","text":"<p>An example sequence using several sampling-related tools:</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"en/structure_sampling.html#common-mistakes","title":"Common Mistakes","text":"Problem Recommendation FPS selects too many similar structures increase the distance threshold or select fewer structures Perturbed structures are unphysical reduce <code>cell_pert</code> and <code>atom_pert</code>, then check minimum distances <code>active.out</code> and <code>active.xyz</code> do not match regenerate both from the same GPUMD active run PCA plot looks strange check whether <code>nep.txt</code> matches the chemical species in both datasets"},{"location":"en/workflow_scripts.html","title":"Workflow Scripts","text":"\ud83d\udd27 Workflow Scripts <p>Workflow scripts automate repetitive preparation steps for DFT, MD, and NEP development.</p> <p>Script Location: <code>Scripts/workflow/</code></p>"},{"location":"en/workflow_scripts.html#interactive-entry","title":"Interactive Entry","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>3) Workflow\n</code></pre> <p>The workflow menu looks like:</p> <pre><code>+---------------------------------------------------------+\n|                      WORKFLOW TOOLS                     |\n+---------------------------------------------------------+\n| 301) SCF batch pretreatment                             |\n| 302) MD sample batch pretreatment (gpumd)               |\n| 303) MD sample batch pretreatment (lmp)                 |\n+---------------------------------------------------------+\n| 000) Return to the main menu                            |\n+---------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Workflow Purpose 301 SCF batch pretreatment Prepare single-point DFT calculations 302 MD sample batch pretreatment (GPUMD) Prepare GPUMD sampling calculations 303 MD sample batch pretreatment (LAMMPS) Prepare LAMMPS sampling calculations"},{"location":"en/workflow_scripts.html#scf-batch-pretreatment","title":"SCF Batch Pretreatment","text":"<p>Use this when you have many structures and want to prepare single-point DFT calculations.</p>"},{"location":"en/workflow_scripts.html#vasp","title":"VASP","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>Before running, put structure files in the current directory. The script checks files in this order:</p> <ol> <li>if one or more <code>.vasp</code> files exist, it processes <code>.vasp</code> files;</li> <li>if both <code>.vasp</code> and <code>.xyz</code> files exist, it prints a notice and only processes <code>.vasp</code> files;</li> <li>if no <code>.vasp</code> file exists and one <code>.xyz</code> file exists, it converts that extxyz file to POSCAR files;</li> <li>if no <code>.vasp</code> file exists and multiple <code>.xyz</code> files exist, it asks you to choose one.</li> </ol> <p>Typical input directory before running:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>INCAR</code>, <code>POTCAR</code>, and <code>KPOINTS</code> in the generated <code>fp/</code> directory after the script creates it. The calculation folders link to files in <code>fp/</code>.</p> <p>The <code>prefix</code> you input during the workflow becomes the calculation folder prefix. When <code>out2xyz</code> is later used to extract results, the folder name is stored as <code>config_type</code> in the extxyz file, which makes it easier to trace where each structure came from.</p>"},{"location":"en/workflow_scripts.html#cp2k","title":"CP2K","text":"<p>CP2K SCF batch pretreatment is available from the workflow menu and can also be called directly:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>The interactive wrapper asks for:</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>Example:</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>The template should be configured to read coordinates from <code>pos.xyz</code>. A reference template is available at:</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>The script creates <code>&lt;prefix&gt;_&lt;index&gt;/</code> directories, writes <code>input.inp</code>, and writes <code>pos.xyz</code> for each structure.</p>"},{"location":"en/workflow_scripts.html#md-sampling-pretreatment","title":"MD Sampling Pretreatment","text":""},{"location":"en/workflow_scripts.html#gpumd","title":"GPUMD","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 302\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. The detection order is the same as the VASP SCF workflow: <code>.vasp</code> files are preferred; if multiple <code>.xyz</code> files are found without <code>.vasp</code>, the script asks you to choose one.</p> <p>Typical input directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>nep.txt</code> and <code>run_*.in</code> files in the generated <code>md/</code> directory. The script links <code>run_1.in</code> to <code>sample_1/run.in</code>, <code>run_2.in</code> to <code>sample_2/run.in</code>, and so on.</p>"},{"location":"en/workflow_scripts.html#lammps","title":"LAMMPS","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 303\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. <code>.vasp</code> files are preferred when both formats exist.</p> <p>After running, the script creates LAMMPS data files in <code>struct_md/</code>, sample folders, and an <code>md/</code> directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>lmprun.in</code> and <code>nep.txt</code> in the generated <code>md/</code> directory.</p>"},{"location":"en/workflow_scripts.html#active-learning-style-workflow","title":"Active-Learning Style Workflow","text":"<p>A common NEP improvement loop is:</p> <ol> <li>run MD with the current <code>nep.txt</code>;</li> <li>collect <code>dump.xyz</code> or <code>active.xyz</code>;</li> <li>remove unphysical structures;</li> <li>select diverse or uncertain structures;</li> <li>run DFT single-point calculations;</li> <li>convert DFT results to extxyz;</li> <li>append new structures to <code>train.xyz</code>;</li> <li>retrain the NEP model.</li> </ol> <p>For the development active-learning script, see Active Learning.</p>"},{"location":"en/workflow_scripts.html#template-based-temperature-series","title":"Template-Based Temperature Series","text":"<p>For a simple temperature series, a shell loop is often enough:</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>Then submit the generated folders according to your local cluster system.</p>"},{"location":"en/workflow_scripts.html#practical-notes","title":"Practical Notes","text":"<ul> <li>Workflow scripts are cluster- and template-dependent. Always test with a small number of structures first.</li> <li>Keep template files (<code>INCAR</code>, <code>KPOINTS</code>, <code>POTCAR</code>, <code>run.in</code>, CP2K inputs) under version control if possible.</li> <li>Check generated folders before submitting a large batch.</li> <li>Use analyzers and sampling scripts before expensive DFT calculations.</li> </ul>"},{"location":"zh/index.html","title":"GPUMDkit \u6559\u7a0b","text":"\ud83d\udcda GPUMDkit \u6559\u7a0b <p>\u6b22\u8fce\u4f7f\u7528 GPUMDkit\uff0c\u8fd9\u662f\u4e00\u4e2a\u9762\u5411 GPUMD \u548c NEP \u7684\u547d\u4ee4\u884c\u5de5\u5177\u5305\u3002</p>"},{"location":"zh/index.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>GPUMDkit \u5e2e\u52a9\u4f60\u5728\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u7814\u7a76\u4e2d\u5b8c\u6210\u5e38\u89c1\u4efb\u52a1\uff0c\u65e0\u9700\u7f16\u5199\u81ea\u5b9a\u4e49\u811a\u672c\u3002\u5b83\u652f\u6301\u683c\u5f0f\u8f6c\u6362\u3001\u7ed3\u6784\u5206\u6790\u3001\u6027\u8d28\u8ba1\u7b97\u3001\u53ef\u89c6\u5316\u548c\u6279\u91cf\u5de5\u4f5c\u6d41\u2014\u2014\u5168\u90e8\u901a\u8fc7\u4e00\u4e2a\u547d\u4ee4\u884c\u5de5\u5177\u5b8c\u6210\u3002</p>"},{"location":"zh/index.html#_2","title":"\u5e38\u89c1\u4efb\u52a1","text":"\u6211\u60f3\u8981... \u6559\u7a0b \u5b89\u88c5 GPUMDkit \u5e76\u8fd0\u884c\u7b2c\u4e00\u4e2a\u547d\u4ee4 \u5feb\u901f\u5165\u95e8 \u5c06 VASP\u3001LAMMPS\u3001CP2K \u6216 CIF \u6587\u4ef6\u8f6c\u6362\u4e3a extxyz \u683c\u5f0f\u8f6c\u6362 \u68c0\u67e5\u7ed3\u6784\u8ddd\u79bb\u3001\u8fc7\u6ee4\u6570\u636e\u96c6\u6216\u67e5\u627e\u5f02\u5e38\u503c \u5206\u6790\u5de5\u5177 \u8ba1\u7b97 MSD\u3001\u79bb\u5b50\u7535\u5bfc\u7387\u6216\u63cf\u8ff0\u7b26 \u8ba1\u7b97\u5668\u811a\u672c \u5206\u6790\u6781\u6027\u6750\u6599\u3001\u94c1\u7535\u4f53\u6216 ABO3 \u4f53\u7cfb \u6781\u6027\u6750\u6599\u5206\u6790 \u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c\u6216\u70ed\u529b\u5b66\u6570\u636e \u7ed8\u56fe\u811a\u672c \u8fd0\u884c\u6279\u91cf DFT \u6216 MD \u6a21\u62df \u5de5\u4f5c\u6d41\u811a\u672c \u4ece\u6570\u636e\u96c6\u4e2d\u9009\u62e9\u4ee3\u8868\u6027\u7ed3\u6784 \u7ed3\u6784\u91c7\u6837 \u6dfb\u52a0\u81ea\u5df1\u7684 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u81ea\u5b9a\u4e49\u547d\u4ee4"},{"location":"zh/index.html#_3","title":"\u51c6\u5907\u5de5\u4f5c","text":""},{"location":"zh/index.html#_4","title":"\u5b89\u88c5","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"zh/index.html#_5","title":"\u4f9d\u8d56","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"zh/index.html#_6","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u6253\u5f00\u83dc\u5355\u540e\uff0c\u6309\u6570\u5b57\u9009\u62e9\u6a21\u5757\u3002</p>"},{"location":"zh/index.html#_7","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n</code></pre> <p>\u4f8b\u5982\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>\u4f7f\u7528 <code>gpumdkit.sh -h</code> \u67e5\u770b\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</p>"},{"location":"zh/index.html#_8","title":"\u6a21\u5757\u6982\u89c8","text":"\u6a21\u5757 \u83dc\u5355 CLI \u63cf\u8ff0 \u683c\u5f0f\u8f6c\u6362 1 <code>-out2xyz</code>, <code>-pos2exyz</code> \u6587\u4ef6\u8f6c\u6362 \u7ed3\u6784\u91c7\u6837 2 <code>-neptrain</code>\u3001\u4ea4\u4e92\u83dc\u5355 \u7ed3\u6784\u91c7\u6837 \u5de5\u4f5c\u6d41 3 - \u6279\u5904\u7406 \u8ba1\u7b97\u5668 4 <code>-calc &lt;\u7c7b\u578b&gt;</code> \u5c5e\u6027\u8ba1\u7b97 \u5206\u6790\u5de5\u5177 5 <code>-range</code>, <code>-min_dist</code> \u7ed3\u6784\u5206\u6790 \u53ef\u89c6\u5316 6 <code>-plt &lt;\u7c7b\u578b&gt;</code> \u7ed8\u56fe\u5de5\u5177 \u5b9e\u7528\u5de5\u5177 7 <code>-time</code>, <code>-clean</code> \u5b9e\u7528\u529f\u80fd"},{"location":"zh/index.html#_9","title":"\u5168\u90e8\u6559\u7a0b","text":"\u6559\u7a0b \u63cf\u8ff0 \u5feb\u901f\u5165\u95e8 \u5b89\u88c5\u548c\u7b2c\u4e00\u6b65 \u547d\u4ee4\u53c2\u8003 \u5e38\u7528 CLI \u548c\u83dc\u5355\u5165\u53e3\u901f\u67e5 \u683c\u5f0f\u8f6c\u6362 \u5728\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362 \u8ba1\u7b97\u5668\u811a\u672c \u8ba1\u7b97\u6750\u6599\u5c5e\u6027 \u5206\u6790\u5de5\u5177 \u7ed3\u6784\u5206\u6790\u548c\u9a8c\u8bc1 \u7ed8\u56fe\u811a\u672c \u7ed8\u56fe\u548c\u53ef\u89c6\u5316 \u5de5\u4f5c\u6d41\u811a\u672c \u6279\u5904\u7406\u548c\u81ea\u52a8\u5316 \u7ed3\u6784\u91c7\u6837 \u7ed3\u6784\u9009\u62e9\u65b9\u6cd5 \u81ea\u5b9a\u4e49\u547d\u4ee4 \u7528\u6237\u81ea\u5b9a\u4e49 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 \u6279\u91cf\u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\u8bf4\u660e \u6781\u6027\u6750\u6599\u5206\u6790 \u94c1\u7535\u548c\u6781\u5316\u76f8\u5173\u5de5\u5177 \u8d21\u732e\u6307\u5357 \u5f00\u53d1\u548c\u8d21\u732e\u8bf4\u660e"},{"location":"zh/index.html#_10","title":"\u94fe\u63a5","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>\u6587\u6863: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html","title":"\u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41","text":"\ud83d\udd01 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 <p><code>workflow_active_learning_dev.sh</code> \u7528\u4e8e\u7ec4\u7ec7\u4e00\u8f6e NEP \u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\uff1a\u8fd0\u884c GPUMD \u5206\u5b50\u52a8\u529b\u5b66\u3001\u7b5b\u9009\u7ed3\u6784\u3001\u62bd\u6837\u3001\u63d0\u4ea4\u7b2c\u4e00\u6027\u539f\u7406\u8ba1\u7b97\uff0c\u5e76\u8fdb\u884c NEP \u9884\u6d4b\u68c0\u67e5\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#_1","title":"\u6982\u89c8","text":"<p>\u8be5\u811a\u672c\u81ea\u52a8\u5316\u4e86 NEP \u4e3b\u52a8\u5b66\u4e60\u7684\u4e00\u8f6e\u8fed\u4ee3\u3002\u5178\u578b\u6d41\u7a0b\u5305\u62ec\uff1a</p> \u6b65\u9aa4 \u64cd\u4f5c \u76ee\u7684 1 \u8fd0\u884c MD \u6a21\u62df \u4f7f\u7528\u5f53\u524d NEP \u6a21\u578b\u751f\u6210\u5019\u9009\u7ed3\u6784 2 \u8fc7\u6ee4\u7ed3\u6784 \u79fb\u9664\u4e0d\u5408\u7406\u7684\u6784\u578b\uff08\u77ed\u8ddd\u79bb\u3001\u5927\u76d2\u5b50\uff09 3 \u91c7\u6837\u7ed3\u6784 \u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\u8fdb\u884c DFT \u8ba1\u7b97 4 \u8fd0\u884c SCF \u8ba1\u7b97 \u8ba1\u7b97 DFT \u53c2\u8003\u80fd\u91cf/\u529b 5 NEP \u9884\u6d4b \u68c0\u67e5\u6a21\u578b\u5728\u65b0\u7ed3\u6784\u4e0a\u7684\u7cbe\u5ea6 <p>\u4e0e\u83dc\u5355\u9a71\u52a8\u7684\u6a21\u5757\u4e0d\u540c\uff0c\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u662f\u4e00\u4e2a\u9700\u8981\u6309\u4f53\u7cfb\u4fee\u6539\u540e\u76f4\u63a5\u8fd0\u884c\u7684 shell \u811a\u672c\uff1a</p> <pre><code>bash Scripts/workflow/workflow_active_learning_dev.sh\n</code></pre> <p>\u4e0b\u9762\u6309\u811a\u672c\u4e2d\u7684\u4e3b\u8981\u4ee3\u7801\u5757\u8bf4\u660e\u6bcf\u4e00\u6b65\u7684\u4f5c\u7528\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#1-slurm","title":"1. SLURM \u8bbe\u7f6e","text":"<p>\u811a\u672c\u5f00\u5934\u5305\u542b\u96c6\u7fa4\u63d0\u4ea4\u53c2\u6570\uff0c\u4f8b\u5982\uff1a</p> <pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>\u8fd9\u4e9b\u53c2\u6570\u9700\u8981\u6839\u636e\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u4fee\u6539\u3002\u5982\u679c\u6ca1\u6709 SLURM \u73af\u5883\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u540e\u53f0\u8fd0\u884c\uff1a</p> <pre><code>nohup bash workflow_active_learning_dev.sh &gt; workflow.log 2&gt;&amp;1 &amp;\n</code></pre>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#2","title":"2. \u57fa\u672c\u8bbe\u7f6e","text":"<p>\u811a\u672c\u4f1a\u8fdb\u5165\u63d0\u4ea4\u76ee\u5f55\uff0c\u5e76\u52a0\u8f7d\u63d0\u4ea4\u6a21\u677f\uff1a</p> <pre><code>cd $SLURM_SUBMIT_DIR\nsource ${GPUMDkit_path}/Scripts/workflow/submit_template.sh\npython_pynep=python\n</code></pre> <ul> <li><code>GPUMDkit_path</code> \u662f\u5b89\u88c5\u811a\u672c\u5199\u5165\u7684 GPUMDkit \u8def\u5f84\u3002</li> <li><code>python_pynep</code> \u4ec5\u7528\u4e8e\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#3","title":"3. \u4e3b\u8981\u53d8\u91cf","text":"<p>\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u9002\u5408\u5df2\u7ecf\u6709\u521d\u59cb <code>nep.txt</code>\u3001<code>nep.in</code>\u3001<code>train.xyz</code> \u548c GPUMD/DFT \u8f93\u5165\u6587\u4ef6\uff0c\u5e76\u5e0c\u671b\u5728\u96c6\u7fa4\u4e0a\u81ea\u52a8\u6269\u5c55\u8bad\u7ec3\u96c6\u7684\u60c5\u51b5\u3002</p> <p>\u811a\u672c\u5f00\u5934\u901a\u5e38\u9700\u8981\u6839\u636e\u4f53\u7cfb\u4fee\u6539\uff1a</p> <pre><code>work_dir=${PWD}\nprefix_name=LiF_iter01\nmin_dist=1.4\nbox_limit=13\nmax_fp_num=50\nsample_method=pynep\npynep_sample_dist=0.01\n</code></pre> <ul> <li><code>prefix_name</code> \u7528\u4e8e\u547d\u540d\u672c\u8f6e\u8ba1\u7b97\u3002</li> <li><code>min_dist</code> \u548c <code>box_limit</code> \u7528\u4e8e\u8fc7\u6ee4\u660e\u663e\u4e0d\u5408\u7406\u7684\u7ed3\u6784\u3002</li> <li><code>max_fp_num</code> \u63a7\u5236\u6700\u591a\u63d0\u4ea4\u591a\u5c11\u4e2a\u5355\u70b9\u8ba1\u7b97\u3002</li> <li><code>sample_method</code> \u53ef\u9009 <code>uniform</code>\u3001<code>random</code> \u6216 <code>pynep</code>\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#4","title":"4. \u68c0\u67e5\u8f93\u5165\u6587\u4ef6","text":"<p>\u5e38\u89c1\u8f93\u5165\u5305\u62ec\uff1a</p> <ul> <li><code>nep.txt</code></li> <li><code>nep.in</code></li> <li><code>train.xyz</code></li> <li><code>run.in</code></li> <li><code>INCAR</code></li> <li><code>POTCAR</code></li> <li><code>KPOINTS</code></li> <li>\u521d\u59cb\u91c7\u6837\u7ed3\u6784\u6587\u4ef6\uff0c\u4f8b\u5982 <code>sample_struct.xyz</code></li> </ul> <p>\u811a\u672c\u4f1a\u628a\u516c\u5171\u8f93\u5165\u79fb\u52a8\u5230 <code>common/</code>\uff0c\u5e76\u521b\u5efa <code>00.modev/</code>\u3001<code>01.select/</code> \u7b49\u5de5\u4f5c\u76ee\u5f55\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#5","title":"5. \u6587\u4ef6\u7ec4\u7ec7","text":"<p>\u811a\u672c\u4f1a\u521b\u5efa\u516c\u5171\u8f93\u5165\u76ee\u5f55\u548c MD \u76ee\u5f55\uff1a</p> <pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <ul> <li><code>00.modev</code>\uff1a\u7528\u4e8e\u8fd0\u884c GPUMD MD \u91c7\u6837\u3002</li> <li><code>common</code>\uff1a\u4fdd\u5b58 <code>nep.txt</code>\u3001<code>run.in</code>\u3001\u7ed3\u6784\u6587\u4ef6\u548c DFT \u8f93\u5165\u6587\u4ef6\u7b49\u516c\u5171\u8d44\u6e90\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#6-md","title":"6. \u63d0\u4ea4 MD \u4efb\u52a1","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>\u811a\u672c\u4f1a\u901a\u8fc7\u63d0\u4ea4\u6a21\u677f\u521b\u5efa\u6570\u7ec4\u4efb\u52a1\u3002\u4e0d\u540c\u96c6\u7fa4\u4e0a\u7684\u63d0\u4ea4\u547d\u4ee4\u548c\u6a21\u677f\u53ef\u80fd\u9700\u8981\u81ea\u5df1\u4fee\u6539\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#7","title":"7. \u68c0\u67e5\u4efb\u52a1\u5b8c\u6210","text":"<p>\u811a\u672c\u4f1a\u6301\u7eed\u68c0\u67e5 <code>00.modev/</code> \u4e0b\u5404\u4e2a <code>sample_*/log</code> \u6587\u4ef6\uff0c\u786e\u8ba4\u662f\u5426\u51fa\u73b0\uff1a</p> <pre><code>Finished running GPUMD.\n</code></pre> <p>\u5982\u679c\u53d1\u73b0 <code>Error</code>\uff0c\u811a\u672c\u4f1a\u505c\u6b62\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#8","title":"8. \u5206\u6790\u548c\u8fc7\u6ee4\u7ed3\u6784","text":"<p>MD \u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u8fdb\u5165 <code>01.select</code>\uff0c\u5bf9 <code>dump.xyz</code> \u4e2d\u7684\u7ed3\u6784\u8fdb\u884c\u7b5b\u9009\u3002\u5e38\u89c1\u68c0\u67e5\u5305\u62ec\uff1a</p> <ul> <li>\u6700\u5c0f\u539f\u5b50\u8ddd\u79bb\uff1b</li> <li>\u6a21\u62df\u76d2\u5b50\u8fb9\u957f\uff1b</li> <li>\u7ed3\u6784\u6570\u91cf\u662f\u5426\u8d85\u8fc7 <code>max_fp_num</code>\u3002</li> </ul> <p>\u8fd9\u4e9b\u6b65\u9aa4\u4f1a\u8c03\u7528 analyzer \u548c sample_structures \u4e2d\u7684\u811a\u672c\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#9","title":"9. \u62bd\u6837\u65b9\u6cd5","text":"<p>\u811a\u672c\u6839\u636e <code>sample_method</code> \u9009\u62e9\u62bd\u6837\u65b9\u5f0f\uff1a</p> <pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <ul> <li><code>uniform</code>\uff1a\u5747\u5300\u62bd\u5e27\uff1b</li> <li><code>random</code>\uff1a\u968f\u673a\u62bd\u5e27\uff1b</li> <li><code>pynep</code>\uff1a\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#10-scf","title":"10. \u63d0\u4ea4 SCF \u8ba1\u7b97","text":"<p>\u62bd\u6837\u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u63d0\u4ea4 VASP \u5355\u70b9\u8ba1\u7b97\uff1a</p> <pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>\u8fd9\u91cc\u7684 <code>prefix_name</code> \u4f1a\u7528\u4e8e\u8ba1\u7b97\u76ee\u5f55\u547d\u540d\uff0c\u4e5f\u65b9\u4fbf\u540e\u7eed\u8ffd\u8e2a\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#11-prediction","title":"11. Prediction \u6b65\u9aa4","text":"<p>\u6700\u540e\u811a\u672c\u4f1a\u63d0\u4ea4 NEP prediction\uff0c\u7528\u4e8e\u68c0\u67e5\u5f53\u524d\u6a21\u578b\u5728\u65b0\u589e\u7ed3\u6784\u4e0a\u7684\u8bef\u5dee\u3002</p> <p>\u8fd9\u4e2a\u811a\u672c\u548c\u8ba1\u7b97\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u4f7f\u7528\u524d\u5efa\u8bae\u5148\u7528\u5c0f\u4f53\u7cfb\u6216\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u4e00\u8f6e\uff0c\u5e76\u68c0\u67e5\u63d0\u4ea4\u6a21\u677f\u3001\u8def\u5f84\u548c\u8f93\u5165\u6587\u4ef6\u662f\u5426\u7b26\u5408\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html","title":"\u5206\u6790\u5de5\u5177","text":"\ud83d\udd0d \u5206\u6790\u5de5\u5177 <p>\u5206\u6790\u811a\u672c\u4e3a extxyz \u6570\u636e\u96c6\u63d0\u4f9b\u7ed3\u6784\u7edf\u8ba1\u3001\u8ddd\u79bb\u68c0\u67e5\u3001\u8fc7\u6ee4\u3001\u6210\u5206\u5206\u6790\u3001\u5f02\u5e38\u68c0\u6d4b\u548c\u65f6\u95f4\u4f30\u7b97\u529f\u80fd\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>\u672c\u6a21\u5757\u5e2e\u52a9\u4f60\u68c0\u67e5\u3001\u8fc7\u6ee4\u548c\u9a8c\u8bc1\u7ed3\u6784\u6570\u636e\u96c6\u3002\u53ef\u4ee5\u68c0\u67e5\u6210\u5206\u3001\u5206\u6790\u6027\u8d28\u8303\u56f4\u3001\u68c0\u6d4b\u77ed\u8ddd\u79bb\u63a5\u89e6\u3001\u6309\u5404\u79cd\u6761\u4ef6\u8fc7\u6ee4\u7ed3\u6784\u3001\u67e5\u627e NEP \u8bad\u7ec3\u6570\u636e\u4e2d\u7684\u5f02\u5e38\u503c\uff0c\u4ee5\u53ca\u4f30\u7b97\u5269\u4f59\u6a21\u62df\u65f6\u95f4\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":"<p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/analyzer/</code></p> <p>\u786e\u4fdd\u5df2\u5b89\u88c5 GPUMDkit\u3002\u5b89\u88c5\u8bf4\u660e\u8bf7\u53c2\u89c1\u5feb\u901f\u5165\u95e8\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_3","title":"\u6982\u89c8","text":"\u4efb\u52a1 \u547d\u4ee4 \u7528\u9014 \u6210\u5206\u5206\u6790 <code>gpumdkit.sh -analyze_comp train.xyz</code> \u6309\u5316\u5b66\u6210\u5206\u5206\u7ec4 \u5316\u5b66\u7269\u79cd <code>gpumdkit.sh -chem_species train.xyz</code> \u5217\u51fa\u6587\u4ef6\u4e2d\u7684\u5143\u7d20 \u6027\u8d28\u8303\u56f4 <code>gpumdkit.sh -range train.xyz force</code> \u68c0\u67e5\u80fd\u91cf/\u529b/virial \u8303\u56f4 \u6700\u77ed\u8ddd\u79bb <code>gpumdkit.sh -min_dist dump.xyz</code> \u5feb\u901f\u8ddd\u79bb\u68c0\u67e5\uff08\u65e0 PBC\uff09 \u6700\u77ed\u8ddd\u79bb\uff08PBC\uff09 <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> \u51c6\u786e\u8ddd\u79bb\u68c0\u67e5\uff08\u542b PBC\uff09 \u7535\u8377\u5e73\u8861 <code>gpumdkit.sh -cbc train.xyz</code> \u6c27\u5316\u6001\u5e73\u8861\u68c0\u67e5 \u8ddd\u79bb\u8fc7\u6ee4 <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> \u79fb\u9664\u77ed\u8ddd\u79bb\u63a5\u89e6\u7684\u7ed3\u6784 \u76d2\u5b50\u8fc7\u6ee4 <code>gpumdkit.sh -filter_box dump.xyz 13</code> \u79fb\u9664\u76d2\u5b50\u8fc7\u5927\u7684\u7ed3\u6784 \u6027\u8d28\u8fc7\u6ee4 <code>gpumdkit.sh -filter_value train.xyz force 20</code> \u6309\u80fd\u91cf/\u529b/virial \u9608\u503c\u8fc7\u6ee4 \u5bf9\u8ddd\u79bb\u8303\u56f4 <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> \u6309\u5bf9\u8ddd\u79bb\u63d0\u53d6\u7ed3\u6784 \u5f02\u5e38\u68c0\u6d4b \u83dc\u5355 502 \u67e5\u627e\u8bad\u7ec3\u96c6\u4e2d\u9ad8 RMSE \u7684\u7ed3\u6784 \u6982\u7387\u5bc6\u5ea6 <code>gpumdkit.sh -pda &lt;\u53c2\u8003\u7ed3\u6784&gt; &lt;\u8f68\u8ff9&gt; &lt;\u5143\u7d20&gt; &lt;\u7f51\u683c\u95f4\u8ddd&gt;</code> 3D \u6982\u7387\u5bc6\u5ea6\u5206\u6790\u6269\u6563\u901a\u9053 GPUMD \u65f6\u95f4 <code>gpumdkit.sh -time gpumd</code> \u4f30\u7b97 GPUMD \u5269\u4f59\u8fd0\u884c\u65f6\u95f4 NEP \u65f6\u95f4 <code>gpumdkit.sh -time nep</code> \u4f30\u7b97 NEP \u5269\u4f59\u8bad\u7ec3\u65f6\u95f4"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_4","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit \u5e76\u9009\u62e9 <code>5) Analyzer</code>\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u5206\u6790\u5de5\u5177\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                    ANALYZER TOOLS                    |\n+------------------------------------------------------+\n| 501) Analyze composition of extxyz                   |\n| 502) Find outliers of extxyz                         |\n| 503) Analyze chemical species of extxyz              |\n| 504) Check charge balance of extxyz                  |\n| 505) Analyze energy/force/virial range               |\n| 506) Filter structures by minimum distance           |\n| 507) Get minimum interatomic distance                |\n| 508) Probability density analysis                    |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5927\u591a\u6570\u5206\u6790\u529f\u80fd\u4e5f\u63d0\u4f9b\u76f4\u63a5 CLI \u8c03\u7528\u65b9\u5f0f\uff0c\u6982\u89c8\u8868\u548c\u540e\u7eed\u5c0f\u8282\u4e2d\u5217\u51fa\u4e86\u5e38\u7528\u547d\u4ee4\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_5","title":"\u6210\u5206\u5206\u6790","text":"<p><code>analyze_composition.py</code> \u5206\u6790 extxyz \u6587\u4ef6\u7684\u6210\u5206\uff0c\u5e76\u5141\u8bb8\u5bfc\u51fa\u5b50\u96c6\u3002</p> <p>\u529f\u80fd\uff1a \u6309\u5316\u5b66\u6210\u5206\u5bf9\u7ed3\u6784\u5206\u7ec4\uff0c\u5e76\u663e\u793a\u6bcf\u79cd\u6210\u5206\u7684\u7ed3\u6784\u6570\u91cf\u3002\u53ef\u4ee5\u6309\u6210\u5206\u5bfc\u51fa\u5b50\u96c6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>501</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>\u5f53 <code>train.xyz</code> \u5305\u542b\u4e0d\u540c\u4f53\u7cfb\u6216\u4e0d\u540c\u5c3a\u5bf8\u7684\u7ed3\u6784\u65f6\u5f88\u6709\u7528\u3002\u53ef\u4ee5\u4ece\u4ea4\u4e92\u63d0\u793a\u4e2d\u6309\u6210\u5206\u5bfc\u51fa\u5b50\u96c6\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_6","title":"\u5316\u5b66\u7269\u79cd","text":"<p><code>analyze_chem_species.py</code> \u5217\u51fa extxyz \u6587\u4ef6\u4e2d\u6240\u6709\u552f\u4e00\u7684\u5316\u5b66\u7269\u79cd\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -chem_species train.xyz\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_7","title":"\u6027\u8d28\u8303\u56f4\u5206\u6790","text":"<p><code>energy_force_virial_analyzer.py</code> \u8ba1\u7b97\u5e76\u53ef\u89c6\u5316 extxyz \u6587\u4ef6\u4e2d\u6027\u8d28\u7684\u8303\u56f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <p>\u652f\u6301\u7684\u6027\u8d28\uff1a <code>energy</code>\u3001<code>force</code>\u3001<code>virial</code></p> <pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist    # \u663e\u793a\u76f4\u65b9\u56fe\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Force range: 0.03210566767721861 to 9.230115912468435\n</code></pre> <p>\u4f7f\u7528 <code>hist</code> \u9009\u9879\uff1a</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_8","title":"\u6700\u77ed\u8ddd\u79bb\u68c0\u67e5","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#pbc","title":"\u65e0 PBC\uff08\u5feb\u901f\uff09","text":"<p><code>get_min_dist.py</code> \u8ba1\u7b97\u4e0d\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u7684\u6700\u77ed\u539f\u5b50\u95f4\u8ddd\u3002\u901f\u5ea6\u5feb\uff0c\u4f46\u5bf9\u5468\u671f\u6027\u4f53\u7cfb\u53ef\u80fd\u4e0d\u51c6\u786e\u3002</p> <p>\u529f\u80fd\uff1a \u62a5\u544a\u6bcf\u5e27\u4e2d\u6bcf\u5bf9\u5143\u7d20\u4e4b\u95f4\u7684\u6700\u77ed\u8ddd\u79bb\uff0c\u5ffd\u7565\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>507</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>+---------------------------+\n|   PBC ignored for speed   |\n| use -min_dist_pbc for PBC |\n+---------------------------+\nMinimum interatomic distances:\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.480     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre> <p>\u8bf4\u660e\uff1a \u7528\u4e8e\u5feb\u901f\u68c0\u67e5\u3002\u5bf9\u4e8e\u5468\u671f\u6027\u4f53\u7cfb\uff0c\u5efa\u8bae\u4f7f\u7528 <code>-min_dist_pbc</code> \u83b7\u5f97\u51c6\u786e\u7ed3\u679c\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#pbc_1","title":"\u542b PBC\uff08\u51c6\u786e\uff09","text":"<p><code>get_min_dist_pbc.py</code> \u8ba1\u7b97\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u7684\u6700\u77ed\u539f\u5b50\u95f4\u8ddd\u3002</p> <p>\u529f\u80fd\uff1a \u62a5\u544a\u6bcf\u5bf9\u5143\u7d20\u4e4b\u95f4\u7684\u6700\u77ed\u8ddd\u79bb\uff0c\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>507</code>\uff0c\u5f53\u63d0\u793a\u662f\u5426\u8003\u8651 PBC \u65f6\u8f93\u5165 <code>y</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_9","title":"\u7ed3\u6784\u8fc7\u6ee4","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_10","title":"\u6309\u6700\u77ed\u8ddd\u79bb\u8fc7\u6ee4","text":"<p><code>filter_structures_by_distance_pbc.py</code> \u79fb\u9664\u4efb\u4f55\u539f\u5b50\u95f4\u8ddd\u4f4e\u4e8e\u9608\u503c\u7684\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>\u79fb\u9664\u4efb\u4f55\u539f\u5b50\u95f4\u8ddd\u4f4e\u4e8e <code>1.0 \u00c5</code> \u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_11","title":"\u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4","text":"<p><code>filter_exyz_by_box.py</code> \u6309\u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>\u4fdd\u7559\u6240\u6709\u76d2\u5b50\u8fb9\u957f\u4f4e\u4e8e <code>13 \u00c5</code> \u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_12","title":"\u6309\u6027\u8d28\u503c\u8fc7\u6ee4","text":"<p><code>filter_exyz_by_value.py</code> \u6309\u80fd\u91cf\u3001\u529b\u6216 virial \u9608\u503c\u8fc7\u6ee4\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <p>\u652f\u6301\u7684\u6027\u8d28\uff1a <code>energy</code>\u3001<code>force</code>\u3001<code>virial</code></p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre> <p>\u8fc7\u6ee4\u6389\u529b\u5206\u91cf\u8d85\u8fc7 <code>20 eV/\u00c5</code>\uff08\u6216\u80fd\u91cf\u8d85\u8fc7 <code>5 eV/atom</code>\uff09\u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_13","title":"\u6309\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4","text":"<p><code>filter_dist_range.py</code> \u63d0\u53d6\u7279\u5b9a\u5143\u7d20\u5bf9\u8ddd\u79bb\u5728\u7ed9\u5b9a\u8303\u56f4\u5185\u7684\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>\u63d0\u53d6 Li-Li \u6700\u77ed\u8ddd\u79bb\u5728 <code>1.8 \u00c5</code> \u5230 <code>2.0 \u00c5</code> \u4e4b\u95f4\u7684\u7ed3\u6784\u3002\u8f93\u51fa\uff1a<code>filtered_Li_Li_1.8_2.0.xyz</code>\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_14","title":"\u7535\u8377\u5e73\u8861\u68c0\u67e5","text":"<p><code>charge_balance_check.py</code> \u68c0\u67e5\u7ed3\u6784\u7684\u6c27\u5316\u6001\u5e73\u8861\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>\u8f93\u51fa\u6587\u4ef6\uff1a</p> <ul> <li><code>balanced.xyz</code> \u2014 \u7535\u8377\u5e73\u8861\u7684\u7ed3\u6784</li> <li><code>unbalanced.xyz</code> \u2014 \u7535\u8377\u4e0d\u5e73\u8861\u7684\u7ed3\u6784</li> <li><code>indices.txt</code> \u2014 \u5e73\u8861\u7ed3\u6784\u7684\u7d22\u5f15</li> </ul> <p>\u9002\u7528\u4e8e\u5177\u6709\u660e\u786e\u6c27\u5316\u6001\u7684\u4f53\u7cfb\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_15","title":"\u5f02\u5e38\u68c0\u6d4b","text":"<p><code>find_outliers.py</code> \u57fa\u4e8e\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u7684 RMSE \u9608\u503c\u67e5\u627e NEP \u8bad\u7ec3\u6570\u636e\u4e2d\u7684\u5f02\u5e38\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>stress_train.out</code>\u3001<code>train.xyz</code></p> <p>\u8fd9\u4e9b\u6587\u4ef6\u5728 NEP \u8bad\u7ec3\u8fc7\u7a0b\u4e2d\u751f\u6210\u3002\u811a\u672c\u6bd4\u8f83 DFT \u4e0e NEP \u7684\u9884\u6d4b\uff0c\u8bc6\u522b\u8bef\u5dee\u8f83\u5927\u7684\u7ed3\u6784\u3002</p> <pre><code># \u4ea4\u4e92\u6a21\u5f0f\ngpumdkit.sh    # \u9009\u62e9\uff1a5) \u5206\u6790\u5de5\u5177 \u2192 502) \u67e5\u627e\u5f02\u5e38\u7ed3\u6784\n</code></pre> <p>\u4ea4\u4e92\u63d0\u793a\uff1a</p> <pre><code>Enter energy RMSE threshold (meV/atom): 1\nEnter force RMSE threshold (meV/\u00c5): 60\nEnter stress RMSE threshold (GPa): 0.03\n</code></pre> <p>\u8f93\u51fa\u6587\u4ef6\uff1a</p> <ul> <li><code>selected.xyz</code> \u2014 \u8d85\u8fc7 RMSE \u9608\u503c\u7684\u7ed3\u6784\uff08\u5f02\u5e38\u503c\uff09</li> <li><code>remained.xyz</code> \u2014 \u5728\u9608\u503c\u5185\u7684\u7ed3\u6784</li> <li><code>selected_remained.png</code> \u2014 \u5bf9\u6bd4\u56fe</li> </ul> <p>\u7528\u9014\uff1a NEP \u8bad\u7ec3\u540e\uff0c\u7528\u6b64\u5de5\u5177\u8bc6\u522b\u5bf9\u8bef\u5dee\u8d21\u732e\u6700\u5927\u7684\u95ee\u9898\u7ed3\u6784\u3002\u79fb\u9664\u6216\u6539\u8fdb\u8fd9\u4e9b\u7ed3\u6784\u4ee5\u63d0\u5347\u8bad\u7ec3\u96c6\u8d28\u91cf\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_16","title":"\u65f6\u95f4\u4f30\u7b97","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#gpumd","title":"GPUMD \u5269\u4f59\u65f6\u95f4","text":"<p><code>time_consuming_gpumd.sh</code> \u4f30\u7b97 GPUMD \u6a21\u62df\u7684\u5269\u4f59\u65f6\u95f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>run.in</code>\u3001<code>thermo.out</code>\uff08\u5728\u5f53\u524d GPUMD \u5de5\u4f5c\u76ee\u5f55\u4e2d\uff09</p> <pre><code>gpumdkit.sh -time gpumd\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>----------------- System Information ----------------\ntotal frames: 1050000\n-----------------------------------------------------\nCurrent Frame  Speed (steps/s)   Total Time       Time Left       Estimated End\n-------------   -------------   -------------   -------------   -----------------\n    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04\n    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#nep","title":"NEP \u5269\u4f59\u65f6\u95f4","text":"<p><code>time_consuming_nep.sh</code> \u4f30\u7b97 NEP \u8bad\u7ec3\u7684\u5269\u4f59\u65f6\u95f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code>\uff08\u5728\u5f53\u524d NEP \u5de5\u4f5c\u76ee\u5f55\u4e2d\uff09</p> <pre><code>gpumdkit.sh -time nep\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>+-----------------+-----------+-----------------+---------------------+\n|       Step      | Time Diff |    Time Left    |    Finish Time      |\n+-----------------+-----------+-----------------+---------------------+\n| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |\n| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |\n| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |\n+-----------------+-----------+-----------------+---------------------+\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_17","title":"\u6982\u7387\u5bc6\u5ea6\u5206\u6790","text":"<p><code>probability_density_analysis.py</code> \u8ba1\u7b97\u79fb\u52a8\u79bb\u5b50\u7684 3D \u6982\u7387\u5bc6\u5ea6\uff0c\u7528\u4e8e\u6269\u6563\u901a\u9053\u5206\u6790\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a \u53c2\u8003\u7ed3\u6784\uff08POSCAR\uff09\u3001\u8f68\u8ff9\u6587\u4ef6\uff08extxyz\uff09</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n</code></pre> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>LLZO.vasp</code> \u53c2\u8003\u7ed3\u6784\uff08POSCAR \u683c\u5f0f\uff09 <code>dump.xyz</code> \u8f68\u8ff9\u6587\u4ef6\uff08extxyz \u683c\u5f0f\uff09 <code>Li</code> \u76ee\u6807\u79fb\u52a8\u79bb\u5b50 <code>0.25</code> \u6982\u7387\u5bc6\u5ea6\u7f51\u683c\u95f4\u8ddd\uff08\u00c5\uff09 <p>\u8f93\u51fa\uff1a <code>probability_density_0.25.vasp</code> \u2014 VASP \u683c\u5f0f\u7684\u6982\u7387\u5bc6\u5ea6\u7f51\u683c\uff0c\u53ef\u7528 VESTA \u7b49\u5de5\u5177\u53ef\u89c6\u5316\u3002</p> <p>\u53ef\u89c6\u5316\u5efa\u8bae\uff1a</p> <ol> <li>\u5728 VESTA \u4e2d\u6253\u5f00 <code>probability_density_0.25.vasp</code></li> <li>\u4f7f\u7528 \"Edit \u2192 Data \u2192 Volumetric Data\" \u8c03\u6574\u7b49\u503c\u9762\u7ea7\u522b</li> <li>\u6309\u6570\u503c\u5bf9\u6982\u7387\u5bc6\u5ea6\u7740\u8272\uff0c\u4ee5\u7a81\u51fa\u4f18\u9009\u6269\u6563\u8def\u5f84</li> <li>\u53e0\u52a0\u6676\u4f53\u7ed3\u6784\u4f5c\u4e3a\u53c2\u8003</li> </ol>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_18","title":"\u793a\u4f8b\u5de5\u4f5c\u6d41","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_19","title":"\u7ed3\u6784\u8d28\u91cf\u68c0\u67e5","text":"<pre><code># 1. \u68c0\u67e5\u6210\u5206\ngpumdkit.sh -analyze_comp train.xyz\n\n# 2. \u68c0\u67e5\u80fd\u91cf/\u529b\u8303\u56f4\ngpumdkit.sh -range train.xyz force hist\n\n# 3. \u68c0\u67e5\u6700\u77ed\u8ddd\u79bb\ngpumdkit.sh -min_dist_pbc train.xyz\n\n# 4. \u67e5\u627e\u5f02\u5e38\u503c\uff08NEP \u8bad\u7ec3\u540e\uff09\n# \u4ea4\u4e92\uff1a5) \u5206\u6790\u5de5\u5177 \u2192 502\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_20","title":"\u7ed3\u6784\u8fc7\u6ee4\u6d41\u6c34\u7ebf","text":"<pre><code># 1. \u6309\u6700\u77ed\u8ddd\u79bb\u8fc7\u6ee4\ngpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n\n# 2. \u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4\ngpumdkit.sh -filter_box filtered_dist_pbc.xyz 13\n\n# 3. \u6309\u529b\u9608\u503c\u8fc7\u6ee4\ngpumdkit.sh -filter_value filtered_box.xyz force 20\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_21","title":"\u6269\u6563\u901a\u9053\u5206\u6790","text":"<pre><code># 1. \u8ba1\u7b97\u6982\u7387\u5bc6\u5ea6\ngpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n\n# 2. \u7528 VESTA \u53ef\u89c6\u5316\n# \u6253\u5f00 probability_density_0.25.vasp\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html","title":"\u547d\u4ee4\u53c2\u8003","text":"\ud83d\udccb \u547d\u4ee4\u53c2\u8003 <p>\u672c\u9875\u5217\u51fa GPUMDkit \u7a33\u5b9a\u7684\u547d\u4ee4\u884c\u5feb\u6377\u5165\u53e3\u3002\u5bf9\u4e8e\u53c2\u6570\u8f83\u591a\u3001\u9700\u8981\u9009\u62e9\u7684\u4efb\u52a1\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528\u4ea4\u4e92\u6a21\u5f0f\u3002</p> <p>\u6e90\u8868\u7ef4\u62a4\u5728 <code>docs/command_reference.tsv</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#gpumdkitsh-h","title":"<code>gpumdkit.sh -h</code> \u8f93\u51fa","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |\n| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_1","title":"\u4e3b\u547d\u4ee4","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-h</code> <code>gpumdkit.sh -h</code> \u663e\u793a\u901a\u7528\u5e2e\u52a9 <code>-update</code> <code>gpumdkit.sh -update</code> \u66f4\u65b0 GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> \u6e05\u7406\u5f53\u524d\u76ee\u5f55\u4e2d\u7684\u5197\u4f59\u6587\u4ef6"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_2","title":"\u683c\u5f0f\u8f6c\u6362","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K \u8f93\u51fa\u8f6c xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR \u8f6c extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF \u8f6c POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF \u8f6c extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR \u8f6c extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz \u591a\u5e27\u8f6c POSCAR \u6587\u4ef6 <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR \u8f6c LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump \u8f6c extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory \u8f6c extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> \u6309\u6676\u80de\u500d\u6570\u6269\u80de <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> \u6309\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> \u6dfb\u52a0 GPUMD group \u6807\u7b7e <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> \u6dfb\u52a0\u7ed3\u6784\u6743\u91cd <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> \u63d0\u53d6\u5355\u5e27 <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> \u6e05\u7406 extxyz \u5197\u4f59\u5c5e\u6027 <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> \u6309\u6bd4\u4f8b\u8303\u56f4\u63d0\u53d6\u5e27"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_3","title":"\u8ba1\u7b97\u5668","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> \u79bb\u5b50\u7535\u5bfc\u7387 <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP \u6027\u8d28\u9884\u6d4b <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP \u63cf\u8ff0\u7b26 <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u57fa\u4e8e NEP \u7684 NEB <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784\u4f18\u5316 <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> \u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> \u90bb\u5c45\u5217\u8868 <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> \u4f4d\u79fb <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> \u5e73\u5747\u7ed3\u6784 <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> \u516b\u9762\u4f53\u503e\u659c <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 \u5c40\u57df\u6781\u5316"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_4","title":"\u5206\u6790\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> \u6027\u8d28\u8303\u56f4\u5206\u6790 <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> \u6210\u5206\u5206\u6790 <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> \u5143\u7d20\u5217\u8868 <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> \u7535\u8377\u5e73\u8861\u68c0\u67e5 <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> \u65e0 PBC \u6700\u5c0f\u8ddd\u79bb <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> \u5e26 PBC \u6700\u5c0f\u8ddd\u79bb <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u5e26 PBC \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> \u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4 <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> \u6027\u8d28\u9608\u503c\u8fc7\u6ee4 <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> \u5143\u7d20\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4 <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> \u6982\u7387\u5bc6\u5ea6\u5206\u6790"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_5","title":"\u53ef\u89c6\u5316","text":"<p>\u4f7f\u7528\uff1a</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>\u5e38\u7528\u7c7b\u578b\u5305\u62ec <code>train</code>\u3001<code>prediction</code>\u3001<code>thermo</code>\u3001<code>msd</code>\u3001<code>sdc</code>\u3001<code>rdf</code>\u3001<code>emd</code>\u3001<code>nemd</code>\u3001<code>hnemd</code>\u3001<code>pdos</code> \u548c <code>plane-grid</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_6","title":"\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> \u76d1\u63a7 GPUMD \u6216 NEP \u8fdb\u5ea6 <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> \u4ea4\u4e92\u5f0f\u4fee\u6539 NEP \u6a21\u578b <code>-pynep</code> <code>gpumdkit.sh -pynep</code> \u5df2\u5f03\u7528\u7684 PyNEP FPS \u91c7\u6837"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html","title":"\u5de5\u4f5c\u6d41\u811a\u672c","text":"\ud83d\udd27 \u5de5\u4f5c\u6d41\u811a\u672c <p>\u5de5\u4f5c\u6d41\u811a\u672c\u7528\u4e8e\u81ea\u52a8\u5316\u91cd\u590d\u6027\u7684 DFT\u3001MD \u548c NEP \u6570\u636e\u51c6\u5907\u6b65\u9aa4\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_1","title":"\u4ea4\u4e92\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>3) Workflow\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+---------------------------------------------------------+\n|                      WORKFLOW TOOLS                     |\n+---------------------------------------------------------+\n| 301) SCF batch pretreatment                             |\n| 302) MD sample batch pretreatment (gpumd)               |\n| 303) MD sample batch pretreatment (lmp)                 |\n+---------------------------------------------------------+\n| 000) Return to the main menu                            |\n+---------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u5de5\u4f5c\u6d41 \u7528\u9014 301 SCF batch pretreatment \u51c6\u5907 DFT \u5355\u70b9\u8ba1\u7b97 302 MD sample batch pretreatment (GPUMD) \u51c6\u5907 GPUMD \u91c7\u6837\u8ba1\u7b97 303 MD sample batch pretreatment (LAMMPS) \u51c6\u5907 LAMMPS \u91c7\u6837\u8ba1\u7b97"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#scf","title":"SCF \u6279\u5904\u7406\u9884\u5904\u7406","text":"<p>\u9002\u7528\u4e8e\u5df2\u6709\u591a\u4e2a\u7ed3\u6784\uff0c\u9700\u8981\u51c6\u5907\u7b2c\u4e00\u6027\u539f\u7406\u5355\u70b9\u8ba1\u7b97\u7684\u60c5\u51b5\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#vasp","title":"VASP","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a\u7ed3\u6784\u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u811a\u672c\u6309\u4ee5\u4e0b\u987a\u5e8f\u68c0\u6d4b\uff1a</p> <ol> <li>\u5982\u679c\u5b58\u5728\u4e00\u4e2a\u6216\u591a\u4e2a <code>.vasp</code> \u6587\u4ef6\uff0c\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c <code>.vasp</code> \u548c <code>.xyz</code> \u540c\u65f6\u5b58\u5728\uff0c\u4f1a\u6253\u5370\u63d0\u793a\uff0c\u5e76\u53ea\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u53ea\u6709\u4e00\u4e2a <code>.xyz</code>\uff0c\u4f1a\u628a\u8fd9\u4e2a extxyz \u8f6c\u4e3a POSCAR \u6587\u4ef6\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</li> </ol> <p>\u8fd0\u884c\u524d\u7684\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>fp/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u7528\u6237\u628a <code>INCAR</code>\u3001<code>POTCAR</code>\u3001<code>KPOINTS</code> \u653e\u5230 <code>fp/</code> \u4e2d\uff0c\u8ba1\u7b97\u76ee\u5f55\u4f1a\u94fe\u63a5\u8fd9\u91cc\u7684\u6587\u4ef6\u3002</p> <p>\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u8f93\u5165\u7684 <code>prefix</code> \u4f1a\u4f5c\u4e3a\u8ba1\u7b97\u6587\u4ef6\u5939\u540d\u524d\u7f00\u3002\u540e\u7eed\u4f7f\u7528 <code>out2xyz</code> \u63d0\u53d6\u7ed3\u679c\u65f6\uff0c\u6587\u4ef6\u5939\u540d\u4f1a\u4f5c\u4e3a <code>config_type</code> \u5199\u5165 extxyz\uff0c\u4fbf\u4e8e\u4e4b\u540e\u68c0\u67e5\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#cp2k","title":"CP2K","text":"<p>CP2K \u53ef\u4ee5\u4ece\u4ea4\u4e92\u83dc\u5355\u8fdb\u5165\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u547d\u4ee4\u884c\u8c03\u7528\uff1a</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4f1a\u8981\u6c42\u8f93\u5165\uff1a</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>CP2K \u6a21\u677f\u5e94\u8bbe\u7f6e\u4e3a\u4ece <code>pos.xyz</code> \u8bfb\u53d6\u5750\u6807\u3002\u53c2\u8003\u6a21\u677f\u5728\uff1a</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>\u811a\u672c\u4f1a\u4e3a\u6bcf\u4e2a\u7ed3\u6784\u751f\u6210 <code>&lt;prefix&gt;_&lt;index&gt;/</code> \u76ee\u5f55\uff0c\u5e76\u5199\u5165 <code>input.inp</code> \u548c <code>pos.xyz</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#md","title":"MD \u91c7\u6837\u9884\u5904\u7406","text":""},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#gpumd","title":"GPUMD","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 302\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u68c0\u6d4b\u987a\u5e8f\u4e0e VASP SCF \u9884\u5904\u7406\u4e00\u81f4\uff1a\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</p> <p>\u8fd0\u884c\u524d\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>md/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>nep.txt</code> \u548c <code>run_*.in</code> \u653e\u5165 <code>md/</code>\u3002\u4f8b\u5982 <code>run_1.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_1/run.in</code>\uff0c<code>run_2.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_2/run.in</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#lammps","title":"LAMMPS","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 303\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\uff1b\u4e24\u79cd\u683c\u5f0f\u540c\u65f6\u5b58\u5728\u65f6\u4f18\u5148\u5904\u7406 <code>.vasp</code>\u3002</p> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>lmprun.in</code> \u548c <code>nep.txt</code> \u653e\u5230 <code>md/</code> \u4e2d\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_2","title":"\u4e3b\u52a8\u5b66\u4e60\u5f0f\u6d41\u7a0b","text":"<p>\u5e38\u89c1 NEP \u6570\u636e\u8fed\u4ee3\u6d41\u7a0b\uff1a</p> <ol> <li>\u4f7f\u7528\u5f53\u524d <code>nep.txt</code> \u8fd0\u884c MD\uff1b</li> <li>\u6536\u96c6 <code>dump.xyz</code> \u6216 <code>active.xyz</code>\uff1b</li> <li>\u5220\u9664\u660e\u663e\u4e0d\u5408\u7406\u7ed3\u6784\uff1b</li> <li>\u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\uff1b</li> <li>\u8fd0\u884c DFT \u5355\u70b9\uff1b</li> <li>\u5c06 DFT \u7ed3\u679c\u8f6c\u6362\u4e3a extxyz\uff1b</li> <li>\u8ffd\u52a0\u5230 <code>train.xyz</code>\uff1b</li> <li>\u91cd\u65b0\u8bad\u7ec3 NEP\u3002</li> </ol> <p>\u66f4\u5b8c\u6574\u7684\u5f00\u53d1\u7248\u4e3b\u52a8\u5b66\u4e60\u811a\u672c\u8bf4\u660e\u89c1 \u4e3b\u52a8\u5b66\u4e60\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_3","title":"\u57fa\u4e8e\u6a21\u677f\u7684\u6e29\u5ea6\u7cfb\u5217","text":"<p>\u5bf9\u4e8e\u7b80\u5355\u7684\u6e29\u5ea6\u7cfb\u5217\u6a21\u62df\uff0c\u4f7f\u7528 shell \u5faa\u73af\u5373\u53ef\uff1a</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>\u7136\u540e\u6839\u636e\u4f60\u7684\u96c6\u7fa4\u7cfb\u7edf\u63d0\u4ea4\u751f\u6210\u7684\u6587\u4ef6\u5939\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_4","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u5de5\u4f5c\u6d41\u811a\u672c\u548c\u96c6\u7fa4\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u6279\u91cf\u63d0\u4ea4\u524d\u5148\u7528\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u3002</li> <li>\u6a21\u677f\u6587\u4ef6\u5982 <code>INCAR</code>\u3001<code>KPOINTS</code>\u3001<code>POTCAR</code>\u3001<code>run.in</code> \u5e94\u4ed4\u7ec6\u68c0\u67e5\u3002</li> <li>\u6279\u91cf DFT \u524d\u5148\u7528\u5206\u6790\u548c\u91c7\u6837\u811a\u672c\u6e05\u7406\u5019\u9009\u7ed3\u6784\u3002</li> </ul>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html","title":"\u5feb\u901f\u5165\u95e8","text":"\ud83d\ude80 \u5feb\u901f\u5165\u95e8 <p>\u672c\u9875\u5e2e\u52a9\u4f60\u5b89\u88c5 GPUMDkit \u5e76\u8fd0\u884c\u7b2c\u4e00\u4e2a\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u6216\u76f4\u63a5\u4f7f\u7528\u547d\u4ee4\u884c\u9009\u9879\u6765\u4f7f\u7528 GPUMDkit\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>GPUMDkit \u4e3a\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u7684\u5e38\u89c1\u4efb\u52a1\u63d0\u4f9b\u7edf\u4e00\u5165\u53e3\u2014\u2014\u683c\u5f0f\u8f6c\u6362\u3001\u7ed3\u6784\u5206\u6790\u3001\u6027\u8d28\u8ba1\u7b97\u548c\u53ef\u89c6\u5316\u2014\u2014\u65e0\u9700\u7f16\u5199\u81ea\u5b9a\u4e49\u811a\u672c\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#1-python","title":"1. \u51c6\u5907 Python \u73af\u5883","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>\u90e8\u5206\u53ef\u9009\u529f\u80fd\u9700\u8981\u989d\u5916\u4f9d\u8d56\uff1a</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>\u5176\u4ed6 Python \u4f9d\u8d56\u7531\u5bf9\u5e94\u811a\u672c\u5728\u8fd0\u884c\u65f6\u5bfc\u5165\u3002\u5982\u679c\u7f3a\u5c11\u67d0\u4e2a\u5305\uff0c\u4f7f\u7528\u5bf9\u5e94\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u63d0\u793a\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#2-gpumdkit","title":"2. \u5b89\u88c5 GPUMDkit","text":"<p>\u514b\u9686\u4ed3\u5e93\u5e76\u8fd0\u884c\u5b89\u88c5\u811a\u672c\uff1a</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre> <p>\u5b89\u88c5\u811a\u672c\u4f1a\u5199\u5165 <code>GPUMDkit_path</code> \u548c <code>PATH</code> \u8bbe\u7f6e\uff0c\u5e76\u5728\u5f53\u524d shell \u4e2d\u52a0\u8f7d\u3002\u9ed8\u8ba4\u5199\u5165 <code>~/.bashrc</code>\uff1b\u5982\u679c\u5f53\u524d shell \u662f zsh\uff0c\u5219\u5199\u5165 <code>~/.zshrc</code>\u3002\u5982\u679c\u68c0\u6d4b\u5230\u5df2\u6709 GPUMDkit \u8def\u5f84\uff0c\u5b89\u88c5\u811a\u672c\u4f1a\u6253\u5370\u65e7\u8def\u5f84\u5e76\u8be2\u95ee\u662f\u5426\u66ff\u6362\uff1b\u4fee\u6539 rc \u6587\u4ef6\u524d\u4f1a\u5148\u521b\u5efa\u5907\u4efd\u3002</p> <p>\u5178\u578b\u5b89\u88c5\u8f93\u51fa\uff1a</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>\u5982\u679c\u4e4b\u524d\u5df2\u7ecf\u5b89\u88c5\u8fc7 GPUMDkit\uff0c\u53ef\u80fd\u4f1a\u770b\u5230\uff1a</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#3","title":"3. \u9a8c\u8bc1\u5b89\u88c5","text":"<pre><code>gpumdkit.sh -h\n</code></pre> <p>\u6b64\u547d\u4ee4\u4f1a\u6253\u5370\u5e2e\u52a9\u8868\uff0c\u5217\u51fa\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_3","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u6253\u5f00\u4e3b\u83dc\u5355\uff1a</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre> <p>\u6309\u6570\u5b57\u9009\u62e9\u6a21\u5757\u3002\u6bcf\u4e2a\u6a21\u5757\u63d0\u4f9b\u5305\u542b\u5177\u4f53\u529f\u80fd\u7684\u5b50\u83dc\u5355\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_4","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<p>\u76f4\u63a5\u547d\u4ee4\u4f7f\u7528\u56fa\u5b9a\u7684\u4f4d\u7f6e\u53c2\u6570\uff1a</p> <pre><code>gpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>\u7b2c\u4e00\u4e2a\u793a\u4f8b\u8bfb\u53d6 <code>POSCAR</code>\uff0c\u5199\u51fa <code>model.xyz</code>\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_5","title":"\u5e38\u89c1\u793a\u4f8b","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#gpumd-group","title":"\u6dfb\u52a0 GPUMD group \u6807\u7b7e","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>group \u6807\u7b7e\u7528\u4e8e\u4e00\u4e9b\u9700\u8981\u539f\u5b50\u5206\u7ec4\u7684 GPUMD \u76f8\u5173\u6d41\u7a0b\u548c\u5206\u6790\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep","title":"\u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep_1","title":"\u7ed8\u5236 NEP \u6d4b\u8bd5\u96c6\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_6","title":"\u7ed8\u5236\u70ed\u529b\u5b66\u91cf","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#msd","title":"\u7ed8\u5236 MSD \u548c\u81ea\u6269\u6563\u7cfb\u6570","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_7","title":"\u8bf4\u660e","text":"<ul> <li>\u4f7f\u7528 <code>gpumdkit.sh -h</code> \u67e5\u770b\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</li> <li>\u4f7f\u7528 <code>gpumdkit.sh -&lt;\u9009\u9879&gt; -h</code> \u83b7\u53d6\u7279\u5b9a\u9009\u9879\u7684\u5e2e\u52a9\uff08\u4f8b\u5982 <code>gpumdkit.sh -plt train -h</code>\uff09\u3002</li> <li>\u5404\u6a21\u5757\u7684\u8be6\u7ec6\u7528\u6cd5\u8bf7\u53c2\u89c1\u9996\u9875\u4e2d\u94fe\u63a5\u7684\u5bf9\u5e94\u6559\u7a0b\u9875\u9762\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html","title":"\u6781\u6027\u6750\u6599\u5206\u6790","text":"\ud83e\uddf2 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u672c\u6559\u7a0b\u4ecb\u7ecd GPUMDkit \u4e2d\u8ba1\u7b97\u5668\u9009\u9879 <code>406-410</code>\uff0c\u4ee5\u53ca <code>plane-grid</code> \u7ed8\u56fe\u6d41\u7a0b\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code> \u548c <code>Scripts/plt_scripts/</code></p> <p>\u672c\u6559\u7a0b\u5305\u542b\u901a\u7528\u5de5\u5177\u548c\u4f53\u7cfb\u76f8\u5173\u5de5\u5177\uff1a</p> <ul> <li><code>nlist</code>\u3001<code>disp</code> \u548c <code>avg-struct</code> \u53ef\u5e7f\u6cdb\u7528\u4e8e\u7ed3\u6784\u548c\u8f68\u8ff9\u5206\u6790\u3002</li> <li><code>oct-tilt</code> \u7528\u4e8e\u516b\u9762\u4f53\u73af\u5883\u5206\u6790\uff0c\u9700\u8981\u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u5468\u56f4\u6709 6 \u4e2a\u8fd1\u90bb\u3002</li> <li><code>pol-abo3</code> \u4e13\u7528\u4e8e <code>ABO3</code> \u4f53\u7cfb\u7684\u6781\u5316\u5206\u6790\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_1","title":"\u6982\u89c8","text":"\u6b65\u9aa4 CLI \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u8f93\u51fa \u6784\u5efa\u8fd1\u90bb\u5217\u8868 <code>gpumdkit.sh -calc nlist ...</code> <code>model.xyz</code> <code>nl-*.dat</code> \u8ba1\u7b97\u4f4d\u79fb <code>gpumdkit.sh -calc disp ...</code> \u8f68\u8ff9 + <code>nl-*.dat</code> <code>displacements.dat</code> \u5e73\u5747\u8f68\u8ff9\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct ...</code> \u8f68\u8ff9 \u5e73\u5747\u7ed3\u6784 extxyz \u516b\u9762\u4f53\u503e\u659c <code>gpumdkit.sh -calc oct-tilt ...</code> \u8f68\u8ff9 + B-O \u8fd1\u90bb\u5217\u8868 \u503e\u659c\u89d2\u6570\u636e\u8868 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 ...</code> \u8f68\u8ff9 + \u8fd1\u90bb\u5217\u8868 \u6781\u5316\u6570\u636e\u8868 plane-grid \u7ed8\u56fe <code>gpumdkit.sh -plt plane-grid ...</code> \u7ed3\u6784 + \u4f4d\u79fb\u6570\u636e \u5e73\u9762\u5256\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_2","title":"\u4f9d\u8d56","text":"<p>\u8fd9\u4e9b\u811a\u672c\u9700\u8981 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_3","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<p>\u9009\u9879 <code>406-410</code> \u662f\u672c\u6559\u7a0b\u4e2d\u7684\u6838\u5fc3\u529f\u80fd\u3002\u4e0b\u9762\u5404\u8282\u4f1a\u8bf4\u660e\u6bcf\u4e2a\u529f\u80fd\u7684\u7528\u9014\u548c\u8fd0\u884c\u65b9\u5f0f\u3002</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 4) Calculators\n</code></pre> <p>\u8ba1\u7b97\u5668\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5b8c\u6574\u53c2\u6570\u8bf4\u660e\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u547d\u4ee4\u67e5\u770b\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#406-calc_neighbor_listpy","title":"406) \u6784\u5efa\u8fd1\u90bb\u5217\u8868 (<code>calc_neighbor_list.py</code>)","text":"<p>\u4e3a\u6307\u5b9a\u4e2d\u5fc3\u5143\u7d20\u548c\u8fd1\u90bb\u5143\u7d20\u6784\u5efa\u8fd1\u90bb\u5217\u8868\u3002</p> <p>\u4f7f\u7528\u573a\u666f\uff1a \u8fd9\u901a\u5e38\u662f\u8fd0\u884c <code>disp</code>\u3001<code>oct-tilt</code> \u548c <code>pol-abo3</code> \u4e4b\u524d\u7684\u7b2c\u4e00\u6b65\uff0c\u56e0\u4e3a\u8fd9\u4e9b\u811a\u672c\u4f1a\u8bfb\u53d6 <code>nl-*.dat</code> \u8fd1\u90bb\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_4","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4e3a\u516b\u9762\u4f53\u5206\u6790\u6784\u5efa Ti-O \u6700\u8fd1 6 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# \u793a\u4f8b 2\uff1a\u4e3a A \u4f4d\u4e2d\u5fc3\u5206\u6790\u6784\u5efa Pb/Sr-O \u6700\u8fd1 12 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_5","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-x, --index</code>\uff1a   \u4ece\u8f93\u5165\u6587\u4ef6\u4e2d\u8bfb\u53d6\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-c, --cutoff</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u641c\u7d22\u622a\u65ad\u8ddd\u79bb\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> <li><code>-n, --neighbor-num</code>\uff08\u5fc5\u9700\uff09\uff1a   \u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u7684\u8fd1\u90bb\u6570\u91cf\u3002</li> <li><code>-d, --defect</code>\uff1a   \u7f3a\u9677\u6a21\u5f0f\u3002\u542f\u7528\u540e\uff0c\u5982\u679c\u8fd1\u90bb\u6570\u91cf\u4e0d\u8db3\uff0c\u7f3a\u5931\u4f4d\u7f6e\u4f1a\u7528\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u586b\u5145\u3002</li> <li><code>-C, --center-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u4e2d\u5fc3\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-E, --neighbor-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u8def\u5f84\u3002\u9ed8\u8ba4\u503c\uff1a<code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_6","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u8fd1\u90bb\u5217\u8868\u6587\u672c\u6587\u4ef6\uff0c\u4f8b\u5982 <code>nl-Ti-O.dat</code>\u3002</li> <li>\u6587\u4ef6\u662f\u4e00\u4e2a\u4e8c\u7ef4\u6574\u6570\u6570\u7ec4\uff0c\u5f62\u72b6\u4e3a <code>(n_center, neighbor_num + 1)</code>\u3002\u6bcf\u4e00\u884c\u5bf9\u5e94\u4e00\u4e2a\u4e2d\u5fc3\u539f\u5b50\uff1a\u7b2c\u4e00\u5217\u662f\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\uff0c\u540e\u7eed\u5217\u662f\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7\uff0c\u6240\u6709\u7f16\u53f7\u5747\u4e3a 1-based\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#407-calc_displacementpy","title":"407) \u4ece\u8f68\u8ff9\u8ba1\u7b97\u4f4d\u79fb (<code>calc_displacement.py</code>)","text":"<p>\u6839\u636e\u8f68\u8ff9\u6216\u6a21\u578b\u7ed3\u6784\u4ee5\u53ca\u8fd1\u90bb\u5217\u8868\uff0c\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_7","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece model.xyz \u8ba1\u7b97\u5355\u5e27\u4f4d\u79fb\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4f7f\u7528 movie.xyz \u7684\u6700\u540e 20% \u5e27\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_8","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7531 <code>nlist</code> \u751f\u6210\u7684\u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u90e8\u5206\u5e27\u3002   \u6574\u6570\u8868\u793a\u6700\u540e <code>N</code> \u5e27\uff1b   <code>0 &lt; value &lt; 1</code> \u8868\u793a\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_9","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>displacements.dat</code>\uff0c\u6216\u4f60\u6307\u5b9a\u7684\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e8c\u7ef4\u6570\u7ec4\uff1a\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u4e09\u5217\u5206\u522b\u4e3a <code>dx</code>\u3001<code>dy</code> \u548c <code>dz</code> \u4f4d\u79fb\u5206\u91cf\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#408-calc_averaged_structurepy","title":"408) \u8ba1\u7b97\u5e73\u5747\u7ed3\u6784 (<code>calc_averaged_structure.py</code>)","text":"<p>\u4ece\u9009\u5b9a\u8f68\u8ff9\u5e27\u751f\u6210\u4e00\u4e2a\u5e73\u5747\u7ed3\u6784\u3002 \u901a\u5e38\u53ef\u5728\u4f53\u7cfb\u5e73\u8861\u540e\u4f7f\u7528\uff1a\u5bf9\u4e8e\u63a5\u8fd1\u5e73\u8861\u7684\u56fa\u4f53\uff0c\u53ef\u4ee5\u5bf9\u76ee\u6807\u6e29\u5ea6\u4e0b\u7684\u4e00\u6bb5\u8f68\u8ff9\u53d6\u5e73\u5747\uff0c\u5e76\u5206\u6790\u8be5\u4ee3\u8868\u6027\u7ed3\u6784\uff0c\u800c\u4e0d\u662f\u9010\u5e27\u5904\u7406\u6bcf\u4e2a snapshot\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_10","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5e73\u5747\u6240\u6709\u5e27\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# \u793a\u4f8b 2\uff1a\u5e73\u5747\u9009\u5b9a\u5e27\u8303\u56f4 (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_11","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u8f68\u8ff9\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>movie.xyz</code>\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>averaged_structure.xyz</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_12","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u5355\u5e27\u5e73\u5747\u7ed3\u6784 extxyz \u6587\u4ef6\u3002</li> <li>\u4f4d\u7f6e\u5e73\u5747\u4f1a\u76f8\u5bf9\u4e8e\u6240\u9009\u7b2c\u4e00\u5e27\u8fdb\u884c MIC/PBC \u4fee\u6b63\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#409-calc_oct_tiltpy","title":"409) \u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c (<code>calc_oct_tilt.py</code>)","text":"<p>\u6839\u636e B-O \u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c\u89d2\u3002 \u8be5\u529f\u80fd\u5e38\u7528\u4e8e\u5206\u6790 <code>ABO3</code> \u4f53\u7cfb\u4e2d\u7684\u516b\u9762\u4f53\u8f6c\u52a8\u6a21\u5f0f\uff0c\u4f8b\u5982 <code>SrTiO3</code> \u548c <code>PbZrO3</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_13","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece\u5355\u5e27\u7ed3\u6784\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4ece\u8f68\u8ff9\u6700\u540e 20% \u5e27\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_14","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>octahedral_tilt.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_15","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>octahedral_tilt.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>theta_x</code>\u3001<code>theta_y</code>\u3001<code>theta_z</code>\uff0c\u5355\u4f4d\u4e3a degree\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#410-abo3-calc_polarization_abo3py","title":"410) \u8ba1\u7b97 ABO3 \u4f53\u7cfb\u6781\u5316 (<code>calc_polarization_abo3.py</code>)","text":"<p>\u8ba1\u7b97 <code>ABO3</code> \u4f53\u7cfb\u7684\u5c40\u57df\u6781\u5316\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_16","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5355\u5e27 ABO3 \u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# \u793a\u4f8b 2\uff1a\u9009\u5b9a\u8f68\u8ff9\u5e27\u8303\u56f4\u4e0a\u7684\u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_17","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>--nl-ba</code>\uff08\u5fc5\u9700\uff09\uff1a   B-A \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>--nl-bo</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>polarization.dat</code>\u3002</li> <li><code>--bec</code>\uff08\u5fc5\u9700\uff09\uff1a   Born \u6709\u6548\u7535\u8377\u9879\uff0c\u683c\u5f0f\u4e3a <code>Element=value</code>\u3002   \u793a\u4f8b\uff1a<code>Pb=2.5 Ti=4.0 O=-2.0</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul> <p>\u91cd\u8981\u68c0\u67e5\uff1a</p> <ul> <li><code>--bec</code> \u5fc5\u987b\u5305\u542b\u8f93\u5165\u7ed3\u6784\u4e2d\u7684\u6240\u6709\u5143\u7d20\u79cd\u7c7b\u3002</li> <li><code>--nl-ba</code> \u548c <code>--nl-bo</code> \u4e2d\u7684\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u5fc5\u987b\u5339\u914d\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_18","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>polarization.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>Px</code>\u3001<code>Py</code>\u3001<code>Pz</code>\uff0c\u5355\u4f4d\u4e3a <code>C/m^2</code>\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u5982\u679c\u603b Born \u7535\u8377\u4e0d\u5e73\u8861\uff0c\u811a\u672c\u4f1a\u6253\u5370 warning\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#plane-grid-plt_plane_gridpy","title":"Plane-grid \u53ef\u89c6\u5316 (<code>plt_plane_grid.py</code>)","text":"<p>\u4f60\u53ef\u4ee5\u53ef\u89c6\u5316 <code>displacements.dat</code> \u6216 <code>polarization.dat</code>\uff1a</p> <pre><code># \u793a\u4f8b 1\uff1aTi \u4f4d\u70b9\u4e0a\u7684\u4f4d\u79fb\u56fe\uff0c\u9009\u62e9\u7b2c\u4e00\u4e2a XY \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# \u793a\u4f8b 2\uff1aPb \u4f4d\u70b9\u4e0a\u7684\u6781\u5316\u56fe\uff0c\u9009\u62e9 XZ \u548c YZ \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>\u53c2\u6570\uff08\u5b8c\u6574\uff09\uff1a</p> <ul> <li><code>-i, --input</code>\uff1a   \u7528\u4e8e\u539f\u5b50\u5e03\u5c40\u548c\u5206\u5c42\u7684\u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-d, --disp</code>\uff1a   \u77e2\u91cf\u573a\u6570\u636e\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-e, --elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7528\u4e8e\u5c06\u77e2\u91cf\u6620\u5c04\u5230\u6676\u683c\u5c42\u4e0a\u7684\u4e2d\u5fc3\u5143\u7d20\u7b26\u53f7\u3002</li> <li><code>-m, --tol</code>\uff1a   \u7f51\u683c\u6620\u5c04\u7684\u5c42\u5bb9\u5dee\u3002\u9ed8\u8ba4\u503c\uff1a<code>1.0</code>\u3002</li> <li><code>-g, --target-size</code>\uff1a   \u671f\u671b\u7f51\u683c\u5927\u5c0f\uff0c\u683c\u5f0f\u4e3a <code>nx ny nz</code>\u3002</li> <li><code>-o, --save-dir</code>\uff1a   \u56fe\u7247\u8f93\u51fa\u76ee\u5f55\u3002\u9ed8\u8ba4\u503c\uff1a<code>plot</code>\u3002</li> <li><code>-f, --frame</code>\uff1a   \u5f53\u77e2\u91cf\u6570\u636e\u5305\u542b\u591a\u5e27\u65f6\uff0c\u8981\u53ef\u89c6\u5316\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>--select-xy</code>\uff1a   \u9009\u5b9a\u7684 XY \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-xz</code>\uff1a   \u9009\u5b9a\u7684 XZ \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-yz</code>\uff1a   \u9009\u5b9a\u7684 YZ \u5c42\u7f16\u53f7\u3002</li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li>\u5982\u679c\u9700\u8981\uff0c\u4f1a\u521b\u5efa\u8f93\u51fa\u76ee\u5f55\u3002</li> <li>\u56fe\u7247\u4fdd\u5b58\u4e3a <code>XY_*.png</code>\u3001<code>XZ_*.png</code>\u3001<code>YZ_*.png</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_19","title":"\u8f93\u51fa\u6587\u4ef6\u4e00\u89c8","text":"\u811a\u672c \u4e3b\u8981\u8f93\u51fa \u4fdd\u5b58\u5185\u5bb9 <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based \u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u548c\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7 <code>calc_displacement.py</code> <code>*.dat</code> \u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\uff08<code>dx dy dz</code>\uff0cAngstrom\uff09 <code>calc_averaged_structure.py</code> <code>*.xyz</code> \u4e00\u4e2a\u5e73\u5747\u7ed3\u6784 <code>calc_oct_tilt.py</code> <code>*.dat</code> \u516b\u9762\u4f53\u503e\u8f6c\u89d2\uff08<code>theta_x theta_y theta_z</code>\uff0cdegree\uff09 <code>calc_polarization_abo3.py</code> <code>*.dat</code> \u5c40\u57df\u6781\u5316\u77e2\u91cf\uff08<code>Px Py Pz</code>\uff0c<code>C/m^2</code>\uff09 <code>plt_plane_grid.py</code> <code>plot/*.png</code> \u6839\u636e\u77e2\u91cf\u573a\u6570\u636e\u7ed8\u5236\u7684 XY/XZ/YZ \u5e73\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_20","title":"\u771f\u5b9e\u6848\u4f8b","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3-","title":"PbTiO3 \u7684\u6e29\u5ea6\u9a71\u52a8\u94c1\u7535-\u987a\u7535\u76f8\u53d8","text":"<p>\u5047\u8bbe\u6240\u6709\u6587\u4ef6\u90fd\u4f4d\u4e8e\u5f53\u524d\u76ee\u5f55 <code>./</code>\uff1a</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> \u662f\u7528\u4e8e\u8fdb\u884c MD \u6a21\u62df\u7684\u521d\u59cb\u7ed3\u6784\u3002\u6bcf\u4e2a <code>TEMP K.xyz</code> \u662f\u5bf9\u5e94\u6e29\u5ea6\u4e0b\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1","title":"\u7b2c 1 \u6b65\uff1a\u4ece\u6bcf\u6761\u8f68\u8ff9\u7684\u540e\u534a\u6bb5\u5f97\u5230\u5e73\u5747\u7ed3\u6784","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>\u8fd9\u4f1a\u5199\u51fa <code>300K-avg.xyz</code>\u3001<code>350K-avg.xyz</code>\u3001...\u3001<code>800K-avg.xyz</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-modelxyz","title":"\u7b2c 2 \u6b65\uff1a\u57fa\u4e8e <code>model.xyz</code> \u6784\u5efa\u8fd1\u90bb\u5217\u8868","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3","title":"\u7b2c 3 \u6b65\uff1a\u4e3a\u6bcf\u4e2a\u6e29\u5ea6\u8ba1\u7b97\u4f4d\u79fb\u548c\u6781\u5316","text":"<p>\u8fd9\u91cc\u4f7f\u7528 Born \u6709\u6548\u7535\u8377\uff08BEC\uff09\uff0c\u4e0d\u662f\u540d\u4e49\u79bb\u5b50\u7535\u8377\u3002\u5bf9\u4e8e\u672c\u4f8b\u4e2d\u7684 PbTiO3\uff1a</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>\u4f60\u53ef\u4ee5\u4ece\u81ea\u5df1\u7684 DFPT \u8ba1\u7b97\u6216\u6587\u732e\u4e2d\u83b7\u5f97 BEC\u3002\u56e0\u6b64\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u548c\u6781\u5316\uff1a</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#4","title":"\u7b2c 4 \u6b65\uff1a\u7ed8\u5236\u5b9e\u7a7a\u95f4\u4f4d\u79fb\u548c\u6781\u5316\u56fe","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#5-","title":"\u7b2c 5 \u6b65\uff1a\u6784\u5efa\u6e29\u5ea6-\u5e8f\u53c2\u91cf\u66f2\u7ebf","text":"<p>\u7ed3\u5408\u6bcf\u4e2a\u6e29\u5ea6\u5e73\u5747\u7ed3\u6784\u7684\u6676\u683c\u4fe1\u606f\u548c\u6781\u5316\u6587\u4ef6\uff08<code>XX-pol.dat</code>\uff09\u8fdb\u884c\u5206\u6790\uff0c\u53ef\u4ee5\u5f97\u5230\u5982\u4e0b\u56fe\uff1a</p> <p>\u8be5\u8d8b\u52bf\u663e\u793a\u5728\u7ea6 <code>600 K</code> \u9644\u8fd1\u53d1\u751f\u660e\u663e\u76f8\u53d8\uff0c\u6b64\u65f6\u6781\u5316\u6d88\u5931\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3srtio3","title":"PbTiO3/SrTiO3 \u8d85\u6676\u683c\u4e2d\u7684\u62d3\u6251\u7ed3\u6784","text":"<p>\u5047\u8bbe <code>movie.xyz</code> \u662f\u5f53\u524d\u76ee\u5f55\u4e0b PbTiO3/SrTiO3 \u8d85\u6676\u683c\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1-25","title":"\u7b2c 1 \u6b65\uff1a\u4f7f\u7528\u6700\u540e 25% \u5e27\u6784\u5efa\u5e73\u5747\u7ed3\u6784","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-ti","title":"\u7b2c 2 \u6b65\uff1a\u6784\u5efa Ti \u8fd1\u90bb\u5217\u8868","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3-plane-grid","title":"\u7b2c 3 \u6b65\uff1a\u7ed8\u5236 plane-grid \u56fe","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>\u8fd9\u4f1a\u5f97\u5230\u4e0e\u524d\u9762\u5c55\u793a\u76f8\u4f3c\u7684\u56fe\u3002\u5728 PTO \u533a\u57df\u53ef\u4ee5\u770b\u5230\u7c7b\u4f3c\u6da1\u65cb\u7684\u6781\u5316\u56fe\u6837\uff0c\u800c STO \u533a\u57df\u7684\u6781\u5316\u63a5\u8fd1\u4e8e\u96f6\u3002</p> <p>\u6ce8\u610f\uff1a\u793a\u4f8b\u56fe\u4f7f\u7528\u4e86\u81ea\u5b9a\u4e49 colormap\u3002GPUMDkit \u9ed8\u8ba4\u8f93\u51fa\u4f7f\u7528\u4e0d\u540c\u98ce\u683c\uff0c\u53ef\u901a\u8fc7\u4fee\u6539\u7ed8\u56fe\u811a\u672c\u8fdb\u884c\u8c03\u6574\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_21","title":"\u5176\u4ed6\u4f53\u7cfb","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#-","title":"\u6709\u673a-\u65e0\u673a\u6742\u5316\u94c1\u7535\u4f53","text":"<p>\u5728\u8bb8\u591a\u6709\u673a-\u65e0\u673a\u94c1\u7535\u4f53\u4e2d\uff0c\u6781\u5316\u4e0e\u5404\u5411\u5f02\u6027\u7684\u5206\u5b50\u5355\u5143\u5bc6\u5207\u76f8\u5173\u3002\u8ddf\u8e2a\u5206\u5b50\u53d6\u5411\u7684\u4e00\u79cd\u5b9e\u7528\u65b9\u6cd5\u662f\u4f7f\u7528\u952e\u77e2\u91cf\u3002</p> <p>\u5bf9\u4e8e TMCM-CdCl3\uff0c\u53ef\u4ee5\u4f7f\u7528 TMCM \u5206\u5b50\u4e2d\u7684 C-Cl \u952e\u65b9\u5411\u4f5c\u4e3a\u53d6\u5411\u4ee3\u7406\uff0c\u5e76\u636e\u6b64\u4f30\u8ba1\u6781\u5316\u6001\uff1a</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p>\u968f\u540e\u53ef\u4ee5\u628a <code>ccl_vectors.dat</code> \u4f5c\u4e3a\u53d6\u5411\u5e8f\u53c2\u91cf\u8fdb\u884c\u5206\u6790\u3002\u66f4\u591a\u7ec6\u8282\u53ef\u53c2\u8003\uff1aPhys. Rev. Lett. 136, 016801\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_22","title":"\u5176\u4ed6\u94c1\u7535\u6750\u6599\u5bb6\u65cf","text":"<p>\u9664 <code>ABO3</code> \u5916\uff0c<code>ferrodispcalc</code> \u4e5f\u53ef\u4ee5\u9002\u914d\u8bb8\u591a\u94c1\u7535\u4f53\u7cfb\uff0c\u5305\u62ec\u6c2e\u5316\u7269\u3001\u6c27\u5316\u94ea\u57fa\u5316\u5408\u7269\u3001\u6709\u673a-\u65e0\u673a\u6742\u5316\u4f53\u7cfb\u4ee5\u53ca\u90e8\u5206\u4e8c\u7ef4\u94c1\u7535\u6750\u6599\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html","title":"\u683c\u5f0f\u8f6c\u6362","text":"\ud83d\udd04 \u683c\u5f0f\u8f6c\u6362 <p>\u683c\u5f0f\u8f6c\u6362\u6a21\u5757\u7528\u4e8e\u5728\u5e38\u89c1\u539f\u5b50\u6a21\u62df\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362\uff0c\u540c\u65f6\u63d0\u4f9b group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u5e27\u63d0\u53d6\u7b49\u5143\u6570\u636e\u5904\u7406\u529f\u80fd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>\u672c\u6a21\u5757\u5728\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u5e38\u7528\u7684\u7ed3\u6784\u548c\u8f68\u8ff9\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8fdb\u884c\u8f6c\u6362\u3002\u652f\u6301 VASP\u3001LAMMPS\u3001CP2K\u3001ABACUS\u3001CIF\u3001ASE \u8f68\u8ff9\u548c extxyz \u683c\u5f0f\u3002\u8fd8\u63d0\u4f9b\u6dfb\u52a0 group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u63d0\u53d6\u5e27\u548c\u6269\u80de\u7b49\u5de5\u5177\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":"<p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/format_conversion/</code></p> <p>\u786e\u4fdd\u5df2\u5b89\u88c5 GPUMDkit\u3002\u5b89\u88c5\u8bf4\u660e\u8bf7\u53c2\u89c1\u5feb\u901f\u5165\u95e8\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_3","title":"\u652f\u6301\u7684\u683c\u5f0f","text":"<ul> <li>VASP\uff1a<code>POSCAR</code>\u3001<code>CONTCAR</code>\u3001<code>OUTCAR</code>\u3001<code>XDATCAR</code></li> <li>LAMMPS\uff1adata \u6587\u4ef6\u548c dump \u8f68\u8ff9</li> <li>CP2K\uff1a\u8f93\u51fa log\u3001\u5750\u6807\u3001\u529b\u548c\u6676\u80de\u6587\u4ef6</li> <li>ABACUS\uff1aSCF/MD \u8f93\u51fa</li> <li>CIF\uff1a\u6676\u4f53\u7ed3\u6784\u6587\u4ef6</li> <li>ASE trajectory\uff1a<code>.traj</code></li> <li>extxyz\uff1aGPUMD \u548c NEP \u5e38\u7528\u7684\u7ed3\u6784\u683c\u5f0f</li> </ul>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_4","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>1) Format Conversion\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_5","title":"\u6bcf\u4e2a\u5165\u53e3\u7684\u4f5c\u7528","text":"\u5165\u53e3 \u529f\u80fd \u9002\u7528\u573a\u666f <code>101</code> VASP OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c \u6279\u91cf\u8f6c\u6362 VASP \u8ba1\u7b97\u76ee\u5f55 <code>102</code> MTP cfg \u8f6c extxyz \u8f6c\u6362 MTP \u6570\u636e <code>103</code> CP2K \u8f6c extxyz \u53ef\u9009\u62e9 log/inp \u8def\u7ebf\u6216 pos/frc/cell \u8def\u7ebf <code>104</code> ABACUS \u8f6c extxyz \u8f6c\u6362 ABACUS SCF \u6216 MD \u8f93\u51fa <code>105</code> extxyz \u8f6c POSCAR \u5c06 extxyz \u6bcf\u4e00\u5e27\u5199\u6210 POSCAR <code>106</code> \u6dfb\u52a0 group \u6807\u7b7e \u4e3a GPUMD \u76f8\u5173\u6d41\u7a0b\u6dfb\u52a0\u539f\u5b50\u5206\u7ec4\u6807\u7b7e <code>107</code> \u6dfb\u52a0\u6743\u91cd \u4fee\u6539\u8bad\u7ec3\u96c6\u7ed3\u6784\u6743\u91cd <code>108</code> \u63d0\u53d6\u5355\u5e27 \u4ece extxyz \u8f68\u8ff9\u5bfc\u51fa\u67d0\u4e00\u5e27 <code>109</code> \u6e05\u7406 XYZ \u4fe1\u606f \u5220\u9664\u591a\u4f59 extxyz \u5c5e\u6027 <code>110</code> \u6269\u80de \u6309\u500d\u6570\u6216\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>out2exyz</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c VASP OUTCAR \u8f6c\u6362\u7684\u53e6\u4e00\u4e2a\u5165\u53e3 <code>pos2exyz</code> POSCAR \u8f6c extxyz \u8f6c\u6362\u5355\u4e2a\u7ed3\u6784 <code>cif2pos</code> CIF \u8f6c POSCAR \u4ece CIF \u51c6\u5907 VASP \u8f93\u5165 <code>cif2exyz</code> CIF \u8f6c extxyz \u4ece CIF \u51c6\u5907 GPUMDkit \u8f93\u5165 <code>xdat2exyz</code> XDATCAR \u8f6c extxyz \u8f6c\u6362 VASP MD \u8f68\u8ff9 <code>pos2lmp</code> POSCAR \u8f6c LAMMPS data \u51c6\u5907 LAMMPS \u8f93\u5165 <code>lmp2exyz</code> LAMMPS dump \u8f6c extxyz \u8f6c\u6362 LAMMPS \u8f68\u8ff9 <code>traj2exyz</code> ASE traj \u8f6c extxyz \u8f6c\u6362 ASE \u8f68\u8ff9"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_6","title":"\u5feb\u901f\u547d\u4ee4\u8868","text":"\u6765\u6e90 \u76ee\u6807 \u547d\u4ee4 OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz POSCAR model.xyz</code> extxyz POSCAR \u6587\u4ef6 <code>gpumdkit.sh -exyz2pos train.xyz</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_7","title":"\u5e38\u89c1\u4f8b\u5b50","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#vasp","title":"\u8f6c\u6362 VASP \u7ed3\u679c","text":"<p>\u529f\u80fd\uff1a \u5728\u76ee\u5f55\u4e2d\u641c\u7d22 VASP OUTCAR \u6587\u4ef6\uff0c\u5e76\u5c06\u5b83\u4eec\u8f6c\u6362\u4e3a\u5355\u4e2a extxyz \u6587\u4ef6\uff0c\u7528\u4e8e NEP \u8bad\u7ec3\u6216\u5206\u6790\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>\u4e5f\u53ef\u4ee5\u4f7f\u7528 Python \u7248\u672c\uff1a</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u683c\u5f0f\u8f6c\u6362\u83dc\u5355\u4e2d\u9009\u62e9 <code>101</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u51fa\uff1a \u5305\u542b\u8f6c\u6362\u540e\u7ed3\u6784\u7684 extxyz \u6587\u4ef6\uff0c\u53ef\u7528\u4e8e NEP \u8bad\u7ec3\u6216\u8fdb\u4e00\u6b65\u5206\u6790\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#group","title":"\u6dfb\u52a0 group \u6807\u7b7e","text":"<p>\u529f\u80fd\uff1a \u4e3a\u7ed3\u6784\u6587\u4ef6\u6dfb\u52a0\u539f\u5b50 group \u6807\u7b7e\u3002\u4e00\u4e9b GPUMD \u76f8\u5173\u6d41\u7a0b\u9700\u8981 group \u6807\u7b7e\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>\u8be5\u547d\u4ee4\u8bfb\u53d6\u8f93\u5165\u7ed3\u6784\uff0c\u5e76\u5199\u51fa\u5e26 group \u4fe1\u606f\u7684 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u683c\u5f0f\u8f6c\u6362\u83dc\u5355\u4e2d\u9009\u62e9 <code>106</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u51fa\uff1a \u6dfb\u52a0\u4e86 group \u6807\u7b7e\u7684 extxyz \u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_8","title":"\u5e38\u7528\u811a\u672c\u8bf4\u660e","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>\u9002\u5408\u628a\u5355\u4e2a VASP \u7ed3\u6784\u8f6c\u6210 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz-poscar","title":"extxyz \u8f6c POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>\u4f1a\u5c06 extxyz \u4e2d\u6240\u6709\u5e27\u8f6c\u6362\u6210 <code>POSCAR_*.vasp</code> \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3\uff1a<code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#lammps-dump-extxyz","title":"LAMMPS dump \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>\u5143\u7d20\u987a\u5e8f\u5fc5\u987b\u5bf9\u5e94 LAMMPS \u4e2d\u7684 atom type ID\u3002\u4f8b\u5982 type 1 \u662f Li\u3001type 2 \u662f Y\u3001type 3 \u662f Cl\uff0c\u5219\u8f93\u5165 <code>Li Y Cl</code>\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#cif","title":"CIF \u8f6c\u6362","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>\u5982\u679c\u540e\u7eed\u9700\u8981 VASP \u8ba1\u7b97\uff0c\u4f7f\u7528 <code>-cif2pos</code>\uff1b\u5982\u679c\u540e\u7eed\u8981\u8fdb\u5165 GPUMDkit \u5206\u6790\uff0c\u4f7f\u7528 <code>-cif2exyz</code>\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_9","title":"\u6dfb\u52a0\u6743\u91cd","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>\u7528\u4e8e\u7ed9\u8bad\u7ec3\u96c6\u7ed3\u6784\u6dfb\u52a0\u6216\u4fee\u6539\u6743\u91cd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_10","title":"\u6269\u80de","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>\u7b2c\u4e00\u79cd\u6309\u6676\u80de\u500d\u6570\u6269\u80de\uff0c\u7b2c\u4e8c\u79cd\u6309\u76ee\u6807\u539f\u5b50\u6570\u81ea\u52a8\u9009\u62e9\u6269\u80de\u65b9\u5f0f\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_11","title":"\u63d0\u53d6\u5355\u5e27","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>\u4ece extxyz \u8f68\u8ff9\u4e2d\u63d0\u53d6\u7b2c <code>1000</code> \u5e27\uff08\u7d22\u5f15\u4ece 0 \u5f00\u59cb\uff09\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz","title":"\u62c6\u5206\u591a\u5e27 extxyz","text":"<p><code>split_single_xyz.py</code> \u5c06\u591a\u5e27 extxyz \u6587\u4ef6\u62c6\u5206\u4e3a\u5355\u5e27\u6587\u4ef6\u3002</p> <pre><code>python Scripts/format_conversion/split_single_xyz.py dump.xyz\n</code></pre> <p>\u751f\u6210 <code>model_0.xyz</code>\u3001<code>model_1.xyz</code>\u3001... \u7b49\u5355\u5e27\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#mtp","title":"MTP \u8f6c\u6362","text":"<p>\u5c06 MTP <code>.cfg</code> \u683c\u5f0f\u8f6c\u6362\u4e3a extxyz\uff1a</p> <pre><code>gpumdkit.sh    # \u9009\u62e9\uff1a1) \u683c\u5f0f\u8f6c\u6362 \u2192 102\n</code></pre> <p>\u4ea4\u4e92\u63d0\u793a\uff1a</p> <pre><code>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;\nExample: train.cfg Pd Ag\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#abacus","title":"ABACUS \u8f6c\u6362","text":"<p>\u5c06 ABACUS \u8f93\u51fa\u8f6c\u6362\u4e3a extxyz\uff1a</p> <pre><code>gpumdkit.sh    # \u9009\u62e9\uff1a1) \u683c\u5f0f\u8f6c\u6362 \u2192 104\n</code></pre> <p>\u83dc\u5355\u63d0\u4f9b\u4e24\u4e2a\u9009\u9879\uff1a</p> <ol> <li>SCF \u8f93\u51fa\uff08<code>running_scf.log</code>\uff09</li> <li>MD \u8f93\u51fa\uff08<code>running_md.log</code>\uff09</li> </ol>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_12","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae LAMMPS \u8f6c\u6362\u540e\u5143\u7d20\u4e0d\u5bf9 \u68c0\u67e5 dump \u6587\u4ef6\u540e\u7684\u5143\u7d20\u987a\u5e8f extxyz \u5143\u6570\u636e\u592a\u591a \u4f7f\u7528 <code>-clean_xyz input.xyz clean.xyz</code> \u63d0\u53d6\u5e27\u4e0d\u5bf9 \u6ce8\u610f\u5e27\u7d22\u5f15\u901a\u5e38\u4ece 0 \u5f00\u59cb"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_13","title":"\u8bf4\u660e","text":"<p>\u5982\u679c\u67d0\u4e2a\u8f6c\u6362\u811a\u672c\u7f3a\u5c11\u6240\u9700 Python \u5305\uff0c\u8fd0\u884c\u8be5\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u76f8\u5e94\u63d0\u793a\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html","title":"\u7ed3\u6784\u91c7\u6837","text":"\ud83d\udce6 \u7ed3\u6784\u91c7\u6837 <p>\u7ed3\u6784\u91c7\u6837\u7528\u4e8e\u4ece\u8f68\u8ff9\u4e2d\u9009\u62e9\u5019\u9009\u7ed3\u6784\u3001\u751f\u6210\u6270\u52a8\u7ed3\u6784\uff0c\u6216\u6839\u636e\u6a21\u578b\u504f\u5dee\u6311\u9009\u503c\u5f97\u8fdb\u4e00\u6b65\u8ba1\u7b97\u7684\u7ed3\u6784\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/sample_structures/</code></p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_1","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>2) Sample Structures\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u65b9\u6cd5 \u7528\u9014 201 uniform/random \u4ece\u8f68\u8ff9\u4e2d\u5747\u5300\u6216\u968f\u673a\u62bd\u5e27 202 PyNEP notice \u53ea\u6253\u5370\u63d0\u793a\uff1b\u771f\u6b63\u8fd0\u884c PyNEP \u8bf7\u7528 <code>gpumdkit.sh -pynep</code> 203 NepTrain FPS \u4f7f\u7528 NepTrain \u63cf\u8ff0\u7b26\u7684 FPS \u91c7\u6837 204 perturb \u4ece POSCAR/CONTCAR \u751f\u6210\u6270\u52a8\u7ed3\u6784 205 force deviation \u4ece active learning \u8f93\u51fa\u4e2d\u9009\u62e9\u9ad8\u504f\u5dee\u7ed3\u6784"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_2","title":"\u5747\u5300/\u968f\u673a\u91c7\u6837","text":"<p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>201</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>\u4f8b\u5982\u8f93\u5165\uff1a</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>\u6216\uff1a</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>uniform</code> / <code>random</code> \u91c7\u6837\u65b9\u6cd5 <code>50</code> / <code>100</code> \u91c7\u6837\u7ed3\u6784\u6570 <code>500</code> \u53ef\u9009\uff0c\u8df3\u8fc7\u524d 500 \u5e27 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#neptrain-fps","title":"NepTrain FPS","text":"<p>NepTrain \u7248\u672c\u7684 FPS\uff1a</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>203</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u5165\uff1a</p> \u6587\u4ef6 \u542b\u4e49 <code>dump.xyz</code> \u5019\u9009\u7ed3\u6784 <code>train.xyz</code> \u5f53\u524d\u8bad\u7ec3\u96c6 <code>nep.txt</code> \u7528\u4e8e\u8ba1\u7b97\u63cf\u8ff0\u7b26\u7684 NEP \u6a21\u578b <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>\u8fd0\u884c\u65f6\u53ef\u4ee5\u9009\u62e9\u6309\u6700\u5c0f\u8ddd\u79bb\u9608\u503c\u91c7\u6837\uff0c\u6216\u6307\u5b9a\u91c7\u6837\u7ed3\u6784\u6570\u3002\u811a\u672c\u968f\u540e\u4f1a\u6253\u5370\uff1a</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>NepTrain</code>\uff0c\u8fd0\u884c\u65f6\u4f1a\u63d0\u793a\u76f8\u5173\u5f15\u7528\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep","title":"PyNEP \u65e7\u5165\u53e3","text":"<p>PyNEP FPS \u4ecd\u7136\u4fdd\u7559\u517c\u5bb9\uff0c\u4f46\u53ea\u901a\u8fc7 <code>-pynep</code> \u5165\u53e3\u8c03\u7528\u3002</p> <p>\u5982\u679c\u5728\u4ea4\u4e92\u83dc\u5355\u4e2d\u9009\u62e9 <code>202</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep_1","title":"\u4e32\u884c PyNEP","text":"<pre><code>python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep_2","title":"\u5e76\u884c PyNEP","text":"<pre><code>python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u6700\u540e\u4e00\u4e2a\u53c2\u6570\u662f CPU \u7ebf\u7a0b\u6570\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#gpumdkit","title":"GPUMDkit \u5165\u53e3","text":"<pre><code>gpumdkit.sh -pynep\n</code></pre> <p>\u968f\u540e\u8f93\u5165\uff1a</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u8fd9\u4e2a\u5165\u53e3\u9700\u8981 <code>pynep</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_3","title":"\u7ed3\u6784\u6270\u52a8","text":"<pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>204</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>POSCAR</code> \u8f93\u5165\u7ed3\u6784 <code>20</code> \u751f\u6210\u7ed3\u6784\u6570 <code>0.03</code> \u6676\u80de\u6270\u52a8\u6bd4\u4f8b <code>0.2</code> \u539f\u5b50\u6270\u52a8\u8ddd\u79bb\uff0c\u5355\u4f4d Angstrom <code>uniform</code> \u6270\u52a8\u65b9\u5f0f\uff0c\u53ef\u9009 <code>normal</code>\u3001<code>uniform</code>\u3001<code>const</code> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>POSCAR_01.vasp</code>\u3001<code>POSCAR_02.vasp</code> \u7b49</li> </ul> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>dpdata</code>\u3002\u4f7f\u7528\u6b64\u529f\u80fd\u65f6\u5efa\u8bae\u5f15\u7528 dpdata \u5305\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_4","title":"\u6700\u5927\u529b\u504f\u5dee\u7ed3\u6784\u9009\u62e9","text":"<p>\u8be5\u529f\u80fd\u9700\u8981\u914d\u5408 GPUMD \u7684 <code>active</code> \u547d\u4ee4\u4f7f\u7528\u3002<code>active</code> \u901a\u8fc7\u59d4\u5458\u4f1a\u8bc4\u5ba1\u673a\u5236\uff0c\u8ba9\u591a\u6761\u52bf\u51fd\u6570\u5bf9\u540c\u4e00\u7ed3\u6784\u8fdb\u884c\u9884\u6d4b\uff0c\u5e76\u8bb0\u5f55\u6bcf\u4e2a\u7ed3\u6784\u7684\u6700\u5927\u529b\u504f\u5dee\u3002<code>select_max_modev.py</code> \u4f1a\u4ece <code>active.out</code> \u548c <code>active.xyz</code> \u4e2d\u9009\u62e9\u529b\u504f\u5dee\u8f83\u5927\u7684\u7ed3\u6784\uff0c\u5199\u5165 <code>selected.xyz</code>\u3002</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>205</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>\u9700\u8981\u5f53\u524d\u76ee\u5f55\u4e0b\u6709\uff1a</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_5","title":"\u5e27\u8303\u56f4\u63d0\u53d6","text":"<p>\u63d0\u53d6\u8f68\u8ff9\u7684\u4e00\u90e8\u5206\u5e27\uff1a</p> <pre><code>python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>\u8fd9\u4f1a\u5199\u5165\u8f68\u8ff9 0% \u5230 80% \u7684\u5e27\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_6","title":"\u793a\u4f8b\u547d\u4ee4","text":"<pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_7","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae FPS \u9009\u51fa\u592a\u591a\u76f8\u4f3c\u7ed3\u6784 \u8c03\u5927\u8ddd\u79bb\u9608\u503c\u6216\u9650\u5236\u6700\u5927\u9009\u62e9\u6570 \u6270\u52a8\u7ed3\u6784\u4e0d\u5408\u7406 \u51cf\u5c0f <code>cell_pert</code> \u548c <code>atom_pert</code> <code>active.out</code> \u548c <code>active.xyz</code> \u4e0d\u5339\u914d \u786e\u4fdd\u6765\u81ea\u540c\u4e00\u6b21 GPUMD active \u8fd0\u884c PCA \u56fe\u5f02\u5e38 \u68c0\u67e5 <code>nep.txt</code> \u662f\u5426\u548c\u4e24\u4e2a\u6570\u636e\u96c6\u5143\u7d20\u4e00\u81f4"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html","title":"\u7ed8\u56fe\u811a\u672c","text":"\ud83d\udcca \u7ed8\u56fe\u811a\u672c <p>\u7ed8\u56fe\u6a21\u5757\u5305\u542b\u4e00\u7cfb\u5217 Python \u811a\u672c\uff0c\u7528\u4e8e\u53ef\u89c6\u5316 GPUMD\u3001NEP \u548c GPUMDkit \u8ba1\u7b97\u5668\u4ea7\u751f\u7684\u6570\u636e\u3002\u6240\u6709\u56fe\u8868\u5747\u53ef\u4ea4\u4e92\u663e\u793a\u6216\u4fdd\u5b58\u4e3a\u9ad8\u5206\u8fa8\u7387 PNG \u6587\u4ef6\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/plt_scripts/</code></p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_1","title":"\u5feb\u901f\u5165\u53e3","text":"<pre><code>gpumdkit.sh -plt              # \u663e\u793a\u6240\u6709\u7ed8\u56fe\u9009\u9879\ngpumdkit.sh -plt &lt;type&gt;       # \u751f\u6210\u6307\u5b9a\u56fe\u8868\ngpumdkit.sh -plt &lt;type&gt; save  # \u4fdd\u5b58\u4e3a PNG\ngpumdkit.sh -plt &lt;type&gt; -h    # \u663e\u793a\u7279\u5b9a\u56fe\u8868\u7684\u5e2e\u52a9\n</code></pre> <p>\u8fd0\u884c <code>gpumdkit.sh -plt</code> \u4f1a\u663e\u793a\u7ed8\u56fe\u547d\u4ee4\u83dc\u5355\uff1a</p> <pre><code>+-----------------------------------------------------------------------------------------------+\n|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |\n+-----------------------------------------------------------------------------------------------+\n|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |\n+-----------------------------------------------------------------------------------------------+\n|                                    NEP Training &amp; Evaluation                                  |\n+-----------------------------------------------------------------------------------------------+\n|  train          - NEP training results           prediction     - NEP prediction results      |\n|  train_test     - NEP train and test results     parity_density - Parity density plot         |\n|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |\n|  charge         - Charge distribution            born_charge    - Born effective charges      |\n|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |\n|  des            - Descriptors                    lr             - Learning rate for gnep      |\n+-----------------------------------------------------------------------------------------------+\n|                                     Diffusion &amp; Transport                                     |\n+-----------------------------------------------------------------------------------------------+\n|  msd            - Mean square displacement       msd_conv       - MSD convergence             |\n|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |\n|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|\n|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |\n|  D_xyz          - Directional Arrhenius D                                                     |\n+-----------------------------------------------------------------------------------------------+\n|                                    MD &amp; Structural Analysis                                   |\n+-----------------------------------------------------------------------------------------------+\n|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |\n|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |\n|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |\n|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |\n|  doas           - Density of atomistic states                                                 |\n+-----------------------------------------------------------------------------------------------+\n|                                        Heat Transport                                         |\n+-----------------------------------------------------------------------------------------------+\n|  emd            - EMD results                    nemd           - NEMD results                |\n|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |\n+-----------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u8bad\u7ec3\u4e0e\u9884\u6d4b","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_trainpy","title":"plt_train.py","text":"<p>\u53ef\u89c6\u5316 NEP \u8bad\u7ec3\u8fc7\u7a0b\uff0c\u5305\u62ec loss \u66f2\u7ebf\u3001RMSE \u6f14\u5316\uff0c\u4ee5\u53ca\u80fd\u91cf/\u529b/virial \u7684 DFT vs NEP parity plot\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code>\u3001<code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_predictionpy","title":"plt_prediction.py","text":"<p>\u53ef\u89c6\u5316\u6d4b\u8bd5\u96c6\u4e0a\u7684 NEP \u9884\u6d4b\u7ed3\u679c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_test.out</code>\u3001<code>force_test.out</code>\u3001<code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test         # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_train_testpy","title":"plt_train_test.py","text":"<p>\u5c06\u8bad\u7ec3\u96c6\u548c\u6d4b\u8bd5\u96c6\u7684 parity plot \u5408\u5e76\u663e\u793a\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code>\u3001<code>energy_test.out</code>\u3001<code>force_test.out</code>\u3001<code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_parity_densitypy","title":"plt_parity_density.py","text":"<p>\u751f\u6210\u57fa\u4e8e\u5bc6\u5ea6\u7684 parity plot\uff0c\u9002\u7528\u4e8e\u5927\u6570\u636e\u96c6\uff08\u6563\u70b9\u56fe\u8fc7\u4e8e\u5bc6\u96c6\u65f6\u66f4\u6613\u9605\u8bfb\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_force_errorspy","title":"plt_force_errors.py","text":"<p>\u53c2\u8003 Liu et al. \u7684\u65b9\u6cd5\u7ed8\u5236\u529b\u8bef\u5dee\u8bc4\u4f30\u6307\u6807\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>force_train.out</code></p> <p>\u663e\u793a\u6307\u6807\uff1a - \u529b\u5927\u5c0f\u8bef\u5dee (delta_F) - \u529b\u89d2\u5ea6\u8bef\u5dee (delta_theta) - \u8bef\u5dee\u5206\u5e03</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_learning_ratepy","title":"plt_learning_rate.py","text":"<p>\u53ef\u89c6\u5316 <code>gnep</code> \u8bad\u7ec3\u8fc7\u7a0b\u4e2d\u7684\u5b66\u4e60\u7387\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code></p> <p>\u6ce8\u610f\uff1a \u4ec5\u9002\u7528\u4e8e <code>gnep</code> \u8bad\u7ec3\u8fc7\u7a0b\u3002</p> <pre><code>gpumdkit.sh -plt lr\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_nep_restartpy","title":"plt_nep_restart.py","text":"<p>\u53ef\u89c6\u5316 <code>nep.restart</code> \u6587\u4ef6\u4e2d\u5b58\u50a8\u7684\u53c2\u6570\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>nep.restart</code></p> <pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_chargepy","title":"plt_charge.py","text":"<p>\u7ed8\u5236 <code>qNEP</code> \u6a21\u578b\u7684\u7535\u8377\u5206\u5e03\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>charge_train.out</code></p> <p>\u91cd\u8981\u63d0\u793a\uff1a \u786e\u4fdd\u8bad\u7ec3\u96c6\u548c\u7535\u8377\u8f93\u51fa\u7684\u539f\u5b50\u6392\u5e8f\u4e00\u81f4\u3002\u5efa\u8bae\u4f7f\u7528\u5168 batch \u8bad\u7ec3\u6216\u5148\u8fd0\u884c\u9884\u6d4b\u6b65\u9aa4\u3002</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_born_chargepy","title":"plt_born_charge.py","text":"<p>\u4e3a\u8bad\u7ec3\u96c6\u548c\u6d4b\u8bd5\u96c6\u521b\u5efa Born \u6709\u6548\u7535\u8377 (BEC) \u7684 parity plot\u3002\u5168\u96f6\u53c2\u8003 BEC \u7684\u7ed3\u6784\u4f1a\u88ab\u8fc7\u6ee4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>bec_train.out</code>\u3001<code>bec_test.out</code></p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec          # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_2","title":"\u70ed\u529b\u5b66\u91cf","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_thermopy","title":"plt_thermo.py","text":"<p>\u7efc\u5408\u53ef\u89c6\u5316\u70ed\u529b\u5b66\u6027\u8d28\u7684\u4e3b\u811a\u672c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_thermo2py-plt_thermo3py","title":"plt_thermo2.py &amp; plt_thermo3.py","text":"<p>\u4e0d\u540c\u98ce\u683c\u7684\u70ed\u529b\u5b66\u91cf\u53ef\u89c6\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_3","title":"\u6269\u6563\u548c\u79bb\u5b50\u8f93\u8fd0","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msdpy","title":"plt_msd.py","text":"<p>\u7ed8\u5236\u5404\u65b9\u5411\u7684\u5747\u65b9\u4f4d\u79fb (MSD)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msd_allpy","title":"plt_msd_all.py","text":"<p>\u5f53 GPUMD \u4e2d\u4f7f\u7528 <code>all_groups</code> \u65f6\uff0c\u5206\u522b\u7ed8\u5236\u6bcf\u79cd\u539f\u5b50\u7684 MSD\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code>\uff08\u9700\u8981\u4f7f\u7528 <code>all_groups</code> \u9009\u9879\u8ba1\u7b97\uff09</p> <p>\u8981\u6c42\uff1a <code>run.in</code> \u4e2d\u7684 <code>compute_msd</code> \u547d\u4ee4\u5fc5\u987b\u4f7f\u7528 <code>all_groups</code>\u3002</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msd_convergence_checkpy","title":"plt_msd_convergence_check.py","text":"<p>\u68c0\u67e5\u4e0d\u540c\u65f6\u95f4\u7a97\u53e3\u4e0b MSD \u8ba1\u7b97\u7684\u6536\u655b\u6027\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd_step*.out</code>\uff08\u9700\u8981\u5728 <code>compute_msd</code> \u4e2d\u4f7f\u7528 <code>save_every</code> \u9009\u9879\uff09</p> <p>\u8981\u6c42\uff1a \u5728 <code>compute_msd</code> \u547d\u4ee4\u4e2d\u4f7f\u7528 <code>save_every</code>\u3002</p> <p>\u7528\u9014\uff1a \u9a8c\u8bc1 MSD \u662f\u5426\u5df2\u5145\u5206\u6536\u655b\u4ee5\u51c6\u786e\u8ba1\u7b97\u6269\u6563\u7cfb\u6570\u3002</p> <pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_sdcpy","title":"plt_sdc.py","text":"<p>\u7ed8\u5236\u81ea\u6269\u6563\u7cfb\u6570 (SDC) \u968f\u65f6\u95f4\u7684\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_arrhenius_dpy","title":"plt_arrhenius_d.py","text":"<p>\u521b\u5efa Arrhenius \u6269\u6563\u7cfb\u6570\u56fe\uff08log10 D vs 1000/T\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>*K/msd.out</code>\uff08\u6bcf\u4e2a\u6e29\u5ea6\u5b50\u76ee\u5f55\u4e0b\u7684 <code>msd.out</code>\uff09</p> <pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D             # \u66ff\u4ee3\u547d\u4ee4\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_arrhenius_sigmapy","title":"plt_arrhenius_sigma.py","text":"<p>\u521b\u5efa Arrhenius \u79bb\u5b50\u7535\u5bfc\u7387\u56fe\uff08ln(\u03c3\u00b7T) vs 1000/T\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code>\uff08\u6bcf\u4e2a\u6e29\u5ea6\u5b50\u76ee\u5f55\uff09</p> <pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma         # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_4","title":"\u70ed\u8f93\u8fd0","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_emdpy","title":"plt_emd.py","text":"<p>\u5206\u6790\u5e76\u7ed8\u5236\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (EMD) \u70ed\u5bfc\u7387\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 EMD \u8f93\u51fa\u6587\u4ef6</p> <pre><code>gpumdkit.sh -plt emd x        # x \u65b9\u5411\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_nemdpy","title":"plt_nemd.py","text":"<p>\u53ef\u89c6\u5316\u975e\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (NEMD) \u70ed\u8f93\u8fd0\u6027\u8d28\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 NEMD \u8f93\u51fa\u6587\u4ef6</p> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u8bf4\u660e <code>real_length</code> \u4f20\u70ed\u533a\u5b9e\u9645\u957f\u5ea6\uff08nm\uff09\uff0c\u8bbe\u4e3a <code>Auto</code> \u53ef\u81ea\u52a8\u8ba1\u7b97 <code>scale_eff_size</code> \u6709\u6548\u622a\u9762\u79ef\u7f29\u653e\u56e0\u5b50\uff08\u9ed8\u8ba4\uff1a1\uff09\u3002\u4e09\u7ef4\u4f53\u76f8\u7528 1\uff1b\u542b\u771f\u7a7a\u5c42\u7684\u4f4e\u7ef4\u4f53\u7cfb\u7528 S_box / S_eff <code>cutoff_freq</code> SHC \u8ba1\u7b97\u7684\u622a\u6b62\u9891\u7387\uff08THz\uff0c\u9ed8\u8ba4\uff1a60\uff09 <code>save</code> \u53ef\u9009\uff0c\u4fdd\u5b58\u56fe\u7247\u4e3a <code>nemd.png</code> <p>\u6ce8\u610f\uff1a \u5982\u679c\u6ca1\u6709 SHC \u6570\u636e\uff0c\u4f7f\u7528 <code>save</code> \u65f6\u8bf7\u5c06 <code>scale_eff_size</code> \u548c <code>cutoff_freq</code> \u8bbe\u4e3a\u4efb\u610f\u5360\u4f4d\u6570\u5b57\u3002</p> <pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_hnemdpy","title":"plt_hnemd.py","text":"<p>\u7ed8\u5236\u975e\u5747\u5300\u975e\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (HNEMD) \u7ed3\u679c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 HNEMD \u8f93\u51fa\u6587\u4ef6</p> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u8bf4\u660e <code>scale_eff_size</code> \u6709\u6548\u622a\u9762\u79ef\u7f29\u653e\u56e0\u5b50\uff08\u9ed8\u8ba4\uff1a1\uff09 <code>cutoff_freq</code> SHC \u8ba1\u7b97\u7684\u622a\u6b62\u9891\u7387\uff08THz\uff0c\u9ed8\u8ba4\uff1a60\uff09 <code>save</code> \u53ef\u9009\uff0c\u4fdd\u5b58\u56fe\u7247\u4e3a <code>hnemd.png</code> <p>\u6ce8\u610f\uff1a \u5982\u679c\u6ca1\u6709 SHC \u6570\u636e\uff0c\u4f7f\u7528 <code>save</code> \u65f6\u8bf7\u5c06 <code>scale_eff_size</code> \u548c <code>cutoff_freq</code> \u8bbe\u4e3a\u4efb\u610f\u5360\u4f4d\u6570\u5b57\u3002</p> <pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_5","title":"\u7ed3\u6784\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_rdfpy","title":"plt_rdf.py","text":"<p>\u7ed8\u5236\u5f84\u5411\u5206\u5e03\u51fd\u6570 (RDF)\uff0c\u5c55\u793a\u539f\u5b50\u5bf9\u5173\u8054\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf               # \u663e\u793a\u6240\u6709 RDF \u5bf9\ngpumdkit.sh -plt rdf &lt;column&gt;      # \u663e\u793a\u7279\u5b9a\u5bf9\n</code></pre> <p>\u5b8c\u6574 RDF \u8f93\u51fa\uff1a</p> <p>\u5355\u5bf9 RDF\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_rdf_pmfpy","title":"plt_rdf_pmf.py","text":"<p>\u7ed8\u5236 RDF \u4e0e\u5e73\u5747\u529b\u52bf (PMF) \u7684\u7ec4\u5408\u56fe\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf_pmf\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_vacpy","title":"plt_vac.py","text":"<p>\u7ed8\u5236\u901f\u5ea6\u81ea\u76f8\u5173\u51fd\u6570 (VAC)\u3002\u53ef\u7528\u4e8e\u5206\u6790\u58f0\u5b50\u6027\u8d28\u548c\u539f\u5b50\u52a8\u529b\u5b66\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>sdc.out</code>\uff08\u7ed8\u56fe\u811a\u672c\u4f1a\u4ece\u8be5\u6587\u4ef6\u4e2d\u8bfb\u53d6 VAC \u76f8\u5173\u5217\uff09</p> <p>\u8f93\u51fa\uff1a \u4ea4\u4e92\u5f0f\u56fe\u8868\u6216 <code>vac.png</code>\uff08\u4f7f\u7528 <code>save</code> \u9009\u9879\u65f6\uff09</p> <pre><code>gpumdkit.sh -plt vac\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_cohesivepy","title":"plt_cohesive.py","text":"<p>\u4ece <code>cohesive.out</code> \u7ed8\u5236\u5185\u805a\u80fd\u66f2\u7ebf\u3002\u53ef\u7528\u4e8e\u5206\u6790\u6676\u683c\u7a33\u5b9a\u6027\u548c\u5e73\u8861\u6676\u683c\u5e38\u6570\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>cohesive.out</code>\uff08\u5404\u5411\u540c\u6027\u7f29\u653e\u56e0\u5b50 vs \u5185\u805a\u80fd\uff09</p> <p>\u8f93\u51fa\uff1a \u4ea4\u4e92\u5f0f\u56fe\u8868\u6216 <code>cohesive.png</code>\uff08\u4f7f\u7528 <code>save</code> \u9009\u9879\u65f6\uff09</p> <pre><code>gpumdkit.sh -plt cohesive\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_net_forcepy","title":"plt_net_force.py","text":"<p>\u7ed8\u5236\u7ed3\u6784\u4e0a\u7684\u51c0\u529b\u5206\u5e03\uff0c\u53ef\u7528\u4e8e\u8bc6\u522b\u95ee\u9898\u6784\u578b\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>\u53c2\u8003\u6587\u732e\uff1a arXiv:2510.19774</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_6","title":"\u58f0\u5b50","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_pdospy","title":"plt_pdos.py","text":"<p>\u8ba1\u7b97\u5e76\u7ed8\u5236\u5f52\u4e00\u5316\u7684\u901f\u5ea6\u81ea\u76f8\u5173\u51fd\u6570 (VAC)\u3001\u58f0\u5b50\u6001\u5bc6\u5ea6 (PDOS) \u548c\u70ed\u5bb9 (Cv)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>model.xyz</code>\u3001<code>run.in</code>\u3001<code>dos.out</code>\u3001<code>mvac.out</code></p> <pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>\u70ed\u5bb9\u8f93\u51fa\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#dimer","title":"\u63cf\u8ff0\u7b26\u3001Dimer \u548c\u5176\u4ed6\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_descriptorspy","title":"plt_descriptors.py","text":"<p>\u4f7f\u7528\u964d\u7ef4\u65b9\u6cd5\uff08PCA \u6216 UMAP\uff09\u53ef\u89c6\u5316\u9ad8\u7ef4 NEP \u63cf\u8ff0\u7b26\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>descriptors.npy</code>\uff08\u7531 <code>gpumdkit.sh -calc des</code> \u751f\u6210\uff09</p> <p>\u65b9\u6cd5\uff1a - <code>pca</code> \u2014 \u4e3b\u6210\u5206\u5206\u6790 - <code>umap</code> \u2014 \u7edf\u4e00\u6d41\u5f62\u903c\u8fd1\u4e0e\u6295\u5f71</p> <pre><code># \u5148\u8ba1\u7b97\u63cf\u8ff0\u7b26\ngpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n\n# \u518d\u53ef\u89c6\u5316\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_descriptors_comparepy","title":"plt_descriptors_compare.py","text":"<p>\u6bd4\u8f83\u591a\u4e2a\u8bad\u7ec3\u96c6\u6216\u6a21\u578b\u7684\u63cf\u8ff0\u7b26\u3002</p> <pre><code>gpumdkit.sh -plt des_compare\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_dimerpy","title":"plt_dimer.py","text":"<p>\u7ed8\u5236\u4e8c\u805a\u4f53\u76f8\u4e92\u4f5c\u7528\u66f2\u7ebf\u3002\u5c06\u4e24\u4e2a\u539f\u5b50\u653e\u5165\u7acb\u65b9\u76d2\u5b50\uff0830 \u00c5\uff09\uff0c\u4f7f\u7528 NEP \u6a21\u578b\u8ba1\u7b97\u52bf\u80fd\u548c\u529b\u968f\u8ddd\u79bb\u7684\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>nep.txt</code></p> <pre><code>gpumdkit.sh -plt dimer &lt;element1&gt; &lt;element2&gt; &lt;nep_model&gt;\ngpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>\u53c2\u8003\u6587\u732e\uff1a J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_doaspy","title":"plt_doas.py","text":"<p>\u7ed8\u5236 Wang et al. \u63d0\u51fa\u7684\u539f\u5b50\u6001\u5bc6\u5ea6 (DOAS)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>doas.out</code>\uff08\u7531 <code>gpumdkit.sh -calc doas</code> \u8ba1\u7b97\uff09</p> <pre><code>gpumdkit.sh -plt doas &lt;doas.out&gt; &lt;species&gt;\ngpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plane-grid","title":"\u6781\u6027\u6750\u6599\u7684 Plane-Grid \u7ed8\u56fe","text":"<p>\u6b64\u5de5\u4f5c\u6d41\u5c06\u4f4d\u79fb\u6216\u6781\u5316\u6570\u636e\u6620\u5c04\u5230\u7f51\u683c\u4e0a\uff0c\u5e76\u7ed8\u5236\u9009\u5b9a\u5e73\u9762\u7684\u8f6e\u5ed3\u3002\u8be6\u7ec6\u7528\u6cd5\u548c\u5b9e\u9645\u6848\u4f8b\u8bf7\u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790\u3002</p> <p>\u4f9d\u8d56\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>\u5178\u578b\u524d\u7f6e\u6b65\u9aa4\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>\u4f7f\u7528\u65b9\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_7","title":"\u5feb\u901f\u53c2\u8003\u8868","text":"\u547d\u4ee4 \u8f93\u5165\u6587\u4ef6 \u7528\u9014 <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP \u8bad\u7ec3\u7ed3\u679c <code>prediction</code> / <code>test</code> <code>*_test.out</code> NEP \u9884\u6d4b\u7ed3\u679c <code>train_test</code> <code>*_train.out</code>, <code>*_test.out</code> \u5408\u5e76 parity plot <code>parity_density</code> <code>*_train.out</code> \u5bc6\u5ea6 parity plot <code>force_errors</code> <code>force_train.out</code> \u529b\u8bef\u5dee\u6307\u6807 <code>lr</code> <code>loss.out</code> (gnep) \u5b66\u4e60\u7387 <code>restart</code> <code>nep.restart</code> \u91cd\u542f\u6587\u4ef6\u53c2\u6570 <code>charge</code> <code>charge_train.out</code> \u7535\u8377\u5206\u5e03 <code>born_charge</code> / <code>bec</code> <code>bec_train.out</code>, <code>bec_test.out</code> Born \u6709\u6548\u7535\u8377 <code>thermo</code> <code>thermo.out</code> \u70ed\u529b\u5b66\u91cf <code>msd</code> <code>msd.out</code> \u5747\u65b9\u4f4d\u79fb <code>msd_all</code> <code>msd.out</code> (all_groups) \u5168\u7ec4\u5206 MSD <code>msd_conv</code> <code>msd_step*.out</code> MSD \u6536\u655b\u6027\u68c0\u67e5 <code>sdc</code> <code>msd.out</code> \u81ea\u6269\u6563\u7cfb\u6570 <code>arrhenius_d</code> / <code>D</code> <code>*K/msd.out</code> Arrhenius \u6269\u6563\u7cfb\u6570 <code>arrhenius_sigma</code> / <code>sigma</code> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> Arrhenius \u79bb\u5b50\u7535\u5bfc\u7387 <code>rdf</code> <code>rdf.out</code> \u5f84\u5411\u5206\u5e03\u51fd\u6570 <code>rdf_pmf</code> <code>rdf.out</code> RDF + \u5e73\u5747\u529b\u52bf <code>vac</code> <code>sdc.out</code> \u901f\u5ea6\u81ea\u76f8\u5173 <code>cohesive</code> <code>cohesive.out</code> \u5185\u805a\u80fd\u66f2\u7ebf <code>net_force</code> <code>train.xyz</code> \u51c0\u529b\u5206\u5e03 <code>doas</code> <code>doas.out</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>des</code> <code>descriptors.npy</code> \u63cf\u8ff0\u7b26 PCA/UMAP <code>dimer</code> <code>nep.txt</code> \u4e8c\u805a\u4f53\u80fd\u91cf/\u529b\u66f2\u7ebf <code>pdos</code> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code> VAC \u548c PDOS <code>emd</code> EMD \u8f93\u51fa EMD \u70ed\u5bfc\u7387 <code>nemd</code> NEMD \u8f93\u51fa NEMD \u70ed\u8f93\u8fd0 <code>hnemd</code> HNEMD \u8f93\u51fa HNEMD \u70ed\u8f93\u8fd0 <code>viscosity</code> \u7c98\u5ea6\u8f93\u51fa \u7c98\u5ea6"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html","title":"\u81ea\u5b9a\u4e49\u547d\u4ee4","text":"\ud83d\udd27 \u81ea\u5b9a\u4e49\u547d\u4ee4 <p>GPUMDkit \u652f\u6301\u4ece ~/.gpumdkit.in \u52a0\u8f7d\u81ea\u5b9a\u4e49\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u628a\u5e38\u7528\u811a\u672c\u6216\u5de5\u4f5c\u6d41\u5c01\u88c5\u6210 <code>custom_</code> \u5f00\u5934\u7684 Bash \u51fd\u6570\uff0c\u7136\u540e\u901a\u8fc7 <code>gpumdkit.sh -\u547d\u4ee4\u540d</code> \u8c03\u7528\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_1","title":"\u8bbe\u7f6e","text":"<p>\u7f16\u8f91\u914d\u7f6e\u6587\u4ef6\uff1a</p> <pre><code>vi ~/.gpumdkit.in\n</code></pre> <p>\u81ea\u5b9a\u4e49\u51fd\u6570\u9700\u8981\u4f7f\u7528 <code>custom_</code> \u524d\u7f00\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_2","title":"\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_3","title":"\u7b80\u5355\u95ee\u5019","text":"<p>\u5728 <code>~/.gpumdkit.in</code> \u4e2d\u5199\u5165\uff1a</p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>\u7136\u540e\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -hello\n</code></pre> <p>\u4f60\u4f1a\u770b\u5230\u7c7b\u4f3c\u8f93\u51fa\uff1a</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_4","title":"\u5e26\u5fc5\u9700\u53c2\u6570\u7684\u547d\u4ee4","text":"<pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -greet Zihan\n</code></pre> <p>\u8f93\u51fa\uff1a</p> <pre><code>Hello, Zihan!\n</code></pre> <p>\u4f20\u9012\u53c2\u6570\u65f6\uff0c\u53ef\u4ee5\u7528 <code>\"$@\"</code> \u5b89\u5168\u5730\u8f6c\u53d1\u6240\u6709\u53c2\u6570\uff1b\u5982\u679c\u9700\u8981\u4ece\u7b2c\u4e00\u4e2a\u53c2\u6570\u5f00\u59cb\u5f15\u7528\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528 <code>${@:1}</code>\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_5","title":"\u8c03\u7528\u5916\u90e8\u811a\u672c","text":"<p>\u5982\u679c\u5e0c\u671b\u50cf\u8c03\u7528 GPUMDkit \u5185\u7f6e\u547d\u4ee4\u4e00\u6837\u8c03\u7528\u81ea\u5df1\u7684\u811a\u672c\uff1a</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -nepanalyse\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_6","title":"\u8fdb\u9636\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_7","title":"\u6279\u5904\u7406\u7ed8\u56fe","text":"<p>\u5bf9\u591a\u4e2a\u76ee\u5f55\u6279\u91cf\u7ed8\u56fe\uff1a</p> <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -batch_plot dir1 dir2 dir3\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_8","title":"\u8bad\u7ec3\u96c6\u5206\u6790\u6d41\u7a0b","text":"<p>\u628a\u591a\u4e2a\u5206\u6790\u547d\u4ee4\u7ec4\u5408\u6210\u4e00\u4e2a\u5165\u53e3\uff1a</p> <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -analyze_training train.xyz\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_9","title":"\u81ea\u5b9a\u4e49\u6570\u636e\u51c6\u5907\u6d41\u7a0b","text":"<pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    gpumdkit.sh -out2xyz ./\n    gpumdkit.sh -filter_value train.xyz force 30\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -prep_training\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_10","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u547d\u4ee4\u540d\u5c3d\u91cf\u6e05\u695a\uff0c\u4f8b\u5982 <code>custom_analyze_training</code> \u6bd4 <code>custom_at</code> \u66f4\u5bb9\u6613\u7ef4\u62a4\u3002</li> <li>\u5bf9\u9700\u8981\u53c2\u6570\u7684\u547d\u4ee4\uff0c\u5efa\u8bae\u5728\u53c2\u6570\u4e3a\u7a7a\u65f6\u6253\u5370\u7528\u6cd5\u63d0\u793a\u3002</li> <li>\u8c03\u7528\u5916\u90e8\u811a\u672c\u65f6\uff0c\u5c3d\u91cf\u7528 <code>\"$@\"</code> \u4fdd\u7559\u53c2\u6570\u4e2d\u7684\u7a7a\u683c\u548c\u7279\u6b8a\u5b57\u7b26\u3002</li> <li>\u6279\u5904\u7406\u76ee\u5f55\u65f6\uff0c\u6ce8\u610f\u4f7f\u7528 <code>cd \"$dir\"</code>\uff0c\u907f\u514d\u8def\u5f84\u4e2d\u6709\u7a7a\u683c\u65f6\u51fa\u9519\u3002</li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html","title":"\u8ba1\u7b97\u5668\u811a\u672c","text":"\ud83e\uddee \u8ba1\u7b97\u5668\u811a\u672c <p>\u8ba1\u7b97\u5668\u6a21\u5757\u7528\u4e8e\u4ece MD \u8f68\u8ff9\u3001NEP \u6a21\u578b\u548c\u7ed3\u6784\u6587\u4ef6\u4e2d\u8ba1\u7b97\u6750\u6599\u6027\u8d28\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code></p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_1","title":"\u529f\u80fd\u6982\u89c8","text":"\u4efb\u52a1 \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u79bb\u5b50\u7535\u5bfc\u7387 <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>\u3001<code>thermo.out</code>\u3001<code>model.xyz</code> MSD <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz \u8f68\u8ff9 NEP \u9884\u6d4b <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP \u6a21\u578b NEP \u63cf\u8ff0\u7b26 <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP \u6a21\u578b DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP \u6a21\u578b NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u521d\u672b\u6001\u7ed3\u6784 \u7ed3\u6784\u4f18\u5316 <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784 + NEP \u6a21\u578b \u90bb\u5c45\u5217\u8868 <code>gpumdkit.sh -calc nlist ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u4f4d\u79fb <code>gpumdkit.sh -calc disp ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u5e73\u5747\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u516b\u9762\u4f53\u503e\u8f6c <code>gpumdkit.sh -calc oct-tilt ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u67e5\u770b\u5b8c\u6574\u5e2e\u52a9\uff1a</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>\u547d\u4ee4\u884c\u5e2e\u52a9\u8868\u7c7b\u4f3c\uff1a</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>4) Calculators</code>\uff0c\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_2","title":"\u79bb\u5b50\u7535\u5bfc\u7387","text":"<pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>401</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>\u5e38\u7528\u8f93\u5165\u6587\u4ef6\uff1a</p> \u6587\u4ef6 \u4f5c\u7528 <code>msd.out</code> \u5fc5\u9700\uff0cMSD \u6570\u636e <code>thermo.out</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u6e29\u5ea6 <code>model.xyz</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u4f53\u79ef\u548c\u79bb\u5b50\u6570 <code>run.in</code> \u53ef\u9009\uff0c\u8bc6\u522b\u6269\u80de\u4fe1\u606f <p>\u5982\u679c\u7f3a\u5c11\u81ea\u52a8\u8bc6\u522b\u6240\u9700\u6587\u4ef6\uff0c\u811a\u672c\u4f1a\u4ea4\u4e92\u5f0f\u8be2\u95ee\u6e29\u5ea6\u3001\u4f53\u79ef\u548c\u79bb\u5b50\u6570\u3002</p> <p>\u624b\u52a8\u6a21\u5f0f\u7684\u63d0\u793a\u7c7b\u4f3c\uff1a</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#msd","title":"\u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD","text":"<pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>412</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>Li</code> \u76ee\u6807\u6269\u6563\u5143\u7d20 <code>10</code> \u5e27\u95f4\u9694\uff0c\u5355\u4f4d fs <code>5000</code> \u53ef\u9009\uff0c\u6700\u5927\u76f8\u5173\u6b65\u6570 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>msd.out</code></li> </ul> <p>\u968f\u540e\u53ef\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u9884\u6d4b\u6027\u8d28","text":"<p><code>calc_properties_with_nep.py</code> \u4f7f\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8ba1\u7b97\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u3002</p> <p>\u4f9d\u8d56\uff1a <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>\u4f7f\u7528\u6b64\u529f\u80fd\u53ef\u4ee5\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8fdb\u884c\u9884\u6d4b\u3002\u5efa\u8bae\u5728\u4f7f\u7528\u524d\u5148\u9a8c\u8bc1\u6a21\u578b\u5728\u76ee\u6807\u7ed3\u6784\u4e0a\u7684\u9884\u6d4b\u8d28\u91cf\u3002</p> <p>\u63d0\u793a\uff1a \u9884\u6d4b\u524d\u53ef\u4ee5\u6e05\u7406 extxyz \u5143\u6570\u636e\uff1a</p> <pre><code>gpumdkit.sh -clean_xyz train.xyz clean_train.xyz\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep_1","title":"NEP \u63cf\u8ff0\u7b26","text":"<pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>\u7528\u9014\u5305\u62ec\uff1a</p> <ul> <li>\u7528 PCA/UMAP \u53ef\u89c6\u5316\u5c40\u57df\u73af\u5883\uff1b</li> <li>\u6bd4\u8f83\u8bad\u7ec3\u96c6\u548c\u5019\u9009\u7ed3\u6784\uff1b</li> <li>\u5224\u65ad\u65b0\u6570\u636e\u662f\u5426\u6269\u5c55\u4e86\u63cf\u8ff0\u7b26\u7a7a\u95f4\u3002</li> </ul> <p>\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#doas","title":"DOAS","text":"<p><code>calc_doas.py</code> \u7528\u4e8e\u8ba1\u7b97 Wang et al. \u63d0\u51fa\u7684 density of atomistic states\u3002</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>\u811a\u672c\u4f1a\uff1a</p> <ol> <li>\u8bfb\u53d6\u6240\u6709\u7ed3\u6784\uff1b</li> <li>\u4f7f\u7528 NEP \u8fdb\u884c\u7ed3\u6784\u4f18\u5316\uff1b</li> <li>\u63d0\u53d6\u6bcf\u4e2a\u539f\u5b50\u7684\u80fd\u91cf\uff1b</li> <li>\u6309\u5143\u7d20\u5206\u7ec4\u8f93\u51fa\uff1b</li> <li>\u7528\u7ed8\u56fe\u811a\u672c\u53ef\u89c6\u5316\u5206\u5e03\u3002</li> </ol>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#neb","title":"NEB \u548c\u7ed3\u6784\u4f18\u5316","text":"<p>NEB\uff1a</p> <pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>\u7ed3\u6784\u4f18\u5316\uff08\u901a\u8fc7 <code>calorine</code>\uff09\uff1a</p> <p>\u4f9d\u8d56\uff1a <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>\u8f93\u51fa\u5305\u62ec\uff1a</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#ovito-rdf","title":"\u4f7f\u7528 OVITO \u8ba1\u7b97 RDF","text":"<p><code>rdf_calculator_ovito.py</code> \u4f7f\u7528 OVITO \u7684\u5206\u6790\u5de5\u5177\u8ba1\u7b97\u5f84\u5411\u5206\u5e03\u51fd\u6570\u3002</p> <p>\u4f9d\u8d56\uff1a OVITO</p> <pre><code>pip install ovito\n</code></pre> <p>\u8f93\u5165\u6587\u4ef6\uff1a \u7ed3\u6784\u6587\u4ef6\uff08\u5355\u5e27\u6216\u8f68\u8ff9\uff09</p> <pre><code>python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400\n</code></pre> <p>\u53c2\u6570\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>trajectory.xyz</code> \u8f93\u5165\u7ed3\u6784\u6587\u4ef6 <code>6.0</code> RDF \u8ba1\u7b97\u7684\u6700\u5927\u8ddd\u79bb\uff08\u00c5\uff09 <code>400</code> \u76f4\u65b9\u56fe\u7684\u5206\u7bb1\u6570 <p>\u53ef\u89c6\u5316\uff1a</p> <pre><code>gpumdkit.sh -plt rdf\n</code></pre> <p>\u6ce8\u610f\uff1a \u5efa\u8bae\u4f18\u5148\u4f7f\u7528 GPUMD \u4e2d\u7684 <code>compute_rdf</code> \u547d\u4ee4\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_3","title":"\u94c1\u7535\u548c\u6781\u6027\u6750\u6599\u5de5\u5177","text":"<p>\u9009\u9879 <code>406\u2013410</code> \u6db5\u76d6\u9499\u949b\u77ff\u548c\u6781\u6027\u6750\u6599\u5206\u6790\uff1a\u8fd1\u90bb\u5217\u8868\u3001\u5c40\u57df\u4f4d\u79fb\u3001\u5e73\u5747\u7ed3\u6784\u3001\u516b\u9762\u4f53\u503e\u8f6c\u548c ABO3 \u6781\u5316\u3002\u8fd9\u4e9b\u5de5\u5177\u57fa\u4e8e <code>ferrodispcalc</code>\u3002</p> <p>\u4f9d\u8d56\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>\u5b8c\u6574\u53c2\u6570\u5217\u8868\u548c\u771f\u5b9e\u5de5\u4f5c\u6d41\u6848\u4f8b\uff08PbTiO3 \u76f8\u53d8\u3001PTO/STO \u8d85\u6676\u683c\u62d3\u6251\u7b49\uff09\u8bf7\u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html","title":"\u8d21\u732e\u6307\u5357","text":"\ud83e\udd1d \u4e3a GPUMDkit \u8d21\u732e\u4ee3\u7801 <p>\u611f\u8c22\u4f60\u6709\u5174\u8da3\u4e3a GPUMDkit \u505a\u51fa\u8d21\u732e\uff01\u6211\u4eec\u611f\u8c22\u4f60\u4e3a\u6539\u5584\u8fd9\u4e2a\u5de5\u5177\u5305\u6240\u4ed8\u51fa\u7684\u65f6\u95f4\u548c\u52aa\u529b\u3002</p> <p> English   \u00a0\u00b7\u00a0   \u7b80\u4f53\u4e2d\u6587 </p> <p><code>GPUMDkit</code> \u662f\u4e00\u4e2a\u5f00\u6e90\u9879\u76ee\uff0c\u6211\u4eec\u6b22\u8fce\u793e\u533a\u7684\u5404\u79cd\u8d21\u732e\uff0c\u65e0\u8bba\u662f\u4fee\u590d bug\u3001\u6dfb\u52a0\u65b0\u529f\u80fd\u3001\u6539\u8fdb\u6587\u6863\u8fd8\u662f\u63d0\u51fa\u5efa\u8bae\u3002</p> <p>\u6ce8\u610f\uff1a\u672c\u6587\u6863\u7684\u6743\u5a01\u7248\u672c\u4f4d\u4e8e\u4ed3\u5e93\u6839\u76ee\u5f55\u7684 <code>CONTRIBUTING.md</code>\u3002\u672c\u6559\u7a0b\u9875\u9762\u540c\u6b65\u5176\u5185\u5bb9\u3002\u4e2d\u6587\u7248\u8bf7\u53c2\u89c1 <code>docs/CONTRIBUTING_zh-CN.md</code>\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_1","title":"\u76ee\u5f55","text":"<ul> <li>\u5f00\u53d1\u89c4\u8303\u4e0e\u51c6\u5219</li> <li>\u62a5\u544a\u95ee\u9898</li> <li>\u529f\u80fd\u5efa\u8bae</li> <li>\u8d21\u732e\u4ee3\u7801</li> <li>Fork \u5e76\u514b\u9686\u4ed3\u5e93</li> <li>\u521b\u5efa\u529f\u80fd\u5206\u652f</li> <li>\u8fdb\u884c\u4fee\u6539<ul> <li>\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e</li> <li>\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e</li> <li>\u66f4\u65b0 Tab \u8865\u5168</li> </ul> </li> <li>\u4ee3\u7801\u98ce\u683c\u4e0e\u6700\u4f73\u5b9e\u8df5</li> <li>\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539</li> <li>\u63d0\u4ea4\u4fe1\u606f</li> <li>\u63a8\u9001\u5e76\u521b\u5efa Pull Request</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_2","title":"\u5f00\u53d1\u89c4\u8303\u4e0e\u51c6\u5219","text":"<p>\u4e3a\u4fdd\u6301\u4ee3\u7801\u8d28\u91cf\u548c\u9879\u76ee\u4e00\u81f4\u6027\uff0c\u8bf7\u9075\u5faa\u4ee5\u4e0b\u51c6\u5219\uff1a</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_3","title":"\u8bed\u8a00\u8981\u6c42","text":"<ul> <li>\u6240\u6709\u4ee3\u7801\u5e94\u4f7f\u7528\u82f1\u6587\u7f16\u5199\uff1a\u5305\u62ec\u53d8\u91cf\u540d\u3001\u51fd\u6570\u540d\u3001\u6ce8\u91ca\u3001\u6587\u6863\u5b57\u7b26\u4e32\u3001\u63d0\u4ea4\u4fe1\u606f\u548c\u6587\u6863\u3002</li> <li>\u867d\u7136\u6211\u4eec\u7406\u89e3\u8d21\u732e\u8005\u6765\u81ea\u4e0d\u540c\u80cc\u666f\uff0c\u4f46\u4f7f\u7528\u82f1\u6587\u80fd\u786e\u4fdd\u4ee3\u7801\u5e93\u5bf9\u6700\u5e7f\u6cdb\u7684\u7528\u6237\u7fa4\u4f53\u53ef\u8bbf\u95ee\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_4","title":"\u6a21\u5757\u5316\u4e0e\u53ef\u590d\u7528\u6027","text":"<ul> <li>\u7f16\u5199\u6a21\u5757\u5316\u548c\u53ef\u590d\u7528\u7684\u4ee3\u7801\uff1a\u51fd\u6570\u548c\u811a\u672c\u7684\u8bbe\u8ba1\u5e94\u5177\u6709\u7075\u6d3b\u6027\u3002</li> <li>\u4f18\u5148\u4f20\u9012\u53c2\u6570\u800c\u975e\u786c\u7f16\u7801\u503c\uff1a\u4f7f\u7528\u51fd\u6570\u53c2\u6570\u3001\u547d\u4ee4\u884c\u53c2\u6570\u6216\u914d\u7f6e\u6587\u4ef6\u6765\u66ff\u4ee3\u786c\u7f16\u7801\u503c\u3002\u4f46\u67d0\u4e9b\u6587\u4ef6\u540d\u7531 GPUMD \u548c NEP \u7a0b\u5e8f\u56fa\u5b9a\u8981\u6c42\uff08\u5982 <code>train.xyz</code>\u3001<code>thermo.out</code>\uff09\uff0c\u8fd9\u4e9b\u53ef\u4ee5\u6309\u9700\u786c\u7f16\u7801\u3002</li> <li>\u793a\u4f8b\uff1a   <pre><code># \u597d\u7684\u505a\u6cd5\uff1a\u63a5\u53d7\u53c2\u6570\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # \u5904\u7406\u903b\u8f91\n}\n\n# \u907f\u514d\uff1a\u786c\u7f16\u7801\u503c\uff08\u9664\u975e GPUMD/NEP \u8981\u6c42\uff09\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # \u5904\u7406\u903b\u8f91\n}\n</code></pre></li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_5","title":"\u4ee3\u7801\u98ce\u683c","text":"<ul> <li>\u7f16\u5199\u6e05\u6670\u3001\u6613\u4e8e\u4ed6\u4eba\u7ef4\u62a4\u548c\u4fee\u6539\u7684\u4ee3\u7801\u3002</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u548c\u51fd\u6570\u540d\u3002</li> <li>\u5728\u5fc5\u8981\u5904\u6dfb\u52a0\u6ce8\u91ca\u4ee5\u89e3\u91ca\u590d\u6742\u903b\u8f91\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_6","title":"\u6587\u6863","text":"<ul> <li>\u786e\u4fdd\u5e2e\u52a9\u4fe1\u606f\uff08\u5982 <code>-h</code> \u6807\u5fd7\uff09\u6e05\u6670\u51c6\u786e\u3002</li> <li>\u6559\u7a0b\u6587\u6863\u4f4d\u4e8e <code>docs/tutorials/en/</code>\uff08\u82f1\u6587\uff09\u548c <code>docs/tutorials/zh/</code>\uff08\u4e2d\u6587\uff09\u3002\u5982\u679c\u4f60\u6dfb\u52a0\u4e86\u65b0\u529f\u80fd\uff0c\u8bf7\u8003\u8651\u66f4\u65b0\u76f8\u5173\u6559\u7a0b\u9875\u9762\u3002</li> <li>\u7f16\u8f91\u6559\u7a0b Markdown \u6587\u4ef6\u540e\uff0c\u4f7f\u7528 <code>mkdocs build -f docs/mkdocs.yml</code> \u91cd\u65b0\u6784\u5efa HTML\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_7","title":"\u62a5\u544a\u95ee\u9898","text":"<p>\u5982\u679c\u4f60\u9047\u5230 bug\uff0c\u8bf7\u901a\u8fc7 GitHub Issues \u5e2e\u52a9\u6211\u4eec\u4fee\u590d\uff1a</p> <ol> <li>\u641c\u7d22\u73b0\u6709 issues \u67e5\u770b\u8be5 bug \u662f\u5426\u5df2\u88ab\u62a5\u544a\u3002</li> <li>\u521b\u5efa\u65b0 issue\uff08\u5982\u679c\u5c1a\u672a\u88ab\u62a5\u544a\uff09\uff1a\u521b\u5efa Issue</li> <li>\u8be6\u7ec6\u63cf\u8ff0\u95ee\u9898\uff0c\u5982\u679c\u53ef\u80fd\u8bf7\u63d0\u4f9b\u6d4b\u8bd5\u6587\u4ef6\u3002</li> </ol> <p>\u4f60\u4e5f\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u65b9\u5f0f\u8054\u7cfb\u6211\u4eec\uff1a - QQ \u7fa4\uff1a825696376 - \u90ae\u7bb1\uff1ayanzihan@westlake.edu.cn - \u811a\u672c\u5f00\u53d1\u8005\uff1a\u8054\u7cfb\u811a\u672c\u5934\u90e8\u5217\u51fa\u7684\u5f00\u53d1\u8005</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_8","title":"\u529f\u80fd\u5efa\u8bae","text":"<p>\u6211\u4eec\u6b22\u8fce\u529f\u80fd\u5efa\u8bae\uff01\u63d0\u51fa\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u641c\u7d22\u73b0\u6709 issues \u67e5\u770b\u662f\u5426\u5df2\u6709\u4eba\u63d0\u51fa\u3002</li> <li>\u521b\u5efa\u65b0\u529f\u80fd\u8bf7\u6c42\uff1a\u521b\u5efa\u529f\u80fd\u8bf7\u6c42 \u5e76 mention @zhyan0603</li> <li>\u6e05\u695a\u63cf\u8ff0\u4f60\u7684\u9700\u6c42 \u5e76\u89e3\u91ca\u5176\u7528\u9014\u3002</li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_9","title":"\u8d21\u732e\u4ee3\u7801","text":""},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#fork","title":"Fork \u5e76\u514b\u9686\u4ed3\u5e93","text":"<ol> <li> <p>\u5728 GitHub \u4e0a Fork \u4ed3\u5e93\uff0c\u70b9\u51fb \u4ed3\u5e93\u9875\u9762 \u53f3\u4e0a\u89d2\u7684 \"Fork\" \u6309\u94ae\u3002</p> </li> <li> <p>\u514b\u9686\u4f60\u7684 fork \u5230\u672c\u5730\uff1a</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>\u8bbe\u7f6e upstream remote \u4ee5\u4fdd\u6301 fork \u540c\u6b65\uff1a    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_10","title":"\u521b\u5efa\u529f\u80fd\u5206\u652f","text":"<p>\u4e3a\u4f60\u7684\u4fee\u6539\u521b\u5efa\u65b0\u5206\u652f\uff1a</p> <pre><code># \u4ece main \u521b\u5efa\u5e76\u5207\u6362\u5230\u65b0\u5206\u652f\ngit checkout -b your-branch-name\n</code></pre> <p>\u5206\u652f\u540d\u79f0\u968f\u610f\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_11","title":"\u8fdb\u884c\u4fee\u6539","text":"<p><code>GPUMDkit</code> \u7684\u7ed3\u6784\u5305\u62ec\uff1a - <code>gpumdkit.sh</code>\uff1a\u4e3b\u5165\u53e3\uff08Bash \u811a\u672c\uff09\uff0c\u5904\u7406\u4ea4\u4e92\u83dc\u5355\u6a21\u5f0f\u548c\u547d\u4ee4\u884c\u6a21\u5f0f - <code>install.sh</code>\uff1a\u5b89\u88c5\u811a\u672c\uff0c\u8bbe\u7f6e\u73af\u5883\u53d8\u91cf\u548c shell \u914d\u7f6e - <code>Scripts/</code>\uff1a\u6309\u529f\u80fd\u7ec4\u7ec7\u7684 Python \u548c Bash \u5b9e\u73b0\u811a\u672c   - <code>plt_scripts/</code>\uff1a\u7ed8\u56fe\u811a\u672c   - <code>calculators/</code>\uff1a\u8ba1\u7b97\u5de5\u5177   - <code>format_conversion/</code>\uff1a\u683c\u5f0f\u8f6c\u6362\u5de5\u5177   - <code>workflow/</code>\uff1a\u5de5\u4f5c\u6d41\u81ea\u52a8\u5316   - <code>sample_structures/</code>\uff1a\u7ed3\u6784\u91c7\u6837\u5de5\u5177   - <code>analyzer/</code>\uff1a\u5206\u6790\u5de5\u5177   - <code>utils/</code>\uff1a\u5b9e\u7528\u51fd\u6570\uff08\u5305\u62ec <code>completion.sh</code> Tab \u8865\u5168\uff09 - <code>src/</code>\uff1a\u4ea4\u4e92\u6a21\u5f0f\u83dc\u5355\u51fd\u6570\u7684 Shell \u811a\u672c   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>skills/</code>\uff1aAI agent \u6280\u80fd\u5b9a\u4e49\uff08\u7528\u4e8e opencode/Claude Code \u96c6\u6210\u7684 SKILL.md \u6587\u4ef6\uff09 - <code>docs/</code>\uff1a\u6587\u6863\u6587\u4ef6   - <code>tutorials/en/</code> \u548c <code>tutorials/zh/</code>\uff1a\u53cc\u8bed\u6559\u7a0b\u9875\u9762   - <code>mkdocs.yml</code>\uff1a\u6784\u5efa\u6559\u7a0b HTML \u7684 MkDocs \u914d\u7f6e   - <code>command_reference.tsv</code>\uff1a\u673a\u5668\u53ef\u8bfb\u7684\u547d\u4ee4\u53c2\u8003   - <code>htmls/</code>\uff1aMkDocs \u751f\u6210\u7684 HTML \u8f93\u51fa</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_12","title":"\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e","text":"<p>\u8981\u6dfb\u52a0\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u8bbf\u95ee\u7684\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u5728\u76f8\u5e94\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a</li> </ol> <pre><code># \u793a\u4f8b\uff1a\u6dfb\u52a0\u65b0\u7684\u683c\u5f0f\u8f6c\u6362\u811a\u672c\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u9075\u5faa\u6a21\u5757\u5316\u51c6\u5219\uff08\u63a5\u53d7\u53c2\u6570\uff0c\u907f\u514d\u786c\u7f16\u7801\uff09\u3002</p> </li> <li> <p>\u5728\u76f8\u5e94\u7684 <code>src/</code> \u6587\u4ef6\u4e2d\u6dfb\u52a0\u5305\u88c5\u51fd\u6570\uff1a    <pre><code># \u793a\u4f8b\uff1a\u7f16\u8f91 src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>\u6dfb\u52a0\u65b0\u51fd\u6570\uff1a    <pre><code>function f111_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input &lt;required_param1&gt; &lt;required_param2&gt;\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -r -a converter_args\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py \"${converter_args[@]}\"\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u66f4\u65b0\u83dc\u5355\u663e\u793a\uff1a    <pre><code># \u627e\u5230 menu() \u51fd\u6570\u5e76\u6309\u9700\u66f4\u65b0\n# \u627e\u5230 array_choice \u6570\u7ec4\u5e76\u6dfb\u52a0\u4f60\u7684\u65b0\u9009\u62e9\u7f16\u53f7\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\" \"107\" \"108\" \"109\" \"110\" \"111\"  # \u6dfb\u52a0 \"111\"\n    # ... \u5176\u4f59\u9009\u62e9\n)\n</code></pre></p> </li> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0 case \u8bed\u53e5\uff1a    <pre><code># \u5728 main() \u51fd\u6570\u4e2d\u627e\u5230\u76f8\u5e94\u7684 case \u8bed\u53e5\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n            \"101\") f101_out2xyz ;;\n            # ... \u73b0\u6709 case ...\n            \"111\") f111_new_converter ;;  # \u6dfb\u52a0\u4f60\u7684 case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_13","title":"\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e","text":"<p>\u8981\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c\u6807\u5fd7\u6216\u5b50\u547d\u4ee4\uff1a</p> <ol> <li> <p>\u5728\u76f8\u5e94\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a    <pre><code># \u793a\u4f8b\uff1a\u6dfb\u52a0\u65b0\u7684\u5206\u6790\u5668\u811a\u672c\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u660e\u786e\u53c2\u6570\u8981\u6c42\uff1a    <pre><code># \u793a\u4f8b\uff1aScripts/analyzer/analyze_bonds.py\nimport sys\n\nif len(sys.argv) != 3:\n    print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n    print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n    sys.exit(1)\n\ninput_file = sys.argv[1]\ncutoff = float(sys.argv[2])\n\n# \u4f60\u7684\u5b9e\u73b0\n</code></pre></p> </li> </ol> <p>\u6ce8\u610f\uff1aGPUMDkit Python \u811a\u672c\u8bbe\u8ba1\u4e3a\u76f4\u63a5\u8fd0\u884c\uff08\u4e0d\u4f5c\u4e3a\u6a21\u5757\u5bfc\u5165\uff09\u3002 \u5982\u679c\u4f60\u613f\u610f\uff0c\u53ef\u4ee5\u4f7f\u7528 <code>main()</code> \u51fd\u6570\u914d\u5408 <code>if __name__ == \"__main__\":</code> \u4fdd\u62a4\uff0c \u4f46\u8fd9\u4e0d\u662f\u5fc5\u9700\u7684\u3002\u5927\u591a\u6570\u73b0\u6709\u811a\u672c\u5728\u6a21\u5757\u7ea7\u522b\u6267\u884c\u3002</p> <ol> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0\u547d\u4ee4\u884c\u6807\u5fd7\u5904\u7406\uff1a    <pre><code># \u627e\u5230\u547d\u4ee4\u884c\u89e3\u6790\u90e8\u5206\uff08\u5927\u7684 \"case $1 in\" \u5757\uff09\n# \u5728\u9002\u5f53\u4f4d\u7f6e\u6dfb\u52a0\u4f60\u7684\u65b0\u6807\u5fd7\n\ncase $1 in\n    # ... \u73b0\u6709 case ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ \"$2\" != \"-h\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py $2 $3\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n        fi ;;\n    # ... \u5176\u4f59 case ...\nesac\n</code></pre></p> </li> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u66f4\u65b0\u5e2e\u52a9\u4fe1\u606f\uff1a    <pre><code># \u627e\u5230 help_info_table() \u51fd\u6570\u5e76\u6dfb\u52a0\u4f60\u7684\u547d\u4ee4\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... \u5176\u4f59\u5e2e\u52a9\u8868 ...\n}\n</code></pre></p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#tab","title":"\u66f4\u65b0 Tab \u8865\u5168","text":"<p>\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c\u6807\u5fd7\u65f6\uff0c\u66f4\u65b0 Tab \u8865\u5168\u811a\u672c\uff1a</p> <pre><code># \u7f16\u8f91 Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>\u5c06\u4f60\u7684\u65b0\u6807\u5fd7\u6dfb\u52a0\u5230 <code>opts</code> \u53d8\u91cf\uff1a <pre><code># \u627e\u5230 local opts=... \u884c\nlocal opts=\"-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...\"\n#                                                        \u5728\u6b64\u6dfb\u52a0\u4f60\u7684\u6807\u5fd7\n</code></pre></p> <p>\u5982\u679c\u4f60\u7684\u6807\u5fd7\u9700\u8981\u6587\u4ef6\u53c2\u6570\uff0c\u5c06\u5176\u6dfb\u52a0\u5230\u73b0\u6709\u7684\u6587\u4ef6\u8865\u5168 case \u4e2d\uff1a <pre><code># \u627e\u5230\u9700\u8981\u6587\u4ef6\u53c2\u6570\u7684 case \u5e76\u7528 | \u6dfb\u52a0\u4f60\u7684\u6807\u5fd7\n-out2xyz|-out2exyz|-...|-your_new_flag)\n    COMPREPLY=($(compgen -f -- \"$cur\")) ;;\n</code></pre></p> <p>\u5982\u679c\u4f60\u7684\u6807\u5fd7\u63a5\u53d7\u4e8c\u7ea7\u9009\u9879\uff08\u5982 <code>-plt</code> \u6216 <code>-calc</code>\uff09\uff0c\u6dfb\u52a0\u65b0 case\uff1a <pre><code>case \"$prev\" in\n    # ... \u73b0\u6709 case ...\n    -your_new_flag)\n        COMPREPLY=($(compgen -W \"option1 option2 option3\" -- \"$cur\")) ;;\n    # ... \u5176\u4f59 case ...\nesac\n</code></pre></p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_14","title":"\u4ee3\u7801\u98ce\u683c\u4e0e\u6700\u4f73\u5b9e\u8df5","text":"<ul> <li>Shell \u811a\u672c\uff1a</li> <li>\u4f7f\u7528 <code>${variable}</code> \u8fdb\u884c\u53d8\u91cf\u5c55\u5f00</li> <li>\u4f7f\u7528 <code>[ ! -z \"$var\" ]</code> \u8fdb\u884c\u975e\u7a7a\u68c0\u67e5\uff08\u9879\u76ee\u7ea6\u5b9a\uff09</li> <li>\u4ea4\u4e92\u51fd\u6570\u5e94\u9075\u5faa banner \u683c\u5f0f\uff1a     <pre><code>echo \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/&lt;category&gt;        |\"\necho \" | Script: &lt;script_name&gt;.py                        |\"\necho \" | Developer: &lt;Name&gt; (&lt;email&gt;)                     |\"\necho \" &gt;-------------------------------------------------&lt;\"\n</code></pre></li> <li>\u4f7f\u7528 <code>read -r -a varname</code> \u8bfb\u53d6\u591a\u8bcd\u8f93\u5165\uff0c\u7136\u540e\u7528 <code>\"${varname[@]}\"</code> \u4f20\u9012</li> <li> <p><code>src/</code> \u4e2d\u7684 Shell \u811a\u672c\u5e94\u4ee5\u6587\u4ef6\u5934\u6ce8\u91ca\u5757\u5f00\u59cb\uff1a     <pre><code># ============================================================\n# GPUMDkit &lt;module name&gt; module\n# Repository: https://github.com/zhyan0603/GPUMDkit\n# Author: &lt;Name&gt; (&lt;email&gt;)\n# ============================================================\n</code></pre></p> </li> <li> <p>Python \u811a\u672c\uff1a</p> </li> <li>\u7f16\u5199\u6e05\u6670\u3001\u53ef\u7ef4\u62a4\u7684\u4ee3\u7801</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u540d</li> <li>\u4f7f\u7528 <code>sys.argv</code> \u8fdb\u884c\u53c2\u6570\u89e3\u6790\uff08\u4e0e\u5927\u591a\u6570\u73b0\u6709\u811a\u672c\u4e00\u81f4\uff09</li> <li>\u63d0\u4f9b\u6e05\u6670\u7684\u4f7f\u7528\u4fe1\u606f\uff1a<code>print(\"Usage: ...\")</code> \u548c <code>print(\"Example: ...\")</code></li> <li>\u5982\u679c\u4f60\u7684\u811a\u672c\u4f7f\u7528\u91cd\u578b/\u7279\u6b8a\u5305\uff08<code>NepTrain</code>\u3001<code>calorine</code>\u3001<code>dpdata</code>\uff09\uff0c\u8bf7\u6dfb\u52a0     <code>print_dependency_notice()</code> \u51fd\u6570\u4ee5\u901a\u77e5\u7528\u6237\u5f15\u7528\u5efa\u8bae</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_15","title":"\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539","text":"<p>\u63d0\u4ea4\u8d21\u732e\u524d\uff0c\u8fd0\u884c\u76f8\u5173\u9a8c\u8bc1\u547d\u4ee4\uff1a</p> <pre><code># Shell \u8bed\u6cd5\u68c0\u67e5\uff08\u59cb\u7ec8\u8fd0\u884c\uff09\nbash -n gpumdkit.sh\nfind src Scripts -name '*.sh' -exec bash -n {} +\n\n# Python \u8bed\u6cd5\u68c0\u67e5\uff08\u9488\u5bf9\u4fee\u6539\u7684 Python \u6587\u4ef6\uff09\npython3 -m py_compile path/to/modified_script.py\n\n# MkDocs \u6784\u5efa\uff08\u5982\u679c\u4fee\u6539\u4e86\u6587\u6863\uff09\nmkdocs build -f docs/mkdocs.yml\n\n# \u68c0\u67e5\u5c3e\u968f\u7a7a\u683c\u95ee\u9898\ngit diff --check\n</code></pre> <p>\u7136\u540e\u6d4b\u8bd5\u529f\u80fd\uff1a</p> <ol> <li> <p>\u6d4b\u8bd5\u4ea4\u4e92\u6a21\u5f0f\uff08\u5982\u9002\u7528\uff09\uff1a    <pre><code>gpumdkit.sh\n# \u5bfc\u822a\u5230\u4f60\u7684\u65b0\u529f\u80fd\u5e76\u5145\u5206\u6d4b\u8bd5\n</code></pre></p> </li> <li> <p>\u6d4b\u8bd5\u547d\u4ee4\u884c\u6a21\u5f0f\uff08\u5982\u9002\u7528\uff09\uff1a    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # \u6d4b\u8bd5\u5e2e\u52a9\u4fe1\u606f\n</code></pre></p> </li> <li> <p>\u6d4b\u8bd5 Tab \u8865\u5168\uff08\u5982\u679c\u4f60\u4fee\u6539\u4e86 <code>completion.sh</code>\uff09\uff1a    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # \u5e94\u663e\u793a\u4f60\u7684\u65b0\u6807\u5fd7\n</code></pre></p> </li> <li> <p>\u7528\u5404\u79cd\u8f93\u5165\u6d4b\u8bd5\uff1a</p> </li> <li>\u7528\u5178\u578b\u8f93\u5165\u6d4b\u8bd5</li> <li>\u7528\u8fb9\u7f18\u60c5\u51b5\u6d4b\u8bd5\uff08\u7a7a\u6587\u4ef6\u3001\u5927\u6587\u4ef6\u7b49\uff09</li> <li> <p>\u6d4b\u8bd5\u9519\u8bef\u5904\u7406\uff08\u7f3a\u5c11\u6587\u4ef6\u3001\u65e0\u6548\u53c2\u6570\uff09</p> </li> <li> <p>\u9a8c\u8bc1\u65e0\u56de\u5f52\uff1a\u786e\u4fdd\u73b0\u6709\u529f\u80fd\u4ecd\u7136\u6b63\u5e38\u5de5\u4f5c\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_16","title":"\u63d0\u4ea4\u4fe1\u606f","text":"<p>\u7f16\u5199\u6e05\u6670\u3001\u63cf\u8ff0\u6027\u7684\u63d0\u4ea4\u4fe1\u606f\u6765\u89e3\u91ca\u4f60\u505a\u4e86\u4ec0\u4e48\u66f4\u6539\u3002\u6ca1\u6709\u4e25\u683c\u7684\u683c\u5f0f\u8981\u6c42\u2014\u2014\u53ea\u8981\u786e\u4fdd\u4f60\u7684\u4fe1\u606f\u662f\u53ef\u7406\u89e3\u7684\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#pull-request","title":"\u63a8\u9001\u5e76\u521b\u5efa Pull Request","text":"<ol> <li> <p>\u63d0\u4ea4\u4f60\u7684\u4fee\u6539\uff1a    <pre><code>git add .\ngit commit -m \"\u4f60\u7684\u63cf\u8ff0\u6027\u4fe1\u606f\"\n</code></pre></p> </li> <li> <p>\u4fdd\u6301\u4f60\u7684\u5206\u652f\u4e0e\u6700\u65b0\u7684 <code>dev</code> \u5206\u652f\u540c\u6b65\uff1a    <pre><code>git fetch origin\ngit rebase origin/dev\n</code></pre></p> </li> <li> <p>\u63a8\u9001\u4f60\u7684\u5206\u652f\u5230\u4f60\u7684 fork\uff1a    <pre><code>git push origin your-branch-name\n</code></pre></p> </li> <li> <p>\u521b\u5efa Pull Request\uff1a</p> </li> <li>\u524d\u5f80 GPUMDkit \u4ed3\u5e93</li> <li>\u70b9\u51fb \"Pull Requests\" \u2192 \"New Pull Request\"</li> <li>\u8bbe\u7f6e\u76ee\u6807\u5206\u652f\u4e3a <code>dev</code> \u8fdb\u884c\u4ee3\u7801\u5ba1\u67e5</li> <li>\u8bbe\u7f6e\u6bd4\u8f83\u5206\u652f\u4e3a\u4f60\u7684\u529f\u80fd\u5206\u652f</li> <li> <p>\u586b\u5199 PR \u63cf\u8ff0\uff1a</p> <ul> <li>\u6807\u9898\uff1a\u7b80\u8981\u63cf\u8ff0\u66f4\u6539</li> <li>\u63cf\u8ff0\uff1a\u8be6\u7ec6\u89e3\u91ca\u66f4\u6539\u5185\u5bb9\u548c\u539f\u56e0</li> <li>\u6d4b\u8bd5\uff1a\u63cf\u8ff0\u4f60\u5982\u4f55\u6d4b\u8bd5\u8fd9\u4e9b\u66f4\u6539</li> </ul> </li> <li> <p>\u56de\u5e94\u5ba1\u67e5\u53cd\u9988\uff1a</p> </li> <li>\u5bf9\u5efa\u8bae\u548c\u5efa\u8bbe\u6027\u6279\u8bc4\u4fdd\u6301\u5f00\u653e</li> <li>\u53ca\u65f6\u8fdb\u884c\u8bf7\u6c42\u7684\u4fee\u6539</li> <li> <p>\u63a8\u9001\u989d\u5916\u63d0\u4ea4\u5230\u4f60\u7684\u5206\u652f\uff08\u5b83\u4eec\u4f1a\u81ea\u52a8\u51fa\u73b0\u5728 PR \u4e2d\uff09</p> </li> <li> <p>\u6279\u51c6\u540e\uff1a\u7ef4\u62a4\u8005\u5c06\u5408\u5e76\u4f60\u7684 PR\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_17","title":"\u6709\u95ee\u9898\u6216\u9700\u8981\u5e2e\u52a9\uff1f","text":"<p>\u5982\u679c\u4f60\u5bf9\u8d21\u732e\u6709\u7591\u95ee\u6216\u9700\u8981\u5e2e\u52a9\uff1a</p> <ul> <li>\u53d1\u8d77\u8ba8\u8bba\uff1a\u4f7f\u7528 GitHub Discussions \u63d0\u51fa\u4e00\u822c\u6027\u95ee\u9898</li> <li>\u5728 issue \u4e2d\u63d0\u95ee\uff1a\u5728\u76f8\u5173 issue \u4e2d\u8bc4\u8bba\u4ee5\u83b7\u53d6\u5177\u4f53\u95ee\u9898\u7684\u5e2e\u52a9</li> <li>\u8054\u7cfb\u7ef4\u62a4\u8005\uff1a\u8054\u7cfb README \u4e2d\u5217\u51fa\u7684\u6838\u5fc3\u5f00\u53d1\u8005</li> </ul> <p>\u518d\u6b21\u611f\u8c22\u4f60\u4e3a <code>GPUMDkit</code> \u505a\u51fa\u8d21\u732e\uff01\u4f60\u7684\u52aa\u529b\u5e2e\u52a9\u8fd9\u4e2a\u5de5\u5177\u5305\u4e3a\u6574\u4e2a GPUMD \u548c NEP \u793e\u533a\u53d8\u5f97\u66f4\u597d\u3002</p>"}]}
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+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"],"fields":{"title":{"boost":1000.0},"text":{"boost":1.0},"tags":{"boost":1000000.0}}},"docs":[{"location":"index.html","title":"Home","text":"\ud83d\udcda GPUMDkit Documentation <p>A practical bilingual tutorial for GPUMDkit, covering installation, command-line tools, interactive workflows, plotting, and analysis utilities.</p>"},{"location":"index.html#language","title":"Language","text":"Language Start Here Command Reference English GPUMDkit Tutorials Command Reference \u7b80\u4f53\u4e2d\u6587 GPUMDkit \u6559\u7a0b \u547d\u4ee4\u53c2\u8003"},{"location":"index.html#what-you-can-learn-here","title":"What You Can Learn Here","text":"<p>This documentation is organized as a practical tutorial rather than only a command list. New users are encouraged to start from the overview and quick start pages, then move to the topic that matches their task.</p> Topic What it Covers Quick Start Installation, environment setup, interactive mode, direct command mode Format Conversion VASP, LAMMPS, CP2K, ABACUS, CIF, extxyz, group labels, weights Sampling Uniform/random sampling, NepTrain FPS, perturbation, force-deviation selection Calculators MSD, ionic conductivity, NEP prediction, descriptors, DOAS, NEB, polarization tools Analyzers Composition checks, distance checks, filters, property range analysis Visualization NEP training plots, MD plots, transport plots, thermal transport plots, example figures Workflows Batch DFT/MD processing and active-learning style workflows <p>For complex operations, use the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>For common operations with fixed arguments, use direct command-line mode:</p> <pre><code>gpumdkit.sh -h\ngpumdkit.sh -plt -h\ngpumdkit.sh -calc -h\n</code></pre>"},{"location":"en/index.html","title":"GPUMDkit Tutorials","text":"\ud83d\udcda GPUMDkit Tutorials <p>Welcome to GPUMDkit, a command-line toolkit for GPUMD and NEP.</p>"},{"location":"en/index.html#what-it-does","title":"What it does","text":"<p>GPUMDkit helps you perform common tasks in computational materials science without writing custom scripts. It supports format conversion, structure analysis, property calculation, visualization, and batch workflows \u2014 all from one command-line tool.</p>"},{"location":"en/index.html#common-tasks","title":"Common Tasks","text":"I want to... Tutorial Install GPUMDkit and run my first command Quick Start Convert VASP, LAMMPS, CP2K, or CIF files to extxyz Format Conversion Check structure distances, filter datasets, or find outliers Analyzer Scripts Calculate MSD, ionic conductivity, or descriptors Calculator Scripts Analyze polar materials, ferroelectrics, or ABO3 systems Polar Material Analysis Plot NEP training results or thermodynamic data Plot Scripts Run batch DFT or MD simulations Workflow Scripts Select representative structures from a dataset Structure Sampling Add my own shortcuts to GPUMDkit Custom Commands"},{"location":"en/index.html#before-you-start","title":"Before you start","text":""},{"location":"en/index.html#installation","title":"Installation","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"en/index.html#dependencies","title":"Dependencies","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"en/index.html#interactive-mode","title":"Interactive mode","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>This opens a menu where you can select modules by number.</p>"},{"location":"en/index.html#cli-mode","title":"CLI mode","text":"<pre><code>gpumdkit.sh -&lt;option&gt; [args...]\n</code></pre> <p>For example:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>Use <code>gpumdkit.sh -h</code> to see all available options.</p>"},{"location":"en/index.html#module-overview","title":"Module Overview","text":"Module Menu CLI Description Format Conversion 1 <code>-out2xyz</code>, <code>-pos2exyz</code> File conversion Sample Structures 2 interactive menu, <code>-frame_range</code>, <code>-pynep</code> (deprecated) Structure sampling Workflow 3 - Batch processing Calculators 4 <code>-calc &lt;type&gt;</code> Property calculations Analyzer 5 <code>-range</code>, <code>-min_dist</code> Structure analysis Visualization 6 <code>-plt &lt;type&gt;</code> Plotting tools Utilities 7 <code>-time</code>, <code>-clean</code> Utility functions"},{"location":"en/index.html#all-tutorials","title":"All Tutorials","text":"Tutorial Description Quick Start Installation and first steps Command Reference One-page CLI and menu reference Format Conversion Convert between file formats Calculator Scripts Compute material properties Analyzer Scripts Structure analysis and validation Plot Scripts Plotting and visualization Workflow Scripts Batch processing and automation Structure Sampling Structure selection methods Custom Commands User-defined GPUMDkit shortcuts Active Learning Workflow Batch active-learning workflow notes Polar Material Analysis Ferroelectric and polarization tools Contributing to GPUMDkit Development notes"},{"location":"en/index.html#links","title":"Links","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>Documentation: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"en/active_learning_workflow.html","title":"Active Learning Workflow","text":"\ud83d\udd01 Active Learning Workflow <p>This tutorial explains the steps and considerations involved in the <code>workflow_active_learning_dev.sh</code> script. The workflow is used to generate, select, and analyze molecular structures, followed by simulations and data collection.</p> <p>Script Location: <code>Scripts/workflow/</code></p>"},{"location":"en/active_learning_workflow.html#overview","title":"Overview","text":"<p>This script automates one iteration of NEP active learning. The typical workflow includes:</p> Step Action Purpose 1 Run MD simulations Generate candidate structures with current NEP model 2 Filter structures Remove unphysical configurations (short distances, large boxes) 3 Sample structures Select diverse or uncertain structures for DFT 4 Run SCF calculations Compute DFT reference energies/forces 5 NEP prediction Check model accuracy on new structures <p>Unlike menu-driven modules, this workflow is a shell script that you customize and run directly:</p> <pre><code>bash Scripts/workflow/workflow_active_learning_dev.sh\n</code></pre> <p>The sections below explain the main blocks in the script and what each part does.</p>"},{"location":"en/active_learning_workflow.html#1-slurm-directives","title":"1. SLURM Directives","text":"<pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>The SLURM directives are used to define how the job will be submitted to the cluster:</p> <ul> <li><code>#SBATCH -p</code> defines the partition, in this case, it's <code>intel-sc3</code> and <code>intel-sc3-32c</code>.</li> <li><code>#SBATCH -q</code> specifies the queue, in this case, <code>huge</code>.</li> <li><code>#SBATCH -N</code> allocates 1 node for the job.</li> <li><code>#SBATCH -J</code> names the job <code>workflow</code>.</li> <li><code>#SBATCH -o</code> defines the output log file as <code>workflow.log</code>.</li> <li><code>--ntasks-per-node=1</code> specifies that only one task should run per node.</li> </ul> <p>NOTE: If your machine does not have the SLURM environment, you can also run the script directly from the command line. For example:</p> <pre><code>nohup bash workflow_active_learning_dev.sh &amp;&gt;workflow.log &amp;\n</code></pre>"},{"location":"en/active_learning_workflow.html#2-basic-setup","title":"2. Basic Setup","text":"<pre><code>cd $SLURM_SUBMIT_DIR \n</code></pre> <p>Ensure the working directory is correct, and that all necessary files are present for the job.</p> <pre><code>source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  # Load the submit template\npython_pynep=python  # Python executable for the deprecated pynep branch if needed\n</code></pre> <ul> <li><code>GPUMDkit_path</code> is the environment variable that stores the path for the <code>GPUMDkit</code> .</li> <li><code>python_pynep</code> points to the Python environment used for the deprecated <code>pynep</code>-related branch if needed.</li> </ul>"},{"location":"en/active_learning_workflow.html#3-variable-definitions","title":"3. Variable Definitions","text":"<pre><code>work_dir=${PWD}  # Set the working directory\nprefix_name=LiF_iter01  # Prefix for calculations\nmin_dist=1.4  # Minimum atom distance\nbox_limit=13  # Simulation box limit\nmax_fp_num=50  # Maximum number of single point calculations\nsample_method=pynep  # Sampling method (options: uniform, random, pynep)\npynep_sample_dist=0.01  # Sampling distance for pynep\n</code></pre> <p>You can customize:</p> <ul> <li><code>prefix_name</code> to reflect the name of your current work.</li> <li><code>min_dist</code>, <code>box_limit</code>, and <code>max_fp_num</code> based on your own system.</li> <li><code>sample_method</code> (choose between <code>uniform</code>, <code>random</code>, or <code>pynep</code>).</li> <li><code>pynep_sample_dist</code> is the sampling distance for <code>pynep</code>.</li> </ul>"},{"location":"en/active_learning_workflow.html#4-check-required-files","title":"4. Check Required Files","text":"<pre><code>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ -f run.in ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then\n    # Check for the required files before proceeding.\nelse\n    echo \"Please put nep.in nep.txt train.xyz run.in INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.\"\n    exit 1\nfi\n</code></pre> <p>Make sure the necessary files (<code>nep.txt</code>, <code>nep.in</code>, <code>train.xyz</code>, <code>run.in</code>, <code>INCAR</code>, <code>POTCAR</code>, <code>KPOINTS</code>) are available in the working directory. If any of these are missing, the script will terminate. <code>train.xyz</code> and <code>nep.txt</code> are used for <code>pynep</code> sampling, and <code>run.in</code> is the simulation parameters of MD in the current iteration.</p>"},{"location":"en/active_learning_workflow.html#5-file-organization","title":"5. File Organization","text":"<pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <p>The script organizes the working files into two folders:</p> <ul> <li><code>00.modev</code>: For molecular dynamics simulation.</li> <li><code>common</code>: For shared resources such as <code>nep.txt</code>, <code>run.in</code>, and the structure files, etc.</li> </ul>"},{"location":"en/active_learning_workflow.html#6-molecular-dynamics-simulation-submission","title":"6. Molecular Dynamics Simulation Submission","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>After preparing the input files, the script submits an array of molecular dynamics (MD) tasks using <code>submit_gpumd_array</code>.</p>"},{"location":"en/active_learning_workflow.html#7-monitoring-task-completion","title":"7. Monitoring Task Completion","text":"<pre><code>while true; do\n    logs=$(find \"${work_dir}/00.modev/\" -type f -name log -path \"*/sample_*/log\")\n    finished_tasks_md=$(grep \"Finished running GPUMD.\" $logs | wc -l)\n    error_tasks_md=$(grep \"Error\" $logs | wc -l)\n\n    if [ \"$error_tasks_md\" -ne 0 ]; then\n        echo \"Error: MD simulation encountered an error.\"\n        exit 1\n    fi\n    if [ $finished_tasks_md -eq $sample_struct_num ]; then\n        break\n    fi\n    sleep 30\ndone\n</code></pre> <p>The script continuously checks whether all MD tasks have finished by searching for a <code>Finished running GPUMD.</code> message in the logs. If an error is encountered, the script terminates.</p>"},{"location":"en/active_learning_workflow.html#8-analysis-and-filtering","title":"8. Analysis and Filtering","text":"<pre><code>mkdir ${work_dir}/01.select\n...\n</code></pre> <p>In the <code>01.select</code> folder, all structures in the trajectory file <code>dump.xyz</code> during the MD process will be analyzed and filtered to avoid the generation of non-physical structures as much as possible. Specifically, the <code>get_min_dist.py</code>, <code>filter_structures_by_distance.py</code> and <code>filter_exyz_by_box.py</code> scripts will be employed to check whether there are situations where the distance between atoms is too close or the simulated box exceeds the limit value, and such structures will be filtered out.</p>"},{"location":"en/active_learning_workflow.html#9-sampling-methods","title":"9. Sampling Methods","text":"<pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <p>The script supports three sampling methods: <code>uniform</code>, <code>random</code>, and <code>pynep</code>. It selects structures according to the chosen method and checks if the number exceeds <code>max_fp_num</code>, ensuring the final structure count is within limits.</p>"},{"location":"en/active_learning_workflow.html#10-scf-calculations","title":"10. SCF Calculations","text":"<pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>After sampling, SCF calculations are submitted using <code>submit_vasp_array</code>. The process is similar to the MD submission, but for SCF calculations.</p>"},{"location":"en/active_learning_workflow.html#11-prediction-step","title":"11. Prediction Step","text":"<pre><code>submit_nep_prediction\n</code></pre> <p>The final step involves submitting the NEP prediction task to check the accuracy of the NEP model. </p> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/analyzer_scripts.html","title":"Analyzer Scripts","text":"\ud83d\udd0d Analyzer Scripts <p>Analyzer scripts provide structure statistics, distance checks, filters, composition analysis, outlier detection, and time estimation for extxyz datasets.</p>"},{"location":"en/analyzer_scripts.html#what-it-does","title":"What it does","text":"<p>This module helps you inspect, filter, and validate structure datasets. You can check composition, analyze property ranges, detect short contacts, filter structures by various criteria, find outliers in NEP training data, and estimate remaining simulation time.</p>"},{"location":"en/analyzer_scripts.html#before-you-start","title":"Before you start","text":"<p>Script location: <code>Scripts/analyzer/</code></p> <p>Make sure GPUMDkit is installed. See Quick Start for installation instructions.</p>"},{"location":"en/analyzer_scripts.html#overview","title":"Overview","text":"Task Command Purpose Composition <code>gpumdkit.sh -analyze_comp train.xyz</code> Group structures by chemical composition Chemical species <code>gpumdkit.sh -chem_species train.xyz</code> List species in a file Property range <code>gpumdkit.sh -range train.xyz force</code> Inspect energy/force/virial range Minimum distance <code>gpumdkit.sh -min_dist dump.xyz</code> Fast distance check without PBC Minimum distance with PBC <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> Accurate distance check with PBC Charge balance <code>gpumdkit.sh -cbc train.xyz</code> Oxidation-state balance check Distance filter <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> Remove structures with short contacts Box filter <code>gpumdkit.sh -filter_box dump.xyz 13</code> Remove structures with too-large box edges Property filter <code>gpumdkit.sh -filter_value train.xyz force 20</code> Filter by energy/force/virial threshold Pair-distance range <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> Extract structures by pair distance Outlier detection Menu 502 Find high-RMSE structures in training set Probability density <code>gpumdkit.sh -pda &lt;ref&gt; &lt;traj&gt; &lt;element&gt; &lt;interval&gt;</code> 3D probability density for diffusion channels GPUMD time <code>gpumdkit.sh -time gpumd</code> Estimate remaining GPUMD run time NEP time <code>gpumdkit.sh -time nep</code> Estimate remaining NEP training time"},{"location":"en/analyzer_scripts.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit and choose <code>5) Analyzer</code>:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>The analyzer menu is:</p> <pre><code>+------------------------------------------------------+\n|                    ANALYZER TOOLS                    |\n+------------------------------------------------------+\n| 501) Analyze composition of extxyz                   |\n| 502) Find outliers of extxyz                         |\n| 503) Analyze chemical species of extxyz              |\n| 504) Check charge balance of extxyz                  |\n| 505) Analyze energy/force/virial range               |\n| 506) Filter structures by minimum distance           |\n| 507) Get minimum interatomic distance                |\n| 508) Probability density analysis                    |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Most analyzer functions also have direct CLI shortcuts, which are listed in the overview table and in the sections below.</p>"},{"location":"en/analyzer_scripts.html#composition-analysis","title":"Composition Analysis","text":"<p><code>analyze_composition.py</code> analyzes the composition of your extxyz file and lets you export subsets.</p> <p>What it does: Groups structures by chemical composition and shows how many structures belong to each composition. You can export subsets by composition.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>Interactive mode: Choose <code>501</code> from the analyzer menu.</p> <p>Output example:</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>This is useful when <code>train.xyz</code> contains structures from different systems or different cell sizes. You can export a subset by composition from the interactive prompt.</p>"},{"location":"en/analyzer_scripts.html#chemical-species","title":"Chemical Species","text":"<p><code>analyze_chem_species.py</code> lists all unique chemical species in an extxyz file.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -chem_species train.xyz\n</code></pre>"},{"location":"en/analyzer_scripts.html#property-range-analysis","title":"Property Range Analysis","text":"<p><code>energy_force_virial_analyzer.py</code> calculates and visualizes the range of properties from an extxyz file.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <p>Supported properties: <code>energy</code>, <code>force</code>, <code>virial</code></p> <pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist    # Show histogram\n</code></pre> <p>Output example:</p> <pre><code>Force range: 0.03210566767721861 to 9.230115912468435\n</code></pre> <p>With <code>hist</code> option:</p>"},{"location":"en/analyzer_scripts.html#minimum-distance-checks","title":"Minimum Distance Checks","text":""},{"location":"en/analyzer_scripts.html#without-pbc-fast","title":"Without PBC (Fast)","text":"<p><code>get_min_dist.py</code> calculates minimum interatomic distances without considering periodic boundary conditions. Fast but may be inaccurate for periodic systems.</p> <p>What it does: Reports the minimum distance between each pair of elements in every frame, ignoring periodic boundary conditions.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>Interactive mode: Choose <code>507</code> from the analyzer menu.</p> <p>Output example:</p> <pre><code>+---------------------------+\n|   PBC ignored for speed   |\n| use -min_dist_pbc for PBC |\n+---------------------------+\nMinimum interatomic distances:\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.480     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre> <p>Notes: Use this for a quick check. For periodic systems, prefer <code>-min_dist_pbc</code> for accurate results.</p>"},{"location":"en/analyzer_scripts.html#with-pbc-accurate","title":"With PBC (Accurate)","text":"<p><code>get_min_dist_pbc.py</code> calculates minimum interatomic distances considering periodic boundary conditions.</p> <p>What it does: Reports the minimum distance between each pair of elements, accounting for periodic boundary conditions.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>Interactive mode: Choose <code>507</code> from the analyzer menu and answer <code>y</code> when asked whether to consider PBC.</p> <p>Output example:</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre>"},{"location":"en/analyzer_scripts.html#filtering-structures","title":"Filtering Structures","text":""},{"location":"en/analyzer_scripts.html#filter-by-minimum-distance","title":"Filter by Minimum Distance","text":"<p><code>filter_structures_by_distance_pbc.py</code> removes structures with any interatomic distance below a threshold.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>This removes structures with any interatomic distance below <code>1.0 \u00c5</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-box-size","title":"Filter by Box Size","text":"<p><code>filter_exyz_by_box.py</code> filters structures by box-edge length.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>This keeps structures where all box edges are below <code>13 \u00c5</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-property-value","title":"Filter by Property Value","text":"<p><code>filter_exyz_by_value.py</code> filters structures by energy, force, or virial threshold.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <p>Supported properties: <code>energy</code>, <code>force</code>, <code>virial</code></p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre> <p>This filters out structures with force components exceeding <code>20 eV/\u00c5</code> (or energy exceeding <code>5 eV/atom</code>).</p>"},{"location":"en/analyzer_scripts.html#filter-by-pair-distance-range","title":"Filter by Pair-Distance Range","text":"<p><code>filter_dist_range.py</code> extracts structures where a specific element-pair distance falls within a given range.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>This extracts structures where the Li-Li minimum distance is between <code>1.8 \u00c5</code> and <code>2.0 \u00c5</code>. Output: <code>filtered_Li_Li_1.8_2.0.xyz</code>.</p>"},{"location":"en/analyzer_scripts.html#charge-balance-check","title":"Charge Balance Check","text":"<p><code>charge_balance_check.py</code> checks the oxidation-state balance of structures.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>Output files:</p> <ul> <li><code>balanced.xyz</code> \u2014 structures with balanced charges</li> <li><code>unbalanced.xyz</code> \u2014 structures with unbalanced charges</li> <li><code>indices.txt</code> \u2014 indices of balanced structures</li> </ul> <p>This is intended for systems where common oxidation states are meaningful.</p>"},{"location":"en/analyzer_scripts.html#outlier-detection","title":"Outlier Detection","text":"<p><code>find_outliers.py</code> finds outlier structures in NEP training data based on RMSE thresholds for energy, force, and stress.</p> <p>Input files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>stress_train.out</code>, <code>train.xyz</code></p> <p>These files are generated during NEP training. The script compares DFT vs NEP predictions and identifies structures with large errors.</p> <pre><code># Interactive mode\ngpumdkit.sh    # Select: 5) Analyzer \u2192 502) Find outliers of extxyz\n</code></pre> <p>Interactive prompts:</p> <pre><code>Enter energy RMSE threshold (meV/atom): 1\nEnter force RMSE threshold (meV/\u00c5): 60\nEnter stress RMSE threshold (GPa): 0.03\n</code></pre> <p>Output files:</p> <ul> <li><code>selected.xyz</code> \u2014 structures exceeding the RMSE thresholds (outliers)</li> <li><code>remained.xyz</code> \u2014 structures within the thresholds</li> <li><code>selected_remained.png</code> \u2014 comparison plot</li> </ul> <p>Use case: After NEP training, use this to identify problematic structures that contribute most to the error. Remove or improve these structures to enhance the training set.</p>"},{"location":"en/analyzer_scripts.html#time-estimation","title":"Time Estimation","text":""},{"location":"en/analyzer_scripts.html#gpumd-remaining-time","title":"GPUMD Remaining Time","text":"<p><code>time_consuming_gpumd.sh</code> estimates the remaining time for a GPUMD simulation.</p> <p>Input files: <code>run.in</code>, <code>thermo.out</code> (in the current GPUMD working directory)</p> <pre><code>gpumdkit.sh -time gpumd\n</code></pre> <p>Output example:</p> <pre><code>----------------- System Information ----------------\ntotal frames: 1050000\n-----------------------------------------------------\nCurrent Frame  Speed (steps/s)   Total Time       Time Left       Estimated End\n-------------   -------------   -------------   -------------   -----------------\n    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04\n    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56\n</code></pre>"},{"location":"en/analyzer_scripts.html#nep-remaining-time","title":"NEP Remaining Time","text":"<p><code>time_consuming_nep.sh</code> estimates the remaining time for NEP training.</p> <p>Input files: <code>loss.out</code> (in the current NEP working directory)</p> <pre><code>gpumdkit.sh -time nep\n</code></pre> <p>Output example:</p> <pre><code>+-----------------+-----------+-----------------+---------------------+\n|       Step      | Time Diff |    Time Left    |    Finish Time      |\n+-----------------+-----------+-----------------+---------------------+\n| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |\n| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |\n| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |\n+-----------------+-----------+-----------------+---------------------+\n</code></pre>"},{"location":"en/analyzer_scripts.html#probability-density-analysis","title":"Probability Density Analysis","text":"<p><code>probability_density_analysis.py</code> calculates 3D probability density of mobile ions for diffusion channel analysis.</p> <p>Input files: Reference structure (POSCAR), trajectory file (extxyz)</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n</code></pre> <p>Arguments:</p> Argument Meaning <code>LLZO.vasp</code> Reference structure (POSCAR format) <code>dump.xyz</code> Trajectory file (extxyz format) <code>Li</code> Target mobile species <code>0.25</code> Grid interval for the probability density (\u00c5) <p>Output: <code>probability_density_0.25.vasp</code> \u2014 probability density grid in VASP format for visualization with VESTA or similar tools.</p> <p>Visualization suggestions:</p> <ol> <li>Open <code>probability_density_0.25.vasp</code> in VESTA</li> <li>Use \"Edit \u2192 Data \u2192 Volumetric Data\" to adjust isosurface levels</li> <li>Color the probability density by value to highlight preferred diffusion pathways</li> <li>Overlay with the crystal structure for context</li> </ol>"},{"location":"en/analyzer_scripts.html#example-workflows","title":"Example Workflows","text":""},{"location":"en/analyzer_scripts.html#structure-quality-check","title":"Structure Quality Check","text":"<pre><code># 1. Check composition\ngpumdkit.sh -analyze_comp train.xyz\n\n# 2. Check energy/force range\ngpumdkit.sh -range train.xyz force hist\n\n# 3. Check minimum distances\ngpumdkit.sh -min_dist_pbc train.xyz\n\n# 4. Find outliers (after NEP training)\n# Interactive: 5) Analyzer \u2192 502\n</code></pre>"},{"location":"en/analyzer_scripts.html#structure-filtering-pipeline","title":"Structure Filtering Pipeline","text":"<pre><code># 1. Filter by minimum distance\ngpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n\n# 2. Filter by box size\ngpumdkit.sh -filter_box filtered_dist_pbc.xyz 13\n\n# 3. Filter by force threshold\ngpumdkit.sh -filter_value filtered_box.xyz force 20\n</code></pre>"},{"location":"en/analyzer_scripts.html#diffusion-channel-analysis","title":"Diffusion Channel Analysis","text":"<pre><code># 1. Calculate probability density\ngpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n\n# 2. Visualize with VESTA\n# Open probability_density_0.25.vasp\n</code></pre>"},{"location":"en/calculator_scripts.html","title":"Calculator Scripts","text":"\ud83e\uddee Calculator Scripts <p>The calculator module contains scripts for computing properties from MD trajectories, NEP models, and structure files.</p> <p>Script Location: <code>Scripts/calculators/</code></p>"},{"location":"en/calculator_scripts.html#overview","title":"Overview","text":"<p>The calculator module can be read as three groups:</p> <ul> <li>Trajectory properties: compute time-dependent quantities such as MSD and ionic conductivity from GPUMD or extxyz trajectories;</li> <li>NEP-assisted calculations: use a NEP model to predict energies/forces/stresses, extract descriptors, calculate DOAS, run NEB, or minimize structures;</li> <li>Polar-material analysis: build neighbor lists and calculate local displacement, averaged structures, octahedral tilt, and local polarization for perovskite or polar systems.</li> </ul> <p>If you are not sure about the required arguments, start from the interactive menu to see the prompt. If the arguments are already clear, use <code>gpumdkit.sh -calc ...</code> directly.</p> Task Command Main Input Ionic conductivity <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>, <code>thermo.out</code>, <code>model.xyz</code> MSD from trajectory <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz trajectory NEP prediction <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP model NEP descriptors <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP model DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP model NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> initial/final structures Minimization <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> structure + NEP model Neighbor list <code>gpumdkit.sh -calc nlist ...</code> see Polar Material Analysis Displacement <code>gpumdkit.sh -calc disp ...</code> see Polar Material Analysis Average structure <code>gpumdkit.sh -calc avg-struct ...</code> see Polar Material Analysis Octahedral tilt <code>gpumdkit.sh -calc oct-tilt ...</code> see Polar Material Analysis ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 ...</code> see Polar Material Analysis <p>For a full command list:</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>The command-line help table looks like:</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>In interactive mode, choose <code>4) Calculators</code>. The menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"en/calculator_scripts.html#ionic-conductivity","title":"Ionic Conductivity","text":"<p><code>calc_ion_conductivity.py</code> calculates ionic diffusivity and conductivity from <code>msd.out</code>.</p>"},{"location":"en/calculator_scripts.html#required-and-optional-files","title":"Required and Optional Files","text":"File Role <code>msd.out</code> Required MSD data <code>thermo.out</code> Optional, used for automatic temperature detection <code>model.xyz</code> Optional, used for volume and ion-count detection <code>run.in</code> Optional, used to detect replication"},{"location":"en/calculator_scripts.html#usage","title":"Usage","text":"<pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>From interactive mode, choose <code>401</code>. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>If automatic files are missing, the script will ask for temperature, volume, and ion count interactively.</p> <p>Interactive prompts in manual mode look like:</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre>"},{"location":"en/calculator_scripts.html#example-output","title":"Example Output","text":"<pre><code>Diffusivity (D):\n  D_x: 4.153e-07 cm^2/s\n  D_y: 4.174e-07 cm^2/s\n  D_z: 2.610e-07 cm^2/s\n  D_total: 3.646e-07 cm^2/s\n------------------------------\nIonic Conductivity:\n  Sigma_x: 2.576e-02 mS/cm\n  Sigma_y: 2.589e-02 mS/cm\n  Sigma_z: 1.619e-02 mS/cm\n  Sigma_total: 2.261e-02 mS/cm\n</code></pre>"},{"location":"en/calculator_scripts.html#mean-square-displacement","title":"Mean Square Displacement","text":"<p><code>calc_msd.py</code> computes MSD directly from an extxyz trajectory.</p> <pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>From interactive mode, choose <code>412</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>Li</code> target mobile species <code>10</code> time interval between frames, in fs <code>5000</code> optional maximum correlation steps <p>Output:</p> <ul> <li><code>msd.out</code></li> </ul> <p>The beginning of <code>msd.out</code> is a text table with time and MSD columns. After generating it, use the plot commands below.</p> <p>You can then plot:</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-property-prediction","title":"NEP Property Prediction","text":"<p><code>calc_properties_with_nep.py</code> calculates energy, force, and stress for structures using a NEP model.</p> <p>Dependency: <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>Use this function to run predictions with a trained NEP model. For best results, validate model quality on your target structures before relying on the output.</p> <p>Tip: Before prediction, you may want to clean the extxyz metadata:</p> <pre><code>gpumdkit.sh -clean_xyz train.xyz clean_train.xyz\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-descriptors","title":"NEP Descriptors","text":"<p><code>calc_descriptors.py</code> extracts NEP descriptors for a selected element.</p> <pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>Use cases:</p> <ul> <li>visualize chemical environments with PCA/UMAP;</li> <li>compare training and candidate structures;</li> <li>inspect whether new data expands descriptor space.</li> </ul> <p>Plot descriptors with:</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/calculator_scripts.html#density-of-atomistic-states","title":"Density of Atomistic States","text":"<p><code>calc_doas.py</code> calculates density of atomistic states (DOAS), following the idea proposed by Wang et al..</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>The script:</p> <ol> <li>reads all structures;</li> <li>relaxes each structure with a NEP calculator;</li> <li>extracts per-atom energies;</li> <li>groups atomic energies by element;</li> <li>writes the grouped values to the output file.</li> </ol> <p>For very large systems, running minimization and atomistic-energy extraction directly in GPUMD can be more efficient.</p>"},{"location":"en/calculator_scripts.html#neb-with-a-nep-model","title":"NEB with a NEP Model","text":"<pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>This runs a NEB calculation with <code>9</code> intermediate images. During execution, the script asks how atoms should be fixed:</p> <ul> <li><code>none</code>: no atoms fixed;</li> <li><code>index</code>: fix atoms by index;</li> <li><code>element</code>: fix all atoms of one element;</li> <li><code>position</code>: fix atoms inside a coordinate range.</li> </ul>"},{"location":"en/calculator_scripts.html#structure-minimization","title":"Structure Minimization","text":"<p><code>calc_minimize.py</code> minimizes a structure using a NEP model through <code>calorine</code>.</p> <p>Dependency: <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input structure, POSCAR/CONTCAR or extxyz <code>nep.txt</code> NEP model <code>0.01</code> optional force convergence threshold in eV/Ang <code>1000</code> optional maximum optimization steps <p>Output:</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"en/calculator_scripts.html#rdf-calculation-with-ovito","title":"RDF Calculation with OVITO","text":"<p><code>rdf_calculator_ovito.py</code> calculates radial distribution function using OVITO's analysis tools.</p> <p>Dependency: OVITO</p> <pre><code>pip install ovito\n</code></pre> <p>Input file: Structure file (single frame or trajectory)</p> <pre><code>python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400\n</code></pre> <p>Parameters:</p> Argument Meaning <code>trajectory.xyz</code> Input structure file <code>6.0</code> Maximum distance for RDF calculation (\u00c5) <code>400</code> Number of histogram bins <p>Visualization:</p> <pre><code>gpumdkit.sh -plt rdf\n</code></pre> <p>Note: It is recommended to use the <code>compute_rdf</code> command directly in GPUMD when possible.</p>"},{"location":"en/calculator_scripts.html#ferroelectric-and-polar-material-tools","title":"Ferroelectric and Polar Material Tools","text":"<p>Options <code>406\u2013410</code> are for perovskite and polar-material analysis. They are commonly used to extract local structural information from MD trajectories before analyzing phase transitions, domain patterns, or polarization textures.</p> <p>This page only gives a quick index for these scripts because they are usually used together. For full workflows and argument details, see Polar Material Analysis.</p> Menu CLI subcommand Purpose Details <code>406</code> <code>gpumdkit.sh -calc nlist ...</code> Build neighbor lists between selected center and neighbor atoms Polar Material Analysis <code>407</code> <code>gpumdkit.sh -calc disp ...</code> Calculate local displacement from a trajectory and neighbor list Polar Material Analysis <code>408</code> <code>gpumdkit.sh -calc avg-struct ...</code> Calculate an averaged structure from a trajectory Polar Material Analysis <code>409</code> <code>gpumdkit.sh -calc oct-tilt ...</code> Calculate octahedral tilt angles Polar Material Analysis <code>410</code> <code>gpumdkit.sh -calc pol-abo3 ...</code> Estimate local ABO3 polarization from Born effective charges Polar Material Analysis <p>Some scripts require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>A typical sequence is to build neighbor lists with <code>nlist</code>, then reuse those lists for displacement, tilt, or polarization calculations. For averaged structures, you can start directly from the trajectory and use the length tolerance to control which frames are included.</p>"},{"location":"en/command_reference.html","title":"Command Reference","text":"\ud83d\udccb Command Reference <p>This page lists the stable GPUMDkit command-line shortcuts. Interactive mode is available for workflows with many choices.</p> <p>The source table is maintained in <code>docs/command_reference.tsv</code>.</p>"},{"location":"en/command_reference.html#gpumdkitsh-h-output","title":"<code>gpumdkit.sh -h</code> Output","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |\n| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/command_reference.html#main","title":"Main","text":"Command Syntax Description <code>-h</code> <code>gpumdkit.sh -h</code> Show general help <code>-update</code> <code>gpumdkit.sh -update</code> Update GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> Clean extra files in the current directory"},{"location":"en/command_reference.html#format-conversion","title":"Format Conversion","text":"Command Syntax Description <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR to extxyz, shell version <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR to extxyz, Python version <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K output to xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR to extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF to POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF to extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR to extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz frames to POSCAR files <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR to LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump to extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory to extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> Replicate by cell factors <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> Replicate toward a target atom count <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> Add GPUMD group labels <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> Add structure weights <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> Extract one frame <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> Remove extra extxyz properties <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> Extract frames by fractional range"},{"location":"en/command_reference.html#calculators","title":"Calculators","text":"Command Syntax Description <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> Ionic conductivity <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP property prediction <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP descriptors <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> Density of atomistic states <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> NEB with a NEP model <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> Structure minimization <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> MSD from trajectory <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> Neighbor lists <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> Displacements <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> Averaged structure <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> Octahedral tilt <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 local polarization"},{"location":"en/command_reference.html#analyzers","title":"Analyzers","text":"Command Syntax Description <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> Property range analysis <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> Composition analysis <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> Chemical species list <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> Charge-balance check <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> Minimum distance without PBC <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> Minimum distance with PBC <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> Distance filtering <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> PBC-aware distance filtering <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> Box-edge filtering <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> Property threshold filtering <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> Element-pair distance range filtering <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> Probability density analysis"},{"location":"en/command_reference.html#visualization","title":"Visualization","text":"<p>Use:</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>Common types include <code>train</code>, <code>prediction</code>, <code>thermo</code>, <code>msd</code>, <code>sdc</code>, <code>rdf</code>, <code>emd</code>, <code>nemd</code>, <code>hnemd</code>, <code>pdos</code>, and <code>plane-grid</code>.</p>"},{"location":"en/command_reference.html#utilities","title":"Utilities","text":"Command Syntax Description <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> Monitor GPUMD or NEP progress <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> Modify NEP models interactively <code>-pynep</code> <code>gpumdkit.sh -pynep</code> Deprecated PyNEP FPS sampling"},{"location":"en/contributing_to_gpumdkit.html","title":"Contributing to GPUMDkit","text":"\ud83e\udd1d Contributing to GPUMDkit <p>Thank you for your interest in contributing to GPUMDkit! We appreciate your time and effort in helping improve this toolkit.</p> <p> English   \u00a0\u00b7\u00a0   \u7b80\u4f53\u4e2d\u6587 </p> <p><code>GPUMDkit</code> is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.</p> <p>Note: The authoritative version of this document is <code>CONTRIBUTING.md</code> in the repository root. This tutorial page mirrors its content.</p>"},{"location":"en/contributing_to_gpumdkit.html#table-of-contents","title":"Table of Contents","text":"<ul> <li>Development Restrictions and Guidelines</li> <li>Reporting Bugs</li> <li>Suggesting Features</li> <li>Contributing Code</li> <li>Fork and Clone the Repository</li> <li>Create a Feature Branch</li> <li>Making Changes<ul> <li>Interactive Mode Contributions</li> <li>Command-Line Mode Contributions</li> <li>Updating Tab Completion</li> </ul> </li> <li>Code Style and Best Practices</li> <li>Testing Your Changes</li> <li>Commit Messages</li> <li>Push and Open a Pull Request</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#development-restrictions-and-guidelines","title":"Development Restrictions and Guidelines","text":"<p>To maintain code quality and consistency across the project, please adhere to these guidelines:</p>"},{"location":"en/contributing_to_gpumdkit.html#language-requirements","title":"Language Requirements","text":"<ul> <li>All code should be written in English: This includes variable names, function names, comments, docstrings, commit messages, and documentation.</li> <li>While we understand that contributors come from diverse backgrounds, using English ensures that the codebase is accessible to the widest possible audience.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#modularity-and-reusability","title":"Modularity and Reusability","text":"<ul> <li>Write modular and reusable code: Functions and scripts should be designed with flexibility in mind.</li> <li>Prefer passing parameters over hardcoding values: Use function arguments, command-line parameters, or configuration files instead of hardcoded values. However, some filenames are required to be fixed by GPUMD and NEP programs (e.g., <code>train.xyz</code>, <code>thermo.out</code>), and these can be hardcoded as needed.</li> <li>Example:    <pre><code># Good: accepts parameters\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # processing logic\n}\n\n# Avoid: hardcoded values (unless required by GPUMD/NEP)\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # processing logic\n}\n</code></pre></li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#code-style","title":"Code Style","text":"<ul> <li>Write code that is clear and easy for others to maintain and modify.</li> <li>Use meaningful variable and function names.</li> <li>Add comments where necessary to explain complex logic.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#documentation","title":"Documentation","text":"<ul> <li>Ensure that help messages (e.g., <code>-h</code> flags) are clear and accurate.</li> <li>Tutorial documentation lives in <code>docs/tutorials/en/</code> (English) and <code>docs/tutorials/zh/</code> (Chinese).   If you add a new feature, consider updating the relevant tutorial page.</li> <li>After editing tutorial markdown files, rebuild the HTML with <code>mkdocs build -f docs/mkdocs.yml</code>.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#reporting-bugs","title":"Reporting Bugs","text":"<p>If you encounter a bug, please help us fix it by reporting it through GitHub Issues:</p> <ol> <li>Search existing issues to see if the bug has already been reported.</li> <li>Open a new issue if it hasn't been reported yet: Create an Issue</li> <li>Describe the problem in detail and provide test files if possible.</li> </ol> <p>You can also reach out to us through: - QQ Group: 825696376 - Email: yanzihan@westlake.edu.cn - Script Developer: Contact the developer listed in the script header</p>"},{"location":"en/contributing_to_gpumdkit.html#suggesting-features","title":"Suggesting Features","text":"<p>We welcome feature suggestions! To propose a new feature:</p> <ol> <li>Search existing issues to see if someone has already suggested it.</li> <li>Open a new feature request: Create a Feature Request and mention @zhyan0603</li> <li>Describe what you need clearly and explain how it would be useful.</li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#contributing-code","title":"Contributing Code","text":""},{"location":"en/contributing_to_gpumdkit.html#fork-and-clone-the-repository","title":"Fork and Clone the Repository","text":"<ol> <li> <p>Fork the repository on GitHub by clicking the \"Fork\" button at the top right of the repository page.</p> </li> <li> <p>Clone your fork to your local machine:</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>Set up the upstream remote to keep your fork in sync:    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#create-a-feature-branch","title":"Create a Feature Branch","text":"<p>Create a new branch for your changes:</p> <pre><code># Create and checkout a new branch from main\ngit checkout -b your-branch-name\n</code></pre> <p>Name your branch as you prefer.</p>"},{"location":"en/contributing_to_gpumdkit.html#making-changes","title":"Making Changes","text":"<p>The structure of <code>GPUMDkit</code> consists of: - <code>gpumdkit.sh</code>: Main entry point (Bash script) handling both interactive menu mode and command-line mode - <code>install.sh</code>: Installation script that sets up environment variables and shell configuration - <code>Scripts/</code>: Python and Bash implementation scripts organized by functionality   - <code>plt_scripts/</code>: Plotting scripts   - <code>calculators/</code>: Calculation utilities   - <code>format_conversion/</code>: Format conversion tools   - <code>workflow/</code>: Workflow automation   - <code>sample_structures/</code>: Structure sampling utilities   - <code>analyzer/</code>: Analysis tools   - <code>utils/</code>: Utility functions (including <code>completion.sh</code> for tab completion) - <code>src/</code>: Shell scripts containing menu functions for interactive mode   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>skills/</code>: AI agent skill definitions (SKILL.md files for opencode/Claude Code integration) - <code>docs/</code>: Documentation files   - <code>tutorials/en/</code> and <code>tutorials/zh/</code>: Bilingual tutorial pages   - <code>mkdocs.yml</code>: MkDocs configuration for building tutorial HTML   - <code>command_reference.tsv</code>: Machine-readable command reference   - <code>htmls/</code>: Generated HTML output from MkDocs</p>"},{"location":"en/contributing_to_gpumdkit.html#interactive-mode-contributions","title":"Interactive Mode Contributions","text":"<p>To add a new feature accessible through the interactive menu:</p> <ol> <li>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:</li> </ol> <pre><code># Example: Add a new format conversion script\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>Implement your functionality following the modularity guidelines (accept parameters, avoid hardcoding).</p> </li> <li> <p>Add a wrapper function in the corresponding <code>src/</code> file:    <pre><code># Example: Edit src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>Add a new function:    <pre><code>function f111_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input &lt;required_param1&gt; &lt;required_param2&gt;\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -r -a converter_args\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py \"${converter_args[@]}\"\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>Update the menu display in <code>gpumdkit.sh</code>:    <pre><code># Find the menu() function and update it if needed\n# Find the array_choice array and add your new choice number\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\" \"107\" \"108\" \"109\" \"110\" \"111\"  # Added \"111\"\n    # ... rest of choices\n)\n</code></pre></p> </li> <li> <p>Add the case statement in <code>gpumdkit.sh</code>:    <pre><code># In the main() function, find the appropriate case statement\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n             \"101\") f101_out2xyz ;;\n             # ... existing cases ...\n             \"111\") f111_new_converter ;;  # Add your case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#command-line-mode-contributions","title":"Command-Line Mode Contributions","text":"<p>To add a new command-line flag or subcommand:</p> <ol> <li> <p>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:    <pre><code># Example: Add a new analyzer script\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>Implement your functionality with clear parameter requirements:    <pre><code># Example: Scripts/analyzer/analyze_bonds.py\nimport sys\n\nif len(sys.argv) != 3:\n    print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n    print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n    sys.exit(1)\n\ninput_file = sys.argv[1]\ncutoff = float(sys.argv[2])\n\n# Your implementation here\n</code></pre></p> </li> </ol> <p>Note: GPUMDkit Python scripts are designed to run directly (not imported as modules). You may use a <code>main()</code> function with <code>if __name__ == \"__main__\":</code> guard if you prefer, but it is not required. Most existing scripts execute at module level.</p> <ol> <li> <p>Add the command-line flag handler in <code>gpumdkit.sh</code>:    <pre><code># Find the command-line parsing section (the large \"case $1 in\" block)\n# Add your new flag in the appropriate location\n\ncase $1 in\n    # ... existing cases ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ \"$2\" != \"-h\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py $2 $3\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n        fi ;;\n    # ... rest of cases ...\nesac\n</code></pre></p> </li> <li> <p>Update the help information in <code>gpumdkit.sh</code>:    <pre><code># Find the help_info_table() function and add your command\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... rest of help table ...\n}\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#updating-tab-completion","title":"Updating Tab Completion","text":"<p>When adding new command-line flags, update the tab completion script:</p> <pre><code># Edit Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>Add your new flag to the <code>opts</code> variable: <pre><code># Find the line with local opts=...\nlocal opts=\"-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...\"\n#                                                        Add your flag here\n</code></pre></p> <p>If your flag requires file arguments, add it to the existing file-completion case: <pre><code># Find the case for file-requiring flags and add yours with |\n-out2xyz|-out2exyz|-...|-your_new_flag)\n    COMPREPLY=($(compgen -f -- \"$cur\")) ;;\n</code></pre></p> <p>If your flag accepts secondary options (like <code>-plt</code> or <code>-calc</code>), add a new case: <pre><code>case \"$prev\" in\n    # ... existing cases ...\n    -your_new_flag)\n        COMPREPLY=($(compgen -W \"option1 option2 option3\" -- \"$cur\")) ;;\n    # ... rest of cases ...\nesac\n</code></pre></p>"},{"location":"en/contributing_to_gpumdkit.html#code-style-and-best-practices","title":"Code Style and Best Practices","text":"<ul> <li>Shell Scripts:</li> <li>Use <code>${variable}</code> for variable expansion</li> <li>Use <code>[ ! -z \"$var\" ]</code> for non-empty checks (project convention)</li> <li>Interactive functions should follow the banner format:     <pre><code>echo \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/&lt;category&gt;        |\"\necho \" | Script: &lt;script_name&gt;.py                        |\"\necho \" | Developer: &lt;Name&gt; (&lt;email&gt;)                     |\"\necho \" &gt;-------------------------------------------------&lt;\"\n</code></pre></li> <li>Use <code>read -r -a varname</code> for multi-word input, then pass with <code>\"${varname[@]}\"</code></li> <li> <p>Shell scripts in <code>src/</code> should start with a file header block:     <pre><code># ============================================================\n# GPUMDkit &lt;module name&gt; module\n# Repository: https://github.com/zhyan0603/GPUMDkit\n# Author: &lt;Name&gt; (&lt;email&gt;)\n# ============================================================\n</code></pre></p> </li> <li> <p>Python Scripts:</p> </li> <li>Write clear, maintainable code</li> <li>Use meaningful variable names</li> <li>Use <code>sys.argv</code> for argument parsing (consistent with most existing scripts)</li> <li>Provide clear usage messages with <code>print(\"Usage: ...\")</code> and <code>print(\"Example: ...\")</code></li> <li>If your script uses heavy/special packages (<code>NepTrain</code>, <code>calorine</code>, <code>dpdata</code>), add a     <code>print_dependency_notice()</code> function to inform users about citation recommendations</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#testing-your-changes","title":"Testing Your Changes","text":"<p>Before submitting your contribution, run the relevant validation commands:</p> <pre><code># Shell syntax checks (always run these)\nbash -n gpumdkit.sh\nfind src Scripts -name '*.sh' -exec bash -n {} +\n\n# Python syntax checks (for modified Python files)\npython3 -m py_compile path/to/modified_script.py\n\n# MkDocs build (if you modified documentation)\nmkdocs build -f docs/mkdocs.yml\n\n# Check for trailing whitespace issues\ngit diff --check\n</code></pre> <p>Then test functionality:</p> <ol> <li> <p>Test interactive mode (if applicable):    <pre><code>gpumdkit.sh\n# Navigate to your new feature and test it thoroughly\n</code></pre></p> </li> <li> <p>Test command-line mode (if applicable):    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # Test help message\n</code></pre></p> </li> <li> <p>Test tab completion (if you modified <code>completion.sh</code>):    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # Should show your new flag\n</code></pre></p> </li> <li> <p>Test with various inputs:</p> </li> <li>Test with typical inputs</li> <li>Test with edge cases (empty files, large files, etc.)</li> <li> <p>Test error handling (missing files, invalid parameters)</p> </li> <li> <p>Verify no regressions: Ensure existing functionality still works correctly.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#commit-messages","title":"Commit Messages","text":"<p>Write clear, descriptive commit messages that explain what you changed. There are no strict format requirements - just make sure your message is understandable.</p>"},{"location":"en/contributing_to_gpumdkit.html#push-and-open-a-pull-request","title":"Push and Open a Pull Request","text":"<ol> <li> <p>Commit your changes:    <pre><code>git add .\ngit commit -m \"your descriptive message\"\n</code></pre></p> </li> <li> <p>Keep your branch updated with the latest <code>dev</code> branch:    <pre><code>git fetch origin\ngit rebase origin/dev\n</code></pre></p> </li> <li> <p>Push your branch to your fork:    <pre><code>git push origin your-branch-name\n</code></pre></p> </li> <li> <p>Open a Pull Request:</p> </li> <li>Go to the GPUMDkit repository</li> <li>Click \"Pull Requests\" \u2192 \"New Pull Request\"</li> <li>Set the base branch to <code>dev</code> for code review</li> <li>Set the compare branch to your feature branch</li> <li> <p>Fill in the PR description with:</p> <ul> <li>Title: Brief description of changes</li> <li>Description: Detailed explanation of what changed and why</li> <li>Testing: Describe how you tested the changes</li> </ul> </li> <li> <p>Respond to review feedback:</p> </li> <li>Be open to suggestions and constructive criticism</li> <li>Make requested changes promptly</li> <li> <p>Push additional commits to your branch (they'll automatically appear in the PR)</p> </li> <li> <p>After approval: A maintainer will merge your PR.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#questions-or-need-help","title":"Questions or Need Help?","text":"<p>If you have questions about contributing or need help with your contribution:</p> <ul> <li>Open a discussion: Use GitHub Discussions for general questions</li> <li>Ask in an issue: Comment on related issues for specific questions</li> <li>Contact maintainers: Reach out to the core developers listed in the README</li> </ul> <p>Thank you again for contributing to <code>GPUMDkit</code>! Your efforts help make this toolkit better for the entire GPUMD and NEP community.</p>"},{"location":"en/custom_commands.html","title":"Custom Commands","text":"\ud83d\udd27 Custom Commands <p>GPUMDkit allows users to extend the command-line interface with custom commands. Define shortcuts for frequently used scripts in your ~/.gpumdkit.in file.</p>"},{"location":"en/custom_commands.html#setup","title":"Setup","text":"<p>Create or edit <code>~/.gpumdkit.in</code>: <pre><code>vi ~/.gpumdkit.in\n</code></pre></p> <p>Define custom functions with the <code>custom_</code> prefix.</p>"},{"location":"en/custom_commands.html#examples","title":"Examples","text":""},{"location":"en/custom_commands.html#simple-greeting","title":"Simple Greeting","text":"<p>Write the following codes in your <code>~/.gpumdkit.in</code> </p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>and run <code>gpumdkit.sh -hello</code>, you will see:</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"en/custom_commands.html#command-with-required-arguments","title":"Command with Required Arguments","text":"<p>For the following function:</p> <pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>and you can add an argument, for example: <code>gpumdkit.sh -greet Zihan</code>, then you will see:</p> <pre><code>Hello, Zihan!\n</code></pre> <p>Passing arguments: Use <code>\"$@\"</code> to forward all arguments safely. Use <code>${@:1}</code> when you need to refer to arguments starting from the first one. </p>"},{"location":"en/custom_commands.html#calling-an-external-script","title":"Calling an External Script","text":"<p>If you want to call an external script like <code>gpumdkit.sh</code>.</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>and run <code>gpumdkit.sh -nepanalyse</code></p>"},{"location":"en/custom_commands.html#advanced-examples","title":"Advanced Examples","text":""},{"location":"en/custom_commands.html#batch-processing","title":"Batch Processing","text":"<p>Process multiple files: <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -batch_plot dir1 dir2 dir3</code></p>"},{"location":"en/custom_commands.html#analysis-pipeline","title":"Analysis Pipeline","text":"<p>Combine multiple operations: <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -analyze_training train.xyz</code></p>"},{"location":"en/custom_commands.html#custom-workflow","title":"Custom Workflow","text":"<p>Automate common workflow: <pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    # Convert VASP outputs\n    gpumdkit.sh -out2xyz ./\n\n    # Filter outliers\n    gpumdkit.sh -filter_value train.xyz force 30\n\n    # Check quality\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -prep_training</code></p>"},{"location":"en/custom_commands.html#tips","title":"Tips","text":"<ul> <li>Use descriptive names: <code>custom_analyze_nep_training</code> is clearer than <code>custom_ant</code></li> <li>Add help messages: Echo usage info when no arguments provided</li> <li>Error handling: Check if required files exist before processing</li> <li>Forward arguments safely: Use <code>\"$@\"</code> to preserve spaces and special characters</li> </ul> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/format_conversion.html","title":"Format Conversion","text":"\ud83d\udd04 Format Conversion <p>GPUMDkit contains utilities for converting common atomistic simulation formats, with extra handling for metadata such as group labels, weights, and frame extraction.</p>"},{"location":"en/format_conversion.html#what-it-does","title":"What it does","text":"<p>This module converts structure and trajectory files between common formats used in computational materials science. It supports VASP, LAMMPS, CP2K, ABACUS, CIF, ASE trajectories, and extxyz. It also provides tools for adding group labels, weights, extracting frames, and replicating structures.</p>"},{"location":"en/format_conversion.html#before-you-start","title":"Before you start","text":"<p>Script location: <code>Scripts/format_conversion/</code></p> <p>Make sure GPUMDkit is installed. See Quick Start for installation instructions.</p>"},{"location":"en/format_conversion.html#supported-formats","title":"Supported formats","text":"<p>The format conversion module covers:</p> <ul> <li>VASP: <code>POSCAR</code>, <code>CONTCAR</code>, <code>OUTCAR</code>, <code>XDATCAR</code></li> <li>LAMMPS: data files and dump trajectories</li> <li>CP2K: output logs, position, force, and cell files</li> <li>ABACUS: SCF/MD logs</li> <li>CIF: crystallographic structure files</li> <li>ASE trajectory: <code>.traj</code></li> <li>extxyz: a common structure format for GPUMD and NEP</li> </ul>"},{"location":"en/format_conversion.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>1) Format Conversion\n</code></pre> <p>The format conversion menu is:</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"en/format_conversion.html#what-each-entry-does","title":"What Each Entry Does","text":"Entry Called script Function When to Use <code>101</code> <code>out2xyz.sh</code> VASP OUTCAR to extxyz, shell version convert VASP calculation directories <code>102</code> <code>mtp2xyz.py</code> MTP cfg to extxyz convert MTP training data <code>103</code> <code>cp2k_log2xyz.py</code> / <code>cp2k2xyz.py</code> CP2K to extxyz choose CP2K log/inp route or pos/frc/cell route <code>104</code> <code>abacus2xyz_scf.sh</code> / <code>abacus2xyz_md.sh</code> ABACUS to extxyz convert ABACUS SCF or MD output <code>105</code> <code>exyz2pos.py</code> extxyz to POSCAR write each extxyz frame as a POSCAR-style file <code>106</code> <code>add_groups.py</code> add group labels add atom group labels for GPUMD-related workflows <code>107</code> <code>add_weight.py</code> add weights assign training weights in extxyz <code>108</code> <code>get_frame.py</code> extract frame export one frame from an extxyz trajectory <code>109</code> <code>clean_xyz.py</code> clean XYZ info remove extra extxyz properties <code>110</code> <code>replicate.py</code> replicate structure build supercells by factors or target atom count <code>out2exyz</code> <code>out2exyz.py</code> OUTCAR to extxyz, Python version alternative VASP OUTCAR converter <code>pos2exyz</code> <code>pos2exyz.py</code> POSCAR to extxyz convert a single structure <code>cif2pos</code> <code>cif2pos.py</code> CIF to POSCAR prepare VASP input from CIF <code>cif2exyz</code> <code>cif2exyz.py</code> CIF to extxyz prepare GPUMDkit input from CIF <code>xdat2exyz</code> <code>xdatcar2exyz.py</code> XDATCAR to extxyz convert VASP MD trajectory <code>pos2lmp</code> <code>pos2lmp.py</code> POSCAR to LAMMPS data prepare LAMMPS input <code>lmp2exyz</code> <code>lmp2exyz.py</code> LAMMPS dump to extxyz convert LAMMPS trajectory <code>traj2exyz</code> <code>traj2exyz.py</code> ASE traj to extxyz convert ASE trajectory"},{"location":"en/format_conversion.html#quick-command-reference","title":"Quick Command Reference","text":"Source Target Command OUTCAR directory extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR directory extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> extxyz POSCAR files <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"en/format_conversion.html#common-examples","title":"Common Examples","text":""},{"location":"en/format_conversion.html#convert-vasp-calculations-to-extxyz","title":"Convert VASP calculations to extxyz","text":"<p>What it does: Searches a directory for VASP OUTCAR files and converts them into a single extxyz file for NEP training or analysis.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>The shell version searches the target directory and converts VASP results into an extxyz file. If you prefer the Python implementation:</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>Interactive mode: Choose <code>101</code> from the format conversion menu. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre> <p>Output: An extxyz file containing the converted structures, suitable for NEP training or further analysis.</p>"},{"location":"en/format_conversion.html#add-group-labels","title":"Add group labels","text":"<p>What it does: Adds atom group labels to a structure file. Group labels are required by some GPUMD-related workflows, such as species-specific MSD or diffusion calculations.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>This command reads the input structure and writes an extxyz file with group information.</p> <p>Interactive mode: Choose <code>106</code> from the format conversion menu. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre> <p>Output: An extxyz file with group labels added.</p>"},{"location":"en/format_conversion.html#script-details","title":"Script Details","text":""},{"location":"en/format_conversion.html#poscar-to-extxyz","title":"POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>Use this when you have a single VASP structure and want an extxyz output.</p> <p>Interactive keyword: <code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#extxyz-to-poscar","title":"extxyz to POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>This converts all frames in an extxyz file into <code>POSCAR_*.vasp</code> files. Frame indices are 0-based in most GPUMDkit scripts, but output filenames are meant for direct inspection and batch calculations.</p> <p>Interactive entry: <code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#lammps-dump-to-extxyz","title":"LAMMPS dump to extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>The element symbols must match the LAMMPS atom type IDs. For example, if type <code>1</code> is Li, type <code>2</code> is Y, and type <code>3</code> is Cl, the order should be <code>Li Y Cl</code>.</p> <p>Interactive keyword: <code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#cif-conversion","title":"CIF conversion","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>Use <code>-cif2pos</code> if you want a VASP-style structure, and <code>-cif2exyz</code> if the next step is GPUMDkit analysis.</p>"},{"location":"en/format_conversion.html#add-weights","title":"Add weights","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>This is useful when you want some structures to have a different training weight in a NEP dataset.</p>"},{"location":"en/format_conversion.html#replicate-structures","title":"Replicate structures","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>The first form uses explicit replication factors. The second form tries to build a supercell close to a target atom count.</p>"},{"location":"en/format_conversion.html#extract-one-frame","title":"Extract one frame","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>This extracts frame index <code>1000</code> from an extxyz trajectory.</p>"},{"location":"en/format_conversion.html#split-multi-frame-extxyz","title":"Split multi-frame extxyz","text":"<p><code>split_single_xyz.py</code> splits an extxyz file into individual frames, each written to a separate file.</p> <pre><code>python Scripts/format_conversion/split_single_xyz.py dump.xyz\n</code></pre> <p>This creates <code>model_0.xyz</code>, <code>model_1.xyz</code>, ... for each frame in the trajectory.</p>"},{"location":"en/format_conversion.html#mtp-conversion","title":"MTP conversion","text":"<p>Convert MTP <code>.cfg</code> format to extxyz:</p> <pre><code>gpumdkit.sh    # Select: 1) Format Conversion \u2192 102\n</code></pre> <p>Interactive prompt:</p> <pre><code>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;\nExample: train.cfg Pd Ag\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#abacus-conversion","title":"ABACUS conversion","text":"<p>Convert ABACUS output to extxyz:</p> <pre><code>gpumdkit.sh    # Select: 1) Format Conversion \u2192 104\n</code></pre> <p>The menu offers two options:</p> <ol> <li>SCF output (<code>running_scf.log</code>)</li> <li>MD output (<code>running_md.log</code>)</li> </ol>"},{"location":"en/format_conversion.html#common-mistakes","title":"Common Mistakes","text":"Problem What to Check LAMMPS elements are wrong Check the element order passed after the dump file A trajectory has strange metadata Try <code>-clean_xyz input.xyz clean.xyz</code> A converted structure looks shifted Inspect PBC/cell information in the source file Frame extraction gives the wrong structure Remember that frame indices are 0-based"},{"location":"en/format_conversion.html#notes","title":"Notes","text":"<p>If a Python package required by a specific converter is missing, Python will report it when that converter is used.</p>"},{"location":"en/plot_scripts.html","title":"Plot Scripts","text":"\ud83d\udcca Plot Scripts <p>The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators. All plots can be displayed interactively or saved as high-resolution PNG files.</p> <p>Script Location: <code>Scripts/plt_scripts/</code></p>"},{"location":"en/plot_scripts.html#quick-access","title":"Quick Access","text":"<pre><code>gpumdkit.sh -plt              # Show all plotting options\ngpumdkit.sh -plt &lt;type&gt;       # Generate a plot\ngpumdkit.sh -plt &lt;type&gt; save  # Save plot as PNG\ngpumdkit.sh -plt &lt;type&gt; -h    # Show help for a specific plot type\n</code></pre> <p>Running <code>gpumdkit.sh -plt</code> prints the plotting command menu:</p> <pre><code>+-----------------------------------------------------------------------------------------------+\n|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |\n+-----------------------------------------------------------------------------------------------+\n|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |\n+-----------------------------------------------------------------------------------------------+\n|                                    NEP Training &amp; Evaluation                                  |\n+-----------------------------------------------------------------------------------------------+\n|  train          - NEP training results           prediction     - NEP prediction results      |\n|  train_test     - NEP train and test results     parity_density - Parity density plot         |\n|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |\n|  charge         - Charge distribution            born_charge    - Born effective charges      |\n|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |\n|  des            - Descriptors                    lr             - Learning rate for gnep      |\n+-----------------------------------------------------------------------------------------------+\n|                                     Diffusion &amp; Transport                                     |\n+-----------------------------------------------------------------------------------------------+\n|  msd            - Mean square displacement       msd_conv       - MSD convergence             |\n|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |\n|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|\n|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |\n|  D_xyz          - Directional Arrhenius D                                                     |\n+-----------------------------------------------------------------------------------------------+\n|                                    MD &amp; Structural Analysis                                   |\n+-----------------------------------------------------------------------------------------------+\n|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |\n|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |\n|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |\n|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |\n|  doas           - Density of atomistic states                                                 |\n+-----------------------------------------------------------------------------------------------+\n|                                        Heat Transport                                         |\n+-----------------------------------------------------------------------------------------------+\n|  emd            - EMD results                    nemd           - NEMD results                |\n|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |\n+-----------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/plot_scripts.html#nep-training-and-prediction","title":"NEP Training and Prediction","text":""},{"location":"en/plot_scripts.html#plt_trainpy","title":"plt_train.py","text":"<p>Visualizes NEP training progress including loss curves, RMSE evolution, and parity plots comparing DFT vs NEP predictions for energy, forces, and stresses.</p> <p>Input Files: <code>loss.out</code>, <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/plot_scripts.html#plt_predictionpy","title":"plt_prediction.py","text":"<p>Visualizes NEP prediction results on the test set.</p> <p>Input Files: <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test         # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#plt_train_testpy","title":"plt_train_test.py","text":"<p>Creates combined parity plots for both training and testing datasets.</p> <p>Input Files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code>, <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"en/plot_scripts.html#plt_parity_densitypy","title":"plt_parity_density.py","text":"<p>Generates density-based parity plots for energies, forces, and stresses. Useful for large datasets where scatter plots become unreadable.</p> <p>Input Files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"en/plot_scripts.html#plt_force_errorspy","title":"plt_force_errors.py","text":"<p>Plots force error evaluation metrics as proposed by Liu et al..</p> <p>Input File: <code>force_train.out</code></p> <p>Metrics Displayed: - Force magnitude errors (delta_F) - Force angle errors (delta_theta) - Distribution of errors</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"en/plot_scripts.html#plt_learning_ratepy","title":"plt_learning_rate.py","text":"<p>Visualizes learning rate during <code>gnep</code> training.</p> <p>Input File: <code>loss.out</code></p> <p>Note: Only for the <code>gnep</code> training process.</p> <pre><code>gpumdkit.sh -plt lr\n</code></pre>"},{"location":"en/plot_scripts.html#plt_nep_restartpy","title":"plt_nep_restart.py","text":"<p>Visualizes parameters stored in the <code>nep.restart</code> file.</p> <p>Input File: <code>nep.restart</code></p> <pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"en/plot_scripts.html#plt_chargepy","title":"plt_charge.py","text":"<p>Plots charge distribution from <code>qNEP</code> model.</p> <p>Input File: <code>charge_train.out</code></p> <p>Important: Ensure consistency between training set and charge output atom ordering. Use full batch training or run prediction step first.</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre>"},{"location":"en/plot_scripts.html#plt_born_chargepy","title":"plt_born_charge.py","text":"<p>Creates parity plots for Born effective charges (BEC) on training and testing datasets. Structures with all-zero reference BEC are filtered out.</p> <p>Input Files: <code>bec_train.out</code>, <code>bec_test.out</code></p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec          # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#thermodynamic-properties","title":"Thermodynamic Properties","text":""},{"location":"en/plot_scripts.html#plt_thermopy","title":"plt_thermo.py","text":"<p>Primary script for comprehensive thermodynamic property visualization.</p> <p>Input File: <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/plot_scripts.html#plt_thermo2py-plt_thermo3py","title":"plt_thermo2.py &amp; plt_thermo3.py","text":"<p>Alternative thermodynamic visualization with different styles.</p> <p>Input File: <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"en/plot_scripts.html#diffusion-and-ionic-transport","title":"Diffusion and Ionic Transport","text":""},{"location":"en/plot_scripts.html#plt_msdpy","title":"plt_msd.py","text":"<p>Plots mean square displacement (MSD) for all directions.</p> <p>Input File: <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"en/plot_scripts.html#plt_msd_allpy","title":"plt_msd_all.py","text":"<p>Plots MSD for all atomic species separately when using <code>all_groups</code> in GPUMD.</p> <p>Input File: <code>msd.out</code> (computed with <code>all_groups</code> option)</p> <p>Requirements: Must use <code>all_groups</code> in the <code>compute_msd</code> command in <code>run.in</code>.</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"en/plot_scripts.html#plt_msd_convergence_checkpy","title":"plt_msd_convergence_check.py","text":"<p>Checks convergence of MSD calculations across different time windows.</p> <p>Input File: <code>msd_step*.out</code> (computed with <code>save_every</code> option)</p> <p>Requirements: Use <code>save_every</code> in the <code>compute_msd</code> command.</p> <p>Purpose: Verify MSD has converged sufficiently for accurate diffusion coefficient calculation.</p> <pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"en/plot_scripts.html#plt_sdcpy","title":"plt_sdc.py","text":"<p>Plots self-diffusion coefficient (SDC) vs time.</p> <p>Input File: <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/plot_scripts.html#plt_arrhenius_dpy","title":"plt_arrhenius_d.py","text":"<p>Creates Arrhenius plot for diffusivity (log10 D vs 1000/T).</p> <p>Input Files: <code>*K/msd.out</code> files (each temperature subdirectory should contain an <code>msd.out</code>)</p> <pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D             # Alternative command\n</code></pre> <p>Output example:</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"en/plot_scripts.html#plt_arrhenius_sigmapy","title":"plt_arrhenius_sigma.py","text":"<p>Creates Arrhenius plot for ionic conductivity (ln(\u03c3\u00b7T) vs 1000/T).</p> <p>Input Files: <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> (each temperature subdirectory)</p> <pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma         # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#heat-transport","title":"Heat Transport","text":""},{"location":"en/plot_scripts.html#plt_emdpy","title":"plt_emd.py","text":"<p>Analyzes and plots thermal conductivity from equilibrium molecular dynamics (EMD).</p> <p>Input Files: EMD output files from GPUMD</p> <pre><code>gpumdkit.sh -plt emd x        # for x direction\n</code></pre>"},{"location":"en/plot_scripts.html#plt_nemdpy","title":"plt_nemd.py","text":"<p>Visualizes non-equilibrium molecular dynamics (NEMD) thermal transport properties.</p> <p>Input Files: NEMD output files from GPUMD</p> <p>Parameters:</p> Parameter Description <code>real_length</code> Real length of heat transfer zone in nm (set to <code>Auto</code> for auto-calculation) <code>scale_eff_size</code> Scale factor for effective cross-sectional area (default: 1). For 3D bulk: use 1. For low-dimensional systems with vacuum: S_box / S_eff <code>cutoff_freq</code> Cutoff frequency for SHC calculation in THz (default: 60) <code>save</code> Optional, save the plot as <code>nemd.png</code> <p>Note: If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p> <pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#plt_hnemdpy","title":"plt_hnemd.py","text":"<p>Plots homogeneous non-equilibrium molecular dynamics (HNEMD) results.</p> <p>Input Files: HNEMD output files from GPUMD</p> <p>Parameters:</p> Parameter Description <code>scale_eff_size</code> Scale factor for effective cross-sectional area (default: 1) <code>cutoff_freq</code> Cutoff frequency for SHC calculation in THz (default: 60) <code>save</code> Optional, save the plot as <code>hnemd.png</code> <p>Note: If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p> <pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#structural-analysis","title":"Structural Analysis","text":""},{"location":"en/plot_scripts.html#plt_rdfpy","title":"plt_rdf.py","text":"<p>Plots radial distribution function (RDF) showing pair correlations.</p> <p>Input File: <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf               # Plot all RDF pairs\ngpumdkit.sh -plt rdf &lt;column&gt;      # Plot specific pair\n</code></pre> <p>Full RDF output:</p> <p>Single pair RDF:</p>"},{"location":"en/plot_scripts.html#plt_rdf_pmfpy","title":"plt_rdf_pmf.py","text":"<p>Plots RDF combined with potential of mean force (PMF).</p> <p>Input File: <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf_pmf\n</code></pre>"},{"location":"en/plot_scripts.html#plt_vacpy","title":"plt_vac.py","text":"<p>Plots velocity autocorrelation function (VAC). Useful for analyzing phonon properties and atomic dynamics.</p> <p>Input File: <code>sdc.out</code> (the VAC columns are read from this file by the plotting script)</p> <p>Output: Interactive plot or <code>vac.png</code> (with <code>save</code> option)</p> <pre><code>gpumdkit.sh -plt vac\n</code></pre>"},{"location":"en/plot_scripts.html#plt_cohesivepy","title":"plt_cohesive.py","text":"<p>Plots cohesive energy curve from <code>cohesive.out</code>. Useful for analyzing lattice stability and equilibrium lattice constants.</p> <p>Input File: <code>cohesive.out</code> (isotropic scaling factor vs cohesive energy)</p> <p>Output: Interactive plot or <code>cohesive.png</code> (with <code>save</code> option)</p> <pre><code>gpumdkit.sh -plt cohesive\n</code></pre>"},{"location":"en/plot_scripts.html#plt_net_forcepy","title":"plt_net_force.py","text":"<p>Plots distribution of net forces on structures, useful for identifying problematic configurations.</p> <p>Input File: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>Reference: arXiv:2510.19774</p>"},{"location":"en/plot_scripts.html#phonons","title":"Phonons","text":""},{"location":"en/plot_scripts.html#plt_pdospy","title":"plt_pdos.py","text":"<p>Calculates and plots normalized VAC, PDOS, and Heat Capacity (Cv).</p> <p>Input Files: <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></p> <pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>Heat capacity output:</p>"},{"location":"en/plot_scripts.html#descriptor-dimer-and-extra-analysis","title":"Descriptor, Dimer, and Extra Analysis","text":""},{"location":"en/plot_scripts.html#plt_descriptorspy","title":"plt_descriptors.py","text":"<p>Visualizes high-dimensional NEP descriptors using dimensionality reduction (PCA or UMAP).</p> <p>Input File: <code>descriptors.npy</code> (generated by <code>gpumdkit.sh -calc des</code>)</p> <p>Methods: - <code>pca</code> \u2014 Principal Component Analysis - <code>umap</code> \u2014 Uniform Manifold Approximation and Projection</p> <pre><code># First generate descriptors\ngpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n\n# Then visualize\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/plot_scripts.html#plt_descriptors_comparepy","title":"plt_descriptors_compare.py","text":"<p>Compares descriptors from multiple training sets or models.</p> <pre><code>gpumdkit.sh -plt des_compare\n</code></pre>"},{"location":"en/plot_scripts.html#plt_dimerpy","title":"plt_dimer.py","text":"<p>Plots dimer interaction curves. Two atoms are placed in a cubic box (30 \u00c5) and the potential energy and force are calculated as a function of dimer distance using a NEP model.</p> <p>Input File: <code>nep.txt</code></p> <pre><code>gpumdkit.sh -plt dimer &lt;element1&gt; &lt;element2&gt; &lt;nep_model&gt;\ngpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>Reference: J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"en/plot_scripts.html#plt_doaspy","title":"plt_doas.py","text":"<p>Plots density of atomistic states (DOAS) proposed by Wang et al..</p> <p>Input File: <code>doas.out</code> (calculated by <code>gpumdkit.sh -calc doas</code>)</p> <pre><code>gpumdkit.sh -plt doas &lt;doas.out&gt; &lt;species&gt;\ngpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"en/plot_scripts.html#plane-grid-plot-for-polar-materials","title":"Plane-Grid Plot for Polar Materials","text":"<p>This workflow maps displacement or polarization data onto a grid and plots selected plane profiles. For detailed usage and real-world examples, see Polar Material Analysis.</p> <p>Dependency:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>Typical upstream steps:</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>Usage:</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre>"},{"location":"en/plot_scripts.html#quick-reference-table","title":"Quick Reference Table","text":"Command Input File(s) Description <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP training plots <code>prediction</code> / <code>test</code> <code>*_test.out</code> NEP prediction plots <code>train_test</code> <code>*_train.out</code>, <code>*_test.out</code> Combined parity plots <code>parity_density</code> <code>*_train.out</code> Density-based parity plots <code>force_errors</code> <code>force_train.out</code> Force error metrics <code>lr</code> <code>loss.out</code> (gnep) Learning rate <code>restart</code> <code>nep.restart</code> Restart file parameters <code>charge</code> <code>charge_train.out</code> Charge distribution <code>born_charge</code> / <code>bec</code> <code>bec_train.out</code>, <code>bec_test.out</code> Born effective charges <code>thermo</code> <code>thermo.out</code> Thermodynamic properties <code>msd</code> <code>msd.out</code> Mean square displacement <code>msd_all</code> <code>msd.out</code> (all_groups) MSD for all species <code>msd_conv</code> <code>msd_step*.out</code> MSD convergence check <code>sdc</code> <code>msd.out</code> Self-diffusion coefficient <code>arrhenius_d</code> / <code>D</code> <code>*K/msd.out</code> Arrhenius diffusivity <code>arrhenius_sigma</code> / <code>sigma</code> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> Arrhenius ionic conductivity <code>rdf</code> <code>rdf.out</code> Radial distribution function <code>rdf_pmf</code> <code>rdf.out</code> RDF + potential of mean force <code>vac</code> <code>sdc.out</code> Velocity autocorrelation <code>cohesive</code> <code>cohesive.out</code> Cohesive energy curve <code>net_force</code> <code>train.xyz</code> Net force distribution <code>doas</code> <code>doas.out</code> Density of atomistic states <code>des</code> <code>descriptors.npy</code> Descriptor PCA/UMAP <code>dimer</code> <code>nep.txt</code> Dimer energy/force curve <code>pdos</code> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code> VAC and PDOS <code>emd</code> EMD outputs EMD thermal conductivity <code>nemd</code> NEMD outputs NEMD thermal transport <code>hnemd</code> HNEMD outputs HNEMD thermal transport <code>viscosity</code> Viscosity outputs Viscosity"},{"location":"en/polar_material_analysis.html","title":"Polar Material Analysis","text":"\ud83e\uddf2 Polar Material Analysis <p>This tutorial covers GPUMDkit calculator options <code>406-410</code> and the <code>plane-grid</code> plotting workflow.</p> <p>Script Location: <code>Scripts/calculators/</code> and <code>Scripts/plt_scripts/</code></p> <p>This tutorial includes both general and system-specific tools:</p> <ul> <li><code>nlist</code>, <code>disp</code>, and <code>avg-struct</code> are broadly useful for structure/trajectory analysis.</li> <li><code>oct-tilt</code> is for octahedral environments (requires 6 neighbors around each center).</li> <li><code>pol-abo3</code> is specific to <code>ABO3</code> polarization analysis.</li> </ul>"},{"location":"en/polar_material_analysis.html#overview","title":"Overview","text":"Step CLI Command Main Input Output Build neighbor list <code>gpumdkit.sh -calc nlist ...</code> <code>model.xyz</code> <code>nl-*.dat</code> Calculate displacement <code>gpumdkit.sh -calc disp ...</code> trajectory + <code>nl-*.dat</code> <code>displacements.dat</code> Average trajectory <code>gpumdkit.sh -calc avg-struct ...</code> trajectory averaged extxyz Octahedral tilt <code>gpumdkit.sh -calc oct-tilt ...</code> trajectory + B-O neighbor list tilt-angle table ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 ...</code> trajectory + neighbor lists polarization table Plane-grid plot <code>gpumdkit.sh -plt plane-grid ...</code> structure + displacement data plane profile plot"},{"location":"en/polar_material_analysis.html#dependency","title":"Dependency","text":"<p>These scripts require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"en/polar_material_analysis.html#interactive-mode-entry","title":"Interactive mode entry","text":"<p>Options <code>406-410</code> are the core functions for this tutorial. The sections below explain when to use each one and how to run it.</p> <pre><code>gpumdkit.sh\n# choose 4) Calculators\n</code></pre> <p>The calculator menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre> <p>For full argument details, use:</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"en/polar_material_analysis.html#406-build-neighbor-list-calc_neighbor_listpy","title":"406) Build neighbor list (<code>calc_neighbor_list.py</code>)","text":"<p>Build neighbor lists for selected center and neighbor elements.</p> <p>When to use it: This is usually the first step before <code>disp</code>, <code>oct-tilt</code>, and <code>pol-abo3</code>, because those scripts read <code>nl-*.dat</code> neighbor files.</p>"},{"location":"en/polar_material_analysis.html#usage","title":"Usage","text":"<pre><code># Example 1: Ti-O nearest 6 neighbors for octahedral analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# Example 2: Pb/Sr-O nearest 12 neighbors for A-site centered analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input structure file. Default: <code>model.xyz</code>.</li> <li><code>-x, --index</code>:   Frame index to read from input. Default: <code>0</code>.</li> <li><code>-c, --cutoff</code> (required):   Neighbor search cutoff (Angstrom).</li> <li><code>-n, --neighbor-num</code> (required):   Number of neighbors per center.</li> <li><code>-d, --defect</code>:   Defect mode. If enabled and neighbors are insufficient, missing slots are filled with the center index.</li> <li><code>-C, --center-elements</code> (required):   Center species list.</li> <li><code>-E, --neighbor-elements</code> (required):   Neighbor species list.</li> <li><code>-o, --output</code>:   Output file path. Default: <code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file","title":"Output file","text":"<ul> <li>Main output: neighbor list text file (for example <code>nl-Ti-O.dat</code>).</li> <li>The file is a 2D integer array with shape <code>(n_center, neighbor_num + 1)</code>. Each row corresponds to one center atom: the first column is the center index, and the remaining columns are its neighbor indices (all 1-based).</li> </ul>"},{"location":"en/polar_material_analysis.html#407-calc-displacement-from-trajectory-calc_displacementpy","title":"407) Calc displacement from trajectory (<code>calc_displacement.py</code>)","text":"<p>Compute local displacement vectors from a trajectory/model and a neighbor list.</p>"},{"location":"en/polar_material_analysis.html#usage_1","title":"Usage","text":"<pre><code># Example 1: single-frame displacement from model.xyz\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# Example 2: use the last 20% frames in movie.xyz\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_1","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   Neighbor list file from <code>nlist</code>.</li> <li><code>-o, --output</code>:   Output file. Default: <code>displacements.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames.   Integer: last <code>N</code> frames.   <code>0 &lt; value &lt; 1</code>: last ratio of frames.</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_1","title":"Output file","text":"<ul> <li>Main output: <code>displacements.dat</code> (or your custom output name).</li> <li>The saved text file is a 2D array: for a single-frame input, its shape is <code>(n_center, 3)</code>; for a multi-frame input, it is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The three columns are <code>dx</code>, <code>dy</code>, and <code>dz</code> displacement components in Angstrom.</li> </ul>"},{"location":"en/polar_material_analysis.html#408-calc-averaged-structure-calc_averaged_structurepy","title":"408) Calc averaged structure (<code>calc_averaged_structure.py</code>)","text":"<p>Generate one averaged structure from selected trajectory frames. Use this after equilibration. For a solid near equilibrium, average a frame window at the target temperature and analyze that representative structure instead of processing every snapshot.</p>"},{"location":"en/polar_material_analysis.html#usage_2","title":"Usage","text":"<pre><code># Example 1: average all frames\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# Example 2: average selected frames (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_2","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input trajectory file. Default: <code>movie.xyz</code>.</li> <li><code>-o, --output</code>:   Output structure file. Default: <code>averaged_structure.xyz</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_2","title":"Output file","text":"<ul> <li>Main output: averaged single-frame extxyz file.</li> <li>Position averaging applies MIC/PBC correction relative to the first selected frame.</li> </ul>"},{"location":"en/polar_material_analysis.html#409-calc-octahedral-tilt-calc_oct_tiltpy","title":"409) Calc octahedral tilt (<code>calc_oct_tilt.py</code>)","text":"<p>Calculate octahedral tilt angles from a B-O neighbor list. This is commonly used to analyze octahedral rotation patterns in <code>ABO3</code> systems, such as <code>SrTiO3</code> and <code>PbZrO3</code>.</p>"},{"location":"en/polar_material_analysis.html#usage_3","title":"Usage","text":"<pre><code># Example 1: octahedral tilt of the TiO6 octahedra from a single frame\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# Example 2: octahedral tilt of the TiO6 octahedra from the last 20% trajectory frames\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_3","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   B-O neighbor list file.</li> <li><code>-o, --output</code>:   Output file. Default: <code>octahedral_tilt.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_3","title":"Output file","text":"<ul> <li>Main output: <code>octahedral_tilt.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>theta_x</code>, <code>theta_y</code>, <code>theta_z</code>, in degree): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#410-calc-polarization-for-abo3-calc_polarization_abo3py","title":"410) Calc polarization for ABO3 (<code>calc_polarization_abo3.py</code>)","text":"<p>Calculate local polarization vectors for <code>ABO3</code> systems.</p>"},{"location":"en/polar_material_analysis.html#usage_4","title":"Usage","text":"<pre><code># Example 1: single-frame ABO3 polarization\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# Example 2: trajectory polarization on a selected frame window\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_4","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>--nl-ba</code> (required):   B-A neighbor list.</li> <li><code>--nl-bo</code> (required):   B-O neighbor list.</li> <li><code>-o, --output</code>:   Output file. Default: <code>polarization.dat</code>.</li> <li><code>--bec</code> (required):   Born effective charge terms in <code>Element=value</code> format.   Example: <code>Pb=2.5 Ti=4.0 O=-2.0</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul> <p>Important checks:</p> <ul> <li><code>--bec</code> must include all element species in the input structure.</li> <li>Center atom indices in <code>--nl-ba</code> and <code>--nl-bo</code> must match.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_4","title":"Output file","text":"<ul> <li>Main output: <code>polarization.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>Px</code>, <code>Py</code>, <code>Pz</code>, in <code>C/m^2</code>): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The script prints a warning if the total Born charge is not balanced.</li> </ul>"},{"location":"en/polar_material_analysis.html#plane-grid-visualization-plt_plane_gridpy","title":"Plane-grid visualization (<code>plt_plane_grid.py</code>)","text":"<p>You can visualize either <code>displacements.dat</code> or <code>polarization.dat</code>:</p> <pre><code># Example 1: displacement map on Ti sites, first XY layer\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# Example 2: polarization map on Pb sites, XZ and YZ layers\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>Arguments (complete):</p> <ul> <li><code>-i, --input</code>:   Input xyz file for atomic layout and layering. Default: <code>model.xyz</code>.</li> <li><code>-d, --disp</code>:   Vector-field data file. Default: <code>displacements.dat</code>.</li> <li><code>-e, --elements</code> (required):   Center element symbols used to map vectors to lattice layers.</li> <li><code>-m, --tol</code>:   Layer tolerance for grid mapping. Default: <code>1.0</code>.</li> <li><code>-g, --target-size</code>:   Expected grid size as <code>nx ny nz</code>.</li> <li><code>-o, --save-dir</code>:   Figure output directory. Default: <code>plot</code>.</li> <li><code>-f, --frame</code>:   Frame index to visualize when vector data has multiple frames. Default: <code>0</code>.</li> <li><code>--select-xy</code>:   Selected XY layer indices.</li> <li><code>--select-xz</code>:   Selected XZ layer indices.</li> <li><code>--select-yz</code>:   Selected YZ layer indices.</li> </ul> <p>Output:</p> <ul> <li>Creates output directory if needed.</li> <li>Saves figures as <code>XY_*.png</code>, <code>XZ_*.png</code>, <code>YZ_*.png</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-files-at-a-glance","title":"Output files at a glance","text":"Script Main output What it stores <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based center index + neighbor indices <code>calc_displacement.py</code> <code>*.dat</code> Local displacement vectors (<code>dx dy dz</code>, Angstrom) <code>calc_averaged_structure.py</code> <code>*.xyz</code> One averaged structure <code>calc_oct_tilt.py</code> <code>*.dat</code> Octahedral tilt angles (<code>theta_x theta_y theta_z</code>, degree) <code>calc_polarization_abo3.py</code> <code>*.dat</code> Local polarization vectors (<code>Px Py Pz</code>, <code>C/m^2</code>) <code>plt_plane_grid.py</code> <code>plot/*.png</code> XY/XZ/YZ plane maps from vector-field data"},{"location":"en/polar_material_analysis.html#real-examples","title":"Real Examples","text":""},{"location":"en/polar_material_analysis.html#temperature-driven-ferroelectric-to-paraelectric-phase-transition-for-pbtio3","title":"Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3","text":"<p>Assume all files are in the current directory <code>./</code>:</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> is the initial structure used to run MD simulations. Each <code>TEMP K.xyz</code> is a trajectory at that temperature.</p>"},{"location":"en/polar_material_analysis.html#step-1-get-averaged-structures-from-the-last-half-of-each-trajectory","title":"Step 1: get averaged structures from the last half of each trajectory","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>This writes <code>300K-avg.xyz</code>, <code>350K-avg.xyz</code>, ..., <code>800K-avg.xyz</code>.</p>"},{"location":"en/polar_material_analysis.html#step-2-build-neighbor-lists-from-modelxyz","title":"Step 2: build neighbor lists from <code>model.xyz</code>","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-compute-displacement-and-polarization-for-each-temperature","title":"Step 3: compute displacement and polarization for each temperature","text":"<p>Use Born effective charges (BEC), not nominal ionic charges. For PbTiO3 in this example:</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>You can obtain BEC from your own DFPT calculation or from literature values. Thus use following commands to compute local displacement and polarization:</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-4-plot-displacement-and-polarization-maps-in-real-space","title":"Step 4: plot displacement and polarization maps in real space","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-5-build-a-temperature-order-parameter-curve","title":"Step 5: build a temperature-order-parameter curve","text":"<p>By analyzing the lattice of each temperature-averaged structure together with its polarization (<code>XX-pol.dat</code>), we can obtain the following figure:</p> <p>The trend shows a clear phase transition around <code>600 K</code>, where the polarization vanishes.</p>"},{"location":"en/polar_material_analysis.html#topological-structure-in-pbtio3srtio3-superlattice","title":"Topological structure in PbTiO3/SrTiO3 superlattice","text":"<p>Assume <code>movie.xyz</code> is the trajectory of the PbTiO3/SrTiO3 superlattice in the current directory.</p>"},{"location":"en/polar_material_analysis.html#step-1-build-an-averaged-structure-from-the-last-25-frames","title":"Step 1: build an averaged structure from the last 25% frames","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-2-build-the-ti-neighbor-list","title":"Step 2: build the Ti neighbor list","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-plot-the-plane-grid-map","title":"Step 3: plot the plane-grid map","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero.</p> <p>Note: the example figure uses a custom colormap. The default GPUMDkit output uses a different style, which can be adjusted by editing the plotting script.</p>"},{"location":"en/polar_material_analysis.html#other-systems","title":"Other Systems","text":""},{"location":"en/polar_material_analysis.html#organic-inorganic-hybrid-ferroelectrics","title":"Organic-inorganic hybrid ferroelectrics","text":"<p>In many organic-inorganic ferroelectrics, polarization is strongly tied to anisotropic molecular units. A practical way to track molecular orientation is to use bond vectors.</p> <p>For TMCM-CdCl3, you can use the C-Cl bond direction of the TMCM molecule as an orientation proxy, then use it to estimate the polarization state:</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p><code>ccl_vectors.dat</code> can then be analyzed as an orientation order parameter. More details could be found at: Phys. Rev. Lett. 136, 016801</p>"},{"location":"en/polar_material_analysis.html#other-ferroelectric-families","title":"Other ferroelectric families","text":"<p>Beyond <code>ABO3</code>, <code>ferrodispcalc</code> can be adapted to many ferroelectric systems, including nitrides, hafnia-based compounds, organic-inorganic hybrids, and some 2D ferroelectrics.</p>"},{"location":"en/quick_start.html","title":"Quick Start","text":"\ud83d\ude80 Quick Start <p>This page helps you install GPUMDkit and run your first commands. You can use GPUMDkit through an interactive menu or direct command-line options.</p>"},{"location":"en/quick_start.html#what-it-does","title":"What it does","text":"<p>GPUMDkit provides a single entry point for common tasks in computational materials science \u2014 format conversion, structure analysis, property calculation, and visualization \u2014 without writing custom scripts.</p>"},{"location":"en/quick_start.html#before-you-start","title":"Before you start","text":""},{"location":"en/quick_start.html#1-prepare-a-python-environment","title":"1. Prepare a Python environment","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>Some optional functions require additional packages:</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>Other Python dependencies are loaded by the corresponding scripts. If a package is missing, Python will report it when that function is used.</p>"},{"location":"en/quick_start.html#2-install-gpumdkit","title":"2. Install GPUMDkit","text":"<p>Clone the repository and run the installer:</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre> <p>The installer writes <code>GPUMDkit_path</code> and <code>PATH</code> settings to your shell configuration and loads them for the current shell. It writes to <code>~/.bashrc</code> by default; if the current shell is zsh, it writes to <code>~/.zshrc</code>. If an existing GPUMDkit path is found, the installer prints the old path and asks whether to replace it. Before changing the rc file, it creates a backup.</p> <p>Typical installation output:</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>If GPUMDkit was installed before, you may see:</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre>"},{"location":"en/quick_start.html#3-verify-the-installation","title":"3. Verify the installation","text":"<pre><code>gpumdkit.sh -h\n</code></pre> <p>This prints a help table listing all available options.</p>"},{"location":"en/quick_start.html#interactive-mode","title":"Interactive mode","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>This opens the main menu:</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre> <p>Select a module by number. Each module provides sub-menus with specific functions.</p>"},{"location":"en/quick_start.html#cli-mode","title":"CLI mode","text":"<p>Direct commands use fixed positional arguments:</p> <pre><code>gpumdkit.sh -&lt;option&gt; [args...]\n</code></pre> <p>Examples:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>The first example reads <code>POSCAR</code> and writes <code>model.xyz</code>.</p>"},{"location":"en/quick_start.html#common-examples","title":"Common examples","text":""},{"location":"en/quick_start.html#convert-a-poscar-to-extxyz","title":"Convert a POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"en/quick_start.html#add-gpumd-group-labels","title":"Add GPUMD group labels","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>Group labels are used by some GPUMD-related workflows that need atom grouping, such as species-specific MSD or diffusion calculations.</p>"},{"location":"en/quick_start.html#plot-nep-training-results","title":"Plot NEP training results","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/quick_start.html#plot-nep-test-results","title":"Plot NEP test results","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"en/quick_start.html#plot-thermodynamic-data","title":"Plot thermodynamic data","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/quick_start.html#plot-msd-and-self-diffusion-coefficient","title":"Plot MSD and self-diffusion coefficient","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/quick_start.html#notes","title":"Notes","text":"<ul> <li>Use <code>gpumdkit.sh -h</code> to see all available options.</li> <li>Use <code>gpumdkit.sh -&lt;option&gt; -h</code> to get help for a specific option (e.g., <code>gpumdkit.sh -plt train -h</code>).</li> <li>For detailed usage of each module, see the corresponding tutorial pages linked in the index.</li> </ul>"},{"location":"en/structure_sampling.html","title":"Structure Sampling","text":"\ud83d\udce6 Structure Sampling <p>Structure sampling is used to select, generate, or filter candidate configurations for NEP training and molecular dynamics workflows.</p> <p>Script Location: <code>Scripts/sample_structures/</code></p>"},{"location":"en/structure_sampling.html#interactive-mode","title":"Interactive Mode","text":"<p>Sampling tasks are usually easier to run from the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>2) Sample Structures\n</code></pre> <p>The menu is:</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Method Use Case 201 Uniform/random sampling quick frame selection from a trajectory 202 PyNEP notice prints a notice; use <code>gpumdkit.sh -pynep</code> to run PyNEP 203 NepTrain FPS descriptor-based FPS with NepTrain 204 Perturb structure generate perturbed structures from POSCAR/CONTCAR 205 Force-deviation selection select structures with high model deviation"},{"location":"en/structure_sampling.html#uniform-and-random-sampling","title":"Uniform and Random Sampling","text":"<p>From interactive mode, choose <code>201</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>Example input:</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>or:</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>uniform</code> / <code>random</code> sampling method <code>50</code> / <code>100</code> number of selected structures <code>500</code> optional number of initial frames to skip <p>Output:</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#farthest-point-sampling-with-neptrain","title":"Farthest Point Sampling with NepTrain","text":"<p>This entry uses NepTrain descriptors for FPS. Choose <code>203</code> in interactive mode, or run the script directly:</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>From interactive mode, choose <code>203</code>. You will see:</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>Inputs:</p> File Meaning <code>dump.xyz</code> candidate structures <code>train.xyz</code> existing training set <code>nep.txt</code> current NEP model used to compute descriptors <p>Outputs:</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>During execution, choose one of two selection modes:</p> <ol> <li>select until the descriptor distance is below a threshold;</li> <li>select a specified number of structures.</li> </ol> <p>The script then prints a selection prompt:</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>This function requires the <code>NepTrain</code> package. If you use this function, we recommend citing the NepTrain paper printed by the script.</p>"},{"location":"en/structure_sampling.html#deprecated-pynep-fps","title":"Deprecated PyNEP FPS","text":"<p>PyNEP FPS is kept for compatibility, but it is only exposed through the direct <code>-pynep</code> entry.</p> <p>If you choose <code>202</code> from the interactive menu, it prints:</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre>"},{"location":"en/structure_sampling.html#serial-pynep","title":"Serial PyNEP","text":"<pre><code>python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"en/structure_sampling.html#parallel-pynep","title":"Parallel PyNEP","text":"<pre><code>python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8\n</code></pre> <p>The last argument is the number of CPU threads.</p>"},{"location":"en/structure_sampling.html#gpumdkit-entry","title":"GPUMDkit Entry","text":"<pre><code>gpumdkit.sh -pynep\n</code></pre> <p>Then input:</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>This entry requires <code>pynep</code> and is kept for compatibility.</p>"},{"location":"en/structure_sampling.html#structure-perturbation","title":"Structure Perturbation","text":"<p>Use perturbation when you want to generate initial structures around a known configuration. Choose <code>204</code> in interactive mode, or run the script directly:</p> <pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>From interactive mode, choose <code>204</code>. You will see:</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input VASP structure <code>20</code> number of perturbed structures <code>0.03</code> cell perturbation fraction <code>0.2</code> atom perturbation distance in Angstrom <code>uniform</code> perturbation style: <code>normal</code>, <code>uniform</code>, or <code>const</code> <p>Output:</p> <ul> <li><code>POSCAR_01.vasp</code>, <code>POSCAR_02.vasp</code>, ...</li> </ul> <p>This function requires <code>dpdata</code>. If you use this function, we recommend citing the dpdata package.</p>"},{"location":"en/structure_sampling.html#force-deviation-selection","title":"Force-Deviation Selection","text":"<p>Use this together with the GPUMD <code>active</code> command. The <code>active</code> command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. <code>select_max_modev.py</code> selects structures with large force deviations from <code>active.out</code> and <code>active.xyz</code>, then writes them to <code>selected.xyz</code>.</p> <p>Choose <code>205</code> in interactive mode, or run the script directly:</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>From interactive mode, choose <code>205</code>. You will see:</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>200</code> maximum number of structures to keep <code>0.15</code> minimum force deviation threshold <p>Required files:</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>Output:</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#frame-range-extraction","title":"Frame Range Extraction","text":"<p><code>frame_range.py</code> is an independent CLI tool and is not part of the interactive sampling menu <code>201\u2013205</code>. Use it when you want to keep only a fraction of a trajectory before sampling, for example after equilibration.</p> <pre><code>gpumdkit.sh -frame_range dump.xyz 0 0.8\npython Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>This writes frames from 0% to 80% of the trajectory. The range arguments are trajectory fractions from <code>0</code> to <code>1</code>.</p>"},{"location":"en/structure_sampling.html#example-commands","title":"Example Commands","text":"<p>An example preprocessing-and-sampling sequence is shown below. The first two commands are analyzer tools; the final step is structure sampling.</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>The final step can also be run from interactive mode by choosing <code>2) Sample Structures -&gt; 203</code>.</p>"},{"location":"en/structure_sampling.html#common-mistakes","title":"Common Mistakes","text":"Problem Recommendation FPS selects too many similar structures increase the distance threshold or select fewer structures Perturbed structures are unphysical reduce <code>cell_pert</code> and <code>atom_pert</code>, then check minimum distances <code>active.out</code> and <code>active.xyz</code> do not match regenerate both from the same GPUMD active run PCA plot looks strange check whether <code>nep.txt</code> matches the chemical species in both datasets"},{"location":"en/workflow_scripts.html","title":"Workflow Scripts","text":"\ud83d\udd27 Workflow Scripts <p>Workflow scripts automate repetitive preparation steps for DFT, MD, and NEP development.</p> <p>Script Location: <code>Scripts/workflow/</code></p>"},{"location":"en/workflow_scripts.html#interactive-entry","title":"Interactive Entry","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>3) Workflow\n</code></pre> <p>The workflow menu looks like:</p> <pre><code>+---------------------------------------------------------+\n|                      WORKFLOW TOOLS                     |\n+---------------------------------------------------------+\n| 301) SCF batch pretreatment                             |\n| 302) MD sample batch pretreatment (gpumd)               |\n| 303) MD sample batch pretreatment (lmp)                 |\n+---------------------------------------------------------+\n| 000) Return to the main menu                            |\n+---------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Workflow Purpose 301 SCF batch pretreatment Prepare single-point DFT calculations 302 MD sample batch pretreatment (GPUMD) Prepare GPUMD sampling calculations 303 MD sample batch pretreatment (LAMMPS) Prepare LAMMPS sampling calculations"},{"location":"en/workflow_scripts.html#scf-batch-pretreatment","title":"SCF Batch Pretreatment","text":"<p>Use this when you have many structures and want to prepare single-point DFT calculations.</p>"},{"location":"en/workflow_scripts.html#vasp","title":"VASP","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>Before running, put structure files in the current directory. The script checks files in this order:</p> <ol> <li>if one or more <code>.vasp</code> files exist, it processes <code>.vasp</code> files;</li> <li>if both <code>.vasp</code> and <code>.xyz</code> files exist, it prints a notice and only processes <code>.vasp</code> files;</li> <li>if no <code>.vasp</code> file exists and one <code>.xyz</code> file exists, it converts that extxyz file to POSCAR files;</li> <li>if no <code>.vasp</code> file exists and multiple <code>.xyz</code> files exist, it asks you to choose one.</li> </ol> <p>Typical input directory before running:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>INCAR</code>, <code>POTCAR</code>, and <code>KPOINTS</code> in the generated <code>fp/</code> directory after the script creates it. The calculation folders link to files in <code>fp/</code>.</p> <p>The <code>prefix</code> you input during the workflow becomes the calculation folder prefix. When <code>out2xyz</code> is later used to extract results, the folder name is stored as <code>config_type</code> in the extxyz file, which makes it easier to trace where each structure came from.</p>"},{"location":"en/workflow_scripts.html#cp2k","title":"CP2K","text":"<p>CP2K SCF batch pretreatment is available from the workflow menu and can also be called directly:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>The interactive wrapper asks for:</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>Example:</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>The template should be configured to read coordinates from <code>pos.xyz</code>. A reference template is available at:</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>The script creates <code>&lt;prefix&gt;_&lt;index&gt;/</code> directories, writes <code>input.inp</code>, and writes <code>pos.xyz</code> for each structure.</p>"},{"location":"en/workflow_scripts.html#md-sampling-pretreatment","title":"MD Sampling Pretreatment","text":""},{"location":"en/workflow_scripts.html#gpumd","title":"GPUMD","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 302\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. The detection order is the same as the VASP SCF workflow: <code>.vasp</code> files are preferred; if multiple <code>.xyz</code> files are found without <code>.vasp</code>, the script asks you to choose one.</p> <p>Typical input directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>nep.txt</code> and <code>run_*.in</code> files in the generated <code>md/</code> directory. The script links <code>run_1.in</code> to <code>sample_1/run.in</code>, <code>run_2.in</code> to <code>sample_2/run.in</code>, and so on.</p>"},{"location":"en/workflow_scripts.html#lammps","title":"LAMMPS","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 303\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. <code>.vasp</code> files are preferred when both formats exist.</p> <p>After running, the script creates LAMMPS data files in <code>struct_md/</code>, sample folders, and an <code>md/</code> directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>lmprun.in</code> and <code>nep.txt</code> in the generated <code>md/</code> directory.</p>"},{"location":"en/workflow_scripts.html#active-learning-style-workflow","title":"Active-Learning Style Workflow","text":"<p>A common NEP improvement loop is:</p> <ol> <li>run MD with the current <code>nep.txt</code>;</li> <li>collect <code>dump.xyz</code> or <code>active.xyz</code>;</li> <li>remove unphysical structures;</li> <li>select diverse or uncertain structures;</li> <li>run DFT single-point calculations;</li> <li>convert DFT results to extxyz;</li> <li>append new structures to <code>train.xyz</code>;</li> <li>retrain the NEP model.</li> </ol> <p>For the development active-learning script, see Active Learning.</p>"},{"location":"en/workflow_scripts.html#template-based-temperature-series","title":"Template-Based Temperature Series","text":"<p>For a simple temperature series, a shell loop is often enough:</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>Then submit the generated folders according to your local cluster system.</p>"},{"location":"en/workflow_scripts.html#practical-notes","title":"Practical Notes","text":"<ul> <li>Workflow scripts are cluster- and template-dependent. Always test with a small number of structures first.</li> <li>Keep template files (<code>INCAR</code>, <code>KPOINTS</code>, <code>POTCAR</code>, <code>run.in</code>, CP2K inputs) under version control if possible.</li> <li>Check generated folders before submitting a large batch.</li> <li>Use analyzers and sampling scripts before expensive DFT calculations.</li> </ul>"},{"location":"zh/index.html","title":"GPUMDkit \u6559\u7a0b","text":"\ud83d\udcda GPUMDkit \u6559\u7a0b <p>\u6b22\u8fce\u4f7f\u7528 GPUMDkit\uff0c\u8fd9\u662f\u4e00\u4e2a\u9762\u5411 GPUMD \u548c NEP \u7684\u547d\u4ee4\u884c\u5de5\u5177\u5305\u3002</p>"},{"location":"zh/index.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>GPUMDkit \u5e2e\u52a9\u4f60\u5728\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u7814\u7a76\u4e2d\u5b8c\u6210\u5e38\u89c1\u4efb\u52a1\uff0c\u65e0\u9700\u7f16\u5199\u81ea\u5b9a\u4e49\u811a\u672c\u3002\u5b83\u652f\u6301\u683c\u5f0f\u8f6c\u6362\u3001\u7ed3\u6784\u5206\u6790\u3001\u6027\u8d28\u8ba1\u7b97\u3001\u53ef\u89c6\u5316\u548c\u6279\u91cf\u5de5\u4f5c\u6d41\u2014\u2014\u5168\u90e8\u901a\u8fc7\u4e00\u4e2a\u547d\u4ee4\u884c\u5de5\u5177\u5b8c\u6210\u3002</p>"},{"location":"zh/index.html#_2","title":"\u5e38\u89c1\u4efb\u52a1","text":"\u6211\u60f3\u8981... \u6559\u7a0b \u5b89\u88c5 GPUMDkit \u5e76\u8fd0\u884c\u7b2c\u4e00\u4e2a\u547d\u4ee4 \u5feb\u901f\u5165\u95e8 \u5c06 VASP\u3001LAMMPS\u3001CP2K \u6216 CIF \u6587\u4ef6\u8f6c\u6362\u4e3a extxyz \u683c\u5f0f\u8f6c\u6362 \u68c0\u67e5\u7ed3\u6784\u8ddd\u79bb\u3001\u8fc7\u6ee4\u6570\u636e\u96c6\u6216\u67e5\u627e\u5f02\u5e38\u503c \u5206\u6790\u5de5\u5177 \u8ba1\u7b97 MSD\u3001\u79bb\u5b50\u7535\u5bfc\u7387\u6216\u63cf\u8ff0\u7b26 \u8ba1\u7b97\u5668\u811a\u672c \u5206\u6790\u6781\u6027\u6750\u6599\u3001\u94c1\u7535\u4f53\u6216 ABO3 \u4f53\u7cfb \u6781\u6027\u6750\u6599\u5206\u6790 \u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c\u6216\u70ed\u529b\u5b66\u6570\u636e \u7ed8\u56fe\u811a\u672c \u8fd0\u884c\u6279\u91cf DFT \u6216 MD \u6a21\u62df \u5de5\u4f5c\u6d41\u811a\u672c \u4ece\u6570\u636e\u96c6\u4e2d\u9009\u62e9\u4ee3\u8868\u6027\u7ed3\u6784 \u7ed3\u6784\u91c7\u6837 \u6dfb\u52a0\u81ea\u5df1\u7684 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u81ea\u5b9a\u4e49\u547d\u4ee4"},{"location":"zh/index.html#_3","title":"\u51c6\u5907\u5de5\u4f5c","text":""},{"location":"zh/index.html#_4","title":"\u5b89\u88c5","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"zh/index.html#_5","title":"\u4f9d\u8d56","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"zh/index.html#_6","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u6253\u5f00\u83dc\u5355\u540e\uff0c\u6309\u6570\u5b57\u9009\u62e9\u6a21\u5757\u3002</p>"},{"location":"zh/index.html#_7","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n</code></pre> <p>\u4f8b\u5982\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>\u4f7f\u7528 <code>gpumdkit.sh -h</code> \u67e5\u770b\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</p>"},{"location":"zh/index.html#_8","title":"\u6a21\u5757\u6982\u89c8","text":"\u6a21\u5757 \u83dc\u5355 CLI \u63cf\u8ff0 \u683c\u5f0f\u8f6c\u6362 1 <code>-out2xyz</code>, <code>-pos2exyz</code> \u6587\u4ef6\u8f6c\u6362 \u7ed3\u6784\u91c7\u6837 2 \u4ea4\u4e92\u83dc\u5355\u3001<code>-frame_range</code>\u3001<code>-pynep</code>\uff08\u5df2\u5f03\u7528\uff09 \u7ed3\u6784\u91c7\u6837 \u5de5\u4f5c\u6d41 3 - \u6279\u5904\u7406 \u8ba1\u7b97\u5668 4 <code>-calc &lt;\u7c7b\u578b&gt;</code> \u5c5e\u6027\u8ba1\u7b97 \u5206\u6790\u5de5\u5177 5 <code>-range</code>, <code>-min_dist</code> \u7ed3\u6784\u5206\u6790 \u53ef\u89c6\u5316 6 <code>-plt &lt;\u7c7b\u578b&gt;</code> \u7ed8\u56fe\u5de5\u5177 \u5b9e\u7528\u5de5\u5177 7 <code>-time</code>, <code>-clean</code> \u5b9e\u7528\u529f\u80fd"},{"location":"zh/index.html#_9","title":"\u5168\u90e8\u6559\u7a0b","text":"\u6559\u7a0b \u63cf\u8ff0 \u5feb\u901f\u5165\u95e8 \u5b89\u88c5\u548c\u7b2c\u4e00\u6b65 \u547d\u4ee4\u53c2\u8003 \u5e38\u7528 CLI \u548c\u83dc\u5355\u5165\u53e3\u901f\u67e5 \u683c\u5f0f\u8f6c\u6362 \u5728\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362 \u8ba1\u7b97\u5668\u811a\u672c \u8ba1\u7b97\u6750\u6599\u5c5e\u6027 \u5206\u6790\u5de5\u5177 \u7ed3\u6784\u5206\u6790\u548c\u9a8c\u8bc1 \u7ed8\u56fe\u811a\u672c \u7ed8\u56fe\u548c\u53ef\u89c6\u5316 \u5de5\u4f5c\u6d41\u811a\u672c \u6279\u5904\u7406\u548c\u81ea\u52a8\u5316 \u7ed3\u6784\u91c7\u6837 \u7ed3\u6784\u9009\u62e9\u65b9\u6cd5 \u81ea\u5b9a\u4e49\u547d\u4ee4 \u7528\u6237\u81ea\u5b9a\u4e49 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 \u6279\u91cf\u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\u8bf4\u660e \u6781\u6027\u6750\u6599\u5206\u6790 \u94c1\u7535\u548c\u6781\u5316\u76f8\u5173\u5de5\u5177 \u8d21\u732e\u6307\u5357 \u5f00\u53d1\u548c\u8d21\u732e\u8bf4\u660e"},{"location":"zh/index.html#_10","title":"\u94fe\u63a5","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>\u6587\u6863: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html","title":"\u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41","text":"\ud83d\udd01 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 <p><code>workflow_active_learning_dev.sh</code> \u7528\u4e8e\u7ec4\u7ec7\u4e00\u8f6e NEP \u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\uff1a\u8fd0\u884c GPUMD \u5206\u5b50\u52a8\u529b\u5b66\u3001\u7b5b\u9009\u7ed3\u6784\u3001\u62bd\u6837\u3001\u63d0\u4ea4\u7b2c\u4e00\u6027\u539f\u7406\u8ba1\u7b97\uff0c\u5e76\u8fdb\u884c NEP \u9884\u6d4b\u68c0\u67e5\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#_1","title":"\u6982\u89c8","text":"<p>\u8be5\u811a\u672c\u81ea\u52a8\u5316\u4e86 NEP \u4e3b\u52a8\u5b66\u4e60\u7684\u4e00\u8f6e\u8fed\u4ee3\u3002\u5178\u578b\u6d41\u7a0b\u5305\u62ec\uff1a</p> \u6b65\u9aa4 \u64cd\u4f5c \u76ee\u7684 1 \u8fd0\u884c MD \u6a21\u62df \u4f7f\u7528\u5f53\u524d NEP \u6a21\u578b\u751f\u6210\u5019\u9009\u7ed3\u6784 2 \u8fc7\u6ee4\u7ed3\u6784 \u79fb\u9664\u4e0d\u5408\u7406\u7684\u6784\u578b\uff08\u77ed\u8ddd\u79bb\u3001\u5927\u76d2\u5b50\uff09 3 \u91c7\u6837\u7ed3\u6784 \u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\u8fdb\u884c DFT \u8ba1\u7b97 4 \u8fd0\u884c SCF \u8ba1\u7b97 \u8ba1\u7b97 DFT \u53c2\u8003\u80fd\u91cf/\u529b 5 NEP \u9884\u6d4b \u68c0\u67e5\u6a21\u578b\u5728\u65b0\u7ed3\u6784\u4e0a\u7684\u7cbe\u5ea6 <p>\u4e0e\u83dc\u5355\u9a71\u52a8\u7684\u6a21\u5757\u4e0d\u540c\uff0c\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u662f\u4e00\u4e2a\u9700\u8981\u6309\u4f53\u7cfb\u4fee\u6539\u540e\u76f4\u63a5\u8fd0\u884c\u7684 shell \u811a\u672c\uff1a</p> <pre><code>bash Scripts/workflow/workflow_active_learning_dev.sh\n</code></pre> <p>\u4e0b\u9762\u6309\u811a\u672c\u4e2d\u7684\u4e3b\u8981\u4ee3\u7801\u5757\u8bf4\u660e\u6bcf\u4e00\u6b65\u7684\u4f5c\u7528\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#1-slurm","title":"1. SLURM \u8bbe\u7f6e","text":"<p>\u811a\u672c\u5f00\u5934\u5305\u542b\u96c6\u7fa4\u63d0\u4ea4\u53c2\u6570\uff0c\u4f8b\u5982\uff1a</p> <pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>\u8fd9\u4e9b\u53c2\u6570\u9700\u8981\u6839\u636e\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u4fee\u6539\u3002\u5982\u679c\u6ca1\u6709 SLURM \u73af\u5883\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u540e\u53f0\u8fd0\u884c\uff1a</p> <pre><code>nohup bash workflow_active_learning_dev.sh &gt; workflow.log 2&gt;&amp;1 &amp;\n</code></pre>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#2","title":"2. \u57fa\u672c\u8bbe\u7f6e","text":"<p>\u811a\u672c\u4f1a\u8fdb\u5165\u63d0\u4ea4\u76ee\u5f55\uff0c\u5e76\u52a0\u8f7d\u63d0\u4ea4\u6a21\u677f\uff1a</p> <pre><code>cd $SLURM_SUBMIT_DIR\nsource ${GPUMDkit_path}/Scripts/workflow/submit_template.sh\npython_pynep=python\n</code></pre> <ul> <li><code>GPUMDkit_path</code> \u662f\u5b89\u88c5\u811a\u672c\u5199\u5165\u7684 GPUMDkit \u8def\u5f84\u3002</li> <li><code>python_pynep</code> \u4ec5\u7528\u4e8e\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#3","title":"3. \u4e3b\u8981\u53d8\u91cf","text":"<p>\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u9002\u5408\u5df2\u7ecf\u6709\u521d\u59cb <code>nep.txt</code>\u3001<code>nep.in</code>\u3001<code>train.xyz</code> \u548c GPUMD/DFT \u8f93\u5165\u6587\u4ef6\uff0c\u5e76\u5e0c\u671b\u5728\u96c6\u7fa4\u4e0a\u81ea\u52a8\u6269\u5c55\u8bad\u7ec3\u96c6\u7684\u60c5\u51b5\u3002</p> <p>\u811a\u672c\u5f00\u5934\u901a\u5e38\u9700\u8981\u6839\u636e\u4f53\u7cfb\u4fee\u6539\uff1a</p> <pre><code>work_dir=${PWD}\nprefix_name=LiF_iter01\nmin_dist=1.4\nbox_limit=13\nmax_fp_num=50\nsample_method=pynep\npynep_sample_dist=0.01\n</code></pre> <ul> <li><code>prefix_name</code> \u7528\u4e8e\u547d\u540d\u672c\u8f6e\u8ba1\u7b97\u3002</li> <li><code>min_dist</code> \u548c <code>box_limit</code> \u7528\u4e8e\u8fc7\u6ee4\u660e\u663e\u4e0d\u5408\u7406\u7684\u7ed3\u6784\u3002</li> <li><code>max_fp_num</code> \u63a7\u5236\u6700\u591a\u63d0\u4ea4\u591a\u5c11\u4e2a\u5355\u70b9\u8ba1\u7b97\u3002</li> <li><code>sample_method</code> \u53ef\u9009 <code>uniform</code>\u3001<code>random</code> \u6216 <code>pynep</code>\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#4","title":"4. \u68c0\u67e5\u8f93\u5165\u6587\u4ef6","text":"<p>\u5e38\u89c1\u8f93\u5165\u5305\u62ec\uff1a</p> <ul> <li><code>nep.txt</code></li> <li><code>nep.in</code></li> <li><code>train.xyz</code></li> <li><code>run.in</code></li> <li><code>INCAR</code></li> <li><code>POTCAR</code></li> <li><code>KPOINTS</code></li> <li>\u521d\u59cb\u91c7\u6837\u7ed3\u6784\u6587\u4ef6\uff0c\u4f8b\u5982 <code>sample_struct.xyz</code></li> </ul> <p>\u811a\u672c\u4f1a\u628a\u516c\u5171\u8f93\u5165\u79fb\u52a8\u5230 <code>common/</code>\uff0c\u5e76\u521b\u5efa <code>00.modev/</code>\u3001<code>01.select/</code> \u7b49\u5de5\u4f5c\u76ee\u5f55\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#5","title":"5. \u6587\u4ef6\u7ec4\u7ec7","text":"<p>\u811a\u672c\u4f1a\u521b\u5efa\u516c\u5171\u8f93\u5165\u76ee\u5f55\u548c MD \u76ee\u5f55\uff1a</p> <pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <ul> <li><code>00.modev</code>\uff1a\u7528\u4e8e\u8fd0\u884c GPUMD MD \u91c7\u6837\u3002</li> <li><code>common</code>\uff1a\u4fdd\u5b58 <code>nep.txt</code>\u3001<code>run.in</code>\u3001\u7ed3\u6784\u6587\u4ef6\u548c DFT \u8f93\u5165\u6587\u4ef6\u7b49\u516c\u5171\u8d44\u6e90\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#6-md","title":"6. \u63d0\u4ea4 MD \u4efb\u52a1","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>\u811a\u672c\u4f1a\u901a\u8fc7\u63d0\u4ea4\u6a21\u677f\u521b\u5efa\u6570\u7ec4\u4efb\u52a1\u3002\u4e0d\u540c\u96c6\u7fa4\u4e0a\u7684\u63d0\u4ea4\u547d\u4ee4\u548c\u6a21\u677f\u53ef\u80fd\u9700\u8981\u81ea\u5df1\u4fee\u6539\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#7","title":"7. \u68c0\u67e5\u4efb\u52a1\u5b8c\u6210","text":"<p>\u811a\u672c\u4f1a\u6301\u7eed\u68c0\u67e5 <code>00.modev/</code> \u4e0b\u5404\u4e2a <code>sample_*/log</code> \u6587\u4ef6\uff0c\u786e\u8ba4\u662f\u5426\u51fa\u73b0\uff1a</p> <pre><code>Finished running GPUMD.\n</code></pre> <p>\u5982\u679c\u53d1\u73b0 <code>Error</code>\uff0c\u811a\u672c\u4f1a\u505c\u6b62\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#8","title":"8. \u5206\u6790\u548c\u8fc7\u6ee4\u7ed3\u6784","text":"<p>MD \u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u8fdb\u5165 <code>01.select</code>\uff0c\u5bf9 <code>dump.xyz</code> \u4e2d\u7684\u7ed3\u6784\u8fdb\u884c\u7b5b\u9009\u3002\u5e38\u89c1\u68c0\u67e5\u5305\u62ec\uff1a</p> <ul> <li>\u6700\u5c0f\u539f\u5b50\u8ddd\u79bb\uff1b</li> <li>\u6a21\u62df\u76d2\u5b50\u8fb9\u957f\uff1b</li> <li>\u7ed3\u6784\u6570\u91cf\u662f\u5426\u8d85\u8fc7 <code>max_fp_num</code>\u3002</li> </ul> <p>\u8fd9\u4e9b\u6b65\u9aa4\u4f1a\u8c03\u7528 analyzer \u548c sample_structures \u4e2d\u7684\u811a\u672c\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#9","title":"9. \u62bd\u6837\u65b9\u6cd5","text":"<p>\u811a\u672c\u6839\u636e <code>sample_method</code> \u9009\u62e9\u62bd\u6837\u65b9\u5f0f\uff1a</p> <pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <ul> <li><code>uniform</code>\uff1a\u5747\u5300\u62bd\u5e27\uff1b</li> <li><code>random</code>\uff1a\u968f\u673a\u62bd\u5e27\uff1b</li> <li><code>pynep</code>\uff1a\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#10-scf","title":"10. \u63d0\u4ea4 SCF \u8ba1\u7b97","text":"<p>\u62bd\u6837\u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u63d0\u4ea4 VASP \u5355\u70b9\u8ba1\u7b97\uff1a</p> <pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>\u8fd9\u91cc\u7684 <code>prefix_name</code> \u4f1a\u7528\u4e8e\u8ba1\u7b97\u76ee\u5f55\u547d\u540d\uff0c\u4e5f\u65b9\u4fbf\u540e\u7eed\u8ffd\u8e2a\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#11-prediction","title":"11. Prediction \u6b65\u9aa4","text":"<p>\u6700\u540e\u811a\u672c\u4f1a\u63d0\u4ea4 NEP prediction\uff0c\u7528\u4e8e\u68c0\u67e5\u5f53\u524d\u6a21\u578b\u5728\u65b0\u589e\u7ed3\u6784\u4e0a\u7684\u8bef\u5dee\u3002</p> <p>\u8fd9\u4e2a\u811a\u672c\u548c\u8ba1\u7b97\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u4f7f\u7528\u524d\u5efa\u8bae\u5148\u7528\u5c0f\u4f53\u7cfb\u6216\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u4e00\u8f6e\uff0c\u5e76\u68c0\u67e5\u63d0\u4ea4\u6a21\u677f\u3001\u8def\u5f84\u548c\u8f93\u5165\u6587\u4ef6\u662f\u5426\u7b26\u5408\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html","title":"\u5206\u6790\u5de5\u5177","text":"\ud83d\udd0d \u5206\u6790\u5de5\u5177 <p>\u5206\u6790\u811a\u672c\u4e3a extxyz \u6570\u636e\u96c6\u63d0\u4f9b\u7ed3\u6784\u7edf\u8ba1\u3001\u8ddd\u79bb\u68c0\u67e5\u3001\u8fc7\u6ee4\u3001\u6210\u5206\u5206\u6790\u3001\u5f02\u5e38\u68c0\u6d4b\u548c\u65f6\u95f4\u4f30\u7b97\u529f\u80fd\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>\u672c\u6a21\u5757\u5e2e\u52a9\u4f60\u68c0\u67e5\u3001\u8fc7\u6ee4\u548c\u9a8c\u8bc1\u7ed3\u6784\u6570\u636e\u96c6\u3002\u53ef\u4ee5\u68c0\u67e5\u6210\u5206\u3001\u5206\u6790\u6027\u8d28\u8303\u56f4\u3001\u68c0\u6d4b\u77ed\u8ddd\u79bb\u63a5\u89e6\u3001\u6309\u5404\u79cd\u6761\u4ef6\u8fc7\u6ee4\u7ed3\u6784\u3001\u67e5\u627e NEP \u8bad\u7ec3\u6570\u636e\u4e2d\u7684\u5f02\u5e38\u503c\uff0c\u4ee5\u53ca\u4f30\u7b97\u5269\u4f59\u6a21\u62df\u65f6\u95f4\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":"<p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/analyzer/</code></p> <p>\u786e\u4fdd\u5df2\u5b89\u88c5 GPUMDkit\u3002\u5b89\u88c5\u8bf4\u660e\u8bf7\u53c2\u89c1\u5feb\u901f\u5165\u95e8\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_3","title":"\u6982\u89c8","text":"\u4efb\u52a1 \u547d\u4ee4 \u7528\u9014 \u6210\u5206\u5206\u6790 <code>gpumdkit.sh -analyze_comp train.xyz</code> \u6309\u5316\u5b66\u6210\u5206\u5206\u7ec4 \u5316\u5b66\u7269\u79cd <code>gpumdkit.sh -chem_species train.xyz</code> \u5217\u51fa\u6587\u4ef6\u4e2d\u7684\u5143\u7d20 \u6027\u8d28\u8303\u56f4 <code>gpumdkit.sh -range train.xyz force</code> \u68c0\u67e5\u80fd\u91cf/\u529b/virial \u8303\u56f4 \u6700\u77ed\u8ddd\u79bb <code>gpumdkit.sh -min_dist dump.xyz</code> \u5feb\u901f\u8ddd\u79bb\u68c0\u67e5\uff08\u65e0 PBC\uff09 \u6700\u77ed\u8ddd\u79bb\uff08PBC\uff09 <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> \u51c6\u786e\u8ddd\u79bb\u68c0\u67e5\uff08\u542b PBC\uff09 \u7535\u8377\u5e73\u8861 <code>gpumdkit.sh -cbc train.xyz</code> \u6c27\u5316\u6001\u5e73\u8861\u68c0\u67e5 \u8ddd\u79bb\u8fc7\u6ee4 <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> \u79fb\u9664\u77ed\u8ddd\u79bb\u63a5\u89e6\u7684\u7ed3\u6784 \u76d2\u5b50\u8fc7\u6ee4 <code>gpumdkit.sh -filter_box dump.xyz 13</code> \u79fb\u9664\u76d2\u5b50\u8fc7\u5927\u7684\u7ed3\u6784 \u6027\u8d28\u8fc7\u6ee4 <code>gpumdkit.sh -filter_value train.xyz force 20</code> \u6309\u80fd\u91cf/\u529b/virial \u9608\u503c\u8fc7\u6ee4 \u5bf9\u8ddd\u79bb\u8303\u56f4 <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> \u6309\u5bf9\u8ddd\u79bb\u63d0\u53d6\u7ed3\u6784 \u5f02\u5e38\u68c0\u6d4b \u83dc\u5355 502 \u67e5\u627e\u8bad\u7ec3\u96c6\u4e2d\u9ad8 RMSE \u7684\u7ed3\u6784 \u6982\u7387\u5bc6\u5ea6 <code>gpumdkit.sh -pda &lt;\u53c2\u8003\u7ed3\u6784&gt; &lt;\u8f68\u8ff9&gt; &lt;\u5143\u7d20&gt; &lt;\u7f51\u683c\u95f4\u8ddd&gt;</code> 3D \u6982\u7387\u5bc6\u5ea6\u5206\u6790\u6269\u6563\u901a\u9053 GPUMD \u65f6\u95f4 <code>gpumdkit.sh -time gpumd</code> \u4f30\u7b97 GPUMD \u5269\u4f59\u8fd0\u884c\u65f6\u95f4 NEP \u65f6\u95f4 <code>gpumdkit.sh -time nep</code> \u4f30\u7b97 NEP \u5269\u4f59\u8bad\u7ec3\u65f6\u95f4"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_4","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit \u5e76\u9009\u62e9 <code>5) Analyzer</code>\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u5206\u6790\u5de5\u5177\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                    ANALYZER TOOLS                    |\n+------------------------------------------------------+\n| 501) Analyze composition of extxyz                   |\n| 502) Find outliers of extxyz                         |\n| 503) Analyze chemical species of extxyz              |\n| 504) Check charge balance of extxyz                  |\n| 505) Analyze energy/force/virial range               |\n| 506) Filter structures by minimum distance           |\n| 507) Get minimum interatomic distance                |\n| 508) Probability density analysis                    |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5927\u591a\u6570\u5206\u6790\u529f\u80fd\u4e5f\u63d0\u4f9b\u76f4\u63a5 CLI \u8c03\u7528\u65b9\u5f0f\uff0c\u6982\u89c8\u8868\u548c\u540e\u7eed\u5c0f\u8282\u4e2d\u5217\u51fa\u4e86\u5e38\u7528\u547d\u4ee4\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_5","title":"\u6210\u5206\u5206\u6790","text":"<p><code>analyze_composition.py</code> \u5206\u6790 extxyz \u6587\u4ef6\u7684\u6210\u5206\uff0c\u5e76\u5141\u8bb8\u5bfc\u51fa\u5b50\u96c6\u3002</p> <p>\u529f\u80fd\uff1a \u6309\u5316\u5b66\u6210\u5206\u5bf9\u7ed3\u6784\u5206\u7ec4\uff0c\u5e76\u663e\u793a\u6bcf\u79cd\u6210\u5206\u7684\u7ed3\u6784\u6570\u91cf\u3002\u53ef\u4ee5\u6309\u6210\u5206\u5bfc\u51fa\u5b50\u96c6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>501</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>\u5f53 <code>train.xyz</code> \u5305\u542b\u4e0d\u540c\u4f53\u7cfb\u6216\u4e0d\u540c\u5c3a\u5bf8\u7684\u7ed3\u6784\u65f6\u5f88\u6709\u7528\u3002\u53ef\u4ee5\u4ece\u4ea4\u4e92\u63d0\u793a\u4e2d\u6309\u6210\u5206\u5bfc\u51fa\u5b50\u96c6\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_6","title":"\u5316\u5b66\u7269\u79cd","text":"<p><code>analyze_chem_species.py</code> \u5217\u51fa extxyz \u6587\u4ef6\u4e2d\u6240\u6709\u552f\u4e00\u7684\u5316\u5b66\u7269\u79cd\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -chem_species train.xyz\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_7","title":"\u6027\u8d28\u8303\u56f4\u5206\u6790","text":"<p><code>energy_force_virial_analyzer.py</code> \u8ba1\u7b97\u5e76\u53ef\u89c6\u5316 extxyz \u6587\u4ef6\u4e2d\u6027\u8d28\u7684\u8303\u56f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <p>\u652f\u6301\u7684\u6027\u8d28\uff1a <code>energy</code>\u3001<code>force</code>\u3001<code>virial</code></p> <pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist    # \u663e\u793a\u76f4\u65b9\u56fe\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Force range: 0.03210566767721861 to 9.230115912468435\n</code></pre> <p>\u4f7f\u7528 <code>hist</code> \u9009\u9879\uff1a</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_8","title":"\u6700\u77ed\u8ddd\u79bb\u68c0\u67e5","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#pbc","title":"\u65e0 PBC\uff08\u5feb\u901f\uff09","text":"<p><code>get_min_dist.py</code> \u8ba1\u7b97\u4e0d\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u7684\u6700\u77ed\u539f\u5b50\u95f4\u8ddd\u3002\u901f\u5ea6\u5feb\uff0c\u4f46\u5bf9\u5468\u671f\u6027\u4f53\u7cfb\u53ef\u80fd\u4e0d\u51c6\u786e\u3002</p> <p>\u529f\u80fd\uff1a \u62a5\u544a\u6bcf\u5e27\u4e2d\u6bcf\u5bf9\u5143\u7d20\u4e4b\u95f4\u7684\u6700\u77ed\u8ddd\u79bb\uff0c\u5ffd\u7565\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>507</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>+---------------------------+\n|   PBC ignored for speed   |\n| use -min_dist_pbc for PBC |\n+---------------------------+\nMinimum interatomic distances:\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.480     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre> <p>\u8bf4\u660e\uff1a \u7528\u4e8e\u5feb\u901f\u68c0\u67e5\u3002\u5bf9\u4e8e\u5468\u671f\u6027\u4f53\u7cfb\uff0c\u5efa\u8bae\u4f7f\u7528 <code>-min_dist_pbc</code> \u83b7\u5f97\u51c6\u786e\u7ed3\u679c\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#pbc_1","title":"\u542b PBC\uff08\u51c6\u786e\uff09","text":"<p><code>get_min_dist_pbc.py</code> \u8ba1\u7b97\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u7684\u6700\u77ed\u539f\u5b50\u95f4\u8ddd\u3002</p> <p>\u529f\u80fd\uff1a \u62a5\u544a\u6bcf\u5bf9\u5143\u7d20\u4e4b\u95f4\u7684\u6700\u77ed\u8ddd\u79bb\uff0c\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>507</code>\uff0c\u5f53\u63d0\u793a\u662f\u5426\u8003\u8651 PBC \u65f6\u8f93\u5165 <code>y</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_9","title":"\u7ed3\u6784\u8fc7\u6ee4","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_10","title":"\u6309\u6700\u77ed\u8ddd\u79bb\u8fc7\u6ee4","text":"<p><code>filter_structures_by_distance_pbc.py</code> \u79fb\u9664\u4efb\u4f55\u539f\u5b50\u95f4\u8ddd\u4f4e\u4e8e\u9608\u503c\u7684\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>\u79fb\u9664\u4efb\u4f55\u539f\u5b50\u95f4\u8ddd\u4f4e\u4e8e <code>1.0 \u00c5</code> \u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_11","title":"\u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4","text":"<p><code>filter_exyz_by_box.py</code> \u6309\u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>\u4fdd\u7559\u6240\u6709\u76d2\u5b50\u8fb9\u957f\u4f4e\u4e8e <code>13 \u00c5</code> \u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_12","title":"\u6309\u6027\u8d28\u503c\u8fc7\u6ee4","text":"<p><code>filter_exyz_by_value.py</code> \u6309\u80fd\u91cf\u3001\u529b\u6216 virial \u9608\u503c\u8fc7\u6ee4\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <p>\u652f\u6301\u7684\u6027\u8d28\uff1a <code>energy</code>\u3001<code>force</code>\u3001<code>virial</code></p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre> <p>\u8fc7\u6ee4\u6389\u529b\u5206\u91cf\u8d85\u8fc7 <code>20 eV/\u00c5</code>\uff08\u6216\u80fd\u91cf\u8d85\u8fc7 <code>5 eV/atom</code>\uff09\u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_13","title":"\u6309\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4","text":"<p><code>filter_dist_range.py</code> \u63d0\u53d6\u7279\u5b9a\u5143\u7d20\u5bf9\u8ddd\u79bb\u5728\u7ed9\u5b9a\u8303\u56f4\u5185\u7684\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>\u63d0\u53d6 Li-Li \u6700\u77ed\u8ddd\u79bb\u5728 <code>1.8 \u00c5</code> \u5230 <code>2.0 \u00c5</code> \u4e4b\u95f4\u7684\u7ed3\u6784\u3002\u8f93\u51fa\uff1a<code>filtered_Li_Li_1.8_2.0.xyz</code>\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_14","title":"\u7535\u8377\u5e73\u8861\u68c0\u67e5","text":"<p><code>charge_balance_check.py</code> \u68c0\u67e5\u7ed3\u6784\u7684\u6c27\u5316\u6001\u5e73\u8861\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>\u8f93\u51fa\u6587\u4ef6\uff1a</p> <ul> <li><code>balanced.xyz</code> \u2014 \u7535\u8377\u5e73\u8861\u7684\u7ed3\u6784</li> <li><code>unbalanced.xyz</code> \u2014 \u7535\u8377\u4e0d\u5e73\u8861\u7684\u7ed3\u6784</li> <li><code>indices.txt</code> \u2014 \u5e73\u8861\u7ed3\u6784\u7684\u7d22\u5f15</li> </ul> <p>\u9002\u7528\u4e8e\u5177\u6709\u660e\u786e\u6c27\u5316\u6001\u7684\u4f53\u7cfb\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_15","title":"\u5f02\u5e38\u68c0\u6d4b","text":"<p><code>find_outliers.py</code> \u57fa\u4e8e\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u7684 RMSE \u9608\u503c\u67e5\u627e NEP \u8bad\u7ec3\u6570\u636e\u4e2d\u7684\u5f02\u5e38\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>stress_train.out</code>\u3001<code>train.xyz</code></p> <p>\u8fd9\u4e9b\u6587\u4ef6\u5728 NEP \u8bad\u7ec3\u8fc7\u7a0b\u4e2d\u751f\u6210\u3002\u811a\u672c\u6bd4\u8f83 DFT \u4e0e NEP \u7684\u9884\u6d4b\uff0c\u8bc6\u522b\u8bef\u5dee\u8f83\u5927\u7684\u7ed3\u6784\u3002</p> <pre><code># \u4ea4\u4e92\u6a21\u5f0f\ngpumdkit.sh    # \u9009\u62e9\uff1a5) \u5206\u6790\u5de5\u5177 \u2192 502) \u67e5\u627e\u5f02\u5e38\u7ed3\u6784\n</code></pre> <p>\u4ea4\u4e92\u63d0\u793a\uff1a</p> <pre><code>Enter energy RMSE threshold (meV/atom): 1\nEnter force RMSE threshold (meV/\u00c5): 60\nEnter stress RMSE threshold (GPa): 0.03\n</code></pre> <p>\u8f93\u51fa\u6587\u4ef6\uff1a</p> <ul> <li><code>selected.xyz</code> \u2014 \u8d85\u8fc7 RMSE \u9608\u503c\u7684\u7ed3\u6784\uff08\u5f02\u5e38\u503c\uff09</li> <li><code>remained.xyz</code> \u2014 \u5728\u9608\u503c\u5185\u7684\u7ed3\u6784</li> <li><code>selected_remained.png</code> \u2014 \u5bf9\u6bd4\u56fe</li> </ul> <p>\u7528\u9014\uff1a NEP \u8bad\u7ec3\u540e\uff0c\u7528\u6b64\u5de5\u5177\u8bc6\u522b\u5bf9\u8bef\u5dee\u8d21\u732e\u6700\u5927\u7684\u95ee\u9898\u7ed3\u6784\u3002\u79fb\u9664\u6216\u6539\u8fdb\u8fd9\u4e9b\u7ed3\u6784\u4ee5\u63d0\u5347\u8bad\u7ec3\u96c6\u8d28\u91cf\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_16","title":"\u65f6\u95f4\u4f30\u7b97","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#gpumd","title":"GPUMD \u5269\u4f59\u65f6\u95f4","text":"<p><code>time_consuming_gpumd.sh</code> \u4f30\u7b97 GPUMD \u6a21\u62df\u7684\u5269\u4f59\u65f6\u95f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>run.in</code>\u3001<code>thermo.out</code>\uff08\u5728\u5f53\u524d GPUMD \u5de5\u4f5c\u76ee\u5f55\u4e2d\uff09</p> <pre><code>gpumdkit.sh -time gpumd\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>----------------- System Information ----------------\ntotal frames: 1050000\n-----------------------------------------------------\nCurrent Frame  Speed (steps/s)   Total Time       Time Left       Estimated End\n-------------   -------------   -------------   -------------   -----------------\n    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04\n    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#nep","title":"NEP \u5269\u4f59\u65f6\u95f4","text":"<p><code>time_consuming_nep.sh</code> \u4f30\u7b97 NEP \u8bad\u7ec3\u7684\u5269\u4f59\u65f6\u95f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code>\uff08\u5728\u5f53\u524d NEP \u5de5\u4f5c\u76ee\u5f55\u4e2d\uff09</p> <pre><code>gpumdkit.sh -time nep\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>+-----------------+-----------+-----------------+---------------------+\n|       Step      | Time Diff |    Time Left    |    Finish Time      |\n+-----------------+-----------+-----------------+---------------------+\n| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |\n| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |\n| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |\n+-----------------+-----------+-----------------+---------------------+\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_17","title":"\u6982\u7387\u5bc6\u5ea6\u5206\u6790","text":"<p><code>probability_density_analysis.py</code> \u8ba1\u7b97\u79fb\u52a8\u79bb\u5b50\u7684 3D \u6982\u7387\u5bc6\u5ea6\uff0c\u7528\u4e8e\u6269\u6563\u901a\u9053\u5206\u6790\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a \u53c2\u8003\u7ed3\u6784\uff08POSCAR\uff09\u3001\u8f68\u8ff9\u6587\u4ef6\uff08extxyz\uff09</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n</code></pre> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>LLZO.vasp</code> \u53c2\u8003\u7ed3\u6784\uff08POSCAR \u683c\u5f0f\uff09 <code>dump.xyz</code> \u8f68\u8ff9\u6587\u4ef6\uff08extxyz \u683c\u5f0f\uff09 <code>Li</code> \u76ee\u6807\u79fb\u52a8\u79bb\u5b50 <code>0.25</code> \u6982\u7387\u5bc6\u5ea6\u7f51\u683c\u95f4\u8ddd\uff08\u00c5\uff09 <p>\u8f93\u51fa\uff1a <code>probability_density_0.25.vasp</code> \u2014 VASP \u683c\u5f0f\u7684\u6982\u7387\u5bc6\u5ea6\u7f51\u683c\uff0c\u53ef\u7528 VESTA \u7b49\u5de5\u5177\u53ef\u89c6\u5316\u3002</p> <p>\u53ef\u89c6\u5316\u5efa\u8bae\uff1a</p> <ol> <li>\u5728 VESTA \u4e2d\u6253\u5f00 <code>probability_density_0.25.vasp</code></li> <li>\u4f7f\u7528 \"Edit \u2192 Data \u2192 Volumetric Data\" \u8c03\u6574\u7b49\u503c\u9762\u7ea7\u522b</li> <li>\u6309\u6570\u503c\u5bf9\u6982\u7387\u5bc6\u5ea6\u7740\u8272\uff0c\u4ee5\u7a81\u51fa\u4f18\u9009\u6269\u6563\u8def\u5f84</li> <li>\u53e0\u52a0\u6676\u4f53\u7ed3\u6784\u4f5c\u4e3a\u53c2\u8003</li> </ol>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_18","title":"\u793a\u4f8b\u5de5\u4f5c\u6d41","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_19","title":"\u7ed3\u6784\u8d28\u91cf\u68c0\u67e5","text":"<pre><code># 1. \u68c0\u67e5\u6210\u5206\ngpumdkit.sh -analyze_comp train.xyz\n\n# 2. \u68c0\u67e5\u80fd\u91cf/\u529b\u8303\u56f4\ngpumdkit.sh -range train.xyz force hist\n\n# 3. \u68c0\u67e5\u6700\u77ed\u8ddd\u79bb\ngpumdkit.sh -min_dist_pbc train.xyz\n\n# 4. \u67e5\u627e\u5f02\u5e38\u503c\uff08NEP \u8bad\u7ec3\u540e\uff09\n# \u4ea4\u4e92\uff1a5) \u5206\u6790\u5de5\u5177 \u2192 502\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_20","title":"\u7ed3\u6784\u8fc7\u6ee4\u6d41\u6c34\u7ebf","text":"<pre><code># 1. \u6309\u6700\u77ed\u8ddd\u79bb\u8fc7\u6ee4\ngpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n\n# 2. \u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4\ngpumdkit.sh -filter_box filtered_dist_pbc.xyz 13\n\n# 3. \u6309\u529b\u9608\u503c\u8fc7\u6ee4\ngpumdkit.sh -filter_value filtered_box.xyz force 20\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_21","title":"\u6269\u6563\u901a\u9053\u5206\u6790","text":"<pre><code># 1. \u8ba1\u7b97\u6982\u7387\u5bc6\u5ea6\ngpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n\n# 2. \u7528 VESTA \u53ef\u89c6\u5316\n# \u6253\u5f00 probability_density_0.25.vasp\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html","title":"\u547d\u4ee4\u53c2\u8003","text":"\ud83d\udccb \u547d\u4ee4\u53c2\u8003 <p>\u672c\u9875\u5217\u51fa GPUMDkit \u7a33\u5b9a\u7684\u547d\u4ee4\u884c\u5feb\u6377\u5165\u53e3\u3002\u5bf9\u4e8e\u53c2\u6570\u8f83\u591a\u3001\u9700\u8981\u9009\u62e9\u7684\u4efb\u52a1\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528\u4ea4\u4e92\u6a21\u5f0f\u3002</p> <p>\u6e90\u8868\u7ef4\u62a4\u5728 <code>docs/command_reference.tsv</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#gpumdkitsh-h","title":"<code>gpumdkit.sh -h</code> \u8f93\u51fa","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |\n| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_1","title":"\u4e3b\u547d\u4ee4","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-h</code> <code>gpumdkit.sh -h</code> \u663e\u793a\u901a\u7528\u5e2e\u52a9 <code>-update</code> <code>gpumdkit.sh -update</code> \u66f4\u65b0 GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> \u6e05\u7406\u5f53\u524d\u76ee\u5f55\u4e2d\u7684\u5197\u4f59\u6587\u4ef6"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_2","title":"\u683c\u5f0f\u8f6c\u6362","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K \u8f93\u51fa\u8f6c xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR \u8f6c extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF \u8f6c POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF \u8f6c extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR \u8f6c extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz \u591a\u5e27\u8f6c POSCAR \u6587\u4ef6 <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR \u8f6c LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump \u8f6c extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory \u8f6c extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> \u6309\u6676\u80de\u500d\u6570\u6269\u80de <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> \u6309\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> \u6dfb\u52a0 GPUMD group \u6807\u7b7e <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> \u6dfb\u52a0\u7ed3\u6784\u6743\u91cd <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> \u63d0\u53d6\u5355\u5e27 <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> \u6e05\u7406 extxyz \u5197\u4f59\u5c5e\u6027 <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> \u6309\u6bd4\u4f8b\u8303\u56f4\u63d0\u53d6\u5e27"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_3","title":"\u8ba1\u7b97\u5668","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> \u79bb\u5b50\u7535\u5bfc\u7387 <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP \u6027\u8d28\u9884\u6d4b <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP \u63cf\u8ff0\u7b26 <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u57fa\u4e8e NEP \u7684 NEB <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784\u4f18\u5316 <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> \u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> \u90bb\u5c45\u5217\u8868 <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> \u4f4d\u79fb <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> \u5e73\u5747\u7ed3\u6784 <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> \u516b\u9762\u4f53\u503e\u659c <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 \u5c40\u57df\u6781\u5316"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_4","title":"\u5206\u6790\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> \u6027\u8d28\u8303\u56f4\u5206\u6790 <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> \u6210\u5206\u5206\u6790 <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> \u5143\u7d20\u5217\u8868 <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> \u7535\u8377\u5e73\u8861\u68c0\u67e5 <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> \u65e0 PBC \u6700\u5c0f\u8ddd\u79bb <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> \u5e26 PBC \u6700\u5c0f\u8ddd\u79bb <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u5e26 PBC \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> \u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4 <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> \u6027\u8d28\u9608\u503c\u8fc7\u6ee4 <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> \u5143\u7d20\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4 <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> \u6982\u7387\u5bc6\u5ea6\u5206\u6790"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_5","title":"\u53ef\u89c6\u5316","text":"<p>\u4f7f\u7528\uff1a</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>\u5e38\u7528\u7c7b\u578b\u5305\u62ec <code>train</code>\u3001<code>prediction</code>\u3001<code>thermo</code>\u3001<code>msd</code>\u3001<code>sdc</code>\u3001<code>rdf</code>\u3001<code>emd</code>\u3001<code>nemd</code>\u3001<code>hnemd</code>\u3001<code>pdos</code> \u548c <code>plane-grid</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_6","title":"\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> \u76d1\u63a7 GPUMD \u6216 NEP \u8fdb\u5ea6 <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> \u4ea4\u4e92\u5f0f\u4fee\u6539 NEP \u6a21\u578b <code>-pynep</code> <code>gpumdkit.sh -pynep</code> \u5df2\u5f03\u7528\u7684 PyNEP FPS \u91c7\u6837"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html","title":"\u5de5\u4f5c\u6d41\u811a\u672c","text":"\ud83d\udd27 \u5de5\u4f5c\u6d41\u811a\u672c <p>\u5de5\u4f5c\u6d41\u811a\u672c\u7528\u4e8e\u81ea\u52a8\u5316\u91cd\u590d\u6027\u7684 DFT\u3001MD \u548c NEP \u6570\u636e\u51c6\u5907\u6b65\u9aa4\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_1","title":"\u4ea4\u4e92\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>3) Workflow\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+---------------------------------------------------------+\n|                      WORKFLOW TOOLS                     |\n+---------------------------------------------------------+\n| 301) SCF batch pretreatment                             |\n| 302) MD sample batch pretreatment (gpumd)               |\n| 303) MD sample batch pretreatment (lmp)                 |\n+---------------------------------------------------------+\n| 000) Return to the main menu                            |\n+---------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u5de5\u4f5c\u6d41 \u7528\u9014 301 SCF batch pretreatment \u51c6\u5907 DFT \u5355\u70b9\u8ba1\u7b97 302 MD sample batch pretreatment (GPUMD) \u51c6\u5907 GPUMD \u91c7\u6837\u8ba1\u7b97 303 MD sample batch pretreatment (LAMMPS) \u51c6\u5907 LAMMPS \u91c7\u6837\u8ba1\u7b97"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#scf","title":"SCF \u6279\u5904\u7406\u9884\u5904\u7406","text":"<p>\u9002\u7528\u4e8e\u5df2\u6709\u591a\u4e2a\u7ed3\u6784\uff0c\u9700\u8981\u51c6\u5907\u7b2c\u4e00\u6027\u539f\u7406\u5355\u70b9\u8ba1\u7b97\u7684\u60c5\u51b5\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#vasp","title":"VASP","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a\u7ed3\u6784\u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u811a\u672c\u6309\u4ee5\u4e0b\u987a\u5e8f\u68c0\u6d4b\uff1a</p> <ol> <li>\u5982\u679c\u5b58\u5728\u4e00\u4e2a\u6216\u591a\u4e2a <code>.vasp</code> \u6587\u4ef6\uff0c\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c <code>.vasp</code> \u548c <code>.xyz</code> \u540c\u65f6\u5b58\u5728\uff0c\u4f1a\u6253\u5370\u63d0\u793a\uff0c\u5e76\u53ea\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u53ea\u6709\u4e00\u4e2a <code>.xyz</code>\uff0c\u4f1a\u628a\u8fd9\u4e2a extxyz \u8f6c\u4e3a POSCAR \u6587\u4ef6\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</li> </ol> <p>\u8fd0\u884c\u524d\u7684\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>fp/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u7528\u6237\u628a <code>INCAR</code>\u3001<code>POTCAR</code>\u3001<code>KPOINTS</code> \u653e\u5230 <code>fp/</code> \u4e2d\uff0c\u8ba1\u7b97\u76ee\u5f55\u4f1a\u94fe\u63a5\u8fd9\u91cc\u7684\u6587\u4ef6\u3002</p> <p>\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u8f93\u5165\u7684 <code>prefix</code> \u4f1a\u4f5c\u4e3a\u8ba1\u7b97\u6587\u4ef6\u5939\u540d\u524d\u7f00\u3002\u540e\u7eed\u4f7f\u7528 <code>out2xyz</code> \u63d0\u53d6\u7ed3\u679c\u65f6\uff0c\u6587\u4ef6\u5939\u540d\u4f1a\u4f5c\u4e3a <code>config_type</code> \u5199\u5165 extxyz\uff0c\u4fbf\u4e8e\u4e4b\u540e\u68c0\u67e5\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#cp2k","title":"CP2K","text":"<p>CP2K \u53ef\u4ee5\u4ece\u4ea4\u4e92\u83dc\u5355\u8fdb\u5165\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u547d\u4ee4\u884c\u8c03\u7528\uff1a</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4f1a\u8981\u6c42\u8f93\u5165\uff1a</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>CP2K \u6a21\u677f\u5e94\u8bbe\u7f6e\u4e3a\u4ece <code>pos.xyz</code> \u8bfb\u53d6\u5750\u6807\u3002\u53c2\u8003\u6a21\u677f\u5728\uff1a</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>\u811a\u672c\u4f1a\u4e3a\u6bcf\u4e2a\u7ed3\u6784\u751f\u6210 <code>&lt;prefix&gt;_&lt;index&gt;/</code> \u76ee\u5f55\uff0c\u5e76\u5199\u5165 <code>input.inp</code> \u548c <code>pos.xyz</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#md","title":"MD \u91c7\u6837\u9884\u5904\u7406","text":""},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#gpumd","title":"GPUMD","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 302\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u68c0\u6d4b\u987a\u5e8f\u4e0e VASP SCF \u9884\u5904\u7406\u4e00\u81f4\uff1a\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</p> <p>\u8fd0\u884c\u524d\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>md/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>nep.txt</code> \u548c <code>run_*.in</code> \u653e\u5165 <code>md/</code>\u3002\u4f8b\u5982 <code>run_1.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_1/run.in</code>\uff0c<code>run_2.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_2/run.in</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#lammps","title":"LAMMPS","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 303\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\uff1b\u4e24\u79cd\u683c\u5f0f\u540c\u65f6\u5b58\u5728\u65f6\u4f18\u5148\u5904\u7406 <code>.vasp</code>\u3002</p> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>lmprun.in</code> \u548c <code>nep.txt</code> \u653e\u5230 <code>md/</code> \u4e2d\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_2","title":"\u4e3b\u52a8\u5b66\u4e60\u5f0f\u6d41\u7a0b","text":"<p>\u5e38\u89c1 NEP \u6570\u636e\u8fed\u4ee3\u6d41\u7a0b\uff1a</p> <ol> <li>\u4f7f\u7528\u5f53\u524d <code>nep.txt</code> \u8fd0\u884c MD\uff1b</li> <li>\u6536\u96c6 <code>dump.xyz</code> \u6216 <code>active.xyz</code>\uff1b</li> <li>\u5220\u9664\u660e\u663e\u4e0d\u5408\u7406\u7ed3\u6784\uff1b</li> <li>\u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\uff1b</li> <li>\u8fd0\u884c DFT \u5355\u70b9\uff1b</li> <li>\u5c06 DFT \u7ed3\u679c\u8f6c\u6362\u4e3a extxyz\uff1b</li> <li>\u8ffd\u52a0\u5230 <code>train.xyz</code>\uff1b</li> <li>\u91cd\u65b0\u8bad\u7ec3 NEP\u3002</li> </ol> <p>\u66f4\u5b8c\u6574\u7684\u5f00\u53d1\u7248\u4e3b\u52a8\u5b66\u4e60\u811a\u672c\u8bf4\u660e\u89c1 \u4e3b\u52a8\u5b66\u4e60\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_3","title":"\u57fa\u4e8e\u6a21\u677f\u7684\u6e29\u5ea6\u7cfb\u5217","text":"<p>\u5bf9\u4e8e\u7b80\u5355\u7684\u6e29\u5ea6\u7cfb\u5217\u6a21\u62df\uff0c\u4f7f\u7528 shell \u5faa\u73af\u5373\u53ef\uff1a</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>\u7136\u540e\u6839\u636e\u4f60\u7684\u96c6\u7fa4\u7cfb\u7edf\u63d0\u4ea4\u751f\u6210\u7684\u6587\u4ef6\u5939\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_4","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u5de5\u4f5c\u6d41\u811a\u672c\u548c\u96c6\u7fa4\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u6279\u91cf\u63d0\u4ea4\u524d\u5148\u7528\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u3002</li> <li>\u6a21\u677f\u6587\u4ef6\u5982 <code>INCAR</code>\u3001<code>KPOINTS</code>\u3001<code>POTCAR</code>\u3001<code>run.in</code> \u5e94\u4ed4\u7ec6\u68c0\u67e5\u3002</li> <li>\u6279\u91cf DFT \u524d\u5148\u7528\u5206\u6790\u548c\u91c7\u6837\u811a\u672c\u6e05\u7406\u5019\u9009\u7ed3\u6784\u3002</li> </ul>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html","title":"\u5feb\u901f\u5165\u95e8","text":"\ud83d\ude80 \u5feb\u901f\u5165\u95e8 <p>\u672c\u9875\u5e2e\u52a9\u4f60\u5b89\u88c5 GPUMDkit \u5e76\u8fd0\u884c\u7b2c\u4e00\u4e2a\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u6216\u76f4\u63a5\u4f7f\u7528\u547d\u4ee4\u884c\u9009\u9879\u6765\u4f7f\u7528 GPUMDkit\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>GPUMDkit \u4e3a\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u7684\u5e38\u89c1\u4efb\u52a1\u63d0\u4f9b\u7edf\u4e00\u5165\u53e3\u2014\u2014\u683c\u5f0f\u8f6c\u6362\u3001\u7ed3\u6784\u5206\u6790\u3001\u6027\u8d28\u8ba1\u7b97\u548c\u53ef\u89c6\u5316\u2014\u2014\u65e0\u9700\u7f16\u5199\u81ea\u5b9a\u4e49\u811a\u672c\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#1-python","title":"1. \u51c6\u5907 Python \u73af\u5883","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>\u90e8\u5206\u53ef\u9009\u529f\u80fd\u9700\u8981\u989d\u5916\u4f9d\u8d56\uff1a</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>\u5176\u4ed6 Python \u4f9d\u8d56\u7531\u5bf9\u5e94\u811a\u672c\u5728\u8fd0\u884c\u65f6\u5bfc\u5165\u3002\u5982\u679c\u7f3a\u5c11\u67d0\u4e2a\u5305\uff0c\u4f7f\u7528\u5bf9\u5e94\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u63d0\u793a\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#2-gpumdkit","title":"2. \u5b89\u88c5 GPUMDkit","text":"<p>\u514b\u9686\u4ed3\u5e93\u5e76\u8fd0\u884c\u5b89\u88c5\u811a\u672c\uff1a</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre> <p>\u5b89\u88c5\u811a\u672c\u4f1a\u5199\u5165 <code>GPUMDkit_path</code> \u548c <code>PATH</code> \u8bbe\u7f6e\uff0c\u5e76\u5728\u5f53\u524d shell \u4e2d\u52a0\u8f7d\u3002\u9ed8\u8ba4\u5199\u5165 <code>~/.bashrc</code>\uff1b\u5982\u679c\u5f53\u524d shell \u662f zsh\uff0c\u5219\u5199\u5165 <code>~/.zshrc</code>\u3002\u5982\u679c\u68c0\u6d4b\u5230\u5df2\u6709 GPUMDkit \u8def\u5f84\uff0c\u5b89\u88c5\u811a\u672c\u4f1a\u6253\u5370\u65e7\u8def\u5f84\u5e76\u8be2\u95ee\u662f\u5426\u66ff\u6362\uff1b\u4fee\u6539 rc \u6587\u4ef6\u524d\u4f1a\u5148\u521b\u5efa\u5907\u4efd\u3002</p> <p>\u5178\u578b\u5b89\u88c5\u8f93\u51fa\uff1a</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>\u5982\u679c\u4e4b\u524d\u5df2\u7ecf\u5b89\u88c5\u8fc7 GPUMDkit\uff0c\u53ef\u80fd\u4f1a\u770b\u5230\uff1a</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#3","title":"3. \u9a8c\u8bc1\u5b89\u88c5","text":"<pre><code>gpumdkit.sh -h\n</code></pre> <p>\u6b64\u547d\u4ee4\u4f1a\u6253\u5370\u5e2e\u52a9\u8868\uff0c\u5217\u51fa\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_3","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u6253\u5f00\u4e3b\u83dc\u5355\uff1a</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre> <p>\u6309\u6570\u5b57\u9009\u62e9\u6a21\u5757\u3002\u6bcf\u4e2a\u6a21\u5757\u63d0\u4f9b\u5305\u542b\u5177\u4f53\u529f\u80fd\u7684\u5b50\u83dc\u5355\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_4","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<p>\u76f4\u63a5\u547d\u4ee4\u4f7f\u7528\u56fa\u5b9a\u7684\u4f4d\u7f6e\u53c2\u6570\uff1a</p> <pre><code>gpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>\u7b2c\u4e00\u4e2a\u793a\u4f8b\u8bfb\u53d6 <code>POSCAR</code>\uff0c\u5199\u51fa <code>model.xyz</code>\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_5","title":"\u5e38\u89c1\u793a\u4f8b","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#gpumd-group","title":"\u6dfb\u52a0 GPUMD group \u6807\u7b7e","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>group \u6807\u7b7e\u7528\u4e8e\u4e00\u4e9b\u9700\u8981\u539f\u5b50\u5206\u7ec4\u7684 GPUMD \u76f8\u5173\u6d41\u7a0b\u548c\u5206\u6790\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep","title":"\u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep_1","title":"\u7ed8\u5236 NEP \u6d4b\u8bd5\u96c6\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_6","title":"\u7ed8\u5236\u70ed\u529b\u5b66\u91cf","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#msd","title":"\u7ed8\u5236 MSD \u548c\u81ea\u6269\u6563\u7cfb\u6570","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_7","title":"\u8bf4\u660e","text":"<ul> <li>\u4f7f\u7528 <code>gpumdkit.sh -h</code> \u67e5\u770b\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</li> <li>\u4f7f\u7528 <code>gpumdkit.sh -&lt;\u9009\u9879&gt; -h</code> \u83b7\u53d6\u7279\u5b9a\u9009\u9879\u7684\u5e2e\u52a9\uff08\u4f8b\u5982 <code>gpumdkit.sh -plt train -h</code>\uff09\u3002</li> <li>\u5404\u6a21\u5757\u7684\u8be6\u7ec6\u7528\u6cd5\u8bf7\u53c2\u89c1\u9996\u9875\u4e2d\u94fe\u63a5\u7684\u5bf9\u5e94\u6559\u7a0b\u9875\u9762\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html","title":"\u6781\u6027\u6750\u6599\u5206\u6790","text":"\ud83e\uddf2 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u672c\u6559\u7a0b\u4ecb\u7ecd GPUMDkit \u4e2d\u8ba1\u7b97\u5668\u9009\u9879 <code>406-410</code>\uff0c\u4ee5\u53ca <code>plane-grid</code> \u7ed8\u56fe\u6d41\u7a0b\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code> \u548c <code>Scripts/plt_scripts/</code></p> <p>\u672c\u6559\u7a0b\u5305\u542b\u901a\u7528\u5de5\u5177\u548c\u4f53\u7cfb\u76f8\u5173\u5de5\u5177\uff1a</p> <ul> <li><code>nlist</code>\u3001<code>disp</code> \u548c <code>avg-struct</code> \u53ef\u5e7f\u6cdb\u7528\u4e8e\u7ed3\u6784\u548c\u8f68\u8ff9\u5206\u6790\u3002</li> <li><code>oct-tilt</code> \u7528\u4e8e\u516b\u9762\u4f53\u73af\u5883\u5206\u6790\uff0c\u9700\u8981\u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u5468\u56f4\u6709 6 \u4e2a\u8fd1\u90bb\u3002</li> <li><code>pol-abo3</code> \u4e13\u7528\u4e8e <code>ABO3</code> \u4f53\u7cfb\u7684\u6781\u5316\u5206\u6790\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_1","title":"\u6982\u89c8","text":"\u6b65\u9aa4 CLI \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u8f93\u51fa \u6784\u5efa\u8fd1\u90bb\u5217\u8868 <code>gpumdkit.sh -calc nlist ...</code> <code>model.xyz</code> <code>nl-*.dat</code> \u8ba1\u7b97\u4f4d\u79fb <code>gpumdkit.sh -calc disp ...</code> \u8f68\u8ff9 + <code>nl-*.dat</code> <code>displacements.dat</code> \u5e73\u5747\u8f68\u8ff9\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct ...</code> \u8f68\u8ff9 \u5e73\u5747\u7ed3\u6784 extxyz \u516b\u9762\u4f53\u503e\u659c <code>gpumdkit.sh -calc oct-tilt ...</code> \u8f68\u8ff9 + B-O \u8fd1\u90bb\u5217\u8868 \u503e\u659c\u89d2\u6570\u636e\u8868 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 ...</code> \u8f68\u8ff9 + \u8fd1\u90bb\u5217\u8868 \u6781\u5316\u6570\u636e\u8868 plane-grid \u7ed8\u56fe <code>gpumdkit.sh -plt plane-grid ...</code> \u7ed3\u6784 + \u4f4d\u79fb\u6570\u636e \u5e73\u9762\u5256\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_2","title":"\u4f9d\u8d56","text":"<p>\u8fd9\u4e9b\u811a\u672c\u9700\u8981 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_3","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<p>\u9009\u9879 <code>406-410</code> \u662f\u672c\u6559\u7a0b\u4e2d\u7684\u6838\u5fc3\u529f\u80fd\u3002\u4e0b\u9762\u5404\u8282\u4f1a\u8bf4\u660e\u6bcf\u4e2a\u529f\u80fd\u7684\u7528\u9014\u548c\u8fd0\u884c\u65b9\u5f0f\u3002</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 4) Calculators\n</code></pre> <p>\u8ba1\u7b97\u5668\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5b8c\u6574\u53c2\u6570\u8bf4\u660e\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u547d\u4ee4\u67e5\u770b\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#406-calc_neighbor_listpy","title":"406) \u6784\u5efa\u8fd1\u90bb\u5217\u8868 (<code>calc_neighbor_list.py</code>)","text":"<p>\u4e3a\u6307\u5b9a\u4e2d\u5fc3\u5143\u7d20\u548c\u8fd1\u90bb\u5143\u7d20\u6784\u5efa\u8fd1\u90bb\u5217\u8868\u3002</p> <p>\u4f7f\u7528\u573a\u666f\uff1a \u8fd9\u901a\u5e38\u662f\u8fd0\u884c <code>disp</code>\u3001<code>oct-tilt</code> \u548c <code>pol-abo3</code> \u4e4b\u524d\u7684\u7b2c\u4e00\u6b65\uff0c\u56e0\u4e3a\u8fd9\u4e9b\u811a\u672c\u4f1a\u8bfb\u53d6 <code>nl-*.dat</code> \u8fd1\u90bb\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_4","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4e3a\u516b\u9762\u4f53\u5206\u6790\u6784\u5efa Ti-O \u6700\u8fd1 6 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# \u793a\u4f8b 2\uff1a\u4e3a A \u4f4d\u4e2d\u5fc3\u5206\u6790\u6784\u5efa Pb/Sr-O \u6700\u8fd1 12 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_5","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-x, --index</code>\uff1a   \u4ece\u8f93\u5165\u6587\u4ef6\u4e2d\u8bfb\u53d6\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-c, --cutoff</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u641c\u7d22\u622a\u65ad\u8ddd\u79bb\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> <li><code>-n, --neighbor-num</code>\uff08\u5fc5\u9700\uff09\uff1a   \u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u7684\u8fd1\u90bb\u6570\u91cf\u3002</li> <li><code>-d, --defect</code>\uff1a   \u7f3a\u9677\u6a21\u5f0f\u3002\u542f\u7528\u540e\uff0c\u5982\u679c\u8fd1\u90bb\u6570\u91cf\u4e0d\u8db3\uff0c\u7f3a\u5931\u4f4d\u7f6e\u4f1a\u7528\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u586b\u5145\u3002</li> <li><code>-C, --center-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u4e2d\u5fc3\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-E, --neighbor-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u8def\u5f84\u3002\u9ed8\u8ba4\u503c\uff1a<code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_6","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u8fd1\u90bb\u5217\u8868\u6587\u672c\u6587\u4ef6\uff0c\u4f8b\u5982 <code>nl-Ti-O.dat</code>\u3002</li> <li>\u6587\u4ef6\u662f\u4e00\u4e2a\u4e8c\u7ef4\u6574\u6570\u6570\u7ec4\uff0c\u5f62\u72b6\u4e3a <code>(n_center, neighbor_num + 1)</code>\u3002\u6bcf\u4e00\u884c\u5bf9\u5e94\u4e00\u4e2a\u4e2d\u5fc3\u539f\u5b50\uff1a\u7b2c\u4e00\u5217\u662f\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\uff0c\u540e\u7eed\u5217\u662f\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7\uff0c\u6240\u6709\u7f16\u53f7\u5747\u4e3a 1-based\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#407-calc_displacementpy","title":"407) \u4ece\u8f68\u8ff9\u8ba1\u7b97\u4f4d\u79fb (<code>calc_displacement.py</code>)","text":"<p>\u6839\u636e\u8f68\u8ff9\u6216\u6a21\u578b\u7ed3\u6784\u4ee5\u53ca\u8fd1\u90bb\u5217\u8868\uff0c\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_7","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece model.xyz \u8ba1\u7b97\u5355\u5e27\u4f4d\u79fb\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4f7f\u7528 movie.xyz \u7684\u6700\u540e 20% \u5e27\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_8","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7531 <code>nlist</code> \u751f\u6210\u7684\u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u90e8\u5206\u5e27\u3002   \u6574\u6570\u8868\u793a\u6700\u540e <code>N</code> \u5e27\uff1b   <code>0 &lt; value &lt; 1</code> \u8868\u793a\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_9","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>displacements.dat</code>\uff0c\u6216\u4f60\u6307\u5b9a\u7684\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e8c\u7ef4\u6570\u7ec4\uff1a\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u4e09\u5217\u5206\u522b\u4e3a <code>dx</code>\u3001<code>dy</code> \u548c <code>dz</code> \u4f4d\u79fb\u5206\u91cf\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#408-calc_averaged_structurepy","title":"408) \u8ba1\u7b97\u5e73\u5747\u7ed3\u6784 (<code>calc_averaged_structure.py</code>)","text":"<p>\u4ece\u9009\u5b9a\u8f68\u8ff9\u5e27\u751f\u6210\u4e00\u4e2a\u5e73\u5747\u7ed3\u6784\u3002 \u901a\u5e38\u53ef\u5728\u4f53\u7cfb\u5e73\u8861\u540e\u4f7f\u7528\uff1a\u5bf9\u4e8e\u63a5\u8fd1\u5e73\u8861\u7684\u56fa\u4f53\uff0c\u53ef\u4ee5\u5bf9\u76ee\u6807\u6e29\u5ea6\u4e0b\u7684\u4e00\u6bb5\u8f68\u8ff9\u53d6\u5e73\u5747\uff0c\u5e76\u5206\u6790\u8be5\u4ee3\u8868\u6027\u7ed3\u6784\uff0c\u800c\u4e0d\u662f\u9010\u5e27\u5904\u7406\u6bcf\u4e2a snapshot\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_10","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5e73\u5747\u6240\u6709\u5e27\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# \u793a\u4f8b 2\uff1a\u5e73\u5747\u9009\u5b9a\u5e27\u8303\u56f4 (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_11","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u8f68\u8ff9\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>movie.xyz</code>\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>averaged_structure.xyz</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_12","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u5355\u5e27\u5e73\u5747\u7ed3\u6784 extxyz \u6587\u4ef6\u3002</li> <li>\u4f4d\u7f6e\u5e73\u5747\u4f1a\u76f8\u5bf9\u4e8e\u6240\u9009\u7b2c\u4e00\u5e27\u8fdb\u884c MIC/PBC \u4fee\u6b63\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#409-calc_oct_tiltpy","title":"409) \u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c (<code>calc_oct_tilt.py</code>)","text":"<p>\u6839\u636e B-O \u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c\u89d2\u3002 \u8be5\u529f\u80fd\u5e38\u7528\u4e8e\u5206\u6790 <code>ABO3</code> \u4f53\u7cfb\u4e2d\u7684\u516b\u9762\u4f53\u8f6c\u52a8\u6a21\u5f0f\uff0c\u4f8b\u5982 <code>SrTiO3</code> \u548c <code>PbZrO3</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_13","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece\u5355\u5e27\u7ed3\u6784\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4ece\u8f68\u8ff9\u6700\u540e 20% \u5e27\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_14","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>octahedral_tilt.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_15","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>octahedral_tilt.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>theta_x</code>\u3001<code>theta_y</code>\u3001<code>theta_z</code>\uff0c\u5355\u4f4d\u4e3a degree\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#410-abo3-calc_polarization_abo3py","title":"410) \u8ba1\u7b97 ABO3 \u4f53\u7cfb\u6781\u5316 (<code>calc_polarization_abo3.py</code>)","text":"<p>\u8ba1\u7b97 <code>ABO3</code> \u4f53\u7cfb\u7684\u5c40\u57df\u6781\u5316\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_16","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5355\u5e27 ABO3 \u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# \u793a\u4f8b 2\uff1a\u9009\u5b9a\u8f68\u8ff9\u5e27\u8303\u56f4\u4e0a\u7684\u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_17","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>--nl-ba</code>\uff08\u5fc5\u9700\uff09\uff1a   B-A \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>--nl-bo</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>polarization.dat</code>\u3002</li> <li><code>--bec</code>\uff08\u5fc5\u9700\uff09\uff1a   Born \u6709\u6548\u7535\u8377\u9879\uff0c\u683c\u5f0f\u4e3a <code>Element=value</code>\u3002   \u793a\u4f8b\uff1a<code>Pb=2.5 Ti=4.0 O=-2.0</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul> <p>\u91cd\u8981\u68c0\u67e5\uff1a</p> <ul> <li><code>--bec</code> \u5fc5\u987b\u5305\u542b\u8f93\u5165\u7ed3\u6784\u4e2d\u7684\u6240\u6709\u5143\u7d20\u79cd\u7c7b\u3002</li> <li><code>--nl-ba</code> \u548c <code>--nl-bo</code> \u4e2d\u7684\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u5fc5\u987b\u5339\u914d\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_18","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>polarization.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>Px</code>\u3001<code>Py</code>\u3001<code>Pz</code>\uff0c\u5355\u4f4d\u4e3a <code>C/m^2</code>\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u5982\u679c\u603b Born \u7535\u8377\u4e0d\u5e73\u8861\uff0c\u811a\u672c\u4f1a\u6253\u5370 warning\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#plane-grid-plt_plane_gridpy","title":"Plane-grid \u53ef\u89c6\u5316 (<code>plt_plane_grid.py</code>)","text":"<p>\u4f60\u53ef\u4ee5\u53ef\u89c6\u5316 <code>displacements.dat</code> \u6216 <code>polarization.dat</code>\uff1a</p> <pre><code># \u793a\u4f8b 1\uff1aTi \u4f4d\u70b9\u4e0a\u7684\u4f4d\u79fb\u56fe\uff0c\u9009\u62e9\u7b2c\u4e00\u4e2a XY \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# \u793a\u4f8b 2\uff1aPb \u4f4d\u70b9\u4e0a\u7684\u6781\u5316\u56fe\uff0c\u9009\u62e9 XZ \u548c YZ \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>\u53c2\u6570\uff08\u5b8c\u6574\uff09\uff1a</p> <ul> <li><code>-i, --input</code>\uff1a   \u7528\u4e8e\u539f\u5b50\u5e03\u5c40\u548c\u5206\u5c42\u7684\u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-d, --disp</code>\uff1a   \u77e2\u91cf\u573a\u6570\u636e\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-e, --elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7528\u4e8e\u5c06\u77e2\u91cf\u6620\u5c04\u5230\u6676\u683c\u5c42\u4e0a\u7684\u4e2d\u5fc3\u5143\u7d20\u7b26\u53f7\u3002</li> <li><code>-m, --tol</code>\uff1a   \u7f51\u683c\u6620\u5c04\u7684\u5c42\u5bb9\u5dee\u3002\u9ed8\u8ba4\u503c\uff1a<code>1.0</code>\u3002</li> <li><code>-g, --target-size</code>\uff1a   \u671f\u671b\u7f51\u683c\u5927\u5c0f\uff0c\u683c\u5f0f\u4e3a <code>nx ny nz</code>\u3002</li> <li><code>-o, --save-dir</code>\uff1a   \u56fe\u7247\u8f93\u51fa\u76ee\u5f55\u3002\u9ed8\u8ba4\u503c\uff1a<code>plot</code>\u3002</li> <li><code>-f, --frame</code>\uff1a   \u5f53\u77e2\u91cf\u6570\u636e\u5305\u542b\u591a\u5e27\u65f6\uff0c\u8981\u53ef\u89c6\u5316\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>--select-xy</code>\uff1a   \u9009\u5b9a\u7684 XY \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-xz</code>\uff1a   \u9009\u5b9a\u7684 XZ \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-yz</code>\uff1a   \u9009\u5b9a\u7684 YZ \u5c42\u7f16\u53f7\u3002</li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li>\u5982\u679c\u9700\u8981\uff0c\u4f1a\u521b\u5efa\u8f93\u51fa\u76ee\u5f55\u3002</li> <li>\u56fe\u7247\u4fdd\u5b58\u4e3a <code>XY_*.png</code>\u3001<code>XZ_*.png</code>\u3001<code>YZ_*.png</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_19","title":"\u8f93\u51fa\u6587\u4ef6\u4e00\u89c8","text":"\u811a\u672c \u4e3b\u8981\u8f93\u51fa \u4fdd\u5b58\u5185\u5bb9 <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based \u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u548c\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7 <code>calc_displacement.py</code> <code>*.dat</code> \u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\uff08<code>dx dy dz</code>\uff0cAngstrom\uff09 <code>calc_averaged_structure.py</code> <code>*.xyz</code> \u4e00\u4e2a\u5e73\u5747\u7ed3\u6784 <code>calc_oct_tilt.py</code> <code>*.dat</code> \u516b\u9762\u4f53\u503e\u8f6c\u89d2\uff08<code>theta_x theta_y theta_z</code>\uff0cdegree\uff09 <code>calc_polarization_abo3.py</code> <code>*.dat</code> \u5c40\u57df\u6781\u5316\u77e2\u91cf\uff08<code>Px Py Pz</code>\uff0c<code>C/m^2</code>\uff09 <code>plt_plane_grid.py</code> <code>plot/*.png</code> \u6839\u636e\u77e2\u91cf\u573a\u6570\u636e\u7ed8\u5236\u7684 XY/XZ/YZ \u5e73\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_20","title":"\u771f\u5b9e\u6848\u4f8b","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3-","title":"PbTiO3 \u7684\u6e29\u5ea6\u9a71\u52a8\u94c1\u7535-\u987a\u7535\u76f8\u53d8","text":"<p>\u5047\u8bbe\u6240\u6709\u6587\u4ef6\u90fd\u4f4d\u4e8e\u5f53\u524d\u76ee\u5f55 <code>./</code>\uff1a</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> \u662f\u7528\u4e8e\u8fdb\u884c MD \u6a21\u62df\u7684\u521d\u59cb\u7ed3\u6784\u3002\u6bcf\u4e2a <code>TEMP K.xyz</code> \u662f\u5bf9\u5e94\u6e29\u5ea6\u4e0b\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1","title":"\u7b2c 1 \u6b65\uff1a\u4ece\u6bcf\u6761\u8f68\u8ff9\u7684\u540e\u534a\u6bb5\u5f97\u5230\u5e73\u5747\u7ed3\u6784","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>\u8fd9\u4f1a\u5199\u51fa <code>300K-avg.xyz</code>\u3001<code>350K-avg.xyz</code>\u3001...\u3001<code>800K-avg.xyz</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-modelxyz","title":"\u7b2c 2 \u6b65\uff1a\u57fa\u4e8e <code>model.xyz</code> \u6784\u5efa\u8fd1\u90bb\u5217\u8868","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3","title":"\u7b2c 3 \u6b65\uff1a\u4e3a\u6bcf\u4e2a\u6e29\u5ea6\u8ba1\u7b97\u4f4d\u79fb\u548c\u6781\u5316","text":"<p>\u8fd9\u91cc\u4f7f\u7528 Born \u6709\u6548\u7535\u8377\uff08BEC\uff09\uff0c\u4e0d\u662f\u540d\u4e49\u79bb\u5b50\u7535\u8377\u3002\u5bf9\u4e8e\u672c\u4f8b\u4e2d\u7684 PbTiO3\uff1a</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>\u4f60\u53ef\u4ee5\u4ece\u81ea\u5df1\u7684 DFPT \u8ba1\u7b97\u6216\u6587\u732e\u4e2d\u83b7\u5f97 BEC\u3002\u56e0\u6b64\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u548c\u6781\u5316\uff1a</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#4","title":"\u7b2c 4 \u6b65\uff1a\u7ed8\u5236\u5b9e\u7a7a\u95f4\u4f4d\u79fb\u548c\u6781\u5316\u56fe","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#5-","title":"\u7b2c 5 \u6b65\uff1a\u6784\u5efa\u6e29\u5ea6-\u5e8f\u53c2\u91cf\u66f2\u7ebf","text":"<p>\u7ed3\u5408\u6bcf\u4e2a\u6e29\u5ea6\u5e73\u5747\u7ed3\u6784\u7684\u6676\u683c\u4fe1\u606f\u548c\u6781\u5316\u6587\u4ef6\uff08<code>XX-pol.dat</code>\uff09\u8fdb\u884c\u5206\u6790\uff0c\u53ef\u4ee5\u5f97\u5230\u5982\u4e0b\u56fe\uff1a</p> <p>\u8be5\u8d8b\u52bf\u663e\u793a\u5728\u7ea6 <code>600 K</code> \u9644\u8fd1\u53d1\u751f\u660e\u663e\u76f8\u53d8\uff0c\u6b64\u65f6\u6781\u5316\u6d88\u5931\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3srtio3","title":"PbTiO3/SrTiO3 \u8d85\u6676\u683c\u4e2d\u7684\u62d3\u6251\u7ed3\u6784","text":"<p>\u5047\u8bbe <code>movie.xyz</code> \u662f\u5f53\u524d\u76ee\u5f55\u4e0b PbTiO3/SrTiO3 \u8d85\u6676\u683c\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1-25","title":"\u7b2c 1 \u6b65\uff1a\u4f7f\u7528\u6700\u540e 25% \u5e27\u6784\u5efa\u5e73\u5747\u7ed3\u6784","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-ti","title":"\u7b2c 2 \u6b65\uff1a\u6784\u5efa Ti \u8fd1\u90bb\u5217\u8868","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3-plane-grid","title":"\u7b2c 3 \u6b65\uff1a\u7ed8\u5236 plane-grid \u56fe","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>\u8fd9\u4f1a\u5f97\u5230\u4e0e\u524d\u9762\u5c55\u793a\u76f8\u4f3c\u7684\u56fe\u3002\u5728 PTO \u533a\u57df\u53ef\u4ee5\u770b\u5230\u7c7b\u4f3c\u6da1\u65cb\u7684\u6781\u5316\u56fe\u6837\uff0c\u800c STO \u533a\u57df\u7684\u6781\u5316\u63a5\u8fd1\u4e8e\u96f6\u3002</p> <p>\u6ce8\u610f\uff1a\u793a\u4f8b\u56fe\u4f7f\u7528\u4e86\u81ea\u5b9a\u4e49 colormap\u3002GPUMDkit \u9ed8\u8ba4\u8f93\u51fa\u4f7f\u7528\u4e0d\u540c\u98ce\u683c\uff0c\u53ef\u901a\u8fc7\u4fee\u6539\u7ed8\u56fe\u811a\u672c\u8fdb\u884c\u8c03\u6574\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_21","title":"\u5176\u4ed6\u4f53\u7cfb","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#-","title":"\u6709\u673a-\u65e0\u673a\u6742\u5316\u94c1\u7535\u4f53","text":"<p>\u5728\u8bb8\u591a\u6709\u673a-\u65e0\u673a\u94c1\u7535\u4f53\u4e2d\uff0c\u6781\u5316\u4e0e\u5404\u5411\u5f02\u6027\u7684\u5206\u5b50\u5355\u5143\u5bc6\u5207\u76f8\u5173\u3002\u8ddf\u8e2a\u5206\u5b50\u53d6\u5411\u7684\u4e00\u79cd\u5b9e\u7528\u65b9\u6cd5\u662f\u4f7f\u7528\u952e\u77e2\u91cf\u3002</p> <p>\u5bf9\u4e8e TMCM-CdCl3\uff0c\u53ef\u4ee5\u4f7f\u7528 TMCM \u5206\u5b50\u4e2d\u7684 C-Cl \u952e\u65b9\u5411\u4f5c\u4e3a\u53d6\u5411\u4ee3\u7406\uff0c\u5e76\u636e\u6b64\u4f30\u8ba1\u6781\u5316\u6001\uff1a</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p>\u968f\u540e\u53ef\u4ee5\u628a <code>ccl_vectors.dat</code> \u4f5c\u4e3a\u53d6\u5411\u5e8f\u53c2\u91cf\u8fdb\u884c\u5206\u6790\u3002\u66f4\u591a\u7ec6\u8282\u53ef\u53c2\u8003\uff1aPhys. Rev. Lett. 136, 016801\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_22","title":"\u5176\u4ed6\u94c1\u7535\u6750\u6599\u5bb6\u65cf","text":"<p>\u9664 <code>ABO3</code> \u5916\uff0c<code>ferrodispcalc</code> \u4e5f\u53ef\u4ee5\u9002\u914d\u8bb8\u591a\u94c1\u7535\u4f53\u7cfb\uff0c\u5305\u62ec\u6c2e\u5316\u7269\u3001\u6c27\u5316\u94ea\u57fa\u5316\u5408\u7269\u3001\u6709\u673a-\u65e0\u673a\u6742\u5316\u4f53\u7cfb\u4ee5\u53ca\u90e8\u5206\u4e8c\u7ef4\u94c1\u7535\u6750\u6599\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html","title":"\u683c\u5f0f\u8f6c\u6362","text":"\ud83d\udd04 \u683c\u5f0f\u8f6c\u6362 <p>\u683c\u5f0f\u8f6c\u6362\u6a21\u5757\u7528\u4e8e\u5728\u5e38\u89c1\u539f\u5b50\u6a21\u62df\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362\uff0c\u540c\u65f6\u63d0\u4f9b group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u5e27\u63d0\u53d6\u7b49\u5143\u6570\u636e\u5904\u7406\u529f\u80fd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>\u672c\u6a21\u5757\u5728\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u5e38\u7528\u7684\u7ed3\u6784\u548c\u8f68\u8ff9\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8fdb\u884c\u8f6c\u6362\u3002\u652f\u6301 VASP\u3001LAMMPS\u3001CP2K\u3001ABACUS\u3001CIF\u3001ASE \u8f68\u8ff9\u548c extxyz \u683c\u5f0f\u3002\u8fd8\u63d0\u4f9b\u6dfb\u52a0 group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u63d0\u53d6\u5e27\u548c\u6269\u80de\u7b49\u5de5\u5177\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":"<p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/format_conversion/</code></p> <p>\u786e\u4fdd\u5df2\u5b89\u88c5 GPUMDkit\u3002\u5b89\u88c5\u8bf4\u660e\u8bf7\u53c2\u89c1\u5feb\u901f\u5165\u95e8\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_3","title":"\u652f\u6301\u7684\u683c\u5f0f","text":"<ul> <li>VASP\uff1a<code>POSCAR</code>\u3001<code>CONTCAR</code>\u3001<code>OUTCAR</code>\u3001<code>XDATCAR</code></li> <li>LAMMPS\uff1adata \u6587\u4ef6\u548c dump \u8f68\u8ff9</li> <li>CP2K\uff1a\u8f93\u51fa log\u3001\u5750\u6807\u3001\u529b\u548c\u6676\u80de\u6587\u4ef6</li> <li>ABACUS\uff1aSCF/MD \u8f93\u51fa</li> <li>CIF\uff1a\u6676\u4f53\u7ed3\u6784\u6587\u4ef6</li> <li>ASE trajectory\uff1a<code>.traj</code></li> <li>extxyz\uff1aGPUMD \u548c NEP \u5e38\u7528\u7684\u7ed3\u6784\u683c\u5f0f</li> </ul>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_4","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>1) Format Conversion\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_5","title":"\u6bcf\u4e2a\u5165\u53e3\u7684\u4f5c\u7528","text":"\u5165\u53e3 \u8c03\u7528\u811a\u672c \u529f\u80fd \u9002\u7528\u573a\u666f <code>101</code> <code>out2xyz.sh</code> VASP OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c \u6279\u91cf\u8f6c\u6362 VASP \u8ba1\u7b97\u76ee\u5f55 <code>102</code> <code>mtp2xyz.py</code> MTP cfg \u8f6c extxyz \u8f6c\u6362 MTP \u6570\u636e <code>103</code> <code>cp2k_log2xyz.py</code> / <code>cp2k2xyz.py</code> CP2K \u8f6c extxyz \u53ef\u9009\u62e9 log/inp \u8def\u7ebf\u6216 pos/frc/cell \u8def\u7ebf <code>104</code> <code>abacus2xyz_scf.sh</code> / <code>abacus2xyz_md.sh</code> ABACUS \u8f6c extxyz \u8f6c\u6362 ABACUS SCF \u6216 MD \u8f93\u51fa <code>105</code> <code>exyz2pos.py</code> extxyz \u8f6c POSCAR \u5c06 extxyz \u6bcf\u4e00\u5e27\u5199\u6210 POSCAR <code>106</code> <code>add_groups.py</code> \u6dfb\u52a0 group \u6807\u7b7e \u4e3a GPUMD \u76f8\u5173\u6d41\u7a0b\u6dfb\u52a0\u539f\u5b50\u5206\u7ec4\u6807\u7b7e <code>107</code> <code>add_weight.py</code> \u6dfb\u52a0\u6743\u91cd \u4fee\u6539\u8bad\u7ec3\u96c6\u7ed3\u6784\u6743\u91cd <code>108</code> <code>get_frame.py</code> \u63d0\u53d6\u5355\u5e27 \u4ece extxyz \u8f68\u8ff9\u5bfc\u51fa\u67d0\u4e00\u5e27 <code>109</code> <code>clean_xyz.py</code> \u6e05\u7406 XYZ \u4fe1\u606f \u5220\u9664\u591a\u4f59 extxyz \u5c5e\u6027 <code>110</code> <code>replicate.py</code> \u6269\u80de \u6309\u500d\u6570\u6216\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>out2exyz</code> <code>out2exyz.py</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c VASP OUTCAR \u8f6c\u6362\u7684\u53e6\u4e00\u4e2a\u5165\u53e3 <code>pos2exyz</code> <code>pos2exyz.py</code> POSCAR \u8f6c extxyz \u8f6c\u6362\u5355\u4e2a\u7ed3\u6784 <code>cif2pos</code> <code>cif2pos.py</code> CIF \u8f6c POSCAR \u4ece CIF \u51c6\u5907 VASP \u8f93\u5165 <code>cif2exyz</code> <code>cif2exyz.py</code> CIF \u8f6c extxyz \u4ece CIF \u51c6\u5907 GPUMDkit \u8f93\u5165 <code>xdat2exyz</code> <code>xdatcar2exyz.py</code> XDATCAR \u8f6c extxyz \u8f6c\u6362 VASP MD \u8f68\u8ff9 <code>pos2lmp</code> <code>pos2lmp.py</code> POSCAR \u8f6c LAMMPS data \u51c6\u5907 LAMMPS \u8f93\u5165 <code>lmp2exyz</code> <code>lmp2exyz.py</code> LAMMPS dump \u8f6c extxyz \u8f6c\u6362 LAMMPS \u8f68\u8ff9 <code>traj2exyz</code> <code>traj2exyz.py</code> ASE traj \u8f6c extxyz \u8f6c\u6362 ASE \u8f68\u8ff9"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_6","title":"\u5feb\u901f\u547d\u4ee4\u8868","text":"\u6765\u6e90 \u76ee\u6807 \u547d\u4ee4 OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz POSCAR model.xyz</code> extxyz POSCAR \u6587\u4ef6 <code>gpumdkit.sh -exyz2pos train.xyz</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_7","title":"\u5e38\u89c1\u4f8b\u5b50","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#vasp","title":"\u8f6c\u6362 VASP \u7ed3\u679c","text":"<p>\u529f\u80fd\uff1a \u5728\u76ee\u5f55\u4e2d\u641c\u7d22 VASP OUTCAR \u6587\u4ef6\uff0c\u5e76\u5c06\u5b83\u4eec\u8f6c\u6362\u4e3a\u5355\u4e2a extxyz \u6587\u4ef6\uff0c\u7528\u4e8e NEP \u8bad\u7ec3\u6216\u5206\u6790\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>\u4e5f\u53ef\u4ee5\u4f7f\u7528 Python \u7248\u672c\uff1a</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u683c\u5f0f\u8f6c\u6362\u83dc\u5355\u4e2d\u9009\u62e9 <code>101</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u51fa\uff1a \u5305\u542b\u8f6c\u6362\u540e\u7ed3\u6784\u7684 extxyz \u6587\u4ef6\uff0c\u53ef\u7528\u4e8e NEP \u8bad\u7ec3\u6216\u8fdb\u4e00\u6b65\u5206\u6790\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#group","title":"\u6dfb\u52a0 group \u6807\u7b7e","text":"<p>\u529f\u80fd\uff1a \u4e3a\u7ed3\u6784\u6587\u4ef6\u6dfb\u52a0\u539f\u5b50 group \u6807\u7b7e\u3002\u4e00\u4e9b GPUMD \u76f8\u5173\u6d41\u7a0b\u9700\u8981 group \u6807\u7b7e\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>\u8be5\u547d\u4ee4\u8bfb\u53d6\u8f93\u5165\u7ed3\u6784\uff0c\u5e76\u5199\u51fa\u5e26 group \u4fe1\u606f\u7684 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u683c\u5f0f\u8f6c\u6362\u83dc\u5355\u4e2d\u9009\u62e9 <code>106</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u51fa\uff1a \u6dfb\u52a0\u4e86 group \u6807\u7b7e\u7684 extxyz \u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_8","title":"\u5e38\u7528\u811a\u672c\u8bf4\u660e","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>\u9002\u5408\u628a\u5355\u4e2a VASP \u7ed3\u6784\u8f6c\u6210 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz-poscar","title":"extxyz \u8f6c POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>\u4f1a\u5c06 extxyz \u4e2d\u6240\u6709\u5e27\u8f6c\u6362\u6210 <code>POSCAR_*.vasp</code> \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3\uff1a<code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#lammps-dump-extxyz","title":"LAMMPS dump \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>\u5143\u7d20\u987a\u5e8f\u5fc5\u987b\u5bf9\u5e94 LAMMPS \u4e2d\u7684 atom type ID\u3002\u4f8b\u5982 type 1 \u662f Li\u3001type 2 \u662f Y\u3001type 3 \u662f Cl\uff0c\u5219\u8f93\u5165 <code>Li Y Cl</code>\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#cif","title":"CIF \u8f6c\u6362","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>\u5982\u679c\u540e\u7eed\u9700\u8981 VASP \u8ba1\u7b97\uff0c\u4f7f\u7528 <code>-cif2pos</code>\uff1b\u5982\u679c\u540e\u7eed\u8981\u8fdb\u5165 GPUMDkit \u5206\u6790\uff0c\u4f7f\u7528 <code>-cif2exyz</code>\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_9","title":"\u6dfb\u52a0\u6743\u91cd","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>\u7528\u4e8e\u7ed9\u8bad\u7ec3\u96c6\u7ed3\u6784\u6dfb\u52a0\u6216\u4fee\u6539\u6743\u91cd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_10","title":"\u6269\u80de","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>\u7b2c\u4e00\u79cd\u6309\u6676\u80de\u500d\u6570\u6269\u80de\uff0c\u7b2c\u4e8c\u79cd\u6309\u76ee\u6807\u539f\u5b50\u6570\u81ea\u52a8\u9009\u62e9\u6269\u80de\u65b9\u5f0f\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_11","title":"\u63d0\u53d6\u5355\u5e27","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>\u4ece extxyz \u8f68\u8ff9\u4e2d\u63d0\u53d6\u7b2c <code>1000</code> \u5e27\uff08\u7d22\u5f15\u4ece 0 \u5f00\u59cb\uff09\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz","title":"\u62c6\u5206\u591a\u5e27 extxyz","text":"<p><code>split_single_xyz.py</code> \u5c06\u591a\u5e27 extxyz \u6587\u4ef6\u62c6\u5206\u4e3a\u5355\u5e27\u6587\u4ef6\u3002</p> <pre><code>python Scripts/format_conversion/split_single_xyz.py dump.xyz\n</code></pre> <p>\u751f\u6210 <code>model_0.xyz</code>\u3001<code>model_1.xyz</code>\u3001... \u7b49\u5355\u5e27\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#mtp","title":"MTP \u8f6c\u6362","text":"<p>\u5c06 MTP <code>.cfg</code> \u683c\u5f0f\u8f6c\u6362\u4e3a extxyz\uff1a</p> <pre><code>gpumdkit.sh    # \u9009\u62e9\uff1a1) \u683c\u5f0f\u8f6c\u6362 \u2192 102\n</code></pre> <p>\u4ea4\u4e92\u63d0\u793a\uff1a</p> <pre><code>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;\nExample: train.cfg Pd Ag\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#abacus","title":"ABACUS \u8f6c\u6362","text":"<p>\u5c06 ABACUS \u8f93\u51fa\u8f6c\u6362\u4e3a extxyz\uff1a</p> <pre><code>gpumdkit.sh    # \u9009\u62e9\uff1a1) \u683c\u5f0f\u8f6c\u6362 \u2192 104\n</code></pre> <p>\u83dc\u5355\u63d0\u4f9b\u4e24\u4e2a\u9009\u9879\uff1a</p> <ol> <li>SCF \u8f93\u51fa\uff08<code>running_scf.log</code>\uff09</li> <li>MD \u8f93\u51fa\uff08<code>running_md.log</code>\uff09</li> </ol>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_12","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae LAMMPS \u8f6c\u6362\u540e\u5143\u7d20\u4e0d\u5bf9 \u68c0\u67e5 dump \u6587\u4ef6\u540e\u7684\u5143\u7d20\u987a\u5e8f extxyz \u5143\u6570\u636e\u592a\u591a \u4f7f\u7528 <code>-clean_xyz input.xyz clean.xyz</code> \u63d0\u53d6\u5e27\u4e0d\u5bf9 \u6ce8\u610f\u5e27\u7d22\u5f15\u901a\u5e38\u4ece 0 \u5f00\u59cb"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_13","title":"\u8bf4\u660e","text":"<p>\u5982\u679c\u67d0\u4e2a\u8f6c\u6362\u811a\u672c\u7f3a\u5c11\u6240\u9700 Python \u5305\uff0c\u8fd0\u884c\u8be5\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u76f8\u5e94\u63d0\u793a\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html","title":"\u7ed3\u6784\u91c7\u6837","text":"\ud83d\udce6 \u7ed3\u6784\u91c7\u6837 <p>\u7ed3\u6784\u91c7\u6837\u7528\u4e8e\u4ece\u8f68\u8ff9\u4e2d\u9009\u62e9\u5019\u9009\u7ed3\u6784\u3001\u751f\u6210\u6270\u52a8\u7ed3\u6784\uff0c\u6216\u6839\u636e\u6a21\u578b\u504f\u5dee\u6311\u9009\u503c\u5f97\u8fdb\u4e00\u6b65\u8ba1\u7b97\u7684\u7ed3\u6784\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/sample_structures/</code></p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_1","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>2) Sample Structures\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u65b9\u6cd5 \u7528\u9014 201 uniform/random \u4ece\u8f68\u8ff9\u4e2d\u5747\u5300\u6216\u968f\u673a\u62bd\u5e27 202 PyNEP notice \u53ea\u6253\u5370\u63d0\u793a\uff1b\u771f\u6b63\u8fd0\u884c PyNEP \u8bf7\u7528 <code>gpumdkit.sh -pynep</code> 203 NepTrain FPS \u4f7f\u7528 NepTrain \u63cf\u8ff0\u7b26\u7684 FPS \u91c7\u6837 204 perturb \u4ece POSCAR/CONTCAR \u751f\u6210\u6270\u52a8\u7ed3\u6784 205 force deviation \u4ece active learning \u8f93\u51fa\u4e2d\u9009\u62e9\u9ad8\u504f\u5dee\u7ed3\u6784"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_2","title":"\u5747\u5300/\u968f\u673a\u91c7\u6837","text":"<p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>201</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>\u4f8b\u5982\u8f93\u5165\uff1a</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>\u6216\uff1a</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>uniform</code> / <code>random</code> \u91c7\u6837\u65b9\u6cd5 <code>50</code> / <code>100</code> \u91c7\u6837\u7ed3\u6784\u6570 <code>500</code> \u53ef\u9009\uff0c\u8df3\u8fc7\u524d 500 \u5e27 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#neptrain-fps","title":"NepTrain FPS","text":"<p>NepTrain \u7248\u672c\u7684 FPS\u3002\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>203</code>\uff1b\u4e5f\u53ef\u4ee5\u76f4\u63a5\u8fd0\u884c\u811a\u672c\uff1a</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>203</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u5165\uff1a</p> \u6587\u4ef6 \u542b\u4e49 <code>dump.xyz</code> \u5019\u9009\u7ed3\u6784 <code>train.xyz</code> \u5f53\u524d\u8bad\u7ec3\u96c6 <code>nep.txt</code> \u7528\u4e8e\u8ba1\u7b97\u63cf\u8ff0\u7b26\u7684 NEP \u6a21\u578b <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>\u8fd0\u884c\u65f6\u53ef\u4ee5\u9009\u62e9\u6309\u6700\u5c0f\u8ddd\u79bb\u9608\u503c\u91c7\u6837\uff0c\u6216\u6307\u5b9a\u91c7\u6837\u7ed3\u6784\u6570\u3002\u811a\u672c\u968f\u540e\u4f1a\u6253\u5370\uff1a</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>NepTrain</code>\uff0c\u8fd0\u884c\u65f6\u4f1a\u63d0\u793a\u76f8\u5173\u5f15\u7528\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep","title":"PyNEP \u65e7\u5165\u53e3","text":"<p>PyNEP FPS \u4ecd\u7136\u4fdd\u7559\u517c\u5bb9\uff0c\u4f46\u53ea\u901a\u8fc7 <code>-pynep</code> \u5165\u53e3\u8c03\u7528\u3002</p> <p>\u5982\u679c\u5728\u4ea4\u4e92\u83dc\u5355\u4e2d\u9009\u62e9 <code>202</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep_1","title":"\u4e32\u884c PyNEP","text":"<pre><code>python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep_2","title":"\u5e76\u884c PyNEP","text":"<pre><code>python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u6700\u540e\u4e00\u4e2a\u53c2\u6570\u662f CPU \u7ebf\u7a0b\u6570\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#gpumdkit","title":"GPUMDkit \u5165\u53e3","text":"<pre><code>gpumdkit.sh -pynep\n</code></pre> <p>\u968f\u540e\u8f93\u5165\uff1a</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u8fd9\u4e2a\u5165\u53e3\u9700\u8981 <code>pynep</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_3","title":"\u7ed3\u6784\u6270\u52a8","text":"<p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>204</code>\uff1b\u4e5f\u53ef\u4ee5\u76f4\u63a5\u8fd0\u884c\u811a\u672c\uff1a</p> <pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>204</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>POSCAR</code> \u8f93\u5165\u7ed3\u6784 <code>20</code> \u751f\u6210\u7ed3\u6784\u6570 <code>0.03</code> \u6676\u80de\u6270\u52a8\u6bd4\u4f8b <code>0.2</code> \u539f\u5b50\u6270\u52a8\u8ddd\u79bb\uff0c\u5355\u4f4d Angstrom <code>uniform</code> \u6270\u52a8\u65b9\u5f0f\uff0c\u53ef\u9009 <code>normal</code>\u3001<code>uniform</code>\u3001<code>const</code> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>POSCAR_01.vasp</code>\u3001<code>POSCAR_02.vasp</code> \u7b49</li> </ul> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>dpdata</code>\u3002\u4f7f\u7528\u6b64\u529f\u80fd\u65f6\u5efa\u8bae\u5f15\u7528 dpdata \u5305\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_4","title":"\u6700\u5927\u529b\u504f\u5dee\u7ed3\u6784\u9009\u62e9","text":"<p>\u8be5\u529f\u80fd\u9700\u8981\u914d\u5408 GPUMD \u7684 <code>active</code> \u547d\u4ee4\u4f7f\u7528\u3002<code>active</code> \u901a\u8fc7\u59d4\u5458\u4f1a\u8bc4\u5ba1\u673a\u5236\uff0c\u8ba9\u591a\u6761\u52bf\u51fd\u6570\u5bf9\u540c\u4e00\u7ed3\u6784\u8fdb\u884c\u9884\u6d4b\uff0c\u5e76\u8bb0\u5f55\u6bcf\u4e2a\u7ed3\u6784\u7684\u6700\u5927\u529b\u504f\u5dee\u3002<code>select_max_modev.py</code> \u4f1a\u4ece <code>active.out</code> \u548c <code>active.xyz</code> \u4e2d\u9009\u62e9\u529b\u504f\u5dee\u8f83\u5927\u7684\u7ed3\u6784\uff0c\u5199\u5165 <code>selected.xyz</code>\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>205</code>\uff1b\u4e5f\u53ef\u4ee5\u76f4\u63a5\u8fd0\u884c\u811a\u672c\uff1a</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>205</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>\u9700\u8981\u5f53\u524d\u76ee\u5f55\u4e0b\u6709\uff1a</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_5","title":"\u5e27\u8303\u56f4\u63d0\u53d6","text":"<p><code>frame_range.py</code> \u662f\u4e00\u4e2a\u72ec\u7acb\u7684 CLI \u5de5\u5177\uff0c\u4e0d\u5728\u7ed3\u6784\u91c7\u6837\u4ea4\u4e92\u83dc\u5355 <code>201\u2013205</code> \u4e2d\u3002\u5b83\u9002\u5408\u5728\u91c7\u6837\u524d\u5148\u622a\u53d6\u8f68\u8ff9\u7684\u4e00\u6bb5\uff0c\u4f8b\u5982\u53ea\u4fdd\u7559\u5e73\u8861\u540e\u7684\u540e\u534a\u6bb5\u8f68\u8ff9\u3002</p> <pre><code>gpumdkit.sh -frame_range dump.xyz 0 0.8\npython Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>\u8fd9\u4f1a\u5199\u5165\u8f68\u8ff9 0% \u5230 80% \u7684\u5e27\u3002\u53c2\u6570\u4f7f\u7528\u8f68\u8ff9\u6bd4\u4f8b\uff0c\u8303\u56f4\u4e3a <code>0</code> \u5230 <code>1</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_6","title":"\u793a\u4f8b\u547d\u4ee4","text":"<p>\u4e0b\u9762\u662f\u4e00\u4e2a\u5e38\u89c1\u7684\u91c7\u6837\u524d\u5904\u7406\u987a\u5e8f\uff1a\u5148\u7528\u5206\u6790\u5de5\u5177\u68c0\u67e5\u548c\u8fc7\u6ee4\u5019\u9009\u8f68\u8ff9\uff0c\u518d\u8fdb\u884c FPS \u91c7\u6837\u3002\u524d\u4e24\u4e2a\u547d\u4ee4\u5c5e\u4e8e\u5206\u6790\u5de5\u5177\uff0c\u6700\u540e\u4e00\u6b65\u5c5e\u4e8e\u672c\u9875\u7684\u7ed3\u6784\u91c7\u6837\u3002</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>\u6700\u540e\u4e00\u6b65\u4e5f\u53ef\u4ee5\u5728\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>2) \u7ed3\u6784\u91c7\u6837 \u2192 203</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_7","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae FPS \u9009\u51fa\u592a\u591a\u76f8\u4f3c\u7ed3\u6784 \u8c03\u5927\u8ddd\u79bb\u9608\u503c\u6216\u9650\u5236\u6700\u5927\u9009\u62e9\u6570 \u6270\u52a8\u7ed3\u6784\u4e0d\u5408\u7406 \u51cf\u5c0f <code>cell_pert</code> \u548c <code>atom_pert</code> <code>active.out</code> \u548c <code>active.xyz</code> \u4e0d\u5339\u914d \u786e\u4fdd\u6765\u81ea\u540c\u4e00\u6b21 GPUMD active \u8fd0\u884c PCA \u56fe\u5f02\u5e38 \u68c0\u67e5 <code>nep.txt</code> \u662f\u5426\u548c\u4e24\u4e2a\u6570\u636e\u96c6\u5143\u7d20\u4e00\u81f4"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html","title":"\u7ed8\u56fe\u811a\u672c","text":"\ud83d\udcca \u7ed8\u56fe\u811a\u672c <p>\u7ed8\u56fe\u6a21\u5757\u5305\u542b\u4e00\u7cfb\u5217 Python \u811a\u672c\uff0c\u7528\u4e8e\u53ef\u89c6\u5316 GPUMD\u3001NEP \u548c GPUMDkit \u8ba1\u7b97\u5668\u4ea7\u751f\u7684\u6570\u636e\u3002\u6240\u6709\u56fe\u8868\u5747\u53ef\u4ea4\u4e92\u663e\u793a\u6216\u4fdd\u5b58\u4e3a\u9ad8\u5206\u8fa8\u7387 PNG \u6587\u4ef6\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/plt_scripts/</code></p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_1","title":"\u5feb\u901f\u5165\u53e3","text":"<pre><code>gpumdkit.sh -plt              # \u663e\u793a\u6240\u6709\u7ed8\u56fe\u9009\u9879\ngpumdkit.sh -plt &lt;type&gt;       # \u751f\u6210\u6307\u5b9a\u56fe\u8868\ngpumdkit.sh -plt &lt;type&gt; save  # \u4fdd\u5b58\u4e3a PNG\ngpumdkit.sh -plt &lt;type&gt; -h    # \u663e\u793a\u7279\u5b9a\u56fe\u8868\u7684\u5e2e\u52a9\n</code></pre> <p>\u8fd0\u884c <code>gpumdkit.sh -plt</code> \u4f1a\u663e\u793a\u7ed8\u56fe\u547d\u4ee4\u83dc\u5355\uff1a</p> <pre><code>+-----------------------------------------------------------------------------------------------+\n|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |\n+-----------------------------------------------------------------------------------------------+\n|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |\n+-----------------------------------------------------------------------------------------------+\n|                                    NEP Training &amp; Evaluation                                  |\n+-----------------------------------------------------------------------------------------------+\n|  train          - NEP training results           prediction     - NEP prediction results      |\n|  train_test     - NEP train and test results     parity_density - Parity density plot         |\n|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |\n|  charge         - Charge distribution            born_charge    - Born effective charges      |\n|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |\n|  des            - Descriptors                    lr             - Learning rate for gnep      |\n+-----------------------------------------------------------------------------------------------+\n|                                     Diffusion &amp; Transport                                     |\n+-----------------------------------------------------------------------------------------------+\n|  msd            - Mean square displacement       msd_conv       - MSD convergence             |\n|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |\n|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|\n|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |\n|  D_xyz          - Directional Arrhenius D                                                     |\n+-----------------------------------------------------------------------------------------------+\n|                                    MD &amp; Structural Analysis                                   |\n+-----------------------------------------------------------------------------------------------+\n|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |\n|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |\n|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |\n|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |\n|  doas           - Density of atomistic states                                                 |\n+-----------------------------------------------------------------------------------------------+\n|                                        Heat Transport                                         |\n+-----------------------------------------------------------------------------------------------+\n|  emd            - EMD results                    nemd           - NEMD results                |\n|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |\n+-----------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u8bad\u7ec3\u4e0e\u9884\u6d4b","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_trainpy","title":"plt_train.py","text":"<p>\u53ef\u89c6\u5316 NEP \u8bad\u7ec3\u8fc7\u7a0b\uff0c\u5305\u62ec loss \u66f2\u7ebf\u3001RMSE \u6f14\u5316\uff0c\u4ee5\u53ca\u80fd\u91cf/\u529b/virial \u7684 DFT vs NEP parity plot\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code>\u3001<code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_predictionpy","title":"plt_prediction.py","text":"<p>\u53ef\u89c6\u5316\u6d4b\u8bd5\u96c6\u4e0a\u7684 NEP \u9884\u6d4b\u7ed3\u679c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_test.out</code>\u3001<code>force_test.out</code>\u3001<code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test         # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_train_testpy","title":"plt_train_test.py","text":"<p>\u5c06\u8bad\u7ec3\u96c6\u548c\u6d4b\u8bd5\u96c6\u7684 parity plot \u5408\u5e76\u663e\u793a\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code>\u3001<code>energy_test.out</code>\u3001<code>force_test.out</code>\u3001<code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_parity_densitypy","title":"plt_parity_density.py","text":"<p>\u751f\u6210\u57fa\u4e8e\u5bc6\u5ea6\u7684 parity plot\uff0c\u9002\u7528\u4e8e\u5927\u6570\u636e\u96c6\uff08\u6563\u70b9\u56fe\u8fc7\u4e8e\u5bc6\u96c6\u65f6\u66f4\u6613\u9605\u8bfb\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_force_errorspy","title":"plt_force_errors.py","text":"<p>\u53c2\u8003 Liu et al. \u7684\u65b9\u6cd5\u7ed8\u5236\u529b\u8bef\u5dee\u8bc4\u4f30\u6307\u6807\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>force_train.out</code></p> <p>\u663e\u793a\u6307\u6807\uff1a - \u529b\u5927\u5c0f\u8bef\u5dee (delta_F) - \u529b\u89d2\u5ea6\u8bef\u5dee (delta_theta) - \u8bef\u5dee\u5206\u5e03</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_learning_ratepy","title":"plt_learning_rate.py","text":"<p>\u53ef\u89c6\u5316 <code>gnep</code> \u8bad\u7ec3\u8fc7\u7a0b\u4e2d\u7684\u5b66\u4e60\u7387\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code></p> <p>\u6ce8\u610f\uff1a \u4ec5\u9002\u7528\u4e8e <code>gnep</code> \u8bad\u7ec3\u8fc7\u7a0b\u3002</p> <pre><code>gpumdkit.sh -plt lr\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_nep_restartpy","title":"plt_nep_restart.py","text":"<p>\u53ef\u89c6\u5316 <code>nep.restart</code> \u6587\u4ef6\u4e2d\u5b58\u50a8\u7684\u53c2\u6570\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>nep.restart</code></p> <pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_chargepy","title":"plt_charge.py","text":"<p>\u7ed8\u5236 <code>qNEP</code> \u6a21\u578b\u7684\u7535\u8377\u5206\u5e03\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>charge_train.out</code></p> <p>\u91cd\u8981\u63d0\u793a\uff1a \u786e\u4fdd\u8bad\u7ec3\u96c6\u548c\u7535\u8377\u8f93\u51fa\u7684\u539f\u5b50\u6392\u5e8f\u4e00\u81f4\u3002\u5efa\u8bae\u4f7f\u7528\u5168 batch \u8bad\u7ec3\u6216\u5148\u8fd0\u884c\u9884\u6d4b\u6b65\u9aa4\u3002</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_born_chargepy","title":"plt_born_charge.py","text":"<p>\u4e3a\u8bad\u7ec3\u96c6\u548c\u6d4b\u8bd5\u96c6\u521b\u5efa Born \u6709\u6548\u7535\u8377 (BEC) \u7684 parity plot\u3002\u5168\u96f6\u53c2\u8003 BEC \u7684\u7ed3\u6784\u4f1a\u88ab\u8fc7\u6ee4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>bec_train.out</code>\u3001<code>bec_test.out</code></p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec          # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_2","title":"\u70ed\u529b\u5b66\u91cf","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_thermopy","title":"plt_thermo.py","text":"<p>\u7efc\u5408\u53ef\u89c6\u5316\u70ed\u529b\u5b66\u6027\u8d28\u7684\u4e3b\u811a\u672c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_thermo2py-plt_thermo3py","title":"plt_thermo2.py &amp; plt_thermo3.py","text":"<p>\u4e0d\u540c\u98ce\u683c\u7684\u70ed\u529b\u5b66\u91cf\u53ef\u89c6\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_3","title":"\u6269\u6563\u548c\u79bb\u5b50\u8f93\u8fd0","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msdpy","title":"plt_msd.py","text":"<p>\u7ed8\u5236\u5404\u65b9\u5411\u7684\u5747\u65b9\u4f4d\u79fb (MSD)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msd_allpy","title":"plt_msd_all.py","text":"<p>\u5f53 GPUMD \u4e2d\u4f7f\u7528 <code>all_groups</code> \u65f6\uff0c\u5206\u522b\u7ed8\u5236\u6bcf\u79cd\u539f\u5b50\u7684 MSD\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code>\uff08\u9700\u8981\u4f7f\u7528 <code>all_groups</code> \u9009\u9879\u8ba1\u7b97\uff09</p> <p>\u8981\u6c42\uff1a <code>run.in</code> \u4e2d\u7684 <code>compute_msd</code> \u547d\u4ee4\u5fc5\u987b\u4f7f\u7528 <code>all_groups</code>\u3002</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msd_convergence_checkpy","title":"plt_msd_convergence_check.py","text":"<p>\u68c0\u67e5\u4e0d\u540c\u65f6\u95f4\u7a97\u53e3\u4e0b MSD \u8ba1\u7b97\u7684\u6536\u655b\u6027\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd_step*.out</code>\uff08\u9700\u8981\u5728 <code>compute_msd</code> \u4e2d\u4f7f\u7528 <code>save_every</code> \u9009\u9879\uff09</p> <p>\u8981\u6c42\uff1a \u5728 <code>compute_msd</code> \u547d\u4ee4\u4e2d\u4f7f\u7528 <code>save_every</code>\u3002</p> <p>\u7528\u9014\uff1a \u9a8c\u8bc1 MSD \u662f\u5426\u5df2\u5145\u5206\u6536\u655b\u4ee5\u51c6\u786e\u8ba1\u7b97\u6269\u6563\u7cfb\u6570\u3002</p> <pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_sdcpy","title":"plt_sdc.py","text":"<p>\u7ed8\u5236\u81ea\u6269\u6563\u7cfb\u6570 (SDC) \u968f\u65f6\u95f4\u7684\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_arrhenius_dpy","title":"plt_arrhenius_d.py","text":"<p>\u521b\u5efa Arrhenius \u6269\u6563\u7cfb\u6570\u56fe\uff08log10 D vs 1000/T\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>*K/msd.out</code>\uff08\u6bcf\u4e2a\u6e29\u5ea6\u5b50\u76ee\u5f55\u4e0b\u7684 <code>msd.out</code>\uff09</p> <pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D             # \u66ff\u4ee3\u547d\u4ee4\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_arrhenius_sigmapy","title":"plt_arrhenius_sigma.py","text":"<p>\u521b\u5efa Arrhenius \u79bb\u5b50\u7535\u5bfc\u7387\u56fe\uff08ln(\u03c3\u00b7T) vs 1000/T\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code>\uff08\u6bcf\u4e2a\u6e29\u5ea6\u5b50\u76ee\u5f55\uff09</p> <pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma         # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_4","title":"\u70ed\u8f93\u8fd0","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_emdpy","title":"plt_emd.py","text":"<p>\u5206\u6790\u5e76\u7ed8\u5236\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (EMD) \u70ed\u5bfc\u7387\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 EMD \u8f93\u51fa\u6587\u4ef6</p> <pre><code>gpumdkit.sh -plt emd x        # x \u65b9\u5411\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_nemdpy","title":"plt_nemd.py","text":"<p>\u53ef\u89c6\u5316\u975e\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (NEMD) \u70ed\u8f93\u8fd0\u6027\u8d28\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 NEMD \u8f93\u51fa\u6587\u4ef6</p> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u8bf4\u660e <code>real_length</code> \u4f20\u70ed\u533a\u5b9e\u9645\u957f\u5ea6\uff08nm\uff09\uff0c\u8bbe\u4e3a <code>Auto</code> \u53ef\u81ea\u52a8\u8ba1\u7b97 <code>scale_eff_size</code> \u6709\u6548\u622a\u9762\u79ef\u7f29\u653e\u56e0\u5b50\uff08\u9ed8\u8ba4\uff1a1\uff09\u3002\u4e09\u7ef4\u4f53\u76f8\u7528 1\uff1b\u542b\u771f\u7a7a\u5c42\u7684\u4f4e\u7ef4\u4f53\u7cfb\u7528 S_box / S_eff <code>cutoff_freq</code> SHC \u8ba1\u7b97\u7684\u622a\u6b62\u9891\u7387\uff08THz\uff0c\u9ed8\u8ba4\uff1a60\uff09 <code>save</code> \u53ef\u9009\uff0c\u4fdd\u5b58\u56fe\u7247\u4e3a <code>nemd.png</code> <p>\u6ce8\u610f\uff1a \u5982\u679c\u6ca1\u6709 SHC \u6570\u636e\uff0c\u4f7f\u7528 <code>save</code> \u65f6\u8bf7\u5c06 <code>scale_eff_size</code> \u548c <code>cutoff_freq</code> \u8bbe\u4e3a\u4efb\u610f\u5360\u4f4d\u6570\u5b57\u3002</p> <pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_hnemdpy","title":"plt_hnemd.py","text":"<p>\u7ed8\u5236\u975e\u5747\u5300\u975e\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (HNEMD) \u7ed3\u679c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 HNEMD \u8f93\u51fa\u6587\u4ef6</p> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u8bf4\u660e <code>scale_eff_size</code> \u6709\u6548\u622a\u9762\u79ef\u7f29\u653e\u56e0\u5b50\uff08\u9ed8\u8ba4\uff1a1\uff09 <code>cutoff_freq</code> SHC \u8ba1\u7b97\u7684\u622a\u6b62\u9891\u7387\uff08THz\uff0c\u9ed8\u8ba4\uff1a60\uff09 <code>save</code> \u53ef\u9009\uff0c\u4fdd\u5b58\u56fe\u7247\u4e3a <code>hnemd.png</code> <p>\u6ce8\u610f\uff1a \u5982\u679c\u6ca1\u6709 SHC \u6570\u636e\uff0c\u4f7f\u7528 <code>save</code> \u65f6\u8bf7\u5c06 <code>scale_eff_size</code> \u548c <code>cutoff_freq</code> \u8bbe\u4e3a\u4efb\u610f\u5360\u4f4d\u6570\u5b57\u3002</p> <pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_5","title":"\u7ed3\u6784\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_rdfpy","title":"plt_rdf.py","text":"<p>\u7ed8\u5236\u5f84\u5411\u5206\u5e03\u51fd\u6570 (RDF)\uff0c\u5c55\u793a\u539f\u5b50\u5bf9\u5173\u8054\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf               # \u663e\u793a\u6240\u6709 RDF \u5bf9\ngpumdkit.sh -plt rdf &lt;column&gt;      # \u663e\u793a\u7279\u5b9a\u5bf9\n</code></pre> <p>\u5b8c\u6574 RDF \u8f93\u51fa\uff1a</p> <p>\u5355\u5bf9 RDF\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_rdf_pmfpy","title":"plt_rdf_pmf.py","text":"<p>\u7ed8\u5236 RDF \u4e0e\u5e73\u5747\u529b\u52bf (PMF) \u7684\u7ec4\u5408\u56fe\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf_pmf\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_vacpy","title":"plt_vac.py","text":"<p>\u7ed8\u5236\u901f\u5ea6\u81ea\u76f8\u5173\u51fd\u6570 (VAC)\u3002\u53ef\u7528\u4e8e\u5206\u6790\u58f0\u5b50\u6027\u8d28\u548c\u539f\u5b50\u52a8\u529b\u5b66\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>sdc.out</code>\uff08\u7ed8\u56fe\u811a\u672c\u4f1a\u4ece\u8be5\u6587\u4ef6\u4e2d\u8bfb\u53d6 VAC \u76f8\u5173\u5217\uff09</p> <p>\u8f93\u51fa\uff1a \u4ea4\u4e92\u5f0f\u56fe\u8868\u6216 <code>vac.png</code>\uff08\u4f7f\u7528 <code>save</code> \u9009\u9879\u65f6\uff09</p> <pre><code>gpumdkit.sh -plt vac\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_cohesivepy","title":"plt_cohesive.py","text":"<p>\u4ece <code>cohesive.out</code> \u7ed8\u5236\u5185\u805a\u80fd\u66f2\u7ebf\u3002\u53ef\u7528\u4e8e\u5206\u6790\u6676\u683c\u7a33\u5b9a\u6027\u548c\u5e73\u8861\u6676\u683c\u5e38\u6570\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>cohesive.out</code>\uff08\u5404\u5411\u540c\u6027\u7f29\u653e\u56e0\u5b50 vs \u5185\u805a\u80fd\uff09</p> <p>\u8f93\u51fa\uff1a \u4ea4\u4e92\u5f0f\u56fe\u8868\u6216 <code>cohesive.png</code>\uff08\u4f7f\u7528 <code>save</code> \u9009\u9879\u65f6\uff09</p> <pre><code>gpumdkit.sh -plt cohesive\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_net_forcepy","title":"plt_net_force.py","text":"<p>\u7ed8\u5236\u7ed3\u6784\u4e0a\u7684\u51c0\u529b\u5206\u5e03\uff0c\u53ef\u7528\u4e8e\u8bc6\u522b\u95ee\u9898\u6784\u578b\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>\u53c2\u8003\u6587\u732e\uff1a arXiv:2510.19774</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_6","title":"\u58f0\u5b50","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_pdospy","title":"plt_pdos.py","text":"<p>\u8ba1\u7b97\u5e76\u7ed8\u5236\u5f52\u4e00\u5316\u7684\u901f\u5ea6\u81ea\u76f8\u5173\u51fd\u6570 (VAC)\u3001\u58f0\u5b50\u6001\u5bc6\u5ea6 (PDOS) \u548c\u70ed\u5bb9 (Cv)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>model.xyz</code>\u3001<code>run.in</code>\u3001<code>dos.out</code>\u3001<code>mvac.out</code></p> <pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>\u70ed\u5bb9\u8f93\u51fa\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#dimer","title":"\u63cf\u8ff0\u7b26\u3001Dimer \u548c\u5176\u4ed6\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_descriptorspy","title":"plt_descriptors.py","text":"<p>\u4f7f\u7528\u964d\u7ef4\u65b9\u6cd5\uff08PCA \u6216 UMAP\uff09\u53ef\u89c6\u5316\u9ad8\u7ef4 NEP \u63cf\u8ff0\u7b26\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>descriptors.npy</code>\uff08\u7531 <code>gpumdkit.sh -calc des</code> \u751f\u6210\uff09</p> <p>\u65b9\u6cd5\uff1a - <code>pca</code> \u2014 \u4e3b\u6210\u5206\u5206\u6790 - <code>umap</code> \u2014 \u7edf\u4e00\u6d41\u5f62\u903c\u8fd1\u4e0e\u6295\u5f71</p> <pre><code># \u5148\u8ba1\u7b97\u63cf\u8ff0\u7b26\ngpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n\n# \u518d\u53ef\u89c6\u5316\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_descriptors_comparepy","title":"plt_descriptors_compare.py","text":"<p>\u6bd4\u8f83\u591a\u4e2a\u8bad\u7ec3\u96c6\u6216\u6a21\u578b\u7684\u63cf\u8ff0\u7b26\u3002</p> <pre><code>gpumdkit.sh -plt des_compare\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_dimerpy","title":"plt_dimer.py","text":"<p>\u7ed8\u5236\u4e8c\u805a\u4f53\u76f8\u4e92\u4f5c\u7528\u66f2\u7ebf\u3002\u5c06\u4e24\u4e2a\u539f\u5b50\u653e\u5165\u7acb\u65b9\u76d2\u5b50\uff0830 \u00c5\uff09\uff0c\u4f7f\u7528 NEP \u6a21\u578b\u8ba1\u7b97\u52bf\u80fd\u548c\u529b\u968f\u8ddd\u79bb\u7684\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>nep.txt</code></p> <pre><code>gpumdkit.sh -plt dimer &lt;element1&gt; &lt;element2&gt; &lt;nep_model&gt;\ngpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>\u53c2\u8003\u6587\u732e\uff1a J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_doaspy","title":"plt_doas.py","text":"<p>\u7ed8\u5236 Wang et al. \u63d0\u51fa\u7684\u539f\u5b50\u6001\u5bc6\u5ea6 (DOAS)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>doas.out</code>\uff08\u7531 <code>gpumdkit.sh -calc doas</code> \u8ba1\u7b97\uff09</p> <pre><code>gpumdkit.sh -plt doas &lt;doas.out&gt; &lt;species&gt;\ngpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plane-grid","title":"\u6781\u6027\u6750\u6599\u7684 Plane-Grid \u7ed8\u56fe","text":"<p>\u6b64\u5de5\u4f5c\u6d41\u5c06\u4f4d\u79fb\u6216\u6781\u5316\u6570\u636e\u6620\u5c04\u5230\u7f51\u683c\u4e0a\uff0c\u5e76\u7ed8\u5236\u9009\u5b9a\u5e73\u9762\u7684\u8f6e\u5ed3\u3002\u8be6\u7ec6\u7528\u6cd5\u548c\u5b9e\u9645\u6848\u4f8b\u8bf7\u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790\u3002</p> <p>\u4f9d\u8d56\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>\u5178\u578b\u524d\u7f6e\u6b65\u9aa4\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>\u4f7f\u7528\u65b9\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_7","title":"\u5feb\u901f\u53c2\u8003\u8868","text":"\u547d\u4ee4 \u8f93\u5165\u6587\u4ef6 \u7528\u9014 <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP \u8bad\u7ec3\u7ed3\u679c <code>prediction</code> / <code>test</code> <code>*_test.out</code> NEP \u9884\u6d4b\u7ed3\u679c <code>train_test</code> <code>*_train.out</code>, <code>*_test.out</code> \u5408\u5e76 parity plot <code>parity_density</code> <code>*_train.out</code> \u5bc6\u5ea6 parity plot <code>force_errors</code> <code>force_train.out</code> \u529b\u8bef\u5dee\u6307\u6807 <code>lr</code> <code>loss.out</code> (gnep) \u5b66\u4e60\u7387 <code>restart</code> <code>nep.restart</code> \u91cd\u542f\u6587\u4ef6\u53c2\u6570 <code>charge</code> <code>charge_train.out</code> \u7535\u8377\u5206\u5e03 <code>born_charge</code> / <code>bec</code> <code>bec_train.out</code>, <code>bec_test.out</code> Born \u6709\u6548\u7535\u8377 <code>thermo</code> <code>thermo.out</code> \u70ed\u529b\u5b66\u91cf <code>msd</code> <code>msd.out</code> \u5747\u65b9\u4f4d\u79fb <code>msd_all</code> <code>msd.out</code> (all_groups) \u5168\u7ec4\u5206 MSD <code>msd_conv</code> <code>msd_step*.out</code> MSD \u6536\u655b\u6027\u68c0\u67e5 <code>sdc</code> <code>msd.out</code> \u81ea\u6269\u6563\u7cfb\u6570 <code>arrhenius_d</code> / <code>D</code> <code>*K/msd.out</code> Arrhenius \u6269\u6563\u7cfb\u6570 <code>arrhenius_sigma</code> / <code>sigma</code> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> Arrhenius \u79bb\u5b50\u7535\u5bfc\u7387 <code>rdf</code> <code>rdf.out</code> \u5f84\u5411\u5206\u5e03\u51fd\u6570 <code>rdf_pmf</code> <code>rdf.out</code> RDF + \u5e73\u5747\u529b\u52bf <code>vac</code> <code>sdc.out</code> \u901f\u5ea6\u81ea\u76f8\u5173 <code>cohesive</code> <code>cohesive.out</code> \u5185\u805a\u80fd\u66f2\u7ebf <code>net_force</code> <code>train.xyz</code> \u51c0\u529b\u5206\u5e03 <code>doas</code> <code>doas.out</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>des</code> <code>descriptors.npy</code> \u63cf\u8ff0\u7b26 PCA/UMAP <code>dimer</code> <code>nep.txt</code> \u4e8c\u805a\u4f53\u80fd\u91cf/\u529b\u66f2\u7ebf <code>pdos</code> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code> VAC \u548c PDOS <code>emd</code> EMD \u8f93\u51fa EMD \u70ed\u5bfc\u7387 <code>nemd</code> NEMD \u8f93\u51fa NEMD \u70ed\u8f93\u8fd0 <code>hnemd</code> HNEMD \u8f93\u51fa HNEMD \u70ed\u8f93\u8fd0 <code>viscosity</code> \u7c98\u5ea6\u8f93\u51fa \u7c98\u5ea6"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html","title":"\u81ea\u5b9a\u4e49\u547d\u4ee4","text":"\ud83d\udd27 \u81ea\u5b9a\u4e49\u547d\u4ee4 <p>GPUMDkit \u652f\u6301\u4ece ~/.gpumdkit.in \u52a0\u8f7d\u81ea\u5b9a\u4e49\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u628a\u5e38\u7528\u811a\u672c\u6216\u5de5\u4f5c\u6d41\u5c01\u88c5\u6210 <code>custom_</code> \u5f00\u5934\u7684 Bash \u51fd\u6570\uff0c\u7136\u540e\u901a\u8fc7 <code>gpumdkit.sh -\u547d\u4ee4\u540d</code> \u8c03\u7528\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_1","title":"\u8bbe\u7f6e","text":"<p>\u7f16\u8f91\u914d\u7f6e\u6587\u4ef6\uff1a</p> <pre><code>vi ~/.gpumdkit.in\n</code></pre> <p>\u81ea\u5b9a\u4e49\u51fd\u6570\u9700\u8981\u4f7f\u7528 <code>custom_</code> \u524d\u7f00\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_2","title":"\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_3","title":"\u7b80\u5355\u95ee\u5019","text":"<p>\u5728 <code>~/.gpumdkit.in</code> \u4e2d\u5199\u5165\uff1a</p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>\u7136\u540e\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -hello\n</code></pre> <p>\u4f60\u4f1a\u770b\u5230\u7c7b\u4f3c\u8f93\u51fa\uff1a</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_4","title":"\u5e26\u5fc5\u9700\u53c2\u6570\u7684\u547d\u4ee4","text":"<pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -greet Zihan\n</code></pre> <p>\u8f93\u51fa\uff1a</p> <pre><code>Hello, Zihan!\n</code></pre> <p>\u4f20\u9012\u53c2\u6570\u65f6\uff0c\u53ef\u4ee5\u7528 <code>\"$@\"</code> \u5b89\u5168\u5730\u8f6c\u53d1\u6240\u6709\u53c2\u6570\uff1b\u5982\u679c\u9700\u8981\u4ece\u7b2c\u4e00\u4e2a\u53c2\u6570\u5f00\u59cb\u5f15\u7528\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528 <code>${@:1}</code>\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_5","title":"\u8c03\u7528\u5916\u90e8\u811a\u672c","text":"<p>\u5982\u679c\u5e0c\u671b\u50cf\u8c03\u7528 GPUMDkit \u5185\u7f6e\u547d\u4ee4\u4e00\u6837\u8c03\u7528\u81ea\u5df1\u7684\u811a\u672c\uff1a</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -nepanalyse\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_6","title":"\u8fdb\u9636\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_7","title":"\u6279\u5904\u7406\u7ed8\u56fe","text":"<p>\u5bf9\u591a\u4e2a\u76ee\u5f55\u6279\u91cf\u7ed8\u56fe\uff1a</p> <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -batch_plot dir1 dir2 dir3\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_8","title":"\u8bad\u7ec3\u96c6\u5206\u6790\u6d41\u7a0b","text":"<p>\u628a\u591a\u4e2a\u5206\u6790\u547d\u4ee4\u7ec4\u5408\u6210\u4e00\u4e2a\u5165\u53e3\uff1a</p> <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -analyze_training train.xyz\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_9","title":"\u81ea\u5b9a\u4e49\u6570\u636e\u51c6\u5907\u6d41\u7a0b","text":"<pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    gpumdkit.sh -out2xyz ./\n    gpumdkit.sh -filter_value train.xyz force 30\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -prep_training\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_10","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u547d\u4ee4\u540d\u5c3d\u91cf\u6e05\u695a\uff0c\u4f8b\u5982 <code>custom_analyze_training</code> \u6bd4 <code>custom_at</code> \u66f4\u5bb9\u6613\u7ef4\u62a4\u3002</li> <li>\u5bf9\u9700\u8981\u53c2\u6570\u7684\u547d\u4ee4\uff0c\u5efa\u8bae\u5728\u53c2\u6570\u4e3a\u7a7a\u65f6\u6253\u5370\u7528\u6cd5\u63d0\u793a\u3002</li> <li>\u8c03\u7528\u5916\u90e8\u811a\u672c\u65f6\uff0c\u5c3d\u91cf\u7528 <code>\"$@\"</code> \u4fdd\u7559\u53c2\u6570\u4e2d\u7684\u7a7a\u683c\u548c\u7279\u6b8a\u5b57\u7b26\u3002</li> <li>\u6279\u5904\u7406\u76ee\u5f55\u65f6\uff0c\u6ce8\u610f\u4f7f\u7528 <code>cd \"$dir\"</code>\uff0c\u907f\u514d\u8def\u5f84\u4e2d\u6709\u7a7a\u683c\u65f6\u51fa\u9519\u3002</li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html","title":"\u8ba1\u7b97\u5668\u811a\u672c","text":"\ud83e\uddee \u8ba1\u7b97\u5668\u811a\u672c <p>\u8ba1\u7b97\u5668\u6a21\u5757\u7528\u4e8e\u4ece MD \u8f68\u8ff9\u3001NEP \u6a21\u578b\u548c\u7ed3\u6784\u6587\u4ef6\u4e2d\u8ba1\u7b97\u6750\u6599\u6027\u8d28\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code></p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_1","title":"\u529f\u80fd\u6982\u89c8","text":"<p>\u8ba1\u7b97\u5668\u6a21\u5757\u5927\u81f4\u53ef\u4ee5\u5206\u4e3a\u4e09\u7c7b\uff1a</p> <ul> <li>\u8f68\u8ff9\u6027\u8d28\uff1a \u4ece GPUMD \u6216 extxyz \u8f68\u8ff9\u8ba1\u7b97 MSD\u3001\u79bb\u5b50\u7535\u5bfc\u7387\u7b49\u65f6\u95f4\u76f8\u5173\u6027\u8d28\uff1b</li> <li>NEP \u8f85\u52a9\u8ba1\u7b97\uff1a \u4f7f\u7528 NEP \u6a21\u578b\u9884\u6d4b\u80fd\u91cf/\u529b/\u5e94\u529b\u3001\u63d0\u53d6\u63cf\u8ff0\u7b26\u3001\u8ba1\u7b97 DOAS\u3001\u8fdb\u884c NEB \u6216\u7ed3\u6784\u4f18\u5316\uff1b</li> <li>\u6781\u6027\u6750\u6599\u5206\u6790\uff1a \u4e3a\u9499\u949b\u77ff\u548c\u6781\u6027\u6750\u6599\u6784\u5efa\u8fd1\u90bb\u5217\u8868\u3001\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u3001\u5e73\u5747\u7ed3\u6784\u3001\u516b\u9762\u4f53\u503e\u8f6c\u548c\u5c40\u57df\u6781\u5316\u3002</li> </ul> <p>\u5982\u679c\u4f60\u8fd8\u4e0d\u719f\u6089\u67d0\u4e2a\u811a\u672c\uff0c\u5efa\u8bae\u5148\u7528\u4ea4\u4e92\u6a21\u5f0f\u67e5\u770b\u8f93\u5165\u63d0\u793a\uff1b\u5982\u679c\u5df2\u7ecf\u77e5\u9053\u53c2\u6570\uff0c\u5219\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528 <code>gpumdkit.sh -calc ...</code> \u8c03\u7528\u3002</p> \u4efb\u52a1 \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u79bb\u5b50\u7535\u5bfc\u7387 <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>\u3001<code>thermo.out</code>\u3001<code>model.xyz</code> MSD <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz \u8f68\u8ff9 NEP \u9884\u6d4b <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP \u6a21\u578b NEP \u63cf\u8ff0\u7b26 <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP \u6a21\u578b DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP \u6a21\u578b NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u521d\u672b\u6001\u7ed3\u6784 \u7ed3\u6784\u4f18\u5316 <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784 + NEP \u6a21\u578b \u90bb\u5c45\u5217\u8868 <code>gpumdkit.sh -calc nlist ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u4f4d\u79fb <code>gpumdkit.sh -calc disp ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u5e73\u5747\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u516b\u9762\u4f53\u503e\u8f6c <code>gpumdkit.sh -calc oct-tilt ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u67e5\u770b\u5b8c\u6574\u5e2e\u52a9\uff1a</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>\u547d\u4ee4\u884c\u5e2e\u52a9\u8868\u7c7b\u4f3c\uff1a</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>4) Calculators</code>\uff0c\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_2","title":"\u79bb\u5b50\u7535\u5bfc\u7387","text":"<p><code>calc_ion_conductivity.py</code> \u4ece <code>msd.out</code> \u8ba1\u7b97\u79bb\u5b50\u6269\u6563\u7cfb\u6570\u548c\u79bb\u5b50\u7535\u5bfc\u7387\u3002</p> <pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>401</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>\u5e38\u7528\u8f93\u5165\u6587\u4ef6\uff1a</p> \u6587\u4ef6 \u4f5c\u7528 <code>msd.out</code> \u5fc5\u9700\uff0cMSD \u6570\u636e <code>thermo.out</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u6e29\u5ea6 <code>model.xyz</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u4f53\u79ef\u548c\u79bb\u5b50\u6570 <code>run.in</code> \u53ef\u9009\uff0c\u8bc6\u522b\u6269\u80de\u4fe1\u606f <p>\u5982\u679c\u7f3a\u5c11\u81ea\u52a8\u8bc6\u522b\u6240\u9700\u6587\u4ef6\uff0c\u811a\u672c\u4f1a\u4ea4\u4e92\u5f0f\u8be2\u95ee\u6e29\u5ea6\u3001\u4f53\u79ef\u548c\u79bb\u5b50\u6570\u3002</p> <p>\u624b\u52a8\u6a21\u5f0f\u7684\u63d0\u793a\u7c7b\u4f3c\uff1a</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Diffusivity (D):\n  D_x: 4.153e-07 cm^2/s\n  D_y: 4.174e-07 cm^2/s\n  D_z: 2.610e-07 cm^2/s\n  D_total: 3.646e-07 cm^2/s\n------------------------------\nIonic Conductivity:\n  Sigma_x: 2.576e-02 mS/cm\n  Sigma_y: 2.589e-02 mS/cm\n  Sigma_z: 1.619e-02 mS/cm\n  Sigma_total: 2.261e-02 mS/cm\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#msd","title":"\u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD","text":"<p><code>calc_msd.py</code> \u53ef\u4ee5\u76f4\u63a5\u4ece extxyz \u8f68\u8ff9\u4e2d\u8ba1\u7b97\u6307\u5b9a\u5143\u7d20\u7684 MSD\u3002</p> <pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>412</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>Li</code> \u76ee\u6807\u6269\u6563\u5143\u7d20 <code>10</code> \u5e27\u95f4\u9694\uff0c\u5355\u4f4d fs <code>5000</code> \u53ef\u9009\uff0c\u6700\u5927\u76f8\u5173\u6b65\u6570 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>msd.out</code></li> </ul> <p><code>msd.out</code> \u7684\u5f00\u5934\u662f\u6587\u672c\u8868\u683c\uff0c\u5305\u542b\u65f6\u95f4\u548c\u4e0d\u540c\u65b9\u5411\u7684 MSD \u5217\u3002\u751f\u6210\u540e\u53ef\u4ee5\u7ee7\u7eed\u4f7f\u7528\u7ed8\u56fe\u547d\u4ee4\u68c0\u67e5\u6269\u6563\u533a\u95f4\u548c\u81ea\u6269\u6563\u7cfb\u6570\u3002</p> <p>\u968f\u540e\u53ef\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u9884\u6d4b\u6027\u8d28","text":"<p><code>calc_properties_with_nep.py</code> \u4f7f\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8ba1\u7b97\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u3002</p> <p>\u4f9d\u8d56\uff1a <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>\u4f7f\u7528\u6b64\u529f\u80fd\u53ef\u4ee5\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8fdb\u884c\u9884\u6d4b\u3002\u5efa\u8bae\u5728\u4f7f\u7528\u524d\u5148\u9a8c\u8bc1\u6a21\u578b\u5728\u76ee\u6807\u7ed3\u6784\u4e0a\u7684\u9884\u6d4b\u8d28\u91cf\uff0c\u518d\u5c06\u8f93\u51fa\u4f5c\u4e3a\u540e\u7eed\u5206\u6790\u6216\u7b5b\u9009\u4f9d\u636e\u3002</p> <p>\u63d0\u793a\uff1a \u9884\u6d4b\u524d\u53ef\u4ee5\u6e05\u7406 extxyz \u5143\u6570\u636e\uff1a</p> <pre><code>gpumdkit.sh -clean_xyz train.xyz clean_train.xyz\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep_1","title":"NEP \u63cf\u8ff0\u7b26","text":"<pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>\u7528\u9014\u5305\u62ec\uff1a</p> <ul> <li>\u7528 PCA/UMAP \u53ef\u89c6\u5316\u5c40\u57df\u73af\u5883\uff1b</li> <li>\u6bd4\u8f83\u8bad\u7ec3\u96c6\u548c\u5019\u9009\u7ed3\u6784\uff1b</li> <li>\u5224\u65ad\u65b0\u6570\u636e\u662f\u5426\u6269\u5c55\u4e86\u63cf\u8ff0\u7b26\u7a7a\u95f4\u3002</li> </ul> <p>\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#doas","title":"DOAS","text":"<p><code>calc_doas.py</code> \u7528\u4e8e\u8ba1\u7b97 Wang et al. \u63d0\u51fa\u7684 density of atomistic states\u3002</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>\u811a\u672c\u4f1a\uff1a</p> <ol> <li>\u8bfb\u53d6\u6240\u6709\u7ed3\u6784\uff1b</li> <li>\u4f7f\u7528 NEP \u8fdb\u884c\u7ed3\u6784\u4f18\u5316\uff1b</li> <li>\u63d0\u53d6\u6bcf\u4e2a\u539f\u5b50\u7684\u80fd\u91cf\uff1b</li> <li>\u6309\u5143\u7d20\u5206\u7ec4\u8f93\u51fa\uff1b</li> <li>\u7528\u7ed8\u56fe\u811a\u672c\u53ef\u89c6\u5316\u5206\u5e03\u3002</li> </ol> <p>\u5bf9\u4e8e\u5f88\u5927\u7684\u4f53\u7cfb\uff0c\u5982\u679c\u4e3b\u8981\u76ee\u7684\u662f\u83b7\u5f97\u4f18\u5316\u540e\u7684\u7ed3\u6784\u548c\u539f\u5b50\u80fd\u91cf\u5206\u5e03\uff0c\u76f4\u63a5\u5728 GPUMD \u4e2d\u5b8c\u6210\u6700\u5c0f\u5316\u548c\u539f\u5b50\u80fd\u91cf\u8f93\u51fa\u901a\u5e38\u4f1a\u66f4\u9ad8\u6548\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#neb","title":"NEB \u548c\u7ed3\u6784\u4f18\u5316","text":"<p>NEB\uff1a</p> <pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>\u8fd9\u4f1a\u4f7f\u7528 NEP \u6a21\u578b\u8fd0\u884c\u542b <code>9</code> \u4e2a\u4e2d\u95f4\u50cf\u7684 NEB \u8ba1\u7b97\u3002\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u811a\u672c\u4f1a\u8be2\u95ee\u539f\u5b50\u56fa\u5b9a\u65b9\u5f0f\uff1a</p> <ul> <li><code>none</code>\uff1a\u4e0d\u56fa\u5b9a\u539f\u5b50\uff1b</li> <li><code>index</code>\uff1a\u6309\u539f\u5b50\u5e8f\u53f7\u56fa\u5b9a\uff1b</li> <li><code>element</code>\uff1a\u56fa\u5b9a\u67d0\u4e00\u79cd\u5143\u7d20\u7684\u6240\u6709\u539f\u5b50\uff1b</li> <li><code>position</code>\uff1a\u56fa\u5b9a\u5750\u6807\u8303\u56f4\u5185\u7684\u539f\u5b50\u3002</li> </ul> <p>\u7ed3\u6784\u4f18\u5316\uff08\u901a\u8fc7 <code>calorine</code>\uff09\uff1a</p> <p>\u4f9d\u8d56\uff1a <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>\u8f93\u51fa\u5305\u62ec\uff1a</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#ovito-rdf","title":"\u4f7f\u7528 OVITO \u8ba1\u7b97 RDF","text":"<p><code>rdf_calculator_ovito.py</code> \u4f7f\u7528 OVITO \u7684\u5206\u6790\u5de5\u5177\u8ba1\u7b97\u5f84\u5411\u5206\u5e03\u51fd\u6570\u3002</p> <p>\u4f9d\u8d56\uff1a OVITO</p> <pre><code>pip install ovito\n</code></pre> <p>\u8f93\u5165\u6587\u4ef6\uff1a \u7ed3\u6784\u6587\u4ef6\uff08\u5355\u5e27\u6216\u8f68\u8ff9\uff09</p> <pre><code>python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400\n</code></pre> <p>\u53c2\u6570\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>trajectory.xyz</code> \u8f93\u5165\u7ed3\u6784\u6587\u4ef6 <code>6.0</code> RDF \u8ba1\u7b97\u7684\u6700\u5927\u8ddd\u79bb\uff08\u00c5\uff09 <code>400</code> \u76f4\u65b9\u56fe\u7684\u5206\u7bb1\u6570 <p>\u53ef\u89c6\u5316\uff1a</p> <pre><code>gpumdkit.sh -plt rdf\n</code></pre> <p>\u6ce8\u610f\uff1a \u5efa\u8bae\u4f18\u5148\u4f7f\u7528 GPUMD \u4e2d\u7684 <code>compute_rdf</code> \u547d\u4ee4\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_3","title":"\u94c1\u7535\u548c\u6781\u6027\u6750\u6599\u5de5\u5177","text":"<p>\u9009\u9879 <code>406\u2013410</code> \u9762\u5411\u9499\u949b\u77ff\u548c\u6781\u6027\u6750\u6599\u5206\u6790\uff0c\u5e38\u7528\u4e8e\u4ece MD \u8f68\u8ff9\u4e2d\u63d0\u53d6\u5c40\u57df\u7ed3\u6784\u4fe1\u606f\uff0c\u7136\u540e\u8fdb\u4e00\u6b65\u5206\u6790\u76f8\u53d8\u3001\u7574\u7ed3\u6784\u6216\u6781\u5316\u7eb9\u7406\u3002</p> <p>\u8fd9\u4e9b\u811a\u672c\u5728\u672c\u9875\u53ea\u505a\u5feb\u901f\u7d22\u5f15\uff0c\u56e0\u4e3a\u5b83\u4eec\u901a\u5e38\u9700\u8981\u7ec4\u5408\u4f7f\u7528\u3002\u63a8\u8350\u9605\u8bfb\u4e13\u9898\u6559\u7a0b\u4e2d\u7684\u5b8c\u6574\u5de5\u4f5c\u6d41\u548c\u53c2\u6570\u8bf4\u660e\uff1a\u6781\u6027\u6750\u6599\u5206\u6790\u3002</p> \u83dc\u5355 CLI \u5b50\u547d\u4ee4 \u4f5c\u7528 \u8be6\u7ec6\u8bf4\u660e <code>406</code> <code>gpumdkit.sh -calc nlist ...</code> \u6784\u5efa\u6307\u5b9a\u4e2d\u5fc3\u539f\u5b50\u548c\u8fd1\u90bb\u539f\u5b50\u4e4b\u95f4\u7684\u8fd1\u90bb\u5217\u8868 \u6781\u6027\u6750\u6599\u5206\u6790 <code>407</code> <code>gpumdkit.sh -calc disp ...</code> \u6839\u636e\u8f68\u8ff9\u548c\u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb \u6781\u6027\u6750\u6599\u5206\u6790 <code>408</code> <code>gpumdkit.sh -calc avg-struct ...</code> \u4ece\u8f68\u8ff9\u4e2d\u8ba1\u7b97\u5e73\u5747\u7ed3\u6784 \u6781\u6027\u6750\u6599\u5206\u6790 <code>409</code> <code>gpumdkit.sh -calc oct-tilt ...</code> \u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c\u89d2 \u6781\u6027\u6750\u6599\u5206\u6790 <code>410</code> <code>gpumdkit.sh -calc pol-abo3 ...</code> \u6839\u636e Born \u6709\u6548\u7535\u8377\u4f30\u7b97 ABO3 \u5c40\u57df\u6781\u5316 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u90e8\u5206\u811a\u672c\u9700\u8981\u5b89\u88c5 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>\u4e00\u4e2a\u5178\u578b\u987a\u5e8f\u662f\u5148\u7528 <code>nlist</code> \u5efa\u7acb\u8fd1\u90bb\u5217\u8868\uff0c\u518d\u7528\u8be5\u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u4f4d\u79fb\u3001\u503e\u8f6c\u6216\u6781\u5316\u3002\u5bf9\u4e8e\u5e73\u5747\u7ed3\u6784\uff0c\u53ef\u4ee5\u76f4\u63a5\u4ece\u8f68\u8ff9\u51fa\u53d1\uff0c\u7528\u957f\u5ea6\u5bb9\u5dee\u63a7\u5236\u54ea\u4e9b\u5e27\u53c2\u4e0e\u5e73\u5747\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html","title":"\u8d21\u732e\u6307\u5357","text":"\ud83e\udd1d \u4e3a GPUMDkit \u8d21\u732e\u4ee3\u7801 <p>\u611f\u8c22\u4f60\u6709\u5174\u8da3\u4e3a GPUMDkit \u505a\u51fa\u8d21\u732e\uff01\u6211\u4eec\u611f\u8c22\u4f60\u4e3a\u6539\u5584\u8fd9\u4e2a\u5de5\u5177\u5305\u6240\u4ed8\u51fa\u7684\u65f6\u95f4\u548c\u52aa\u529b\u3002</p> <p> English   \u00a0\u00b7\u00a0   \u7b80\u4f53\u4e2d\u6587 </p> <p><code>GPUMDkit</code> \u662f\u4e00\u4e2a\u5f00\u6e90\u9879\u76ee\uff0c\u6211\u4eec\u6b22\u8fce\u793e\u533a\u7684\u5404\u79cd\u8d21\u732e\uff0c\u65e0\u8bba\u662f\u4fee\u590d bug\u3001\u6dfb\u52a0\u65b0\u529f\u80fd\u3001\u6539\u8fdb\u6587\u6863\u8fd8\u662f\u63d0\u51fa\u5efa\u8bae\u3002</p> <p>\u6ce8\u610f\uff1a\u672c\u6587\u6863\u7684\u6743\u5a01\u7248\u672c\u4f4d\u4e8e\u4ed3\u5e93\u6839\u76ee\u5f55\u7684 <code>CONTRIBUTING.md</code>\u3002\u672c\u6559\u7a0b\u9875\u9762\u540c\u6b65\u5176\u5185\u5bb9\u3002\u4e2d\u6587\u7248\u8bf7\u53c2\u89c1 <code>docs/CONTRIBUTING_zh-CN.md</code>\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_1","title":"\u76ee\u5f55","text":"<ul> <li>\u5f00\u53d1\u89c4\u8303\u4e0e\u51c6\u5219</li> <li>\u62a5\u544a\u95ee\u9898</li> <li>\u529f\u80fd\u5efa\u8bae</li> <li>\u8d21\u732e\u4ee3\u7801</li> <li>Fork \u5e76\u514b\u9686\u4ed3\u5e93</li> <li>\u521b\u5efa\u529f\u80fd\u5206\u652f</li> <li>\u8fdb\u884c\u4fee\u6539<ul> <li>\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e</li> <li>\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e</li> <li>\u66f4\u65b0 Tab \u8865\u5168</li> </ul> </li> <li>\u4ee3\u7801\u98ce\u683c\u4e0e\u6700\u4f73\u5b9e\u8df5</li> <li>\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539</li> <li>\u63d0\u4ea4\u4fe1\u606f</li> <li>\u63a8\u9001\u5e76\u521b\u5efa Pull Request</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_2","title":"\u5f00\u53d1\u89c4\u8303\u4e0e\u51c6\u5219","text":"<p>\u4e3a\u4fdd\u6301\u4ee3\u7801\u8d28\u91cf\u548c\u9879\u76ee\u4e00\u81f4\u6027\uff0c\u8bf7\u9075\u5faa\u4ee5\u4e0b\u51c6\u5219\uff1a</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_3","title":"\u8bed\u8a00\u8981\u6c42","text":"<ul> <li>\u6240\u6709\u4ee3\u7801\u5e94\u4f7f\u7528\u82f1\u6587\u7f16\u5199\uff1a\u5305\u62ec\u53d8\u91cf\u540d\u3001\u51fd\u6570\u540d\u3001\u6ce8\u91ca\u3001\u6587\u6863\u5b57\u7b26\u4e32\u3001\u63d0\u4ea4\u4fe1\u606f\u548c\u6587\u6863\u3002</li> <li>\u867d\u7136\u6211\u4eec\u7406\u89e3\u8d21\u732e\u8005\u6765\u81ea\u4e0d\u540c\u80cc\u666f\uff0c\u4f46\u4f7f\u7528\u82f1\u6587\u80fd\u786e\u4fdd\u4ee3\u7801\u5e93\u5bf9\u6700\u5e7f\u6cdb\u7684\u7528\u6237\u7fa4\u4f53\u53ef\u8bbf\u95ee\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_4","title":"\u6a21\u5757\u5316\u4e0e\u53ef\u590d\u7528\u6027","text":"<ul> <li>\u7f16\u5199\u6a21\u5757\u5316\u548c\u53ef\u590d\u7528\u7684\u4ee3\u7801\uff1a\u51fd\u6570\u548c\u811a\u672c\u7684\u8bbe\u8ba1\u5e94\u5177\u6709\u7075\u6d3b\u6027\u3002</li> <li>\u4f18\u5148\u4f20\u9012\u53c2\u6570\u800c\u975e\u786c\u7f16\u7801\u503c\uff1a\u4f7f\u7528\u51fd\u6570\u53c2\u6570\u3001\u547d\u4ee4\u884c\u53c2\u6570\u6216\u914d\u7f6e\u6587\u4ef6\u6765\u66ff\u4ee3\u786c\u7f16\u7801\u503c\u3002\u4f46\u67d0\u4e9b\u6587\u4ef6\u540d\u7531 GPUMD \u548c NEP \u7a0b\u5e8f\u56fa\u5b9a\u8981\u6c42\uff08\u5982 <code>train.xyz</code>\u3001<code>thermo.out</code>\uff09\uff0c\u8fd9\u4e9b\u53ef\u4ee5\u6309\u9700\u786c\u7f16\u7801\u3002</li> <li>\u793a\u4f8b\uff1a   <pre><code># \u597d\u7684\u505a\u6cd5\uff1a\u63a5\u53d7\u53c2\u6570\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # \u5904\u7406\u903b\u8f91\n}\n\n# \u907f\u514d\uff1a\u786c\u7f16\u7801\u503c\uff08\u9664\u975e GPUMD/NEP \u8981\u6c42\uff09\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # \u5904\u7406\u903b\u8f91\n}\n</code></pre></li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_5","title":"\u4ee3\u7801\u98ce\u683c","text":"<ul> <li>\u7f16\u5199\u6e05\u6670\u3001\u6613\u4e8e\u4ed6\u4eba\u7ef4\u62a4\u548c\u4fee\u6539\u7684\u4ee3\u7801\u3002</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u548c\u51fd\u6570\u540d\u3002</li> <li>\u5728\u5fc5\u8981\u5904\u6dfb\u52a0\u6ce8\u91ca\u4ee5\u89e3\u91ca\u590d\u6742\u903b\u8f91\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_6","title":"\u6587\u6863","text":"<ul> <li>\u786e\u4fdd\u5e2e\u52a9\u4fe1\u606f\uff08\u5982 <code>-h</code> \u6807\u5fd7\uff09\u6e05\u6670\u51c6\u786e\u3002</li> <li>\u6559\u7a0b\u6587\u6863\u4f4d\u4e8e <code>docs/tutorials/en/</code>\uff08\u82f1\u6587\uff09\u548c <code>docs/tutorials/zh/</code>\uff08\u4e2d\u6587\uff09\u3002\u5982\u679c\u4f60\u6dfb\u52a0\u4e86\u65b0\u529f\u80fd\uff0c\u8bf7\u8003\u8651\u66f4\u65b0\u76f8\u5173\u6559\u7a0b\u9875\u9762\u3002</li> <li>\u7f16\u8f91\u6559\u7a0b Markdown \u6587\u4ef6\u540e\uff0c\u4f7f\u7528 <code>mkdocs build -f docs/mkdocs.yml</code> \u91cd\u65b0\u6784\u5efa HTML\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_7","title":"\u62a5\u544a\u95ee\u9898","text":"<p>\u5982\u679c\u4f60\u9047\u5230 bug\uff0c\u8bf7\u901a\u8fc7 GitHub Issues \u5e2e\u52a9\u6211\u4eec\u4fee\u590d\uff1a</p> <ol> <li>\u641c\u7d22\u73b0\u6709 issues \u67e5\u770b\u8be5 bug \u662f\u5426\u5df2\u88ab\u62a5\u544a\u3002</li> <li>\u521b\u5efa\u65b0 issue\uff08\u5982\u679c\u5c1a\u672a\u88ab\u62a5\u544a\uff09\uff1a\u521b\u5efa Issue</li> <li>\u8be6\u7ec6\u63cf\u8ff0\u95ee\u9898\uff0c\u5982\u679c\u53ef\u80fd\u8bf7\u63d0\u4f9b\u6d4b\u8bd5\u6587\u4ef6\u3002</li> </ol> <p>\u4f60\u4e5f\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u65b9\u5f0f\u8054\u7cfb\u6211\u4eec\uff1a - QQ \u7fa4\uff1a825696376 - \u90ae\u7bb1\uff1ayanzihan@westlake.edu.cn - \u811a\u672c\u5f00\u53d1\u8005\uff1a\u8054\u7cfb\u811a\u672c\u5934\u90e8\u5217\u51fa\u7684\u5f00\u53d1\u8005</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_8","title":"\u529f\u80fd\u5efa\u8bae","text":"<p>\u6211\u4eec\u6b22\u8fce\u529f\u80fd\u5efa\u8bae\uff01\u63d0\u51fa\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u641c\u7d22\u73b0\u6709 issues \u67e5\u770b\u662f\u5426\u5df2\u6709\u4eba\u63d0\u51fa\u3002</li> <li>\u521b\u5efa\u65b0\u529f\u80fd\u8bf7\u6c42\uff1a\u521b\u5efa\u529f\u80fd\u8bf7\u6c42 \u5e76 mention @zhyan0603</li> <li>\u6e05\u695a\u63cf\u8ff0\u4f60\u7684\u9700\u6c42 \u5e76\u89e3\u91ca\u5176\u7528\u9014\u3002</li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_9","title":"\u8d21\u732e\u4ee3\u7801","text":""},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#fork","title":"Fork \u5e76\u514b\u9686\u4ed3\u5e93","text":"<ol> <li> <p>\u5728 GitHub \u4e0a Fork \u4ed3\u5e93\uff0c\u70b9\u51fb \u4ed3\u5e93\u9875\u9762 \u53f3\u4e0a\u89d2\u7684 \"Fork\" \u6309\u94ae\u3002</p> </li> <li> <p>\u514b\u9686\u4f60\u7684 fork \u5230\u672c\u5730\uff1a</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>\u8bbe\u7f6e upstream remote \u4ee5\u4fdd\u6301 fork \u540c\u6b65\uff1a    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_10","title":"\u521b\u5efa\u529f\u80fd\u5206\u652f","text":"<p>\u4e3a\u4f60\u7684\u4fee\u6539\u521b\u5efa\u65b0\u5206\u652f\uff1a</p> <pre><code># \u4ece main \u521b\u5efa\u5e76\u5207\u6362\u5230\u65b0\u5206\u652f\ngit checkout -b your-branch-name\n</code></pre> <p>\u5206\u652f\u540d\u79f0\u968f\u610f\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_11","title":"\u8fdb\u884c\u4fee\u6539","text":"<p><code>GPUMDkit</code> \u7684\u7ed3\u6784\u5305\u62ec\uff1a - <code>gpumdkit.sh</code>\uff1a\u4e3b\u5165\u53e3\uff08Bash \u811a\u672c\uff09\uff0c\u5904\u7406\u4ea4\u4e92\u83dc\u5355\u6a21\u5f0f\u548c\u547d\u4ee4\u884c\u6a21\u5f0f - <code>install.sh</code>\uff1a\u5b89\u88c5\u811a\u672c\uff0c\u8bbe\u7f6e\u73af\u5883\u53d8\u91cf\u548c shell \u914d\u7f6e - <code>Scripts/</code>\uff1a\u6309\u529f\u80fd\u7ec4\u7ec7\u7684 Python \u548c Bash \u5b9e\u73b0\u811a\u672c   - <code>plt_scripts/</code>\uff1a\u7ed8\u56fe\u811a\u672c   - <code>calculators/</code>\uff1a\u8ba1\u7b97\u5de5\u5177   - <code>format_conversion/</code>\uff1a\u683c\u5f0f\u8f6c\u6362\u5de5\u5177   - <code>workflow/</code>\uff1a\u5de5\u4f5c\u6d41\u81ea\u52a8\u5316   - <code>sample_structures/</code>\uff1a\u7ed3\u6784\u91c7\u6837\u5de5\u5177   - <code>analyzer/</code>\uff1a\u5206\u6790\u5de5\u5177   - <code>utils/</code>\uff1a\u5b9e\u7528\u51fd\u6570\uff08\u5305\u62ec <code>completion.sh</code> Tab \u8865\u5168\uff09 - <code>src/</code>\uff1a\u4ea4\u4e92\u6a21\u5f0f\u83dc\u5355\u51fd\u6570\u7684 Shell \u811a\u672c   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>skills/</code>\uff1aAI agent \u6280\u80fd\u5b9a\u4e49\uff08\u7528\u4e8e opencode/Claude Code \u96c6\u6210\u7684 SKILL.md \u6587\u4ef6\uff09 - <code>docs/</code>\uff1a\u6587\u6863\u6587\u4ef6   - <code>tutorials/en/</code> \u548c <code>tutorials/zh/</code>\uff1a\u53cc\u8bed\u6559\u7a0b\u9875\u9762   - <code>mkdocs.yml</code>\uff1a\u6784\u5efa\u6559\u7a0b HTML \u7684 MkDocs \u914d\u7f6e   - <code>command_reference.tsv</code>\uff1a\u673a\u5668\u53ef\u8bfb\u7684\u547d\u4ee4\u53c2\u8003   - <code>htmls/</code>\uff1aMkDocs \u751f\u6210\u7684 HTML \u8f93\u51fa</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_12","title":"\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e","text":"<p>\u8981\u6dfb\u52a0\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u8bbf\u95ee\u7684\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u5728\u76f8\u5e94\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a</li> </ol> <pre><code># \u793a\u4f8b\uff1a\u6dfb\u52a0\u65b0\u7684\u683c\u5f0f\u8f6c\u6362\u811a\u672c\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u9075\u5faa\u6a21\u5757\u5316\u51c6\u5219\uff08\u63a5\u53d7\u53c2\u6570\uff0c\u907f\u514d\u786c\u7f16\u7801\uff09\u3002</p> </li> <li> <p>\u5728\u76f8\u5e94\u7684 <code>src/</code> \u6587\u4ef6\u4e2d\u6dfb\u52a0\u5305\u88c5\u51fd\u6570\uff1a    <pre><code># \u793a\u4f8b\uff1a\u7f16\u8f91 src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>\u6dfb\u52a0\u65b0\u51fd\u6570\uff1a    <pre><code>function f111_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input &lt;required_param1&gt; &lt;required_param2&gt;\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -r -a converter_args\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py \"${converter_args[@]}\"\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u66f4\u65b0\u83dc\u5355\u663e\u793a\uff1a    <pre><code># \u627e\u5230 menu() \u51fd\u6570\u5e76\u6309\u9700\u66f4\u65b0\n# \u627e\u5230 array_choice \u6570\u7ec4\u5e76\u6dfb\u52a0\u4f60\u7684\u65b0\u9009\u62e9\u7f16\u53f7\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\" \"107\" \"108\" \"109\" \"110\" \"111\"  # \u6dfb\u52a0 \"111\"\n    # ... \u5176\u4f59\u9009\u62e9\n)\n</code></pre></p> </li> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0 case \u8bed\u53e5\uff1a    <pre><code># \u5728 main() \u51fd\u6570\u4e2d\u627e\u5230\u76f8\u5e94\u7684 case \u8bed\u53e5\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n            \"101\") f101_out2xyz ;;\n            # ... \u73b0\u6709 case ...\n            \"111\") f111_new_converter ;;  # \u6dfb\u52a0\u4f60\u7684 case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_13","title":"\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e","text":"<p>\u8981\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c\u6807\u5fd7\u6216\u5b50\u547d\u4ee4\uff1a</p> <ol> <li> <p>\u5728\u76f8\u5e94\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a    <pre><code># \u793a\u4f8b\uff1a\u6dfb\u52a0\u65b0\u7684\u5206\u6790\u5668\u811a\u672c\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u660e\u786e\u53c2\u6570\u8981\u6c42\uff1a    <pre><code># \u793a\u4f8b\uff1aScripts/analyzer/analyze_bonds.py\nimport sys\n\nif len(sys.argv) != 3:\n    print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n    print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n    sys.exit(1)\n\ninput_file = sys.argv[1]\ncutoff = float(sys.argv[2])\n\n# \u4f60\u7684\u5b9e\u73b0\n</code></pre></p> </li> </ol> <p>\u6ce8\u610f\uff1aGPUMDkit Python \u811a\u672c\u8bbe\u8ba1\u4e3a\u76f4\u63a5\u8fd0\u884c\uff08\u4e0d\u4f5c\u4e3a\u6a21\u5757\u5bfc\u5165\uff09\u3002 \u5982\u679c\u4f60\u613f\u610f\uff0c\u53ef\u4ee5\u4f7f\u7528 <code>main()</code> \u51fd\u6570\u914d\u5408 <code>if __name__ == \"__main__\":</code> \u4fdd\u62a4\uff0c \u4f46\u8fd9\u4e0d\u662f\u5fc5\u9700\u7684\u3002\u5927\u591a\u6570\u73b0\u6709\u811a\u672c\u5728\u6a21\u5757\u7ea7\u522b\u6267\u884c\u3002</p> <ol> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0\u547d\u4ee4\u884c\u6807\u5fd7\u5904\u7406\uff1a    <pre><code># \u627e\u5230\u547d\u4ee4\u884c\u89e3\u6790\u90e8\u5206\uff08\u5927\u7684 \"case $1 in\" \u5757\uff09\n# \u5728\u9002\u5f53\u4f4d\u7f6e\u6dfb\u52a0\u4f60\u7684\u65b0\u6807\u5fd7\n\ncase $1 in\n    # ... \u73b0\u6709 case ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ \"$2\" != \"-h\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py $2 $3\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n        fi ;;\n    # ... \u5176\u4f59 case ...\nesac\n</code></pre></p> </li> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u66f4\u65b0\u5e2e\u52a9\u4fe1\u606f\uff1a    <pre><code># \u627e\u5230 help_info_table() \u51fd\u6570\u5e76\u6dfb\u52a0\u4f60\u7684\u547d\u4ee4\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... \u5176\u4f59\u5e2e\u52a9\u8868 ...\n}\n</code></pre></p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#tab","title":"\u66f4\u65b0 Tab \u8865\u5168","text":"<p>\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c\u6807\u5fd7\u65f6\uff0c\u66f4\u65b0 Tab \u8865\u5168\u811a\u672c\uff1a</p> <pre><code># \u7f16\u8f91 Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>\u5c06\u4f60\u7684\u65b0\u6807\u5fd7\u6dfb\u52a0\u5230 <code>opts</code> \u53d8\u91cf\uff1a <pre><code># \u627e\u5230 local opts=... \u884c\nlocal opts=\"-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...\"\n#                                                        \u5728\u6b64\u6dfb\u52a0\u4f60\u7684\u6807\u5fd7\n</code></pre></p> <p>\u5982\u679c\u4f60\u7684\u6807\u5fd7\u9700\u8981\u6587\u4ef6\u53c2\u6570\uff0c\u5c06\u5176\u6dfb\u52a0\u5230\u73b0\u6709\u7684\u6587\u4ef6\u8865\u5168 case \u4e2d\uff1a <pre><code># \u627e\u5230\u9700\u8981\u6587\u4ef6\u53c2\u6570\u7684 case \u5e76\u7528 | \u6dfb\u52a0\u4f60\u7684\u6807\u5fd7\n-out2xyz|-out2exyz|-...|-your_new_flag)\n    COMPREPLY=($(compgen -f -- \"$cur\")) ;;\n</code></pre></p> <p>\u5982\u679c\u4f60\u7684\u6807\u5fd7\u63a5\u53d7\u4e8c\u7ea7\u9009\u9879\uff08\u5982 <code>-plt</code> \u6216 <code>-calc</code>\uff09\uff0c\u6dfb\u52a0\u65b0 case\uff1a <pre><code>case \"$prev\" in\n    # ... \u73b0\u6709 case ...\n    -your_new_flag)\n        COMPREPLY=($(compgen -W \"option1 option2 option3\" -- \"$cur\")) ;;\n    # ... \u5176\u4f59 case ...\nesac\n</code></pre></p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_14","title":"\u4ee3\u7801\u98ce\u683c\u4e0e\u6700\u4f73\u5b9e\u8df5","text":"<ul> <li>Shell \u811a\u672c\uff1a</li> <li>\u4f7f\u7528 <code>${variable}</code> \u8fdb\u884c\u53d8\u91cf\u5c55\u5f00</li> <li>\u4f7f\u7528 <code>[ ! -z \"$var\" ]</code> \u8fdb\u884c\u975e\u7a7a\u68c0\u67e5\uff08\u9879\u76ee\u7ea6\u5b9a\uff09</li> <li>\u4ea4\u4e92\u51fd\u6570\u5e94\u9075\u5faa banner \u683c\u5f0f\uff1a     <pre><code>echo \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/&lt;category&gt;        |\"\necho \" | Script: &lt;script_name&gt;.py                        |\"\necho \" | Developer: &lt;Name&gt; (&lt;email&gt;)                     |\"\necho \" &gt;-------------------------------------------------&lt;\"\n</code></pre></li> <li>\u4f7f\u7528 <code>read -r -a varname</code> \u8bfb\u53d6\u591a\u8bcd\u8f93\u5165\uff0c\u7136\u540e\u7528 <code>\"${varname[@]}\"</code> \u4f20\u9012</li> <li> <p><code>src/</code> \u4e2d\u7684 Shell \u811a\u672c\u5e94\u4ee5\u6587\u4ef6\u5934\u6ce8\u91ca\u5757\u5f00\u59cb\uff1a     <pre><code># ============================================================\n# GPUMDkit &lt;module name&gt; module\n# Repository: https://github.com/zhyan0603/GPUMDkit\n# Author: &lt;Name&gt; (&lt;email&gt;)\n# ============================================================\n</code></pre></p> </li> <li> <p>Python \u811a\u672c\uff1a</p> </li> <li>\u7f16\u5199\u6e05\u6670\u3001\u53ef\u7ef4\u62a4\u7684\u4ee3\u7801</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u540d</li> <li>\u4f7f\u7528 <code>sys.argv</code> \u8fdb\u884c\u53c2\u6570\u89e3\u6790\uff08\u4e0e\u5927\u591a\u6570\u73b0\u6709\u811a\u672c\u4e00\u81f4\uff09</li> <li>\u63d0\u4f9b\u6e05\u6670\u7684\u4f7f\u7528\u4fe1\u606f\uff1a<code>print(\"Usage: ...\")</code> \u548c <code>print(\"Example: ...\")</code></li> <li>\u5982\u679c\u4f60\u7684\u811a\u672c\u4f7f\u7528\u91cd\u578b/\u7279\u6b8a\u5305\uff08<code>NepTrain</code>\u3001<code>calorine</code>\u3001<code>dpdata</code>\uff09\uff0c\u8bf7\u6dfb\u52a0     <code>print_dependency_notice()</code> \u51fd\u6570\u4ee5\u901a\u77e5\u7528\u6237\u5f15\u7528\u5efa\u8bae</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_15","title":"\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539","text":"<p>\u63d0\u4ea4\u8d21\u732e\u524d\uff0c\u8fd0\u884c\u76f8\u5173\u9a8c\u8bc1\u547d\u4ee4\uff1a</p> <pre><code># Shell \u8bed\u6cd5\u68c0\u67e5\uff08\u59cb\u7ec8\u8fd0\u884c\uff09\nbash -n gpumdkit.sh\nfind src Scripts -name '*.sh' -exec bash -n {} +\n\n# Python \u8bed\u6cd5\u68c0\u67e5\uff08\u9488\u5bf9\u4fee\u6539\u7684 Python \u6587\u4ef6\uff09\npython3 -m py_compile path/to/modified_script.py\n\n# MkDocs \u6784\u5efa\uff08\u5982\u679c\u4fee\u6539\u4e86\u6587\u6863\uff09\nmkdocs build -f docs/mkdocs.yml\n\n# \u68c0\u67e5\u5c3e\u968f\u7a7a\u683c\u95ee\u9898\ngit diff --check\n</code></pre> <p>\u7136\u540e\u6d4b\u8bd5\u529f\u80fd\uff1a</p> <ol> <li> <p>\u6d4b\u8bd5\u4ea4\u4e92\u6a21\u5f0f\uff08\u5982\u9002\u7528\uff09\uff1a    <pre><code>gpumdkit.sh\n# \u5bfc\u822a\u5230\u4f60\u7684\u65b0\u529f\u80fd\u5e76\u5145\u5206\u6d4b\u8bd5\n</code></pre></p> </li> <li> <p>\u6d4b\u8bd5\u547d\u4ee4\u884c\u6a21\u5f0f\uff08\u5982\u9002\u7528\uff09\uff1a    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # \u6d4b\u8bd5\u5e2e\u52a9\u4fe1\u606f\n</code></pre></p> </li> <li> <p>\u6d4b\u8bd5 Tab \u8865\u5168\uff08\u5982\u679c\u4f60\u4fee\u6539\u4e86 <code>completion.sh</code>\uff09\uff1a    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # \u5e94\u663e\u793a\u4f60\u7684\u65b0\u6807\u5fd7\n</code></pre></p> </li> <li> <p>\u7528\u5404\u79cd\u8f93\u5165\u6d4b\u8bd5\uff1a</p> </li> <li>\u7528\u5178\u578b\u8f93\u5165\u6d4b\u8bd5</li> <li>\u7528\u8fb9\u7f18\u60c5\u51b5\u6d4b\u8bd5\uff08\u7a7a\u6587\u4ef6\u3001\u5927\u6587\u4ef6\u7b49\uff09</li> <li> <p>\u6d4b\u8bd5\u9519\u8bef\u5904\u7406\uff08\u7f3a\u5c11\u6587\u4ef6\u3001\u65e0\u6548\u53c2\u6570\uff09</p> </li> <li> <p>\u9a8c\u8bc1\u65e0\u56de\u5f52\uff1a\u786e\u4fdd\u73b0\u6709\u529f\u80fd\u4ecd\u7136\u6b63\u5e38\u5de5\u4f5c\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_16","title":"\u63d0\u4ea4\u4fe1\u606f","text":"<p>\u7f16\u5199\u6e05\u6670\u3001\u63cf\u8ff0\u6027\u7684\u63d0\u4ea4\u4fe1\u606f\u6765\u89e3\u91ca\u4f60\u505a\u4e86\u4ec0\u4e48\u66f4\u6539\u3002\u6ca1\u6709\u4e25\u683c\u7684\u683c\u5f0f\u8981\u6c42\u2014\u2014\u53ea\u8981\u786e\u4fdd\u4f60\u7684\u4fe1\u606f\u662f\u53ef\u7406\u89e3\u7684\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#pull-request","title":"\u63a8\u9001\u5e76\u521b\u5efa Pull Request","text":"<ol> <li> <p>\u63d0\u4ea4\u4f60\u7684\u4fee\u6539\uff1a    <pre><code>git add .\ngit commit -m \"\u4f60\u7684\u63cf\u8ff0\u6027\u4fe1\u606f\"\n</code></pre></p> </li> <li> <p>\u4fdd\u6301\u4f60\u7684\u5206\u652f\u4e0e\u6700\u65b0\u7684 <code>dev</code> \u5206\u652f\u540c\u6b65\uff1a    <pre><code>git fetch origin\ngit rebase origin/dev\n</code></pre></p> </li> <li> <p>\u63a8\u9001\u4f60\u7684\u5206\u652f\u5230\u4f60\u7684 fork\uff1a    <pre><code>git push origin your-branch-name\n</code></pre></p> </li> <li> <p>\u521b\u5efa Pull Request\uff1a</p> </li> <li>\u524d\u5f80 GPUMDkit \u4ed3\u5e93</li> <li>\u70b9\u51fb \"Pull Requests\" \u2192 \"New Pull Request\"</li> <li>\u8bbe\u7f6e\u76ee\u6807\u5206\u652f\u4e3a <code>dev</code> \u8fdb\u884c\u4ee3\u7801\u5ba1\u67e5</li> <li>\u8bbe\u7f6e\u6bd4\u8f83\u5206\u652f\u4e3a\u4f60\u7684\u529f\u80fd\u5206\u652f</li> <li> <p>\u586b\u5199 PR \u63cf\u8ff0\uff1a</p> <ul> <li>\u6807\u9898\uff1a\u7b80\u8981\u63cf\u8ff0\u66f4\u6539</li> <li>\u63cf\u8ff0\uff1a\u8be6\u7ec6\u89e3\u91ca\u66f4\u6539\u5185\u5bb9\u548c\u539f\u56e0</li> <li>\u6d4b\u8bd5\uff1a\u63cf\u8ff0\u4f60\u5982\u4f55\u6d4b\u8bd5\u8fd9\u4e9b\u66f4\u6539</li> </ul> </li> <li> <p>\u56de\u5e94\u5ba1\u67e5\u53cd\u9988\uff1a</p> </li> <li>\u5bf9\u5efa\u8bae\u548c\u5efa\u8bbe\u6027\u6279\u8bc4\u4fdd\u6301\u5f00\u653e</li> <li>\u53ca\u65f6\u8fdb\u884c\u8bf7\u6c42\u7684\u4fee\u6539</li> <li> <p>\u63a8\u9001\u989d\u5916\u63d0\u4ea4\u5230\u4f60\u7684\u5206\u652f\uff08\u5b83\u4eec\u4f1a\u81ea\u52a8\u51fa\u73b0\u5728 PR \u4e2d\uff09</p> </li> <li> <p>\u6279\u51c6\u540e\uff1a\u7ef4\u62a4\u8005\u5c06\u5408\u5e76\u4f60\u7684 PR\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_17","title":"\u6709\u95ee\u9898\u6216\u9700\u8981\u5e2e\u52a9\uff1f","text":"<p>\u5982\u679c\u4f60\u5bf9\u8d21\u732e\u6709\u7591\u95ee\u6216\u9700\u8981\u5e2e\u52a9\uff1a</p> <ul> <li>\u53d1\u8d77\u8ba8\u8bba\uff1a\u4f7f\u7528 GitHub Discussions \u63d0\u51fa\u4e00\u822c\u6027\u95ee\u9898</li> <li>\u5728 issue \u4e2d\u63d0\u95ee\uff1a\u5728\u76f8\u5173 issue \u4e2d\u8bc4\u8bba\u4ee5\u83b7\u53d6\u5177\u4f53\u95ee\u9898\u7684\u5e2e\u52a9</li> <li>\u8054\u7cfb\u7ef4\u62a4\u8005\uff1a\u8054\u7cfb README \u4e2d\u5217\u51fa\u7684\u6838\u5fc3\u5f00\u53d1\u8005</li> </ul> <p>\u518d\u6b21\u611f\u8c22\u4f60\u4e3a <code>GPUMDkit</code> \u505a\u51fa\u8d21\u732e\uff01\u4f60\u7684\u52aa\u529b\u5e2e\u52a9\u8fd9\u4e2a\u5de5\u5177\u5305\u4e3a\u6574\u4e2a GPUMD \u548c NEP \u793e\u533a\u53d8\u5f97\u66f4\u597d\u3002</p>"}]}
\ No newline at end of file
diff --git a/docs/htmls/sitemap.xml b/docs/htmls/sitemap.xml
index 28a7dd6..bd1616c 100644
--- a/docs/htmls/sitemap.xml
+++ b/docs/htmls/sitemap.xml
@@ -2,110 +2,110 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/index.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/index.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/active_learning_workflow.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/analyzer_scripts.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/calculator_scripts.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/command_reference.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/contributing_to_gpumdkit.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/custom_commands.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/format_conversion.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/plot_scripts.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/polar_material_analysis.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/quick_start.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/structure_sampling.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/workflow_scripts.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/index.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html</loc>
-         <lastmod>2026-06-30</lastmod>
+         <lastmod>2026-07-01</lastmod>
     </url>
 </urlset>
\ No newline at end of file
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diff --git a/docs/htmls/zh/index.html b/docs/htmls/zh/index.html
index 3add00d..744ae68 100644
--- a/docs/htmls/zh/index.html
+++ b/docs/htmls/zh/index.html
@@ -1576,7 +1576,7 @@ <h2 id="_8">模块概览</h2>
 <tr>
 <td>结构采样</td>
 <td>2</td>
-<td><code>-neptrain</code>、交互菜单</td>
+<td>交互菜单、<code>-frame_range</code>、<code>-pynep</code>（已弃用）</td>
 <td>结构采样</td>
 </tr>
 <tr>
diff --git "a/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html" "b/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html"
index e1819d1..02e073d 100644
--- "a/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html"
+++ "b/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html"
@@ -1817,6 +1817,7 @@ <h3 id="_5">每个入口的作用</h3>
 <thead>
 <tr>
 <th>入口</th>
+<th>调用脚本</th>
 <th>功能</th>
 <th>适用场景</th>
 </tr>
@@ -1824,91 +1825,109 @@ <h3 id="_5">每个入口的作用</h3>
 <tbody>
 <tr>
 <td><code>101</code></td>
+<td><code>out2xyz.sh</code></td>
 <td>VASP OUTCAR 转 extxyz，shell 版本</td>
 <td>批量转换 VASP 计算目录</td>
 </tr>
 <tr>
 <td><code>102</code></td>
+<td><code>mtp2xyz.py</code></td>
 <td>MTP cfg 转 extxyz</td>
 <td>转换 MTP 数据</td>
 </tr>
 <tr>
 <td><code>103</code></td>
+<td><code>cp2k_log2xyz.py</code> / <code>cp2k2xyz.py</code></td>
 <td>CP2K 转 extxyz</td>
 <td>可选择 log/inp 路线或 pos/frc/cell 路线</td>
 </tr>
 <tr>
 <td><code>104</code></td>
+<td><code>abacus2xyz_scf.sh</code> / <code>abacus2xyz_md.sh</code></td>
 <td>ABACUS 转 extxyz</td>
 <td>转换 ABACUS SCF 或 MD 输出</td>
 </tr>
 <tr>
 <td><code>105</code></td>
+<td><code>exyz2pos.py</code></td>
 <td>extxyz 转 POSCAR</td>
 <td>将 extxyz 每一帧写成 POSCAR</td>
 </tr>
 <tr>
 <td><code>106</code></td>
+<td><code>add_groups.py</code></td>
 <td>添加 group 标签</td>
 <td>为 GPUMD 相关流程添加原子分组标签</td>
 </tr>
 <tr>
 <td><code>107</code></td>
+<td><code>add_weight.py</code></td>
 <td>添加权重</td>
 <td>修改训练集结构权重</td>
 </tr>
 <tr>
 <td><code>108</code></td>
+<td><code>get_frame.py</code></td>
 <td>提取单帧</td>
 <td>从 extxyz 轨迹导出某一帧</td>
 </tr>
 <tr>
 <td><code>109</code></td>
+<td><code>clean_xyz.py</code></td>
 <td>清理 XYZ 信息</td>
 <td>删除多余 extxyz 属性</td>
 </tr>
 <tr>
 <td><code>110</code></td>
+<td><code>replicate.py</code></td>
 <td>扩胞</td>
 <td>按倍数或目标原子数扩胞</td>
 </tr>
 <tr>
 <td><code>out2exyz</code></td>
+<td><code>out2exyz.py</code></td>
 <td>OUTCAR 转 extxyz，Python 版本</td>
 <td>VASP OUTCAR 转换的另一个入口</td>
 </tr>
 <tr>
 <td><code>pos2exyz</code></td>
+<td><code>pos2exyz.py</code></td>
 <td>POSCAR 转 extxyz</td>
 <td>转换单个结构</td>
 </tr>
 <tr>
 <td><code>cif2pos</code></td>
+<td><code>cif2pos.py</code></td>
 <td>CIF 转 POSCAR</td>
 <td>从 CIF 准备 VASP 输入</td>
 </tr>
 <tr>
 <td><code>cif2exyz</code></td>
+<td><code>cif2exyz.py</code></td>
 <td>CIF 转 extxyz</td>
 <td>从 CIF 准备 GPUMDkit 输入</td>
 </tr>
 <tr>
 <td><code>xdat2exyz</code></td>
+<td><code>xdatcar2exyz.py</code></td>
 <td>XDATCAR 转 extxyz</td>
 <td>转换 VASP MD 轨迹</td>
 </tr>
 <tr>
 <td><code>pos2lmp</code></td>
+<td><code>pos2lmp.py</code></td>
 <td>POSCAR 转 LAMMPS data</td>
 <td>准备 LAMMPS 输入</td>
 </tr>
 <tr>
 <td><code>lmp2exyz</code></td>
+<td><code>lmp2exyz.py</code></td>
 <td>LAMMPS dump 转 extxyz</td>
 <td>转换 LAMMPS 轨迹</td>
 </tr>
 <tr>
 <td><code>traj2exyz</code></td>
+<td><code>traj2exyz.py</code></td>
 <td>ASE traj 转 extxyz</td>
 <td>转换 ASE 轨迹</td>
 </tr>
diff --git "a/docs/htmls/zh/\347\273\223\346\236\204\351\207\207\346\240\267.html" "b/docs/htmls/zh/\347\273\223\346\236\204\351\207\207\346\240\267.html"
index 7fd034e..942825c 100644
--- "a/docs/htmls/zh/\347\273\223\346\236\204\351\207\207\346\240\267.html"
+++ "b/docs/htmls/zh/\347\273\223\346\236\204\351\207\207\346\240\267.html"
@@ -1631,7 +1631,7 @@ <h2 id="_2">均匀/随机采样</h2>
 <li><code>sampled_structures.xyz</code></li>
 </ul>
 <h2 id="neptrain-fps">NepTrain FPS</h2>
-<p>NepTrain 版本的 FPS：</p>
+<p>NepTrain 版本的 FPS。交互模式选择 <code>203</code>；也可以直接运行脚本：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
 </code></pre></div>
 <p>交互模式选择 <code>203</code>，会看到：</p>
@@ -1703,6 +1703,7 @@ <h3 id="gpumdkit">GPUMDkit 入口</h3>
 </code></pre></div>
 <p>这个入口需要 <code>pynep</code>。</p>
 <h2 id="_3">结构扰动</h2>
+<p>交互模式选择 <code>204</code>；也可以直接运行脚本：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>python<span class="w"> </span>Scripts/sample_structures/perturb_structure.py<span class="w"> </span>POSCAR<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">0</span>.03<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>uniform
 </code></pre></div>
 <p>交互模式选择 <code>204</code>，会看到：</p>
@@ -1749,6 +1750,7 @@ <h2 id="_3">结构扰动</h2>
 <p>该功能需要 <code>dpdata</code>。使用此功能时建议引用 dpdata 包。</p>
 <h2 id="_4">最大力偏差结构选择</h2>
 <p>该功能需要配合 GPUMD 的 <code>active</code> 命令使用。<code>active</code> 通过委员会评审机制，让多条势函数对同一结构进行预测，并记录每个结构的最大力偏差。<code>select_max_modev.py</code> 会从 <code>active.out</code> 和 <code>active.xyz</code> 中选择力偏差较大的结构，写入 <code>selected.xyz</code>。</p>
+<p>交互模式选择 <code>205</code>；也可以直接运行脚本：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>python<span class="w"> </span>Scripts/sample_structures/select_max_modev.py<span class="w"> </span><span class="m">200</span><span class="w"> </span><span class="m">0</span>.15
 </code></pre></div>
 <p>交互模式选择 <code>205</code>，会看到：</p>
@@ -1769,15 +1771,18 @@ <h2 id="_4">最大力偏差结构选择</h2>
 <li><code>selected.xyz</code></li>
 </ul>
 <h2 id="_5">帧范围提取</h2>
-<p>提取轨迹的一部分帧：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>python<span class="w"> </span>Scripts/sample_structures/frame_range.py<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span>.8
+<p><code>frame_range.py</code> 是一个独立的 CLI 工具，不在结构采样交互菜单 <code>201–205</code> 中。它适合在采样前先截取轨迹的一段，例如只保留平衡后的后半段轨迹。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-frame_range<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span>.8
+<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a>python<span class="w"> </span>Scripts/sample_structures/frame_range.py<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span>.8
 </code></pre></div>
-<p>这会写入轨迹 0% 到 80% 的帧。</p>
+<p>这会写入轨迹 0% 到 80% 的帧。参数使用轨迹比例，范围为 <code>0</code> 到 <code>1</code>。</p>
 <h2 id="_6">示例命令</h2>
+<p>下面是一个常见的采样前处理顺序：先用分析工具检查和过滤候选轨迹，再进行 FPS 采样。前两个命令属于<a href="%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html">分析工具</a>，最后一步属于本页的结构采样。</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>gpumdkit.sh<span class="w"> </span>-min_dist_pbc<span class="w"> </span>dump.xyz
 <a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>gpumdkit.sh<span class="w"> </span>-filter_box<span class="w"> </span>dump.xyz<span class="w"> </span><span class="m">13</span>
 <a id="__codelineno-19-3" name="__codelineno-19-3" href="#__codelineno-19-3"></a>python<span class="w"> </span>Scripts/sample_structures/neptrain_select_structs.py<span class="w"> </span>dump.xyz<span class="w"> </span>train.xyz<span class="w"> </span>nep.txt
 </code></pre></div>
+<p>最后一步也可以在交互模式中选择 <code>2) 结构采样 → 203</code>。</p>
 <h2 id="_7">常见问题</h2>
 <table>
 <thead>
diff --git "a/docs/htmls/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.html" "b/docs/htmls/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.html"
index 467d935..531c057 100644
--- "a/docs/htmls/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.html"
+++ "b/docs/htmls/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.html"
@@ -1451,6 +1451,13 @@ <h1>🧮 计算器脚本</h1>
 
 <p><strong>脚本位置：</strong> <code>Scripts/calculators/</code></p>
 <h2 id="_1">功能概览</h2>
+<p>计算器模块大致可以分为三类：</p>
+<ul>
+<li><strong>轨迹性质：</strong> 从 GPUMD 或 extxyz 轨迹计算 MSD、离子电导率等时间相关性质；</li>
+<li><strong>NEP 辅助计算：</strong> 使用 NEP 模型预测能量/力/应力、提取描述符、计算 DOAS、进行 NEB 或结构优化；</li>
+<li><strong>极性材料分析：</strong> 为钙钛矿和极性材料构建近邻列表、计算局域位移、平均结构、八面体倾转和局域极化。</li>
+</ul>
+<p>如果你还不熟悉某个脚本，建议先用交互模式查看输入提示；如果已经知道参数，则可以直接使用 <code>gpumdkit.sh -calc ...</code> 调用。</p>
 <table>
 <thead>
 <tr>
@@ -1567,6 +1574,7 @@ <h2 id="_1">功能概览</h2>
 <a id="__codelineno-2-19" name="__codelineno-2-19" href="#__codelineno-2-19"></a>Input the function number:
 </code></pre></div>
 <h2 id="_2">离子电导率</h2>
+<p><code>calc_ion_conductivity.py</code> 从 <code>msd.out</code> 计算离子扩散系数和离子电导率。</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>ionic-cond<span class="w"> </span>Li<span class="w"> </span><span class="m">1</span>
 </code></pre></div>
 <p>交互模式选择 <code>401</code>，会看到：</p>
@@ -1614,15 +1622,29 @@ <h2 id="_2">离子电导率</h2>
 <a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a>Enter system volume (in A^3):
 <a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>Enter number of ions:
 </code></pre></div>
+<p>输出示例：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>Diffusivity (D):
+<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>  D_x: 4.153e-07 cm^2/s
+<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>  D_y: 4.174e-07 cm^2/s
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>  D_z: 2.610e-07 cm^2/s
+<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a>  D_total: 3.646e-07 cm^2/s
+<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>------------------------------
+<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a>Ionic Conductivity:
+<a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a>  Sigma_x: 2.576e-02 mS/cm
+<a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a>  Sigma_y: 2.589e-02 mS/cm
+<a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a>  Sigma_z: 1.619e-02 mS/cm
+<a id="__codelineno-6-11" name="__codelineno-6-11" href="#__codelineno-6-11"></a>  Sigma_total: 2.261e-02 mS/cm
+</code></pre></div>
 <h2 id="msd">从轨迹计算 MSD</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
-<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">5000</span>
+<p><code>calc_msd.py</code> 可以直接从 extxyz 轨迹中计算指定元素的 MSD。</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>dump.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">5000</span>
 </code></pre></div>
 <p>交互模式选择 <code>412</code>，会看到：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]
-<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>  Optional argument: max_corr_steps (default: frame number)
-<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>Example: dump.xyz Li 10
-<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>------------&gt;&gt;
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]
+<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>  Optional argument: max_corr_steps (default: frame number)
+<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>Example: dump.xyz Li 10
+<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a>------------&gt;&gt;
 </code></pre></div>
 <p>参数含义：</p>
 <table>
@@ -1655,9 +1677,10 @@ <h2 id="msd">从轨迹计算 MSD</h2>
 <ul>
 <li><code>msd.out</code></li>
 </ul>
+<p><code>msd.out</code> 的开头是文本表格，包含时间和不同方向的 MSD 列。生成后可以继续使用绘图命令检查扩散区间和自扩散系数。</p>
 <p>随后可绘图：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
-<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
@@ -1667,16 +1690,16 @@ <h2 id="msd">从轨迹计算 MSD</h2>
 <h2 id="nep">NEP 预测性质</h2>
 <p><code>calc_properties_with_nep.py</code> 使用训练好的 NEP 模型计算能量、力和应力。</p>
 <p><strong>依赖：</strong> <code>calorine</code></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>pip<span class="w"> </span>install<span class="w"> </span>calorine
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>pip<span class="w"> </span>install<span class="w"> </span>calorine
 </code></pre></div>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nep<span class="w"> </span>structures.xyz<span class="w"> </span>predictions.xyz<span class="w"> </span>nep.txt
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nep<span class="w"> </span>structures.xyz<span class="w"> </span>predictions.xyz<span class="w"> </span>nep.txt
 </code></pre></div>
-<p>使用此功能可以用训练好的 NEP 模型进行预测。建议在使用前先验证模型在目标结构上的预测质量。</p>
+<p>使用此功能可以用训练好的 NEP 模型进行预测。建议在使用前先验证模型在目标结构上的预测质量，再将输出作为后续分析或筛选依据。</p>
 <p><strong>提示：</strong> 预测前可以清理 extxyz 元数据：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-clean_xyz<span class="w"> </span>train.xyz<span class="w"> </span>clean_train.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-clean_xyz<span class="w"> </span>train.xyz<span class="w"> </span>clean_train.xyz
 </code></pre></div>
 <h2 id="nep_1">NEP 描述符</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>des<span class="w"> </span>train.xyz<span class="w"> </span>descriptors.npy<span class="w"> </span>nep.txt<span class="w"> </span>Li
 </code></pre></div>
 <p>用途包括：</p>
 <ul>
@@ -1685,8 +1708,8 @@ <h2 id="nep_1">NEP 描述符</h2>
 <li>判断新数据是否扩展了描述符空间。</li>
 </ul>
 <p>绘图：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
-<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>pca
+<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des<span class="w"> </span>umap
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/des_umap.png" alt="Descriptor UMAP" width="52%" />
@@ -1694,8 +1717,8 @@ <h2 id="nep_1">NEP 描述符</h2>
 
 <h2 id="doas">DOAS</h2>
 <p><code>calc_doas.py</code> 用于计算 <a href="https://doi.org/10.1002/anie.202215544">Wang et al.</a> 提出的 density of atomistic states。</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>doas<span class="w"> </span>structures.xyz<span class="w"> </span>nep.txt<span class="w"> </span>doas.out
-<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>doas<span class="w"> </span>structures.xyz<span class="w"> </span>nep.txt<span class="w"> </span>doas.out
+<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
 </code></pre></div>
 <p>脚本会：</p>
 <ol>
@@ -1705,19 +1728,27 @@ <h2 id="doas">DOAS</h2>
 <li>按元素分组输出；</li>
 <li>用绘图脚本可视化分布。</li>
 </ol>
+<p>对于很大的体系，如果主要目的是获得优化后的结构和原子能量分布，直接在 GPUMD 中完成最小化和原子能量输出通常会更高效。</p>
 <div align="center">
   <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
 </div>
 
 <h2 id="neb">NEB 和结构优化</h2>
 <p>NEB：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>neb<span class="w"> </span>initial.xyz<span class="w"> </span>final.xyz<span class="w"> </span><span class="m">9</span><span class="w"> </span>nep.txt
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>neb<span class="w"> </span>initial.xyz<span class="w"> </span>final.xyz<span class="w"> </span><span class="m">9</span><span class="w"> </span>nep.txt
 </code></pre></div>
+<p>这会使用 NEP 模型运行含 <code>9</code> 个中间像的 NEB 计算。运行过程中脚本会询问原子固定方式：</p>
+<ul>
+<li><code>none</code>：不固定原子；</li>
+<li><code>index</code>：按原子序号固定；</li>
+<li><code>element</code>：固定某一种元素的所有原子；</li>
+<li><code>position</code>：固定坐标范围内的原子。</li>
+</ul>
 <p>结构优化（通过 <code>calorine</code>）：</p>
 <p><strong>依赖：</strong> <code>calorine</code></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>pip<span class="w"> </span>install<span class="w"> </span>calorine
+<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>pip<span class="w"> </span>install<span class="w"> </span>calorine
 </code></pre></div>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>minimize<span class="w"> </span>POSCAR<span class="w"> </span>nep.txt<span class="w"> </span><span class="m">0</span>.01<span class="w"> </span><span class="m">1000</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>minimize<span class="w"> </span>POSCAR<span class="w"> </span>nep.txt<span class="w"> </span><span class="m">0</span>.01<span class="w"> </span><span class="m">1000</span>
 </code></pre></div>
 <p>输出包括：</p>
 <ul>
@@ -1727,10 +1758,10 @@ <h2 id="neb">NEB 和结构优化</h2>
 <h2 id="ovito-rdf">使用 OVITO 计算 RDF</h2>
 <p><code>rdf_calculator_ovito.py</code> 使用 OVITO 的分析工具计算径向分布函数。</p>
 <p><strong>依赖：</strong> OVITO</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a>pip<span class="w"> </span>install<span class="w"> </span>ovito
+<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>pip<span class="w"> </span>install<span class="w"> </span>ovito
 </code></pre></div>
 <p><strong>输入文件：</strong> 结构文件（单帧或轨迹）</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a>python<span class="w"> </span>Scripts/calculators/rdf_calculator_ovito.py<span class="w"> </span>trajectory.xyz<span class="w"> </span><span class="m">6</span>.0<span class="w"> </span><span class="m">400</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>python<span class="w"> </span>Scripts/calculators/rdf_calculator_ovito.py<span class="w"> </span>trajectory.xyz<span class="w"> </span><span class="m">6</span>.0<span class="w"> </span><span class="m">400</span>
 </code></pre></div>
 <p><strong>参数：</strong></p>
 <table>
@@ -1756,15 +1787,58 @@ <h2 id="ovito-rdf">使用 OVITO 计算 RDF</h2>
 </tbody>
 </table>
 <p><strong>可视化：</strong></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf
+<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>rdf
 </code></pre></div>
 <p><strong>注意：</strong> 建议优先使用 GPUMD 中的 <code>compute_rdf</code> 命令。</p>
 <h2 id="_3">铁电和极性材料工具</h2>
-<p>选项 <code>406–410</code> 涵盖钙钛矿和极性材料分析：近邻列表、局域位移、平均结构、八面体倾转和 ABO3 极化。这些工具基于 <code>ferrodispcalc</code>。</p>
-<p><strong>依赖：</strong></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
+<p>选项 <code>406–410</code> 面向钙钛矿和极性材料分析，常用于从 MD 轨迹中提取局域结构信息，然后进一步分析相变、畴结构或极化纹理。</p>
+<p>这些脚本在本页只做快速索引，因为它们通常需要组合使用。推荐阅读专题教程中的完整工作流和参数说明：<strong><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></strong>。</p>
+<table>
+<thead>
+<tr>
+<th>菜单</th>
+<th>CLI 子命令</th>
+<th>作用</th>
+<th>详细说明</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>406</code></td>
+<td><code>gpumdkit.sh -calc nlist ...</code></td>
+<td>构建指定中心原子和近邻原子之间的近邻列表</td>
+<td><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
+</tr>
+<tr>
+<td><code>407</code></td>
+<td><code>gpumdkit.sh -calc disp ...</code></td>
+<td>根据轨迹和近邻列表计算局域位移</td>
+<td><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
+</tr>
+<tr>
+<td><code>408</code></td>
+<td><code>gpumdkit.sh -calc avg-struct ...</code></td>
+<td>从轨迹中计算平均结构</td>
+<td><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
+</tr>
+<tr>
+<td><code>409</code></td>
+<td><code>gpumdkit.sh -calc oct-tilt ...</code></td>
+<td>计算八面体倾转角</td>
+<td><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
+</tr>
+<tr>
+<td><code>410</code></td>
+<td><code>gpumdkit.sh -calc pol-abo3 ...</code></td>
+<td>根据 Born 有效电荷估算 ABO3 局域极化</td>
+<td><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></td>
+</tr>
+</tbody>
+</table>
+<p>部分脚本需要安装 <code>ferrodispcalc</code>：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
 </code></pre></div>
-<p>完整参数列表和真实工作流案例（PbTiO3 相变、PTO/STO 超晶格拓扑等）请参见 <strong><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></strong>。</p>
+<p>一个典型顺序是先用 <code>nlist</code> 建立近邻列表，再用该近邻列表计算位移、倾转或极化。对于平均结构，可以直接从轨迹出发，用长度容差控制哪些帧参与平均。</p>
 
 
 
diff --git a/docs/tutorials/en/calculator_scripts.md b/docs/tutorials/en/calculator_scripts.md
index 5763b48..a8698f1 100644
--- a/docs/tutorials/en/calculator_scripts.md
+++ b/docs/tutorials/en/calculator_scripts.md
@@ -7,6 +7,14 @@
 
 ## Overview
 
+The calculator module can be read as three groups:
+
+- **Trajectory properties:** compute time-dependent quantities such as MSD and ionic conductivity from GPUMD or extxyz trajectories;
+- **NEP-assisted calculations:** use a NEP model to predict energies/forces/stresses, extract descriptors, calculate DOAS, run NEB, or minimize structures;
+- **Polar-material analysis:** build neighbor lists and calculate local displacement, averaged structures, octahedral tilt, and local polarization for perovskite or polar systems.
+
+If you are not sure about the required arguments, start from the interactive menu to see the prompt. If the arguments are already clear, use `gpumdkit.sh -calc ...` directly.
+
 | Task | Command | Main Input |
 |------|---------|------------|
 | Ionic conductivity | `gpumdkit.sh -calc ionic-cond <element> <charge>` | `msd.out`, `thermo.out`, `model.xyz` |
@@ -327,12 +335,22 @@ gpumdkit.sh -plt rdf
 
 ## Ferroelectric and Polar Material Tools
 
-Options `406–410` cover perovskite and polar-material analysis: neighbor lists, local displacements, averaged structures, octahedral tilt, and ABO3 polarization. These tools are built on `ferrodispcalc`.
+Options `406–410` are for perovskite and polar-material analysis. They are commonly used to extract local structural information from MD trajectories before analyzing phase transitions, domain patterns, or polarization textures.
+
+This page only gives a quick index for these scripts because they are usually used together. For full workflows and argument details, see **[Polar Material Analysis](polar_material_analysis.md)**.
+
+| Menu | CLI subcommand | Purpose | Details |
+|------|----------------|---------|---------|
+| `406` | `gpumdkit.sh -calc nlist ...` | Build neighbor lists between selected center and neighbor atoms | [Polar Material Analysis](polar_material_analysis.md) |
+| `407` | `gpumdkit.sh -calc disp ...` | Calculate local displacement from a trajectory and neighbor list | [Polar Material Analysis](polar_material_analysis.md) |
+| `408` | `gpumdkit.sh -calc avg-struct ...` | Calculate an averaged structure from a trajectory | [Polar Material Analysis](polar_material_analysis.md) |
+| `409` | `gpumdkit.sh -calc oct-tilt ...` | Calculate octahedral tilt angles | [Polar Material Analysis](polar_material_analysis.md) |
+| `410` | `gpumdkit.sh -calc pol-abo3 ...` | Estimate local ABO3 polarization from Born effective charges | [Polar Material Analysis](polar_material_analysis.md) |
 
-**Dependency:**
+Some scripts require `ferrodispcalc`:
 
 ```bash
 pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
 ```
 
-For complete argument lists, real-world workflow examples (PbTiO3 phase transition, PTO/STO superlattice topology, etc.), see **[Polar Material Analysis](polar_material_analysis.md)**.
+A typical sequence is to build neighbor lists with `nlist`, then reuse those lists for displacement, tilt, or polarization calculations. For averaged structures, you can start directly from the trajectory and use the length tolerance to control which frames are included.
diff --git a/docs/tutorials/en/format_conversion.md b/docs/tutorials/en/format_conversion.md
index f912c48..f80e2e2 100644
--- a/docs/tutorials/en/format_conversion.md
+++ b/docs/tutorials/en/format_conversion.md
@@ -63,26 +63,26 @@ Input the function number or converter keyword:
 
 ### What Each Entry Does
 
-| Entry | Function | When to Use |
-|-------|----------|-------------|
-| `101` | VASP OUTCAR to extxyz, shell version | convert VASP calculation directories |
-| `102` | MTP cfg to extxyz | convert MTP training data |
-| `103` | CP2K to extxyz | choose CP2K log/inp route or pos/frc/cell route |
-| `104` | ABACUS to extxyz | convert ABACUS SCF or MD output |
-| `105` | extxyz to POSCAR | write each extxyz frame as a POSCAR-style file |
-| `106` | add group labels | add atom group labels for GPUMD-related workflows |
-| `107` | add weights | assign training weights in extxyz |
-| `108` | extract frame | export one frame from an extxyz trajectory |
-| `109` | clean XYZ info | remove extra extxyz properties |
-| `110` | replicate structure | build supercells by factors or target atom count |
-| `out2exyz` | OUTCAR to extxyz, Python version | alternative VASP OUTCAR converter |
-| `pos2exyz` | POSCAR to extxyz | convert a single structure |
-| `cif2pos` | CIF to POSCAR | prepare VASP input from CIF |
-| `cif2exyz` | CIF to extxyz | prepare GPUMDkit input from CIF |
-| `xdat2exyz` | XDATCAR to extxyz | convert VASP MD trajectory |
-| `pos2lmp` | POSCAR to LAMMPS data | prepare LAMMPS input |
-| `lmp2exyz` | LAMMPS dump to extxyz | convert LAMMPS trajectory |
-| `traj2exyz` | ASE traj to extxyz | convert ASE trajectory |
+| Entry | Called script | Function | When to Use |
+|-------|---------------|----------|-------------|
+| `101` | `out2xyz.sh` | VASP OUTCAR to extxyz, shell version | convert VASP calculation directories |
+| `102` | `mtp2xyz.py` | MTP cfg to extxyz | convert MTP training data |
+| `103` | `cp2k_log2xyz.py` / `cp2k2xyz.py` | CP2K to extxyz | choose CP2K log/inp route or pos/frc/cell route |
+| `104` | `abacus2xyz_scf.sh` / `abacus2xyz_md.sh` | ABACUS to extxyz | convert ABACUS SCF or MD output |
+| `105` | `exyz2pos.py` | extxyz to POSCAR | write each extxyz frame as a POSCAR-style file |
+| `106` | `add_groups.py` | add group labels | add atom group labels for GPUMD-related workflows |
+| `107` | `add_weight.py` | add weights | assign training weights in extxyz |
+| `108` | `get_frame.py` | extract frame | export one frame from an extxyz trajectory |
+| `109` | `clean_xyz.py` | clean XYZ info | remove extra extxyz properties |
+| `110` | `replicate.py` | replicate structure | build supercells by factors or target atom count |
+| `out2exyz` | `out2exyz.py` | OUTCAR to extxyz, Python version | alternative VASP OUTCAR converter |
+| `pos2exyz` | `pos2exyz.py` | POSCAR to extxyz | convert a single structure |
+| `cif2pos` | `cif2pos.py` | CIF to POSCAR | prepare VASP input from CIF |
+| `cif2exyz` | `cif2exyz.py` | CIF to extxyz | prepare GPUMDkit input from CIF |
+| `xdat2exyz` | `xdatcar2exyz.py` | XDATCAR to extxyz | convert VASP MD trajectory |
+| `pos2lmp` | `pos2lmp.py` | POSCAR to LAMMPS data | prepare LAMMPS input |
+| `lmp2exyz` | `lmp2exyz.py` | LAMMPS dump to extxyz | convert LAMMPS trajectory |
+| `traj2exyz` | `traj2exyz.py` | ASE traj to extxyz | convert ASE trajectory |
 
 ## Quick Command Reference
 
diff --git a/docs/tutorials/en/index.md b/docs/tutorials/en/index.md
index 03dc970..d729439 100644
--- a/docs/tutorials/en/index.md
+++ b/docs/tutorials/en/index.md
@@ -68,7 +68,7 @@ Use `gpumdkit.sh -h` to see all available options.
 | Module | Menu | CLI | Description |
 |--------|------|-----|-------------|
 | Format Conversion | 1 | `-out2xyz`, `-pos2exyz` | File conversion |
-| Sample Structures | 2 | `-neptrain`, interactive menu | Structure sampling |
+| Sample Structures | 2 | interactive menu, `-frame_range`, `-pynep` (deprecated) | Structure sampling |
 | Workflow | 3 | - | Batch processing |
 | Calculators | 4 | `-calc <type>` | Property calculations |
 | Analyzer | 5 | `-range`, `-min_dist` | Structure analysis |
diff --git a/docs/tutorials/en/structure_sampling.md b/docs/tutorials/en/structure_sampling.md
index c1a7627..08f40d3 100644
--- a/docs/tutorials/en/structure_sampling.md
+++ b/docs/tutorials/en/structure_sampling.md
@@ -85,7 +85,7 @@ Output:
 
 ## Farthest Point Sampling with NepTrain
 
-This entry uses NepTrain descriptors for FPS.
+This entry uses NepTrain descriptors for FPS. Choose `203` in interactive mode, or run the script directly:
 
 ```bash
 python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
@@ -177,7 +177,7 @@ This entry requires `pynep` and is kept for compatibility.
 
 ## Structure Perturbation
 
-Use perturbation when you want to generate initial structures around a known configuration.
+Use perturbation when you want to generate initial structures around a known configuration. Choose `204` in interactive mode, or run the script directly:
 
 ```bash
 python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
@@ -212,6 +212,8 @@ This function requires `dpdata`. If you use this function, we recommend citing t
 
 Use this together with the GPUMD `active` command. The `active` command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. `select_max_modev.py` selects structures with large force deviations from `active.out` and `active.xyz`, then writes them to `selected.xyz`.
 
+Choose `205` in interactive mode, or run the script directly:
+
 ```bash
 python Scripts/sample_structures/select_max_modev.py 200 0.15
 ```
@@ -245,17 +247,18 @@ Output:
 
 ## Frame Range Extraction
 
-Use this to extract a fraction of a trajectory:
+`frame_range.py` is an independent CLI tool and is not part of the interactive sampling menu `201–205`. Use it when you want to keep only a fraction of a trajectory before sampling, for example after equilibration.
 
 ```bash
+gpumdkit.sh -frame_range dump.xyz 0 0.8
 python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
 ```
 
-This writes frames from 0% to 80% of the trajectory.
+This writes frames from 0% to 80% of the trajectory. The range arguments are trajectory fractions from `0` to `1`.
 
 ## Example Commands
 
-An example sequence using several sampling-related tools:
+An example preprocessing-and-sampling sequence is shown below. The first two commands are analyzer tools; the final step is structure sampling.
 
 ```bash
 gpumdkit.sh -min_dist_pbc dump.xyz
@@ -263,6 +266,8 @@ gpumdkit.sh -filter_box dump.xyz 13
 python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
 ```
 
+The final step can also be run from interactive mode by choosing `2) Sample Structures -> 203`.
+
 ## Common Mistakes
 
 | Problem | Recommendation |
diff --git a/docs/tutorials/zh/index.md b/docs/tutorials/zh/index.md
index ba71e98..7ba7749 100644
--- a/docs/tutorials/zh/index.md
+++ b/docs/tutorials/zh/index.md
@@ -68,7 +68,7 @@ gpumdkit.sh -calc msd trajectory.xyz Li 10
 | 模块 | 菜单 | CLI | 描述 |
 |------|------|-----|------|
 | 格式转换 | 1 | `-out2xyz`, `-pos2exyz` | 文件转换 |
-| 结构采样 | 2 | `-neptrain`、交互菜单 | 结构采样 |
+| 结构采样 | 2 | 交互菜单、`-frame_range`、`-pynep`（已弃用） | 结构采样 |
 | 工作流 | 3 | - | 批处理 |
 | 计算器 | 4 | `-calc <类型>` | 属性计算 |
 | 分析工具 | 5 | `-range`, `-min_dist` | 结构分析 |
diff --git "a/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md" "b/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
index d69fcf8..0237a30 100644
--- "a/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
+++ "b/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
@@ -61,26 +61,26 @@ Input the function number or converter keyword:
 
 ### 每个入口的作用
 
-| 入口 | 功能 | 适用场景 |
-|------|------|----------|
-| `101` | VASP OUTCAR 转 extxyz，shell 版本 | 批量转换 VASP 计算目录 |
-| `102` | MTP cfg 转 extxyz | 转换 MTP 数据 |
-| `103` | CP2K 转 extxyz | 可选择 log/inp 路线或 pos/frc/cell 路线 |
-| `104` | ABACUS 转 extxyz | 转换 ABACUS SCF 或 MD 输出 |
-| `105` | extxyz 转 POSCAR | 将 extxyz 每一帧写成 POSCAR |
-| `106` | 添加 group 标签 | 为 GPUMD 相关流程添加原子分组标签 |
-| `107` | 添加权重 | 修改训练集结构权重 |
-| `108` | 提取单帧 | 从 extxyz 轨迹导出某一帧 |
-| `109` | 清理 XYZ 信息 | 删除多余 extxyz 属性 |
-| `110` | 扩胞 | 按倍数或目标原子数扩胞 |
-| `out2exyz` | OUTCAR 转 extxyz，Python 版本 | VASP OUTCAR 转换的另一个入口 |
-| `pos2exyz` | POSCAR 转 extxyz | 转换单个结构 |
-| `cif2pos` | CIF 转 POSCAR | 从 CIF 准备 VASP 输入 |
-| `cif2exyz` | CIF 转 extxyz | 从 CIF 准备 GPUMDkit 输入 |
-| `xdat2exyz` | XDATCAR 转 extxyz | 转换 VASP MD 轨迹 |
-| `pos2lmp` | POSCAR 转 LAMMPS data | 准备 LAMMPS 输入 |
-| `lmp2exyz` | LAMMPS dump 转 extxyz | 转换 LAMMPS 轨迹 |
-| `traj2exyz` | ASE traj 转 extxyz | 转换 ASE 轨迹 |
+| 入口 | 调用脚本 | 功能 | 适用场景 |
+|------|----------|------|----------|
+| `101` | `out2xyz.sh` | VASP OUTCAR 转 extxyz，shell 版本 | 批量转换 VASP 计算目录 |
+| `102` | `mtp2xyz.py` | MTP cfg 转 extxyz | 转换 MTP 数据 |
+| `103` | `cp2k_log2xyz.py` / `cp2k2xyz.py` | CP2K 转 extxyz | 可选择 log/inp 路线或 pos/frc/cell 路线 |
+| `104` | `abacus2xyz_scf.sh` / `abacus2xyz_md.sh` | ABACUS 转 extxyz | 转换 ABACUS SCF 或 MD 输出 |
+| `105` | `exyz2pos.py` | extxyz 转 POSCAR | 将 extxyz 每一帧写成 POSCAR |
+| `106` | `add_groups.py` | 添加 group 标签 | 为 GPUMD 相关流程添加原子分组标签 |
+| `107` | `add_weight.py` | 添加权重 | 修改训练集结构权重 |
+| `108` | `get_frame.py` | 提取单帧 | 从 extxyz 轨迹导出某一帧 |
+| `109` | `clean_xyz.py` | 清理 XYZ 信息 | 删除多余 extxyz 属性 |
+| `110` | `replicate.py` | 扩胞 | 按倍数或目标原子数扩胞 |
+| `out2exyz` | `out2exyz.py` | OUTCAR 转 extxyz，Python 版本 | VASP OUTCAR 转换的另一个入口 |
+| `pos2exyz` | `pos2exyz.py` | POSCAR 转 extxyz | 转换单个结构 |
+| `cif2pos` | `cif2pos.py` | CIF 转 POSCAR | 从 CIF 准备 VASP 输入 |
+| `cif2exyz` | `cif2exyz.py` | CIF 转 extxyz | 从 CIF 准备 GPUMDkit 输入 |
+| `xdat2exyz` | `xdatcar2exyz.py` | XDATCAR 转 extxyz | 转换 VASP MD 轨迹 |
+| `pos2lmp` | `pos2lmp.py` | POSCAR 转 LAMMPS data | 准备 LAMMPS 输入 |
+| `lmp2exyz` | `lmp2exyz.py` | LAMMPS dump 转 extxyz | 转换 LAMMPS 轨迹 |
+| `traj2exyz` | `traj2exyz.py` | ASE traj 转 extxyz | 转换 ASE 轨迹 |
 
 ## 快速命令表
 
diff --git "a/docs/tutorials/zh/\347\273\223\346\236\204\351\207\207\346\240\267.md" "b/docs/tutorials/zh/\347\273\223\346\236\204\351\207\207\346\240\267.md"
index 57dc0da..1ac0f65 100644
--- "a/docs/tutorials/zh/\347\273\223\346\236\204\351\207\207\346\240\267.md"
+++ "b/docs/tutorials/zh/\347\273\223\346\236\204\351\207\207\346\240\267.md"
@@ -83,7 +83,7 @@ dump.xyz random 100 500
 
 ## NepTrain FPS
 
-NepTrain 版本的 FPS：
+NepTrain 版本的 FPS。交互模式选择 `203`；也可以直接运行脚本：
 
 ```bash
 python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
@@ -170,6 +170,8 @@ dump.xyz train.xyz nep.txt 8
 
 ## 结构扰动
 
+交互模式选择 `204`；也可以直接运行脚本：
+
 ```bash
 python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform
 ```
@@ -203,6 +205,8 @@ Example: POSCAR 20 0.03 0.2 uniform
 
 该功能需要配合 GPUMD 的 `active` 命令使用。`active` 通过委员会评审机制，让多条势函数对同一结构进行预测，并记录每个结构的最大力偏差。`select_max_modev.py` 会从 `active.out` 和 `active.xyz` 中选择力偏差较大的结构，写入 `selected.xyz`。
 
+交互模式选择 `205`；也可以直接运行脚本：
+
 ```bash
 python Scripts/sample_structures/select_max_modev.py 200 0.15
 ```
@@ -229,22 +233,27 @@ Input <structs_num> <threshold> (eg. 200 0.15)
 
 ## 帧范围提取
 
-提取轨迹的一部分帧：
+`frame_range.py` 是一个独立的 CLI 工具，不在结构采样交互菜单 `201–205` 中。它适合在采样前先截取轨迹的一段，例如只保留平衡后的后半段轨迹。
 
 ```bash
+gpumdkit.sh -frame_range dump.xyz 0 0.8
 python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
 ```
 
-这会写入轨迹 0% 到 80% 的帧。
+这会写入轨迹 0% 到 80% 的帧。参数使用轨迹比例，范围为 `0` 到 `1`。
 
 ## 示例命令
 
+下面是一个常见的采样前处理顺序：先用分析工具检查和过滤候选轨迹，再进行 FPS 采样。前两个命令属于[分析工具](分析工具.md)，最后一步属于本页的结构采样。
+
 ```bash
 gpumdkit.sh -min_dist_pbc dump.xyz
 gpumdkit.sh -filter_box dump.xyz 13
 python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt
 ```
 
+最后一步也可以在交互模式中选择 `2) 结构采样 → 203`。
+
 ## 常见问题
 
 | 问题 | 建议 |
diff --git "a/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md" "b/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md"
index c8889b5..f429595 100644
--- "a/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md"
+++ "b/docs/tutorials/zh/\350\256\241\347\256\227\345\231\250\350\204\232\346\234\254.md"
@@ -7,6 +7,14 @@
 
 ## 功能概览
 
+计算器模块大致可以分为三类：
+
+- **轨迹性质：** 从 GPUMD 或 extxyz 轨迹计算 MSD、离子电导率等时间相关性质；
+- **NEP 辅助计算：** 使用 NEP 模型预测能量/力/应力、提取描述符、计算 DOAS、进行 NEB 或结构优化；
+- **极性材料分析：** 为钙钛矿和极性材料构建近邻列表、计算局域位移、平均结构、八面体倾转和局域极化。
+
+如果你还不熟悉某个脚本，建议先用交互模式查看输入提示；如果已经知道参数，则可以直接使用 `gpumdkit.sh -calc ...` 调用。
+
 | 任务 | 命令 | 主要输入 |
 |------|------|----------|
 | 离子电导率 | `gpumdkit.sh -calc ionic-cond <element> <charge>` | `msd.out`、`thermo.out`、`model.xyz` |
@@ -77,6 +85,8 @@ Input the function number:
 
 ## 离子电导率
 
+`calc_ion_conductivity.py` 从 `msd.out` 计算离子扩散系数和离子电导率。
+
 ```bash
 gpumdkit.sh -calc ionic-cond Li 1
 ```
@@ -115,8 +125,26 @@ Enter system volume (in A^3):
 Enter number of ions:
 ```
 
+输出示例：
+
+```text
+Diffusivity (D):
+  D_x: 4.153e-07 cm^2/s
+  D_y: 4.174e-07 cm^2/s
+  D_z: 2.610e-07 cm^2/s
+  D_total: 3.646e-07 cm^2/s
+------------------------------
+Ionic Conductivity:
+  Sigma_x: 2.576e-02 mS/cm
+  Sigma_y: 2.589e-02 mS/cm
+  Sigma_z: 1.619e-02 mS/cm
+  Sigma_total: 2.261e-02 mS/cm
+```
+
 ## 从轨迹计算 MSD
 
+`calc_msd.py` 可以直接从 extxyz 轨迹中计算指定元素的 MSD。
+
 ```bash
 gpumdkit.sh -calc msd dump.xyz Li 10
 gpumdkit.sh -calc msd dump.xyz Li 10 5000
@@ -144,6 +172,8 @@ Example: dump.xyz Li 10
 
 - `msd.out`
 
+`msd.out` 的开头是文本表格，包含时间和不同方向的 MSD 列。生成后可以继续使用绘图命令检查扩散区间和自扩散系数。
+
 随后可绘图：
 
 ```bash
@@ -170,7 +200,7 @@ pip install calorine
 gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt
 ```
 
-使用此功能可以用训练好的 NEP 模型进行预测。建议在使用前先验证模型在目标结构上的预测质量。
+使用此功能可以用训练好的 NEP 模型进行预测。建议在使用前先验证模型在目标结构上的预测质量，再将输出作为后续分析或筛选依据。
 
 **提示：** 预测前可以清理 extxyz 元数据：
 
@@ -218,6 +248,8 @@ gpumdkit.sh -plt doas doas.out Li
 4. 按元素分组输出；
 5. 用绘图脚本可视化分布。
 
+对于很大的体系，如果主要目的是获得优化后的结构和原子能量分布，直接在 GPUMD 中完成最小化和原子能量输出通常会更高效。
+
 <div align="center">
   <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
 </div>
@@ -230,6 +262,13 @@ NEB：
 gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt
 ```
 
+这会使用 NEP 模型运行含 `9` 个中间像的 NEB 计算。运行过程中脚本会询问原子固定方式：
+
+- `none`：不固定原子；
+- `index`：按原子序号固定；
+- `element`：固定某一种元素的所有原子；
+- `position`：固定坐标范围内的原子。
+
 结构优化（通过 `calorine`）：
 
 **依赖：** `calorine`
@@ -281,12 +320,22 @@ gpumdkit.sh -plt rdf
 
 ## 铁电和极性材料工具
 
-选项 `406–410` 涵盖钙钛矿和极性材料分析：近邻列表、局域位移、平均结构、八面体倾转和 ABO3 极化。这些工具基于 `ferrodispcalc`。
+选项 `406–410` 面向钙钛矿和极性材料分析，常用于从 MD 轨迹中提取局域结构信息，然后进一步分析相变、畴结构或极化纹理。
+
+这些脚本在本页只做快速索引，因为它们通常需要组合使用。推荐阅读专题教程中的完整工作流和参数说明：**[极性材料分析](极性材料分析.md)**。
+
+| 菜单 | CLI 子命令 | 作用 | 详细说明 |
+|------|------------|------|----------|
+| `406` | `gpumdkit.sh -calc nlist ...` | 构建指定中心原子和近邻原子之间的近邻列表 | [极性材料分析](极性材料分析.md) |
+| `407` | `gpumdkit.sh -calc disp ...` | 根据轨迹和近邻列表计算局域位移 | [极性材料分析](极性材料分析.md) |
+| `408` | `gpumdkit.sh -calc avg-struct ...` | 从轨迹中计算平均结构 | [极性材料分析](极性材料分析.md) |
+| `409` | `gpumdkit.sh -calc oct-tilt ...` | 计算八面体倾转角 | [极性材料分析](极性材料分析.md) |
+| `410` | `gpumdkit.sh -calc pol-abo3 ...` | 根据 Born 有效电荷估算 ABO3 局域极化 | [极性材料分析](极性材料分析.md) |
 
-**依赖：**
+部分脚本需要安装 `ferrodispcalc`：
 
 ```bash
 pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git
 ```
 
-完整参数列表和真实工作流案例（PbTiO3 相变、PTO/STO 超晶格拓扑等）请参见 **[极性材料分析](极性材料分析.md)**。
+一个典型顺序是先用 `nlist` 建立近邻列表，再用该近邻列表计算位移、倾转或极化。对于平均结构，可以直接从轨迹出发，用长度容差控制哪些帧参与平均。
diff --git a/gpumdkit.sh b/gpumdkit.sh
index dfc744b..8b292f9 100755
--- a/gpumdkit.sh
+++ b/gpumdkit.sh
@@ -40,6 +40,16 @@ echo " 7) Utilities                  8) Developing...       "
 echo " 0) Exit                                              "
 }
 
+function read_menu_choice(){
+    local __target_var="$1"
+    local __input
+    if ! IFS= read -r -p " " __input; then
+        echo " Input closed. Exiting."
+        return 1
+    fi
+    printf -v "$__target_var" '%s' "$__input"
+}
+
 # Function main
 function main(){
     echo " ------------>>"
@@ -54,12 +64,12 @@ function main(){
         "7" "701"
         "8"
     ) 
-    read -p " " choice
+    read_menu_choice choice || return 1
     while ! echo "${array_choice[@]}" | grep -wq "$choice" 
     do
       echo " ------------>>"
       echo " Please reinput function number:"
-      read -p " " choice
+      read_menu_choice choice || return 1
     done
 
     case "${choice:0:1}" in
diff --git a/skills/gpumdkit-analyzers/SKILL.md b/skills/gpumdkit-analyzers/SKILL.md
index fa6d3d1..19bffb0 100644
--- a/skills/gpumdkit-analyzers/SKILL.md
+++ b/skills/gpumdkit-analyzers/SKILL.md
@@ -17,7 +17,7 @@ allowed-tools: Bash(gpumdkit *) Bash(python3 *)
 |------|---------|-------------|
 | Composition Analysis | `-analyze_comp` | Group structures by composition |
 | Outlier Detection | Menu 502 | Find high-error structures |
-| Chemical Species | Menu 503 | List unique elements |
+| Chemical Species | `-chem_species` or Menu 503 | List unique elements |
 | Charge Balance | `-cbc` | Check oxidation-state balance |
 | Property Range | `-range` | Energy/force/virial statistics |
 | Distance Filter | `-filter_dist` or Menu 506 | Filter by minimum distance (no PBC) |
@@ -76,8 +76,11 @@ gpumdkit.sh -cbc train.xyz
 
 ### Chemical Species Identification
 ```bash
-# List unique elements (interactive mode)
-gpumdkit.sh  # Select: 5) Analyzer -> 503
+# List unique elements
+gpumdkit.sh -chem_species train.xyz
+
+# Interactive mode also works:
+# gpumdkit.sh  # Select: 5) Analyzer -> 503
 
 # Output: Sorted list of all elements in the file
 ```
@@ -198,13 +201,6 @@ gpumdkit.sh -time gpumd
 gpumdkit.sh -time nep
 ```
 
-### Volume Analysis
-```bash
-# Get average volume per temperature
-python Scripts/analyzer/get_volume.py
-# Requires: */K/thermo.out directories
-```
-
 ## CLI Flag Reference
 
 | Flag | Description | Syntax |
@@ -213,6 +209,7 @@ python Scripts/analyzer/get_volume.py
 | `-range` | Property range | `gpumdkit.sh -range <file> <prop>` |
 | `-min_dist` | Min distance (no PBC) | `gpumdkit.sh -min_dist <file>` |
 | `-min_dist_pbc` | Min distance (PBC) | `gpumdkit.sh -min_dist_pbc <file>` |
+| `-chem_species` | Chemical species list | `gpumdkit.sh -chem_species <file>` |
 | `-cbc` | Charge balance | `gpumdkit.sh -cbc <file>` |
 | `-filter_dist` | Filter by minimum distance | `gpumdkit.sh -filter_dist <file> <min_dist>` |
 | `-filter_dist_pbc` | Filter by minimum distance with PBC | `gpumdkit.sh -filter_dist_pbc <file> <min_dist>` |
diff --git a/skills/gpumdkit-sampling/SKILL.md b/skills/gpumdkit-sampling/SKILL.md
index 68ee56e..c0fc39c 100644
--- a/skills/gpumdkit-sampling/SKILL.md
+++ b/skills/gpumdkit-sampling/SKILL.md
@@ -136,11 +136,14 @@ python Scripts/sample_structures/select_max_modev.py 200 0.15
 ### Frame Range Extraction
 
 ```bash
-# Direct Python execution
+# GPUMDkit CLI
+gpumdkit.sh -frame_range <input.xyz> <start_fraction> <end_fraction>
+
+# Direct Python execution also works
 python Scripts/sample_structures/frame_range.py <input.xyz> <start_fraction> <end_fraction>
 
 # Example: Extract first 80% of frames
-python Scripts/sample_structures/frame_range.py dump.xyz 0 0.8
+gpumdkit.sh -frame_range dump.xyz 0 0.8
 
 # Output: dump_0.00_0.80.xyz
 ```
diff --git a/src/f1_format_conversions.sh b/src/f1_format_conversions.sh
index 984d9d7..6b25908 100644
--- a/src/f1_format_conversions.sh
+++ b/src/f1_format_conversions.sh
@@ -83,7 +83,7 @@ echo " Choose the script to use:"
 echo " 1) cp2k_log2xyz.py (from log and inp/xyz files)"
 echo " 2) cp2k2xyz.py (from pos.xyz, frc.xyz, cell.cell files)"
 echo " ------------>>"
-read -p " " cp2k_script_choice
+read_menu_choice cp2k_script_choice || return 1
 if [ "$cp2k_script_choice" == "1" ]; then
     cp2k2xyz_chenhua
 elif [ "$cp2k_script_choice" == "2" ]; then
@@ -105,12 +105,12 @@ echo " Choose the type of ABACUS calculation:"
 echo " 1) SCF calculation"
 echo " 2) MD calculation"
 echo " ------------>>"
-read -p " " abacus_type
+read_menu_choice abacus_type || return 1
 if [ "$abacus_type" == "1" ]; then
     echo " Input the directory containing running_scf.log"
     echo " Example: ./ "
     echo " ------------>>"
-    read -p " " dir_abacus_scf
+    read_menu_choice dir_abacus_scf || return 1
     echo " ---------------------------------------------------"
     bash ${GPUMDkit_path}/Scripts/format_conversion/abacus2xyz_scf.sh ${dir_abacus_scf}
     echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/abacus2xyz_scf.sh"
@@ -118,7 +118,7 @@ if [ "$abacus_type" == "1" ]; then
 elif [ "$abacus_type" == "2" ]; then
     echo " Input the directory containing running_md.log and MD_dump file"
     echo " ------------>>"
-    read -p " " dir_abacus_md
+    read_menu_choice dir_abacus_md || return 1
     echo " ---------------------------------------------------"
     bash ${GPUMDkit_path}/Scripts/format_conversion/abacus2xyz_md.sh ${dir_abacus_md}
     echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/abacus2xyz_md.sh"
@@ -392,12 +392,12 @@ valid_menu_choices=(
     "000" "101" "102" "103" "104" "105" "106" "107" "108" "109" "110" \
     "out2exyz" "pos2exyz" "cif2pos" "cif2exyz" "xdat2exyz" "pos2lmp" "lmp2exyz" "traj2exyz"
 ) 
-read -p " " num_choice
+read_menu_choice num_choice || return 1
 while ! echo "${valid_menu_choices[@]}" | grep -wq "$num_choice" 
 do
   echo " ------------>>"
   echo " Please reinput function number or converter keyword..."
-  read -p " " num_choice
+  read_menu_choice num_choice || return 1
 done
 
 case $num_choice in
diff --git a/src/f2_sample_structures.sh b/src/f2_sample_structures.sh
index f340144..64020e4 100644
--- a/src/f2_sample_structures.sh
+++ b/src/f2_sample_structures.sh
@@ -140,12 +140,12 @@ echo " +------------------------------------------------------+"
 echo " Input the function number:"
 
 valid_menu_choices=("000" "201" "202" "203" "204" "205")
-read -p " " num_choice
+read_menu_choice num_choice || return 1
 while ! echo "${valid_menu_choices[@]}" | grep -wq "$num_choice"
 do
   echo " ------------>>"
   echo " Please reinput function number..."
-  read -p " " num_choice
+  read_menu_choice num_choice || return 1
 done
 
 case $num_choice in
diff --git a/src/f3_workflows.sh b/src/f3_workflows.sh
index ae8fcec..8e1b2d2 100644
--- a/src/f3_workflows.sh
+++ b/src/f3_workflows.sh
@@ -19,17 +19,20 @@ echo " | to read coordinates from 'pos.xyz'.             |"
 echo " | Refer to Scripts/workflow/cp2k_template.inp     |"
 echo " >-------------------------------------------------<"
 
-read -p " Are you ready to continue? [y/N]: " confirm
+if ! IFS= read -r -p " Are you ready to continue? [y/N]: " confirm; then
+    echo " Input closed. Exiting."
+    return 1
+fi
 if [[ "$confirm" != [yY]* ]]; then
     echo " Operation cancelled. Exiting..."
-    exit
+    return
 fi
 
 echo " ---------------------------------------------------"
 echo " Input <extxyz_file> <template.inp> <prefix_name>"
 echo " Example: dump.xyz template.inp H2O"
 echo " ------------>>"
-read -p " " input_results
+read_menu_choice input_results || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/workflow/scf_batch_pretreatment_cp2k.py ${input_results}
 echo " Code path: ${GPUMDkit_path}/Scripts/workflow/scf_batch_pretreatment_cp2k.py"
@@ -46,12 +49,12 @@ function f301_scf_batch_pretreatment(){
     echo " +-------------------------------------------------------------+"
     echo " Input the function number:"
     valid_menu_choices=("1" "2")
-    read -p " " num_choice
+    read_menu_choice num_choice || return 1
     while ! echo "${valid_menu_choices[@]}" | grep -wq "$num_choice"
     do
       echo " ------------>>"
       echo " Please reinput function number..."
-      read -p " " num_choice
+      read_menu_choice num_choice || return 1
     done   
     case $num_choice in
         "1")
@@ -78,12 +81,12 @@ echo " +---------------------------------------------------------+"
 echo " Input the function number:"
 
 valid_menu_choices=("000" "301" "302" "303")
-read -p " " num_choice
+read_menu_choice num_choice || return 1
 while ! echo "${valid_menu_choices[@]}" | grep -wq "$num_choice"
 do
   echo " ------------>>"
   echo " Please reinput function number..."
-  read -p " " num_choice
+  read_menu_choice num_choice || return 1
 done
 
 case $num_choice in
diff --git a/src/f4_calculators.sh b/src/f4_calculators.sh
index 930a36c..9a2b848 100644
--- a/src/f4_calculators.sh
+++ b/src/f4_calculators.sh
@@ -15,7 +15,7 @@ echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
 echo " >-------------------------------------------------<"
 echo " Input <element> <charge> (eg. Li 1)"
 echo " ------------>>"
-read -p " " ion_cond_choice
+read_menu_choice ion_cond_choice || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_ion_conductivity.py ${ion_cond_choice}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_ion_conductivity.py"
@@ -32,7 +32,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> <output.xyz> <nep_model> "
 echo " Example: input.xyz output.xyz nep.txt"
 echo " ------------>>"
-read -p " " input_calc_properties
+read_menu_choice input_calc_properties || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_properties_with_nep.py ${input_calc_properties}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_properties_with_nep.py"
@@ -49,7 +49,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> <output.npy> <nep_model> <element>"
 echo " Example: train.xyz des_Li.npy nep.txt Li"
 echo " ------------>>"
-read -p " " input_calc_descriptors
+read_menu_choice input_calc_descriptors || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_descriptors.py ${input_calc_descriptors}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_descriptors.py"
@@ -66,7 +66,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> <nep_model> <output_file>"
 echo " Example: dump.xyz nep.txt doas.out"
 echo " ------------>>"
-read -p " " input_calc_doas
+read_menu_choice input_calc_doas || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_doas.py ${input_calc_doas}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_doas.py"
@@ -83,7 +83,7 @@ echo " >-------------------------------------------------<"
 echo " Input <initial_struct> <final_struct> <n_image> <nep_model>"
 echo " Example: IS.xyz FS.xyz 5 nep.txt"
 echo " ------------>>"
-read -p " " input_calc_neb
+read_menu_choice input_calc_neb || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/neb_calculation.py ${input_calc_neb}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/neb_calculation.py"
@@ -100,7 +100,7 @@ echo " >-------------------------------------------------<"
 echo " Input script arguments (eg. -c 4 -n 12 -C Pb Sr -E O)"
 echo " See https://gpumdkit.cn/htmls/polar_material_analysis.html for details"
 echo " ------------>>"
-read -p " " input_calc_neighbor_list
+read_menu_choice input_calc_neighbor_list || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_neighbor_list.py ${input_calc_neighbor_list}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_neighbor_list.py"
@@ -117,7 +117,7 @@ echo " >-------------------------------------------------<"
 echo " Input script arguments (eg. -i movie.xyz -n nl-Pb-O.dat -o displacements.dat)"
 echo " See https://gpumdkit.cn/htmls/polar_material_analysis.html for details"
 echo " ------------>>"
-read -p " " input_calc_displacement
+read_menu_choice input_calc_displacement || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_displacement.py ${input_calc_displacement}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_displacement.py"
@@ -134,7 +134,7 @@ echo " >-------------------------------------------------<"
 echo " Input script arguments (eg. -i movie.xyz -l 0.2 -o averaged_structure.xyz)"
 echo " See https://gpumdkit.cn/htmls/polar_material_analysis.html for details"
 echo " ------------>>"
-read -p " " input_calc_averaged_structure
+read_menu_choice input_calc_averaged_structure || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_averaged_structure.py ${input_calc_averaged_structure}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_averaged_structure.py"
@@ -151,7 +151,7 @@ echo " >-------------------------------------------------<"
 echo " Input script arguments (eg. -i model.xyz -n nl-Ti-O.dat -o octahedral_tilt.dat)"
 echo " See https://gpumdkit.cn/htmls/polar_material_analysis.html for details"
 echo " ------------>>"
-read -p " " input_calc_oct_tilt
+read_menu_choice input_calc_oct_tilt || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_oct_tilt.py ${input_calc_oct_tilt}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_oct_tilt.py"
@@ -168,7 +168,7 @@ echo " >-------------------------------------------------<"
 echo " Input script arguments (eg. --nl-ba nl-Ti-A.dat --nl-bo nl-Ti-O.dat --bec Pb=2.5 Sr=2.0 Ti=4.0 O=-2.0)"
 echo " See https://gpumdkit.cn/htmls/polar_material_analysis.html for details"
 echo " ------------>>"
-read -p " " input_calc_polarization_abo3
+read_menu_choice input_calc_polarization_abo3 || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_polarization_abo3.py ${input_calc_polarization_abo3}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_polarization_abo3.py"
@@ -188,7 +188,7 @@ echo "  fmax: Force convergence threshold in eV/Ang (default: 0.01)"
 echo "  max_steps: Maximum number of optimization steps (default: 1000)"
 echo " Example: POSCAR nep.txt 0.01 1000"
 echo " ------------>>"
-read -p " " input_minimize_structure
+read_menu_choice input_minimize_structure || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_minimize.py ${input_minimize_structure}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_minimize.py"
@@ -205,7 +205,7 @@ echo " Input <extxyz_file> <element_symbol> <dt_fs> [max_corr_steps]"
 echo "   Optional argument: max_corr_steps (default: frame number)"
 echo " Example: dump.xyz Li 10"
 echo " ------------>>"
-read -p " " input_calc_msd
+read_menu_choice input_calc_msd || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_msd.py ${input_calc_msd}
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_msd.py"
@@ -235,12 +235,12 @@ echo " +----------------------------------------------------------+"
 echo " Input the function number:"
 
 valid_menu_choices=("000" "401" "402" "403" "404" "405" "406" "407" "408" "409" "410" "411" "412")
-read -p " " num_choice
+read_menu_choice num_choice || return 1
 while ! echo "${valid_menu_choices[@]}" | grep -wq "$num_choice"
 do
   echo " ------------>>"
   echo " Please reinput function number..."
-  read -p " " num_choice
+  read_menu_choice num_choice || return 1
 done
 
 case $num_choice in
diff --git a/src/f5_analyzers.sh b/src/f5_analyzers.sh
index 29982cc..ff2f176 100644
--- a/src/f5_analyzers.sh
+++ b/src/f5_analyzers.sh
@@ -16,7 +16,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> you want to analyze"
 echo " Example: train.xyz"
 echo " ------------>>"
-read -p " " input_extxyz
+read_menu_choice input_extxyz || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/analyzer/analyze_composition.py ${input_extxyz}
 echo " Code path: ${GPUMDkit_path}/Scripts/analyzer/analyze_composition.py"
@@ -31,6 +31,8 @@ echo " | Script: find_outliers.py                        |"
 echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
 echo " >-------------------------------------------------<"
 echo " Input the threshold of RMSE to identify outliers"
+echo " Required files: train.xyz, energy_train.out, force_train.out, stress_train.out"
+echo " The script will ask for energy (meV/atom), force (meV/Angstrom), and stress (GPa) thresholds."
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/analyzer/find_outliers.py
 echo " Code path: ${GPUMDkit_path}/Scripts/analyzer/find_outliers.py"
@@ -47,7 +49,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> you want to analyze"
 echo " Example: train.xyz"
 echo " ------------>>"
-read -p " " input_extxyz
+read_menu_choice input_extxyz || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/analyzer/analyze_chem_species.py ${input_extxyz}
 echo " Code path: ${GPUMDkit_path}/Scripts/analyzer/analyze_chem_species.py"
@@ -64,7 +66,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> you want to analyze"
 echo " Example: train.xyz"
 echo " ------------>>"
-read -p " " input_extxyz
+read_menu_choice input_extxyz || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/analyzer/charge_balance_check.py ${input_extxyz}
 echo " Code path: ${GPUMDkit_path}/Scripts/analyzer/charge_balance_check.py"
@@ -81,10 +83,11 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> and property (energy/force/virial)"
 echo " Example: train.xyz force"
 echo " ------------>>"
-read -p " " input_extxyz property_name
+read_menu_choice analyzer_args || return 1
+read -r input_extxyz property_name <<< "${analyzer_args}"
 echo " Plot histogram? (y/n)"
 echo " ------------>>"
-read -p " " if_hist
+read_menu_choice if_hist || return 1
 echo " ---------------------------------------------------"
 if [ "$if_hist" == "y" ] || [ "$if_hist" == "Y" ]; then
   python ${GPUMDkit_path}/Scripts/analyzer/energy_force_virial_analyzer.py ${input_extxyz} ${property_name} hist
@@ -105,7 +108,8 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> and <min_dist>"
 echo " Example: dump.xyz 1.5"
 echo " ------------>>"
-read -p " " input_extxyz min_dist
+read_menu_choice filter_args || return 1
+read -r input_extxyz min_dist <<< "${filter_args}"
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/analyzer/filter_structures_by_distance.py ${input_extxyz} ${min_dist}
 echo " Code path: ${GPUMDkit_path}/Scripts/analyzer/filter_structures_by_distance.py"
@@ -122,10 +126,10 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> you want to analyze"
 echo " Example: dump.xyz"
 echo " ------------>>"
-read -p " " input_extxyz
+read_menu_choice input_extxyz || return 1
 echo " Consider PBC? (y/n)"
 echo " ------------>>"
-read -p " " consider_pbc
+read_menu_choice consider_pbc || return 1
 echo " ---------------------------------------------------"
 if [ "$consider_pbc" == "y" ] || [ "$consider_pbc" == "Y" ]; then
   python ${GPUMDkit_path}/Scripts/analyzer/get_min_dist_pbc.py ${input_extxyz}
@@ -147,7 +151,8 @@ echo " >-------------------------------------------------<"
 echo " Input <ref_struct> <trajectory_file> <species> <interval>"
 echo " Example: LLZO.vasp dump.xyz Li 0.25"
 echo " ------------>>"
-read -p " " ref_struct trajectory_file species interval
+read_menu_choice pda_args || return 1
+read -r ref_struct trajectory_file species interval <<< "${pda_args}"
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/analyzer/probability_density_analysis.py ${ref_struct} ${trajectory_file} ${species} ${interval}
 echo " Code path: ${GPUMDkit_path}/Scripts/analyzer/probability_density_analysis.py"
@@ -173,12 +178,12 @@ echo " +------------------------------------------------------+"
 echo " Input the function number:"
 
 arry_num_choice=("000" "501" "502" "503" "504" "505" "506" "507" "508") 
-read -p " " num_choice
+read_menu_choice num_choice || return 1
 while ! echo "${arry_num_choice[@]}" | grep -wq "$num_choice" 
 do
   echo " ------------>>"
   echo " Please reinput function number..."
-  read -p " " num_choice
+  read_menu_choice num_choice || return 1
 done
 
 case $num_choice in
diff --git a/src/f7_utilities.sh b/src/f7_utilities.sh
index f826e28..8a7a34d 100644
--- a/src/f7_utilities.sh
+++ b/src/f7_utilities.sh
@@ -15,7 +15,7 @@ echo " >-------------------------------------------------<"
 echo " Input mode: gpumd, nep or gnep"
 echo " Example: gpumd"
 echo " ------------>>"
-read -p " " time_mode
+read_menu_choice time_mode || return 1
 echo " ---------------------------------------------------"
 case $time_mode in
     gpumd) bash ${analyzer_path}/time_consuming_gpumd.sh ;;
@@ -38,12 +38,12 @@ echo " +------------------------------------------------------+"
 echo " Input the function number:"
 
 valid_menu_choices=("000" "701")
-read -p " " num_choice
+read_menu_choice num_choice || return 1
 while ! echo "${valid_menu_choices[@]}" | grep -wq "$num_choice"
 do
   echo " ------------>>"
   echo " Please reinput function number..."
-  read -p " " num_choice
+  read_menu_choice num_choice || return 1
 done
 
 case $num_choice in

From 32ee60d081f31bc4793b2422a313c91520ae7683 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Wed, 1 Jul 2026 17:21:45 +0800
Subject: [PATCH 15/24] update

---
 .gitignore                                    |  13 +
 README.md                                     |   2 +-
 Scripts/README.md                             |   2 +-
 Scripts/analyzer/charge_balance_check.py      |  22 +-
 Scripts/calculators/calc_ion_conductivity.py  |   4 +-
 Scripts/calculators/calc_msd.py               |   3 -
 Scripts/format_conversion/cp2k_log2xyz.py     |   2 +-
 Scripts/format_conversion/exyz2lmp.py         |   2 -
 Scripts/format_conversion/lmp2exyz.py         |   1 -
 Scripts/format_conversion/out2exyz.py         |   2 +-
 .../plt_scripts/plt_descriptors_compare.py    |   1 -
 Scripts/plt_scripts/plt_nemd.py               |   1 -
 Scripts/plt_scripts/plt_net_force.py          |   2 +-
 Scripts/sample_structures/README.md           |   2 +-
 Scripts/sample_structures/select_max_modev.py |   2 +-
 Scripts/utils/clean_extra_files.sh            |  69 +++--
 Scripts/utils/update_gpumdkit.sh              |  29 +-
 Scripts/workflow/README.md                    |   2 +-
 .../md_sample_batch_pretreatment_gpumd.sh     |  21 +-
 .../md_sample_batch_pretreatment_lmp.sh       |  13 +-
 .../workflow/scf_batch_pretreatment_vasp.sh   |  15 +-
 docs/README_zh-CN.md                          |   2 +-
 docs/tutorials/en/active_learning_workflow.md |  20 +-
 docs/tutorials/en/command_reference.md        |   2 +-
 docs/tutorials/en/custom_commands.md          |   2 +-
 docs/tutorials/en/index.md                    |   1 +
 docs/tutorials/en/plot_scripts.md             |  16 +-
 docs/tutorials/en/quick_start.md              |  26 +-
 docs/tutorials/en/troubleshooting.md          | 128 ++++++++
 docs/tutorials/zh/index.md                    |   1 +
 ...40\345\267\245\344\275\234\346\265\201.md" |  18 +-
 ...75\344\273\244\345\217\202\350\200\203.md" |   2 +-
 ...53\351\200\237\345\205\245\351\227\250.md" |  26 +-
 ...05\351\232\234\346\216\222\351\231\244.md" | 128 ++++++++
 ...74\345\274\217\350\275\254\346\215\242.md" |   1 +
 ...30\345\233\276\350\204\232\346\234\254.md" |  18 +-
 ...32\344\271\211\345\221\275\344\273\244.md" |   4 +
 gpumdkit.sh                                   | 138 +++++----
 skills/AGENTS.md                              | 274 ++++++++++++++++++
 skills/README.md                              |  12 +-
 skills/gpumdkit-contributing/SKILL.md         | 128 +++++++-
 skills/gpumdkit-main/SKILL.md                 |   2 +-
 skills/gpumdkit-visualization/SKILL.md        |  14 +-
 src/README.md                                 |   3 +-
 src/f1_format_conversions.sh                  |  34 +--
 src/f2_sample_structures.sh                   |  10 +-
 src/f5_analyzers.sh                           |   4 +-
 src/f6_plots.sh                               |   2 +-
 48 files changed, 979 insertions(+), 247 deletions(-)
 create mode 100644 docs/tutorials/en/troubleshooting.md
 create mode 100644 "docs/tutorials/zh/\346\225\205\351\232\234\346\216\222\351\231\244.md"
 create mode 100644 skills/AGENTS.md

diff --git a/.gitignore b/.gitignore
index 4314cfc..ecc80b6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,3 +22,16 @@ Thumbs.db
 # Temporary / generated files
 *.log
 temp_*.xyz
+
+# additional hygiene patterns
+*.tmp
+*.bak
+*~
+*.egg
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+htmlcov/
+.omo/
+.claude/
diff --git a/README.md b/README.md
index 1ad6b62..692cc5b 100644
--- a/README.md
+++ b/README.md
@@ -110,7 +110,7 @@ There are two options, <u>*interactive mode*</u> and <u>*command-line mode*</u>
      1) Format Conversion          2) Sample Structures
      3) Workflow                   4) Calculators
      5) Analyzer                   6) Visualization
-     7) Utilities                  8) Developing...
+     7) Utilities                  8) Help                
      0) Exit
      ------------>>
      Input the function number:
diff --git a/Scripts/README.md b/Scripts/README.md
index 32b50b1..51497ab 100644
--- a/Scripts/README.md
+++ b/Scripts/README.md
@@ -149,7 +149,7 @@ Navigate through numbered menus to access different functionalities.
   1) Format Conversion          2) Sample Structures
   3) Workflow                   4) Calculators
   5) Analyzer                   6) Visualization
-  7) Utilities                  8) Developing...
+  7) Utilities                  8) Help                
   0) Exit
  ------------>>
  Input the function number:
diff --git a/Scripts/analyzer/charge_balance_check.py b/Scripts/analyzer/charge_balance_check.py
index 78dc779..91f0cdc 100644
--- a/Scripts/analyzer/charge_balance_check.py
+++ b/Scripts/analyzer/charge_balance_check.py
@@ -116,9 +116,18 @@ def main():
     
     # Check oxidation states for unique compositions
     with Pool() as pool:
-        oxi_results = dict(tqdm(pool.imap_unordered(check_oxidation_state, unique_compositions),
-                                total=len(unique_compositions),
-                                desc="Checking oxidation states"))
+        oxi_results = {}
+        oxi_errors = {}
+        for result in tqdm(pool.imap_unordered(check_oxidation_state, unique_compositions),
+                           total=len(unique_compositions),
+                           desc="Checking oxidation states"):
+            if len(result) == 3:
+                comp_str, _, error = result
+                oxi_results[comp_str] = False
+                oxi_errors[comp_str] = error
+            else:
+                comp_str, is_balanced = result
+                oxi_results[comp_str] = is_balanced
     
     # Assign oxidation state results to structures
     balanced_structures = []
@@ -139,11 +148,10 @@ def main():
             continue
         
         result = oxi_results[comp_str]
-        if isinstance(result, tuple):
-            # Error case
-            comp_str, is_balanced, error = result
+        if comp_str in oxi_errors:
+            # Error case, pymatgen couldn't determine oxidation states
             atoms.info["oxidation_state"] = "unbalanced"
-            atoms.info["error"] = error
+            atoms.info["error"] = oxi_errors[comp_str]
             unbalanced_structures.append(atoms)
             unbalanced_indices.append(idx)
         elif result:
diff --git a/Scripts/calculators/calc_ion_conductivity.py b/Scripts/calculators/calc_ion_conductivity.py
index 09bbb69..95c1d29 100644
--- a/Scripts/calculators/calc_ion_conductivity.py
+++ b/Scripts/calculators/calc_ion_conductivity.py
@@ -104,8 +104,8 @@ def calculate_diffusivity_and_conductivity(filepath, structure_volume, species_c
     dts, msd_x, msd_y, msd_z, msd_total = read_msd_file(filepath)
 
     # Use a portion of the MSD data for fitting
-    start = int(len(dts) * 0.1)  # Start at 10% of the data
-    end = int(len(dts) * 0.4)  # End at 40% of the data
+    start = int(len(dts) * 0.4)  # Start at 40% of the data
+    end = int(len(dts) * 0.8)  # End at 80% of the data
 
     # Linear fit to obtain slopes for x, y, z, and total MSD
     k_x, _ = np.polyfit(dts[start:end], msd_x[start:end], 1)
diff --git a/Scripts/calculators/calc_msd.py b/Scripts/calculators/calc_msd.py
index 42f1a52..7a2c7ef 100644
--- a/Scripts/calculators/calc_msd.py
+++ b/Scripts/calculators/calc_msd.py
@@ -332,7 +332,6 @@ def calculate_msd_from_extxyz(extxyz_file, element_symbol, dt_fs, max_corr_steps
     # Coordinate wrapping check
     # ------------------------------------------------------------------
     print(" ")
-    # print(" "+ "-" * 60)
     if cell is not None:
         is_wrapped = check_wrapped_coordinates(all_positions, cell)
         if is_wrapped:
@@ -349,7 +348,6 @@ def calculate_msd_from_extxyz(extxyz_file, element_symbol, dt_fs, max_corr_steps
     # MSD calculation
     # ------------------------------------------------------------------
     print(" ")
-    # print(" "+ "-" * 60)
     if n_frames < 3:
         print(" Error: At least 3 frames are required for MSD, "
               " but only %d found." % n_frames)
@@ -379,7 +377,6 @@ def calculate_msd_from_extxyz(extxyz_file, element_symbol, dt_fs, max_corr_steps
     # Write output
     # ------------------------------------------------------------------
     print(" ")
-    # print(" "+ "-" * 60)
     output_file = "msd.out"
     header = ("msd.out by GPUMDkit\n"
                "Element: %s  |  dt: %.4f fs  |  Frames: %d  |  Atoms: %d\n"
diff --git a/Scripts/format_conversion/cp2k_log2xyz.py b/Scripts/format_conversion/cp2k_log2xyz.py
index c4655f0..65c73ba 100644
--- a/Scripts/format_conversion/cp2k_log2xyz.py
+++ b/Scripts/format_conversion/cp2k_log2xyz.py
@@ -42,7 +42,7 @@ def extract_atoms_lattice_xyz(lines):
         if m := re.search(r'Lattice="([^"]+)"', '\n'.join(lines)):
             lat = [float(x) for x in m.group(1).split()]
         return atoms, lat
-    except: return [], []
+    except (ValueError, IndexError): return [], []
 
 def extract_atoms_lattice_inp(text):
     atoms, lat = [], [0.0]*9
diff --git a/Scripts/format_conversion/exyz2lmp.py b/Scripts/format_conversion/exyz2lmp.py
index 97b9644..6d857c8 100644
--- a/Scripts/format_conversion/exyz2lmp.py
+++ b/Scripts/format_conversion/exyz2lmp.py
@@ -81,8 +81,6 @@ def convert_extxyz_to_lammps_data(extxyz_file, lammps_data_file):
             atom_type = symbol_to_type[atom.symbol]
             x, y, z = atom.position
             f.write(f"{atom_id} {atom_type} {x} {y} {z}\n")
-    
-#   print(f"Conversion complete! {extxyz_file} has been converted to {lammps_data_file}")
 
 if __name__ == '__main__':
     args = sys.argv[1:]
diff --git a/Scripts/format_conversion/lmp2exyz.py b/Scripts/format_conversion/lmp2exyz.py
index 6d78ce4..450aab5 100644
--- a/Scripts/format_conversion/lmp2exyz.py
+++ b/Scripts/format_conversion/lmp2exyz.py
@@ -62,7 +62,6 @@ def lmp2exyz(dump_file, elements):
     # Write to extxyz file
     extxyz_file = 'dump.xyz'
     write(extxyz_file, frames, format='extxyz')
-#   print(f" Converted {dump_file} to {extxyz_file}")
 
 if __name__ == '__main__':
     dump_file = sys.argv[1]
diff --git a/Scripts/format_conversion/out2exyz.py b/Scripts/format_conversion/out2exyz.py
index bf7d84e..5451c3d 100644
--- a/Scripts/format_conversion/out2exyz.py
+++ b/Scripts/format_conversion/out2exyz.py
@@ -120,7 +120,7 @@ def is_converged(outcar_path):
     
     try:
         atoms = read(file_path, format='vasp-out', index=":")
-    except:
+    except Exception:
         err_list.append(file_path)
         continue
     
diff --git a/Scripts/plt_scripts/plt_descriptors_compare.py b/Scripts/plt_scripts/plt_descriptors_compare.py
index b57b663..f44e6bc 100644
--- a/Scripts/plt_scripts/plt_descriptors_compare.py
+++ b/Scripts/plt_scripts/plt_descriptors_compare.py
@@ -130,7 +130,6 @@ def print_progress_bar(iteration, total, prefix='', suffix='', decimals=1, lengt
     # Save descriptors
     # output_file = f"{os.path.splitext(xyz_file)[0]}_descriptors.npy"
     # np.save(output_file, file_descriptors)
-    # print(f"Saved descriptors to '{output_file}' (shape: {file_descriptors.shape})")
 
 # Check if any descriptors were collected
 if not all_descriptors:
diff --git a/Scripts/plt_scripts/plt_nemd.py b/Scripts/plt_scripts/plt_nemd.py
index 6494dfc..0ed0ae9 100644
--- a/Scripts/plt_scripts/plt_nemd.py
+++ b/Scripts/plt_scripts/plt_nemd.py
@@ -287,7 +287,6 @@ def _print_nemd_results(self, Reformed_NEMD_data, Length):
         print("NEMD Thermal Conductivity Results")
         print("=" * 70)
         print(f"\nEffective length: {Length:.4f} nm")
-        # print(f"Scale_vacuum: {self.scale_vacuum}")
         print(f"Scale_eff_size: {self.scale_eff_size}\n")
         print(f"Thermal conductance G = {Reformed_NEMD_data['G'][0, -2]:.6f} ± {Reformed_NEMD_data['G'][0, -1]:.6f} MW/m²K")
         print(f"Thermal conductivity κ = {Reformed_NEMD_data['k'][0, -2]:.6f} ± {Reformed_NEMD_data['k'][0, -1]:.6f} W/mK")
diff --git a/Scripts/plt_scripts/plt_net_force.py b/Scripts/plt_scripts/plt_net_force.py
index 75d90e2..074ab7b 100644
--- a/Scripts/plt_scripts/plt_net_force.py
+++ b/Scripts/plt_scripts/plt_net_force.py
@@ -39,7 +39,7 @@ def parse_xyz_file(xyz_file):
             # Read number of atoms
             try:
                 num_atoms = int(lines[i].strip())
-            except:
+            except (ValueError, IndexError):
                 i += 1
                 continue
             
diff --git a/Scripts/sample_structures/README.md b/Scripts/sample_structures/README.md
index 511ca8a..6525345 100644
--- a/Scripts/sample_structures/README.md
+++ b/Scripts/sample_structures/README.md
@@ -33,7 +33,7 @@ Structure sampling is crucial for creating diverse configurations. These scripts
   1) Format Conversion          2) Sample Structures
   3) Workflow                   4) Calculators
   5) Analyzer                   6) Visualization
-  7) Utilities                  8) Developing...
+  7) Utilities                  8) Help                
   0) Exit
  ------------>>
  Input the function number:
diff --git a/Scripts/sample_structures/select_max_modev.py b/Scripts/sample_structures/select_max_modev.py
index 7753db7..2fcac5e 100644
--- a/Scripts/sample_structures/select_max_modev.py
+++ b/Scripts/sample_structures/select_max_modev.py
@@ -108,7 +108,7 @@ def extract_xyz_structures(xyz_file, indices, output_xyz_file):
     atoms_list = read(xyz_file, index=':')  # Read all structures as a list of ASE atoms objects
 
     # Extract the corresponding structures based on the indices from the filtered list
-    selected_atoms = [atoms_list[i] for i in indices]
+    selected_atoms = [atoms_list[filtered_indices[i]] for i in indices]
     
     # Write the selected structures to the output .xyz file
     write(output_xyz_file, selected_atoms)
diff --git a/Scripts/utils/clean_extra_files.sh b/Scripts/utils/clean_extra_files.sh
index 8fc905f..c030602 100644
--- a/Scripts/utils/clean_extra_files.sh
+++ b/Scripts/utils/clean_extra_files.sh
@@ -5,10 +5,15 @@
 function clean_extra_files(){
 keep_files=("run.in" "nep.in" "model.xyz" "nep.txt" "train.xyz" "test.xyz")
 keep_patterns=("*sub*" "*.sh" "*slurm")
-all_files=$(ls)
 delete_files=()
 
-for file in $all_files; do
+# Build the deletion list using a glob (avoids parsing `ls` output),
+# considering only regular files (matches the net effect of plain `ls`,
+# where subdirectory names would have failed `rm -f` anyway).
+for file in *; do
+    [ -e "$file" ] || continue
+    [ -f "$file" ] || continue
+
     # Check if the file matches any keep_files or keep_patterns
     keep=false
     for keep_file in "${keep_files[@]}"; do
@@ -32,50 +37,68 @@ done
 
 # Display files to delete
 if [ ${#delete_files[@]} -eq 0 ]; then
-    echo "No files to delete."
+    echo " No files to delete."
     return 0
 else
-    echo "The following files will be deleted:"
-    echo "---------------------------------------"
+    echo " The following files will be deleted:"
+    echo " ----------------------------------------------------"
     for file in "${delete_files[@]}"; do
-        echo -n "$file "
+        echo "   ${file}"
     done
-    echo -e "\n---------------------------------------"
+    echo " ----------------------------------------------------"
 fi
 
 # Ask user for confirmation or additional files to keep
-echo "Do you want to delete all these files?"
-echo "y/yes to delete, n/no to cancel, or input files to keep (separated by spaces):"
-read user_input
+echo " +------------------------------------------------------+"
+echo " | Do you want to delete all these files?              |"
+echo " |   y / yes : delete all                              |"
+echo " |   n / no  : cancel                                   |"
+echo " |   or input filenames to keep (space-separated)       |"
+echo " +------------------------------------------------------+"
+if ! IFS= read -r -p " " user_input; then
+    echo " Input closed. No files were deleted."
+    return 1
+fi
 
 # Process user input
 if [[ "$user_input" == "y" || "$user_input" == "yes" ]]; then
-    echo "Deleting the files..."
+    echo " Deleting the files..."
     for file in "${delete_files[@]}"; do
         rm -f "$file"
     done
-    echo "Files deleted."
+    echo " Files deleted."
 elif [[ "$user_input" == "n" || "$user_input" == "no" ]]; then
-    echo "Operation canceled. No files were deleted."
+    echo " Operation canceled. No files were deleted."
     return 0
 else
-    # Add extra files to keep based on user input
-    extra_keep_files=($user_input)
-    for extra_file in "${extra_keep_files[@]}"; do
-        delete_files=("${delete_files[@]/$extra_file}")
+    # Add extra files to keep based on user input.
+    # Tokenize and exclude by whole-word match (NOT substring removal,
+    # which would corrupt names sharing a substring with the keep input).
+    read -r -a extra_keep_files <<< "$user_input"
+    new_delete_files=()
+    for df in "${delete_files[@]}"; do
+        skip=false
+        for ek in "${extra_keep_files[@]}"; do
+            if [ "$df" = "$ek" ]; then
+                skip=true
+                break
+            fi
+        done
+        if [ "$skip" = false ]; then
+            new_delete_files+=("$df")
+        fi
     done
+    delete_files=("${new_delete_files[@]}")
 
     # Delete remaining files
     if [ ${#delete_files[@]} -eq 0 ]; then
-        echo "No files to delete after processing extra keep files."
+        echo " No files to delete after processing extra keep files."
     else
-        echo "Deleting remaining files..."
+        echo " Deleting remaining files..."
         for file in "${delete_files[@]}"; do
-            if [ -n "$file" ]; then
-                rm -f "$file"
-            fi
+            rm -f "$file"
         done
-        echo "Files deleted."
+        echo " Files deleted."
     fi
 fi
 }
\ No newline at end of file
diff --git a/Scripts/utils/update_gpumdkit.sh b/Scripts/utils/update_gpumdkit.sh
index aefb60d..237e422 100644
--- a/Scripts/utils/update_gpumdkit.sh
+++ b/Scripts/utils/update_gpumdkit.sh
@@ -1,21 +1,24 @@
 # check for updates
 function update_gpumdkit(){
+# Save the caller's working directory so it can be restored on success.
+__update_orig_pwd="$PWD"
+
 # Check if in a Git repository; if not, try to switch to GPUMDkit_path
 if ! git rev-parse --is-inside-work-tree > /dev/null 2>&1; then
     if [ -z "$GPUMDkit_path" ]; then
-        echo "Error: Not in a Git repository and GPUMDkit_path environment variable is not set."
+        echo " Error: Not in a Git repository and GPUMDkit_path environment variable is not set."
         exit 1
     fi
     if [ ! -d "$GPUMDkit_path" ]; then
-        echo "Error: Directory $GPUMDkit_path does not exist."
+        echo " Error: Directory $GPUMDkit_path does not exist."
         exit 1
     fi
     cd "$GPUMDkit_path" || {
-        echo "Error: Failed to change directory to $GPUMDkit_path."
+        echo " Error: Failed to change directory to $GPUMDkit_path."
         exit 1
     }
     if ! git rev-parse --is-inside-work-tree > /dev/null 2>&1; then
-        echo "Error: $GPUMDkit_path is not a Git repository."
+        echo " Error: $GPUMDkit_path is not a Git repository."
         exit 1
     fi
 fi
@@ -23,7 +26,7 @@ fi
 # Get current branch name
 current_branch=$(git rev-parse --abbrev-ref HEAD)
 if [ -z "$current_branch" ]; then
-    echo "Error: Unable to determine current branch."
+    echo " Error: Unable to determine current branch."
     exit 1
 fi
 
@@ -35,23 +38,27 @@ remote_commit=$(git ls-remote https://github.com/zhyan0603/GPUMDkit.git "$curren
 
 # Check if remote commit was retrieved successfully
 if [ -z "$remote_commit" ]; then
-    echo "Error: Unable to fetch remote repository information."
-    echo "Check network or branch name ($current_branch)."
+    echo " Error: Unable to fetch remote repository information."
+    echo " Check network or branch name ($current_branch)."
     exit 1
 fi
 
 # Compare local and remote commits
 if [ "$local_commit" = "$remote_commit" ]; then
-    echo "No updates available: Local $current_branch branch is up to date."
+    echo " No updates available: Local $current_branch branch is up to date."
 else
-    echo "Updates detected, pulling latest code for branch $current_branch..."
+    echo " Updates detected, pulling latest code for branch $current_branch..."
 
     # Pull latest code
     if git pull origin "$current_branch"; then
-        echo "Code successfully updated."
+        echo " Code successfully updated."
     else
-        echo "Error: Failed to pull code. Check Git configuration or network connection."
+        echo " Error: Failed to pull code. Check Git configuration or network connection."
+        cd "$__update_orig_pwd" 2>/dev/null
         exit 1
     fi
 fi
+
+# Restore the caller's working directory on success.
+cd "$__update_orig_pwd" 2>/dev/null
 }
\ No newline at end of file
diff --git a/Scripts/workflow/README.md b/Scripts/workflow/README.md
index 349f111..60d7ab8 100644
--- a/Scripts/workflow/README.md
+++ b/Scripts/workflow/README.md
@@ -32,7 +32,7 @@ Access workflow tools through `gpumdkit.sh` interactive mode:
   1) Format Conversion          2) Sample Structures
   3) Workflow                   4) Calculators
   5) Analyzer                   6) Visualization
-  7) Utilities                  8) Developing...
+  7) Utilities                  8) Help                
   0) Exit
  ------------>>
  Input the function number:
diff --git a/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh b/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
index 7d057f0..ae69f11 100644
--- a/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
+++ b/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
@@ -61,6 +61,7 @@ function f302_md_sample_batch_pretreatment_gpumd(){
 	                fi
 	                echo " Invalid selection. Please choose one XYZ file."
 	            done
+	            [ -n "$xyz_file" ] || { echo " Input closed. Exiting."; return 1; }
 	        fi
 	        echo " Splitting ${xyz_file#./} to model_*.xyz using GPUMDkit..."
 	        python ${GPUMDkit_path}/Scripts/format_conversion/split_single_xyz.py "$xyz_file"
@@ -81,7 +82,7 @@ function f302_md_sample_batch_pretreatment_gpumd(){
     # Ask user for directory name prefix
     echo " >-------------------------------------------------<"
     echo " | This function calls the script in Scripts       |"
-    echo " | Script: md_sample_batch_pretreatment.sh         |"
+    echo " | Script: md_sample_batch_pretreatment_gpumd.sh   |"
     echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
     echo " >-------------------------------------------------<"
 
@@ -99,7 +100,7 @@ function f302_md_sample_batch_pretreatment_gpumd(){
         cd ..
     done
 
-    # Create the presub.sh file for VASP self-consistency calculations
+    # Create the presub.sh file for GPUMD MD sampling
     cat > presub.sh <<-EOF
 	#!/bin/bash
 
@@ -116,13 +117,13 @@ function f302_md_sample_batch_pretreatment_gpumd(){
     # Make presub.sh executable
     chmod +x presub.sh
 
-	echo " >----------------------------------------------------<"
-	echo " | ATTENTION: Place run_*.in and nep.txt in 'md' Dir. |"
-	echo " >----------------------------------------------------<"
-	echo " | You need to provide MD control parameter files in  |"
-	echo " | the format run_*.in (e.g., run_1.in, run_2.in),    |"
-	echo " | each corresponding to a sample (e.g., sample_1,    |"
-	echo " | sample_2) for molecular dynamics simulations.      |"
-	echo " >----------------------------------------------------<"
+    echo " >---------------------------------------------------------<"
+    echo " |    ATTENTION: Place run_*.in and nep.txt in 'md' Dir.   |"
+    echo " >---------------------------------------------------------<"
+    echo " |    You need to provide MD control parameter files in    |"
+    echo " |    the format run_*.in (e.g., run_1.in, run_2.in),      |"
+    echo " |    each corresponding to a sample (e.g., sample_1,      |"
+    echo " |    sample_2) for molecular dynamics simulations.        |"
+    echo " >---------------------------------------------------------<"
 
 }
diff --git a/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh b/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
index 735cab1..3cc7c8a 100644
--- a/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
+++ b/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
@@ -63,6 +63,7 @@ function f303_md_sample_batch_pretreatment_lmp(){
 	                fi
 	                echo " Invalid selection. Please choose one XYZ file."
 	            done
+	            [ -n "$xyz_file" ] || { echo " Input closed. Exiting."; return 1; }
 	        fi
 	        echo " Splitting ${xyz_file#./} to model_*.xyz using GPUMDkit..."
 	        python ${GPUMDkit_path}/Scripts/format_conversion/split_single_xyz.py "$xyz_file"
@@ -111,7 +112,7 @@ function f303_md_sample_batch_pretreatment_lmp(){
         cd ..
     done
 
-    # Create the presub.sh file for VASP self-consistency calculations
+    # Create the presub.sh file for LAMMPS MD sampling
     cat > presub.sh <<-EOF
 	#!/bin/bash
 
@@ -128,9 +129,9 @@ function f303_md_sample_batch_pretreatment_lmp(){
     # Make presub.sh executable
     chmod +x presub.sh
 
-    echo " >--------------------------------------------------<"
-    echo " ATTENTION: Place lmprun.in and nep.txt in 'md' Dir. "
-    echo " ATTENTION: Place lmprun.in and nep.txt in 'md' Dir. "
-    echo " ATTENTION: Place lmprun.in and nep.txt in 'md' Dir. "
-    echo " >--------------------------------------------------<"
+    echo " >---------------------------------------------------------<"
+    echo " | ATTENTION: Place lmprun.in and nep.txt in 'md' Dir.     |"
+    echo " | ATTENTION: Place lmprun.in and nep.txt in 'md' Dir.     |"
+    echo " | ATTENTION: Place lmprun.in and nep.txt in 'md' Dir.     |"
+    echo " >---------------------------------------------------------<"
 }
diff --git a/Scripts/workflow/scf_batch_pretreatment_vasp.sh b/Scripts/workflow/scf_batch_pretreatment_vasp.sh
index f67329d..0c92556 100644
--- a/Scripts/workflow/scf_batch_pretreatment_vasp.sh
+++ b/Scripts/workflow/scf_batch_pretreatment_vasp.sh
@@ -53,6 +53,7 @@ function vasp_scf_batch_pretreatment(){
 	                fi
 	                echo " Invalid selection. Please choose one XYZ file."
 	            done
+	            [ -n "$xyz_file" ] || { echo " Input closed. Exiting."; return 1; }
 	        fi
 	        echo " Converting ${xyz_file#./} to POSCAR files using GPUMDkit..."
 	        python ${GPUMDkit_path}/Scripts/format_conversion/exyz2pos.py "$xyz_file"
@@ -73,7 +74,7 @@ function vasp_scf_batch_pretreatment(){
     # Ask user for directory name prefix
     echo " >-------------------------------------------------<"
     echo " | This function calls the script in Scripts       |"
-    echo " | Script: scf_batch_pretreatment.sh               |"
+    echo " | Script: scf_batch_pretreatment_vasp.sh          |"
     echo " | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |"
     echo " >-------------------------------------------------<"
     echo " We recommend using the prefix to locate the structure."
@@ -81,7 +82,7 @@ function vasp_scf_batch_pretreatment(){
     echo " config_type=<prefix>_<ID>"
     echo " ------------>>"
     echo " Please enter the prefix of directory (e.g. FAPBI3_iter01)"
-    read -p " " prefix
+    read_menu_choice prefix || return 1
 
     # Create fp directory
     mkdir -p fp
@@ -113,9 +114,9 @@ function vasp_scf_batch_pretreatment(){
     # Make presub.sh executable
     chmod +x presub.sh
 
-    echo " >-----------------------------------------------------<"
-    echo " ATTENTION: Place POTCAR, KPOINTS and INCAR in 'fp' Dir."
-    echo " ATTENTION: Place POTCAR, KPOINTS and INCAR in 'fp' Dir."
-    echo " ATTENTION: Place POTCAR, KPOINTS and INCAR in 'fp' Dir."
-    echo " >-----------------------------------------------------<"
+    echo " >---------------------------------------------------------<"
+    echo " | ATTENTION: Place POTCAR, KPOINTS and INCAR in 'fp' Dir. |"
+    echo " | ATTENTION: Place POTCAR, KPOINTS and INCAR in 'fp' Dir. |"
+    echo " | ATTENTION: Place POTCAR, KPOINTS and INCAR in 'fp' Dir. |"
+    echo " >---------------------------------------------------------<"
 }
diff --git a/docs/README_zh-CN.md b/docs/README_zh-CN.md
index 9de2a48..7f5c4b2 100644
--- a/docs/README_zh-CN.md
+++ b/docs/README_zh-CN.md
@@ -111,7 +111,7 @@ wget https://github.com/zhyan0603/GPUMDkit/archive/refs/heads/main.zip
       1) Format Conversion          2) Sample Structures
       3) Workflow                   4) Calculators
       5) Analyzer                   6) Visualization
-      7) Utilities                  8) Developing...
+      7) Utilities                  8) Help                
       0) Exit
       ------------>>
       Input the function number:
diff --git a/docs/tutorials/en/active_learning_workflow.md b/docs/tutorials/en/active_learning_workflow.md
index 724ce96..8416290 100644
--- a/docs/tutorials/en/active_learning_workflow.md
+++ b/docs/tutorials/en/active_learning_workflow.md
@@ -94,37 +94,37 @@ You can customize:
 ## 4. **Check Required Files**
 
 ```
-if [ -f nep.txt ] && [ -f nep.in ] && [ -f train.xyz ] && [ -f run.in ] && [ -f INCAR ] && [ -f POTCAR ] ; then
+if [ -f nep.txt ] && [ -f nep.in ] && [ -f train.xyz ] && [ "$(find . -maxdepth 1 -name 'run_*.in' | wc -l)" -ge 1 ] && [ -f INCAR ] && [ -f POTCAR ] ; then
     # Check for the required files before proceeding.
 else
-    echo "Please put nep.in nep.txt train.xyz run.in INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory."
+    echo "Please put nep.in nep.txt train.xyz run_*.in (eg. run_1.in, run_2.in, ...) INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory."
     exit 1
 fi
 ```
 
-Make sure the necessary files (`nep.txt`, `nep.in`, `train.xyz`, `run.in`, `INCAR`, `POTCAR`, `KPOINTS`) are available in the working directory. If any of these are missing, the script will terminate. `train.xyz` and `nep.txt` are used for `pynep` sampling, and `run.in` is the simulation parameters of MD in the current iteration.
+Make sure the necessary files (`nep.txt`, `nep.in`, `train.xyz`, `run_*.in` (e.g., `run_1.in`, `run_2.in`, ...), `INCAR`, `POTCAR`, `KPOINTS`) are available in the working directory. If any of these are missing, the script will terminate. `train.xyz` and `nep.txt` are always required as prerequisites for NEP model operation, and `run_*.in` files define the simulation parameters of MD in the current iteration.
 
 ------
 
 ## 5. **File Organization**
 
 ```
-mkdir 00.modev common
-mv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common
-cp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev
+mkdir 00.md common
+mv ${work_dir}/{nep.txt,nep.in,*.xyz,run_*.in,INCAR,KPOINTS,POTCAR} ./common
+cp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.md
 ```
 
 The script organizes the working files into two folders:
 
-- `00.modev`: For molecular dynamics simulation.
-- `common`: For shared resources such as `nep.txt`, `run.in`, and the structure files, etc.
+- `00.md`: For molecular dynamics simulation.
+- `common`: For shared resources such as `nep.txt`, `run_*.in` files, and the structure files, etc.
 
 ------
 
 ## 6. **Molecular Dynamics Simulation Submission**
 
 ```
-submit_gpumd_array modev ${sample_struct_num}
+submit_gpumd_array md ${sample_struct_num}
 sbatch submit.slurm
 ```
 
@@ -136,7 +136,7 @@ After preparing the input files, the script submits an array of molecular dynami
 
 ```
 while true; do
-    logs=$(find "${work_dir}/00.modev/" -type f -name log -path "*/sample_*/log")
+    logs=$(find "${work_dir}/00.md/" -type f -name log -path "*/sample_*/log")
     finished_tasks_md=$(grep "Finished running GPUMD." $logs | wc -l)
     error_tasks_md=$(grep "Error" $logs | wc -l)
 
diff --git a/docs/tutorials/en/command_reference.md b/docs/tutorials/en/command_reference.md
index fa22bed..f8f6119 100644
--- a/docs/tutorials/en/command_reference.md
+++ b/docs/tutorials/en/command_reference.md
@@ -116,7 +116,7 @@ gpumdkit.sh -plt <type> [options]
 gpumdkit.sh -plt -h
 ```
 
-Common types include `train`, `prediction`, `thermo`, `msd`, `sdc`, `rdf`, `emd`, `nemd`, `hnemd`, `pdos`, and `plane-grid`.
+Common types include `train`, `prediction` (alias: `test`), `thermo`, `msd`, `sdc`, `rdf`, `emd`, `nemd`, `hnemd`, `pdos`, and `plane-grid`.
 
 ## Utilities
 
diff --git a/docs/tutorials/en/custom_commands.md b/docs/tutorials/en/custom_commands.md
index 9be5bd6..49856ce 100644
--- a/docs/tutorials/en/custom_commands.md
+++ b/docs/tutorials/en/custom_commands.md
@@ -16,7 +16,7 @@ Define custom functions with the `custom_` prefix.
 
 ### Simple Greeting
 
-Write the following codes in your `~/.gpumdkit.in` 
+Write the following code in your `~/.gpumdkit.in` 
 
 ```bash
 custom_hello() {
diff --git a/docs/tutorials/en/index.md b/docs/tutorials/en/index.md
index d729439..18207b1 100644
--- a/docs/tutorials/en/index.md
+++ b/docs/tutorials/en/index.md
@@ -91,6 +91,7 @@ Use `gpumdkit.sh -h` to see all available options.
 | [Active Learning Workflow](active_learning_workflow.md) | Batch active-learning workflow notes |
 | [Polar Material Analysis](polar_material_analysis.md) | Ferroelectric and polarization tools |
 | [Contributing to GPUMDkit](contributing_to_gpumdkit.md) | Development notes |
+| [Troubleshooting](troubleshooting.md) | Common issues, diagnostics, and fixes |
 
 ## Links
 
diff --git a/docs/tutorials/en/plot_scripts.md b/docs/tutorials/en/plot_scripts.md
index 73a4933..82bc3e6 100644
--- a/docs/tutorials/en/plot_scripts.md
+++ b/docs/tutorials/en/plot_scripts.md
@@ -38,6 +38,7 @@ Running `gpumdkit.sh -plt` prints the plotting command menu:
 |  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|
 |  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |
 |  D_xyz          - Directional Arrhenius D                                                     |
+|  doas           - Density of atomistic states                                                 |
 +-----------------------------------------------------------------------------------------------+
 |                                    MD & Structural Analysis                                   |
 +-----------------------------------------------------------------------------------------------+
@@ -45,13 +46,16 @@ Running `gpumdkit.sh -plt` prints the plotting command menu:
 |  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
 |  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
 |  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
-|  doas           - Density of atomistic states                                                 |
 +-----------------------------------------------------------------------------------------------+
 |                                        Heat Transport                                         |
 +-----------------------------------------------------------------------------------------------+
 |  emd            - EMD results                    nemd           - NEMD results                |
 |  hnemd          - HNEMD results                  viscosity      - Viscosity                   |
 +-----------------------------------------------------------------------------------------------+
+|                                          Phonons                                              |
++-----------------------------------------------------------------------------------------------+
+|  pdos           - VAC and PDOS                                                                |
++-----------------------------------------------------------------------------------------------+
 ```
 
 ---
@@ -563,16 +567,6 @@ gpumdkit.sh -plt des umap
 
 ---
 
-### plt_descriptors_compare.py
-
-Compares descriptors from multiple training sets or models.
-
-```bash
-gpumdkit.sh -plt des_compare
-```
-
----
-
 ### plt_dimer.py
 
 Plots dimer interaction curves. Two atoms are placed in a cubic box (30 Å) and the potential energy and force are calculated as a function of dimer distance using a NEP model.
diff --git a/docs/tutorials/en/quick_start.md b/docs/tutorials/en/quick_start.md
index de72e2a..0e92e02 100644
--- a/docs/tutorials/en/quick_start.md
+++ b/docs/tutorials/en/quick_start.md
@@ -100,7 +100,7 @@ This opens the main menu:
  1) Format Conversion          2) Sample Structures
  3) Workflow                   4) Calculators
  5) Analyzer                   6) Visualization
- 7) Utilities                  8) Developing...
+ 7) Utilities                  8) Help                
  0) Exit
  ------------>>
  Input the function number:
@@ -126,6 +126,30 @@ gpumdkit.sh -calc msd trajectory.xyz Li 10
 
 The first example reads `POSCAR` and writes `model.xyz`.
 
+## Hello World Example
+
+A minimal end-to-end check that your install works — create a tiny silicon POSCAR, convert it to extxyz, and inspect the output:
+
+```bash
+cat > POSCAR << 'EOF'
+Si
+1.0
+0 2.715 2.715
+2.715 0 2.715
+2.715 2.715 0
+Si
+1
+direct
+0 0 0
+EOF
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+head model.xyz
+```
+
+If `model.xyz` shows a single Si atom with lattice info, your install works.
+
+> **What is extxyz?** extxyz is the extended XYZ format: line 1 is the atom count, line 2 contains the lattice and per-structure properties (energy/forces/virial as needed), and lines 3+ list each atom with its per-atom properties. It is the native training-data format for NEP.
+
 ## Common examples
 
 ### Convert a POSCAR to extxyz
diff --git a/docs/tutorials/en/troubleshooting.md b/docs/tutorials/en/troubleshooting.md
new file mode 100644
index 0000000..fc352d0
--- /dev/null
+++ b/docs/tutorials/en/troubleshooting.md
@@ -0,0 +1,128 @@
+<div align="center">
+  <h1>🛠️ Troubleshooting</h1>
+  <p style="text-align: justify;">This page collects the most common problems users hit when installing or running GPUMDkit, with a quick diagnostic command and fix for each. If your issue is not listed here, see <a href="#getting-more-help">Getting More Help</a> at the bottom.</p>
+</div>
+
+## Common Issues
+
+### 1. After install, `gpumdkit.sh: command not found` in a new terminal
+
+**Symptom:** Opening a fresh terminal and typing `gpumdkit.sh` gives `command not found`, even though installation appeared to succeed.
+
+**Diagnostic:**
+
+```bash
+echo $GPUMDkit_path
+```
+
+This should print the install directory. If it is empty or wrong, your shell did not load the environment variables.
+
+**Fix:**
+
+```bash
+source ~/.bashrc        # on Linux / bash
+source ~/.zshrc         # on macOS / zsh
+```
+
+If the variable is still empty after sourcing, run the installer again from the GPUMDkit directory:
+
+```bash
+cd /path/to/GPUMDkit
+bash install.sh
+```
+
+---
+
+### 2. Plot crashes with `FileNotFoundError: loss.out` (or `thermo.out`, `msd.out`, etc.)
+
+**Symptom:** Running `gpumdkit.sh -plt <type>` fails with a `FileNotFoundError` for an `.out` file.
+
+**Diagnostic:**
+
+```bash
+ls *.out
+```
+
+If nothing is listed, you are not in the directory that holds the GPUMD/NEP output files.
+
+**Fix:**
+
+```bash
+cd /path/to/your/simulation/run
+gpumdkit.sh -plt <type>
+```
+
+Always run `-plt` from the directory containing the output files, or pass the correct path.
+
+---
+
+### 3. `No module named 'calorine'` (or `'neptrain'`, `'dpdata'`) when running certain calculators
+
+**Symptom:** A calculator or converter aborts with `ModuleNotFoundError: No module named 'calorine'` (or `neptrain`, `dpdata`).
+
+**Diagnostic:**
+
+```bash
+pip list | grep -iE 'calorine|neptrain|dpdata'
+```
+
+If the package is missing, install it.
+
+**Fix:**
+
+```bash
+pip install calorine neptrain dpdata
+```
+
+Or, if you use conda, run the equivalent `conda install` / `pip install` inside your activated `gpumdkit` environment. Make sure the environment is activated before running GPUMDkit.
+
+---
+
+### 4. MSD plot oscillates wildly instead of showing linear diffusion
+
+**Symptom:** The MSD curve is noisy or oscillates instead of growing roughly linearly with time, giving an unreliable diffusion coefficient.
+
+**Diagnostic:**
+
+Check the actual frame interval used in the simulation:
+
+```bash
+head thermo.out
+```
+
+Compare the sampling interval there with the `dt_fs` value you passed to `-calc msd`.
+
+**Fix:**
+
+- Ensure `dt_fs` passed to `gpumdkit.sh -calc msd` equals the real MD timestep multiplied by the sample (output) interval — not just the MD timestep alone.
+- Confirm the trajectory is long enough for the diffusion timescale of your system.
+- Note that solids at low temperature may genuinely not show a linear MSD regime (the atoms are localized); this is physical, not a bug.
+
+---
+
+### 5. `-out2xyz` or `-pos2exyz` says "No files found"
+
+**Symptom:** A format-conversion command reports that no input files were found, even though you expected them to be there.
+
+**Diagnostic:**
+
+```bash
+ls *.vasp *.xyz *.OUTCAR
+```
+
+If nothing matches, you are either in the wrong directory or the file extensions do not match what the command expects.
+
+**Fix:**
+
+- `cd` into the directory that actually contains your structure files before running the conversion.
+- Verify the file extensions match the expected ones (e.g., `POSCAR`, `*.vasp`, `OUTCAR`, `*.xyz`).
+
+---
+
+## Getting More Help
+
+If none of the above solves your problem:
+
+- **Issue tracker:** Open an issue at <https://github.com/zhyan0603/GPUMDkit/issues> (please include the full command you ran and the error message).
+- **Email:** Zihan YAN — <yanzihan@westlake.edu.cn>
+- **QQ group:** 825696376 — for community discussion and quick help.
diff --git a/docs/tutorials/zh/index.md b/docs/tutorials/zh/index.md
index 7ba7749..5b1069a 100644
--- a/docs/tutorials/zh/index.md
+++ b/docs/tutorials/zh/index.md
@@ -91,6 +91,7 @@ gpumdkit.sh -calc msd trajectory.xyz Li 10
 | [主动学习工作流](主动学习工作流.md) | 批量主动学习流程说明 |
 | [极性材料分析](极性材料分析.md) | 铁电和极化相关工具 |
 | [贡献指南](贡献指南.md) | 开发和贡献说明 |
+| [故障排除](故障排除.md) | 常见问题、诊断和修复方法 |
 
 ## 链接
 
diff --git "a/docs/tutorials/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.md" "b/docs/tutorials/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.md"
index a6d5574..c9fe0b2 100644
--- "a/docs/tutorials/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.md"
+++ "b/docs/tutorials/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.md"
@@ -86,31 +86,31 @@ pynep_sample_dist=0.01
 - `nep.txt`
 - `nep.in`
 - `train.xyz`
-- `run.in`
+- `run_*.in`（如 `run_1.in`、`run_2.in` 等）
 - `INCAR`
 - `POTCAR`
 - `KPOINTS`
 - 初始采样结构文件，例如 `sample_struct.xyz`
 
-脚本会把公共输入移动到 `common/`，并创建 `00.modev/`、`01.select/` 等工作目录。
+脚本会把公共输入移动到 `common/`，并创建 `00.md/`、`01.select/` 等工作目录。
 
 ## 5. 文件组织
 
 脚本会创建公共输入目录和 MD 目录：
 
 ```bash
-mkdir 00.modev common
-mv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common
-cp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev
+mkdir 00.md common
+mv ${work_dir}/{nep.txt,nep.in,*.xyz,run_*.in,INCAR,KPOINTS,POTCAR} ./common
+cp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.md
 ```
 
-- `00.modev`：用于运行 GPUMD MD 采样。
-- `common`：保存 `nep.txt`、`run.in`、结构文件和 DFT 输入文件等公共资源。
+- `00.md`：用于运行 GPUMD MD 采样。
+- `common`：保存 `nep.txt`、`run_*.in` 文件、结构文件和 DFT 输入文件等公共资源。
 
 ## 6. 提交 MD 任务
 
 ```bash
-submit_gpumd_array modev ${sample_struct_num}
+submit_gpumd_array md ${sample_struct_num}
 sbatch submit.slurm
 ```
 
@@ -118,7 +118,7 @@ sbatch submit.slurm
 
 ## 7. 检查任务完成
 
-脚本会持续检查 `00.modev/` 下各个 `sample_*/log` 文件，确认是否出现：
+脚本会持续检查 `00.md/` 下各个 `sample_*/log` 文件，确认是否出现：
 
 ```bash
 Finished running GPUMD.
diff --git "a/docs/tutorials/zh/\345\221\275\344\273\244\345\217\202\350\200\203.md" "b/docs/tutorials/zh/\345\221\275\344\273\244\345\217\202\350\200\203.md"
index 22d5d53..15d6d93 100644
--- "a/docs/tutorials/zh/\345\221\275\344\273\244\345\217\202\350\200\203.md"
+++ "b/docs/tutorials/zh/\345\221\275\344\273\244\345\217\202\350\200\203.md"
@@ -116,7 +116,7 @@ gpumdkit.sh -plt <type> [options]
 gpumdkit.sh -plt -h
 ```
 
-常用类型包括 `train`、`prediction`、`thermo`、`msd`、`sdc`、`rdf`、`emd`、`nemd`、`hnemd`、`pdos` 和 `plane-grid`。
+常用类型包括 `train`、`prediction`（别名：`test`）、`thermo`、`msd`、`sdc`、`rdf`、`emd`、`nemd`、`hnemd`、`pdos` 和 `plane-grid`。
 
 ## 工具
 
diff --git "a/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md" "b/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md"
index 854491d..bc966d5 100644
--- "a/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md"
+++ "b/docs/tutorials/zh/\345\277\253\351\200\237\345\205\245\351\227\250.md"
@@ -100,7 +100,7 @@ gpumdkit.sh
  1) Format Conversion          2) Sample Structures
  3) Workflow                   4) Calculators
  5) Analyzer                   6) Visualization
- 7) Utilities                  8) Developing...
+ 7) Utilities                  8) Help                
  0) Exit
  ------------>>
  Input the function number:
@@ -126,6 +126,30 @@ gpumdkit.sh -calc msd trajectory.xyz Li 10
 
 第一个示例读取 `POSCAR`，写出 `model.xyz`。
 
+## Hello World 示例
+
+一个最小化的端到端检查，确认安装是否正常——创建一个极小的硅 POSCAR，转换为 extxyz，并查看输出：
+
+```bash
+cat > POSCAR << 'EOF'
+Si
+1.0
+0 2.715 2.715
+2.715 0 2.715
+2.715 2.715 0
+Si
+1
+direct
+0 0 0
+EOF
+gpumdkit.sh -pos2exyz POSCAR model.xyz
+head model.xyz
+```
+
+如果 `model.xyz` 显示一个 Si 原子及晶格信息，说明安装成功。
+
+> **什么是 extxyz？** extxyz 是扩展 XYZ 格式：第 1 行是原子数，第 2 行包含晶格及结构级属性（按需包含能量/力/维里），第 3 行及以后是每个原子及其原子级属性。它是 NEP 的原生训练数据格式。
+
 ## 常见示例
 
 ### POSCAR 转 extxyz
diff --git "a/docs/tutorials/zh/\346\225\205\351\232\234\346\216\222\351\231\244.md" "b/docs/tutorials/zh/\346\225\205\351\232\234\346\216\222\351\231\244.md"
new file mode 100644
index 0000000..775ebf4
--- /dev/null
+++ "b/docs/tutorials/zh/\346\225\205\351\232\234\346\216\222\351\231\244.md"
@@ -0,0 +1,128 @@
+<div align="center">
+  <h1>🛠️ 故障排除</h1>
+  <p style="text-align: justify;">本页收集了用户在安装或运行 GPUMDkit 时最常遇到的问题，每个问题都给出了快速诊断命令和修复方法。如果此处未列出你的问题，请参见页面底部的<a href="#获取更多帮助">获取更多帮助</a>。</p>
+</div>
+
+## 常见问题
+
+### 1. 安装后在新终端中提示 `gpumdkit.sh: command not found`
+
+**症状：** 打开新终端输入 `gpumdkit.sh` 时提示 `command not found`，尽管安装过程看似成功。
+
+**诊断：**
+
+```bash
+echo $GPUMDkit_path
+```
+
+应打印出安装目录。如果为空或不正确，说明 shell 未加载环境变量。
+
+**修复：**
+
+```bash
+source ~/.bashrc        # Linux / bash
+source ~/.zshrc         # macOS / zsh
+```
+
+如果 source 后变量仍为空，请在 GPUMDkit 目录下重新运行安装脚本：
+
+```bash
+cd /path/to/GPUMDkit
+bash install.sh
+```
+
+---
+
+### 2. 绘图时报错 `FileNotFoundError: loss.out`（或 `thermo.out`、`msd.out` 等）
+
+**症状：** 运行 `gpumdkit.sh -plt <type>` 时因找不到某个 `.out` 文件而报 `FileNotFoundError`。
+
+**诊断：**
+
+```bash
+ls *.out
+```
+
+如果没有输出，说明当前目录不包含 GPUMD/NEP 的输出文件。
+
+**修复：**
+
+```bash
+cd /path/to/your/simulation/run
+gpumdkit.sh -plt <type>
+```
+
+务必在包含输出文件的目录中运行 `-plt`，或传入正确的路径。
+
+---
+
+### 3. 运行某些计算器时报 `No module named 'calorine'`（或 `'neptrain'`、`'dpdata'`）
+
+**症状：** 计算器或转换器中止并报 `ModuleNotFoundError: No module named 'calorine'`（或 `neptrain`、`dpdata`）。
+
+**诊断：**
+
+```bash
+pip list | grep -iE 'calorine|neptrain|dpdata'
+```
+
+如果缺少该包，请安装。
+
+**修复：**
+
+```bash
+pip install calorine neptrain dpdata
+```
+
+如果使用 conda，请在已激活的 `gpumdkit` 环境中运行对应的 `conda install` 或 `pip install`。运行 GPUMDkit 前请确保环境已激活。
+
+---
+
+### 4. MSD 曲线剧烈震荡而非线性扩散
+
+**症状：** MSD 曲线噪声很大或来回震荡，没有随时间近似线性增长，导致扩散系数不可靠。
+
+**诊断：**
+
+检查模拟中实际使用的帧间隔：
+
+```bash
+head thermo.out
+```
+
+将那里的采样间隔与你传给 `-calc msd` 的 `dt_fs` 进行对比。
+
+**修复：**
+
+- 确保传给 `gpumdkit.sh -calc msd` 的 `dt_fs` 等于真实 MD 时间步长乘以采样（输出）间隔，而不仅仅是 MD 时间步长。
+- 确认轨迹长度足以覆盖你体系的扩散时间尺度。
+- 注意：低温下固体可能确实不会出现线性 MSD 区域（原子被局域化），这是物理现象，不是 bug。
+
+---
+
+### 5. `-out2xyz` 或 `-pos2exyz` 提示 "No files found"
+
+**症状：** 格式转换命令报告找不到输入文件，尽管你预期文件就在那里。
+
+**诊断：**
+
+```bash
+ls *.vasp *.xyz *.OUTCAR
+```
+
+如果没有匹配项，说明你所在目录不对，或文件扩展名与命令预期的不一致。
+
+**修复：**
+
+- 运行转换前先 `cd` 到实际包含结构文件的目录。
+- 确认文件扩展名与预期一致（例如 `POSCAR`、`*.vasp`、`OUTCAR`、`*.xyz`）。
+
+---
+
+## 获取更多帮助
+
+如果以上方法均未解决问题：
+
+- **Issue 跟踪器：** 在 <https://github.com/zhyan0603/GPUMDkit/issues> 提交 issue（请附上你运行的完整命令和错误信息）。
+- **邮件：** Zihan YAN — <yanzihan@westlake.edu.cn>
+- **QQ 群：** 825696376 — 用于社区交流和快速帮助。
diff --git "a/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md" "b/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
index 0237a30..e14a4dd 100644
--- "a/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
+++ "b/docs/tutorials/zh/\346\240\274\345\274\217\350\275\254\346\215\242.md"
@@ -287,6 +287,7 @@ gpumdkit.sh    # 选择：1) 格式转换 → 104
 |------|------|
 | LAMMPS 转换后元素不对 | 检查 dump 文件后的元素顺序 |
 | extxyz 元数据太多 | 使用 `-clean_xyz input.xyz clean.xyz` |
+| 转换后的结构看起来偏移 | 检查源文件中的周期性边界条件/晶胞信息 |
 | 提取帧不对 | 注意帧索引通常从 0 开始 |
 
 ## 说明
diff --git "a/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md" "b/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md"
index da213f4..6dc5b54 100644
--- "a/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md"
+++ "b/docs/tutorials/zh/\347\273\230\345\233\276\350\204\232\346\234\254.md"
@@ -38,6 +38,7 @@ gpumdkit.sh -plt <type> -h    # 显示特定图表的帮助
 |  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|
 |  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |
 |  D_xyz          - Directional Arrhenius D                                                     |
+|  doas           - Density of atomistic states                                                 |
 +-----------------------------------------------------------------------------------------------+
 |                                    MD & Structural Analysis                                   |
 +-----------------------------------------------------------------------------------------------+
@@ -45,13 +46,16 @@ gpumdkit.sh -plt <type> -h    # 显示特定图表的帮助
 |  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
 |  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
 |  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
-|  doas           - Density of atomistic states                                                 |
 +-----------------------------------------------------------------------------------------------+
 |                                        Heat Transport                                         |
 +-----------------------------------------------------------------------------------------------+
 |  emd            - EMD results                    nemd           - NEMD results                |
 |  hnemd          - HNEMD results                  viscosity      - Viscosity                   |
 +-----------------------------------------------------------------------------------------------+
+|                                          Phonons                                              |
++-----------------------------------------------------------------------------------------------+
+|  pdos           - VAC and PDOS                                                                |
++-----------------------------------------------------------------------------------------------+
 ```
 
 ---
@@ -402,7 +406,7 @@ gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]
 
 ### plt_hnemd.py
 
-绘制非均匀非平衡分子动力学 (HNEMD) 结果。
+绘制均匀非平衡分子动力学 (HNEMD) 结果。
 
 **输入文件：** GPUMD 的 HNEMD 输出文件
 
@@ -563,16 +567,6 @@ gpumdkit.sh -plt des umap
 
 ---
 
-### plt_descriptors_compare.py
-
-比较多个训练集或模型的描述符。
-
-```bash
-gpumdkit.sh -plt des_compare
-```
-
----
-
 ### plt_dimer.py
 
 绘制二聚体相互作用曲线。将两个原子放入立方盒子（30 Å），使用 NEP 模型计算势能和力随距离的变化。
diff --git "a/docs/tutorials/zh/\350\207\252\345\256\232\344\271\211\345\221\275\344\273\244.md" "b/docs/tutorials/zh/\350\207\252\345\256\232\344\271\211\345\221\275\344\273\244.md"
index 832b6a0..1c575e6 100644
--- "a/docs/tutorials/zh/\350\207\252\345\256\232\344\271\211\345\221\275\344\273\244.md"
+++ "b/docs/tutorials/zh/\350\207\252\345\256\232\344\271\211\345\221\275\344\273\244.md"
@@ -150,3 +150,7 @@ gpumdkit.sh -prep_training
 - 对需要参数的命令，建议在参数为空时打印用法提示。
 - 调用外部脚本时，尽量用 `"$@"` 保留参数中的空格和特殊字符。
 - 批处理目录时，注意使用 `cd "$dir"`，避免路径中有空格时出错。
+
+---
+
+感谢你使用 `GPUMDkit`！如有任何问题或需要进一步帮助，欢迎在我们的 GitHub 仓库提 issue 或联系 Zihan YAN (yanzihan@westlake.edu.cn)。
diff --git a/gpumdkit.sh b/gpumdkit.sh
index 8b292f9..6887329 100755
--- a/gpumdkit.sh
+++ b/gpumdkit.sh
@@ -36,7 +36,7 @@ echo " ---------------------- GPUMD ------------------------"
 echo " 1) Format Conversion          2) Sample Structures   "
 echo " 3) Workflow                   4) Calculators         "
 echo " 5) Analyzer                   6) Visualization       "
-echo " 7) Utilities                  8) Developing...       "
+echo " 7) Utilities                  8) Help                "
 echo " 0) Exit                                              "
 }
 
@@ -50,6 +50,13 @@ function read_menu_choice(){
     printf -v "$__target_var" '%s' "$__input"
 }
 
+function read_menu_array(){
+    if ! read -r -a "$1"; then
+        echo " Input closed. Exiting."
+        return 1
+    fi
+}
+
 # Function main
 function main(){
     echo " ------------>>"
@@ -161,7 +168,9 @@ function main(){
             esac ;;
         "8")
             echo " ------------>>"
-            echo " This module is under development. Coming soon."
+            echo " GPUMDkit Version ${VERSION}"
+            echo " ------------------------------------------------------------"
+            help_info_table
             ;;
         *)
             echo " Incorrect Options"
@@ -176,76 +185,76 @@ function main(){
 # It will show the usage of each function
 
 function help_info_table(){
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "|                          GPUMDkit ${VERSION} Command Help                               |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "|                                          MAIN FUNCTIONS                                               |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "| -h            Show this help table            | -plt <type>        Plot and visualization tools       |"
-    echo "| -calc <type>  Calculator tools                | -time <gpumd|nep>  Time-consuming analyzer            |"
-    echo "| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "|                                         FORMAT CONVERSION                                             |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "| -out2xyz      OUTCAR -> extxyz (shell)        | -out2exyz          OUTCAR -> extxyz (python)          |"
-    echo "| -cp2k2xyz     CP2K log -> xyz                 | -xdat2exyz         XDATCAR -> extxyz                  |"
-    echo "| -cif2pos      cif -> POSCAR                   | -cif2exyz          cif -> extxyz                      |"
-    echo "| -pos2exyz     POSCAR -> extxyz                | -exyz2pos          extxyz -> POSCAR                   |"
-    echo "| -pos2lmp      POSCAR -> LAMMPS data           | -lmp2exyz          LAMMPS dump -> extxyz              |"
-    echo "| -traj2exyz    ASE traj -> extxyz              | -replicate         Replicate structure                |"
-    echo "| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |"
-    echo "| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |"
-    echo "| -frame_range  Extract frames by range         |                                                       |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "|                                            ANALYSIS                                                   |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |"
-    echo "| -chem_species Analyze chemical species        | -cbc               Charge balance check               |"
-    echo "| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |"
-    echo "| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |"
-    echo "| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |"
-    echo "| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "| Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " |                          GPUMDkit ${VERSION} Command Help                               |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " |                                          MAIN FUNCTIONS                                               |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " | -h            Show this help table            | -plt <type>        Plot and visualization tools       |"
+    echo " | -calc <type>  Calculator tools                | -time <gpumd|nep>  Time-consuming analyzer            |"
+    echo " | -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " |                                         FORMAT CONVERSION                                             |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " | -out2xyz      OUTCAR -> extxyz (shell)        | -out2exyz          OUTCAR -> extxyz (python)          |"
+    echo " | -cp2k2xyz     CP2K log -> xyz                 | -xdat2exyz         XDATCAR -> extxyz                  |"
+    echo " | -cif2pos      cif -> POSCAR                   | -cif2exyz          cif -> extxyz                      |"
+    echo " | -pos2exyz     POSCAR -> extxyz                | -exyz2pos          extxyz -> POSCAR                   |"
+    echo " | -pos2lmp      POSCAR -> LAMMPS data           | -lmp2exyz          LAMMPS dump -> extxyz              |"
+    echo " | -traj2exyz    ASE traj -> extxyz              | -replicate         Replicate structure                |"
+    echo " | -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |"
+    echo " | -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |"
+    echo " | -frame_range  Extract frames by range         |                                                       |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " |                                            ANALYSIS                                                   |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " | -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |"
+    echo " | -chem_species Analyze chemical species        | -cbc               Charge balance check               |"
+    echo " | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |"
+    echo " | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |"
+    echo " | -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |"
+    echo " | -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
 }
 
 function calculator_help_table(){
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "|                                      CALCULATOR TOOLS                                                 |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "| Usage: gpumdkit.sh -calc <type> [args...]                                                             |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "| ionic-cond <element> <charge>                 Calculate ionic conductivity from MSD data              |"
-    echo "| nep <input.xyz> <output.xyz> <nep_model>      Calculate energy/force/virial with a NEP model          |"
-    echo "| des <input.xyz> <output.npy> <nep_model> <el> Calculate NEP descriptors for one element               |"
-    echo "| doas <input.xyz> <nep_model> <output.txt>     Calculate density of atomistic states                   |"
-    echo "| neb <initial.xyz> <final.xyz> <n_images> <nep> Run NEB calculation with a NEP model                   |"
-    echo "| minimize <structure> <nep_model> [fmax] [n]   Minimize a structure with a NEP model                   |"
-    echo "| msd <trajectory.xyz> <element> <dt_fs> [n]    Calculate MSD from an extxyz trajectory                 |"
-    echo "| nlist [script args...]                        Build neighbor lists                                    |"
-    echo "| disp [script args...]                         Calculate displacement from trajectory                  |"
-    echo "| avg-struct [script args...]                   Calculate averaged structure                            |"
-    echo "| oct-tilt [script args...]                     Calculate octahedral tilt                               |"
-    echo "| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
-    echo "| Examples: gpumdkit.sh -calc ionic-cond Li 1                                                           |"
-    echo "|           gpumdkit.sh -calc msd dump.xyz Li 10                                                        |"
-    echo "|           gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O                                  |"
-    echo "+-------------------------------------------------------------------------------------------------------+"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " |                                      CALCULATOR TOOLS                                                 |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " | Usage: gpumdkit.sh -calc <type> [args...]                                                             |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " | ionic-cond <element> <charge>                 Calculate ionic conductivity from MSD data              |"
+    echo " | nep <input.xyz> <output.xyz> <nep_model>      Calculate energy/force/virial with a NEP model          |"
+    echo " | des <input.xyz> <output.npy> <nep_model> <el> Calculate NEP descriptors for one element               |"
+    echo " | doas <input.xyz> <nep_model> <output.txt>     Calculate density of atomistic states                   |"
+    echo " | neb <initial.xyz> <final.xyz> <n_images> <nep> Run NEB calculation with a NEP model                   |"
+    echo " | minimize <structure> <nep_model> [fmax] [n]   Minimize a structure with a NEP model                   |"
+    echo " | msd <trajectory.xyz> <element> <dt_fs> [n]    Calculate MSD from an extxyz trajectory                 |"
+    echo " | nlist [script args...]                        Build neighbor lists                                    |"
+    echo " | disp [script args...]                         Calculate displacement from trajectory                  |"
+    echo " | avg-struct [script args...]                   Calculate averaged structure                            |"
+    echo " | oct-tilt [script args...]                     Calculate octahedral tilt                               |"
+    echo " | pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
+    echo " | Examples: gpumdkit.sh -calc ionic-cond Li 1                                                           |"
+    echo " |           gpumdkit.sh -calc msd dump.xyz Li 10                                                        |"
+    echo " |           gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Ti -E O                                  |"
+    echo " +-------------------------------------------------------------------------------------------------------+"
 }
 
 function citation(){
 echo " +------------------------------------------------------+"
 echo " |           THANK YOU FOR USING GPUMDKIT               |"
 echo " +------------------------------------------------------+"
-echo " │ If you find it useful, please cite our paper:        │"
-echo " │                                                      │"
-echo " │ GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP  │"
+echo " | If you find it useful, please cite our paper:        |"
+echo " |                                                      |"
+echo " | GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP  |"
 echo " |           MGE Advances, 2026, 4, e70074              |"
-echo " |       (https://doi.org/10.1002/mgea.70074)           │"
-echo " │                                                      │"
-echo " |     Welcome to join our QQ group (825696376) !       │"
+echo " |       (https://doi.org/10.1002/mgea.70074)           |"
+echo " |                                                      |"
+echo " |     Welcome to join our QQ group (825696376) !       |"
 echo " +------------------------------------------------------+"
 }
 
@@ -326,7 +335,10 @@ if [ ! -z "$1" ]; then
                         echo " | set and charge_train.out.                                |"
                         echo " +----------------------------------------------------------+"
                         python ${plt_path}/plt_charge.py $3 ;;
-                    *) source ${GPUMDkit_path}/src/f6_plots.sh; f6_plots_two_column; exit 1 ;;
+                    *)
+                        echo " Unknown plot type: $2"
+                        echo " Available types are listed below."
+                        source ${GPUMDkit_path}/src/f6_plots.sh; f6_plots_two_column; exit 1 ;;
                 esac
             else
                 source ${GPUMDkit_path}/src/f6_plots.sh
diff --git a/skills/AGENTS.md b/skills/AGENTS.md
new file mode 100644
index 0000000..82df07b
--- /dev/null
+++ b/skills/AGENTS.md
@@ -0,0 +1,274 @@
+# GPUMDkit — AI Agent Knowledge File
+
+> This document records architecture, conventions, preferences, and known pitfalls of the GPUMDkit project for future AI agents. Last updated: 2026-07-01 (project VERSION="1.5.6 (dev)").
+
+## Project Overview
+
+GPUMDkit is a Bash + Python command-line toolkit for GPUMD and NEP. It provides format conversion, structure sampling, workflows, property calculation, plotting, and analysis utilities. The entry point is `gpumdkit.sh` (dual-mode: interactive menu + CLI).
+
+**Repository**: https://github.com/zhyan0603/GPUMDkit
+**Primary Author**: Zihan YAN (yanzihan@westlake.edu.cn)
+**Citation**: MGE Advances, 2026, 4, e70074
+
+## Architecture
+
+```
+gpumdkit.sh          ← Main entry point: menu rendering + CLI dispatch
+  │
+  ├── src/f1_format_conversions.sh  ← Interactive menu wrappers (f101-f110 + keyword converters)
+  ├── src/f2_sample_structures.sh   ← f201-f205
+  ├── src/f3_workflows.sh           ← f301-f303
+  ├── src/f4_calculators.sh         ← f401-f412
+  ├── src/f5_analyzers.sh           ← f501-f508
+  ├── src/f6_plots.sh               ← f6_plots_one_column / f6_plots_two_column (dynamic layout)
+  │     └── Layout is selected based on terminal width
+  ├── src/f7_utilities.sh           ← f701
+  │
+  └── Scripts/                      ← Implementation scripts
+        ├── format_conversion/      ← Python/Bash converters
+        ├── sample_structures/      ← Sampling utilities
+        ├── calculators/            ← Calculators (MSD, ionic conductivity, NEB, descriptors, ...)
+        ├── analyzer/               ← Analyzers (composition, distance, filter, ...)
+        ├── plt_scripts/            ← Plotting (35 scripts)
+        ├── workflow/               ← Workflows (SCF pretreatment, active learning)
+        └── utils/                  ← Update, clean, completion, NEP modifier
+```
+
+## Key Files
+
+| File | Purpose |
+|------|---------|
+| `gpumdkit.sh` | Main entry: defines `GPUMDkit_path`, `menu()`, `main()`, `help_info_table()`, `calculator_help_table()`, `citation()`, CLI `case`, `read_menu_choice()`, `read_menu_array()`, `run_python_script()` |
+| `src/fN_*.sh` | Interactive menu modules. Each defines `fN_category()` display functions and leaf `fNXX_*` wrapper functions with `valid_menu_choices` validation loops. |
+| `Scripts/utils/completion.sh` | Bash TAB completion |
+| `Scripts/utils/update_gpumdkit.sh` | Update command |
+| `Scripts/utils/clean_extra_files.sh` | Clean command |
+| `install.sh` | Installation (writes `GPUMDkit_path` to bashrc/zshrc) |
+| `docs/tutorials/en/*.md` + `zh/*.md` | Bilingual tutorials (13 pairs + index + troubleshooting) |
+| `skills/*/SKILL.md` | AI agent skill definitions |
+| `~/.gpumdkit.in` | User custom commands |
+
+## Variable Reference
+
+```bash
+GPUMDkit_path          # Set by user; points to GPUMDkit root directory
+VERSION                # "1.5.6 (dev) (2026-06-17)" (only in gpumdkit.sh)
+plt_path               # ${GPUMDkit_path}/Scripts/plt_scripts
+analyzer_path          # ${GPUMDkit_path}/Scripts/analyzer
+calc_path              # ${GPUMDkit_path}/Scripts/calculators
+workflow_path          # ${GPUMDkit_path}/Scripts/workflow
+format_conv_path       # ${GPUMDkit_path}/Scripts/format_conversion
+utils_path             # ${GPUMDkit_path}/Scripts/utils
+sample_path            # ${GPUMDkit_path}/Scripts/sample_structures
+```
+
+## Shell Script Conventions
+
+### Entry Point / Dispatch
+
+**Interactive**: `gpumdkit.sh` (no args) → `menu()` → `main()` reads choice → first character of choice selects module → nested `case` calls `fNXX_*` functions → after function returns, `citation()` runs → script exits (no loop back to menu).
+
+**CLI**: `gpumdkit.sh -flag [args]` → dispatched via `case $1 in`.
+
+### Read Conventions (EOF Safety)
+
+**Always use the EOF-safe helpers defined in `gpumdkit.sh`:**
+
+- `read_menu_choice var || return 1` — reads a single line into a variable
+- `read_menu_array arr || return 1` — reads whitespace-separated tokens into an array
+
+**Never use bare `read -p " "` or `read -r -a`.** On closed stdin (pipe, redirect, /dev/null), bare read silently hangs or returns empty values without detection. The helpers print `" Input closed. Exiting."` and return 1.
+
+### Menu Conventions
+
+- Validation array: always named `valid_menu_choices`
+- Validation loop: `while ! echo "${valid_menu_choices[@]}" | grep -wq "$num_choice"; do ...; done`
+- Return to main menu: `case ... "000") menu; main ;;` (recursive)
+
+### Box Drawing Styles
+
+- **Menu boxes**: `+---+` style, constructed with sequential `echo` lines.
+- **Script banners**: `>----<` style, inner width 49 dashes (53 chars total including `>` and `<`). Content uses ` | ... |` wrapper.
+- **Input prompt marker**: `echo " ------------>>"` before any `read_menu_choice` or `read_menu_array`.
+
+### Error Message Style
+
+**Every user-facing `echo` must start with a space character:**
+
+```bash
+echo " Error: GPUMDkit_path is not set."        # ✓ Correct
+echo " Error: Unable to determine current branch."  # ✓ Correct
+echo "Error: ..."   # ✗ Wrong — missing leading space
+
+# Normal informational messages also use leading space:
+echo " Deleting the files..."   # ✓
+echo " Operation canceled."     # ✓
+```
+
+### ASCII Only Box Drawing
+
+All border characters must be pure ASCII: `|`, `+`, `-`, `/`, `\`, `>`, `<`. **Never use** Unicode box-drawing characters like `│` (U+2502) — they render as mojibake on non-UTF-8 terminals.
+
+### Function Naming
+
+- Interactive entry functions: `f<Module><Number>_<descriptive_name>` (e.g., `f101_out2xyz`, `f302_md_sample_batch_pretreatment_gpumd`)
+- Menu display functions: `f<Module>_<module_name>` (e.g., `f1_format_conversion`, `f4_calculators`)
+- Utility functions: lowercase snake_case (e.g., `clean_extra_files`, `update_gpumdkit`)
+- `run_python_script` (helper in gpumdkit.sh): prints author + path banner, then calls `python "$@"`
+
+### Other Shell Conventions
+
+- Non-empty check: `[ ! -z "$var" ]` (project convention)
+- CLI help flag check: `[ "$2" != "-h" ]`
+- `"${@:2}"` / `"${@:3}"` patterns for argument forwarding
+- `run_python_script "Author" /path/to/script.py "${@:2}"` used in CLI branches
+- Functions are `source`d into the current shell; `type -t` can verify definition
+
+## Python Script Conventions
+
+- **Scripts are designed to run standalone, not to be imported.** Module-level `sys.exit(1)`, `input()`, `plt.show()` etc. are all acceptable.
+- **Arguments**: prefer `sys.argv` positional (88% of scripts), `argparse` only for complex flag-heavy scripts (12%).
+- **`np.loadtxt()` default `comments='#'`** handles GPUMD's newer output files that have `#` header lines automatically. No extra handling needed.
+- **`np.savetxt(header=...)`** auto-prefixes the header string with `# `. Writers and readers are pair-compatible.
+- **File header docstring**: all scripts over 50 lines should have a module-level docstring (Script / Author / Purpose / Usage).
+- **Error exits**: `print(" Error: ..."); sys.exit(1)` — do not raise raw exceptions.
+- `ase.io.read` provides reasonably clear errors when files are missing; this can serve as a minimal defense.
+
+## Documentation Conventions
+
+- **Tutorials**: `docs/tutorials/en/` + `zh/` bilingual. Any feature change should update the corresponding tutorial page in both languages.
+- **SKILL.md**: `skills/<category>/SKILL.md` with YAML frontmatter (the `name` field must match the directory name exactly).
+- **Help tables**: `help_info_table()` and `calculator_help_table()` in `gpumdkit.sh` — CLI flag tables must be kept in sync manually.
+
+## Contributor Rules
+
+### Must Do
+
+1. All CLI help text and tutorial `echo`/`print` messages start with a **space** character.
+2. All box-drawing characters must be **pure ASCII** (no `│` or other Unicode).
+3. All interactive input reads must go through `read_menu_choice` or `read_menu_array` (**never** bare `read`).
+4. Menu validation arrays must be named `valid_menu_choices`.
+5. Script banners must name the **exact** filename (no abbreviations or wrong suffixes).
+6. Changes must not break existing functionality — **minimum-invasion principle**.
+7. After any change, validate with `bash -n` and `python3 -m py_compile`.
+
+### Do NOT Do (explicitly rejected by maintainer)
+
+| Rejected | Rationale |
+|---|---|
+| Force `if __name__ == "__main__":` on Python scripts | Scripts are standalone; main guards are unnecessary churn |
+| Replace `from pylab import *` with explicit imports | Keep as-is |
+| Unify `-plt` "save" argument position | Different scripts have different arg counts; inflexible |
+| Unify DPI (e.g., 150 → 300) across plotting scripts | Keep per-script DPI |
+| Change `exit` → `return` in workflow sourced scripts | Keep as-is |
+| Make interactive mode loop back to menu after one function | Intentionally single-shot |
+| Add `-filter_value` / `-filter_range` / `-get_volume` / `-re_atoms` to help table | Intentionally undocumented |
+| Add color / ANSI escape codes | User rejected; keep monochrome |
+| Add debug examples to every tutorial page | Keep tutorials lean |
+| Change MSD fitting range without maintainer approval | 40%-80% is the settled range; changing it is a scientific decision |
+| Add `des_compare` to CLI | Script exists but not exposed |
+| Add extra troubleshooting FAQ items | Keep the 5-item set |
+
+### macOS / Cross-Platform Notes
+
+- macOS ships **bash 3.2** (no `local -n` nameref). Use `read -a "$varname"` for array reads.
+- macOS **sed is BSD**, not GNU. For cross-platform sed, use `perl -i -pe` instead.
+- **zsh does not support `read -a`** (bash-only). All scripts run under bash.
+- `timeout` command is unavailable on macOS. Rely on EOF-safe `read_menu_choice` / `read_menu_array` to avoid hangs.
+
+## Key Data Flows
+
+### Interactive Mode
+
+```
+User runs: gpumdkit.sh
+         → menu() prints menu
+         → main() reads choice
+         → ${choice:0:1} selects module (1-7)
+         → source src/fN_*.sh
+         → nested case calls fNXX_* function
+         → Function: echo banner → read_menu_choice/read_menu_array for args → python/bash runs script
+         → Return to main → citation() → script exits
+```
+
+### CLI Mode
+
+```
+User runs: gpumdkit.sh -flag args
+         → case $1 in
+         → source / python / bash dispatches to script
+         → ${@:2} or ${@:3} forwards arguments
+         → exit
+```
+
+### Custom Commands (~/.gpumdkit.in)
+
+```
+gpumdkit.sh -mycommand args
+         → alias_key="${1#-}"        → "mycommand"
+         → func_name="custom_${alias_key}" → "custom_mycommand"
+         → source ~/.gpumdkit.in
+         → custom_mycommand "$@"
+```
+
+## GPUMD/NEP Output File Behavior
+
+- **`#` comment lines**: GPUMD now prints `#`-prefixed comment lines at the start of `.out` files (e.g., msd.out). `np.loadtxt()` default `comments='#'` handles these automatically — all 35+ reading scripts are SAFE.
+- **`np.savetxt(header=...)`**: auto-prefixes the header with `# `. Writers (like `calc_msd.py`) and readers (like `plt_msd.py`) are pair-compatible.
+- **`.out` column counts vary by compute command**: msd.out may have 4 or 7 columns depending on whether `compute_sdc` was enabled. Scripts with hardcoded column assumptions (`plt_sdc.py`, `plt_msd_sdc.py` assume 7) will crash on 4-column files. See "Known Pitfalls" below.
+
+## Known Pitfalls
+
+1. **`plt_sdc.py` / `plt_msd_sdc.py`**: hardcode 7-column msd.out. Crashes with `IndexError` when only `compute_msd` (4 columns) was used. These are the most common script crashes for GPUMD users.
+2. **`plt_arrhenius_sigma.py` / `_xyz.py`**: hardcode `z = 1` (species charge). Produces **wrong conductivity values** (off by z²) for multivalent ions (Mg²⁺, Ca²⁺, Al³⁺, etc.).
+3. **`plt_emd.py` / `plt_nemd.py` / `plt_hnemd.py` / `plt_pdos.py`**: call `plt.show()` without Agg backend detection. Crash with `TclError` on headless servers/SSH. The other 34 plotting scripts all have proper Agg detection.
+4. **`plt_rdf_pmf.py`**: calls `input()` when run without arguments — hangs in non-interactive mode. `gpumdkit.sh -plt rdf_pmf` (no extra args) triggers this.
+5. **~30 plotting scripts** use `np.loadtxt()` / `open()` without file-existence checks. Users running from the wrong directory get cryptic tracebacks instead of friendly "file not found" messages.
+6. **macOS bash 3.2**: no `local -n` nameref. Use alternative patterns (read -a "$varname", eval, or herestring redirection).
+
+## Design Decisions (recent fixes — do not revert)
+
+- **`calc_ion_conductivity.py` lines 107-108**: MSD fitting range is now 40%-80% (was 10%-40%). The Arrhenius plotting scripts also use 40%-80%. This is a settled scientific choice.
+- **`select_max_modev.py` line 111**: The index mapping `atoms_list[filtered_indices[i]]` was recently fixed from a bug (`atoms_list[i]`). The old version silently selected the wrong structures.
+- **`charge_balance_check.py` lines 118-131**: Now uses a manual loop instead of `dict()` to handle 3-tuple error returns from `check_oxidation_state()`. The `dict()` constructor crashes on 3-tuples.
+- **`clean_extra_files.sh`**: Uses whole-word matching for the keep-exclusion logic, not substring removal. Substring removal (`${var/pattern/}`) corrupts filenames that share substrings with the keep input.
+- **`clean_extra_files.sh`**: `read user_input` changed to EOF-safe read with `|| return 1`. On EOF (closed stdin), the old code would proceed to `rm -f` the entire deletion list.
+- **`src/f6_plots.sh`**: `doas` is now in the "Diffusion & Transport" section of `f6_plots_two_column` (previously was in "MD & Structural Analysis"). Both one-column and two-column layouts are now consistent.
+- **All workflow ATTENTION blocks**: standardized to uniform width (57 dashes inner), with consistent `|` bar edges.
+
+## Verification Checklist
+
+```bash
+# Shell syntax
+bash -n gpumdkit.sh
+find src Scripts -name '*.sh' -exec bash -n {} +
+
+# Python syntax
+python3 -m py_compile <modified_file>
+
+# Interactive menu paths
+echo "0" | bash gpumdkit.sh                         # Exit
+printf '8\n0\n' | bash gpumdkit.sh                   # About/Help → Exit
+
+# CLI paths
+bash gpumdkit.sh -h >/dev/null                       # Help table
+bash gpumdkit.sh -plt badtype 2>&1                    # Should print "Unknown plot type"
+bash gpumdkit.sh -plt -h >/dev/null                   # Plot list
+
+# Documentation build
+mkdocs build -f docs/mkdocs.yml
+```
+
+## Quick Reference: Skill Files
+
+| Skill | Directory | Purpose |
+|-------|-----------|---------|
+| Main | `skills/gpumdkit-main/SKILL.md` | Entry point and project overview |
+| Format Conversion | `skills/gpumdkit-format-conversion/SKILL.md` | Structure file conversion |
+| Calculators | `skills/gpumdkit-calculators/SKILL.md` | Material property calculations |
+| Analyzers | `skills/gpumdkit-analyzers/SKILL.md` | Structure analysis and validation |
+| Visualization | `skills/gpumdkit-visualization/SKILL.md` | Plotting and visualization |
+| Workflows | `skills/gpumdkit-workflows/SKILL.md` | Batch processing and automation |
+| Sampling | `skills/gpumdkit-sampling/SKILL.md` | Structure sampling and selection |
+| Contributing | `skills/gpumdkit-contributing/SKILL.md` | Conventions and adding new features |
+| Agents | `skills/AGENTS.md` | This file — AI agent project knowledge |
diff --git a/skills/README.md b/skills/README.md
index 342d42c..e424873 100644
--- a/skills/README.md
+++ b/skills/README.md
@@ -20,17 +20,7 @@ to effectively use GPUMDkit functionality.
 
 ### opencode (Recommended)
 
-Configure in `opencode.json` to load skills directly from the skills directory:
-
-```json
-{
-  "skills": {
-    "paths": ["./skills"]
-  }
-}
-```
-
-Or create symlinks manually:
+Create symlinks manually:
 
 ```bash
 # Run from GPUMDkit root directory
diff --git a/skills/gpumdkit-contributing/SKILL.md b/skills/gpumdkit-contributing/SKILL.md
index bf07508..c81a058 100644
--- a/skills/gpumdkit-contributing/SKILL.md
+++ b/skills/gpumdkit-contributing/SKILL.md
@@ -79,7 +79,7 @@ echo " >-------------------------------------------------<"
 echo " Input <param1> <param2> [optional_param3]"
 echo " Example: input.xyz nep.txt"
 echo " ------------>>"
-read -r -a feature_args
+read_menu_choice feature_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_new_feature.py "${feature_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_new_feature.py"
@@ -88,16 +88,19 @@ echo " ---------------------------------------------------"
 ```
 
 Key conventions:
-- Banner uses `>-----<` and `| ... |` format
+- Banner uses `>-----<` and `| ... |` format (49 dashes inner, 53 chars total)
 - `echo " Input <...>"` describes parameters
-- `echo " Example: ..."` shows a concrete example (not "Examp:")
-- `read -r -a varname` reads into an array
+- `echo " Example: ..."` shows a concrete example
+- Use `read_menu_choice var || return 1` for single-value input, `read_menu_array arr || return 1` for array input
+- **Never use bare `read -p` or `read -r -a`** — these hang on closed stdin. The helpers are defined in `gpumdkit.sh`
 - `"${varname[@]}"` passes all arguments properly quoted
 - Function name format: `f<Category><Number>_<descriptive_name>`
+- **Script banner must name the EXACT filename** (not an abbreviation or wrong suffix)
+- All banners use uniform width: 49 dashes inner (lines 82-86 style). Inconsistent widths (51/52/53/56) should be normalized when touching a file.
 
 ### Step 3: Register in `gpumdkit.sh`
 
-1. Add the choice number to `array_choice` (line ~47)
+1. Add the choice number to `array_choice` (line ~64)
 2. Add the case in the `main()` function's nested case statement:
    ```bash
    "413") f413_new_feature ;;
@@ -147,7 +150,7 @@ echo "| -new_flag  Description of new flag           | -existing_flag    Descrip
 Edit `Scripts/utils/completion.sh`:
 
 1. Add `-new_flag` to the `opts` string (line 16)
-2. If it needs file completion, add it to the `|`-separated case (line 33):
+2. If it needs file completion, add it to the `|`-separated case (line 38):
    ```bash
    -out2xyz|-...|-new_flag)
        COMPREPLY=($(compgen -f -- "$cur")) ;;
@@ -212,8 +215,8 @@ Do NOT add notices for common packages like `ase`, `numpy`, `pymatgen`.
 ### Error messages
 
 ```python
-# Good
-print("Error: File 'input.xyz' not found.")
+# Good (leading space, clear message, sys.exit)
+print(" Error: File 'input.xyz' not found.")
 sys.exit(1)
 
 # Avoid
@@ -258,7 +261,7 @@ echo " >-------------------------------------------------<"
 echo " Input <param1> <param2>"
 echo " Example: input.xyz nep.txt"
 echo " ------------>>"
-read -r -a feature_args
+read_menu_choice feature_args || return 1   # EOF-safe; see project conventions
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/calculators/calc_new_feature.py "${feature_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/calculators/calc_new_feature.py"
@@ -266,6 +269,113 @@ echo " ---------------------------------------------------"
 }
 ```
 
+## Project Conventions & Personal Preferences
+
+These are the maintainer's conventions. Follow them strictly.
+
+### Echo / Print Leading Space
+
+**Every user-facing `echo`/`print` must start with a space.**
+
+```bash
+# ✓ Correct
+echo " Error: File not found."
+echo " Deleting the files..."
+echo " Operation canceled."
+
+# ✗ Wrong
+echo "Error: File not found."
+```
+
+```python
+# ✓ Correct
+print(" Error: 'input.xyz' not found.")
+print(" Deleting the files...")
+
+# ✗ Wrong
+print("Error: 'input.xyz' not found.")
+```
+
+This applies to ALL script types: interactive wrappers, workflow scripts, utility messages, tutorial transcripts, and Python print() output. The only exception is the `" ------------>>"` prompt marker which starts with a space by design.
+
+### ASCII Only Box Drawing
+
+All border characters must be pure ASCII: `|`, `+`, `-`, `/`, `\`, `>`, `<`. **Never use** Unicode box-drawing characters like `│` (U+2502) — they render as mojibake on non-UTF-8 terminals.
+
+### EOF-Safe Input
+
+All interactive input must go through the helpers defined in `gpumdkit.sh`:
+
+- `read_menu_choice var || return 1` — reads a single line into a variable
+- `read_menu_array arr || return 1` — reads whitespace-separated tokens into an array
+
+**Never use bare `read -p` or `read -r -a`.** When stdin is closed (pipe, redirect, /dev/null), bare read silently succeeds with empty/unset values or hangs forever. The helpers print `" Input closed. Exiting."` and return 1.
+
+### Menu Validation
+
+- Validation array: always named `valid_menu_choices`
+- Validation loop: `while ! echo "${valid_menu_choices[@]}" | grep -wq "$num_choice"; do ...; done`
+- Return-to-main-menu: `case ... "000") menu; main ;;`
+
+### Script Banners
+
+The info banner displayed before running a script follows this exact format:
+
+```bash
+echo " >-------------------------------------------------<"   # exactly 49 dashes
+echo " | Calling the script in Scripts/<category>       |"
+echo " | Script: <exact_filename>                         |"   # MUST match actual filename
+echo " | Developer: Name (email)                          |"
+echo " >-------------------------------------------------<"
+```
+
+- The script name in the banner **must be the exact filename** (e.g., `scf_batch_pretreatment_vasp.sh`, not `scf_batch_pretreatment.sh`)
+- Width: 49 dashes inner (53 chars total between `>` and `<`). Keep uniform across projects.
+
+### The Prompt Arrow
+
+User input follows the marker pattern: `echo " ------------>>"` before reading input. This is consistent across all interactive functions.
+
+### Error Message Format
+
+Shell: `echo " Error: <message>."` — leading space, capital E, colon, period at end.
+Python: `print(" Error: <message>."); sys.exit(1)` — same format, always call sys.exit after.
+
+### What NOT to Propose or Do
+
+These changes have been **explicitly rejected** by the project maintainer. Do not suggest them.
+
+| Rejected | Reason |
+|---|---|
+| Add `if __name__ == "__main__":` to Python scripts | Scripts run standalone; main guard is unnecessary |
+| Replace `from pylab import *` with explicit imports | Keep as-is |
+| Unify `-plt` "save" argument position | Different scripts have different arg counts; keep flexible |
+| Unify DPI (150 → 300) across plotting scripts | Keep per-script DPI settings |
+| Change `exit` → `return` in workflow sourced scripts | Keep as-is |
+| Add `-filter_value` / `-filter_range` / `-get_volume` / `-re_atoms` to the help table | Intentionally undocumented |
+| Make interactive mode loop back to menu after one function | Keeps shots single-shot; designed this way |
+| Add color/ANSI escape codes | User explicitly rejected; keep monochrome |
+| Add debug examples to every tutorial page | Unnecessary; keep tutorials lean |
+| Change MSD fitting range arbitrarily | Scientific choice; ask maintainer first |
+| Add `des_compare` to CLI | Script exists but user chose not to expose it |
+
+### macOS / Cross-Platform Notes
+
+- macOS ships **bash 3.2** (no `local -n` nameref). Use `read -a "$varname"` with eval or herestring instead of namerefs.
+- macOS **sed is BSD**, not GNU. Cross-platform sed: use `perl -i -pe` instead.
+- **zsh does not support `read -a`** (bash-only). All scripts run under bash.
+- `timeout` command is not available on macOS. Use background jobs or rely on EOF-safe read.
+
+### Specific Design Decisions
+
+- **calc_ion_conductivity.py**: MSD fitting range is 40%-80% of data (lines 107-108). The Arrhenius plotting scripts use the same range. Do not change without maintainer approval.
+- **clean_extra_files.sh**: Keep-substring deletion uses **whole-word matching**, NOT substring removal. Do not regress to `${var/pattern/}` substring removal (it corrupts filenames sharing substrings).
+- **troubleshooting.md**: Only 5 FAQ items. Do not expand without asking.
+- **select_max_modev.py line 111**: The index mapping `atoms_list[filtered_indices[i]]` was recently fixed from a bug (`atoms_list[i]`). Do not undo.
+- **charge_balance_check.py lines 118-131**: Now uses manual loop instead of `dict()` to handle 3-tuple error returns. Do not revert to `dict()`.
+
+---
+
 ## Validation Checklist
 
 Before committing, run these checks:
diff --git a/skills/gpumdkit-main/SKILL.md b/skills/gpumdkit-main/SKILL.md
index 1392c31..aafc634 100644
--- a/skills/gpumdkit-main/SKILL.md
+++ b/skills/gpumdkit-main/SKILL.md
@@ -1,5 +1,5 @@
 ---
-name: gpumdkit
+name: gpumdkit-main
 description: >
   Use when working with GPUMD molecular dynamics or NEP potentials for computational materials science.
   Provides format conversion, structure analysis, visualization, calculation tools, and workflow automation.
diff --git a/skills/gpumdkit-visualization/SKILL.md b/skills/gpumdkit-visualization/SKILL.md
index 60bb237..a800e52 100644
--- a/skills/gpumdkit-visualization/SKILL.md
+++ b/skills/gpumdkit-visualization/SKILL.md
@@ -21,7 +21,7 @@ gpumdkit.sh -plt <type> -h           # Get help for specific plot
 
 ## Plot Categories
 
-### NEP Training & Evaluation (12 plot types)
+### NEP Training & Evaluation (13 plot types)
 
 | Command | Input Files | Description |
 |---------|-------------|-------------|
@@ -53,7 +53,7 @@ gpumdkit.sh -plt des umap
 gpumdkit.sh -plt dimer Li Li nep.txt
 ```
 
-### Transport Properties (9 plot types)
+### Transport Properties (10 plot types)
 
 | Command | Input Files | Description |
 |---------|-------------|-------------|
@@ -66,6 +66,7 @@ gpumdkit.sh -plt dimer Li Li nep.txt
 | `D` / `arrhenius_d` | `*K/` directories | Arrhenius diffusivity |
 | `sigma_xyz` | `*K/` directories | Directional Arrhenius conductivity |
 | `D_xyz` | `*K/` directories | Directional Arrhenius diffusivity |
+| `doas` | `doas.out` | Density of atomistic states |
 
 ```bash
 # MSD and diffusion
@@ -80,9 +81,12 @@ gpumdkit.sh -plt msd_all Li P S
 # Directory structure: 300K/, 350K/, 400K/, ... each containing msd.out
 gpumdkit.sh -plt arrhenius_sigma
 gpumdkit.sh -plt arrhenius_d
+
+# DOAS visualization (requires prior calculation)
+gpumdkit.sh -plt doas doas.out Li
 ```
 
-### Structural Analysis (10 plot types)
+### Structural Analysis (9 plot types)
 
 | Command | Input Files | Description |
 |---------|-------------|-------------|
@@ -94,7 +98,6 @@ gpumdkit.sh -plt arrhenius_d
 | `vac` | `sdc.out` | Velocity autocorrelation |
 | `cohesive` | `cohesive.out` | Cohesive energy curve |
 | `net_force` | extxyz file | Net force distribution |
-| `doas` | `doas.out` | Density of atomistic states |
 | `plane-grid` | `model.xyz`, `displacements.dat` | Displacement grid visualization |
 
 ```bash
@@ -106,9 +109,6 @@ gpumdkit.sh -plt rdf
 gpumdkit.sh -plt rdf 2              # Specific column
 gpumdkit.sh -plt rdf_pmf 300        # With PMF at 300K
 
-# DOAS visualization (requires prior calculation)
-gpumdkit.sh -plt doas doas.out Li
-
 # Plane-grid displacement
 gpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Pb Sr
 ```
diff --git a/src/README.md b/src/README.md
index 3c2cce6..ccc04d0 100644
--- a/src/README.md
+++ b/src/README.md
@@ -117,12 +117,13 @@ then you will see:
 
         GPUMDkit Version 1.5.6 (dev) (2026-06-17)
   Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)
+ Main Contributors: Denan LI, Xin WU, Zhoulin LIU & Chen HUA
 
  ----------------------- GPUMD -----------------------
   1) Format Conversion          2) Sample Structures
   3) Workflow                   4) Calculators
   5) Analyzer                   6) Visualization
-  7) Utilities                  8) Developing...
+  7) Utilities                  8) Help                
   0) Exit
  ------------>>
  Input the function number:
diff --git a/src/f1_format_conversions.sh b/src/f1_format_conversions.sh
index 6b25908..bf07a8b 100644
--- a/src/f1_format_conversions.sh
+++ b/src/f1_format_conversions.sh
@@ -16,7 +16,7 @@ echo " >-------------------------------------------------<"
 echo " Input the directory containing OUTCARs"
 echo " Example: ./ "
 echo " ------------>>"
-read -p " " dir_outcars
+read_menu_choice dir_outcars || return 1
 echo " ---------------------------------------------------"
 bash ${GPUMDkit_path}/Scripts/format_conversion/out2xyz.sh ${dir_outcars}
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/out2xyz.sh"
@@ -33,7 +33,7 @@ echo " >-------------------------------------------------<"
 echo " Input <filename.cfg> <Symbol1 Symbol2 Symbol3 ...>"
 echo " Example: train.cfg Pd Ag"
 echo " ------------>>"
-read -p " " mtp_variables
+read_menu_choice mtp_variables || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/mtp2xyz.py ${mtp_variables}
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/mtp2xyz.py"
@@ -64,7 +64,7 @@ echo " | Developer: Ke XU (kickhsu@gmail.com)            |"
 echo " >-------------------------------------------------<"
 echo " Input [pos.xyz] [frc.xyz] [cell.cell] [-shifted yes/no] "
 echo " ------------>>"
-read -p " " cp2k_choice
+read_menu_choice cp2k_choice || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/cp2k2xyz.py ${cp2k_choice}
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/cp2k2xyz.py"
@@ -139,7 +139,7 @@ echo " >-------------------------------------------------<"
 echo " Input the name of extxyz"
 echo " Example: ./train.xyz "
 echo " ------------>>"
-read -p " " filename
+read_menu_choice filename || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/exyz2pos.py ${filename}
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/exyz2pos.py"
@@ -156,7 +156,7 @@ echo " >-------------------------------------------------<"
 echo " Input <POSCAR> <element1> <element2> ..."
 echo " Example: POSCAR Li Y Cl"
 echo " ------------>>"
-read -r -a addgroup_args
+read_menu_array addgroup_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/add_groups.py "${addgroup_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/add_groups.py"
@@ -173,7 +173,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> <output.xyz> <weight>"
 echo " Example: train.xyz train_weighted.xyz 5"
 echo " ------------>>"
-read -r -a addweight_args
+read_menu_array addweight_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/add_weight.py "${addweight_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/add_weight.py"
@@ -190,7 +190,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> <frame_number>"
 echo " Example: train.xyz 1"
 echo " ------------>>"
-read -r -a getframe_args
+read_menu_array getframe_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/get_frame.py "${getframe_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/get_frame.py"
@@ -207,7 +207,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.xyz> <output.xyz>"
 echo " Example: train.xyz train_clean.xyz"
 echo " ------------>>"
-read -r -a cleanxyz_args
+read_menu_array cleanxyz_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/clean_xyz.py "${cleanxyz_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/clean_xyz.py"
@@ -225,7 +225,7 @@ echo " Input <inputfile> <outputfile> <a b c / target_num>"
 echo " Example 1: POSCAR POSCAR_222.vasp 2 2 2"
 echo " Example 2: POSCAR POSCAR_256.vasp 256"
 echo " ------------>>"
-read -r -a replicate_args
+read_menu_array replicate_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/replicate.py "${replicate_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/replicate.py"
@@ -242,7 +242,7 @@ echo " >-------------------------------------------------<"
 echo " Input the directory containing OUTCARs"
 echo " Example: ./ "
 echo " ------------>>"
-read -r -p " " dir_outcars
+read_menu_choice dir_outcars || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/out2exyz.py "${dir_outcars}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/out2exyz.py"
@@ -259,7 +259,7 @@ echo " >-------------------------------------------------<"
 echo " Input <POSCAR> <output.xyz>"
 echo " Example: POSCAR model.xyz"
 echo " ------------>>"
-read -r -a pos2extxyz_args
+read_menu_array pos2extxyz_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/pos2exyz.py "${pos2extxyz_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/pos2exyz.py"
@@ -276,7 +276,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.cif> <output.vasp>"
 echo " Example: input.cif POSCAR.vasp"
 echo " ------------>>"
-read -r -a cif2pos_args
+read_menu_array cif2pos_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/cif2pos.py "${cif2pos_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/cif2pos.py"
@@ -293,7 +293,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.cif> <output.xyz>"
 echo " Example: input.cif model.xyz"
 echo " ------------>>"
-read -r -a cif2extxyz_args
+read_menu_array cif2extxyz_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/cif2exyz.py "${cif2extxyz_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/cif2exyz.py"
@@ -310,7 +310,7 @@ echo " >-------------------------------------------------<"
 echo " Input <XDATCAR> <output.xyz>"
 echo " Example: XDATCAR dump.xyz"
 echo " ------------>>"
-read -r -a xdatcar_args
+read_menu_array xdatcar_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/xdatcar2exyz.py "${xdatcar_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/xdatcar2exyz.py"
@@ -327,7 +327,7 @@ echo " >-------------------------------------------------<"
 echo " Input <POSCAR> <lammps.data>"
 echo " Example: POSCAR lammps.data"
 echo " ------------>>"
-read -r -a pos2lmp_args
+read_menu_array pos2lmp_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/pos2lmp.py "${pos2lmp_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/pos2lmp.py"
@@ -344,7 +344,7 @@ echo " >-------------------------------------------------<"
 echo " Input <dump_file> <element1> <element2> ..."
 echo " Example: dump.lammpstrj Li O"
 echo " ------------>>"
-read -r -a lmp2extxyz_args
+read_menu_array lmp2extxyz_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/lmp2exyz.py "${lmp2extxyz_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/lmp2exyz.py"
@@ -361,7 +361,7 @@ echo " >-------------------------------------------------<"
 echo " Input <input.traj> <output.xyz>"
 echo " Example: input.traj output.xyz"
 echo " ------------>>"
-read -r -a traj2extxyz_args
+read_menu_array traj2extxyz_args || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/format_conversion/traj2exyz.py "${traj2extxyz_args[@]}"
 echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/traj2exyz.py"
diff --git a/src/f2_sample_structures.sh b/src/f2_sample_structures.sh
index 64020e4..471aa80 100644
--- a/src/f2_sample_structures.sh
+++ b/src/f2_sample_structures.sh
@@ -18,7 +18,7 @@ echo " [skip_num]: number of initial frames to skip, default value is 0"
 echo " Sampling_method: 'uniform' or 'random'"
 echo " Example: train.xyz uniform 50 "
 echo " ------------>>"
-read -p " " sample_choice
+read_menu_choice sample_choice || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/sample_structures/sample_structures.py ${sample_choice}
 echo " Code path: ${GPUMDkit_path}/Scripts/sample_structures/sample_structures.py"
@@ -55,7 +55,7 @@ echo " Input <sample.xyz> <train.xyz> <nep_model> <threads>"
 echo " Example: dump.xyz train.xyz nep.txt 8"
 echo " <threads>: number of CPU threads to use"
 echo " ------------>>"
-read -p " " sample_choice
+read_menu_choice sample_choice || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/sample_structures/parallel_pynep_select_structs.py ${sample_choice}
 echo " Code path: ${GPUMDkit_path}/Scripts/sample_structures/parallel_pynep_select_structs.py"
@@ -72,7 +72,7 @@ echo " >-------------------------------------------------<"
 echo " Input <sample.xyz> <train.xyz> <nep_model>"
 echo " Example: dump.xyz train.xyz nep.txt "
 echo " ------------>>"
-read -p " " sample_choice
+read_menu_choice sample_choice || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/sample_structures/neptrain_select_structs.py ${sample_choice}
 rm -f dpdispatcher.log
@@ -97,7 +97,7 @@ echo " Input <input.vasp> <pert_num> <cell_pert_fraction> <atom_pert_distance> <
 echo " The default parameters for perturb are 20 0.03 0.2 uniform"
 echo " Example: POSCAR 20 0.03 0.2 uniform"
 echo " ------------>>"
-read -p " " perturb_choice
+read_menu_choice perturb_choice || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/sample_structures/perturb_structure.py ${perturb_choice}
 echo " Code path: ${GPUMDkit_path}/Scripts/sample_structures/perturb_structure.py"
@@ -117,7 +117,7 @@ echo " |     generated by the active command in gpumd.      |"
 echo " +----------------------------------------------------+"
 echo " Input <structs_num> <threshold> (eg. 200 0.15)"
 echo " ------------>>"
-read -p " " modev_choice
+read_menu_choice modev_choice || return 1
 echo " ---------------------------------------------------"
 python ${GPUMDkit_path}/Scripts/sample_structures/select_max_modev.py ${modev_choice}
 echo " Code path: ${GPUMDkit_path}/Scripts/sample_structures/select_max_modev.py"
diff --git a/src/f5_analyzers.sh b/src/f5_analyzers.sh
index ff2f176..7be7883 100644
--- a/src/f5_analyzers.sh
+++ b/src/f5_analyzers.sh
@@ -177,9 +177,9 @@ echo " | 000) Return to the main menu                         |"
 echo " +------------------------------------------------------+"
 echo " Input the function number:"
 
-arry_num_choice=("000" "501" "502" "503" "504" "505" "506" "507" "508") 
+valid_menu_choices=("000" "501" "502" "503" "504" "505" "506" "507" "508") 
 read_menu_choice num_choice || return 1
-while ! echo "${arry_num_choice[@]}" | grep -wq "$num_choice" 
+while ! echo "${valid_menu_choices[@]}" | grep -wq "$num_choice" 
 do
   echo " ------------>>"
   echo " Please reinput function number..."
diff --git a/src/f6_plots.sh b/src/f6_plots.sh
index 87cb7e4..dc42a81 100644
--- a/src/f6_plots.sh
+++ b/src/f6_plots.sh
@@ -90,6 +90,7 @@ function f6_plots_two_column(){
     echo " |  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|"
     echo " |  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |"
     echo " |  D_xyz          - Directional Arrhenius D                                                     |"
+    echo " |  doas           - Density of atomistic states                                                 |"
     echo " +-----------------------------------------------------------------------------------------------+"
     echo " |                                    MD & Structural Analysis                                   |"
     echo " +-----------------------------------------------------------------------------------------------+"
@@ -97,7 +98,6 @@ function f6_plots_two_column(){
     echo " |  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |"
     echo " |  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |"
     echo " |  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |"
-    echo " |  doas           - Density of atomistic states                                                 |"
     echo " +-----------------------------------------------------------------------------------------------+"
     echo " |                                        Heat Transport                                         |"
     echo " +-----------------------------------------------------------------------------------------------+"

From 065ec4c6f07c5112522eca538ffbfa9499786db8 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Wed, 1 Jul 2026 17:34:05 +0800
Subject: [PATCH 16/24] update

---
 docs/htmls/en/active_learning_workflow.html   |  20 +--
 docs/htmls/en/command_reference.html          |   2 +-
 docs/htmls/en/custom_commands.html            |   2 +-
 docs/htmls/en/plot_scripts.html               |  67 +++------
 docs/htmls/en/quick_start.html                |  58 ++++++--
 docs/htmls/search/search_index.json           |   2 +-
 ...\345\267\245\344\275\234\346\265\201.html" |  18 +--
 ...\344\273\244\345\217\202\350\200\203.html" |   2 +-
 ...\351\200\237\345\205\245\351\227\250.html" |  58 ++++++--
 ...\345\274\217\350\275\254\346\215\242.html" |   4 +
 ...\345\233\276\350\204\232\346\234\254.html" |  69 ++++------
 ...\344\271\211\345\221\275\344\273\244.html" |   2 +
 ...\347\214\256\346\214\207\345\215\227.html" | 114 ++++++++--------
 docs/mkdocs.yml                               |   1 +
 docs/tutorials/en/index.md                    |   1 -
 docs/tutorials/en/troubleshooting.md          | 128 ------------------
 docs/tutorials/zh/index.md                    |   1 -
 ...05\351\232\234\346\216\222\351\231\244.md" | 128 ------------------
 ...41\347\214\256\346\214\207\345\215\227.md" |  28 ++--
 19 files changed, 246 insertions(+), 459 deletions(-)
 delete mode 100644 docs/tutorials/en/troubleshooting.md
 delete mode 100644 "docs/tutorials/zh/\346\225\205\351\232\234\346\216\222\351\231\244.md"

diff --git a/docs/htmls/en/active_learning_workflow.html b/docs/htmls/en/active_learning_workflow.html
index fe2ad79..ef4662c 100644
--- a/docs/htmls/en/active_learning_workflow.html
+++ b/docs/htmls/en/active_learning_workflow.html
@@ -1609,35 +1609,35 @@ <h2 id="3-variable-definitions">3. <strong>Variable Definitions</strong></h2>
 </ul>
 <hr />
 <h2 id="4-check-required-files">4. <strong>Check Required Files</strong></h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ -f run.in ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ &quot;$(find . -maxdepth 1 -name &#39;run_*.in&#39; | wc -l)&quot; -ge 1 ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then
 <a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>    # Check for the required files before proceeding.
 <a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>else
-<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>    echo &quot;Please put nep.in nep.txt train.xyz run.in INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.&quot;
+<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>    echo &quot;Please put nep.in nep.txt train.xyz run_*.in (eg. run_1.in, run_2.in, ...) INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.&quot;
 <a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a>    exit 1
 <a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>fi
 </code></pre></div>
-<p>Make sure the necessary files (<code>nep.txt</code>, <code>nep.in</code>, <code>train.xyz</code>, <code>run.in</code>, <code>INCAR</code>, <code>POTCAR</code>, <code>KPOINTS</code>) are available in the working directory. If any of these are missing, the script will terminate. <code>train.xyz</code> and <code>nep.txt</code> are used for <code>pynep</code> sampling, and <code>run.in</code> is the simulation parameters of MD in the current iteration.</p>
+<p>Make sure the necessary files (<code>nep.txt</code>, <code>nep.in</code>, <code>train.xyz</code>, <code>run_*.in</code> (e.g., <code>run_1.in</code>, <code>run_2.in</code>, ...), <code>INCAR</code>, <code>POTCAR</code>, <code>KPOINTS</code>) are available in the working directory. If any of these are missing, the script will terminate. <code>train.xyz</code> and <code>nep.txt</code> are always required as prerequisites for NEP model operation, and <code>run_*.in</code> files define the simulation parameters of MD in the current iteration.</p>
 <hr />
 <h2 id="5-file-organization">5. <strong>File Organization</strong></h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>mkdir 00.modev common
-<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>mv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common
-<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>cp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev
+<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>mkdir 00.md common
+<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>mv ${work_dir}/{nep.txt,nep.in,*.xyz,run_*.in,INCAR,KPOINTS,POTCAR} ./common
+<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>cp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.md
 </code></pre></div>
 <p>The script organizes the working files into two folders:</p>
 <ul>
-<li><code>00.modev</code>: For molecular dynamics simulation.</li>
-<li><code>common</code>: For shared resources such as <code>nep.txt</code>, <code>run.in</code>, and the structure files, etc.</li>
+<li><code>00.md</code>: For molecular dynamics simulation.</li>
+<li><code>common</code>: For shared resources such as <code>nep.txt</code>, <code>run_*.in</code> files, and the structure files, etc.</li>
 </ul>
 <hr />
 <h2 id="6-molecular-dynamics-simulation-submission">6. <strong>Molecular Dynamics Simulation Submission</strong></h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>submit_gpumd_array modev ${sample_struct_num}
+<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>submit_gpumd_array md ${sample_struct_num}
 <a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>sbatch submit.slurm
 </code></pre></div>
 <p>After preparing the input files, the script submits an array of molecular dynamics (MD) tasks using <code>submit_gpumd_array</code>.</p>
 <hr />
 <h2 id="7-monitoring-task-completion">7. <strong>Monitoring Task Completion</strong></h2>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>while true; do
-<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>    logs=$(find &quot;${work_dir}/00.modev/&quot; -type f -name log -path &quot;*/sample_*/log&quot;)
+<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>    logs=$(find &quot;${work_dir}/00.md/&quot; -type f -name log -path &quot;*/sample_*/log&quot;)
 <a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>    finished_tasks_md=$(grep &quot;Finished running GPUMD.&quot; $logs | wc -l)
 <a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a>    error_tasks_md=$(grep &quot;Error&quot; $logs | wc -l)
 <a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>
diff --git a/docs/htmls/en/command_reference.html b/docs/htmls/en/command_reference.html
index 897633e..ecfaf34 100644
--- a/docs/htmls/en/command_reference.html
+++ b/docs/htmls/en/command_reference.html
@@ -1718,7 +1718,7 @@ <h2 id="visualization">Visualization</h2>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span><span class="o">[</span>options<span class="o">]</span>
 <a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>-h
 </code></pre></div>
-<p>Common types include <code>train</code>, <code>prediction</code>, <code>thermo</code>, <code>msd</code>, <code>sdc</code>, <code>rdf</code>, <code>emd</code>, <code>nemd</code>, <code>hnemd</code>, <code>pdos</code>, and <code>plane-grid</code>.</p>
+<p>Common types include <code>train</code>, <code>prediction</code> (alias: <code>test</code>), <code>thermo</code>, <code>msd</code>, <code>sdc</code>, <code>rdf</code>, <code>emd</code>, <code>nemd</code>, <code>hnemd</code>, <code>pdos</code>, and <code>plane-grid</code>.</p>
 <h2 id="utilities">Utilities</h2>
 <table>
 <thead>
diff --git a/docs/htmls/en/custom_commands.html b/docs/htmls/en/custom_commands.html
index b72fd19..da64d4f 100644
--- a/docs/htmls/en/custom_commands.html
+++ b/docs/htmls/en/custom_commands.html
@@ -1502,7 +1502,7 @@ <h2 id="setup">Setup</h2>
 <p>Define custom functions with the <code>custom_</code> prefix.</p>
 <h2 id="examples">Examples</h2>
 <h3 id="simple-greeting">Simple Greeting</h3>
-<p>Write the following codes in your <code>~/.gpumdkit.in</code> </p>
+<p>Write the following code in your <code>~/.gpumdkit.in</code> </p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>custom_hello<span class="o">()</span><span class="w"> </span><span class="o">{</span>
 <a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Hello, GPUMDkit user! This is a custom command.&quot;</span>
 <a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="w">    </span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Current GPUMDkit path: </span><span class="si">${</span><span class="nv">GPUMDkit_path</span><span class="si">}</span><span class="s2">&quot;</span>
diff --git a/docs/htmls/en/plot_scripts.html b/docs/htmls/en/plot_scripts.html
index 4a26f0e..5f29bdc 100644
--- a/docs/htmls/en/plot_scripts.html
+++ b/docs/htmls/en/plot_scripts.html
@@ -1076,17 +1076,6 @@
     </span>
   </a>
   
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#plt_descriptors_comparepy" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        plt_descriptors_compare.py
-      
-    </span>
-  </a>
-  
 </li>
         
           <li class="md-nav__item">
@@ -2128,17 +2117,6 @@
     </span>
   </a>
   
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#plt_descriptors_comparepy" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        plt_descriptors_compare.py
-      
-    </span>
-  </a>
-  
 </li>
         
           <li class="md-nav__item">
@@ -2244,20 +2222,24 @@ <h2 id="quick-access">Quick Access</h2>
 <a id="__codelineno-1-19" name="__codelineno-1-19" href="#__codelineno-1-19"></a>|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|
 <a id="__codelineno-1-20" name="__codelineno-1-20" href="#__codelineno-1-20"></a>|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |
 <a id="__codelineno-1-21" name="__codelineno-1-21" href="#__codelineno-1-21"></a>|  D_xyz          - Directional Arrhenius D                                                     |
-<a id="__codelineno-1-22" name="__codelineno-1-22" href="#__codelineno-1-22"></a>+-----------------------------------------------------------------------------------------------+
-<a id="__codelineno-1-23" name="__codelineno-1-23" href="#__codelineno-1-23"></a>|                                    MD &amp; Structural Analysis                                   |
-<a id="__codelineno-1-24" name="__codelineno-1-24" href="#__codelineno-1-24"></a>+-----------------------------------------------------------------------------------------------+
-<a id="__codelineno-1-25" name="__codelineno-1-25" href="#__codelineno-1-25"></a>|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |
-<a id="__codelineno-1-26" name="__codelineno-1-26" href="#__codelineno-1-26"></a>|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
-<a id="__codelineno-1-27" name="__codelineno-1-27" href="#__codelineno-1-27"></a>|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
-<a id="__codelineno-1-28" name="__codelineno-1-28" href="#__codelineno-1-28"></a>|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
-<a id="__codelineno-1-29" name="__codelineno-1-29" href="#__codelineno-1-29"></a>|  doas           - Density of atomistic states                                                 |
+<a id="__codelineno-1-22" name="__codelineno-1-22" href="#__codelineno-1-22"></a>|  doas           - Density of atomistic states                                                 |
+<a id="__codelineno-1-23" name="__codelineno-1-23" href="#__codelineno-1-23"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-24" name="__codelineno-1-24" href="#__codelineno-1-24"></a>|                                    MD &amp; Structural Analysis                                   |
+<a id="__codelineno-1-25" name="__codelineno-1-25" href="#__codelineno-1-25"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-26" name="__codelineno-1-26" href="#__codelineno-1-26"></a>|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |
+<a id="__codelineno-1-27" name="__codelineno-1-27" href="#__codelineno-1-27"></a>|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
+<a id="__codelineno-1-28" name="__codelineno-1-28" href="#__codelineno-1-28"></a>|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
+<a id="__codelineno-1-29" name="__codelineno-1-29" href="#__codelineno-1-29"></a>|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
 <a id="__codelineno-1-30" name="__codelineno-1-30" href="#__codelineno-1-30"></a>+-----------------------------------------------------------------------------------------------+
 <a id="__codelineno-1-31" name="__codelineno-1-31" href="#__codelineno-1-31"></a>|                                        Heat Transport                                         |
 <a id="__codelineno-1-32" name="__codelineno-1-32" href="#__codelineno-1-32"></a>+-----------------------------------------------------------------------------------------------+
 <a id="__codelineno-1-33" name="__codelineno-1-33" href="#__codelineno-1-33"></a>|  emd            - EMD results                    nemd           - NEMD results                |
 <a id="__codelineno-1-34" name="__codelineno-1-34" href="#__codelineno-1-34"></a>|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |
 <a id="__codelineno-1-35" name="__codelineno-1-35" href="#__codelineno-1-35"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-36" name="__codelineno-1-36" href="#__codelineno-1-36"></a>|                                          Phonons                                              |
+<a id="__codelineno-1-37" name="__codelineno-1-37" href="#__codelineno-1-37"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-38" name="__codelineno-1-38" href="#__codelineno-1-38"></a>|  pdos           - VAC and PDOS                                                                |
+<a id="__codelineno-1-39" name="__codelineno-1-39" href="#__codelineno-1-39"></a>+-----------------------------------------------------------------------------------------------+
 </code></pre></div>
 <hr />
 <h2 id="nep-training-and-prediction">NEP Training and Prediction</h2>
@@ -2612,17 +2594,12 @@ <h3 id="plt_descriptorspy">plt_descriptors.py</h3>
   <img src="../../Gallery/des_umap.png" alt="UMAP descriptor visualization" width="52%" />
 </div>
 
-<hr />
-<h3 id="plt_descriptors_comparepy">plt_descriptors_compare.py</h3>
-<p>Compares descriptors from multiple training sets or models.</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-30-1" name="__codelineno-30-1" href="#__codelineno-30-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des_compare
-</code></pre></div>
 <hr />
 <h3 id="plt_dimerpy">plt_dimer.py</h3>
 <p>Plots dimer interaction curves. Two atoms are placed in a cubic box (30 Å) and the potential energy and force are calculated as a function of dimer distance using a NEP model.</p>
 <p><strong>Input File:</strong> <code>nep.txt</code></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-31-1" name="__codelineno-31-1" href="#__codelineno-31-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>&lt;element1&gt;<span class="w"> </span>&lt;element2&gt;<span class="w"> </span>&lt;nep_model&gt;
-<a id="__codelineno-31-2" name="__codelineno-31-2" href="#__codelineno-31-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span>nep.txt
+<div class="highlight"><pre><span></span><code><a id="__codelineno-30-1" name="__codelineno-30-1" href="#__codelineno-30-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>&lt;element1&gt;<span class="w"> </span>&lt;element2&gt;<span class="w"> </span>&lt;nep_model&gt;
+<a id="__codelineno-30-2" name="__codelineno-30-2" href="#__codelineno-30-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span>nep.txt
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/dimer_nep.png" alt="Dimer NEP curve" width="45%" />
@@ -2634,8 +2611,8 @@ <h3 id="plt_dimerpy">plt_dimer.py</h3>
 <h3 id="plt_doaspy">plt_doas.py</h3>
 <p>Plots density of atomistic states (DOAS) proposed by <a href="https://doi.org/10.1002/anie.202215544">Wang et al.</a>.</p>
 <p><strong>Input File:</strong> <code>doas.out</code> (calculated by <code>gpumdkit.sh -calc doas</code>)</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-32-1" name="__codelineno-32-1" href="#__codelineno-32-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>&lt;doas.out&gt;<span class="w"> </span>&lt;species&gt;
-<a id="__codelineno-32-2" name="__codelineno-32-2" href="#__codelineno-32-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
+<div class="highlight"><pre><span></span><code><a id="__codelineno-31-1" name="__codelineno-31-1" href="#__codelineno-31-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>&lt;doas.out&gt;<span class="w"> </span>&lt;species&gt;
+<a id="__codelineno-31-2" name="__codelineno-31-2" href="#__codelineno-31-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
@@ -2645,16 +2622,16 @@ <h3 id="plt_doaspy">plt_doas.py</h3>
 <h2 id="plane-grid-plot-for-polar-materials">Plane-Grid Plot for Polar Materials</h2>
 <p>This workflow maps displacement or polarization data onto a grid and plots selected plane profiles. For detailed usage and real-world examples, see <strong><a href="polar_material_analysis.html">Polar Material Analysis</a></strong>.</p>
 <p><strong>Dependency:</strong></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-33-1" name="__codelineno-33-1" href="#__codelineno-33-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
+<div class="highlight"><pre><span></span><code><a id="__codelineno-32-1" name="__codelineno-32-1" href="#__codelineno-32-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
 </code></pre></div>
 <p><strong>Typical upstream steps:</strong></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-34-1" name="__codelineno-34-1" href="#__codelineno-34-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span><span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
-<a id="__codelineno-34-2" name="__codelineno-34-2" href="#__codelineno-34-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Pb_Sr-O.dat<span class="w"> </span>-o<span class="w"> </span>displacements.dat
-<a id="__codelineno-34-3" name="__codelineno-34-3" href="#__codelineno-34-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-33-1" name="__codelineno-33-1" href="#__codelineno-33-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span><span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
+<a id="__codelineno-33-2" name="__codelineno-33-2" href="#__codelineno-33-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Pb_Sr-O.dat<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+<a id="__codelineno-33-3" name="__codelineno-33-3" href="#__codelineno-33-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
 </code></pre></div>
 <p><strong>Usage:</strong></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-35-1" name="__codelineno-35-1" href="#__codelineno-35-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr
-<a id="__codelineno-35-2" name="__codelineno-35-2" href="#__codelineno-35-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-34-1" name="__codelineno-34-1" href="#__codelineno-34-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr
+<a id="__codelineno-34-2" name="__codelineno-34-2" href="#__codelineno-34-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span>
 </code></pre></div>
 <hr />
 <h2 id="quick-reference-table">Quick Reference Table</h2>
diff --git a/docs/htmls/en/quick_start.html b/docs/htmls/en/quick_start.html
index 006095f..cd00ff6 100644
--- a/docs/htmls/en/quick_start.html
+++ b/docs/htmls/en/quick_start.html
@@ -541,6 +541,17 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#hello-world-example" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Hello World Example
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1484,6 +1495,17 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#hello-world-example" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Hello World Example
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1672,7 +1694,7 @@ <h2 id="interactive-mode">Interactive mode</h2>
 <a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a> 1) Format Conversion          2) Sample Structures
 <a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a> 3) Workflow                   4) Calculators
 <a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a> 5) Analyzer                   6) Visualization
-<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a> 7) Utilities                  8) Developing...
+<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a> 7) Utilities                  8) Help                
 <a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a> 0) Exit
 <a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a> ------------&gt;&gt;
 <a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a> Input the function number:
@@ -1688,38 +1710,58 @@ <h2 id="cli-mode">CLI mode</h2>
 <a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>trajectory.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
 </code></pre></div>
 <p>The first example reads <code>POSCAR</code> and writes <code>model.xyz</code>.</p>
+<h2 id="hello-world-example">Hello World Example</h2>
+<p>A minimal end-to-end check that your install works — create a tiny silicon POSCAR, convert it to extxyz, and inspect the output:</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>cat<span class="w"> </span>&gt;<span class="w"> </span>POSCAR<span class="w"> </span><span class="s">&lt;&lt; &#39;EOF&#39;</span>
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a><span class="s">Si</span>
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a><span class="s">1.0</span>
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="s">0 2.715 2.715</span>
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a><span class="s">2.715 0 2.715</span>
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a><span class="s">2.715 2.715 0</span>
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a><span class="s">Si</span>
+<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a><span class="s">1</span>
+<a id="__codelineno-10-9" name="__codelineno-10-9" href="#__codelineno-10-9"></a><span class="s">direct</span>
+<a id="__codelineno-10-10" name="__codelineno-10-10" href="#__codelineno-10-10"></a><span class="s">0 0 0</span>
+<a id="__codelineno-10-11" name="__codelineno-10-11" href="#__codelineno-10-11"></a><span class="s">EOF</span>
+<a id="__codelineno-10-12" name="__codelineno-10-12" href="#__codelineno-10-12"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<a id="__codelineno-10-13" name="__codelineno-10-13" href="#__codelineno-10-13"></a>head<span class="w"> </span>model.xyz
+</code></pre></div>
+<p>If <code>model.xyz</code> shows a single Si atom with lattice info, your install works.</p>
+<blockquote>
+<p><strong>What is extxyz?</strong> extxyz is the extended XYZ format: line 1 is the atom count, line 2 contains the lattice and per-structure properties (energy/forces/virial as needed), and lines 3+ list each atom with its per-atom properties. It is the native training-data format for NEP.</p>
+</blockquote>
 <h2 id="common-examples">Common examples</h2>
 <h3 id="convert-a-poscar-to-extxyz">Convert a POSCAR to extxyz</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
 </code></pre></div>
 <h3 id="add-gpumd-group-labels">Add GPUMD group labels</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
 </code></pre></div>
 <p>Group labels are used by some GPUMD-related workflows that need atom grouping, such as species-specific MSD or diffusion calculations.</p>
 <h3 id="plot-nep-training-results">Plot NEP training results</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/train.png" alt="NEP training results" width="72%" />
 </div>
 
 <h3 id="plot-nep-test-results">Plot NEP test results</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/prediction.png" alt="NEP test results" width="72%" />
 </div>
 
 <h3 id="plot-thermodynamic-data">Plot thermodynamic data</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/thermo.png" alt="Thermo plot" width="72%" />
 </div>
 
 <h3 id="plot-msd-and-self-diffusion-coefficient">Plot MSD and self-diffusion coefficient</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
-<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
diff --git a/docs/htmls/search/search_index.json b/docs/htmls/search/search_index.json
index 0d1ff60..0632bd3 100644
--- a/docs/htmls/search/search_index.json
+++ b/docs/htmls/search/search_index.json
@@ -1 +1 @@
-{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"],"fields":{"title":{"boost":1000.0},"text":{"boost":1.0},"tags":{"boost":1000000.0}}},"docs":[{"location":"index.html","title":"Home","text":"\ud83d\udcda GPUMDkit Documentation <p>A practical bilingual tutorial for GPUMDkit, covering installation, command-line tools, interactive workflows, plotting, and analysis utilities.</p>"},{"location":"index.html#language","title":"Language","text":"Language Start Here Command Reference English GPUMDkit Tutorials Command Reference \u7b80\u4f53\u4e2d\u6587 GPUMDkit \u6559\u7a0b \u547d\u4ee4\u53c2\u8003"},{"location":"index.html#what-you-can-learn-here","title":"What You Can Learn Here","text":"<p>This documentation is organized as a practical tutorial rather than only a command list. New users are encouraged to start from the overview and quick start pages, then move to the topic that matches their task.</p> Topic What it Covers Quick Start Installation, environment setup, interactive mode, direct command mode Format Conversion VASP, LAMMPS, CP2K, ABACUS, CIF, extxyz, group labels, weights Sampling Uniform/random sampling, NepTrain FPS, perturbation, force-deviation selection Calculators MSD, ionic conductivity, NEP prediction, descriptors, DOAS, NEB, polarization tools Analyzers Composition checks, distance checks, filters, property range analysis Visualization NEP training plots, MD plots, transport plots, thermal transport plots, example figures Workflows Batch DFT/MD processing and active-learning style workflows <p>For complex operations, use the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>For common operations with fixed arguments, use direct command-line mode:</p> <pre><code>gpumdkit.sh -h\ngpumdkit.sh -plt -h\ngpumdkit.sh -calc -h\n</code></pre>"},{"location":"en/index.html","title":"GPUMDkit Tutorials","text":"\ud83d\udcda GPUMDkit Tutorials <p>Welcome to GPUMDkit, a command-line toolkit for GPUMD and NEP.</p>"},{"location":"en/index.html#what-it-does","title":"What it does","text":"<p>GPUMDkit helps you perform common tasks in computational materials science without writing custom scripts. It supports format conversion, structure analysis, property calculation, visualization, and batch workflows \u2014 all from one command-line tool.</p>"},{"location":"en/index.html#common-tasks","title":"Common Tasks","text":"I want to... Tutorial Install GPUMDkit and run my first command Quick Start Convert VASP, LAMMPS, CP2K, or CIF files to extxyz Format Conversion Check structure distances, filter datasets, or find outliers Analyzer Scripts Calculate MSD, ionic conductivity, or descriptors Calculator Scripts Analyze polar materials, ferroelectrics, or ABO3 systems Polar Material Analysis Plot NEP training results or thermodynamic data Plot Scripts Run batch DFT or MD simulations Workflow Scripts Select representative structures from a dataset Structure Sampling Add my own shortcuts to GPUMDkit Custom Commands"},{"location":"en/index.html#before-you-start","title":"Before you start","text":""},{"location":"en/index.html#installation","title":"Installation","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"en/index.html#dependencies","title":"Dependencies","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"en/index.html#interactive-mode","title":"Interactive mode","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>This opens a menu where you can select modules by number.</p>"},{"location":"en/index.html#cli-mode","title":"CLI mode","text":"<pre><code>gpumdkit.sh -&lt;option&gt; [args...]\n</code></pre> <p>For example:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>Use <code>gpumdkit.sh -h</code> to see all available options.</p>"},{"location":"en/index.html#module-overview","title":"Module Overview","text":"Module Menu CLI Description Format Conversion 1 <code>-out2xyz</code>, <code>-pos2exyz</code> File conversion Sample Structures 2 interactive menu, <code>-frame_range</code>, <code>-pynep</code> (deprecated) Structure sampling Workflow 3 - Batch processing Calculators 4 <code>-calc &lt;type&gt;</code> Property calculations Analyzer 5 <code>-range</code>, <code>-min_dist</code> Structure analysis Visualization 6 <code>-plt &lt;type&gt;</code> Plotting tools Utilities 7 <code>-time</code>, <code>-clean</code> Utility functions"},{"location":"en/index.html#all-tutorials","title":"All Tutorials","text":"Tutorial Description Quick Start Installation and first steps Command Reference One-page CLI and menu reference Format Conversion Convert between file formats Calculator Scripts Compute material properties Analyzer Scripts Structure analysis and validation Plot Scripts Plotting and visualization Workflow Scripts Batch processing and automation Structure Sampling Structure selection methods Custom Commands User-defined GPUMDkit shortcuts Active Learning Workflow Batch active-learning workflow notes Polar Material Analysis Ferroelectric and polarization tools Contributing to GPUMDkit Development notes"},{"location":"en/index.html#links","title":"Links","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>Documentation: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"en/active_learning_workflow.html","title":"Active Learning Workflow","text":"\ud83d\udd01 Active Learning Workflow <p>This tutorial explains the steps and considerations involved in the <code>workflow_active_learning_dev.sh</code> script. The workflow is used to generate, select, and analyze molecular structures, followed by simulations and data collection.</p> <p>Script Location: <code>Scripts/workflow/</code></p>"},{"location":"en/active_learning_workflow.html#overview","title":"Overview","text":"<p>This script automates one iteration of NEP active learning. The typical workflow includes:</p> Step Action Purpose 1 Run MD simulations Generate candidate structures with current NEP model 2 Filter structures Remove unphysical configurations (short distances, large boxes) 3 Sample structures Select diverse or uncertain structures for DFT 4 Run SCF calculations Compute DFT reference energies/forces 5 NEP prediction Check model accuracy on new structures <p>Unlike menu-driven modules, this workflow is a shell script that you customize and run directly:</p> <pre><code>bash Scripts/workflow/workflow_active_learning_dev.sh\n</code></pre> <p>The sections below explain the main blocks in the script and what each part does.</p>"},{"location":"en/active_learning_workflow.html#1-slurm-directives","title":"1. SLURM Directives","text":"<pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>The SLURM directives are used to define how the job will be submitted to the cluster:</p> <ul> <li><code>#SBATCH -p</code> defines the partition, in this case, it's <code>intel-sc3</code> and <code>intel-sc3-32c</code>.</li> <li><code>#SBATCH -q</code> specifies the queue, in this case, <code>huge</code>.</li> <li><code>#SBATCH -N</code> allocates 1 node for the job.</li> <li><code>#SBATCH -J</code> names the job <code>workflow</code>.</li> <li><code>#SBATCH -o</code> defines the output log file as <code>workflow.log</code>.</li> <li><code>--ntasks-per-node=1</code> specifies that only one task should run per node.</li> </ul> <p>NOTE: If your machine does not have the SLURM environment, you can also run the script directly from the command line. For example:</p> <pre><code>nohup bash workflow_active_learning_dev.sh &amp;&gt;workflow.log &amp;\n</code></pre>"},{"location":"en/active_learning_workflow.html#2-basic-setup","title":"2. Basic Setup","text":"<pre><code>cd $SLURM_SUBMIT_DIR \n</code></pre> <p>Ensure the working directory is correct, and that all necessary files are present for the job.</p> <pre><code>source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  # Load the submit template\npython_pynep=python  # Python executable for the deprecated pynep branch if needed\n</code></pre> <ul> <li><code>GPUMDkit_path</code> is the environment variable that stores the path for the <code>GPUMDkit</code> .</li> <li><code>python_pynep</code> points to the Python environment used for the deprecated <code>pynep</code>-related branch if needed.</li> </ul>"},{"location":"en/active_learning_workflow.html#3-variable-definitions","title":"3. Variable Definitions","text":"<pre><code>work_dir=${PWD}  # Set the working directory\nprefix_name=LiF_iter01  # Prefix for calculations\nmin_dist=1.4  # Minimum atom distance\nbox_limit=13  # Simulation box limit\nmax_fp_num=50  # Maximum number of single point calculations\nsample_method=pynep  # Sampling method (options: uniform, random, pynep)\npynep_sample_dist=0.01  # Sampling distance for pynep\n</code></pre> <p>You can customize:</p> <ul> <li><code>prefix_name</code> to reflect the name of your current work.</li> <li><code>min_dist</code>, <code>box_limit</code>, and <code>max_fp_num</code> based on your own system.</li> <li><code>sample_method</code> (choose between <code>uniform</code>, <code>random</code>, or <code>pynep</code>).</li> <li><code>pynep_sample_dist</code> is the sampling distance for <code>pynep</code>.</li> </ul>"},{"location":"en/active_learning_workflow.html#4-check-required-files","title":"4. Check Required Files","text":"<pre><code>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ -f run.in ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then\n    # Check for the required files before proceeding.\nelse\n    echo \"Please put nep.in nep.txt train.xyz run.in INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.\"\n    exit 1\nfi\n</code></pre> <p>Make sure the necessary files (<code>nep.txt</code>, <code>nep.in</code>, <code>train.xyz</code>, <code>run.in</code>, <code>INCAR</code>, <code>POTCAR</code>, <code>KPOINTS</code>) are available in the working directory. If any of these are missing, the script will terminate. <code>train.xyz</code> and <code>nep.txt</code> are used for <code>pynep</code> sampling, and <code>run.in</code> is the simulation parameters of MD in the current iteration.</p>"},{"location":"en/active_learning_workflow.html#5-file-organization","title":"5. File Organization","text":"<pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <p>The script organizes the working files into two folders:</p> <ul> <li><code>00.modev</code>: For molecular dynamics simulation.</li> <li><code>common</code>: For shared resources such as <code>nep.txt</code>, <code>run.in</code>, and the structure files, etc.</li> </ul>"},{"location":"en/active_learning_workflow.html#6-molecular-dynamics-simulation-submission","title":"6. Molecular Dynamics Simulation Submission","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>After preparing the input files, the script submits an array of molecular dynamics (MD) tasks using <code>submit_gpumd_array</code>.</p>"},{"location":"en/active_learning_workflow.html#7-monitoring-task-completion","title":"7. Monitoring Task Completion","text":"<pre><code>while true; do\n    logs=$(find \"${work_dir}/00.modev/\" -type f -name log -path \"*/sample_*/log\")\n    finished_tasks_md=$(grep \"Finished running GPUMD.\" $logs | wc -l)\n    error_tasks_md=$(grep \"Error\" $logs | wc -l)\n\n    if [ \"$error_tasks_md\" -ne 0 ]; then\n        echo \"Error: MD simulation encountered an error.\"\n        exit 1\n    fi\n    if [ $finished_tasks_md -eq $sample_struct_num ]; then\n        break\n    fi\n    sleep 30\ndone\n</code></pre> <p>The script continuously checks whether all MD tasks have finished by searching for a <code>Finished running GPUMD.</code> message in the logs. If an error is encountered, the script terminates.</p>"},{"location":"en/active_learning_workflow.html#8-analysis-and-filtering","title":"8. Analysis and Filtering","text":"<pre><code>mkdir ${work_dir}/01.select\n...\n</code></pre> <p>In the <code>01.select</code> folder, all structures in the trajectory file <code>dump.xyz</code> during the MD process will be analyzed and filtered to avoid the generation of non-physical structures as much as possible. Specifically, the <code>get_min_dist.py</code>, <code>filter_structures_by_distance.py</code> and <code>filter_exyz_by_box.py</code> scripts will be employed to check whether there are situations where the distance between atoms is too close or the simulated box exceeds the limit value, and such structures will be filtered out.</p>"},{"location":"en/active_learning_workflow.html#9-sampling-methods","title":"9. Sampling Methods","text":"<pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <p>The script supports three sampling methods: <code>uniform</code>, <code>random</code>, and <code>pynep</code>. It selects structures according to the chosen method and checks if the number exceeds <code>max_fp_num</code>, ensuring the final structure count is within limits.</p>"},{"location":"en/active_learning_workflow.html#10-scf-calculations","title":"10. SCF Calculations","text":"<pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>After sampling, SCF calculations are submitted using <code>submit_vasp_array</code>. The process is similar to the MD submission, but for SCF calculations.</p>"},{"location":"en/active_learning_workflow.html#11-prediction-step","title":"11. Prediction Step","text":"<pre><code>submit_nep_prediction\n</code></pre> <p>The final step involves submitting the NEP prediction task to check the accuracy of the NEP model. </p> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/analyzer_scripts.html","title":"Analyzer Scripts","text":"\ud83d\udd0d Analyzer Scripts <p>Analyzer scripts provide structure statistics, distance checks, filters, composition analysis, outlier detection, and time estimation for extxyz datasets.</p>"},{"location":"en/analyzer_scripts.html#what-it-does","title":"What it does","text":"<p>This module helps you inspect, filter, and validate structure datasets. You can check composition, analyze property ranges, detect short contacts, filter structures by various criteria, find outliers in NEP training data, and estimate remaining simulation time.</p>"},{"location":"en/analyzer_scripts.html#before-you-start","title":"Before you start","text":"<p>Script location: <code>Scripts/analyzer/</code></p> <p>Make sure GPUMDkit is installed. See Quick Start for installation instructions.</p>"},{"location":"en/analyzer_scripts.html#overview","title":"Overview","text":"Task Command Purpose Composition <code>gpumdkit.sh -analyze_comp train.xyz</code> Group structures by chemical composition Chemical species <code>gpumdkit.sh -chem_species train.xyz</code> List species in a file Property range <code>gpumdkit.sh -range train.xyz force</code> Inspect energy/force/virial range Minimum distance <code>gpumdkit.sh -min_dist dump.xyz</code> Fast distance check without PBC Minimum distance with PBC <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> Accurate distance check with PBC Charge balance <code>gpumdkit.sh -cbc train.xyz</code> Oxidation-state balance check Distance filter <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> Remove structures with short contacts Box filter <code>gpumdkit.sh -filter_box dump.xyz 13</code> Remove structures with too-large box edges Property filter <code>gpumdkit.sh -filter_value train.xyz force 20</code> Filter by energy/force/virial threshold Pair-distance range <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> Extract structures by pair distance Outlier detection Menu 502 Find high-RMSE structures in training set Probability density <code>gpumdkit.sh -pda &lt;ref&gt; &lt;traj&gt; &lt;element&gt; &lt;interval&gt;</code> 3D probability density for diffusion channels GPUMD time <code>gpumdkit.sh -time gpumd</code> Estimate remaining GPUMD run time NEP time <code>gpumdkit.sh -time nep</code> Estimate remaining NEP training time"},{"location":"en/analyzer_scripts.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit and choose <code>5) Analyzer</code>:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>The analyzer menu is:</p> <pre><code>+------------------------------------------------------+\n|                    ANALYZER TOOLS                    |\n+------------------------------------------------------+\n| 501) Analyze composition of extxyz                   |\n| 502) Find outliers of extxyz                         |\n| 503) Analyze chemical species of extxyz              |\n| 504) Check charge balance of extxyz                  |\n| 505) Analyze energy/force/virial range               |\n| 506) Filter structures by minimum distance           |\n| 507) Get minimum interatomic distance                |\n| 508) Probability density analysis                    |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Most analyzer functions also have direct CLI shortcuts, which are listed in the overview table and in the sections below.</p>"},{"location":"en/analyzer_scripts.html#composition-analysis","title":"Composition Analysis","text":"<p><code>analyze_composition.py</code> analyzes the composition of your extxyz file and lets you export subsets.</p> <p>What it does: Groups structures by chemical composition and shows how many structures belong to each composition. You can export subsets by composition.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>Interactive mode: Choose <code>501</code> from the analyzer menu.</p> <p>Output example:</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>This is useful when <code>train.xyz</code> contains structures from different systems or different cell sizes. You can export a subset by composition from the interactive prompt.</p>"},{"location":"en/analyzer_scripts.html#chemical-species","title":"Chemical Species","text":"<p><code>analyze_chem_species.py</code> lists all unique chemical species in an extxyz file.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -chem_species train.xyz\n</code></pre>"},{"location":"en/analyzer_scripts.html#property-range-analysis","title":"Property Range Analysis","text":"<p><code>energy_force_virial_analyzer.py</code> calculates and visualizes the range of properties from an extxyz file.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <p>Supported properties: <code>energy</code>, <code>force</code>, <code>virial</code></p> <pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist    # Show histogram\n</code></pre> <p>Output example:</p> <pre><code>Force range: 0.03210566767721861 to 9.230115912468435\n</code></pre> <p>With <code>hist</code> option:</p>"},{"location":"en/analyzer_scripts.html#minimum-distance-checks","title":"Minimum Distance Checks","text":""},{"location":"en/analyzer_scripts.html#without-pbc-fast","title":"Without PBC (Fast)","text":"<p><code>get_min_dist.py</code> calculates minimum interatomic distances without considering periodic boundary conditions. Fast but may be inaccurate for periodic systems.</p> <p>What it does: Reports the minimum distance between each pair of elements in every frame, ignoring periodic boundary conditions.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>Interactive mode: Choose <code>507</code> from the analyzer menu.</p> <p>Output example:</p> <pre><code>+---------------------------+\n|   PBC ignored for speed   |\n| use -min_dist_pbc for PBC |\n+---------------------------+\nMinimum interatomic distances:\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.480     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre> <p>Notes: Use this for a quick check. For periodic systems, prefer <code>-min_dist_pbc</code> for accurate results.</p>"},{"location":"en/analyzer_scripts.html#with-pbc-accurate","title":"With PBC (Accurate)","text":"<p><code>get_min_dist_pbc.py</code> calculates minimum interatomic distances considering periodic boundary conditions.</p> <p>What it does: Reports the minimum distance between each pair of elements, accounting for periodic boundary conditions.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>Interactive mode: Choose <code>507</code> from the analyzer menu and answer <code>y</code> when asked whether to consider PBC.</p> <p>Output example:</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre>"},{"location":"en/analyzer_scripts.html#filtering-structures","title":"Filtering Structures","text":""},{"location":"en/analyzer_scripts.html#filter-by-minimum-distance","title":"Filter by Minimum Distance","text":"<p><code>filter_structures_by_distance_pbc.py</code> removes structures with any interatomic distance below a threshold.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>This removes structures with any interatomic distance below <code>1.0 \u00c5</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-box-size","title":"Filter by Box Size","text":"<p><code>filter_exyz_by_box.py</code> filters structures by box-edge length.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>This keeps structures where all box edges are below <code>13 \u00c5</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-property-value","title":"Filter by Property Value","text":"<p><code>filter_exyz_by_value.py</code> filters structures by energy, force, or virial threshold.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <p>Supported properties: <code>energy</code>, <code>force</code>, <code>virial</code></p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre> <p>This filters out structures with force components exceeding <code>20 eV/\u00c5</code> (or energy exceeding <code>5 eV/atom</code>).</p>"},{"location":"en/analyzer_scripts.html#filter-by-pair-distance-range","title":"Filter by Pair-Distance Range","text":"<p><code>filter_dist_range.py</code> extracts structures where a specific element-pair distance falls within a given range.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>This extracts structures where the Li-Li minimum distance is between <code>1.8 \u00c5</code> and <code>2.0 \u00c5</code>. Output: <code>filtered_Li_Li_1.8_2.0.xyz</code>.</p>"},{"location":"en/analyzer_scripts.html#charge-balance-check","title":"Charge Balance Check","text":"<p><code>charge_balance_check.py</code> checks the oxidation-state balance of structures.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>Output files:</p> <ul> <li><code>balanced.xyz</code> \u2014 structures with balanced charges</li> <li><code>unbalanced.xyz</code> \u2014 structures with unbalanced charges</li> <li><code>indices.txt</code> \u2014 indices of balanced structures</li> </ul> <p>This is intended for systems where common oxidation states are meaningful.</p>"},{"location":"en/analyzer_scripts.html#outlier-detection","title":"Outlier Detection","text":"<p><code>find_outliers.py</code> finds outlier structures in NEP training data based on RMSE thresholds for energy, force, and stress.</p> <p>Input files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>stress_train.out</code>, <code>train.xyz</code></p> <p>These files are generated during NEP training. The script compares DFT vs NEP predictions and identifies structures with large errors.</p> <pre><code># Interactive mode\ngpumdkit.sh    # Select: 5) Analyzer \u2192 502) Find outliers of extxyz\n</code></pre> <p>Interactive prompts:</p> <pre><code>Enter energy RMSE threshold (meV/atom): 1\nEnter force RMSE threshold (meV/\u00c5): 60\nEnter stress RMSE threshold (GPa): 0.03\n</code></pre> <p>Output files:</p> <ul> <li><code>selected.xyz</code> \u2014 structures exceeding the RMSE thresholds (outliers)</li> <li><code>remained.xyz</code> \u2014 structures within the thresholds</li> <li><code>selected_remained.png</code> \u2014 comparison plot</li> </ul> <p>Use case: After NEP training, use this to identify problematic structures that contribute most to the error. Remove or improve these structures to enhance the training set.</p>"},{"location":"en/analyzer_scripts.html#time-estimation","title":"Time Estimation","text":""},{"location":"en/analyzer_scripts.html#gpumd-remaining-time","title":"GPUMD Remaining Time","text":"<p><code>time_consuming_gpumd.sh</code> estimates the remaining time for a GPUMD simulation.</p> <p>Input files: <code>run.in</code>, <code>thermo.out</code> (in the current GPUMD working directory)</p> <pre><code>gpumdkit.sh -time gpumd\n</code></pre> <p>Output example:</p> <pre><code>----------------- System Information ----------------\ntotal frames: 1050000\n-----------------------------------------------------\nCurrent Frame  Speed (steps/s)   Total Time       Time Left       Estimated End\n-------------   -------------   -------------   -------------   -----------------\n    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04\n    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56\n</code></pre>"},{"location":"en/analyzer_scripts.html#nep-remaining-time","title":"NEP Remaining Time","text":"<p><code>time_consuming_nep.sh</code> estimates the remaining time for NEP training.</p> <p>Input files: <code>loss.out</code> (in the current NEP working directory)</p> <pre><code>gpumdkit.sh -time nep\n</code></pre> <p>Output example:</p> <pre><code>+-----------------+-----------+-----------------+---------------------+\n|       Step      | Time Diff |    Time Left    |    Finish Time      |\n+-----------------+-----------+-----------------+---------------------+\n| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |\n| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |\n| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |\n+-----------------+-----------+-----------------+---------------------+\n</code></pre>"},{"location":"en/analyzer_scripts.html#probability-density-analysis","title":"Probability Density Analysis","text":"<p><code>probability_density_analysis.py</code> calculates 3D probability density of mobile ions for diffusion channel analysis.</p> <p>Input files: Reference structure (POSCAR), trajectory file (extxyz)</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n</code></pre> <p>Arguments:</p> Argument Meaning <code>LLZO.vasp</code> Reference structure (POSCAR format) <code>dump.xyz</code> Trajectory file (extxyz format) <code>Li</code> Target mobile species <code>0.25</code> Grid interval for the probability density (\u00c5) <p>Output: <code>probability_density_0.25.vasp</code> \u2014 probability density grid in VASP format for visualization with VESTA or similar tools.</p> <p>Visualization suggestions:</p> <ol> <li>Open <code>probability_density_0.25.vasp</code> in VESTA</li> <li>Use \"Edit \u2192 Data \u2192 Volumetric Data\" to adjust isosurface levels</li> <li>Color the probability density by value to highlight preferred diffusion pathways</li> <li>Overlay with the crystal structure for context</li> </ol>"},{"location":"en/analyzer_scripts.html#example-workflows","title":"Example Workflows","text":""},{"location":"en/analyzer_scripts.html#structure-quality-check","title":"Structure Quality Check","text":"<pre><code># 1. Check composition\ngpumdkit.sh -analyze_comp train.xyz\n\n# 2. Check energy/force range\ngpumdkit.sh -range train.xyz force hist\n\n# 3. Check minimum distances\ngpumdkit.sh -min_dist_pbc train.xyz\n\n# 4. Find outliers (after NEP training)\n# Interactive: 5) Analyzer \u2192 502\n</code></pre>"},{"location":"en/analyzer_scripts.html#structure-filtering-pipeline","title":"Structure Filtering Pipeline","text":"<pre><code># 1. Filter by minimum distance\ngpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n\n# 2. Filter by box size\ngpumdkit.sh -filter_box filtered_dist_pbc.xyz 13\n\n# 3. Filter by force threshold\ngpumdkit.sh -filter_value filtered_box.xyz force 20\n</code></pre>"},{"location":"en/analyzer_scripts.html#diffusion-channel-analysis","title":"Diffusion Channel Analysis","text":"<pre><code># 1. Calculate probability density\ngpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n\n# 2. Visualize with VESTA\n# Open probability_density_0.25.vasp\n</code></pre>"},{"location":"en/calculator_scripts.html","title":"Calculator Scripts","text":"\ud83e\uddee Calculator Scripts <p>The calculator module contains scripts for computing properties from MD trajectories, NEP models, and structure files.</p> <p>Script Location: <code>Scripts/calculators/</code></p>"},{"location":"en/calculator_scripts.html#overview","title":"Overview","text":"<p>The calculator module can be read as three groups:</p> <ul> <li>Trajectory properties: compute time-dependent quantities such as MSD and ionic conductivity from GPUMD or extxyz trajectories;</li> <li>NEP-assisted calculations: use a NEP model to predict energies/forces/stresses, extract descriptors, calculate DOAS, run NEB, or minimize structures;</li> <li>Polar-material analysis: build neighbor lists and calculate local displacement, averaged structures, octahedral tilt, and local polarization for perovskite or polar systems.</li> </ul> <p>If you are not sure about the required arguments, start from the interactive menu to see the prompt. If the arguments are already clear, use <code>gpumdkit.sh -calc ...</code> directly.</p> Task Command Main Input Ionic conductivity <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>, <code>thermo.out</code>, <code>model.xyz</code> MSD from trajectory <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz trajectory NEP prediction <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP model NEP descriptors <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP model DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP model NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> initial/final structures Minimization <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> structure + NEP model Neighbor list <code>gpumdkit.sh -calc nlist ...</code> see Polar Material Analysis Displacement <code>gpumdkit.sh -calc disp ...</code> see Polar Material Analysis Average structure <code>gpumdkit.sh -calc avg-struct ...</code> see Polar Material Analysis Octahedral tilt <code>gpumdkit.sh -calc oct-tilt ...</code> see Polar Material Analysis ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 ...</code> see Polar Material Analysis <p>For a full command list:</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>The command-line help table looks like:</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>In interactive mode, choose <code>4) Calculators</code>. The menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"en/calculator_scripts.html#ionic-conductivity","title":"Ionic Conductivity","text":"<p><code>calc_ion_conductivity.py</code> calculates ionic diffusivity and conductivity from <code>msd.out</code>.</p>"},{"location":"en/calculator_scripts.html#required-and-optional-files","title":"Required and Optional Files","text":"File Role <code>msd.out</code> Required MSD data <code>thermo.out</code> Optional, used for automatic temperature detection <code>model.xyz</code> Optional, used for volume and ion-count detection <code>run.in</code> Optional, used to detect replication"},{"location":"en/calculator_scripts.html#usage","title":"Usage","text":"<pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>From interactive mode, choose <code>401</code>. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>If automatic files are missing, the script will ask for temperature, volume, and ion count interactively.</p> <p>Interactive prompts in manual mode look like:</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre>"},{"location":"en/calculator_scripts.html#example-output","title":"Example Output","text":"<pre><code>Diffusivity (D):\n  D_x: 4.153e-07 cm^2/s\n  D_y: 4.174e-07 cm^2/s\n  D_z: 2.610e-07 cm^2/s\n  D_total: 3.646e-07 cm^2/s\n------------------------------\nIonic Conductivity:\n  Sigma_x: 2.576e-02 mS/cm\n  Sigma_y: 2.589e-02 mS/cm\n  Sigma_z: 1.619e-02 mS/cm\n  Sigma_total: 2.261e-02 mS/cm\n</code></pre>"},{"location":"en/calculator_scripts.html#mean-square-displacement","title":"Mean Square Displacement","text":"<p><code>calc_msd.py</code> computes MSD directly from an extxyz trajectory.</p> <pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>From interactive mode, choose <code>412</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>Li</code> target mobile species <code>10</code> time interval between frames, in fs <code>5000</code> optional maximum correlation steps <p>Output:</p> <ul> <li><code>msd.out</code></li> </ul> <p>The beginning of <code>msd.out</code> is a text table with time and MSD columns. After generating it, use the plot commands below.</p> <p>You can then plot:</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-property-prediction","title":"NEP Property Prediction","text":"<p><code>calc_properties_with_nep.py</code> calculates energy, force, and stress for structures using a NEP model.</p> <p>Dependency: <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>Use this function to run predictions with a trained NEP model. For best results, validate model quality on your target structures before relying on the output.</p> <p>Tip: Before prediction, you may want to clean the extxyz metadata:</p> <pre><code>gpumdkit.sh -clean_xyz train.xyz clean_train.xyz\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-descriptors","title":"NEP Descriptors","text":"<p><code>calc_descriptors.py</code> extracts NEP descriptors for a selected element.</p> <pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>Use cases:</p> <ul> <li>visualize chemical environments with PCA/UMAP;</li> <li>compare training and candidate structures;</li> <li>inspect whether new data expands descriptor space.</li> </ul> <p>Plot descriptors with:</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/calculator_scripts.html#density-of-atomistic-states","title":"Density of Atomistic States","text":"<p><code>calc_doas.py</code> calculates density of atomistic states (DOAS), following the idea proposed by Wang et al..</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>The script:</p> <ol> <li>reads all structures;</li> <li>relaxes each structure with a NEP calculator;</li> <li>extracts per-atom energies;</li> <li>groups atomic energies by element;</li> <li>writes the grouped values to the output file.</li> </ol> <p>For very large systems, running minimization and atomistic-energy extraction directly in GPUMD can be more efficient.</p>"},{"location":"en/calculator_scripts.html#neb-with-a-nep-model","title":"NEB with a NEP Model","text":"<pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>This runs a NEB calculation with <code>9</code> intermediate images. During execution, the script asks how atoms should be fixed:</p> <ul> <li><code>none</code>: no atoms fixed;</li> <li><code>index</code>: fix atoms by index;</li> <li><code>element</code>: fix all atoms of one element;</li> <li><code>position</code>: fix atoms inside a coordinate range.</li> </ul>"},{"location":"en/calculator_scripts.html#structure-minimization","title":"Structure Minimization","text":"<p><code>calc_minimize.py</code> minimizes a structure using a NEP model through <code>calorine</code>.</p> <p>Dependency: <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input structure, POSCAR/CONTCAR or extxyz <code>nep.txt</code> NEP model <code>0.01</code> optional force convergence threshold in eV/Ang <code>1000</code> optional maximum optimization steps <p>Output:</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"en/calculator_scripts.html#rdf-calculation-with-ovito","title":"RDF Calculation with OVITO","text":"<p><code>rdf_calculator_ovito.py</code> calculates radial distribution function using OVITO's analysis tools.</p> <p>Dependency: OVITO</p> <pre><code>pip install ovito\n</code></pre> <p>Input file: Structure file (single frame or trajectory)</p> <pre><code>python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400\n</code></pre> <p>Parameters:</p> Argument Meaning <code>trajectory.xyz</code> Input structure file <code>6.0</code> Maximum distance for RDF calculation (\u00c5) <code>400</code> Number of histogram bins <p>Visualization:</p> <pre><code>gpumdkit.sh -plt rdf\n</code></pre> <p>Note: It is recommended to use the <code>compute_rdf</code> command directly in GPUMD when possible.</p>"},{"location":"en/calculator_scripts.html#ferroelectric-and-polar-material-tools","title":"Ferroelectric and Polar Material Tools","text":"<p>Options <code>406\u2013410</code> are for perovskite and polar-material analysis. They are commonly used to extract local structural information from MD trajectories before analyzing phase transitions, domain patterns, or polarization textures.</p> <p>This page only gives a quick index for these scripts because they are usually used together. For full workflows and argument details, see Polar Material Analysis.</p> Menu CLI subcommand Purpose Details <code>406</code> <code>gpumdkit.sh -calc nlist ...</code> Build neighbor lists between selected center and neighbor atoms Polar Material Analysis <code>407</code> <code>gpumdkit.sh -calc disp ...</code> Calculate local displacement from a trajectory and neighbor list Polar Material Analysis <code>408</code> <code>gpumdkit.sh -calc avg-struct ...</code> Calculate an averaged structure from a trajectory Polar Material Analysis <code>409</code> <code>gpumdkit.sh -calc oct-tilt ...</code> Calculate octahedral tilt angles Polar Material Analysis <code>410</code> <code>gpumdkit.sh -calc pol-abo3 ...</code> Estimate local ABO3 polarization from Born effective charges Polar Material Analysis <p>Some scripts require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>A typical sequence is to build neighbor lists with <code>nlist</code>, then reuse those lists for displacement, tilt, or polarization calculations. For averaged structures, you can start directly from the trajectory and use the length tolerance to control which frames are included.</p>"},{"location":"en/command_reference.html","title":"Command Reference","text":"\ud83d\udccb Command Reference <p>This page lists the stable GPUMDkit command-line shortcuts. Interactive mode is available for workflows with many choices.</p> <p>The source table is maintained in <code>docs/command_reference.tsv</code>.</p>"},{"location":"en/command_reference.html#gpumdkitsh-h-output","title":"<code>gpumdkit.sh -h</code> Output","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |\n| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/command_reference.html#main","title":"Main","text":"Command Syntax Description <code>-h</code> <code>gpumdkit.sh -h</code> Show general help <code>-update</code> <code>gpumdkit.sh -update</code> Update GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> Clean extra files in the current directory"},{"location":"en/command_reference.html#format-conversion","title":"Format Conversion","text":"Command Syntax Description <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR to extxyz, shell version <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR to extxyz, Python version <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K output to xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR to extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF to POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF to extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR to extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz frames to POSCAR files <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR to LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump to extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory to extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> Replicate by cell factors <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> Replicate toward a target atom count <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> Add GPUMD group labels <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> Add structure weights <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> Extract one frame <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> Remove extra extxyz properties <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> Extract frames by fractional range"},{"location":"en/command_reference.html#calculators","title":"Calculators","text":"Command Syntax Description <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> Ionic conductivity <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP property prediction <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP descriptors <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> Density of atomistic states <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> NEB with a NEP model <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> Structure minimization <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> MSD from trajectory <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> Neighbor lists <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> Displacements <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> Averaged structure <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> Octahedral tilt <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 local polarization"},{"location":"en/command_reference.html#analyzers","title":"Analyzers","text":"Command Syntax Description <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> Property range analysis <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> Composition analysis <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> Chemical species list <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> Charge-balance check <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> Minimum distance without PBC <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> Minimum distance with PBC <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> Distance filtering <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> PBC-aware distance filtering <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> Box-edge filtering <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> Property threshold filtering <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> Element-pair distance range filtering <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> Probability density analysis"},{"location":"en/command_reference.html#visualization","title":"Visualization","text":"<p>Use:</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>Common types include <code>train</code>, <code>prediction</code>, <code>thermo</code>, <code>msd</code>, <code>sdc</code>, <code>rdf</code>, <code>emd</code>, <code>nemd</code>, <code>hnemd</code>, <code>pdos</code>, and <code>plane-grid</code>.</p>"},{"location":"en/command_reference.html#utilities","title":"Utilities","text":"Command Syntax Description <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> Monitor GPUMD or NEP progress <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> Modify NEP models interactively <code>-pynep</code> <code>gpumdkit.sh -pynep</code> Deprecated PyNEP FPS sampling"},{"location":"en/contributing_to_gpumdkit.html","title":"Contributing to GPUMDkit","text":"\ud83e\udd1d Contributing to GPUMDkit <p>Thank you for your interest in contributing to GPUMDkit! We appreciate your time and effort in helping improve this toolkit.</p> <p> English   \u00a0\u00b7\u00a0   \u7b80\u4f53\u4e2d\u6587 </p> <p><code>GPUMDkit</code> is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.</p> <p>Note: The authoritative version of this document is <code>CONTRIBUTING.md</code> in the repository root. This tutorial page mirrors its content.</p>"},{"location":"en/contributing_to_gpumdkit.html#table-of-contents","title":"Table of Contents","text":"<ul> <li>Development Restrictions and Guidelines</li> <li>Reporting Bugs</li> <li>Suggesting Features</li> <li>Contributing Code</li> <li>Fork and Clone the Repository</li> <li>Create a Feature Branch</li> <li>Making Changes<ul> <li>Interactive Mode Contributions</li> <li>Command-Line Mode Contributions</li> <li>Updating Tab Completion</li> </ul> </li> <li>Code Style and Best Practices</li> <li>Testing Your Changes</li> <li>Commit Messages</li> <li>Push and Open a Pull Request</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#development-restrictions-and-guidelines","title":"Development Restrictions and Guidelines","text":"<p>To maintain code quality and consistency across the project, please adhere to these guidelines:</p>"},{"location":"en/contributing_to_gpumdkit.html#language-requirements","title":"Language Requirements","text":"<ul> <li>All code should be written in English: This includes variable names, function names, comments, docstrings, commit messages, and documentation.</li> <li>While we understand that contributors come from diverse backgrounds, using English ensures that the codebase is accessible to the widest possible audience.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#modularity-and-reusability","title":"Modularity and Reusability","text":"<ul> <li>Write modular and reusable code: Functions and scripts should be designed with flexibility in mind.</li> <li>Prefer passing parameters over hardcoding values: Use function arguments, command-line parameters, or configuration files instead of hardcoded values. However, some filenames are required to be fixed by GPUMD and NEP programs (e.g., <code>train.xyz</code>, <code>thermo.out</code>), and these can be hardcoded as needed.</li> <li>Example:    <pre><code># Good: accepts parameters\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # processing logic\n}\n\n# Avoid: hardcoded values (unless required by GPUMD/NEP)\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # processing logic\n}\n</code></pre></li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#code-style","title":"Code Style","text":"<ul> <li>Write code that is clear and easy for others to maintain and modify.</li> <li>Use meaningful variable and function names.</li> <li>Add comments where necessary to explain complex logic.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#documentation","title":"Documentation","text":"<ul> <li>Ensure that help messages (e.g., <code>-h</code> flags) are clear and accurate.</li> <li>Tutorial documentation lives in <code>docs/tutorials/en/</code> (English) and <code>docs/tutorials/zh/</code> (Chinese).   If you add a new feature, consider updating the relevant tutorial page.</li> <li>After editing tutorial markdown files, rebuild the HTML with <code>mkdocs build -f docs/mkdocs.yml</code>.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#reporting-bugs","title":"Reporting Bugs","text":"<p>If you encounter a bug, please help us fix it by reporting it through GitHub Issues:</p> <ol> <li>Search existing issues to see if the bug has already been reported.</li> <li>Open a new issue if it hasn't been reported yet: Create an Issue</li> <li>Describe the problem in detail and provide test files if possible.</li> </ol> <p>You can also reach out to us through: - QQ Group: 825696376 - Email: yanzihan@westlake.edu.cn - Script Developer: Contact the developer listed in the script header</p>"},{"location":"en/contributing_to_gpumdkit.html#suggesting-features","title":"Suggesting Features","text":"<p>We welcome feature suggestions! To propose a new feature:</p> <ol> <li>Search existing issues to see if someone has already suggested it.</li> <li>Open a new feature request: Create a Feature Request and mention @zhyan0603</li> <li>Describe what you need clearly and explain how it would be useful.</li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#contributing-code","title":"Contributing Code","text":""},{"location":"en/contributing_to_gpumdkit.html#fork-and-clone-the-repository","title":"Fork and Clone the Repository","text":"<ol> <li> <p>Fork the repository on GitHub by clicking the \"Fork\" button at the top right of the repository page.</p> </li> <li> <p>Clone your fork to your local machine:</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>Set up the upstream remote to keep your fork in sync:    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#create-a-feature-branch","title":"Create a Feature Branch","text":"<p>Create a new branch for your changes:</p> <pre><code># Create and checkout a new branch from main\ngit checkout -b your-branch-name\n</code></pre> <p>Name your branch as you prefer.</p>"},{"location":"en/contributing_to_gpumdkit.html#making-changes","title":"Making Changes","text":"<p>The structure of <code>GPUMDkit</code> consists of: - <code>gpumdkit.sh</code>: Main entry point (Bash script) handling both interactive menu mode and command-line mode - <code>install.sh</code>: Installation script that sets up environment variables and shell configuration - <code>Scripts/</code>: Python and Bash implementation scripts organized by functionality   - <code>plt_scripts/</code>: Plotting scripts   - <code>calculators/</code>: Calculation utilities   - <code>format_conversion/</code>: Format conversion tools   - <code>workflow/</code>: Workflow automation   - <code>sample_structures/</code>: Structure sampling utilities   - <code>analyzer/</code>: Analysis tools   - <code>utils/</code>: Utility functions (including <code>completion.sh</code> for tab completion) - <code>src/</code>: Shell scripts containing menu functions for interactive mode   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>skills/</code>: AI agent skill definitions (SKILL.md files for opencode/Claude Code integration) - <code>docs/</code>: Documentation files   - <code>tutorials/en/</code> and <code>tutorials/zh/</code>: Bilingual tutorial pages   - <code>mkdocs.yml</code>: MkDocs configuration for building tutorial HTML   - <code>command_reference.tsv</code>: Machine-readable command reference   - <code>htmls/</code>: Generated HTML output from MkDocs</p>"},{"location":"en/contributing_to_gpumdkit.html#interactive-mode-contributions","title":"Interactive Mode Contributions","text":"<p>To add a new feature accessible through the interactive menu:</p> <ol> <li>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:</li> </ol> <pre><code># Example: Add a new format conversion script\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>Implement your functionality following the modularity guidelines (accept parameters, avoid hardcoding).</p> </li> <li> <p>Add a wrapper function in the corresponding <code>src/</code> file:    <pre><code># Example: Edit src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>Add a new function:    <pre><code>function f111_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input &lt;required_param1&gt; &lt;required_param2&gt;\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -r -a converter_args\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py \"${converter_args[@]}\"\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>Update the menu display in <code>gpumdkit.sh</code>:    <pre><code># Find the menu() function and update it if needed\n# Find the array_choice array and add your new choice number\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\" \"107\" \"108\" \"109\" \"110\" \"111\"  # Added \"111\"\n    # ... rest of choices\n)\n</code></pre></p> </li> <li> <p>Add the case statement in <code>gpumdkit.sh</code>:    <pre><code># In the main() function, find the appropriate case statement\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n             \"101\") f101_out2xyz ;;\n             # ... existing cases ...\n             \"111\") f111_new_converter ;;  # Add your case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#command-line-mode-contributions","title":"Command-Line Mode Contributions","text":"<p>To add a new command-line flag or subcommand:</p> <ol> <li> <p>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:    <pre><code># Example: Add a new analyzer script\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>Implement your functionality with clear parameter requirements:    <pre><code># Example: Scripts/analyzer/analyze_bonds.py\nimport sys\n\nif len(sys.argv) != 3:\n    print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n    print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n    sys.exit(1)\n\ninput_file = sys.argv[1]\ncutoff = float(sys.argv[2])\n\n# Your implementation here\n</code></pre></p> </li> </ol> <p>Note: GPUMDkit Python scripts are designed to run directly (not imported as modules). You may use a <code>main()</code> function with <code>if __name__ == \"__main__\":</code> guard if you prefer, but it is not required. Most existing scripts execute at module level.</p> <ol> <li> <p>Add the command-line flag handler in <code>gpumdkit.sh</code>:    <pre><code># Find the command-line parsing section (the large \"case $1 in\" block)\n# Add your new flag in the appropriate location\n\ncase $1 in\n    # ... existing cases ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ \"$2\" != \"-h\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py $2 $3\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n        fi ;;\n    # ... rest of cases ...\nesac\n</code></pre></p> </li> <li> <p>Update the help information in <code>gpumdkit.sh</code>:    <pre><code># Find the help_info_table() function and add your command\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... rest of help table ...\n}\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#updating-tab-completion","title":"Updating Tab Completion","text":"<p>When adding new command-line flags, update the tab completion script:</p> <pre><code># Edit Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>Add your new flag to the <code>opts</code> variable: <pre><code># Find the line with local opts=...\nlocal opts=\"-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...\"\n#                                                        Add your flag here\n</code></pre></p> <p>If your flag requires file arguments, add it to the existing file-completion case: <pre><code># Find the case for file-requiring flags and add yours with |\n-out2xyz|-out2exyz|-...|-your_new_flag)\n    COMPREPLY=($(compgen -f -- \"$cur\")) ;;\n</code></pre></p> <p>If your flag accepts secondary options (like <code>-plt</code> or <code>-calc</code>), add a new case: <pre><code>case \"$prev\" in\n    # ... existing cases ...\n    -your_new_flag)\n        COMPREPLY=($(compgen -W \"option1 option2 option3\" -- \"$cur\")) ;;\n    # ... rest of cases ...\nesac\n</code></pre></p>"},{"location":"en/contributing_to_gpumdkit.html#code-style-and-best-practices","title":"Code Style and Best Practices","text":"<ul> <li>Shell Scripts:</li> <li>Use <code>${variable}</code> for variable expansion</li> <li>Use <code>[ ! -z \"$var\" ]</code> for non-empty checks (project convention)</li> <li>Interactive functions should follow the banner format:     <pre><code>echo \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/&lt;category&gt;        |\"\necho \" | Script: &lt;script_name&gt;.py                        |\"\necho \" | Developer: &lt;Name&gt; (&lt;email&gt;)                     |\"\necho \" &gt;-------------------------------------------------&lt;\"\n</code></pre></li> <li>Use <code>read -r -a varname</code> for multi-word input, then pass with <code>\"${varname[@]}\"</code></li> <li> <p>Shell scripts in <code>src/</code> should start with a file header block:     <pre><code># ============================================================\n# GPUMDkit &lt;module name&gt; module\n# Repository: https://github.com/zhyan0603/GPUMDkit\n# Author: &lt;Name&gt; (&lt;email&gt;)\n# ============================================================\n</code></pre></p> </li> <li> <p>Python Scripts:</p> </li> <li>Write clear, maintainable code</li> <li>Use meaningful variable names</li> <li>Use <code>sys.argv</code> for argument parsing (consistent with most existing scripts)</li> <li>Provide clear usage messages with <code>print(\"Usage: ...\")</code> and <code>print(\"Example: ...\")</code></li> <li>If your script uses heavy/special packages (<code>NepTrain</code>, <code>calorine</code>, <code>dpdata</code>), add a     <code>print_dependency_notice()</code> function to inform users about citation recommendations</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#testing-your-changes","title":"Testing Your Changes","text":"<p>Before submitting your contribution, run the relevant validation commands:</p> <pre><code># Shell syntax checks (always run these)\nbash -n gpumdkit.sh\nfind src Scripts -name '*.sh' -exec bash -n {} +\n\n# Python syntax checks (for modified Python files)\npython3 -m py_compile path/to/modified_script.py\n\n# MkDocs build (if you modified documentation)\nmkdocs build -f docs/mkdocs.yml\n\n# Check for trailing whitespace issues\ngit diff --check\n</code></pre> <p>Then test functionality:</p> <ol> <li> <p>Test interactive mode (if applicable):    <pre><code>gpumdkit.sh\n# Navigate to your new feature and test it thoroughly\n</code></pre></p> </li> <li> <p>Test command-line mode (if applicable):    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # Test help message\n</code></pre></p> </li> <li> <p>Test tab completion (if you modified <code>completion.sh</code>):    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # Should show your new flag\n</code></pre></p> </li> <li> <p>Test with various inputs:</p> </li> <li>Test with typical inputs</li> <li>Test with edge cases (empty files, large files, etc.)</li> <li> <p>Test error handling (missing files, invalid parameters)</p> </li> <li> <p>Verify no regressions: Ensure existing functionality still works correctly.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#commit-messages","title":"Commit Messages","text":"<p>Write clear, descriptive commit messages that explain what you changed. There are no strict format requirements - just make sure your message is understandable.</p>"},{"location":"en/contributing_to_gpumdkit.html#push-and-open-a-pull-request","title":"Push and Open a Pull Request","text":"<ol> <li> <p>Commit your changes:    <pre><code>git add .\ngit commit -m \"your descriptive message\"\n</code></pre></p> </li> <li> <p>Keep your branch updated with the latest <code>dev</code> branch:    <pre><code>git fetch origin\ngit rebase origin/dev\n</code></pre></p> </li> <li> <p>Push your branch to your fork:    <pre><code>git push origin your-branch-name\n</code></pre></p> </li> <li> <p>Open a Pull Request:</p> </li> <li>Go to the GPUMDkit repository</li> <li>Click \"Pull Requests\" \u2192 \"New Pull Request\"</li> <li>Set the base branch to <code>dev</code> for code review</li> <li>Set the compare branch to your feature branch</li> <li> <p>Fill in the PR description with:</p> <ul> <li>Title: Brief description of changes</li> <li>Description: Detailed explanation of what changed and why</li> <li>Testing: Describe how you tested the changes</li> </ul> </li> <li> <p>Respond to review feedback:</p> </li> <li>Be open to suggestions and constructive criticism</li> <li>Make requested changes promptly</li> <li> <p>Push additional commits to your branch (they'll automatically appear in the PR)</p> </li> <li> <p>After approval: A maintainer will merge your PR.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#questions-or-need-help","title":"Questions or Need Help?","text":"<p>If you have questions about contributing or need help with your contribution:</p> <ul> <li>Open a discussion: Use GitHub Discussions for general questions</li> <li>Ask in an issue: Comment on related issues for specific questions</li> <li>Contact maintainers: Reach out to the core developers listed in the README</li> </ul> <p>Thank you again for contributing to <code>GPUMDkit</code>! Your efforts help make this toolkit better for the entire GPUMD and NEP community.</p>"},{"location":"en/custom_commands.html","title":"Custom Commands","text":"\ud83d\udd27 Custom Commands <p>GPUMDkit allows users to extend the command-line interface with custom commands. Define shortcuts for frequently used scripts in your ~/.gpumdkit.in file.</p>"},{"location":"en/custom_commands.html#setup","title":"Setup","text":"<p>Create or edit <code>~/.gpumdkit.in</code>: <pre><code>vi ~/.gpumdkit.in\n</code></pre></p> <p>Define custom functions with the <code>custom_</code> prefix.</p>"},{"location":"en/custom_commands.html#examples","title":"Examples","text":""},{"location":"en/custom_commands.html#simple-greeting","title":"Simple Greeting","text":"<p>Write the following codes in your <code>~/.gpumdkit.in</code> </p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>and run <code>gpumdkit.sh -hello</code>, you will see:</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"en/custom_commands.html#command-with-required-arguments","title":"Command with Required Arguments","text":"<p>For the following function:</p> <pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>and you can add an argument, for example: <code>gpumdkit.sh -greet Zihan</code>, then you will see:</p> <pre><code>Hello, Zihan!\n</code></pre> <p>Passing arguments: Use <code>\"$@\"</code> to forward all arguments safely. Use <code>${@:1}</code> when you need to refer to arguments starting from the first one. </p>"},{"location":"en/custom_commands.html#calling-an-external-script","title":"Calling an External Script","text":"<p>If you want to call an external script like <code>gpumdkit.sh</code>.</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>and run <code>gpumdkit.sh -nepanalyse</code></p>"},{"location":"en/custom_commands.html#advanced-examples","title":"Advanced Examples","text":""},{"location":"en/custom_commands.html#batch-processing","title":"Batch Processing","text":"<p>Process multiple files: <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -batch_plot dir1 dir2 dir3</code></p>"},{"location":"en/custom_commands.html#analysis-pipeline","title":"Analysis Pipeline","text":"<p>Combine multiple operations: <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -analyze_training train.xyz</code></p>"},{"location":"en/custom_commands.html#custom-workflow","title":"Custom Workflow","text":"<p>Automate common workflow: <pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    # Convert VASP outputs\n    gpumdkit.sh -out2xyz ./\n\n    # Filter outliers\n    gpumdkit.sh -filter_value train.xyz force 30\n\n    # Check quality\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -prep_training</code></p>"},{"location":"en/custom_commands.html#tips","title":"Tips","text":"<ul> <li>Use descriptive names: <code>custom_analyze_nep_training</code> is clearer than <code>custom_ant</code></li> <li>Add help messages: Echo usage info when no arguments provided</li> <li>Error handling: Check if required files exist before processing</li> <li>Forward arguments safely: Use <code>\"$@\"</code> to preserve spaces and special characters</li> </ul> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/format_conversion.html","title":"Format Conversion","text":"\ud83d\udd04 Format Conversion <p>GPUMDkit contains utilities for converting common atomistic simulation formats, with extra handling for metadata such as group labels, weights, and frame extraction.</p>"},{"location":"en/format_conversion.html#what-it-does","title":"What it does","text":"<p>This module converts structure and trajectory files between common formats used in computational materials science. It supports VASP, LAMMPS, CP2K, ABACUS, CIF, ASE trajectories, and extxyz. It also provides tools for adding group labels, weights, extracting frames, and replicating structures.</p>"},{"location":"en/format_conversion.html#before-you-start","title":"Before you start","text":"<p>Script location: <code>Scripts/format_conversion/</code></p> <p>Make sure GPUMDkit is installed. See Quick Start for installation instructions.</p>"},{"location":"en/format_conversion.html#supported-formats","title":"Supported formats","text":"<p>The format conversion module covers:</p> <ul> <li>VASP: <code>POSCAR</code>, <code>CONTCAR</code>, <code>OUTCAR</code>, <code>XDATCAR</code></li> <li>LAMMPS: data files and dump trajectories</li> <li>CP2K: output logs, position, force, and cell files</li> <li>ABACUS: SCF/MD logs</li> <li>CIF: crystallographic structure files</li> <li>ASE trajectory: <code>.traj</code></li> <li>extxyz: a common structure format for GPUMD and NEP</li> </ul>"},{"location":"en/format_conversion.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>1) Format Conversion\n</code></pre> <p>The format conversion menu is:</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"en/format_conversion.html#what-each-entry-does","title":"What Each Entry Does","text":"Entry Called script Function When to Use <code>101</code> <code>out2xyz.sh</code> VASP OUTCAR to extxyz, shell version convert VASP calculation directories <code>102</code> <code>mtp2xyz.py</code> MTP cfg to extxyz convert MTP training data <code>103</code> <code>cp2k_log2xyz.py</code> / <code>cp2k2xyz.py</code> CP2K to extxyz choose CP2K log/inp route or pos/frc/cell route <code>104</code> <code>abacus2xyz_scf.sh</code> / <code>abacus2xyz_md.sh</code> ABACUS to extxyz convert ABACUS SCF or MD output <code>105</code> <code>exyz2pos.py</code> extxyz to POSCAR write each extxyz frame as a POSCAR-style file <code>106</code> <code>add_groups.py</code> add group labels add atom group labels for GPUMD-related workflows <code>107</code> <code>add_weight.py</code> add weights assign training weights in extxyz <code>108</code> <code>get_frame.py</code> extract frame export one frame from an extxyz trajectory <code>109</code> <code>clean_xyz.py</code> clean XYZ info remove extra extxyz properties <code>110</code> <code>replicate.py</code> replicate structure build supercells by factors or target atom count <code>out2exyz</code> <code>out2exyz.py</code> OUTCAR to extxyz, Python version alternative VASP OUTCAR converter <code>pos2exyz</code> <code>pos2exyz.py</code> POSCAR to extxyz convert a single structure <code>cif2pos</code> <code>cif2pos.py</code> CIF to POSCAR prepare VASP input from CIF <code>cif2exyz</code> <code>cif2exyz.py</code> CIF to extxyz prepare GPUMDkit input from CIF <code>xdat2exyz</code> <code>xdatcar2exyz.py</code> XDATCAR to extxyz convert VASP MD trajectory <code>pos2lmp</code> <code>pos2lmp.py</code> POSCAR to LAMMPS data prepare LAMMPS input <code>lmp2exyz</code> <code>lmp2exyz.py</code> LAMMPS dump to extxyz convert LAMMPS trajectory <code>traj2exyz</code> <code>traj2exyz.py</code> ASE traj to extxyz convert ASE trajectory"},{"location":"en/format_conversion.html#quick-command-reference","title":"Quick Command Reference","text":"Source Target Command OUTCAR directory extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR directory extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> extxyz POSCAR files <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"en/format_conversion.html#common-examples","title":"Common Examples","text":""},{"location":"en/format_conversion.html#convert-vasp-calculations-to-extxyz","title":"Convert VASP calculations to extxyz","text":"<p>What it does: Searches a directory for VASP OUTCAR files and converts them into a single extxyz file for NEP training or analysis.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>The shell version searches the target directory and converts VASP results into an extxyz file. If you prefer the Python implementation:</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>Interactive mode: Choose <code>101</code> from the format conversion menu. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre> <p>Output: An extxyz file containing the converted structures, suitable for NEP training or further analysis.</p>"},{"location":"en/format_conversion.html#add-group-labels","title":"Add group labels","text":"<p>What it does: Adds atom group labels to a structure file. Group labels are required by some GPUMD-related workflows, such as species-specific MSD or diffusion calculations.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>This command reads the input structure and writes an extxyz file with group information.</p> <p>Interactive mode: Choose <code>106</code> from the format conversion menu. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre> <p>Output: An extxyz file with group labels added.</p>"},{"location":"en/format_conversion.html#script-details","title":"Script Details","text":""},{"location":"en/format_conversion.html#poscar-to-extxyz","title":"POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>Use this when you have a single VASP structure and want an extxyz output.</p> <p>Interactive keyword: <code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#extxyz-to-poscar","title":"extxyz to POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>This converts all frames in an extxyz file into <code>POSCAR_*.vasp</code> files. Frame indices are 0-based in most GPUMDkit scripts, but output filenames are meant for direct inspection and batch calculations.</p> <p>Interactive entry: <code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#lammps-dump-to-extxyz","title":"LAMMPS dump to extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>The element symbols must match the LAMMPS atom type IDs. For example, if type <code>1</code> is Li, type <code>2</code> is Y, and type <code>3</code> is Cl, the order should be <code>Li Y Cl</code>.</p> <p>Interactive keyword: <code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#cif-conversion","title":"CIF conversion","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>Use <code>-cif2pos</code> if you want a VASP-style structure, and <code>-cif2exyz</code> if the next step is GPUMDkit analysis.</p>"},{"location":"en/format_conversion.html#add-weights","title":"Add weights","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>This is useful when you want some structures to have a different training weight in a NEP dataset.</p>"},{"location":"en/format_conversion.html#replicate-structures","title":"Replicate structures","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>The first form uses explicit replication factors. The second form tries to build a supercell close to a target atom count.</p>"},{"location":"en/format_conversion.html#extract-one-frame","title":"Extract one frame","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>This extracts frame index <code>1000</code> from an extxyz trajectory.</p>"},{"location":"en/format_conversion.html#split-multi-frame-extxyz","title":"Split multi-frame extxyz","text":"<p><code>split_single_xyz.py</code> splits an extxyz file into individual frames, each written to a separate file.</p> <pre><code>python Scripts/format_conversion/split_single_xyz.py dump.xyz\n</code></pre> <p>This creates <code>model_0.xyz</code>, <code>model_1.xyz</code>, ... for each frame in the trajectory.</p>"},{"location":"en/format_conversion.html#mtp-conversion","title":"MTP conversion","text":"<p>Convert MTP <code>.cfg</code> format to extxyz:</p> <pre><code>gpumdkit.sh    # Select: 1) Format Conversion \u2192 102\n</code></pre> <p>Interactive prompt:</p> <pre><code>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;\nExample: train.cfg Pd Ag\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#abacus-conversion","title":"ABACUS conversion","text":"<p>Convert ABACUS output to extxyz:</p> <pre><code>gpumdkit.sh    # Select: 1) Format Conversion \u2192 104\n</code></pre> <p>The menu offers two options:</p> <ol> <li>SCF output (<code>running_scf.log</code>)</li> <li>MD output (<code>running_md.log</code>)</li> </ol>"},{"location":"en/format_conversion.html#common-mistakes","title":"Common Mistakes","text":"Problem What to Check LAMMPS elements are wrong Check the element order passed after the dump file A trajectory has strange metadata Try <code>-clean_xyz input.xyz clean.xyz</code> A converted structure looks shifted Inspect PBC/cell information in the source file Frame extraction gives the wrong structure Remember that frame indices are 0-based"},{"location":"en/format_conversion.html#notes","title":"Notes","text":"<p>If a Python package required by a specific converter is missing, Python will report it when that converter is used.</p>"},{"location":"en/plot_scripts.html","title":"Plot Scripts","text":"\ud83d\udcca Plot Scripts <p>The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators. All plots can be displayed interactively or saved as high-resolution PNG files.</p> <p>Script Location: <code>Scripts/plt_scripts/</code></p>"},{"location":"en/plot_scripts.html#quick-access","title":"Quick Access","text":"<pre><code>gpumdkit.sh -plt              # Show all plotting options\ngpumdkit.sh -plt &lt;type&gt;       # Generate a plot\ngpumdkit.sh -plt &lt;type&gt; save  # Save plot as PNG\ngpumdkit.sh -plt &lt;type&gt; -h    # Show help for a specific plot type\n</code></pre> <p>Running <code>gpumdkit.sh -plt</code> prints the plotting command menu:</p> <pre><code>+-----------------------------------------------------------------------------------------------+\n|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |\n+-----------------------------------------------------------------------------------------------+\n|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |\n+-----------------------------------------------------------------------------------------------+\n|                                    NEP Training &amp; Evaluation                                  |\n+-----------------------------------------------------------------------------------------------+\n|  train          - NEP training results           prediction     - NEP prediction results      |\n|  train_test     - NEP train and test results     parity_density - Parity density plot         |\n|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |\n|  charge         - Charge distribution            born_charge    - Born effective charges      |\n|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |\n|  des            - Descriptors                    lr             - Learning rate for gnep      |\n+-----------------------------------------------------------------------------------------------+\n|                                     Diffusion &amp; Transport                                     |\n+-----------------------------------------------------------------------------------------------+\n|  msd            - Mean square displacement       msd_conv       - MSD convergence             |\n|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |\n|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|\n|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |\n|  D_xyz          - Directional Arrhenius D                                                     |\n+-----------------------------------------------------------------------------------------------+\n|                                    MD &amp; Structural Analysis                                   |\n+-----------------------------------------------------------------------------------------------+\n|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |\n|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |\n|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |\n|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |\n|  doas           - Density of atomistic states                                                 |\n+-----------------------------------------------------------------------------------------------+\n|                                        Heat Transport                                         |\n+-----------------------------------------------------------------------------------------------+\n|  emd            - EMD results                    nemd           - NEMD results                |\n|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |\n+-----------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/plot_scripts.html#nep-training-and-prediction","title":"NEP Training and Prediction","text":""},{"location":"en/plot_scripts.html#plt_trainpy","title":"plt_train.py","text":"<p>Visualizes NEP training progress including loss curves, RMSE evolution, and parity plots comparing DFT vs NEP predictions for energy, forces, and stresses.</p> <p>Input Files: <code>loss.out</code>, <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/plot_scripts.html#plt_predictionpy","title":"plt_prediction.py","text":"<p>Visualizes NEP prediction results on the test set.</p> <p>Input Files: <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test         # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#plt_train_testpy","title":"plt_train_test.py","text":"<p>Creates combined parity plots for both training and testing datasets.</p> <p>Input Files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code>, <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"en/plot_scripts.html#plt_parity_densitypy","title":"plt_parity_density.py","text":"<p>Generates density-based parity plots for energies, forces, and stresses. Useful for large datasets where scatter plots become unreadable.</p> <p>Input Files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"en/plot_scripts.html#plt_force_errorspy","title":"plt_force_errors.py","text":"<p>Plots force error evaluation metrics as proposed by Liu et al..</p> <p>Input File: <code>force_train.out</code></p> <p>Metrics Displayed: - Force magnitude errors (delta_F) - Force angle errors (delta_theta) - Distribution of errors</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"en/plot_scripts.html#plt_learning_ratepy","title":"plt_learning_rate.py","text":"<p>Visualizes learning rate during <code>gnep</code> training.</p> <p>Input File: <code>loss.out</code></p> <p>Note: Only for the <code>gnep</code> training process.</p> <pre><code>gpumdkit.sh -plt lr\n</code></pre>"},{"location":"en/plot_scripts.html#plt_nep_restartpy","title":"plt_nep_restart.py","text":"<p>Visualizes parameters stored in the <code>nep.restart</code> file.</p> <p>Input File: <code>nep.restart</code></p> <pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"en/plot_scripts.html#plt_chargepy","title":"plt_charge.py","text":"<p>Plots charge distribution from <code>qNEP</code> model.</p> <p>Input File: <code>charge_train.out</code></p> <p>Important: Ensure consistency between training set and charge output atom ordering. Use full batch training or run prediction step first.</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre>"},{"location":"en/plot_scripts.html#plt_born_chargepy","title":"plt_born_charge.py","text":"<p>Creates parity plots for Born effective charges (BEC) on training and testing datasets. Structures with all-zero reference BEC are filtered out.</p> <p>Input Files: <code>bec_train.out</code>, <code>bec_test.out</code></p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec          # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#thermodynamic-properties","title":"Thermodynamic Properties","text":""},{"location":"en/plot_scripts.html#plt_thermopy","title":"plt_thermo.py","text":"<p>Primary script for comprehensive thermodynamic property visualization.</p> <p>Input File: <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/plot_scripts.html#plt_thermo2py-plt_thermo3py","title":"plt_thermo2.py &amp; plt_thermo3.py","text":"<p>Alternative thermodynamic visualization with different styles.</p> <p>Input File: <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"en/plot_scripts.html#diffusion-and-ionic-transport","title":"Diffusion and Ionic Transport","text":""},{"location":"en/plot_scripts.html#plt_msdpy","title":"plt_msd.py","text":"<p>Plots mean square displacement (MSD) for all directions.</p> <p>Input File: <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"en/plot_scripts.html#plt_msd_allpy","title":"plt_msd_all.py","text":"<p>Plots MSD for all atomic species separately when using <code>all_groups</code> in GPUMD.</p> <p>Input File: <code>msd.out</code> (computed with <code>all_groups</code> option)</p> <p>Requirements: Must use <code>all_groups</code> in the <code>compute_msd</code> command in <code>run.in</code>.</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"en/plot_scripts.html#plt_msd_convergence_checkpy","title":"plt_msd_convergence_check.py","text":"<p>Checks convergence of MSD calculations across different time windows.</p> <p>Input File: <code>msd_step*.out</code> (computed with <code>save_every</code> option)</p> <p>Requirements: Use <code>save_every</code> in the <code>compute_msd</code> command.</p> <p>Purpose: Verify MSD has converged sufficiently for accurate diffusion coefficient calculation.</p> <pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"en/plot_scripts.html#plt_sdcpy","title":"plt_sdc.py","text":"<p>Plots self-diffusion coefficient (SDC) vs time.</p> <p>Input File: <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/plot_scripts.html#plt_arrhenius_dpy","title":"plt_arrhenius_d.py","text":"<p>Creates Arrhenius plot for diffusivity (log10 D vs 1000/T).</p> <p>Input Files: <code>*K/msd.out</code> files (each temperature subdirectory should contain an <code>msd.out</code>)</p> <pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D             # Alternative command\n</code></pre> <p>Output example:</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"en/plot_scripts.html#plt_arrhenius_sigmapy","title":"plt_arrhenius_sigma.py","text":"<p>Creates Arrhenius plot for ionic conductivity (ln(\u03c3\u00b7T) vs 1000/T).</p> <p>Input Files: <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> (each temperature subdirectory)</p> <pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma         # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#heat-transport","title":"Heat Transport","text":""},{"location":"en/plot_scripts.html#plt_emdpy","title":"plt_emd.py","text":"<p>Analyzes and plots thermal conductivity from equilibrium molecular dynamics (EMD).</p> <p>Input Files: EMD output files from GPUMD</p> <pre><code>gpumdkit.sh -plt emd x        # for x direction\n</code></pre>"},{"location":"en/plot_scripts.html#plt_nemdpy","title":"plt_nemd.py","text":"<p>Visualizes non-equilibrium molecular dynamics (NEMD) thermal transport properties.</p> <p>Input Files: NEMD output files from GPUMD</p> <p>Parameters:</p> Parameter Description <code>real_length</code> Real length of heat transfer zone in nm (set to <code>Auto</code> for auto-calculation) <code>scale_eff_size</code> Scale factor for effective cross-sectional area (default: 1). For 3D bulk: use 1. For low-dimensional systems with vacuum: S_box / S_eff <code>cutoff_freq</code> Cutoff frequency for SHC calculation in THz (default: 60) <code>save</code> Optional, save the plot as <code>nemd.png</code> <p>Note: If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p> <pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#plt_hnemdpy","title":"plt_hnemd.py","text":"<p>Plots homogeneous non-equilibrium molecular dynamics (HNEMD) results.</p> <p>Input Files: HNEMD output files from GPUMD</p> <p>Parameters:</p> Parameter Description <code>scale_eff_size</code> Scale factor for effective cross-sectional area (default: 1) <code>cutoff_freq</code> Cutoff frequency for SHC calculation in THz (default: 60) <code>save</code> Optional, save the plot as <code>hnemd.png</code> <p>Note: If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p> <pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#structural-analysis","title":"Structural Analysis","text":""},{"location":"en/plot_scripts.html#plt_rdfpy","title":"plt_rdf.py","text":"<p>Plots radial distribution function (RDF) showing pair correlations.</p> <p>Input File: <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf               # Plot all RDF pairs\ngpumdkit.sh -plt rdf &lt;column&gt;      # Plot specific pair\n</code></pre> <p>Full RDF output:</p> <p>Single pair RDF:</p>"},{"location":"en/plot_scripts.html#plt_rdf_pmfpy","title":"plt_rdf_pmf.py","text":"<p>Plots RDF combined with potential of mean force (PMF).</p> <p>Input File: <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf_pmf\n</code></pre>"},{"location":"en/plot_scripts.html#plt_vacpy","title":"plt_vac.py","text":"<p>Plots velocity autocorrelation function (VAC). Useful for analyzing phonon properties and atomic dynamics.</p> <p>Input File: <code>sdc.out</code> (the VAC columns are read from this file by the plotting script)</p> <p>Output: Interactive plot or <code>vac.png</code> (with <code>save</code> option)</p> <pre><code>gpumdkit.sh -plt vac\n</code></pre>"},{"location":"en/plot_scripts.html#plt_cohesivepy","title":"plt_cohesive.py","text":"<p>Plots cohesive energy curve from <code>cohesive.out</code>. Useful for analyzing lattice stability and equilibrium lattice constants.</p> <p>Input File: <code>cohesive.out</code> (isotropic scaling factor vs cohesive energy)</p> <p>Output: Interactive plot or <code>cohesive.png</code> (with <code>save</code> option)</p> <pre><code>gpumdkit.sh -plt cohesive\n</code></pre>"},{"location":"en/plot_scripts.html#plt_net_forcepy","title":"plt_net_force.py","text":"<p>Plots distribution of net forces on structures, useful for identifying problematic configurations.</p> <p>Input File: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>Reference: arXiv:2510.19774</p>"},{"location":"en/plot_scripts.html#phonons","title":"Phonons","text":""},{"location":"en/plot_scripts.html#plt_pdospy","title":"plt_pdos.py","text":"<p>Calculates and plots normalized VAC, PDOS, and Heat Capacity (Cv).</p> <p>Input Files: <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></p> <pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>Heat capacity output:</p>"},{"location":"en/plot_scripts.html#descriptor-dimer-and-extra-analysis","title":"Descriptor, Dimer, and Extra Analysis","text":""},{"location":"en/plot_scripts.html#plt_descriptorspy","title":"plt_descriptors.py","text":"<p>Visualizes high-dimensional NEP descriptors using dimensionality reduction (PCA or UMAP).</p> <p>Input File: <code>descriptors.npy</code> (generated by <code>gpumdkit.sh -calc des</code>)</p> <p>Methods: - <code>pca</code> \u2014 Principal Component Analysis - <code>umap</code> \u2014 Uniform Manifold Approximation and Projection</p> <pre><code># First generate descriptors\ngpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n\n# Then visualize\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/plot_scripts.html#plt_descriptors_comparepy","title":"plt_descriptors_compare.py","text":"<p>Compares descriptors from multiple training sets or models.</p> <pre><code>gpumdkit.sh -plt des_compare\n</code></pre>"},{"location":"en/plot_scripts.html#plt_dimerpy","title":"plt_dimer.py","text":"<p>Plots dimer interaction curves. Two atoms are placed in a cubic box (30 \u00c5) and the potential energy and force are calculated as a function of dimer distance using a NEP model.</p> <p>Input File: <code>nep.txt</code></p> <pre><code>gpumdkit.sh -plt dimer &lt;element1&gt; &lt;element2&gt; &lt;nep_model&gt;\ngpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>Reference: J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"en/plot_scripts.html#plt_doaspy","title":"plt_doas.py","text":"<p>Plots density of atomistic states (DOAS) proposed by Wang et al..</p> <p>Input File: <code>doas.out</code> (calculated by <code>gpumdkit.sh -calc doas</code>)</p> <pre><code>gpumdkit.sh -plt doas &lt;doas.out&gt; &lt;species&gt;\ngpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"en/plot_scripts.html#plane-grid-plot-for-polar-materials","title":"Plane-Grid Plot for Polar Materials","text":"<p>This workflow maps displacement or polarization data onto a grid and plots selected plane profiles. For detailed usage and real-world examples, see Polar Material Analysis.</p> <p>Dependency:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>Typical upstream steps:</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>Usage:</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre>"},{"location":"en/plot_scripts.html#quick-reference-table","title":"Quick Reference Table","text":"Command Input File(s) Description <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP training plots <code>prediction</code> / <code>test</code> <code>*_test.out</code> NEP prediction plots <code>train_test</code> <code>*_train.out</code>, <code>*_test.out</code> Combined parity plots <code>parity_density</code> <code>*_train.out</code> Density-based parity plots <code>force_errors</code> <code>force_train.out</code> Force error metrics <code>lr</code> <code>loss.out</code> (gnep) Learning rate <code>restart</code> <code>nep.restart</code> Restart file parameters <code>charge</code> <code>charge_train.out</code> Charge distribution <code>born_charge</code> / <code>bec</code> <code>bec_train.out</code>, <code>bec_test.out</code> Born effective charges <code>thermo</code> <code>thermo.out</code> Thermodynamic properties <code>msd</code> <code>msd.out</code> Mean square displacement <code>msd_all</code> <code>msd.out</code> (all_groups) MSD for all species <code>msd_conv</code> <code>msd_step*.out</code> MSD convergence check <code>sdc</code> <code>msd.out</code> Self-diffusion coefficient <code>arrhenius_d</code> / <code>D</code> <code>*K/msd.out</code> Arrhenius diffusivity <code>arrhenius_sigma</code> / <code>sigma</code> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> Arrhenius ionic conductivity <code>rdf</code> <code>rdf.out</code> Radial distribution function <code>rdf_pmf</code> <code>rdf.out</code> RDF + potential of mean force <code>vac</code> <code>sdc.out</code> Velocity autocorrelation <code>cohesive</code> <code>cohesive.out</code> Cohesive energy curve <code>net_force</code> <code>train.xyz</code> Net force distribution <code>doas</code> <code>doas.out</code> Density of atomistic states <code>des</code> <code>descriptors.npy</code> Descriptor PCA/UMAP <code>dimer</code> <code>nep.txt</code> Dimer energy/force curve <code>pdos</code> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code> VAC and PDOS <code>emd</code> EMD outputs EMD thermal conductivity <code>nemd</code> NEMD outputs NEMD thermal transport <code>hnemd</code> HNEMD outputs HNEMD thermal transport <code>viscosity</code> Viscosity outputs Viscosity"},{"location":"en/polar_material_analysis.html","title":"Polar Material Analysis","text":"\ud83e\uddf2 Polar Material Analysis <p>This tutorial covers GPUMDkit calculator options <code>406-410</code> and the <code>plane-grid</code> plotting workflow.</p> <p>Script Location: <code>Scripts/calculators/</code> and <code>Scripts/plt_scripts/</code></p> <p>This tutorial includes both general and system-specific tools:</p> <ul> <li><code>nlist</code>, <code>disp</code>, and <code>avg-struct</code> are broadly useful for structure/trajectory analysis.</li> <li><code>oct-tilt</code> is for octahedral environments (requires 6 neighbors around each center).</li> <li><code>pol-abo3</code> is specific to <code>ABO3</code> polarization analysis.</li> </ul>"},{"location":"en/polar_material_analysis.html#overview","title":"Overview","text":"Step CLI Command Main Input Output Build neighbor list <code>gpumdkit.sh -calc nlist ...</code> <code>model.xyz</code> <code>nl-*.dat</code> Calculate displacement <code>gpumdkit.sh -calc disp ...</code> trajectory + <code>nl-*.dat</code> <code>displacements.dat</code> Average trajectory <code>gpumdkit.sh -calc avg-struct ...</code> trajectory averaged extxyz Octahedral tilt <code>gpumdkit.sh -calc oct-tilt ...</code> trajectory + B-O neighbor list tilt-angle table ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 ...</code> trajectory + neighbor lists polarization table Plane-grid plot <code>gpumdkit.sh -plt plane-grid ...</code> structure + displacement data plane profile plot"},{"location":"en/polar_material_analysis.html#dependency","title":"Dependency","text":"<p>These scripts require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"en/polar_material_analysis.html#interactive-mode-entry","title":"Interactive mode entry","text":"<p>Options <code>406-410</code> are the core functions for this tutorial. The sections below explain when to use each one and how to run it.</p> <pre><code>gpumdkit.sh\n# choose 4) Calculators\n</code></pre> <p>The calculator menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre> <p>For full argument details, use:</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"en/polar_material_analysis.html#406-build-neighbor-list-calc_neighbor_listpy","title":"406) Build neighbor list (<code>calc_neighbor_list.py</code>)","text":"<p>Build neighbor lists for selected center and neighbor elements.</p> <p>When to use it: This is usually the first step before <code>disp</code>, <code>oct-tilt</code>, and <code>pol-abo3</code>, because those scripts read <code>nl-*.dat</code> neighbor files.</p>"},{"location":"en/polar_material_analysis.html#usage","title":"Usage","text":"<pre><code># Example 1: Ti-O nearest 6 neighbors for octahedral analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# Example 2: Pb/Sr-O nearest 12 neighbors for A-site centered analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input structure file. Default: <code>model.xyz</code>.</li> <li><code>-x, --index</code>:   Frame index to read from input. Default: <code>0</code>.</li> <li><code>-c, --cutoff</code> (required):   Neighbor search cutoff (Angstrom).</li> <li><code>-n, --neighbor-num</code> (required):   Number of neighbors per center.</li> <li><code>-d, --defect</code>:   Defect mode. If enabled and neighbors are insufficient, missing slots are filled with the center index.</li> <li><code>-C, --center-elements</code> (required):   Center species list.</li> <li><code>-E, --neighbor-elements</code> (required):   Neighbor species list.</li> <li><code>-o, --output</code>:   Output file path. Default: <code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file","title":"Output file","text":"<ul> <li>Main output: neighbor list text file (for example <code>nl-Ti-O.dat</code>).</li> <li>The file is a 2D integer array with shape <code>(n_center, neighbor_num + 1)</code>. Each row corresponds to one center atom: the first column is the center index, and the remaining columns are its neighbor indices (all 1-based).</li> </ul>"},{"location":"en/polar_material_analysis.html#407-calc-displacement-from-trajectory-calc_displacementpy","title":"407) Calc displacement from trajectory (<code>calc_displacement.py</code>)","text":"<p>Compute local displacement vectors from a trajectory/model and a neighbor list.</p>"},{"location":"en/polar_material_analysis.html#usage_1","title":"Usage","text":"<pre><code># Example 1: single-frame displacement from model.xyz\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# Example 2: use the last 20% frames in movie.xyz\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_1","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   Neighbor list file from <code>nlist</code>.</li> <li><code>-o, --output</code>:   Output file. Default: <code>displacements.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames.   Integer: last <code>N</code> frames.   <code>0 &lt; value &lt; 1</code>: last ratio of frames.</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_1","title":"Output file","text":"<ul> <li>Main output: <code>displacements.dat</code> (or your custom output name).</li> <li>The saved text file is a 2D array: for a single-frame input, its shape is <code>(n_center, 3)</code>; for a multi-frame input, it is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The three columns are <code>dx</code>, <code>dy</code>, and <code>dz</code> displacement components in Angstrom.</li> </ul>"},{"location":"en/polar_material_analysis.html#408-calc-averaged-structure-calc_averaged_structurepy","title":"408) Calc averaged structure (<code>calc_averaged_structure.py</code>)","text":"<p>Generate one averaged structure from selected trajectory frames. Use this after equilibration. For a solid near equilibrium, average a frame window at the target temperature and analyze that representative structure instead of processing every snapshot.</p>"},{"location":"en/polar_material_analysis.html#usage_2","title":"Usage","text":"<pre><code># Example 1: average all frames\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# Example 2: average selected frames (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_2","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input trajectory file. Default: <code>movie.xyz</code>.</li> <li><code>-o, --output</code>:   Output structure file. Default: <code>averaged_structure.xyz</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_2","title":"Output file","text":"<ul> <li>Main output: averaged single-frame extxyz file.</li> <li>Position averaging applies MIC/PBC correction relative to the first selected frame.</li> </ul>"},{"location":"en/polar_material_analysis.html#409-calc-octahedral-tilt-calc_oct_tiltpy","title":"409) Calc octahedral tilt (<code>calc_oct_tilt.py</code>)","text":"<p>Calculate octahedral tilt angles from a B-O neighbor list. This is commonly used to analyze octahedral rotation patterns in <code>ABO3</code> systems, such as <code>SrTiO3</code> and <code>PbZrO3</code>.</p>"},{"location":"en/polar_material_analysis.html#usage_3","title":"Usage","text":"<pre><code># Example 1: octahedral tilt of the TiO6 octahedra from a single frame\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# Example 2: octahedral tilt of the TiO6 octahedra from the last 20% trajectory frames\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_3","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   B-O neighbor list file.</li> <li><code>-o, --output</code>:   Output file. Default: <code>octahedral_tilt.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_3","title":"Output file","text":"<ul> <li>Main output: <code>octahedral_tilt.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>theta_x</code>, <code>theta_y</code>, <code>theta_z</code>, in degree): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#410-calc-polarization-for-abo3-calc_polarization_abo3py","title":"410) Calc polarization for ABO3 (<code>calc_polarization_abo3.py</code>)","text":"<p>Calculate local polarization vectors for <code>ABO3</code> systems.</p>"},{"location":"en/polar_material_analysis.html#usage_4","title":"Usage","text":"<pre><code># Example 1: single-frame ABO3 polarization\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# Example 2: trajectory polarization on a selected frame window\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_4","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>--nl-ba</code> (required):   B-A neighbor list.</li> <li><code>--nl-bo</code> (required):   B-O neighbor list.</li> <li><code>-o, --output</code>:   Output file. Default: <code>polarization.dat</code>.</li> <li><code>--bec</code> (required):   Born effective charge terms in <code>Element=value</code> format.   Example: <code>Pb=2.5 Ti=4.0 O=-2.0</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul> <p>Important checks:</p> <ul> <li><code>--bec</code> must include all element species in the input structure.</li> <li>Center atom indices in <code>--nl-ba</code> and <code>--nl-bo</code> must match.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_4","title":"Output file","text":"<ul> <li>Main output: <code>polarization.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>Px</code>, <code>Py</code>, <code>Pz</code>, in <code>C/m^2</code>): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The script prints a warning if the total Born charge is not balanced.</li> </ul>"},{"location":"en/polar_material_analysis.html#plane-grid-visualization-plt_plane_gridpy","title":"Plane-grid visualization (<code>plt_plane_grid.py</code>)","text":"<p>You can visualize either <code>displacements.dat</code> or <code>polarization.dat</code>:</p> <pre><code># Example 1: displacement map on Ti sites, first XY layer\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# Example 2: polarization map on Pb sites, XZ and YZ layers\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>Arguments (complete):</p> <ul> <li><code>-i, --input</code>:   Input xyz file for atomic layout and layering. Default: <code>model.xyz</code>.</li> <li><code>-d, --disp</code>:   Vector-field data file. Default: <code>displacements.dat</code>.</li> <li><code>-e, --elements</code> (required):   Center element symbols used to map vectors to lattice layers.</li> <li><code>-m, --tol</code>:   Layer tolerance for grid mapping. Default: <code>1.0</code>.</li> <li><code>-g, --target-size</code>:   Expected grid size as <code>nx ny nz</code>.</li> <li><code>-o, --save-dir</code>:   Figure output directory. Default: <code>plot</code>.</li> <li><code>-f, --frame</code>:   Frame index to visualize when vector data has multiple frames. Default: <code>0</code>.</li> <li><code>--select-xy</code>:   Selected XY layer indices.</li> <li><code>--select-xz</code>:   Selected XZ layer indices.</li> <li><code>--select-yz</code>:   Selected YZ layer indices.</li> </ul> <p>Output:</p> <ul> <li>Creates output directory if needed.</li> <li>Saves figures as <code>XY_*.png</code>, <code>XZ_*.png</code>, <code>YZ_*.png</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-files-at-a-glance","title":"Output files at a glance","text":"Script Main output What it stores <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based center index + neighbor indices <code>calc_displacement.py</code> <code>*.dat</code> Local displacement vectors (<code>dx dy dz</code>, Angstrom) <code>calc_averaged_structure.py</code> <code>*.xyz</code> One averaged structure <code>calc_oct_tilt.py</code> <code>*.dat</code> Octahedral tilt angles (<code>theta_x theta_y theta_z</code>, degree) <code>calc_polarization_abo3.py</code> <code>*.dat</code> Local polarization vectors (<code>Px Py Pz</code>, <code>C/m^2</code>) <code>plt_plane_grid.py</code> <code>plot/*.png</code> XY/XZ/YZ plane maps from vector-field data"},{"location":"en/polar_material_analysis.html#real-examples","title":"Real Examples","text":""},{"location":"en/polar_material_analysis.html#temperature-driven-ferroelectric-to-paraelectric-phase-transition-for-pbtio3","title":"Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3","text":"<p>Assume all files are in the current directory <code>./</code>:</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> is the initial structure used to run MD simulations. Each <code>TEMP K.xyz</code> is a trajectory at that temperature.</p>"},{"location":"en/polar_material_analysis.html#step-1-get-averaged-structures-from-the-last-half-of-each-trajectory","title":"Step 1: get averaged structures from the last half of each trajectory","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>This writes <code>300K-avg.xyz</code>, <code>350K-avg.xyz</code>, ..., <code>800K-avg.xyz</code>.</p>"},{"location":"en/polar_material_analysis.html#step-2-build-neighbor-lists-from-modelxyz","title":"Step 2: build neighbor lists from <code>model.xyz</code>","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-compute-displacement-and-polarization-for-each-temperature","title":"Step 3: compute displacement and polarization for each temperature","text":"<p>Use Born effective charges (BEC), not nominal ionic charges. For PbTiO3 in this example:</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>You can obtain BEC from your own DFPT calculation or from literature values. Thus use following commands to compute local displacement and polarization:</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-4-plot-displacement-and-polarization-maps-in-real-space","title":"Step 4: plot displacement and polarization maps in real space","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-5-build-a-temperature-order-parameter-curve","title":"Step 5: build a temperature-order-parameter curve","text":"<p>By analyzing the lattice of each temperature-averaged structure together with its polarization (<code>XX-pol.dat</code>), we can obtain the following figure:</p> <p>The trend shows a clear phase transition around <code>600 K</code>, where the polarization vanishes.</p>"},{"location":"en/polar_material_analysis.html#topological-structure-in-pbtio3srtio3-superlattice","title":"Topological structure in PbTiO3/SrTiO3 superlattice","text":"<p>Assume <code>movie.xyz</code> is the trajectory of the PbTiO3/SrTiO3 superlattice in the current directory.</p>"},{"location":"en/polar_material_analysis.html#step-1-build-an-averaged-structure-from-the-last-25-frames","title":"Step 1: build an averaged structure from the last 25% frames","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-2-build-the-ti-neighbor-list","title":"Step 2: build the Ti neighbor list","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-plot-the-plane-grid-map","title":"Step 3: plot the plane-grid map","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero.</p> <p>Note: the example figure uses a custom colormap. The default GPUMDkit output uses a different style, which can be adjusted by editing the plotting script.</p>"},{"location":"en/polar_material_analysis.html#other-systems","title":"Other Systems","text":""},{"location":"en/polar_material_analysis.html#organic-inorganic-hybrid-ferroelectrics","title":"Organic-inorganic hybrid ferroelectrics","text":"<p>In many organic-inorganic ferroelectrics, polarization is strongly tied to anisotropic molecular units. A practical way to track molecular orientation is to use bond vectors.</p> <p>For TMCM-CdCl3, you can use the C-Cl bond direction of the TMCM molecule as an orientation proxy, then use it to estimate the polarization state:</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p><code>ccl_vectors.dat</code> can then be analyzed as an orientation order parameter. More details could be found at: Phys. Rev. Lett. 136, 016801</p>"},{"location":"en/polar_material_analysis.html#other-ferroelectric-families","title":"Other ferroelectric families","text":"<p>Beyond <code>ABO3</code>, <code>ferrodispcalc</code> can be adapted to many ferroelectric systems, including nitrides, hafnia-based compounds, organic-inorganic hybrids, and some 2D ferroelectrics.</p>"},{"location":"en/quick_start.html","title":"Quick Start","text":"\ud83d\ude80 Quick Start <p>This page helps you install GPUMDkit and run your first commands. You can use GPUMDkit through an interactive menu or direct command-line options.</p>"},{"location":"en/quick_start.html#what-it-does","title":"What it does","text":"<p>GPUMDkit provides a single entry point for common tasks in computational materials science \u2014 format conversion, structure analysis, property calculation, and visualization \u2014 without writing custom scripts.</p>"},{"location":"en/quick_start.html#before-you-start","title":"Before you start","text":""},{"location":"en/quick_start.html#1-prepare-a-python-environment","title":"1. Prepare a Python environment","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>Some optional functions require additional packages:</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>Other Python dependencies are loaded by the corresponding scripts. If a package is missing, Python will report it when that function is used.</p>"},{"location":"en/quick_start.html#2-install-gpumdkit","title":"2. Install GPUMDkit","text":"<p>Clone the repository and run the installer:</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre> <p>The installer writes <code>GPUMDkit_path</code> and <code>PATH</code> settings to your shell configuration and loads them for the current shell. It writes to <code>~/.bashrc</code> by default; if the current shell is zsh, it writes to <code>~/.zshrc</code>. If an existing GPUMDkit path is found, the installer prints the old path and asks whether to replace it. Before changing the rc file, it creates a backup.</p> <p>Typical installation output:</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>If GPUMDkit was installed before, you may see:</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre>"},{"location":"en/quick_start.html#3-verify-the-installation","title":"3. Verify the installation","text":"<pre><code>gpumdkit.sh -h\n</code></pre> <p>This prints a help table listing all available options.</p>"},{"location":"en/quick_start.html#interactive-mode","title":"Interactive mode","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>This opens the main menu:</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre> <p>Select a module by number. Each module provides sub-menus with specific functions.</p>"},{"location":"en/quick_start.html#cli-mode","title":"CLI mode","text":"<p>Direct commands use fixed positional arguments:</p> <pre><code>gpumdkit.sh -&lt;option&gt; [args...]\n</code></pre> <p>Examples:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>The first example reads <code>POSCAR</code> and writes <code>model.xyz</code>.</p>"},{"location":"en/quick_start.html#common-examples","title":"Common examples","text":""},{"location":"en/quick_start.html#convert-a-poscar-to-extxyz","title":"Convert a POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"en/quick_start.html#add-gpumd-group-labels","title":"Add GPUMD group labels","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>Group labels are used by some GPUMD-related workflows that need atom grouping, such as species-specific MSD or diffusion calculations.</p>"},{"location":"en/quick_start.html#plot-nep-training-results","title":"Plot NEP training results","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/quick_start.html#plot-nep-test-results","title":"Plot NEP test results","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"en/quick_start.html#plot-thermodynamic-data","title":"Plot thermodynamic data","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/quick_start.html#plot-msd-and-self-diffusion-coefficient","title":"Plot MSD and self-diffusion coefficient","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/quick_start.html#notes","title":"Notes","text":"<ul> <li>Use <code>gpumdkit.sh -h</code> to see all available options.</li> <li>Use <code>gpumdkit.sh -&lt;option&gt; -h</code> to get help for a specific option (e.g., <code>gpumdkit.sh -plt train -h</code>).</li> <li>For detailed usage of each module, see the corresponding tutorial pages linked in the index.</li> </ul>"},{"location":"en/structure_sampling.html","title":"Structure Sampling","text":"\ud83d\udce6 Structure Sampling <p>Structure sampling is used to select, generate, or filter candidate configurations for NEP training and molecular dynamics workflows.</p> <p>Script Location: <code>Scripts/sample_structures/</code></p>"},{"location":"en/structure_sampling.html#interactive-mode","title":"Interactive Mode","text":"<p>Sampling tasks are usually easier to run from the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>2) Sample Structures\n</code></pre> <p>The menu is:</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Method Use Case 201 Uniform/random sampling quick frame selection from a trajectory 202 PyNEP notice prints a notice; use <code>gpumdkit.sh -pynep</code> to run PyNEP 203 NepTrain FPS descriptor-based FPS with NepTrain 204 Perturb structure generate perturbed structures from POSCAR/CONTCAR 205 Force-deviation selection select structures with high model deviation"},{"location":"en/structure_sampling.html#uniform-and-random-sampling","title":"Uniform and Random Sampling","text":"<p>From interactive mode, choose <code>201</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>Example input:</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>or:</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>uniform</code> / <code>random</code> sampling method <code>50</code> / <code>100</code> number of selected structures <code>500</code> optional number of initial frames to skip <p>Output:</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#farthest-point-sampling-with-neptrain","title":"Farthest Point Sampling with NepTrain","text":"<p>This entry uses NepTrain descriptors for FPS. Choose <code>203</code> in interactive mode, or run the script directly:</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>From interactive mode, choose <code>203</code>. You will see:</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>Inputs:</p> File Meaning <code>dump.xyz</code> candidate structures <code>train.xyz</code> existing training set <code>nep.txt</code> current NEP model used to compute descriptors <p>Outputs:</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>During execution, choose one of two selection modes:</p> <ol> <li>select until the descriptor distance is below a threshold;</li> <li>select a specified number of structures.</li> </ol> <p>The script then prints a selection prompt:</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>This function requires the <code>NepTrain</code> package. If you use this function, we recommend citing the NepTrain paper printed by the script.</p>"},{"location":"en/structure_sampling.html#deprecated-pynep-fps","title":"Deprecated PyNEP FPS","text":"<p>PyNEP FPS is kept for compatibility, but it is only exposed through the direct <code>-pynep</code> entry.</p> <p>If you choose <code>202</code> from the interactive menu, it prints:</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre>"},{"location":"en/structure_sampling.html#serial-pynep","title":"Serial PyNEP","text":"<pre><code>python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"en/structure_sampling.html#parallel-pynep","title":"Parallel PyNEP","text":"<pre><code>python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8\n</code></pre> <p>The last argument is the number of CPU threads.</p>"},{"location":"en/structure_sampling.html#gpumdkit-entry","title":"GPUMDkit Entry","text":"<pre><code>gpumdkit.sh -pynep\n</code></pre> <p>Then input:</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>This entry requires <code>pynep</code> and is kept for compatibility.</p>"},{"location":"en/structure_sampling.html#structure-perturbation","title":"Structure Perturbation","text":"<p>Use perturbation when you want to generate initial structures around a known configuration. Choose <code>204</code> in interactive mode, or run the script directly:</p> <pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>From interactive mode, choose <code>204</code>. You will see:</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input VASP structure <code>20</code> number of perturbed structures <code>0.03</code> cell perturbation fraction <code>0.2</code> atom perturbation distance in Angstrom <code>uniform</code> perturbation style: <code>normal</code>, <code>uniform</code>, or <code>const</code> <p>Output:</p> <ul> <li><code>POSCAR_01.vasp</code>, <code>POSCAR_02.vasp</code>, ...</li> </ul> <p>This function requires <code>dpdata</code>. If you use this function, we recommend citing the dpdata package.</p>"},{"location":"en/structure_sampling.html#force-deviation-selection","title":"Force-Deviation Selection","text":"<p>Use this together with the GPUMD <code>active</code> command. The <code>active</code> command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. <code>select_max_modev.py</code> selects structures with large force deviations from <code>active.out</code> and <code>active.xyz</code>, then writes them to <code>selected.xyz</code>.</p> <p>Choose <code>205</code> in interactive mode, or run the script directly:</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>From interactive mode, choose <code>205</code>. You will see:</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>200</code> maximum number of structures to keep <code>0.15</code> minimum force deviation threshold <p>Required files:</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>Output:</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#frame-range-extraction","title":"Frame Range Extraction","text":"<p><code>frame_range.py</code> is an independent CLI tool and is not part of the interactive sampling menu <code>201\u2013205</code>. Use it when you want to keep only a fraction of a trajectory before sampling, for example after equilibration.</p> <pre><code>gpumdkit.sh -frame_range dump.xyz 0 0.8\npython Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>This writes frames from 0% to 80% of the trajectory. The range arguments are trajectory fractions from <code>0</code> to <code>1</code>.</p>"},{"location":"en/structure_sampling.html#example-commands","title":"Example Commands","text":"<p>An example preprocessing-and-sampling sequence is shown below. The first two commands are analyzer tools; the final step is structure sampling.</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>The final step can also be run from interactive mode by choosing <code>2) Sample Structures -&gt; 203</code>.</p>"},{"location":"en/structure_sampling.html#common-mistakes","title":"Common Mistakes","text":"Problem Recommendation FPS selects too many similar structures increase the distance threshold or select fewer structures Perturbed structures are unphysical reduce <code>cell_pert</code> and <code>atom_pert</code>, then check minimum distances <code>active.out</code> and <code>active.xyz</code> do not match regenerate both from the same GPUMD active run PCA plot looks strange check whether <code>nep.txt</code> matches the chemical species in both datasets"},{"location":"en/workflow_scripts.html","title":"Workflow Scripts","text":"\ud83d\udd27 Workflow Scripts <p>Workflow scripts automate repetitive preparation steps for DFT, MD, and NEP development.</p> <p>Script Location: <code>Scripts/workflow/</code></p>"},{"location":"en/workflow_scripts.html#interactive-entry","title":"Interactive Entry","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>3) Workflow\n</code></pre> <p>The workflow menu looks like:</p> <pre><code>+---------------------------------------------------------+\n|                      WORKFLOW TOOLS                     |\n+---------------------------------------------------------+\n| 301) SCF batch pretreatment                             |\n| 302) MD sample batch pretreatment (gpumd)               |\n| 303) MD sample batch pretreatment (lmp)                 |\n+---------------------------------------------------------+\n| 000) Return to the main menu                            |\n+---------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Workflow Purpose 301 SCF batch pretreatment Prepare single-point DFT calculations 302 MD sample batch pretreatment (GPUMD) Prepare GPUMD sampling calculations 303 MD sample batch pretreatment (LAMMPS) Prepare LAMMPS sampling calculations"},{"location":"en/workflow_scripts.html#scf-batch-pretreatment","title":"SCF Batch Pretreatment","text":"<p>Use this when you have many structures and want to prepare single-point DFT calculations.</p>"},{"location":"en/workflow_scripts.html#vasp","title":"VASP","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>Before running, put structure files in the current directory. The script checks files in this order:</p> <ol> <li>if one or more <code>.vasp</code> files exist, it processes <code>.vasp</code> files;</li> <li>if both <code>.vasp</code> and <code>.xyz</code> files exist, it prints a notice and only processes <code>.vasp</code> files;</li> <li>if no <code>.vasp</code> file exists and one <code>.xyz</code> file exists, it converts that extxyz file to POSCAR files;</li> <li>if no <code>.vasp</code> file exists and multiple <code>.xyz</code> files exist, it asks you to choose one.</li> </ol> <p>Typical input directory before running:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>INCAR</code>, <code>POTCAR</code>, and <code>KPOINTS</code> in the generated <code>fp/</code> directory after the script creates it. The calculation folders link to files in <code>fp/</code>.</p> <p>The <code>prefix</code> you input during the workflow becomes the calculation folder prefix. When <code>out2xyz</code> is later used to extract results, the folder name is stored as <code>config_type</code> in the extxyz file, which makes it easier to trace where each structure came from.</p>"},{"location":"en/workflow_scripts.html#cp2k","title":"CP2K","text":"<p>CP2K SCF batch pretreatment is available from the workflow menu and can also be called directly:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>The interactive wrapper asks for:</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>Example:</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>The template should be configured to read coordinates from <code>pos.xyz</code>. A reference template is available at:</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>The script creates <code>&lt;prefix&gt;_&lt;index&gt;/</code> directories, writes <code>input.inp</code>, and writes <code>pos.xyz</code> for each structure.</p>"},{"location":"en/workflow_scripts.html#md-sampling-pretreatment","title":"MD Sampling Pretreatment","text":""},{"location":"en/workflow_scripts.html#gpumd","title":"GPUMD","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 302\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. The detection order is the same as the VASP SCF workflow: <code>.vasp</code> files are preferred; if multiple <code>.xyz</code> files are found without <code>.vasp</code>, the script asks you to choose one.</p> <p>Typical input directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>nep.txt</code> and <code>run_*.in</code> files in the generated <code>md/</code> directory. The script links <code>run_1.in</code> to <code>sample_1/run.in</code>, <code>run_2.in</code> to <code>sample_2/run.in</code>, and so on.</p>"},{"location":"en/workflow_scripts.html#lammps","title":"LAMMPS","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 303\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. <code>.vasp</code> files are preferred when both formats exist.</p> <p>After running, the script creates LAMMPS data files in <code>struct_md/</code>, sample folders, and an <code>md/</code> directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>lmprun.in</code> and <code>nep.txt</code> in the generated <code>md/</code> directory.</p>"},{"location":"en/workflow_scripts.html#active-learning-style-workflow","title":"Active-Learning Style Workflow","text":"<p>A common NEP improvement loop is:</p> <ol> <li>run MD with the current <code>nep.txt</code>;</li> <li>collect <code>dump.xyz</code> or <code>active.xyz</code>;</li> <li>remove unphysical structures;</li> <li>select diverse or uncertain structures;</li> <li>run DFT single-point calculations;</li> <li>convert DFT results to extxyz;</li> <li>append new structures to <code>train.xyz</code>;</li> <li>retrain the NEP model.</li> </ol> <p>For the development active-learning script, see Active Learning.</p>"},{"location":"en/workflow_scripts.html#template-based-temperature-series","title":"Template-Based Temperature Series","text":"<p>For a simple temperature series, a shell loop is often enough:</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>Then submit the generated folders according to your local cluster system.</p>"},{"location":"en/workflow_scripts.html#practical-notes","title":"Practical Notes","text":"<ul> <li>Workflow scripts are cluster- and template-dependent. Always test with a small number of structures first.</li> <li>Keep template files (<code>INCAR</code>, <code>KPOINTS</code>, <code>POTCAR</code>, <code>run.in</code>, CP2K inputs) under version control if possible.</li> <li>Check generated folders before submitting a large batch.</li> <li>Use analyzers and sampling scripts before expensive DFT calculations.</li> </ul>"},{"location":"zh/index.html","title":"GPUMDkit \u6559\u7a0b","text":"\ud83d\udcda GPUMDkit \u6559\u7a0b <p>\u6b22\u8fce\u4f7f\u7528 GPUMDkit\uff0c\u8fd9\u662f\u4e00\u4e2a\u9762\u5411 GPUMD \u548c NEP \u7684\u547d\u4ee4\u884c\u5de5\u5177\u5305\u3002</p>"},{"location":"zh/index.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>GPUMDkit \u5e2e\u52a9\u4f60\u5728\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u7814\u7a76\u4e2d\u5b8c\u6210\u5e38\u89c1\u4efb\u52a1\uff0c\u65e0\u9700\u7f16\u5199\u81ea\u5b9a\u4e49\u811a\u672c\u3002\u5b83\u652f\u6301\u683c\u5f0f\u8f6c\u6362\u3001\u7ed3\u6784\u5206\u6790\u3001\u6027\u8d28\u8ba1\u7b97\u3001\u53ef\u89c6\u5316\u548c\u6279\u91cf\u5de5\u4f5c\u6d41\u2014\u2014\u5168\u90e8\u901a\u8fc7\u4e00\u4e2a\u547d\u4ee4\u884c\u5de5\u5177\u5b8c\u6210\u3002</p>"},{"location":"zh/index.html#_2","title":"\u5e38\u89c1\u4efb\u52a1","text":"\u6211\u60f3\u8981... \u6559\u7a0b \u5b89\u88c5 GPUMDkit \u5e76\u8fd0\u884c\u7b2c\u4e00\u4e2a\u547d\u4ee4 \u5feb\u901f\u5165\u95e8 \u5c06 VASP\u3001LAMMPS\u3001CP2K \u6216 CIF \u6587\u4ef6\u8f6c\u6362\u4e3a extxyz \u683c\u5f0f\u8f6c\u6362 \u68c0\u67e5\u7ed3\u6784\u8ddd\u79bb\u3001\u8fc7\u6ee4\u6570\u636e\u96c6\u6216\u67e5\u627e\u5f02\u5e38\u503c \u5206\u6790\u5de5\u5177 \u8ba1\u7b97 MSD\u3001\u79bb\u5b50\u7535\u5bfc\u7387\u6216\u63cf\u8ff0\u7b26 \u8ba1\u7b97\u5668\u811a\u672c \u5206\u6790\u6781\u6027\u6750\u6599\u3001\u94c1\u7535\u4f53\u6216 ABO3 \u4f53\u7cfb \u6781\u6027\u6750\u6599\u5206\u6790 \u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c\u6216\u70ed\u529b\u5b66\u6570\u636e \u7ed8\u56fe\u811a\u672c \u8fd0\u884c\u6279\u91cf DFT \u6216 MD \u6a21\u62df \u5de5\u4f5c\u6d41\u811a\u672c \u4ece\u6570\u636e\u96c6\u4e2d\u9009\u62e9\u4ee3\u8868\u6027\u7ed3\u6784 \u7ed3\u6784\u91c7\u6837 \u6dfb\u52a0\u81ea\u5df1\u7684 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u81ea\u5b9a\u4e49\u547d\u4ee4"},{"location":"zh/index.html#_3","title":"\u51c6\u5907\u5de5\u4f5c","text":""},{"location":"zh/index.html#_4","title":"\u5b89\u88c5","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"zh/index.html#_5","title":"\u4f9d\u8d56","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"zh/index.html#_6","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u6253\u5f00\u83dc\u5355\u540e\uff0c\u6309\u6570\u5b57\u9009\u62e9\u6a21\u5757\u3002</p>"},{"location":"zh/index.html#_7","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n</code></pre> <p>\u4f8b\u5982\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>\u4f7f\u7528 <code>gpumdkit.sh -h</code> \u67e5\u770b\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</p>"},{"location":"zh/index.html#_8","title":"\u6a21\u5757\u6982\u89c8","text":"\u6a21\u5757 \u83dc\u5355 CLI \u63cf\u8ff0 \u683c\u5f0f\u8f6c\u6362 1 <code>-out2xyz</code>, <code>-pos2exyz</code> \u6587\u4ef6\u8f6c\u6362 \u7ed3\u6784\u91c7\u6837 2 \u4ea4\u4e92\u83dc\u5355\u3001<code>-frame_range</code>\u3001<code>-pynep</code>\uff08\u5df2\u5f03\u7528\uff09 \u7ed3\u6784\u91c7\u6837 \u5de5\u4f5c\u6d41 3 - \u6279\u5904\u7406 \u8ba1\u7b97\u5668 4 <code>-calc &lt;\u7c7b\u578b&gt;</code> \u5c5e\u6027\u8ba1\u7b97 \u5206\u6790\u5de5\u5177 5 <code>-range</code>, <code>-min_dist</code> \u7ed3\u6784\u5206\u6790 \u53ef\u89c6\u5316 6 <code>-plt &lt;\u7c7b\u578b&gt;</code> \u7ed8\u56fe\u5de5\u5177 \u5b9e\u7528\u5de5\u5177 7 <code>-time</code>, <code>-clean</code> \u5b9e\u7528\u529f\u80fd"},{"location":"zh/index.html#_9","title":"\u5168\u90e8\u6559\u7a0b","text":"\u6559\u7a0b \u63cf\u8ff0 \u5feb\u901f\u5165\u95e8 \u5b89\u88c5\u548c\u7b2c\u4e00\u6b65 \u547d\u4ee4\u53c2\u8003 \u5e38\u7528 CLI \u548c\u83dc\u5355\u5165\u53e3\u901f\u67e5 \u683c\u5f0f\u8f6c\u6362 \u5728\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362 \u8ba1\u7b97\u5668\u811a\u672c \u8ba1\u7b97\u6750\u6599\u5c5e\u6027 \u5206\u6790\u5de5\u5177 \u7ed3\u6784\u5206\u6790\u548c\u9a8c\u8bc1 \u7ed8\u56fe\u811a\u672c \u7ed8\u56fe\u548c\u53ef\u89c6\u5316 \u5de5\u4f5c\u6d41\u811a\u672c \u6279\u5904\u7406\u548c\u81ea\u52a8\u5316 \u7ed3\u6784\u91c7\u6837 \u7ed3\u6784\u9009\u62e9\u65b9\u6cd5 \u81ea\u5b9a\u4e49\u547d\u4ee4 \u7528\u6237\u81ea\u5b9a\u4e49 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 \u6279\u91cf\u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\u8bf4\u660e \u6781\u6027\u6750\u6599\u5206\u6790 \u94c1\u7535\u548c\u6781\u5316\u76f8\u5173\u5de5\u5177 \u8d21\u732e\u6307\u5357 \u5f00\u53d1\u548c\u8d21\u732e\u8bf4\u660e"},{"location":"zh/index.html#_10","title":"\u94fe\u63a5","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>\u6587\u6863: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html","title":"\u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41","text":"\ud83d\udd01 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 <p><code>workflow_active_learning_dev.sh</code> \u7528\u4e8e\u7ec4\u7ec7\u4e00\u8f6e NEP \u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\uff1a\u8fd0\u884c GPUMD \u5206\u5b50\u52a8\u529b\u5b66\u3001\u7b5b\u9009\u7ed3\u6784\u3001\u62bd\u6837\u3001\u63d0\u4ea4\u7b2c\u4e00\u6027\u539f\u7406\u8ba1\u7b97\uff0c\u5e76\u8fdb\u884c NEP \u9884\u6d4b\u68c0\u67e5\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#_1","title":"\u6982\u89c8","text":"<p>\u8be5\u811a\u672c\u81ea\u52a8\u5316\u4e86 NEP \u4e3b\u52a8\u5b66\u4e60\u7684\u4e00\u8f6e\u8fed\u4ee3\u3002\u5178\u578b\u6d41\u7a0b\u5305\u62ec\uff1a</p> \u6b65\u9aa4 \u64cd\u4f5c \u76ee\u7684 1 \u8fd0\u884c MD \u6a21\u62df \u4f7f\u7528\u5f53\u524d NEP \u6a21\u578b\u751f\u6210\u5019\u9009\u7ed3\u6784 2 \u8fc7\u6ee4\u7ed3\u6784 \u79fb\u9664\u4e0d\u5408\u7406\u7684\u6784\u578b\uff08\u77ed\u8ddd\u79bb\u3001\u5927\u76d2\u5b50\uff09 3 \u91c7\u6837\u7ed3\u6784 \u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\u8fdb\u884c DFT \u8ba1\u7b97 4 \u8fd0\u884c SCF \u8ba1\u7b97 \u8ba1\u7b97 DFT \u53c2\u8003\u80fd\u91cf/\u529b 5 NEP \u9884\u6d4b \u68c0\u67e5\u6a21\u578b\u5728\u65b0\u7ed3\u6784\u4e0a\u7684\u7cbe\u5ea6 <p>\u4e0e\u83dc\u5355\u9a71\u52a8\u7684\u6a21\u5757\u4e0d\u540c\uff0c\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u662f\u4e00\u4e2a\u9700\u8981\u6309\u4f53\u7cfb\u4fee\u6539\u540e\u76f4\u63a5\u8fd0\u884c\u7684 shell \u811a\u672c\uff1a</p> <pre><code>bash Scripts/workflow/workflow_active_learning_dev.sh\n</code></pre> <p>\u4e0b\u9762\u6309\u811a\u672c\u4e2d\u7684\u4e3b\u8981\u4ee3\u7801\u5757\u8bf4\u660e\u6bcf\u4e00\u6b65\u7684\u4f5c\u7528\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#1-slurm","title":"1. SLURM \u8bbe\u7f6e","text":"<p>\u811a\u672c\u5f00\u5934\u5305\u542b\u96c6\u7fa4\u63d0\u4ea4\u53c2\u6570\uff0c\u4f8b\u5982\uff1a</p> <pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>\u8fd9\u4e9b\u53c2\u6570\u9700\u8981\u6839\u636e\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u4fee\u6539\u3002\u5982\u679c\u6ca1\u6709 SLURM \u73af\u5883\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u540e\u53f0\u8fd0\u884c\uff1a</p> <pre><code>nohup bash workflow_active_learning_dev.sh &gt; workflow.log 2&gt;&amp;1 &amp;\n</code></pre>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#2","title":"2. \u57fa\u672c\u8bbe\u7f6e","text":"<p>\u811a\u672c\u4f1a\u8fdb\u5165\u63d0\u4ea4\u76ee\u5f55\uff0c\u5e76\u52a0\u8f7d\u63d0\u4ea4\u6a21\u677f\uff1a</p> <pre><code>cd $SLURM_SUBMIT_DIR\nsource ${GPUMDkit_path}/Scripts/workflow/submit_template.sh\npython_pynep=python\n</code></pre> <ul> <li><code>GPUMDkit_path</code> \u662f\u5b89\u88c5\u811a\u672c\u5199\u5165\u7684 GPUMDkit \u8def\u5f84\u3002</li> <li><code>python_pynep</code> \u4ec5\u7528\u4e8e\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#3","title":"3. \u4e3b\u8981\u53d8\u91cf","text":"<p>\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u9002\u5408\u5df2\u7ecf\u6709\u521d\u59cb <code>nep.txt</code>\u3001<code>nep.in</code>\u3001<code>train.xyz</code> \u548c GPUMD/DFT \u8f93\u5165\u6587\u4ef6\uff0c\u5e76\u5e0c\u671b\u5728\u96c6\u7fa4\u4e0a\u81ea\u52a8\u6269\u5c55\u8bad\u7ec3\u96c6\u7684\u60c5\u51b5\u3002</p> <p>\u811a\u672c\u5f00\u5934\u901a\u5e38\u9700\u8981\u6839\u636e\u4f53\u7cfb\u4fee\u6539\uff1a</p> <pre><code>work_dir=${PWD}\nprefix_name=LiF_iter01\nmin_dist=1.4\nbox_limit=13\nmax_fp_num=50\nsample_method=pynep\npynep_sample_dist=0.01\n</code></pre> <ul> <li><code>prefix_name</code> \u7528\u4e8e\u547d\u540d\u672c\u8f6e\u8ba1\u7b97\u3002</li> <li><code>min_dist</code> \u548c <code>box_limit</code> \u7528\u4e8e\u8fc7\u6ee4\u660e\u663e\u4e0d\u5408\u7406\u7684\u7ed3\u6784\u3002</li> <li><code>max_fp_num</code> \u63a7\u5236\u6700\u591a\u63d0\u4ea4\u591a\u5c11\u4e2a\u5355\u70b9\u8ba1\u7b97\u3002</li> <li><code>sample_method</code> \u53ef\u9009 <code>uniform</code>\u3001<code>random</code> \u6216 <code>pynep</code>\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#4","title":"4. \u68c0\u67e5\u8f93\u5165\u6587\u4ef6","text":"<p>\u5e38\u89c1\u8f93\u5165\u5305\u62ec\uff1a</p> <ul> <li><code>nep.txt</code></li> <li><code>nep.in</code></li> <li><code>train.xyz</code></li> <li><code>run.in</code></li> <li><code>INCAR</code></li> <li><code>POTCAR</code></li> <li><code>KPOINTS</code></li> <li>\u521d\u59cb\u91c7\u6837\u7ed3\u6784\u6587\u4ef6\uff0c\u4f8b\u5982 <code>sample_struct.xyz</code></li> </ul> <p>\u811a\u672c\u4f1a\u628a\u516c\u5171\u8f93\u5165\u79fb\u52a8\u5230 <code>common/</code>\uff0c\u5e76\u521b\u5efa <code>00.modev/</code>\u3001<code>01.select/</code> \u7b49\u5de5\u4f5c\u76ee\u5f55\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#5","title":"5. \u6587\u4ef6\u7ec4\u7ec7","text":"<p>\u811a\u672c\u4f1a\u521b\u5efa\u516c\u5171\u8f93\u5165\u76ee\u5f55\u548c MD \u76ee\u5f55\uff1a</p> <pre><code>mkdir 00.modev common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.modev\n</code></pre> <ul> <li><code>00.modev</code>\uff1a\u7528\u4e8e\u8fd0\u884c GPUMD MD \u91c7\u6837\u3002</li> <li><code>common</code>\uff1a\u4fdd\u5b58 <code>nep.txt</code>\u3001<code>run.in</code>\u3001\u7ed3\u6784\u6587\u4ef6\u548c DFT \u8f93\u5165\u6587\u4ef6\u7b49\u516c\u5171\u8d44\u6e90\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#6-md","title":"6. \u63d0\u4ea4 MD \u4efb\u52a1","text":"<pre><code>submit_gpumd_array modev ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>\u811a\u672c\u4f1a\u901a\u8fc7\u63d0\u4ea4\u6a21\u677f\u521b\u5efa\u6570\u7ec4\u4efb\u52a1\u3002\u4e0d\u540c\u96c6\u7fa4\u4e0a\u7684\u63d0\u4ea4\u547d\u4ee4\u548c\u6a21\u677f\u53ef\u80fd\u9700\u8981\u81ea\u5df1\u4fee\u6539\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#7","title":"7. \u68c0\u67e5\u4efb\u52a1\u5b8c\u6210","text":"<p>\u811a\u672c\u4f1a\u6301\u7eed\u68c0\u67e5 <code>00.modev/</code> \u4e0b\u5404\u4e2a <code>sample_*/log</code> \u6587\u4ef6\uff0c\u786e\u8ba4\u662f\u5426\u51fa\u73b0\uff1a</p> <pre><code>Finished running GPUMD.\n</code></pre> <p>\u5982\u679c\u53d1\u73b0 <code>Error</code>\uff0c\u811a\u672c\u4f1a\u505c\u6b62\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#8","title":"8. \u5206\u6790\u548c\u8fc7\u6ee4\u7ed3\u6784","text":"<p>MD \u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u8fdb\u5165 <code>01.select</code>\uff0c\u5bf9 <code>dump.xyz</code> \u4e2d\u7684\u7ed3\u6784\u8fdb\u884c\u7b5b\u9009\u3002\u5e38\u89c1\u68c0\u67e5\u5305\u62ec\uff1a</p> <ul> <li>\u6700\u5c0f\u539f\u5b50\u8ddd\u79bb\uff1b</li> <li>\u6a21\u62df\u76d2\u5b50\u8fb9\u957f\uff1b</li> <li>\u7ed3\u6784\u6570\u91cf\u662f\u5426\u8d85\u8fc7 <code>max_fp_num</code>\u3002</li> </ul> <p>\u8fd9\u4e9b\u6b65\u9aa4\u4f1a\u8c03\u7528 analyzer \u548c sample_structures \u4e2d\u7684\u811a\u672c\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#9","title":"9. \u62bd\u6837\u65b9\u6cd5","text":"<p>\u811a\u672c\u6839\u636e <code>sample_method</code> \u9009\u62e9\u62bd\u6837\u65b9\u5f0f\uff1a</p> <pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <ul> <li><code>uniform</code>\uff1a\u5747\u5300\u62bd\u5e27\uff1b</li> <li><code>random</code>\uff1a\u968f\u673a\u62bd\u5e27\uff1b</li> <li><code>pynep</code>\uff1a\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#10-scf","title":"10. \u63d0\u4ea4 SCF \u8ba1\u7b97","text":"<p>\u62bd\u6837\u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u63d0\u4ea4 VASP \u5355\u70b9\u8ba1\u7b97\uff1a</p> <pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>\u8fd9\u91cc\u7684 <code>prefix_name</code> \u4f1a\u7528\u4e8e\u8ba1\u7b97\u76ee\u5f55\u547d\u540d\uff0c\u4e5f\u65b9\u4fbf\u540e\u7eed\u8ffd\u8e2a\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#11-prediction","title":"11. Prediction \u6b65\u9aa4","text":"<p>\u6700\u540e\u811a\u672c\u4f1a\u63d0\u4ea4 NEP prediction\uff0c\u7528\u4e8e\u68c0\u67e5\u5f53\u524d\u6a21\u578b\u5728\u65b0\u589e\u7ed3\u6784\u4e0a\u7684\u8bef\u5dee\u3002</p> <p>\u8fd9\u4e2a\u811a\u672c\u548c\u8ba1\u7b97\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u4f7f\u7528\u524d\u5efa\u8bae\u5148\u7528\u5c0f\u4f53\u7cfb\u6216\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u4e00\u8f6e\uff0c\u5e76\u68c0\u67e5\u63d0\u4ea4\u6a21\u677f\u3001\u8def\u5f84\u548c\u8f93\u5165\u6587\u4ef6\u662f\u5426\u7b26\u5408\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html","title":"\u5206\u6790\u5de5\u5177","text":"\ud83d\udd0d \u5206\u6790\u5de5\u5177 <p>\u5206\u6790\u811a\u672c\u4e3a extxyz \u6570\u636e\u96c6\u63d0\u4f9b\u7ed3\u6784\u7edf\u8ba1\u3001\u8ddd\u79bb\u68c0\u67e5\u3001\u8fc7\u6ee4\u3001\u6210\u5206\u5206\u6790\u3001\u5f02\u5e38\u68c0\u6d4b\u548c\u65f6\u95f4\u4f30\u7b97\u529f\u80fd\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>\u672c\u6a21\u5757\u5e2e\u52a9\u4f60\u68c0\u67e5\u3001\u8fc7\u6ee4\u548c\u9a8c\u8bc1\u7ed3\u6784\u6570\u636e\u96c6\u3002\u53ef\u4ee5\u68c0\u67e5\u6210\u5206\u3001\u5206\u6790\u6027\u8d28\u8303\u56f4\u3001\u68c0\u6d4b\u77ed\u8ddd\u79bb\u63a5\u89e6\u3001\u6309\u5404\u79cd\u6761\u4ef6\u8fc7\u6ee4\u7ed3\u6784\u3001\u67e5\u627e NEP \u8bad\u7ec3\u6570\u636e\u4e2d\u7684\u5f02\u5e38\u503c\uff0c\u4ee5\u53ca\u4f30\u7b97\u5269\u4f59\u6a21\u62df\u65f6\u95f4\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":"<p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/analyzer/</code></p> <p>\u786e\u4fdd\u5df2\u5b89\u88c5 GPUMDkit\u3002\u5b89\u88c5\u8bf4\u660e\u8bf7\u53c2\u89c1\u5feb\u901f\u5165\u95e8\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_3","title":"\u6982\u89c8","text":"\u4efb\u52a1 \u547d\u4ee4 \u7528\u9014 \u6210\u5206\u5206\u6790 <code>gpumdkit.sh -analyze_comp train.xyz</code> \u6309\u5316\u5b66\u6210\u5206\u5206\u7ec4 \u5316\u5b66\u7269\u79cd <code>gpumdkit.sh -chem_species train.xyz</code> \u5217\u51fa\u6587\u4ef6\u4e2d\u7684\u5143\u7d20 \u6027\u8d28\u8303\u56f4 <code>gpumdkit.sh -range train.xyz force</code> \u68c0\u67e5\u80fd\u91cf/\u529b/virial \u8303\u56f4 \u6700\u77ed\u8ddd\u79bb <code>gpumdkit.sh -min_dist dump.xyz</code> \u5feb\u901f\u8ddd\u79bb\u68c0\u67e5\uff08\u65e0 PBC\uff09 \u6700\u77ed\u8ddd\u79bb\uff08PBC\uff09 <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> \u51c6\u786e\u8ddd\u79bb\u68c0\u67e5\uff08\u542b PBC\uff09 \u7535\u8377\u5e73\u8861 <code>gpumdkit.sh -cbc train.xyz</code> \u6c27\u5316\u6001\u5e73\u8861\u68c0\u67e5 \u8ddd\u79bb\u8fc7\u6ee4 <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> \u79fb\u9664\u77ed\u8ddd\u79bb\u63a5\u89e6\u7684\u7ed3\u6784 \u76d2\u5b50\u8fc7\u6ee4 <code>gpumdkit.sh -filter_box dump.xyz 13</code> \u79fb\u9664\u76d2\u5b50\u8fc7\u5927\u7684\u7ed3\u6784 \u6027\u8d28\u8fc7\u6ee4 <code>gpumdkit.sh -filter_value train.xyz force 20</code> \u6309\u80fd\u91cf/\u529b/virial \u9608\u503c\u8fc7\u6ee4 \u5bf9\u8ddd\u79bb\u8303\u56f4 <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> \u6309\u5bf9\u8ddd\u79bb\u63d0\u53d6\u7ed3\u6784 \u5f02\u5e38\u68c0\u6d4b \u83dc\u5355 502 \u67e5\u627e\u8bad\u7ec3\u96c6\u4e2d\u9ad8 RMSE \u7684\u7ed3\u6784 \u6982\u7387\u5bc6\u5ea6 <code>gpumdkit.sh -pda &lt;\u53c2\u8003\u7ed3\u6784&gt; &lt;\u8f68\u8ff9&gt; &lt;\u5143\u7d20&gt; &lt;\u7f51\u683c\u95f4\u8ddd&gt;</code> 3D \u6982\u7387\u5bc6\u5ea6\u5206\u6790\u6269\u6563\u901a\u9053 GPUMD \u65f6\u95f4 <code>gpumdkit.sh -time gpumd</code> \u4f30\u7b97 GPUMD \u5269\u4f59\u8fd0\u884c\u65f6\u95f4 NEP \u65f6\u95f4 <code>gpumdkit.sh -time nep</code> \u4f30\u7b97 NEP \u5269\u4f59\u8bad\u7ec3\u65f6\u95f4"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_4","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit \u5e76\u9009\u62e9 <code>5) Analyzer</code>\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u5206\u6790\u5de5\u5177\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                    ANALYZER TOOLS                    |\n+------------------------------------------------------+\n| 501) Analyze composition of extxyz                   |\n| 502) Find outliers of extxyz                         |\n| 503) Analyze chemical species of extxyz              |\n| 504) Check charge balance of extxyz                  |\n| 505) Analyze energy/force/virial range               |\n| 506) Filter structures by minimum distance           |\n| 507) Get minimum interatomic distance                |\n| 508) Probability density analysis                    |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5927\u591a\u6570\u5206\u6790\u529f\u80fd\u4e5f\u63d0\u4f9b\u76f4\u63a5 CLI \u8c03\u7528\u65b9\u5f0f\uff0c\u6982\u89c8\u8868\u548c\u540e\u7eed\u5c0f\u8282\u4e2d\u5217\u51fa\u4e86\u5e38\u7528\u547d\u4ee4\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_5","title":"\u6210\u5206\u5206\u6790","text":"<p><code>analyze_composition.py</code> \u5206\u6790 extxyz \u6587\u4ef6\u7684\u6210\u5206\uff0c\u5e76\u5141\u8bb8\u5bfc\u51fa\u5b50\u96c6\u3002</p> <p>\u529f\u80fd\uff1a \u6309\u5316\u5b66\u6210\u5206\u5bf9\u7ed3\u6784\u5206\u7ec4\uff0c\u5e76\u663e\u793a\u6bcf\u79cd\u6210\u5206\u7684\u7ed3\u6784\u6570\u91cf\u3002\u53ef\u4ee5\u6309\u6210\u5206\u5bfc\u51fa\u5b50\u96c6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>501</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>\u5f53 <code>train.xyz</code> \u5305\u542b\u4e0d\u540c\u4f53\u7cfb\u6216\u4e0d\u540c\u5c3a\u5bf8\u7684\u7ed3\u6784\u65f6\u5f88\u6709\u7528\u3002\u53ef\u4ee5\u4ece\u4ea4\u4e92\u63d0\u793a\u4e2d\u6309\u6210\u5206\u5bfc\u51fa\u5b50\u96c6\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_6","title":"\u5316\u5b66\u7269\u79cd","text":"<p><code>analyze_chem_species.py</code> \u5217\u51fa extxyz \u6587\u4ef6\u4e2d\u6240\u6709\u552f\u4e00\u7684\u5316\u5b66\u7269\u79cd\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -chem_species train.xyz\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_7","title":"\u6027\u8d28\u8303\u56f4\u5206\u6790","text":"<p><code>energy_force_virial_analyzer.py</code> \u8ba1\u7b97\u5e76\u53ef\u89c6\u5316 extxyz \u6587\u4ef6\u4e2d\u6027\u8d28\u7684\u8303\u56f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <p>\u652f\u6301\u7684\u6027\u8d28\uff1a <code>energy</code>\u3001<code>force</code>\u3001<code>virial</code></p> <pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist    # \u663e\u793a\u76f4\u65b9\u56fe\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Force range: 0.03210566767721861 to 9.230115912468435\n</code></pre> <p>\u4f7f\u7528 <code>hist</code> \u9009\u9879\uff1a</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_8","title":"\u6700\u77ed\u8ddd\u79bb\u68c0\u67e5","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#pbc","title":"\u65e0 PBC\uff08\u5feb\u901f\uff09","text":"<p><code>get_min_dist.py</code> \u8ba1\u7b97\u4e0d\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u7684\u6700\u77ed\u539f\u5b50\u95f4\u8ddd\u3002\u901f\u5ea6\u5feb\uff0c\u4f46\u5bf9\u5468\u671f\u6027\u4f53\u7cfb\u53ef\u80fd\u4e0d\u51c6\u786e\u3002</p> <p>\u529f\u80fd\uff1a \u62a5\u544a\u6bcf\u5e27\u4e2d\u6bcf\u5bf9\u5143\u7d20\u4e4b\u95f4\u7684\u6700\u77ed\u8ddd\u79bb\uff0c\u5ffd\u7565\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>507</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>+---------------------------+\n|   PBC ignored for speed   |\n| use -min_dist_pbc for PBC |\n+---------------------------+\nMinimum interatomic distances:\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.480     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre> <p>\u8bf4\u660e\uff1a \u7528\u4e8e\u5feb\u901f\u68c0\u67e5\u3002\u5bf9\u4e8e\u5468\u671f\u6027\u4f53\u7cfb\uff0c\u5efa\u8bae\u4f7f\u7528 <code>-min_dist_pbc</code> \u83b7\u5f97\u51c6\u786e\u7ed3\u679c\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#pbc_1","title":"\u542b PBC\uff08\u51c6\u786e\uff09","text":"<p><code>get_min_dist_pbc.py</code> \u8ba1\u7b97\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u7684\u6700\u77ed\u539f\u5b50\u95f4\u8ddd\u3002</p> <p>\u529f\u80fd\uff1a \u62a5\u544a\u6bcf\u5bf9\u5143\u7d20\u4e4b\u95f4\u7684\u6700\u77ed\u8ddd\u79bb\uff0c\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>507</code>\uff0c\u5f53\u63d0\u793a\u662f\u5426\u8003\u8651 PBC \u65f6\u8f93\u5165 <code>y</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_9","title":"\u7ed3\u6784\u8fc7\u6ee4","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_10","title":"\u6309\u6700\u77ed\u8ddd\u79bb\u8fc7\u6ee4","text":"<p><code>filter_structures_by_distance_pbc.py</code> \u79fb\u9664\u4efb\u4f55\u539f\u5b50\u95f4\u8ddd\u4f4e\u4e8e\u9608\u503c\u7684\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>\u79fb\u9664\u4efb\u4f55\u539f\u5b50\u95f4\u8ddd\u4f4e\u4e8e <code>1.0 \u00c5</code> \u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_11","title":"\u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4","text":"<p><code>filter_exyz_by_box.py</code> \u6309\u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>\u4fdd\u7559\u6240\u6709\u76d2\u5b50\u8fb9\u957f\u4f4e\u4e8e <code>13 \u00c5</code> \u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_12","title":"\u6309\u6027\u8d28\u503c\u8fc7\u6ee4","text":"<p><code>filter_exyz_by_value.py</code> \u6309\u80fd\u91cf\u3001\u529b\u6216 virial \u9608\u503c\u8fc7\u6ee4\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <p>\u652f\u6301\u7684\u6027\u8d28\uff1a <code>energy</code>\u3001<code>force</code>\u3001<code>virial</code></p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre> <p>\u8fc7\u6ee4\u6389\u529b\u5206\u91cf\u8d85\u8fc7 <code>20 eV/\u00c5</code>\uff08\u6216\u80fd\u91cf\u8d85\u8fc7 <code>5 eV/atom</code>\uff09\u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_13","title":"\u6309\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4","text":"<p><code>filter_dist_range.py</code> \u63d0\u53d6\u7279\u5b9a\u5143\u7d20\u5bf9\u8ddd\u79bb\u5728\u7ed9\u5b9a\u8303\u56f4\u5185\u7684\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>\u63d0\u53d6 Li-Li \u6700\u77ed\u8ddd\u79bb\u5728 <code>1.8 \u00c5</code> \u5230 <code>2.0 \u00c5</code> \u4e4b\u95f4\u7684\u7ed3\u6784\u3002\u8f93\u51fa\uff1a<code>filtered_Li_Li_1.8_2.0.xyz</code>\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_14","title":"\u7535\u8377\u5e73\u8861\u68c0\u67e5","text":"<p><code>charge_balance_check.py</code> \u68c0\u67e5\u7ed3\u6784\u7684\u6c27\u5316\u6001\u5e73\u8861\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>\u8f93\u51fa\u6587\u4ef6\uff1a</p> <ul> <li><code>balanced.xyz</code> \u2014 \u7535\u8377\u5e73\u8861\u7684\u7ed3\u6784</li> <li><code>unbalanced.xyz</code> \u2014 \u7535\u8377\u4e0d\u5e73\u8861\u7684\u7ed3\u6784</li> <li><code>indices.txt</code> \u2014 \u5e73\u8861\u7ed3\u6784\u7684\u7d22\u5f15</li> </ul> <p>\u9002\u7528\u4e8e\u5177\u6709\u660e\u786e\u6c27\u5316\u6001\u7684\u4f53\u7cfb\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_15","title":"\u5f02\u5e38\u68c0\u6d4b","text":"<p><code>find_outliers.py</code> \u57fa\u4e8e\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u7684 RMSE \u9608\u503c\u67e5\u627e NEP \u8bad\u7ec3\u6570\u636e\u4e2d\u7684\u5f02\u5e38\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>stress_train.out</code>\u3001<code>train.xyz</code></p> <p>\u8fd9\u4e9b\u6587\u4ef6\u5728 NEP \u8bad\u7ec3\u8fc7\u7a0b\u4e2d\u751f\u6210\u3002\u811a\u672c\u6bd4\u8f83 DFT \u4e0e NEP \u7684\u9884\u6d4b\uff0c\u8bc6\u522b\u8bef\u5dee\u8f83\u5927\u7684\u7ed3\u6784\u3002</p> <pre><code># \u4ea4\u4e92\u6a21\u5f0f\ngpumdkit.sh    # \u9009\u62e9\uff1a5) \u5206\u6790\u5de5\u5177 \u2192 502) \u67e5\u627e\u5f02\u5e38\u7ed3\u6784\n</code></pre> <p>\u4ea4\u4e92\u63d0\u793a\uff1a</p> <pre><code>Enter energy RMSE threshold (meV/atom): 1\nEnter force RMSE threshold (meV/\u00c5): 60\nEnter stress RMSE threshold (GPa): 0.03\n</code></pre> <p>\u8f93\u51fa\u6587\u4ef6\uff1a</p> <ul> <li><code>selected.xyz</code> \u2014 \u8d85\u8fc7 RMSE \u9608\u503c\u7684\u7ed3\u6784\uff08\u5f02\u5e38\u503c\uff09</li> <li><code>remained.xyz</code> \u2014 \u5728\u9608\u503c\u5185\u7684\u7ed3\u6784</li> <li><code>selected_remained.png</code> \u2014 \u5bf9\u6bd4\u56fe</li> </ul> <p>\u7528\u9014\uff1a NEP \u8bad\u7ec3\u540e\uff0c\u7528\u6b64\u5de5\u5177\u8bc6\u522b\u5bf9\u8bef\u5dee\u8d21\u732e\u6700\u5927\u7684\u95ee\u9898\u7ed3\u6784\u3002\u79fb\u9664\u6216\u6539\u8fdb\u8fd9\u4e9b\u7ed3\u6784\u4ee5\u63d0\u5347\u8bad\u7ec3\u96c6\u8d28\u91cf\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_16","title":"\u65f6\u95f4\u4f30\u7b97","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#gpumd","title":"GPUMD \u5269\u4f59\u65f6\u95f4","text":"<p><code>time_consuming_gpumd.sh</code> \u4f30\u7b97 GPUMD \u6a21\u62df\u7684\u5269\u4f59\u65f6\u95f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>run.in</code>\u3001<code>thermo.out</code>\uff08\u5728\u5f53\u524d GPUMD \u5de5\u4f5c\u76ee\u5f55\u4e2d\uff09</p> <pre><code>gpumdkit.sh -time gpumd\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>----------------- System Information ----------------\ntotal frames: 1050000\n-----------------------------------------------------\nCurrent Frame  Speed (steps/s)   Total Time       Time Left       Estimated End\n-------------   -------------   -------------   -------------   -----------------\n    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04\n    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#nep","title":"NEP \u5269\u4f59\u65f6\u95f4","text":"<p><code>time_consuming_nep.sh</code> \u4f30\u7b97 NEP \u8bad\u7ec3\u7684\u5269\u4f59\u65f6\u95f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code>\uff08\u5728\u5f53\u524d NEP \u5de5\u4f5c\u76ee\u5f55\u4e2d\uff09</p> <pre><code>gpumdkit.sh -time nep\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>+-----------------+-----------+-----------------+---------------------+\n|       Step      | Time Diff |    Time Left    |    Finish Time      |\n+-----------------+-----------+-----------------+---------------------+\n| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |\n| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |\n| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |\n+-----------------+-----------+-----------------+---------------------+\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_17","title":"\u6982\u7387\u5bc6\u5ea6\u5206\u6790","text":"<p><code>probability_density_analysis.py</code> \u8ba1\u7b97\u79fb\u52a8\u79bb\u5b50\u7684 3D \u6982\u7387\u5bc6\u5ea6\uff0c\u7528\u4e8e\u6269\u6563\u901a\u9053\u5206\u6790\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a \u53c2\u8003\u7ed3\u6784\uff08POSCAR\uff09\u3001\u8f68\u8ff9\u6587\u4ef6\uff08extxyz\uff09</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n</code></pre> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>LLZO.vasp</code> \u53c2\u8003\u7ed3\u6784\uff08POSCAR \u683c\u5f0f\uff09 <code>dump.xyz</code> \u8f68\u8ff9\u6587\u4ef6\uff08extxyz \u683c\u5f0f\uff09 <code>Li</code> \u76ee\u6807\u79fb\u52a8\u79bb\u5b50 <code>0.25</code> \u6982\u7387\u5bc6\u5ea6\u7f51\u683c\u95f4\u8ddd\uff08\u00c5\uff09 <p>\u8f93\u51fa\uff1a <code>probability_density_0.25.vasp</code> \u2014 VASP \u683c\u5f0f\u7684\u6982\u7387\u5bc6\u5ea6\u7f51\u683c\uff0c\u53ef\u7528 VESTA \u7b49\u5de5\u5177\u53ef\u89c6\u5316\u3002</p> <p>\u53ef\u89c6\u5316\u5efa\u8bae\uff1a</p> <ol> <li>\u5728 VESTA \u4e2d\u6253\u5f00 <code>probability_density_0.25.vasp</code></li> <li>\u4f7f\u7528 \"Edit \u2192 Data \u2192 Volumetric Data\" \u8c03\u6574\u7b49\u503c\u9762\u7ea7\u522b</li> <li>\u6309\u6570\u503c\u5bf9\u6982\u7387\u5bc6\u5ea6\u7740\u8272\uff0c\u4ee5\u7a81\u51fa\u4f18\u9009\u6269\u6563\u8def\u5f84</li> <li>\u53e0\u52a0\u6676\u4f53\u7ed3\u6784\u4f5c\u4e3a\u53c2\u8003</li> </ol>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_18","title":"\u793a\u4f8b\u5de5\u4f5c\u6d41","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_19","title":"\u7ed3\u6784\u8d28\u91cf\u68c0\u67e5","text":"<pre><code># 1. \u68c0\u67e5\u6210\u5206\ngpumdkit.sh -analyze_comp train.xyz\n\n# 2. \u68c0\u67e5\u80fd\u91cf/\u529b\u8303\u56f4\ngpumdkit.sh -range train.xyz force hist\n\n# 3. \u68c0\u67e5\u6700\u77ed\u8ddd\u79bb\ngpumdkit.sh -min_dist_pbc train.xyz\n\n# 4. \u67e5\u627e\u5f02\u5e38\u503c\uff08NEP \u8bad\u7ec3\u540e\uff09\n# \u4ea4\u4e92\uff1a5) \u5206\u6790\u5de5\u5177 \u2192 502\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_20","title":"\u7ed3\u6784\u8fc7\u6ee4\u6d41\u6c34\u7ebf","text":"<pre><code># 1. \u6309\u6700\u77ed\u8ddd\u79bb\u8fc7\u6ee4\ngpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n\n# 2. \u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4\ngpumdkit.sh -filter_box filtered_dist_pbc.xyz 13\n\n# 3. \u6309\u529b\u9608\u503c\u8fc7\u6ee4\ngpumdkit.sh -filter_value filtered_box.xyz force 20\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_21","title":"\u6269\u6563\u901a\u9053\u5206\u6790","text":"<pre><code># 1. \u8ba1\u7b97\u6982\u7387\u5bc6\u5ea6\ngpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n\n# 2. \u7528 VESTA \u53ef\u89c6\u5316\n# \u6253\u5f00 probability_density_0.25.vasp\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html","title":"\u547d\u4ee4\u53c2\u8003","text":"\ud83d\udccb \u547d\u4ee4\u53c2\u8003 <p>\u672c\u9875\u5217\u51fa GPUMDkit \u7a33\u5b9a\u7684\u547d\u4ee4\u884c\u5feb\u6377\u5165\u53e3\u3002\u5bf9\u4e8e\u53c2\u6570\u8f83\u591a\u3001\u9700\u8981\u9009\u62e9\u7684\u4efb\u52a1\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528\u4ea4\u4e92\u6a21\u5f0f\u3002</p> <p>\u6e90\u8868\u7ef4\u62a4\u5728 <code>docs/command_reference.tsv</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#gpumdkitsh-h","title":"<code>gpumdkit.sh -h</code> \u8f93\u51fa","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |\n| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_1","title":"\u4e3b\u547d\u4ee4","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-h</code> <code>gpumdkit.sh -h</code> \u663e\u793a\u901a\u7528\u5e2e\u52a9 <code>-update</code> <code>gpumdkit.sh -update</code> \u66f4\u65b0 GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> \u6e05\u7406\u5f53\u524d\u76ee\u5f55\u4e2d\u7684\u5197\u4f59\u6587\u4ef6"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_2","title":"\u683c\u5f0f\u8f6c\u6362","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K \u8f93\u51fa\u8f6c xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR \u8f6c extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF \u8f6c POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF \u8f6c extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR \u8f6c extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz \u591a\u5e27\u8f6c POSCAR \u6587\u4ef6 <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR \u8f6c LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump \u8f6c extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory \u8f6c extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> \u6309\u6676\u80de\u500d\u6570\u6269\u80de <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> \u6309\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> \u6dfb\u52a0 GPUMD group \u6807\u7b7e <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> \u6dfb\u52a0\u7ed3\u6784\u6743\u91cd <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> \u63d0\u53d6\u5355\u5e27 <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> \u6e05\u7406 extxyz \u5197\u4f59\u5c5e\u6027 <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> \u6309\u6bd4\u4f8b\u8303\u56f4\u63d0\u53d6\u5e27"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_3","title":"\u8ba1\u7b97\u5668","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> \u79bb\u5b50\u7535\u5bfc\u7387 <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP \u6027\u8d28\u9884\u6d4b <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP \u63cf\u8ff0\u7b26 <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u57fa\u4e8e NEP \u7684 NEB <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784\u4f18\u5316 <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> \u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> \u90bb\u5c45\u5217\u8868 <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> \u4f4d\u79fb <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> \u5e73\u5747\u7ed3\u6784 <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> \u516b\u9762\u4f53\u503e\u659c <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 \u5c40\u57df\u6781\u5316"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_4","title":"\u5206\u6790\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> \u6027\u8d28\u8303\u56f4\u5206\u6790 <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> \u6210\u5206\u5206\u6790 <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> \u5143\u7d20\u5217\u8868 <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> \u7535\u8377\u5e73\u8861\u68c0\u67e5 <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> \u65e0 PBC \u6700\u5c0f\u8ddd\u79bb <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> \u5e26 PBC \u6700\u5c0f\u8ddd\u79bb <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u5e26 PBC \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> \u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4 <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> \u6027\u8d28\u9608\u503c\u8fc7\u6ee4 <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> \u5143\u7d20\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4 <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> \u6982\u7387\u5bc6\u5ea6\u5206\u6790"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_5","title":"\u53ef\u89c6\u5316","text":"<p>\u4f7f\u7528\uff1a</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>\u5e38\u7528\u7c7b\u578b\u5305\u62ec <code>train</code>\u3001<code>prediction</code>\u3001<code>thermo</code>\u3001<code>msd</code>\u3001<code>sdc</code>\u3001<code>rdf</code>\u3001<code>emd</code>\u3001<code>nemd</code>\u3001<code>hnemd</code>\u3001<code>pdos</code> \u548c <code>plane-grid</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_6","title":"\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> \u76d1\u63a7 GPUMD \u6216 NEP \u8fdb\u5ea6 <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> \u4ea4\u4e92\u5f0f\u4fee\u6539 NEP \u6a21\u578b <code>-pynep</code> <code>gpumdkit.sh -pynep</code> \u5df2\u5f03\u7528\u7684 PyNEP FPS \u91c7\u6837"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html","title":"\u5de5\u4f5c\u6d41\u811a\u672c","text":"\ud83d\udd27 \u5de5\u4f5c\u6d41\u811a\u672c <p>\u5de5\u4f5c\u6d41\u811a\u672c\u7528\u4e8e\u81ea\u52a8\u5316\u91cd\u590d\u6027\u7684 DFT\u3001MD \u548c NEP \u6570\u636e\u51c6\u5907\u6b65\u9aa4\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_1","title":"\u4ea4\u4e92\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>3) Workflow\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+---------------------------------------------------------+\n|                      WORKFLOW TOOLS                     |\n+---------------------------------------------------------+\n| 301) SCF batch pretreatment                             |\n| 302) MD sample batch pretreatment (gpumd)               |\n| 303) MD sample batch pretreatment (lmp)                 |\n+---------------------------------------------------------+\n| 000) Return to the main menu                            |\n+---------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u5de5\u4f5c\u6d41 \u7528\u9014 301 SCF batch pretreatment \u51c6\u5907 DFT \u5355\u70b9\u8ba1\u7b97 302 MD sample batch pretreatment (GPUMD) \u51c6\u5907 GPUMD \u91c7\u6837\u8ba1\u7b97 303 MD sample batch pretreatment (LAMMPS) \u51c6\u5907 LAMMPS \u91c7\u6837\u8ba1\u7b97"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#scf","title":"SCF \u6279\u5904\u7406\u9884\u5904\u7406","text":"<p>\u9002\u7528\u4e8e\u5df2\u6709\u591a\u4e2a\u7ed3\u6784\uff0c\u9700\u8981\u51c6\u5907\u7b2c\u4e00\u6027\u539f\u7406\u5355\u70b9\u8ba1\u7b97\u7684\u60c5\u51b5\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#vasp","title":"VASP","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a\u7ed3\u6784\u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u811a\u672c\u6309\u4ee5\u4e0b\u987a\u5e8f\u68c0\u6d4b\uff1a</p> <ol> <li>\u5982\u679c\u5b58\u5728\u4e00\u4e2a\u6216\u591a\u4e2a <code>.vasp</code> \u6587\u4ef6\uff0c\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c <code>.vasp</code> \u548c <code>.xyz</code> \u540c\u65f6\u5b58\u5728\uff0c\u4f1a\u6253\u5370\u63d0\u793a\uff0c\u5e76\u53ea\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u53ea\u6709\u4e00\u4e2a <code>.xyz</code>\uff0c\u4f1a\u628a\u8fd9\u4e2a extxyz \u8f6c\u4e3a POSCAR \u6587\u4ef6\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</li> </ol> <p>\u8fd0\u884c\u524d\u7684\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>fp/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u7528\u6237\u628a <code>INCAR</code>\u3001<code>POTCAR</code>\u3001<code>KPOINTS</code> \u653e\u5230 <code>fp/</code> \u4e2d\uff0c\u8ba1\u7b97\u76ee\u5f55\u4f1a\u94fe\u63a5\u8fd9\u91cc\u7684\u6587\u4ef6\u3002</p> <p>\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u8f93\u5165\u7684 <code>prefix</code> \u4f1a\u4f5c\u4e3a\u8ba1\u7b97\u6587\u4ef6\u5939\u540d\u524d\u7f00\u3002\u540e\u7eed\u4f7f\u7528 <code>out2xyz</code> \u63d0\u53d6\u7ed3\u679c\u65f6\uff0c\u6587\u4ef6\u5939\u540d\u4f1a\u4f5c\u4e3a <code>config_type</code> \u5199\u5165 extxyz\uff0c\u4fbf\u4e8e\u4e4b\u540e\u68c0\u67e5\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#cp2k","title":"CP2K","text":"<p>CP2K \u53ef\u4ee5\u4ece\u4ea4\u4e92\u83dc\u5355\u8fdb\u5165\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u547d\u4ee4\u884c\u8c03\u7528\uff1a</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4f1a\u8981\u6c42\u8f93\u5165\uff1a</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>CP2K \u6a21\u677f\u5e94\u8bbe\u7f6e\u4e3a\u4ece <code>pos.xyz</code> \u8bfb\u53d6\u5750\u6807\u3002\u53c2\u8003\u6a21\u677f\u5728\uff1a</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>\u811a\u672c\u4f1a\u4e3a\u6bcf\u4e2a\u7ed3\u6784\u751f\u6210 <code>&lt;prefix&gt;_&lt;index&gt;/</code> \u76ee\u5f55\uff0c\u5e76\u5199\u5165 <code>input.inp</code> \u548c <code>pos.xyz</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#md","title":"MD \u91c7\u6837\u9884\u5904\u7406","text":""},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#gpumd","title":"GPUMD","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 302\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u68c0\u6d4b\u987a\u5e8f\u4e0e VASP SCF \u9884\u5904\u7406\u4e00\u81f4\uff1a\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</p> <p>\u8fd0\u884c\u524d\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>md/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>nep.txt</code> \u548c <code>run_*.in</code> \u653e\u5165 <code>md/</code>\u3002\u4f8b\u5982 <code>run_1.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_1/run.in</code>\uff0c<code>run_2.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_2/run.in</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#lammps","title":"LAMMPS","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 303\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\uff1b\u4e24\u79cd\u683c\u5f0f\u540c\u65f6\u5b58\u5728\u65f6\u4f18\u5148\u5904\u7406 <code>.vasp</code>\u3002</p> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>lmprun.in</code> \u548c <code>nep.txt</code> \u653e\u5230 <code>md/</code> \u4e2d\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_2","title":"\u4e3b\u52a8\u5b66\u4e60\u5f0f\u6d41\u7a0b","text":"<p>\u5e38\u89c1 NEP \u6570\u636e\u8fed\u4ee3\u6d41\u7a0b\uff1a</p> <ol> <li>\u4f7f\u7528\u5f53\u524d <code>nep.txt</code> \u8fd0\u884c MD\uff1b</li> <li>\u6536\u96c6 <code>dump.xyz</code> \u6216 <code>active.xyz</code>\uff1b</li> <li>\u5220\u9664\u660e\u663e\u4e0d\u5408\u7406\u7ed3\u6784\uff1b</li> <li>\u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\uff1b</li> <li>\u8fd0\u884c DFT \u5355\u70b9\uff1b</li> <li>\u5c06 DFT \u7ed3\u679c\u8f6c\u6362\u4e3a extxyz\uff1b</li> <li>\u8ffd\u52a0\u5230 <code>train.xyz</code>\uff1b</li> <li>\u91cd\u65b0\u8bad\u7ec3 NEP\u3002</li> </ol> <p>\u66f4\u5b8c\u6574\u7684\u5f00\u53d1\u7248\u4e3b\u52a8\u5b66\u4e60\u811a\u672c\u8bf4\u660e\u89c1 \u4e3b\u52a8\u5b66\u4e60\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_3","title":"\u57fa\u4e8e\u6a21\u677f\u7684\u6e29\u5ea6\u7cfb\u5217","text":"<p>\u5bf9\u4e8e\u7b80\u5355\u7684\u6e29\u5ea6\u7cfb\u5217\u6a21\u62df\uff0c\u4f7f\u7528 shell \u5faa\u73af\u5373\u53ef\uff1a</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>\u7136\u540e\u6839\u636e\u4f60\u7684\u96c6\u7fa4\u7cfb\u7edf\u63d0\u4ea4\u751f\u6210\u7684\u6587\u4ef6\u5939\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_4","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u5de5\u4f5c\u6d41\u811a\u672c\u548c\u96c6\u7fa4\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u6279\u91cf\u63d0\u4ea4\u524d\u5148\u7528\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u3002</li> <li>\u6a21\u677f\u6587\u4ef6\u5982 <code>INCAR</code>\u3001<code>KPOINTS</code>\u3001<code>POTCAR</code>\u3001<code>run.in</code> \u5e94\u4ed4\u7ec6\u68c0\u67e5\u3002</li> <li>\u6279\u91cf DFT \u524d\u5148\u7528\u5206\u6790\u548c\u91c7\u6837\u811a\u672c\u6e05\u7406\u5019\u9009\u7ed3\u6784\u3002</li> </ul>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html","title":"\u5feb\u901f\u5165\u95e8","text":"\ud83d\ude80 \u5feb\u901f\u5165\u95e8 <p>\u672c\u9875\u5e2e\u52a9\u4f60\u5b89\u88c5 GPUMDkit \u5e76\u8fd0\u884c\u7b2c\u4e00\u4e2a\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u6216\u76f4\u63a5\u4f7f\u7528\u547d\u4ee4\u884c\u9009\u9879\u6765\u4f7f\u7528 GPUMDkit\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>GPUMDkit \u4e3a\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u7684\u5e38\u89c1\u4efb\u52a1\u63d0\u4f9b\u7edf\u4e00\u5165\u53e3\u2014\u2014\u683c\u5f0f\u8f6c\u6362\u3001\u7ed3\u6784\u5206\u6790\u3001\u6027\u8d28\u8ba1\u7b97\u548c\u53ef\u89c6\u5316\u2014\u2014\u65e0\u9700\u7f16\u5199\u81ea\u5b9a\u4e49\u811a\u672c\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#1-python","title":"1. \u51c6\u5907 Python \u73af\u5883","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>\u90e8\u5206\u53ef\u9009\u529f\u80fd\u9700\u8981\u989d\u5916\u4f9d\u8d56\uff1a</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>\u5176\u4ed6 Python \u4f9d\u8d56\u7531\u5bf9\u5e94\u811a\u672c\u5728\u8fd0\u884c\u65f6\u5bfc\u5165\u3002\u5982\u679c\u7f3a\u5c11\u67d0\u4e2a\u5305\uff0c\u4f7f\u7528\u5bf9\u5e94\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u63d0\u793a\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#2-gpumdkit","title":"2. \u5b89\u88c5 GPUMDkit","text":"<p>\u514b\u9686\u4ed3\u5e93\u5e76\u8fd0\u884c\u5b89\u88c5\u811a\u672c\uff1a</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre> <p>\u5b89\u88c5\u811a\u672c\u4f1a\u5199\u5165 <code>GPUMDkit_path</code> \u548c <code>PATH</code> \u8bbe\u7f6e\uff0c\u5e76\u5728\u5f53\u524d shell \u4e2d\u52a0\u8f7d\u3002\u9ed8\u8ba4\u5199\u5165 <code>~/.bashrc</code>\uff1b\u5982\u679c\u5f53\u524d shell \u662f zsh\uff0c\u5219\u5199\u5165 <code>~/.zshrc</code>\u3002\u5982\u679c\u68c0\u6d4b\u5230\u5df2\u6709 GPUMDkit \u8def\u5f84\uff0c\u5b89\u88c5\u811a\u672c\u4f1a\u6253\u5370\u65e7\u8def\u5f84\u5e76\u8be2\u95ee\u662f\u5426\u66ff\u6362\uff1b\u4fee\u6539 rc \u6587\u4ef6\u524d\u4f1a\u5148\u521b\u5efa\u5907\u4efd\u3002</p> <p>\u5178\u578b\u5b89\u88c5\u8f93\u51fa\uff1a</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>\u5982\u679c\u4e4b\u524d\u5df2\u7ecf\u5b89\u88c5\u8fc7 GPUMDkit\uff0c\u53ef\u80fd\u4f1a\u770b\u5230\uff1a</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#3","title":"3. \u9a8c\u8bc1\u5b89\u88c5","text":"<pre><code>gpumdkit.sh -h\n</code></pre> <p>\u6b64\u547d\u4ee4\u4f1a\u6253\u5370\u5e2e\u52a9\u8868\uff0c\u5217\u51fa\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_3","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u6253\u5f00\u4e3b\u83dc\u5355\uff1a</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Developing...\n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre> <p>\u6309\u6570\u5b57\u9009\u62e9\u6a21\u5757\u3002\u6bcf\u4e2a\u6a21\u5757\u63d0\u4f9b\u5305\u542b\u5177\u4f53\u529f\u80fd\u7684\u5b50\u83dc\u5355\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_4","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<p>\u76f4\u63a5\u547d\u4ee4\u4f7f\u7528\u56fa\u5b9a\u7684\u4f4d\u7f6e\u53c2\u6570\uff1a</p> <pre><code>gpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>\u7b2c\u4e00\u4e2a\u793a\u4f8b\u8bfb\u53d6 <code>POSCAR</code>\uff0c\u5199\u51fa <code>model.xyz</code>\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_5","title":"\u5e38\u89c1\u793a\u4f8b","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#gpumd-group","title":"\u6dfb\u52a0 GPUMD group \u6807\u7b7e","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>group \u6807\u7b7e\u7528\u4e8e\u4e00\u4e9b\u9700\u8981\u539f\u5b50\u5206\u7ec4\u7684 GPUMD \u76f8\u5173\u6d41\u7a0b\u548c\u5206\u6790\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep","title":"\u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep_1","title":"\u7ed8\u5236 NEP \u6d4b\u8bd5\u96c6\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_6","title":"\u7ed8\u5236\u70ed\u529b\u5b66\u91cf","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#msd","title":"\u7ed8\u5236 MSD \u548c\u81ea\u6269\u6563\u7cfb\u6570","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_7","title":"\u8bf4\u660e","text":"<ul> <li>\u4f7f\u7528 <code>gpumdkit.sh -h</code> \u67e5\u770b\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</li> <li>\u4f7f\u7528 <code>gpumdkit.sh -&lt;\u9009\u9879&gt; -h</code> \u83b7\u53d6\u7279\u5b9a\u9009\u9879\u7684\u5e2e\u52a9\uff08\u4f8b\u5982 <code>gpumdkit.sh -plt train -h</code>\uff09\u3002</li> <li>\u5404\u6a21\u5757\u7684\u8be6\u7ec6\u7528\u6cd5\u8bf7\u53c2\u89c1\u9996\u9875\u4e2d\u94fe\u63a5\u7684\u5bf9\u5e94\u6559\u7a0b\u9875\u9762\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html","title":"\u6781\u6027\u6750\u6599\u5206\u6790","text":"\ud83e\uddf2 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u672c\u6559\u7a0b\u4ecb\u7ecd GPUMDkit \u4e2d\u8ba1\u7b97\u5668\u9009\u9879 <code>406-410</code>\uff0c\u4ee5\u53ca <code>plane-grid</code> \u7ed8\u56fe\u6d41\u7a0b\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code> \u548c <code>Scripts/plt_scripts/</code></p> <p>\u672c\u6559\u7a0b\u5305\u542b\u901a\u7528\u5de5\u5177\u548c\u4f53\u7cfb\u76f8\u5173\u5de5\u5177\uff1a</p> <ul> <li><code>nlist</code>\u3001<code>disp</code> \u548c <code>avg-struct</code> \u53ef\u5e7f\u6cdb\u7528\u4e8e\u7ed3\u6784\u548c\u8f68\u8ff9\u5206\u6790\u3002</li> <li><code>oct-tilt</code> \u7528\u4e8e\u516b\u9762\u4f53\u73af\u5883\u5206\u6790\uff0c\u9700\u8981\u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u5468\u56f4\u6709 6 \u4e2a\u8fd1\u90bb\u3002</li> <li><code>pol-abo3</code> \u4e13\u7528\u4e8e <code>ABO3</code> \u4f53\u7cfb\u7684\u6781\u5316\u5206\u6790\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_1","title":"\u6982\u89c8","text":"\u6b65\u9aa4 CLI \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u8f93\u51fa \u6784\u5efa\u8fd1\u90bb\u5217\u8868 <code>gpumdkit.sh -calc nlist ...</code> <code>model.xyz</code> <code>nl-*.dat</code> \u8ba1\u7b97\u4f4d\u79fb <code>gpumdkit.sh -calc disp ...</code> \u8f68\u8ff9 + <code>nl-*.dat</code> <code>displacements.dat</code> \u5e73\u5747\u8f68\u8ff9\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct ...</code> \u8f68\u8ff9 \u5e73\u5747\u7ed3\u6784 extxyz \u516b\u9762\u4f53\u503e\u659c <code>gpumdkit.sh -calc oct-tilt ...</code> \u8f68\u8ff9 + B-O \u8fd1\u90bb\u5217\u8868 \u503e\u659c\u89d2\u6570\u636e\u8868 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 ...</code> \u8f68\u8ff9 + \u8fd1\u90bb\u5217\u8868 \u6781\u5316\u6570\u636e\u8868 plane-grid \u7ed8\u56fe <code>gpumdkit.sh -plt plane-grid ...</code> \u7ed3\u6784 + \u4f4d\u79fb\u6570\u636e \u5e73\u9762\u5256\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_2","title":"\u4f9d\u8d56","text":"<p>\u8fd9\u4e9b\u811a\u672c\u9700\u8981 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_3","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<p>\u9009\u9879 <code>406-410</code> \u662f\u672c\u6559\u7a0b\u4e2d\u7684\u6838\u5fc3\u529f\u80fd\u3002\u4e0b\u9762\u5404\u8282\u4f1a\u8bf4\u660e\u6bcf\u4e2a\u529f\u80fd\u7684\u7528\u9014\u548c\u8fd0\u884c\u65b9\u5f0f\u3002</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 4) Calculators\n</code></pre> <p>\u8ba1\u7b97\u5668\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5b8c\u6574\u53c2\u6570\u8bf4\u660e\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u547d\u4ee4\u67e5\u770b\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#406-calc_neighbor_listpy","title":"406) \u6784\u5efa\u8fd1\u90bb\u5217\u8868 (<code>calc_neighbor_list.py</code>)","text":"<p>\u4e3a\u6307\u5b9a\u4e2d\u5fc3\u5143\u7d20\u548c\u8fd1\u90bb\u5143\u7d20\u6784\u5efa\u8fd1\u90bb\u5217\u8868\u3002</p> <p>\u4f7f\u7528\u573a\u666f\uff1a \u8fd9\u901a\u5e38\u662f\u8fd0\u884c <code>disp</code>\u3001<code>oct-tilt</code> \u548c <code>pol-abo3</code> \u4e4b\u524d\u7684\u7b2c\u4e00\u6b65\uff0c\u56e0\u4e3a\u8fd9\u4e9b\u811a\u672c\u4f1a\u8bfb\u53d6 <code>nl-*.dat</code> \u8fd1\u90bb\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_4","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4e3a\u516b\u9762\u4f53\u5206\u6790\u6784\u5efa Ti-O \u6700\u8fd1 6 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# \u793a\u4f8b 2\uff1a\u4e3a A \u4f4d\u4e2d\u5fc3\u5206\u6790\u6784\u5efa Pb/Sr-O \u6700\u8fd1 12 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_5","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-x, --index</code>\uff1a   \u4ece\u8f93\u5165\u6587\u4ef6\u4e2d\u8bfb\u53d6\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-c, --cutoff</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u641c\u7d22\u622a\u65ad\u8ddd\u79bb\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> <li><code>-n, --neighbor-num</code>\uff08\u5fc5\u9700\uff09\uff1a   \u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u7684\u8fd1\u90bb\u6570\u91cf\u3002</li> <li><code>-d, --defect</code>\uff1a   \u7f3a\u9677\u6a21\u5f0f\u3002\u542f\u7528\u540e\uff0c\u5982\u679c\u8fd1\u90bb\u6570\u91cf\u4e0d\u8db3\uff0c\u7f3a\u5931\u4f4d\u7f6e\u4f1a\u7528\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u586b\u5145\u3002</li> <li><code>-C, --center-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u4e2d\u5fc3\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-E, --neighbor-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u8def\u5f84\u3002\u9ed8\u8ba4\u503c\uff1a<code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_6","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u8fd1\u90bb\u5217\u8868\u6587\u672c\u6587\u4ef6\uff0c\u4f8b\u5982 <code>nl-Ti-O.dat</code>\u3002</li> <li>\u6587\u4ef6\u662f\u4e00\u4e2a\u4e8c\u7ef4\u6574\u6570\u6570\u7ec4\uff0c\u5f62\u72b6\u4e3a <code>(n_center, neighbor_num + 1)</code>\u3002\u6bcf\u4e00\u884c\u5bf9\u5e94\u4e00\u4e2a\u4e2d\u5fc3\u539f\u5b50\uff1a\u7b2c\u4e00\u5217\u662f\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\uff0c\u540e\u7eed\u5217\u662f\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7\uff0c\u6240\u6709\u7f16\u53f7\u5747\u4e3a 1-based\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#407-calc_displacementpy","title":"407) \u4ece\u8f68\u8ff9\u8ba1\u7b97\u4f4d\u79fb (<code>calc_displacement.py</code>)","text":"<p>\u6839\u636e\u8f68\u8ff9\u6216\u6a21\u578b\u7ed3\u6784\u4ee5\u53ca\u8fd1\u90bb\u5217\u8868\uff0c\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_7","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece model.xyz \u8ba1\u7b97\u5355\u5e27\u4f4d\u79fb\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4f7f\u7528 movie.xyz \u7684\u6700\u540e 20% \u5e27\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_8","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7531 <code>nlist</code> \u751f\u6210\u7684\u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u90e8\u5206\u5e27\u3002   \u6574\u6570\u8868\u793a\u6700\u540e <code>N</code> \u5e27\uff1b   <code>0 &lt; value &lt; 1</code> \u8868\u793a\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_9","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>displacements.dat</code>\uff0c\u6216\u4f60\u6307\u5b9a\u7684\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e8c\u7ef4\u6570\u7ec4\uff1a\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u4e09\u5217\u5206\u522b\u4e3a <code>dx</code>\u3001<code>dy</code> \u548c <code>dz</code> \u4f4d\u79fb\u5206\u91cf\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#408-calc_averaged_structurepy","title":"408) \u8ba1\u7b97\u5e73\u5747\u7ed3\u6784 (<code>calc_averaged_structure.py</code>)","text":"<p>\u4ece\u9009\u5b9a\u8f68\u8ff9\u5e27\u751f\u6210\u4e00\u4e2a\u5e73\u5747\u7ed3\u6784\u3002 \u901a\u5e38\u53ef\u5728\u4f53\u7cfb\u5e73\u8861\u540e\u4f7f\u7528\uff1a\u5bf9\u4e8e\u63a5\u8fd1\u5e73\u8861\u7684\u56fa\u4f53\uff0c\u53ef\u4ee5\u5bf9\u76ee\u6807\u6e29\u5ea6\u4e0b\u7684\u4e00\u6bb5\u8f68\u8ff9\u53d6\u5e73\u5747\uff0c\u5e76\u5206\u6790\u8be5\u4ee3\u8868\u6027\u7ed3\u6784\uff0c\u800c\u4e0d\u662f\u9010\u5e27\u5904\u7406\u6bcf\u4e2a snapshot\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_10","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5e73\u5747\u6240\u6709\u5e27\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# \u793a\u4f8b 2\uff1a\u5e73\u5747\u9009\u5b9a\u5e27\u8303\u56f4 (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_11","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u8f68\u8ff9\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>movie.xyz</code>\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>averaged_structure.xyz</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_12","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u5355\u5e27\u5e73\u5747\u7ed3\u6784 extxyz \u6587\u4ef6\u3002</li> <li>\u4f4d\u7f6e\u5e73\u5747\u4f1a\u76f8\u5bf9\u4e8e\u6240\u9009\u7b2c\u4e00\u5e27\u8fdb\u884c MIC/PBC \u4fee\u6b63\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#409-calc_oct_tiltpy","title":"409) \u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c (<code>calc_oct_tilt.py</code>)","text":"<p>\u6839\u636e B-O \u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c\u89d2\u3002 \u8be5\u529f\u80fd\u5e38\u7528\u4e8e\u5206\u6790 <code>ABO3</code> \u4f53\u7cfb\u4e2d\u7684\u516b\u9762\u4f53\u8f6c\u52a8\u6a21\u5f0f\uff0c\u4f8b\u5982 <code>SrTiO3</code> \u548c <code>PbZrO3</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_13","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece\u5355\u5e27\u7ed3\u6784\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4ece\u8f68\u8ff9\u6700\u540e 20% \u5e27\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_14","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>octahedral_tilt.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_15","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>octahedral_tilt.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>theta_x</code>\u3001<code>theta_y</code>\u3001<code>theta_z</code>\uff0c\u5355\u4f4d\u4e3a degree\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#410-abo3-calc_polarization_abo3py","title":"410) \u8ba1\u7b97 ABO3 \u4f53\u7cfb\u6781\u5316 (<code>calc_polarization_abo3.py</code>)","text":"<p>\u8ba1\u7b97 <code>ABO3</code> \u4f53\u7cfb\u7684\u5c40\u57df\u6781\u5316\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_16","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5355\u5e27 ABO3 \u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# \u793a\u4f8b 2\uff1a\u9009\u5b9a\u8f68\u8ff9\u5e27\u8303\u56f4\u4e0a\u7684\u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_17","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>--nl-ba</code>\uff08\u5fc5\u9700\uff09\uff1a   B-A \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>--nl-bo</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>polarization.dat</code>\u3002</li> <li><code>--bec</code>\uff08\u5fc5\u9700\uff09\uff1a   Born \u6709\u6548\u7535\u8377\u9879\uff0c\u683c\u5f0f\u4e3a <code>Element=value</code>\u3002   \u793a\u4f8b\uff1a<code>Pb=2.5 Ti=4.0 O=-2.0</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul> <p>\u91cd\u8981\u68c0\u67e5\uff1a</p> <ul> <li><code>--bec</code> \u5fc5\u987b\u5305\u542b\u8f93\u5165\u7ed3\u6784\u4e2d\u7684\u6240\u6709\u5143\u7d20\u79cd\u7c7b\u3002</li> <li><code>--nl-ba</code> \u548c <code>--nl-bo</code> \u4e2d\u7684\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u5fc5\u987b\u5339\u914d\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_18","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>polarization.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>Px</code>\u3001<code>Py</code>\u3001<code>Pz</code>\uff0c\u5355\u4f4d\u4e3a <code>C/m^2</code>\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u5982\u679c\u603b Born \u7535\u8377\u4e0d\u5e73\u8861\uff0c\u811a\u672c\u4f1a\u6253\u5370 warning\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#plane-grid-plt_plane_gridpy","title":"Plane-grid \u53ef\u89c6\u5316 (<code>plt_plane_grid.py</code>)","text":"<p>\u4f60\u53ef\u4ee5\u53ef\u89c6\u5316 <code>displacements.dat</code> \u6216 <code>polarization.dat</code>\uff1a</p> <pre><code># \u793a\u4f8b 1\uff1aTi \u4f4d\u70b9\u4e0a\u7684\u4f4d\u79fb\u56fe\uff0c\u9009\u62e9\u7b2c\u4e00\u4e2a XY \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# \u793a\u4f8b 2\uff1aPb \u4f4d\u70b9\u4e0a\u7684\u6781\u5316\u56fe\uff0c\u9009\u62e9 XZ \u548c YZ \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>\u53c2\u6570\uff08\u5b8c\u6574\uff09\uff1a</p> <ul> <li><code>-i, --input</code>\uff1a   \u7528\u4e8e\u539f\u5b50\u5e03\u5c40\u548c\u5206\u5c42\u7684\u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-d, --disp</code>\uff1a   \u77e2\u91cf\u573a\u6570\u636e\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-e, --elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7528\u4e8e\u5c06\u77e2\u91cf\u6620\u5c04\u5230\u6676\u683c\u5c42\u4e0a\u7684\u4e2d\u5fc3\u5143\u7d20\u7b26\u53f7\u3002</li> <li><code>-m, --tol</code>\uff1a   \u7f51\u683c\u6620\u5c04\u7684\u5c42\u5bb9\u5dee\u3002\u9ed8\u8ba4\u503c\uff1a<code>1.0</code>\u3002</li> <li><code>-g, --target-size</code>\uff1a   \u671f\u671b\u7f51\u683c\u5927\u5c0f\uff0c\u683c\u5f0f\u4e3a <code>nx ny nz</code>\u3002</li> <li><code>-o, --save-dir</code>\uff1a   \u56fe\u7247\u8f93\u51fa\u76ee\u5f55\u3002\u9ed8\u8ba4\u503c\uff1a<code>plot</code>\u3002</li> <li><code>-f, --frame</code>\uff1a   \u5f53\u77e2\u91cf\u6570\u636e\u5305\u542b\u591a\u5e27\u65f6\uff0c\u8981\u53ef\u89c6\u5316\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>--select-xy</code>\uff1a   \u9009\u5b9a\u7684 XY \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-xz</code>\uff1a   \u9009\u5b9a\u7684 XZ \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-yz</code>\uff1a   \u9009\u5b9a\u7684 YZ \u5c42\u7f16\u53f7\u3002</li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li>\u5982\u679c\u9700\u8981\uff0c\u4f1a\u521b\u5efa\u8f93\u51fa\u76ee\u5f55\u3002</li> <li>\u56fe\u7247\u4fdd\u5b58\u4e3a <code>XY_*.png</code>\u3001<code>XZ_*.png</code>\u3001<code>YZ_*.png</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_19","title":"\u8f93\u51fa\u6587\u4ef6\u4e00\u89c8","text":"\u811a\u672c \u4e3b\u8981\u8f93\u51fa \u4fdd\u5b58\u5185\u5bb9 <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based \u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u548c\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7 <code>calc_displacement.py</code> <code>*.dat</code> \u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\uff08<code>dx dy dz</code>\uff0cAngstrom\uff09 <code>calc_averaged_structure.py</code> <code>*.xyz</code> \u4e00\u4e2a\u5e73\u5747\u7ed3\u6784 <code>calc_oct_tilt.py</code> <code>*.dat</code> \u516b\u9762\u4f53\u503e\u8f6c\u89d2\uff08<code>theta_x theta_y theta_z</code>\uff0cdegree\uff09 <code>calc_polarization_abo3.py</code> <code>*.dat</code> \u5c40\u57df\u6781\u5316\u77e2\u91cf\uff08<code>Px Py Pz</code>\uff0c<code>C/m^2</code>\uff09 <code>plt_plane_grid.py</code> <code>plot/*.png</code> \u6839\u636e\u77e2\u91cf\u573a\u6570\u636e\u7ed8\u5236\u7684 XY/XZ/YZ \u5e73\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_20","title":"\u771f\u5b9e\u6848\u4f8b","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3-","title":"PbTiO3 \u7684\u6e29\u5ea6\u9a71\u52a8\u94c1\u7535-\u987a\u7535\u76f8\u53d8","text":"<p>\u5047\u8bbe\u6240\u6709\u6587\u4ef6\u90fd\u4f4d\u4e8e\u5f53\u524d\u76ee\u5f55 <code>./</code>\uff1a</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> \u662f\u7528\u4e8e\u8fdb\u884c MD \u6a21\u62df\u7684\u521d\u59cb\u7ed3\u6784\u3002\u6bcf\u4e2a <code>TEMP K.xyz</code> \u662f\u5bf9\u5e94\u6e29\u5ea6\u4e0b\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1","title":"\u7b2c 1 \u6b65\uff1a\u4ece\u6bcf\u6761\u8f68\u8ff9\u7684\u540e\u534a\u6bb5\u5f97\u5230\u5e73\u5747\u7ed3\u6784","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>\u8fd9\u4f1a\u5199\u51fa <code>300K-avg.xyz</code>\u3001<code>350K-avg.xyz</code>\u3001...\u3001<code>800K-avg.xyz</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-modelxyz","title":"\u7b2c 2 \u6b65\uff1a\u57fa\u4e8e <code>model.xyz</code> \u6784\u5efa\u8fd1\u90bb\u5217\u8868","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3","title":"\u7b2c 3 \u6b65\uff1a\u4e3a\u6bcf\u4e2a\u6e29\u5ea6\u8ba1\u7b97\u4f4d\u79fb\u548c\u6781\u5316","text":"<p>\u8fd9\u91cc\u4f7f\u7528 Born \u6709\u6548\u7535\u8377\uff08BEC\uff09\uff0c\u4e0d\u662f\u540d\u4e49\u79bb\u5b50\u7535\u8377\u3002\u5bf9\u4e8e\u672c\u4f8b\u4e2d\u7684 PbTiO3\uff1a</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>\u4f60\u53ef\u4ee5\u4ece\u81ea\u5df1\u7684 DFPT \u8ba1\u7b97\u6216\u6587\u732e\u4e2d\u83b7\u5f97 BEC\u3002\u56e0\u6b64\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u548c\u6781\u5316\uff1a</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#4","title":"\u7b2c 4 \u6b65\uff1a\u7ed8\u5236\u5b9e\u7a7a\u95f4\u4f4d\u79fb\u548c\u6781\u5316\u56fe","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#5-","title":"\u7b2c 5 \u6b65\uff1a\u6784\u5efa\u6e29\u5ea6-\u5e8f\u53c2\u91cf\u66f2\u7ebf","text":"<p>\u7ed3\u5408\u6bcf\u4e2a\u6e29\u5ea6\u5e73\u5747\u7ed3\u6784\u7684\u6676\u683c\u4fe1\u606f\u548c\u6781\u5316\u6587\u4ef6\uff08<code>XX-pol.dat</code>\uff09\u8fdb\u884c\u5206\u6790\uff0c\u53ef\u4ee5\u5f97\u5230\u5982\u4e0b\u56fe\uff1a</p> <p>\u8be5\u8d8b\u52bf\u663e\u793a\u5728\u7ea6 <code>600 K</code> \u9644\u8fd1\u53d1\u751f\u660e\u663e\u76f8\u53d8\uff0c\u6b64\u65f6\u6781\u5316\u6d88\u5931\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3srtio3","title":"PbTiO3/SrTiO3 \u8d85\u6676\u683c\u4e2d\u7684\u62d3\u6251\u7ed3\u6784","text":"<p>\u5047\u8bbe <code>movie.xyz</code> \u662f\u5f53\u524d\u76ee\u5f55\u4e0b PbTiO3/SrTiO3 \u8d85\u6676\u683c\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1-25","title":"\u7b2c 1 \u6b65\uff1a\u4f7f\u7528\u6700\u540e 25% \u5e27\u6784\u5efa\u5e73\u5747\u7ed3\u6784","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-ti","title":"\u7b2c 2 \u6b65\uff1a\u6784\u5efa Ti \u8fd1\u90bb\u5217\u8868","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3-plane-grid","title":"\u7b2c 3 \u6b65\uff1a\u7ed8\u5236 plane-grid \u56fe","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>\u8fd9\u4f1a\u5f97\u5230\u4e0e\u524d\u9762\u5c55\u793a\u76f8\u4f3c\u7684\u56fe\u3002\u5728 PTO \u533a\u57df\u53ef\u4ee5\u770b\u5230\u7c7b\u4f3c\u6da1\u65cb\u7684\u6781\u5316\u56fe\u6837\uff0c\u800c STO \u533a\u57df\u7684\u6781\u5316\u63a5\u8fd1\u4e8e\u96f6\u3002</p> <p>\u6ce8\u610f\uff1a\u793a\u4f8b\u56fe\u4f7f\u7528\u4e86\u81ea\u5b9a\u4e49 colormap\u3002GPUMDkit \u9ed8\u8ba4\u8f93\u51fa\u4f7f\u7528\u4e0d\u540c\u98ce\u683c\uff0c\u53ef\u901a\u8fc7\u4fee\u6539\u7ed8\u56fe\u811a\u672c\u8fdb\u884c\u8c03\u6574\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_21","title":"\u5176\u4ed6\u4f53\u7cfb","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#-","title":"\u6709\u673a-\u65e0\u673a\u6742\u5316\u94c1\u7535\u4f53","text":"<p>\u5728\u8bb8\u591a\u6709\u673a-\u65e0\u673a\u94c1\u7535\u4f53\u4e2d\uff0c\u6781\u5316\u4e0e\u5404\u5411\u5f02\u6027\u7684\u5206\u5b50\u5355\u5143\u5bc6\u5207\u76f8\u5173\u3002\u8ddf\u8e2a\u5206\u5b50\u53d6\u5411\u7684\u4e00\u79cd\u5b9e\u7528\u65b9\u6cd5\u662f\u4f7f\u7528\u952e\u77e2\u91cf\u3002</p> <p>\u5bf9\u4e8e TMCM-CdCl3\uff0c\u53ef\u4ee5\u4f7f\u7528 TMCM \u5206\u5b50\u4e2d\u7684 C-Cl \u952e\u65b9\u5411\u4f5c\u4e3a\u53d6\u5411\u4ee3\u7406\uff0c\u5e76\u636e\u6b64\u4f30\u8ba1\u6781\u5316\u6001\uff1a</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p>\u968f\u540e\u53ef\u4ee5\u628a <code>ccl_vectors.dat</code> \u4f5c\u4e3a\u53d6\u5411\u5e8f\u53c2\u91cf\u8fdb\u884c\u5206\u6790\u3002\u66f4\u591a\u7ec6\u8282\u53ef\u53c2\u8003\uff1aPhys. Rev. Lett. 136, 016801\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_22","title":"\u5176\u4ed6\u94c1\u7535\u6750\u6599\u5bb6\u65cf","text":"<p>\u9664 <code>ABO3</code> \u5916\uff0c<code>ferrodispcalc</code> \u4e5f\u53ef\u4ee5\u9002\u914d\u8bb8\u591a\u94c1\u7535\u4f53\u7cfb\uff0c\u5305\u62ec\u6c2e\u5316\u7269\u3001\u6c27\u5316\u94ea\u57fa\u5316\u5408\u7269\u3001\u6709\u673a-\u65e0\u673a\u6742\u5316\u4f53\u7cfb\u4ee5\u53ca\u90e8\u5206\u4e8c\u7ef4\u94c1\u7535\u6750\u6599\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html","title":"\u683c\u5f0f\u8f6c\u6362","text":"\ud83d\udd04 \u683c\u5f0f\u8f6c\u6362 <p>\u683c\u5f0f\u8f6c\u6362\u6a21\u5757\u7528\u4e8e\u5728\u5e38\u89c1\u539f\u5b50\u6a21\u62df\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362\uff0c\u540c\u65f6\u63d0\u4f9b group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u5e27\u63d0\u53d6\u7b49\u5143\u6570\u636e\u5904\u7406\u529f\u80fd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>\u672c\u6a21\u5757\u5728\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u5e38\u7528\u7684\u7ed3\u6784\u548c\u8f68\u8ff9\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8fdb\u884c\u8f6c\u6362\u3002\u652f\u6301 VASP\u3001LAMMPS\u3001CP2K\u3001ABACUS\u3001CIF\u3001ASE \u8f68\u8ff9\u548c extxyz \u683c\u5f0f\u3002\u8fd8\u63d0\u4f9b\u6dfb\u52a0 group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u63d0\u53d6\u5e27\u548c\u6269\u80de\u7b49\u5de5\u5177\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":"<p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/format_conversion/</code></p> <p>\u786e\u4fdd\u5df2\u5b89\u88c5 GPUMDkit\u3002\u5b89\u88c5\u8bf4\u660e\u8bf7\u53c2\u89c1\u5feb\u901f\u5165\u95e8\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_3","title":"\u652f\u6301\u7684\u683c\u5f0f","text":"<ul> <li>VASP\uff1a<code>POSCAR</code>\u3001<code>CONTCAR</code>\u3001<code>OUTCAR</code>\u3001<code>XDATCAR</code></li> <li>LAMMPS\uff1adata \u6587\u4ef6\u548c dump \u8f68\u8ff9</li> <li>CP2K\uff1a\u8f93\u51fa log\u3001\u5750\u6807\u3001\u529b\u548c\u6676\u80de\u6587\u4ef6</li> <li>ABACUS\uff1aSCF/MD \u8f93\u51fa</li> <li>CIF\uff1a\u6676\u4f53\u7ed3\u6784\u6587\u4ef6</li> <li>ASE trajectory\uff1a<code>.traj</code></li> <li>extxyz\uff1aGPUMD \u548c NEP \u5e38\u7528\u7684\u7ed3\u6784\u683c\u5f0f</li> </ul>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_4","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>1) Format Conversion\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_5","title":"\u6bcf\u4e2a\u5165\u53e3\u7684\u4f5c\u7528","text":"\u5165\u53e3 \u8c03\u7528\u811a\u672c \u529f\u80fd \u9002\u7528\u573a\u666f <code>101</code> <code>out2xyz.sh</code> VASP OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c \u6279\u91cf\u8f6c\u6362 VASP \u8ba1\u7b97\u76ee\u5f55 <code>102</code> <code>mtp2xyz.py</code> MTP cfg \u8f6c extxyz \u8f6c\u6362 MTP \u6570\u636e <code>103</code> <code>cp2k_log2xyz.py</code> / <code>cp2k2xyz.py</code> CP2K \u8f6c extxyz \u53ef\u9009\u62e9 log/inp \u8def\u7ebf\u6216 pos/frc/cell \u8def\u7ebf <code>104</code> <code>abacus2xyz_scf.sh</code> / <code>abacus2xyz_md.sh</code> ABACUS \u8f6c extxyz \u8f6c\u6362 ABACUS SCF \u6216 MD \u8f93\u51fa <code>105</code> <code>exyz2pos.py</code> extxyz \u8f6c POSCAR \u5c06 extxyz \u6bcf\u4e00\u5e27\u5199\u6210 POSCAR <code>106</code> <code>add_groups.py</code> \u6dfb\u52a0 group \u6807\u7b7e \u4e3a GPUMD \u76f8\u5173\u6d41\u7a0b\u6dfb\u52a0\u539f\u5b50\u5206\u7ec4\u6807\u7b7e <code>107</code> <code>add_weight.py</code> \u6dfb\u52a0\u6743\u91cd \u4fee\u6539\u8bad\u7ec3\u96c6\u7ed3\u6784\u6743\u91cd <code>108</code> <code>get_frame.py</code> \u63d0\u53d6\u5355\u5e27 \u4ece extxyz \u8f68\u8ff9\u5bfc\u51fa\u67d0\u4e00\u5e27 <code>109</code> <code>clean_xyz.py</code> \u6e05\u7406 XYZ \u4fe1\u606f \u5220\u9664\u591a\u4f59 extxyz \u5c5e\u6027 <code>110</code> <code>replicate.py</code> \u6269\u80de \u6309\u500d\u6570\u6216\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>out2exyz</code> <code>out2exyz.py</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c VASP OUTCAR \u8f6c\u6362\u7684\u53e6\u4e00\u4e2a\u5165\u53e3 <code>pos2exyz</code> <code>pos2exyz.py</code> POSCAR \u8f6c extxyz \u8f6c\u6362\u5355\u4e2a\u7ed3\u6784 <code>cif2pos</code> <code>cif2pos.py</code> CIF \u8f6c POSCAR \u4ece CIF \u51c6\u5907 VASP \u8f93\u5165 <code>cif2exyz</code> <code>cif2exyz.py</code> CIF \u8f6c extxyz \u4ece CIF \u51c6\u5907 GPUMDkit \u8f93\u5165 <code>xdat2exyz</code> <code>xdatcar2exyz.py</code> XDATCAR \u8f6c extxyz \u8f6c\u6362 VASP MD \u8f68\u8ff9 <code>pos2lmp</code> <code>pos2lmp.py</code> POSCAR \u8f6c LAMMPS data \u51c6\u5907 LAMMPS \u8f93\u5165 <code>lmp2exyz</code> <code>lmp2exyz.py</code> LAMMPS dump \u8f6c extxyz \u8f6c\u6362 LAMMPS \u8f68\u8ff9 <code>traj2exyz</code> <code>traj2exyz.py</code> ASE traj \u8f6c extxyz \u8f6c\u6362 ASE \u8f68\u8ff9"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_6","title":"\u5feb\u901f\u547d\u4ee4\u8868","text":"\u6765\u6e90 \u76ee\u6807 \u547d\u4ee4 OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz POSCAR model.xyz</code> extxyz POSCAR \u6587\u4ef6 <code>gpumdkit.sh -exyz2pos train.xyz</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_7","title":"\u5e38\u89c1\u4f8b\u5b50","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#vasp","title":"\u8f6c\u6362 VASP \u7ed3\u679c","text":"<p>\u529f\u80fd\uff1a \u5728\u76ee\u5f55\u4e2d\u641c\u7d22 VASP OUTCAR \u6587\u4ef6\uff0c\u5e76\u5c06\u5b83\u4eec\u8f6c\u6362\u4e3a\u5355\u4e2a extxyz \u6587\u4ef6\uff0c\u7528\u4e8e NEP \u8bad\u7ec3\u6216\u5206\u6790\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>\u4e5f\u53ef\u4ee5\u4f7f\u7528 Python \u7248\u672c\uff1a</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u683c\u5f0f\u8f6c\u6362\u83dc\u5355\u4e2d\u9009\u62e9 <code>101</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u51fa\uff1a \u5305\u542b\u8f6c\u6362\u540e\u7ed3\u6784\u7684 extxyz \u6587\u4ef6\uff0c\u53ef\u7528\u4e8e NEP \u8bad\u7ec3\u6216\u8fdb\u4e00\u6b65\u5206\u6790\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#group","title":"\u6dfb\u52a0 group \u6807\u7b7e","text":"<p>\u529f\u80fd\uff1a \u4e3a\u7ed3\u6784\u6587\u4ef6\u6dfb\u52a0\u539f\u5b50 group \u6807\u7b7e\u3002\u4e00\u4e9b GPUMD \u76f8\u5173\u6d41\u7a0b\u9700\u8981 group \u6807\u7b7e\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>\u8be5\u547d\u4ee4\u8bfb\u53d6\u8f93\u5165\u7ed3\u6784\uff0c\u5e76\u5199\u51fa\u5e26 group \u4fe1\u606f\u7684 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u683c\u5f0f\u8f6c\u6362\u83dc\u5355\u4e2d\u9009\u62e9 <code>106</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u51fa\uff1a \u6dfb\u52a0\u4e86 group \u6807\u7b7e\u7684 extxyz \u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_8","title":"\u5e38\u7528\u811a\u672c\u8bf4\u660e","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>\u9002\u5408\u628a\u5355\u4e2a VASP \u7ed3\u6784\u8f6c\u6210 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz-poscar","title":"extxyz \u8f6c POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>\u4f1a\u5c06 extxyz \u4e2d\u6240\u6709\u5e27\u8f6c\u6362\u6210 <code>POSCAR_*.vasp</code> \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3\uff1a<code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#lammps-dump-extxyz","title":"LAMMPS dump \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>\u5143\u7d20\u987a\u5e8f\u5fc5\u987b\u5bf9\u5e94 LAMMPS \u4e2d\u7684 atom type ID\u3002\u4f8b\u5982 type 1 \u662f Li\u3001type 2 \u662f Y\u3001type 3 \u662f Cl\uff0c\u5219\u8f93\u5165 <code>Li Y Cl</code>\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#cif","title":"CIF \u8f6c\u6362","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>\u5982\u679c\u540e\u7eed\u9700\u8981 VASP \u8ba1\u7b97\uff0c\u4f7f\u7528 <code>-cif2pos</code>\uff1b\u5982\u679c\u540e\u7eed\u8981\u8fdb\u5165 GPUMDkit \u5206\u6790\uff0c\u4f7f\u7528 <code>-cif2exyz</code>\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_9","title":"\u6dfb\u52a0\u6743\u91cd","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>\u7528\u4e8e\u7ed9\u8bad\u7ec3\u96c6\u7ed3\u6784\u6dfb\u52a0\u6216\u4fee\u6539\u6743\u91cd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_10","title":"\u6269\u80de","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>\u7b2c\u4e00\u79cd\u6309\u6676\u80de\u500d\u6570\u6269\u80de\uff0c\u7b2c\u4e8c\u79cd\u6309\u76ee\u6807\u539f\u5b50\u6570\u81ea\u52a8\u9009\u62e9\u6269\u80de\u65b9\u5f0f\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_11","title":"\u63d0\u53d6\u5355\u5e27","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>\u4ece extxyz \u8f68\u8ff9\u4e2d\u63d0\u53d6\u7b2c <code>1000</code> \u5e27\uff08\u7d22\u5f15\u4ece 0 \u5f00\u59cb\uff09\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz","title":"\u62c6\u5206\u591a\u5e27 extxyz","text":"<p><code>split_single_xyz.py</code> \u5c06\u591a\u5e27 extxyz \u6587\u4ef6\u62c6\u5206\u4e3a\u5355\u5e27\u6587\u4ef6\u3002</p> <pre><code>python Scripts/format_conversion/split_single_xyz.py dump.xyz\n</code></pre> <p>\u751f\u6210 <code>model_0.xyz</code>\u3001<code>model_1.xyz</code>\u3001... \u7b49\u5355\u5e27\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#mtp","title":"MTP \u8f6c\u6362","text":"<p>\u5c06 MTP <code>.cfg</code> \u683c\u5f0f\u8f6c\u6362\u4e3a extxyz\uff1a</p> <pre><code>gpumdkit.sh    # \u9009\u62e9\uff1a1) \u683c\u5f0f\u8f6c\u6362 \u2192 102\n</code></pre> <p>\u4ea4\u4e92\u63d0\u793a\uff1a</p> <pre><code>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;\nExample: train.cfg Pd Ag\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#abacus","title":"ABACUS \u8f6c\u6362","text":"<p>\u5c06 ABACUS \u8f93\u51fa\u8f6c\u6362\u4e3a extxyz\uff1a</p> <pre><code>gpumdkit.sh    # \u9009\u62e9\uff1a1) \u683c\u5f0f\u8f6c\u6362 \u2192 104\n</code></pre> <p>\u83dc\u5355\u63d0\u4f9b\u4e24\u4e2a\u9009\u9879\uff1a</p> <ol> <li>SCF \u8f93\u51fa\uff08<code>running_scf.log</code>\uff09</li> <li>MD \u8f93\u51fa\uff08<code>running_md.log</code>\uff09</li> </ol>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_12","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae LAMMPS \u8f6c\u6362\u540e\u5143\u7d20\u4e0d\u5bf9 \u68c0\u67e5 dump \u6587\u4ef6\u540e\u7684\u5143\u7d20\u987a\u5e8f extxyz \u5143\u6570\u636e\u592a\u591a \u4f7f\u7528 <code>-clean_xyz input.xyz clean.xyz</code> \u63d0\u53d6\u5e27\u4e0d\u5bf9 \u6ce8\u610f\u5e27\u7d22\u5f15\u901a\u5e38\u4ece 0 \u5f00\u59cb"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_13","title":"\u8bf4\u660e","text":"<p>\u5982\u679c\u67d0\u4e2a\u8f6c\u6362\u811a\u672c\u7f3a\u5c11\u6240\u9700 Python \u5305\uff0c\u8fd0\u884c\u8be5\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u76f8\u5e94\u63d0\u793a\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html","title":"\u7ed3\u6784\u91c7\u6837","text":"\ud83d\udce6 \u7ed3\u6784\u91c7\u6837 <p>\u7ed3\u6784\u91c7\u6837\u7528\u4e8e\u4ece\u8f68\u8ff9\u4e2d\u9009\u62e9\u5019\u9009\u7ed3\u6784\u3001\u751f\u6210\u6270\u52a8\u7ed3\u6784\uff0c\u6216\u6839\u636e\u6a21\u578b\u504f\u5dee\u6311\u9009\u503c\u5f97\u8fdb\u4e00\u6b65\u8ba1\u7b97\u7684\u7ed3\u6784\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/sample_structures/</code></p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_1","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>2) Sample Structures\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u65b9\u6cd5 \u7528\u9014 201 uniform/random \u4ece\u8f68\u8ff9\u4e2d\u5747\u5300\u6216\u968f\u673a\u62bd\u5e27 202 PyNEP notice \u53ea\u6253\u5370\u63d0\u793a\uff1b\u771f\u6b63\u8fd0\u884c PyNEP \u8bf7\u7528 <code>gpumdkit.sh -pynep</code> 203 NepTrain FPS \u4f7f\u7528 NepTrain \u63cf\u8ff0\u7b26\u7684 FPS \u91c7\u6837 204 perturb \u4ece POSCAR/CONTCAR \u751f\u6210\u6270\u52a8\u7ed3\u6784 205 force deviation \u4ece active learning \u8f93\u51fa\u4e2d\u9009\u62e9\u9ad8\u504f\u5dee\u7ed3\u6784"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_2","title":"\u5747\u5300/\u968f\u673a\u91c7\u6837","text":"<p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>201</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>\u4f8b\u5982\u8f93\u5165\uff1a</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>\u6216\uff1a</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>uniform</code> / <code>random</code> \u91c7\u6837\u65b9\u6cd5 <code>50</code> / <code>100</code> \u91c7\u6837\u7ed3\u6784\u6570 <code>500</code> \u53ef\u9009\uff0c\u8df3\u8fc7\u524d 500 \u5e27 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#neptrain-fps","title":"NepTrain FPS","text":"<p>NepTrain \u7248\u672c\u7684 FPS\u3002\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>203</code>\uff1b\u4e5f\u53ef\u4ee5\u76f4\u63a5\u8fd0\u884c\u811a\u672c\uff1a</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>203</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u5165\uff1a</p> \u6587\u4ef6 \u542b\u4e49 <code>dump.xyz</code> \u5019\u9009\u7ed3\u6784 <code>train.xyz</code> \u5f53\u524d\u8bad\u7ec3\u96c6 <code>nep.txt</code> \u7528\u4e8e\u8ba1\u7b97\u63cf\u8ff0\u7b26\u7684 NEP \u6a21\u578b <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>\u8fd0\u884c\u65f6\u53ef\u4ee5\u9009\u62e9\u6309\u6700\u5c0f\u8ddd\u79bb\u9608\u503c\u91c7\u6837\uff0c\u6216\u6307\u5b9a\u91c7\u6837\u7ed3\u6784\u6570\u3002\u811a\u672c\u968f\u540e\u4f1a\u6253\u5370\uff1a</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>NepTrain</code>\uff0c\u8fd0\u884c\u65f6\u4f1a\u63d0\u793a\u76f8\u5173\u5f15\u7528\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep","title":"PyNEP \u65e7\u5165\u53e3","text":"<p>PyNEP FPS \u4ecd\u7136\u4fdd\u7559\u517c\u5bb9\uff0c\u4f46\u53ea\u901a\u8fc7 <code>-pynep</code> \u5165\u53e3\u8c03\u7528\u3002</p> <p>\u5982\u679c\u5728\u4ea4\u4e92\u83dc\u5355\u4e2d\u9009\u62e9 <code>202</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep_1","title":"\u4e32\u884c PyNEP","text":"<pre><code>python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep_2","title":"\u5e76\u884c PyNEP","text":"<pre><code>python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u6700\u540e\u4e00\u4e2a\u53c2\u6570\u662f CPU \u7ebf\u7a0b\u6570\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#gpumdkit","title":"GPUMDkit \u5165\u53e3","text":"<pre><code>gpumdkit.sh -pynep\n</code></pre> <p>\u968f\u540e\u8f93\u5165\uff1a</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u8fd9\u4e2a\u5165\u53e3\u9700\u8981 <code>pynep</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_3","title":"\u7ed3\u6784\u6270\u52a8","text":"<p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>204</code>\uff1b\u4e5f\u53ef\u4ee5\u76f4\u63a5\u8fd0\u884c\u811a\u672c\uff1a</p> <pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>204</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>POSCAR</code> \u8f93\u5165\u7ed3\u6784 <code>20</code> \u751f\u6210\u7ed3\u6784\u6570 <code>0.03</code> \u6676\u80de\u6270\u52a8\u6bd4\u4f8b <code>0.2</code> \u539f\u5b50\u6270\u52a8\u8ddd\u79bb\uff0c\u5355\u4f4d Angstrom <code>uniform</code> \u6270\u52a8\u65b9\u5f0f\uff0c\u53ef\u9009 <code>normal</code>\u3001<code>uniform</code>\u3001<code>const</code> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>POSCAR_01.vasp</code>\u3001<code>POSCAR_02.vasp</code> \u7b49</li> </ul> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>dpdata</code>\u3002\u4f7f\u7528\u6b64\u529f\u80fd\u65f6\u5efa\u8bae\u5f15\u7528 dpdata \u5305\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_4","title":"\u6700\u5927\u529b\u504f\u5dee\u7ed3\u6784\u9009\u62e9","text":"<p>\u8be5\u529f\u80fd\u9700\u8981\u914d\u5408 GPUMD \u7684 <code>active</code> \u547d\u4ee4\u4f7f\u7528\u3002<code>active</code> \u901a\u8fc7\u59d4\u5458\u4f1a\u8bc4\u5ba1\u673a\u5236\uff0c\u8ba9\u591a\u6761\u52bf\u51fd\u6570\u5bf9\u540c\u4e00\u7ed3\u6784\u8fdb\u884c\u9884\u6d4b\uff0c\u5e76\u8bb0\u5f55\u6bcf\u4e2a\u7ed3\u6784\u7684\u6700\u5927\u529b\u504f\u5dee\u3002<code>select_max_modev.py</code> \u4f1a\u4ece <code>active.out</code> \u548c <code>active.xyz</code> \u4e2d\u9009\u62e9\u529b\u504f\u5dee\u8f83\u5927\u7684\u7ed3\u6784\uff0c\u5199\u5165 <code>selected.xyz</code>\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>205</code>\uff1b\u4e5f\u53ef\u4ee5\u76f4\u63a5\u8fd0\u884c\u811a\u672c\uff1a</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>205</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>\u9700\u8981\u5f53\u524d\u76ee\u5f55\u4e0b\u6709\uff1a</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_5","title":"\u5e27\u8303\u56f4\u63d0\u53d6","text":"<p><code>frame_range.py</code> \u662f\u4e00\u4e2a\u72ec\u7acb\u7684 CLI \u5de5\u5177\uff0c\u4e0d\u5728\u7ed3\u6784\u91c7\u6837\u4ea4\u4e92\u83dc\u5355 <code>201\u2013205</code> \u4e2d\u3002\u5b83\u9002\u5408\u5728\u91c7\u6837\u524d\u5148\u622a\u53d6\u8f68\u8ff9\u7684\u4e00\u6bb5\uff0c\u4f8b\u5982\u53ea\u4fdd\u7559\u5e73\u8861\u540e\u7684\u540e\u534a\u6bb5\u8f68\u8ff9\u3002</p> <pre><code>gpumdkit.sh -frame_range dump.xyz 0 0.8\npython Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>\u8fd9\u4f1a\u5199\u5165\u8f68\u8ff9 0% \u5230 80% \u7684\u5e27\u3002\u53c2\u6570\u4f7f\u7528\u8f68\u8ff9\u6bd4\u4f8b\uff0c\u8303\u56f4\u4e3a <code>0</code> \u5230 <code>1</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_6","title":"\u793a\u4f8b\u547d\u4ee4","text":"<p>\u4e0b\u9762\u662f\u4e00\u4e2a\u5e38\u89c1\u7684\u91c7\u6837\u524d\u5904\u7406\u987a\u5e8f\uff1a\u5148\u7528\u5206\u6790\u5de5\u5177\u68c0\u67e5\u548c\u8fc7\u6ee4\u5019\u9009\u8f68\u8ff9\uff0c\u518d\u8fdb\u884c FPS \u91c7\u6837\u3002\u524d\u4e24\u4e2a\u547d\u4ee4\u5c5e\u4e8e\u5206\u6790\u5de5\u5177\uff0c\u6700\u540e\u4e00\u6b65\u5c5e\u4e8e\u672c\u9875\u7684\u7ed3\u6784\u91c7\u6837\u3002</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>\u6700\u540e\u4e00\u6b65\u4e5f\u53ef\u4ee5\u5728\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>2) \u7ed3\u6784\u91c7\u6837 \u2192 203</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_7","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae FPS \u9009\u51fa\u592a\u591a\u76f8\u4f3c\u7ed3\u6784 \u8c03\u5927\u8ddd\u79bb\u9608\u503c\u6216\u9650\u5236\u6700\u5927\u9009\u62e9\u6570 \u6270\u52a8\u7ed3\u6784\u4e0d\u5408\u7406 \u51cf\u5c0f <code>cell_pert</code> \u548c <code>atom_pert</code> <code>active.out</code> \u548c <code>active.xyz</code> \u4e0d\u5339\u914d \u786e\u4fdd\u6765\u81ea\u540c\u4e00\u6b21 GPUMD active \u8fd0\u884c PCA \u56fe\u5f02\u5e38 \u68c0\u67e5 <code>nep.txt</code> \u662f\u5426\u548c\u4e24\u4e2a\u6570\u636e\u96c6\u5143\u7d20\u4e00\u81f4"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html","title":"\u7ed8\u56fe\u811a\u672c","text":"\ud83d\udcca \u7ed8\u56fe\u811a\u672c <p>\u7ed8\u56fe\u6a21\u5757\u5305\u542b\u4e00\u7cfb\u5217 Python \u811a\u672c\uff0c\u7528\u4e8e\u53ef\u89c6\u5316 GPUMD\u3001NEP \u548c GPUMDkit \u8ba1\u7b97\u5668\u4ea7\u751f\u7684\u6570\u636e\u3002\u6240\u6709\u56fe\u8868\u5747\u53ef\u4ea4\u4e92\u663e\u793a\u6216\u4fdd\u5b58\u4e3a\u9ad8\u5206\u8fa8\u7387 PNG \u6587\u4ef6\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/plt_scripts/</code></p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_1","title":"\u5feb\u901f\u5165\u53e3","text":"<pre><code>gpumdkit.sh -plt              # \u663e\u793a\u6240\u6709\u7ed8\u56fe\u9009\u9879\ngpumdkit.sh -plt &lt;type&gt;       # \u751f\u6210\u6307\u5b9a\u56fe\u8868\ngpumdkit.sh -plt &lt;type&gt; save  # \u4fdd\u5b58\u4e3a PNG\ngpumdkit.sh -plt &lt;type&gt; -h    # \u663e\u793a\u7279\u5b9a\u56fe\u8868\u7684\u5e2e\u52a9\n</code></pre> <p>\u8fd0\u884c <code>gpumdkit.sh -plt</code> \u4f1a\u663e\u793a\u7ed8\u56fe\u547d\u4ee4\u83dc\u5355\uff1a</p> <pre><code>+-----------------------------------------------------------------------------------------------+\n|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |\n+-----------------------------------------------------------------------------------------------+\n|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |\n+-----------------------------------------------------------------------------------------------+\n|                                    NEP Training &amp; Evaluation                                  |\n+-----------------------------------------------------------------------------------------------+\n|  train          - NEP training results           prediction     - NEP prediction results      |\n|  train_test     - NEP train and test results     parity_density - Parity density plot         |\n|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |\n|  charge         - Charge distribution            born_charge    - Born effective charges      |\n|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |\n|  des            - Descriptors                    lr             - Learning rate for gnep      |\n+-----------------------------------------------------------------------------------------------+\n|                                     Diffusion &amp; Transport                                     |\n+-----------------------------------------------------------------------------------------------+\n|  msd            - Mean square displacement       msd_conv       - MSD convergence             |\n|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |\n|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|\n|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |\n|  D_xyz          - Directional Arrhenius D                                                     |\n+-----------------------------------------------------------------------------------------------+\n|                                    MD &amp; Structural Analysis                                   |\n+-----------------------------------------------------------------------------------------------+\n|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |\n|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |\n|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |\n|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |\n|  doas           - Density of atomistic states                                                 |\n+-----------------------------------------------------------------------------------------------+\n|                                        Heat Transport                                         |\n+-----------------------------------------------------------------------------------------------+\n|  emd            - EMD results                    nemd           - NEMD results                |\n|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |\n+-----------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u8bad\u7ec3\u4e0e\u9884\u6d4b","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_trainpy","title":"plt_train.py","text":"<p>\u53ef\u89c6\u5316 NEP \u8bad\u7ec3\u8fc7\u7a0b\uff0c\u5305\u62ec loss \u66f2\u7ebf\u3001RMSE \u6f14\u5316\uff0c\u4ee5\u53ca\u80fd\u91cf/\u529b/virial \u7684 DFT vs NEP parity plot\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code>\u3001<code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_predictionpy","title":"plt_prediction.py","text":"<p>\u53ef\u89c6\u5316\u6d4b\u8bd5\u96c6\u4e0a\u7684 NEP \u9884\u6d4b\u7ed3\u679c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_test.out</code>\u3001<code>force_test.out</code>\u3001<code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test         # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_train_testpy","title":"plt_train_test.py","text":"<p>\u5c06\u8bad\u7ec3\u96c6\u548c\u6d4b\u8bd5\u96c6\u7684 parity plot \u5408\u5e76\u663e\u793a\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code>\u3001<code>energy_test.out</code>\u3001<code>force_test.out</code>\u3001<code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_parity_densitypy","title":"plt_parity_density.py","text":"<p>\u751f\u6210\u57fa\u4e8e\u5bc6\u5ea6\u7684 parity plot\uff0c\u9002\u7528\u4e8e\u5927\u6570\u636e\u96c6\uff08\u6563\u70b9\u56fe\u8fc7\u4e8e\u5bc6\u96c6\u65f6\u66f4\u6613\u9605\u8bfb\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_force_errorspy","title":"plt_force_errors.py","text":"<p>\u53c2\u8003 Liu et al. \u7684\u65b9\u6cd5\u7ed8\u5236\u529b\u8bef\u5dee\u8bc4\u4f30\u6307\u6807\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>force_train.out</code></p> <p>\u663e\u793a\u6307\u6807\uff1a - \u529b\u5927\u5c0f\u8bef\u5dee (delta_F) - \u529b\u89d2\u5ea6\u8bef\u5dee (delta_theta) - \u8bef\u5dee\u5206\u5e03</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_learning_ratepy","title":"plt_learning_rate.py","text":"<p>\u53ef\u89c6\u5316 <code>gnep</code> \u8bad\u7ec3\u8fc7\u7a0b\u4e2d\u7684\u5b66\u4e60\u7387\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code></p> <p>\u6ce8\u610f\uff1a \u4ec5\u9002\u7528\u4e8e <code>gnep</code> \u8bad\u7ec3\u8fc7\u7a0b\u3002</p> <pre><code>gpumdkit.sh -plt lr\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_nep_restartpy","title":"plt_nep_restart.py","text":"<p>\u53ef\u89c6\u5316 <code>nep.restart</code> \u6587\u4ef6\u4e2d\u5b58\u50a8\u7684\u53c2\u6570\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>nep.restart</code></p> <pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_chargepy","title":"plt_charge.py","text":"<p>\u7ed8\u5236 <code>qNEP</code> \u6a21\u578b\u7684\u7535\u8377\u5206\u5e03\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>charge_train.out</code></p> <p>\u91cd\u8981\u63d0\u793a\uff1a \u786e\u4fdd\u8bad\u7ec3\u96c6\u548c\u7535\u8377\u8f93\u51fa\u7684\u539f\u5b50\u6392\u5e8f\u4e00\u81f4\u3002\u5efa\u8bae\u4f7f\u7528\u5168 batch \u8bad\u7ec3\u6216\u5148\u8fd0\u884c\u9884\u6d4b\u6b65\u9aa4\u3002</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_born_chargepy","title":"plt_born_charge.py","text":"<p>\u4e3a\u8bad\u7ec3\u96c6\u548c\u6d4b\u8bd5\u96c6\u521b\u5efa Born \u6709\u6548\u7535\u8377 (BEC) \u7684 parity plot\u3002\u5168\u96f6\u53c2\u8003 BEC \u7684\u7ed3\u6784\u4f1a\u88ab\u8fc7\u6ee4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>bec_train.out</code>\u3001<code>bec_test.out</code></p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec          # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_2","title":"\u70ed\u529b\u5b66\u91cf","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_thermopy","title":"plt_thermo.py","text":"<p>\u7efc\u5408\u53ef\u89c6\u5316\u70ed\u529b\u5b66\u6027\u8d28\u7684\u4e3b\u811a\u672c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_thermo2py-plt_thermo3py","title":"plt_thermo2.py &amp; plt_thermo3.py","text":"<p>\u4e0d\u540c\u98ce\u683c\u7684\u70ed\u529b\u5b66\u91cf\u53ef\u89c6\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_3","title":"\u6269\u6563\u548c\u79bb\u5b50\u8f93\u8fd0","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msdpy","title":"plt_msd.py","text":"<p>\u7ed8\u5236\u5404\u65b9\u5411\u7684\u5747\u65b9\u4f4d\u79fb (MSD)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msd_allpy","title":"plt_msd_all.py","text":"<p>\u5f53 GPUMD \u4e2d\u4f7f\u7528 <code>all_groups</code> \u65f6\uff0c\u5206\u522b\u7ed8\u5236\u6bcf\u79cd\u539f\u5b50\u7684 MSD\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code>\uff08\u9700\u8981\u4f7f\u7528 <code>all_groups</code> \u9009\u9879\u8ba1\u7b97\uff09</p> <p>\u8981\u6c42\uff1a <code>run.in</code> \u4e2d\u7684 <code>compute_msd</code> \u547d\u4ee4\u5fc5\u987b\u4f7f\u7528 <code>all_groups</code>\u3002</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msd_convergence_checkpy","title":"plt_msd_convergence_check.py","text":"<p>\u68c0\u67e5\u4e0d\u540c\u65f6\u95f4\u7a97\u53e3\u4e0b MSD \u8ba1\u7b97\u7684\u6536\u655b\u6027\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd_step*.out</code>\uff08\u9700\u8981\u5728 <code>compute_msd</code> \u4e2d\u4f7f\u7528 <code>save_every</code> \u9009\u9879\uff09</p> <p>\u8981\u6c42\uff1a \u5728 <code>compute_msd</code> \u547d\u4ee4\u4e2d\u4f7f\u7528 <code>save_every</code>\u3002</p> <p>\u7528\u9014\uff1a \u9a8c\u8bc1 MSD \u662f\u5426\u5df2\u5145\u5206\u6536\u655b\u4ee5\u51c6\u786e\u8ba1\u7b97\u6269\u6563\u7cfb\u6570\u3002</p> <pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_sdcpy","title":"plt_sdc.py","text":"<p>\u7ed8\u5236\u81ea\u6269\u6563\u7cfb\u6570 (SDC) \u968f\u65f6\u95f4\u7684\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_arrhenius_dpy","title":"plt_arrhenius_d.py","text":"<p>\u521b\u5efa Arrhenius \u6269\u6563\u7cfb\u6570\u56fe\uff08log10 D vs 1000/T\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>*K/msd.out</code>\uff08\u6bcf\u4e2a\u6e29\u5ea6\u5b50\u76ee\u5f55\u4e0b\u7684 <code>msd.out</code>\uff09</p> <pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D             # \u66ff\u4ee3\u547d\u4ee4\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_arrhenius_sigmapy","title":"plt_arrhenius_sigma.py","text":"<p>\u521b\u5efa Arrhenius \u79bb\u5b50\u7535\u5bfc\u7387\u56fe\uff08ln(\u03c3\u00b7T) vs 1000/T\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code>\uff08\u6bcf\u4e2a\u6e29\u5ea6\u5b50\u76ee\u5f55\uff09</p> <pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma         # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_4","title":"\u70ed\u8f93\u8fd0","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_emdpy","title":"plt_emd.py","text":"<p>\u5206\u6790\u5e76\u7ed8\u5236\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (EMD) \u70ed\u5bfc\u7387\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 EMD \u8f93\u51fa\u6587\u4ef6</p> <pre><code>gpumdkit.sh -plt emd x        # x \u65b9\u5411\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_nemdpy","title":"plt_nemd.py","text":"<p>\u53ef\u89c6\u5316\u975e\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (NEMD) \u70ed\u8f93\u8fd0\u6027\u8d28\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 NEMD \u8f93\u51fa\u6587\u4ef6</p> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u8bf4\u660e <code>real_length</code> \u4f20\u70ed\u533a\u5b9e\u9645\u957f\u5ea6\uff08nm\uff09\uff0c\u8bbe\u4e3a <code>Auto</code> \u53ef\u81ea\u52a8\u8ba1\u7b97 <code>scale_eff_size</code> \u6709\u6548\u622a\u9762\u79ef\u7f29\u653e\u56e0\u5b50\uff08\u9ed8\u8ba4\uff1a1\uff09\u3002\u4e09\u7ef4\u4f53\u76f8\u7528 1\uff1b\u542b\u771f\u7a7a\u5c42\u7684\u4f4e\u7ef4\u4f53\u7cfb\u7528 S_box / S_eff <code>cutoff_freq</code> SHC \u8ba1\u7b97\u7684\u622a\u6b62\u9891\u7387\uff08THz\uff0c\u9ed8\u8ba4\uff1a60\uff09 <code>save</code> \u53ef\u9009\uff0c\u4fdd\u5b58\u56fe\u7247\u4e3a <code>nemd.png</code> <p>\u6ce8\u610f\uff1a \u5982\u679c\u6ca1\u6709 SHC \u6570\u636e\uff0c\u4f7f\u7528 <code>save</code> \u65f6\u8bf7\u5c06 <code>scale_eff_size</code> \u548c <code>cutoff_freq</code> \u8bbe\u4e3a\u4efb\u610f\u5360\u4f4d\u6570\u5b57\u3002</p> <pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_hnemdpy","title":"plt_hnemd.py","text":"<p>\u7ed8\u5236\u975e\u5747\u5300\u975e\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (HNEMD) \u7ed3\u679c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 HNEMD \u8f93\u51fa\u6587\u4ef6</p> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u8bf4\u660e <code>scale_eff_size</code> \u6709\u6548\u622a\u9762\u79ef\u7f29\u653e\u56e0\u5b50\uff08\u9ed8\u8ba4\uff1a1\uff09 <code>cutoff_freq</code> SHC \u8ba1\u7b97\u7684\u622a\u6b62\u9891\u7387\uff08THz\uff0c\u9ed8\u8ba4\uff1a60\uff09 <code>save</code> \u53ef\u9009\uff0c\u4fdd\u5b58\u56fe\u7247\u4e3a <code>hnemd.png</code> <p>\u6ce8\u610f\uff1a \u5982\u679c\u6ca1\u6709 SHC \u6570\u636e\uff0c\u4f7f\u7528 <code>save</code> \u65f6\u8bf7\u5c06 <code>scale_eff_size</code> \u548c <code>cutoff_freq</code> \u8bbe\u4e3a\u4efb\u610f\u5360\u4f4d\u6570\u5b57\u3002</p> <pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_5","title":"\u7ed3\u6784\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_rdfpy","title":"plt_rdf.py","text":"<p>\u7ed8\u5236\u5f84\u5411\u5206\u5e03\u51fd\u6570 (RDF)\uff0c\u5c55\u793a\u539f\u5b50\u5bf9\u5173\u8054\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf               # \u663e\u793a\u6240\u6709 RDF \u5bf9\ngpumdkit.sh -plt rdf &lt;column&gt;      # \u663e\u793a\u7279\u5b9a\u5bf9\n</code></pre> <p>\u5b8c\u6574 RDF \u8f93\u51fa\uff1a</p> <p>\u5355\u5bf9 RDF\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_rdf_pmfpy","title":"plt_rdf_pmf.py","text":"<p>\u7ed8\u5236 RDF \u4e0e\u5e73\u5747\u529b\u52bf (PMF) \u7684\u7ec4\u5408\u56fe\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf_pmf\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_vacpy","title":"plt_vac.py","text":"<p>\u7ed8\u5236\u901f\u5ea6\u81ea\u76f8\u5173\u51fd\u6570 (VAC)\u3002\u53ef\u7528\u4e8e\u5206\u6790\u58f0\u5b50\u6027\u8d28\u548c\u539f\u5b50\u52a8\u529b\u5b66\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>sdc.out</code>\uff08\u7ed8\u56fe\u811a\u672c\u4f1a\u4ece\u8be5\u6587\u4ef6\u4e2d\u8bfb\u53d6 VAC \u76f8\u5173\u5217\uff09</p> <p>\u8f93\u51fa\uff1a \u4ea4\u4e92\u5f0f\u56fe\u8868\u6216 <code>vac.png</code>\uff08\u4f7f\u7528 <code>save</code> \u9009\u9879\u65f6\uff09</p> <pre><code>gpumdkit.sh -plt vac\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_cohesivepy","title":"plt_cohesive.py","text":"<p>\u4ece <code>cohesive.out</code> \u7ed8\u5236\u5185\u805a\u80fd\u66f2\u7ebf\u3002\u53ef\u7528\u4e8e\u5206\u6790\u6676\u683c\u7a33\u5b9a\u6027\u548c\u5e73\u8861\u6676\u683c\u5e38\u6570\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>cohesive.out</code>\uff08\u5404\u5411\u540c\u6027\u7f29\u653e\u56e0\u5b50 vs \u5185\u805a\u80fd\uff09</p> <p>\u8f93\u51fa\uff1a \u4ea4\u4e92\u5f0f\u56fe\u8868\u6216 <code>cohesive.png</code>\uff08\u4f7f\u7528 <code>save</code> \u9009\u9879\u65f6\uff09</p> <pre><code>gpumdkit.sh -plt cohesive\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_net_forcepy","title":"plt_net_force.py","text":"<p>\u7ed8\u5236\u7ed3\u6784\u4e0a\u7684\u51c0\u529b\u5206\u5e03\uff0c\u53ef\u7528\u4e8e\u8bc6\u522b\u95ee\u9898\u6784\u578b\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>\u53c2\u8003\u6587\u732e\uff1a arXiv:2510.19774</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_6","title":"\u58f0\u5b50","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_pdospy","title":"plt_pdos.py","text":"<p>\u8ba1\u7b97\u5e76\u7ed8\u5236\u5f52\u4e00\u5316\u7684\u901f\u5ea6\u81ea\u76f8\u5173\u51fd\u6570 (VAC)\u3001\u58f0\u5b50\u6001\u5bc6\u5ea6 (PDOS) \u548c\u70ed\u5bb9 (Cv)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>model.xyz</code>\u3001<code>run.in</code>\u3001<code>dos.out</code>\u3001<code>mvac.out</code></p> <pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>\u70ed\u5bb9\u8f93\u51fa\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#dimer","title":"\u63cf\u8ff0\u7b26\u3001Dimer \u548c\u5176\u4ed6\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_descriptorspy","title":"plt_descriptors.py","text":"<p>\u4f7f\u7528\u964d\u7ef4\u65b9\u6cd5\uff08PCA \u6216 UMAP\uff09\u53ef\u89c6\u5316\u9ad8\u7ef4 NEP \u63cf\u8ff0\u7b26\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>descriptors.npy</code>\uff08\u7531 <code>gpumdkit.sh -calc des</code> \u751f\u6210\uff09</p> <p>\u65b9\u6cd5\uff1a - <code>pca</code> \u2014 \u4e3b\u6210\u5206\u5206\u6790 - <code>umap</code> \u2014 \u7edf\u4e00\u6d41\u5f62\u903c\u8fd1\u4e0e\u6295\u5f71</p> <pre><code># \u5148\u8ba1\u7b97\u63cf\u8ff0\u7b26\ngpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n\n# \u518d\u53ef\u89c6\u5316\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_descriptors_comparepy","title":"plt_descriptors_compare.py","text":"<p>\u6bd4\u8f83\u591a\u4e2a\u8bad\u7ec3\u96c6\u6216\u6a21\u578b\u7684\u63cf\u8ff0\u7b26\u3002</p> <pre><code>gpumdkit.sh -plt des_compare\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_dimerpy","title":"plt_dimer.py","text":"<p>\u7ed8\u5236\u4e8c\u805a\u4f53\u76f8\u4e92\u4f5c\u7528\u66f2\u7ebf\u3002\u5c06\u4e24\u4e2a\u539f\u5b50\u653e\u5165\u7acb\u65b9\u76d2\u5b50\uff0830 \u00c5\uff09\uff0c\u4f7f\u7528 NEP \u6a21\u578b\u8ba1\u7b97\u52bf\u80fd\u548c\u529b\u968f\u8ddd\u79bb\u7684\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>nep.txt</code></p> <pre><code>gpumdkit.sh -plt dimer &lt;element1&gt; &lt;element2&gt; &lt;nep_model&gt;\ngpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>\u53c2\u8003\u6587\u732e\uff1a J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_doaspy","title":"plt_doas.py","text":"<p>\u7ed8\u5236 Wang et al. \u63d0\u51fa\u7684\u539f\u5b50\u6001\u5bc6\u5ea6 (DOAS)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>doas.out</code>\uff08\u7531 <code>gpumdkit.sh -calc doas</code> \u8ba1\u7b97\uff09</p> <pre><code>gpumdkit.sh -plt doas &lt;doas.out&gt; &lt;species&gt;\ngpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plane-grid","title":"\u6781\u6027\u6750\u6599\u7684 Plane-Grid \u7ed8\u56fe","text":"<p>\u6b64\u5de5\u4f5c\u6d41\u5c06\u4f4d\u79fb\u6216\u6781\u5316\u6570\u636e\u6620\u5c04\u5230\u7f51\u683c\u4e0a\uff0c\u5e76\u7ed8\u5236\u9009\u5b9a\u5e73\u9762\u7684\u8f6e\u5ed3\u3002\u8be6\u7ec6\u7528\u6cd5\u548c\u5b9e\u9645\u6848\u4f8b\u8bf7\u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790\u3002</p> <p>\u4f9d\u8d56\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>\u5178\u578b\u524d\u7f6e\u6b65\u9aa4\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>\u4f7f\u7528\u65b9\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_7","title":"\u5feb\u901f\u53c2\u8003\u8868","text":"\u547d\u4ee4 \u8f93\u5165\u6587\u4ef6 \u7528\u9014 <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP \u8bad\u7ec3\u7ed3\u679c <code>prediction</code> / <code>test</code> <code>*_test.out</code> NEP \u9884\u6d4b\u7ed3\u679c <code>train_test</code> <code>*_train.out</code>, <code>*_test.out</code> \u5408\u5e76 parity plot <code>parity_density</code> <code>*_train.out</code> \u5bc6\u5ea6 parity plot <code>force_errors</code> <code>force_train.out</code> \u529b\u8bef\u5dee\u6307\u6807 <code>lr</code> <code>loss.out</code> (gnep) \u5b66\u4e60\u7387 <code>restart</code> <code>nep.restart</code> \u91cd\u542f\u6587\u4ef6\u53c2\u6570 <code>charge</code> <code>charge_train.out</code> \u7535\u8377\u5206\u5e03 <code>born_charge</code> / <code>bec</code> <code>bec_train.out</code>, <code>bec_test.out</code> Born \u6709\u6548\u7535\u8377 <code>thermo</code> <code>thermo.out</code> \u70ed\u529b\u5b66\u91cf <code>msd</code> <code>msd.out</code> \u5747\u65b9\u4f4d\u79fb <code>msd_all</code> <code>msd.out</code> (all_groups) \u5168\u7ec4\u5206 MSD <code>msd_conv</code> <code>msd_step*.out</code> MSD \u6536\u655b\u6027\u68c0\u67e5 <code>sdc</code> <code>msd.out</code> \u81ea\u6269\u6563\u7cfb\u6570 <code>arrhenius_d</code> / <code>D</code> <code>*K/msd.out</code> Arrhenius \u6269\u6563\u7cfb\u6570 <code>arrhenius_sigma</code> / <code>sigma</code> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> Arrhenius \u79bb\u5b50\u7535\u5bfc\u7387 <code>rdf</code> <code>rdf.out</code> \u5f84\u5411\u5206\u5e03\u51fd\u6570 <code>rdf_pmf</code> <code>rdf.out</code> RDF + \u5e73\u5747\u529b\u52bf <code>vac</code> <code>sdc.out</code> \u901f\u5ea6\u81ea\u76f8\u5173 <code>cohesive</code> <code>cohesive.out</code> \u5185\u805a\u80fd\u66f2\u7ebf <code>net_force</code> <code>train.xyz</code> \u51c0\u529b\u5206\u5e03 <code>doas</code> <code>doas.out</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>des</code> <code>descriptors.npy</code> \u63cf\u8ff0\u7b26 PCA/UMAP <code>dimer</code> <code>nep.txt</code> \u4e8c\u805a\u4f53\u80fd\u91cf/\u529b\u66f2\u7ebf <code>pdos</code> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code> VAC \u548c PDOS <code>emd</code> EMD \u8f93\u51fa EMD \u70ed\u5bfc\u7387 <code>nemd</code> NEMD \u8f93\u51fa NEMD \u70ed\u8f93\u8fd0 <code>hnemd</code> HNEMD \u8f93\u51fa HNEMD \u70ed\u8f93\u8fd0 <code>viscosity</code> \u7c98\u5ea6\u8f93\u51fa \u7c98\u5ea6"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html","title":"\u81ea\u5b9a\u4e49\u547d\u4ee4","text":"\ud83d\udd27 \u81ea\u5b9a\u4e49\u547d\u4ee4 <p>GPUMDkit \u652f\u6301\u4ece ~/.gpumdkit.in \u52a0\u8f7d\u81ea\u5b9a\u4e49\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u628a\u5e38\u7528\u811a\u672c\u6216\u5de5\u4f5c\u6d41\u5c01\u88c5\u6210 <code>custom_</code> \u5f00\u5934\u7684 Bash \u51fd\u6570\uff0c\u7136\u540e\u901a\u8fc7 <code>gpumdkit.sh -\u547d\u4ee4\u540d</code> \u8c03\u7528\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_1","title":"\u8bbe\u7f6e","text":"<p>\u7f16\u8f91\u914d\u7f6e\u6587\u4ef6\uff1a</p> <pre><code>vi ~/.gpumdkit.in\n</code></pre> <p>\u81ea\u5b9a\u4e49\u51fd\u6570\u9700\u8981\u4f7f\u7528 <code>custom_</code> \u524d\u7f00\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_2","title":"\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_3","title":"\u7b80\u5355\u95ee\u5019","text":"<p>\u5728 <code>~/.gpumdkit.in</code> \u4e2d\u5199\u5165\uff1a</p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>\u7136\u540e\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -hello\n</code></pre> <p>\u4f60\u4f1a\u770b\u5230\u7c7b\u4f3c\u8f93\u51fa\uff1a</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_4","title":"\u5e26\u5fc5\u9700\u53c2\u6570\u7684\u547d\u4ee4","text":"<pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -greet Zihan\n</code></pre> <p>\u8f93\u51fa\uff1a</p> <pre><code>Hello, Zihan!\n</code></pre> <p>\u4f20\u9012\u53c2\u6570\u65f6\uff0c\u53ef\u4ee5\u7528 <code>\"$@\"</code> \u5b89\u5168\u5730\u8f6c\u53d1\u6240\u6709\u53c2\u6570\uff1b\u5982\u679c\u9700\u8981\u4ece\u7b2c\u4e00\u4e2a\u53c2\u6570\u5f00\u59cb\u5f15\u7528\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528 <code>${@:1}</code>\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_5","title":"\u8c03\u7528\u5916\u90e8\u811a\u672c","text":"<p>\u5982\u679c\u5e0c\u671b\u50cf\u8c03\u7528 GPUMDkit \u5185\u7f6e\u547d\u4ee4\u4e00\u6837\u8c03\u7528\u81ea\u5df1\u7684\u811a\u672c\uff1a</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -nepanalyse\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_6","title":"\u8fdb\u9636\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_7","title":"\u6279\u5904\u7406\u7ed8\u56fe","text":"<p>\u5bf9\u591a\u4e2a\u76ee\u5f55\u6279\u91cf\u7ed8\u56fe\uff1a</p> <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -batch_plot dir1 dir2 dir3\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_8","title":"\u8bad\u7ec3\u96c6\u5206\u6790\u6d41\u7a0b","text":"<p>\u628a\u591a\u4e2a\u5206\u6790\u547d\u4ee4\u7ec4\u5408\u6210\u4e00\u4e2a\u5165\u53e3\uff1a</p> <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -analyze_training train.xyz\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_9","title":"\u81ea\u5b9a\u4e49\u6570\u636e\u51c6\u5907\u6d41\u7a0b","text":"<pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    gpumdkit.sh -out2xyz ./\n    gpumdkit.sh -filter_value train.xyz force 30\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -prep_training\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_10","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u547d\u4ee4\u540d\u5c3d\u91cf\u6e05\u695a\uff0c\u4f8b\u5982 <code>custom_analyze_training</code> \u6bd4 <code>custom_at</code> \u66f4\u5bb9\u6613\u7ef4\u62a4\u3002</li> <li>\u5bf9\u9700\u8981\u53c2\u6570\u7684\u547d\u4ee4\uff0c\u5efa\u8bae\u5728\u53c2\u6570\u4e3a\u7a7a\u65f6\u6253\u5370\u7528\u6cd5\u63d0\u793a\u3002</li> <li>\u8c03\u7528\u5916\u90e8\u811a\u672c\u65f6\uff0c\u5c3d\u91cf\u7528 <code>\"$@\"</code> \u4fdd\u7559\u53c2\u6570\u4e2d\u7684\u7a7a\u683c\u548c\u7279\u6b8a\u5b57\u7b26\u3002</li> <li>\u6279\u5904\u7406\u76ee\u5f55\u65f6\uff0c\u6ce8\u610f\u4f7f\u7528 <code>cd \"$dir\"</code>\uff0c\u907f\u514d\u8def\u5f84\u4e2d\u6709\u7a7a\u683c\u65f6\u51fa\u9519\u3002</li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html","title":"\u8ba1\u7b97\u5668\u811a\u672c","text":"\ud83e\uddee \u8ba1\u7b97\u5668\u811a\u672c <p>\u8ba1\u7b97\u5668\u6a21\u5757\u7528\u4e8e\u4ece MD \u8f68\u8ff9\u3001NEP \u6a21\u578b\u548c\u7ed3\u6784\u6587\u4ef6\u4e2d\u8ba1\u7b97\u6750\u6599\u6027\u8d28\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code></p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_1","title":"\u529f\u80fd\u6982\u89c8","text":"<p>\u8ba1\u7b97\u5668\u6a21\u5757\u5927\u81f4\u53ef\u4ee5\u5206\u4e3a\u4e09\u7c7b\uff1a</p> <ul> <li>\u8f68\u8ff9\u6027\u8d28\uff1a \u4ece GPUMD \u6216 extxyz \u8f68\u8ff9\u8ba1\u7b97 MSD\u3001\u79bb\u5b50\u7535\u5bfc\u7387\u7b49\u65f6\u95f4\u76f8\u5173\u6027\u8d28\uff1b</li> <li>NEP \u8f85\u52a9\u8ba1\u7b97\uff1a \u4f7f\u7528 NEP \u6a21\u578b\u9884\u6d4b\u80fd\u91cf/\u529b/\u5e94\u529b\u3001\u63d0\u53d6\u63cf\u8ff0\u7b26\u3001\u8ba1\u7b97 DOAS\u3001\u8fdb\u884c NEB \u6216\u7ed3\u6784\u4f18\u5316\uff1b</li> <li>\u6781\u6027\u6750\u6599\u5206\u6790\uff1a \u4e3a\u9499\u949b\u77ff\u548c\u6781\u6027\u6750\u6599\u6784\u5efa\u8fd1\u90bb\u5217\u8868\u3001\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u3001\u5e73\u5747\u7ed3\u6784\u3001\u516b\u9762\u4f53\u503e\u8f6c\u548c\u5c40\u57df\u6781\u5316\u3002</li> </ul> <p>\u5982\u679c\u4f60\u8fd8\u4e0d\u719f\u6089\u67d0\u4e2a\u811a\u672c\uff0c\u5efa\u8bae\u5148\u7528\u4ea4\u4e92\u6a21\u5f0f\u67e5\u770b\u8f93\u5165\u63d0\u793a\uff1b\u5982\u679c\u5df2\u7ecf\u77e5\u9053\u53c2\u6570\uff0c\u5219\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528 <code>gpumdkit.sh -calc ...</code> \u8c03\u7528\u3002</p> \u4efb\u52a1 \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u79bb\u5b50\u7535\u5bfc\u7387 <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>\u3001<code>thermo.out</code>\u3001<code>model.xyz</code> MSD <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz \u8f68\u8ff9 NEP \u9884\u6d4b <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP \u6a21\u578b NEP \u63cf\u8ff0\u7b26 <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP \u6a21\u578b DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP \u6a21\u578b NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u521d\u672b\u6001\u7ed3\u6784 \u7ed3\u6784\u4f18\u5316 <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784 + NEP \u6a21\u578b \u90bb\u5c45\u5217\u8868 <code>gpumdkit.sh -calc nlist ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u4f4d\u79fb <code>gpumdkit.sh -calc disp ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u5e73\u5747\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u516b\u9762\u4f53\u503e\u8f6c <code>gpumdkit.sh -calc oct-tilt ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u67e5\u770b\u5b8c\u6574\u5e2e\u52a9\uff1a</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>\u547d\u4ee4\u884c\u5e2e\u52a9\u8868\u7c7b\u4f3c\uff1a</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>4) Calculators</code>\uff0c\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_2","title":"\u79bb\u5b50\u7535\u5bfc\u7387","text":"<p><code>calc_ion_conductivity.py</code> \u4ece <code>msd.out</code> \u8ba1\u7b97\u79bb\u5b50\u6269\u6563\u7cfb\u6570\u548c\u79bb\u5b50\u7535\u5bfc\u7387\u3002</p> <pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>401</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>\u5e38\u7528\u8f93\u5165\u6587\u4ef6\uff1a</p> \u6587\u4ef6 \u4f5c\u7528 <code>msd.out</code> \u5fc5\u9700\uff0cMSD \u6570\u636e <code>thermo.out</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u6e29\u5ea6 <code>model.xyz</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u4f53\u79ef\u548c\u79bb\u5b50\u6570 <code>run.in</code> \u53ef\u9009\uff0c\u8bc6\u522b\u6269\u80de\u4fe1\u606f <p>\u5982\u679c\u7f3a\u5c11\u81ea\u52a8\u8bc6\u522b\u6240\u9700\u6587\u4ef6\uff0c\u811a\u672c\u4f1a\u4ea4\u4e92\u5f0f\u8be2\u95ee\u6e29\u5ea6\u3001\u4f53\u79ef\u548c\u79bb\u5b50\u6570\u3002</p> <p>\u624b\u52a8\u6a21\u5f0f\u7684\u63d0\u793a\u7c7b\u4f3c\uff1a</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Diffusivity (D):\n  D_x: 4.153e-07 cm^2/s\n  D_y: 4.174e-07 cm^2/s\n  D_z: 2.610e-07 cm^2/s\n  D_total: 3.646e-07 cm^2/s\n------------------------------\nIonic Conductivity:\n  Sigma_x: 2.576e-02 mS/cm\n  Sigma_y: 2.589e-02 mS/cm\n  Sigma_z: 1.619e-02 mS/cm\n  Sigma_total: 2.261e-02 mS/cm\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#msd","title":"\u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD","text":"<p><code>calc_msd.py</code> \u53ef\u4ee5\u76f4\u63a5\u4ece extxyz \u8f68\u8ff9\u4e2d\u8ba1\u7b97\u6307\u5b9a\u5143\u7d20\u7684 MSD\u3002</p> <pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>412</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>Li</code> \u76ee\u6807\u6269\u6563\u5143\u7d20 <code>10</code> \u5e27\u95f4\u9694\uff0c\u5355\u4f4d fs <code>5000</code> \u53ef\u9009\uff0c\u6700\u5927\u76f8\u5173\u6b65\u6570 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>msd.out</code></li> </ul> <p><code>msd.out</code> \u7684\u5f00\u5934\u662f\u6587\u672c\u8868\u683c\uff0c\u5305\u542b\u65f6\u95f4\u548c\u4e0d\u540c\u65b9\u5411\u7684 MSD \u5217\u3002\u751f\u6210\u540e\u53ef\u4ee5\u7ee7\u7eed\u4f7f\u7528\u7ed8\u56fe\u547d\u4ee4\u68c0\u67e5\u6269\u6563\u533a\u95f4\u548c\u81ea\u6269\u6563\u7cfb\u6570\u3002</p> <p>\u968f\u540e\u53ef\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u9884\u6d4b\u6027\u8d28","text":"<p><code>calc_properties_with_nep.py</code> \u4f7f\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8ba1\u7b97\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u3002</p> <p>\u4f9d\u8d56\uff1a <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>\u4f7f\u7528\u6b64\u529f\u80fd\u53ef\u4ee5\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8fdb\u884c\u9884\u6d4b\u3002\u5efa\u8bae\u5728\u4f7f\u7528\u524d\u5148\u9a8c\u8bc1\u6a21\u578b\u5728\u76ee\u6807\u7ed3\u6784\u4e0a\u7684\u9884\u6d4b\u8d28\u91cf\uff0c\u518d\u5c06\u8f93\u51fa\u4f5c\u4e3a\u540e\u7eed\u5206\u6790\u6216\u7b5b\u9009\u4f9d\u636e\u3002</p> <p>\u63d0\u793a\uff1a \u9884\u6d4b\u524d\u53ef\u4ee5\u6e05\u7406 extxyz \u5143\u6570\u636e\uff1a</p> <pre><code>gpumdkit.sh -clean_xyz train.xyz clean_train.xyz\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep_1","title":"NEP \u63cf\u8ff0\u7b26","text":"<pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>\u7528\u9014\u5305\u62ec\uff1a</p> <ul> <li>\u7528 PCA/UMAP \u53ef\u89c6\u5316\u5c40\u57df\u73af\u5883\uff1b</li> <li>\u6bd4\u8f83\u8bad\u7ec3\u96c6\u548c\u5019\u9009\u7ed3\u6784\uff1b</li> <li>\u5224\u65ad\u65b0\u6570\u636e\u662f\u5426\u6269\u5c55\u4e86\u63cf\u8ff0\u7b26\u7a7a\u95f4\u3002</li> </ul> <p>\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#doas","title":"DOAS","text":"<p><code>calc_doas.py</code> \u7528\u4e8e\u8ba1\u7b97 Wang et al. \u63d0\u51fa\u7684 density of atomistic states\u3002</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>\u811a\u672c\u4f1a\uff1a</p> <ol> <li>\u8bfb\u53d6\u6240\u6709\u7ed3\u6784\uff1b</li> <li>\u4f7f\u7528 NEP \u8fdb\u884c\u7ed3\u6784\u4f18\u5316\uff1b</li> <li>\u63d0\u53d6\u6bcf\u4e2a\u539f\u5b50\u7684\u80fd\u91cf\uff1b</li> <li>\u6309\u5143\u7d20\u5206\u7ec4\u8f93\u51fa\uff1b</li> <li>\u7528\u7ed8\u56fe\u811a\u672c\u53ef\u89c6\u5316\u5206\u5e03\u3002</li> </ol> <p>\u5bf9\u4e8e\u5f88\u5927\u7684\u4f53\u7cfb\uff0c\u5982\u679c\u4e3b\u8981\u76ee\u7684\u662f\u83b7\u5f97\u4f18\u5316\u540e\u7684\u7ed3\u6784\u548c\u539f\u5b50\u80fd\u91cf\u5206\u5e03\uff0c\u76f4\u63a5\u5728 GPUMD \u4e2d\u5b8c\u6210\u6700\u5c0f\u5316\u548c\u539f\u5b50\u80fd\u91cf\u8f93\u51fa\u901a\u5e38\u4f1a\u66f4\u9ad8\u6548\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#neb","title":"NEB \u548c\u7ed3\u6784\u4f18\u5316","text":"<p>NEB\uff1a</p> <pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>\u8fd9\u4f1a\u4f7f\u7528 NEP \u6a21\u578b\u8fd0\u884c\u542b <code>9</code> \u4e2a\u4e2d\u95f4\u50cf\u7684 NEB \u8ba1\u7b97\u3002\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u811a\u672c\u4f1a\u8be2\u95ee\u539f\u5b50\u56fa\u5b9a\u65b9\u5f0f\uff1a</p> <ul> <li><code>none</code>\uff1a\u4e0d\u56fa\u5b9a\u539f\u5b50\uff1b</li> <li><code>index</code>\uff1a\u6309\u539f\u5b50\u5e8f\u53f7\u56fa\u5b9a\uff1b</li> <li><code>element</code>\uff1a\u56fa\u5b9a\u67d0\u4e00\u79cd\u5143\u7d20\u7684\u6240\u6709\u539f\u5b50\uff1b</li> <li><code>position</code>\uff1a\u56fa\u5b9a\u5750\u6807\u8303\u56f4\u5185\u7684\u539f\u5b50\u3002</li> </ul> <p>\u7ed3\u6784\u4f18\u5316\uff08\u901a\u8fc7 <code>calorine</code>\uff09\uff1a</p> <p>\u4f9d\u8d56\uff1a <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>\u8f93\u51fa\u5305\u62ec\uff1a</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#ovito-rdf","title":"\u4f7f\u7528 OVITO \u8ba1\u7b97 RDF","text":"<p><code>rdf_calculator_ovito.py</code> \u4f7f\u7528 OVITO \u7684\u5206\u6790\u5de5\u5177\u8ba1\u7b97\u5f84\u5411\u5206\u5e03\u51fd\u6570\u3002</p> <p>\u4f9d\u8d56\uff1a OVITO</p> <pre><code>pip install ovito\n</code></pre> <p>\u8f93\u5165\u6587\u4ef6\uff1a \u7ed3\u6784\u6587\u4ef6\uff08\u5355\u5e27\u6216\u8f68\u8ff9\uff09</p> <pre><code>python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400\n</code></pre> <p>\u53c2\u6570\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>trajectory.xyz</code> \u8f93\u5165\u7ed3\u6784\u6587\u4ef6 <code>6.0</code> RDF \u8ba1\u7b97\u7684\u6700\u5927\u8ddd\u79bb\uff08\u00c5\uff09 <code>400</code> \u76f4\u65b9\u56fe\u7684\u5206\u7bb1\u6570 <p>\u53ef\u89c6\u5316\uff1a</p> <pre><code>gpumdkit.sh -plt rdf\n</code></pre> <p>\u6ce8\u610f\uff1a \u5efa\u8bae\u4f18\u5148\u4f7f\u7528 GPUMD \u4e2d\u7684 <code>compute_rdf</code> \u547d\u4ee4\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_3","title":"\u94c1\u7535\u548c\u6781\u6027\u6750\u6599\u5de5\u5177","text":"<p>\u9009\u9879 <code>406\u2013410</code> \u9762\u5411\u9499\u949b\u77ff\u548c\u6781\u6027\u6750\u6599\u5206\u6790\uff0c\u5e38\u7528\u4e8e\u4ece MD \u8f68\u8ff9\u4e2d\u63d0\u53d6\u5c40\u57df\u7ed3\u6784\u4fe1\u606f\uff0c\u7136\u540e\u8fdb\u4e00\u6b65\u5206\u6790\u76f8\u53d8\u3001\u7574\u7ed3\u6784\u6216\u6781\u5316\u7eb9\u7406\u3002</p> <p>\u8fd9\u4e9b\u811a\u672c\u5728\u672c\u9875\u53ea\u505a\u5feb\u901f\u7d22\u5f15\uff0c\u56e0\u4e3a\u5b83\u4eec\u901a\u5e38\u9700\u8981\u7ec4\u5408\u4f7f\u7528\u3002\u63a8\u8350\u9605\u8bfb\u4e13\u9898\u6559\u7a0b\u4e2d\u7684\u5b8c\u6574\u5de5\u4f5c\u6d41\u548c\u53c2\u6570\u8bf4\u660e\uff1a\u6781\u6027\u6750\u6599\u5206\u6790\u3002</p> \u83dc\u5355 CLI \u5b50\u547d\u4ee4 \u4f5c\u7528 \u8be6\u7ec6\u8bf4\u660e <code>406</code> <code>gpumdkit.sh -calc nlist ...</code> \u6784\u5efa\u6307\u5b9a\u4e2d\u5fc3\u539f\u5b50\u548c\u8fd1\u90bb\u539f\u5b50\u4e4b\u95f4\u7684\u8fd1\u90bb\u5217\u8868 \u6781\u6027\u6750\u6599\u5206\u6790 <code>407</code> <code>gpumdkit.sh -calc disp ...</code> \u6839\u636e\u8f68\u8ff9\u548c\u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb \u6781\u6027\u6750\u6599\u5206\u6790 <code>408</code> <code>gpumdkit.sh -calc avg-struct ...</code> \u4ece\u8f68\u8ff9\u4e2d\u8ba1\u7b97\u5e73\u5747\u7ed3\u6784 \u6781\u6027\u6750\u6599\u5206\u6790 <code>409</code> <code>gpumdkit.sh -calc oct-tilt ...</code> \u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c\u89d2 \u6781\u6027\u6750\u6599\u5206\u6790 <code>410</code> <code>gpumdkit.sh -calc pol-abo3 ...</code> \u6839\u636e Born \u6709\u6548\u7535\u8377\u4f30\u7b97 ABO3 \u5c40\u57df\u6781\u5316 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u90e8\u5206\u811a\u672c\u9700\u8981\u5b89\u88c5 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>\u4e00\u4e2a\u5178\u578b\u987a\u5e8f\u662f\u5148\u7528 <code>nlist</code> \u5efa\u7acb\u8fd1\u90bb\u5217\u8868\uff0c\u518d\u7528\u8be5\u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u4f4d\u79fb\u3001\u503e\u8f6c\u6216\u6781\u5316\u3002\u5bf9\u4e8e\u5e73\u5747\u7ed3\u6784\uff0c\u53ef\u4ee5\u76f4\u63a5\u4ece\u8f68\u8ff9\u51fa\u53d1\uff0c\u7528\u957f\u5ea6\u5bb9\u5dee\u63a7\u5236\u54ea\u4e9b\u5e27\u53c2\u4e0e\u5e73\u5747\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html","title":"\u8d21\u732e\u6307\u5357","text":"\ud83e\udd1d \u4e3a GPUMDkit \u8d21\u732e\u4ee3\u7801 <p>\u611f\u8c22\u4f60\u6709\u5174\u8da3\u4e3a GPUMDkit \u505a\u51fa\u8d21\u732e\uff01\u6211\u4eec\u611f\u8c22\u4f60\u4e3a\u6539\u5584\u8fd9\u4e2a\u5de5\u5177\u5305\u6240\u4ed8\u51fa\u7684\u65f6\u95f4\u548c\u52aa\u529b\u3002</p> <p> English   \u00a0\u00b7\u00a0   \u7b80\u4f53\u4e2d\u6587 </p> <p><code>GPUMDkit</code> \u662f\u4e00\u4e2a\u5f00\u6e90\u9879\u76ee\uff0c\u6211\u4eec\u6b22\u8fce\u793e\u533a\u7684\u5404\u79cd\u8d21\u732e\uff0c\u65e0\u8bba\u662f\u4fee\u590d bug\u3001\u6dfb\u52a0\u65b0\u529f\u80fd\u3001\u6539\u8fdb\u6587\u6863\u8fd8\u662f\u63d0\u51fa\u5efa\u8bae\u3002</p> <p>\u6ce8\u610f\uff1a\u672c\u6587\u6863\u7684\u6743\u5a01\u7248\u672c\u4f4d\u4e8e\u4ed3\u5e93\u6839\u76ee\u5f55\u7684 <code>CONTRIBUTING.md</code>\u3002\u672c\u6559\u7a0b\u9875\u9762\u540c\u6b65\u5176\u5185\u5bb9\u3002\u4e2d\u6587\u7248\u8bf7\u53c2\u89c1 <code>docs/CONTRIBUTING_zh-CN.md</code>\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_1","title":"\u76ee\u5f55","text":"<ul> <li>\u5f00\u53d1\u89c4\u8303\u4e0e\u51c6\u5219</li> <li>\u62a5\u544a\u95ee\u9898</li> <li>\u529f\u80fd\u5efa\u8bae</li> <li>\u8d21\u732e\u4ee3\u7801</li> <li>Fork \u5e76\u514b\u9686\u4ed3\u5e93</li> <li>\u521b\u5efa\u529f\u80fd\u5206\u652f</li> <li>\u8fdb\u884c\u4fee\u6539<ul> <li>\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e</li> <li>\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e</li> <li>\u66f4\u65b0 Tab \u8865\u5168</li> </ul> </li> <li>\u4ee3\u7801\u98ce\u683c\u4e0e\u6700\u4f73\u5b9e\u8df5</li> <li>\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539</li> <li>\u63d0\u4ea4\u4fe1\u606f</li> <li>\u63a8\u9001\u5e76\u521b\u5efa Pull Request</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_2","title":"\u5f00\u53d1\u89c4\u8303\u4e0e\u51c6\u5219","text":"<p>\u4e3a\u4fdd\u6301\u4ee3\u7801\u8d28\u91cf\u548c\u9879\u76ee\u4e00\u81f4\u6027\uff0c\u8bf7\u9075\u5faa\u4ee5\u4e0b\u51c6\u5219\uff1a</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_3","title":"\u8bed\u8a00\u8981\u6c42","text":"<ul> <li>\u6240\u6709\u4ee3\u7801\u5e94\u4f7f\u7528\u82f1\u6587\u7f16\u5199\uff1a\u5305\u62ec\u53d8\u91cf\u540d\u3001\u51fd\u6570\u540d\u3001\u6ce8\u91ca\u3001\u6587\u6863\u5b57\u7b26\u4e32\u3001\u63d0\u4ea4\u4fe1\u606f\u548c\u6587\u6863\u3002</li> <li>\u867d\u7136\u6211\u4eec\u7406\u89e3\u8d21\u732e\u8005\u6765\u81ea\u4e0d\u540c\u80cc\u666f\uff0c\u4f46\u4f7f\u7528\u82f1\u6587\u80fd\u786e\u4fdd\u4ee3\u7801\u5e93\u5bf9\u6700\u5e7f\u6cdb\u7684\u7528\u6237\u7fa4\u4f53\u53ef\u8bbf\u95ee\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_4","title":"\u6a21\u5757\u5316\u4e0e\u53ef\u590d\u7528\u6027","text":"<ul> <li>\u7f16\u5199\u6a21\u5757\u5316\u548c\u53ef\u590d\u7528\u7684\u4ee3\u7801\uff1a\u51fd\u6570\u548c\u811a\u672c\u7684\u8bbe\u8ba1\u5e94\u5177\u6709\u7075\u6d3b\u6027\u3002</li> <li>\u4f18\u5148\u4f20\u9012\u53c2\u6570\u800c\u975e\u786c\u7f16\u7801\u503c\uff1a\u4f7f\u7528\u51fd\u6570\u53c2\u6570\u3001\u547d\u4ee4\u884c\u53c2\u6570\u6216\u914d\u7f6e\u6587\u4ef6\u6765\u66ff\u4ee3\u786c\u7f16\u7801\u503c\u3002\u4f46\u67d0\u4e9b\u6587\u4ef6\u540d\u7531 GPUMD \u548c NEP \u7a0b\u5e8f\u56fa\u5b9a\u8981\u6c42\uff08\u5982 <code>train.xyz</code>\u3001<code>thermo.out</code>\uff09\uff0c\u8fd9\u4e9b\u53ef\u4ee5\u6309\u9700\u786c\u7f16\u7801\u3002</li> <li>\u793a\u4f8b\uff1a   <pre><code># \u597d\u7684\u505a\u6cd5\uff1a\u63a5\u53d7\u53c2\u6570\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # \u5904\u7406\u903b\u8f91\n}\n\n# \u907f\u514d\uff1a\u786c\u7f16\u7801\u503c\uff08\u9664\u975e GPUMD/NEP \u8981\u6c42\uff09\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # \u5904\u7406\u903b\u8f91\n}\n</code></pre></li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_5","title":"\u4ee3\u7801\u98ce\u683c","text":"<ul> <li>\u7f16\u5199\u6e05\u6670\u3001\u6613\u4e8e\u4ed6\u4eba\u7ef4\u62a4\u548c\u4fee\u6539\u7684\u4ee3\u7801\u3002</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u548c\u51fd\u6570\u540d\u3002</li> <li>\u5728\u5fc5\u8981\u5904\u6dfb\u52a0\u6ce8\u91ca\u4ee5\u89e3\u91ca\u590d\u6742\u903b\u8f91\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_6","title":"\u6587\u6863","text":"<ul> <li>\u786e\u4fdd\u5e2e\u52a9\u4fe1\u606f\uff08\u5982 <code>-h</code> \u6807\u5fd7\uff09\u6e05\u6670\u51c6\u786e\u3002</li> <li>\u6559\u7a0b\u6587\u6863\u4f4d\u4e8e <code>docs/tutorials/en/</code>\uff08\u82f1\u6587\uff09\u548c <code>docs/tutorials/zh/</code>\uff08\u4e2d\u6587\uff09\u3002\u5982\u679c\u4f60\u6dfb\u52a0\u4e86\u65b0\u529f\u80fd\uff0c\u8bf7\u8003\u8651\u66f4\u65b0\u76f8\u5173\u6559\u7a0b\u9875\u9762\u3002</li> <li>\u7f16\u8f91\u6559\u7a0b Markdown \u6587\u4ef6\u540e\uff0c\u4f7f\u7528 <code>mkdocs build -f docs/mkdocs.yml</code> \u91cd\u65b0\u6784\u5efa HTML\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_7","title":"\u62a5\u544a\u95ee\u9898","text":"<p>\u5982\u679c\u4f60\u9047\u5230 bug\uff0c\u8bf7\u901a\u8fc7 GitHub Issues \u5e2e\u52a9\u6211\u4eec\u4fee\u590d\uff1a</p> <ol> <li>\u641c\u7d22\u73b0\u6709 issues \u67e5\u770b\u8be5 bug \u662f\u5426\u5df2\u88ab\u62a5\u544a\u3002</li> <li>\u521b\u5efa\u65b0 issue\uff08\u5982\u679c\u5c1a\u672a\u88ab\u62a5\u544a\uff09\uff1a\u521b\u5efa Issue</li> <li>\u8be6\u7ec6\u63cf\u8ff0\u95ee\u9898\uff0c\u5982\u679c\u53ef\u80fd\u8bf7\u63d0\u4f9b\u6d4b\u8bd5\u6587\u4ef6\u3002</li> </ol> <p>\u4f60\u4e5f\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u65b9\u5f0f\u8054\u7cfb\u6211\u4eec\uff1a - QQ \u7fa4\uff1a825696376 - \u90ae\u7bb1\uff1ayanzihan@westlake.edu.cn - \u811a\u672c\u5f00\u53d1\u8005\uff1a\u8054\u7cfb\u811a\u672c\u5934\u90e8\u5217\u51fa\u7684\u5f00\u53d1\u8005</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_8","title":"\u529f\u80fd\u5efa\u8bae","text":"<p>\u6211\u4eec\u6b22\u8fce\u529f\u80fd\u5efa\u8bae\uff01\u63d0\u51fa\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u641c\u7d22\u73b0\u6709 issues \u67e5\u770b\u662f\u5426\u5df2\u6709\u4eba\u63d0\u51fa\u3002</li> <li>\u521b\u5efa\u65b0\u529f\u80fd\u8bf7\u6c42\uff1a\u521b\u5efa\u529f\u80fd\u8bf7\u6c42 \u5e76 mention @zhyan0603</li> <li>\u6e05\u695a\u63cf\u8ff0\u4f60\u7684\u9700\u6c42 \u5e76\u89e3\u91ca\u5176\u7528\u9014\u3002</li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_9","title":"\u8d21\u732e\u4ee3\u7801","text":""},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#fork","title":"Fork \u5e76\u514b\u9686\u4ed3\u5e93","text":"<ol> <li> <p>\u5728 GitHub \u4e0a Fork \u4ed3\u5e93\uff0c\u70b9\u51fb \u4ed3\u5e93\u9875\u9762 \u53f3\u4e0a\u89d2\u7684 \"Fork\" \u6309\u94ae\u3002</p> </li> <li> <p>\u514b\u9686\u4f60\u7684 fork \u5230\u672c\u5730\uff1a</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>\u8bbe\u7f6e upstream remote \u4ee5\u4fdd\u6301 fork \u540c\u6b65\uff1a    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_10","title":"\u521b\u5efa\u529f\u80fd\u5206\u652f","text":"<p>\u4e3a\u4f60\u7684\u4fee\u6539\u521b\u5efa\u65b0\u5206\u652f\uff1a</p> <pre><code># \u4ece main \u521b\u5efa\u5e76\u5207\u6362\u5230\u65b0\u5206\u652f\ngit checkout -b your-branch-name\n</code></pre> <p>\u5206\u652f\u540d\u79f0\u968f\u610f\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_11","title":"\u8fdb\u884c\u4fee\u6539","text":"<p><code>GPUMDkit</code> \u7684\u7ed3\u6784\u5305\u62ec\uff1a - <code>gpumdkit.sh</code>\uff1a\u4e3b\u5165\u53e3\uff08Bash \u811a\u672c\uff09\uff0c\u5904\u7406\u4ea4\u4e92\u83dc\u5355\u6a21\u5f0f\u548c\u547d\u4ee4\u884c\u6a21\u5f0f - <code>install.sh</code>\uff1a\u5b89\u88c5\u811a\u672c\uff0c\u8bbe\u7f6e\u73af\u5883\u53d8\u91cf\u548c shell \u914d\u7f6e - <code>Scripts/</code>\uff1a\u6309\u529f\u80fd\u7ec4\u7ec7\u7684 Python \u548c Bash \u5b9e\u73b0\u811a\u672c   - <code>plt_scripts/</code>\uff1a\u7ed8\u56fe\u811a\u672c   - <code>calculators/</code>\uff1a\u8ba1\u7b97\u5de5\u5177   - <code>format_conversion/</code>\uff1a\u683c\u5f0f\u8f6c\u6362\u5de5\u5177   - <code>workflow/</code>\uff1a\u5de5\u4f5c\u6d41\u81ea\u52a8\u5316   - <code>sample_structures/</code>\uff1a\u7ed3\u6784\u91c7\u6837\u5de5\u5177   - <code>analyzer/</code>\uff1a\u5206\u6790\u5de5\u5177   - <code>utils/</code>\uff1a\u5b9e\u7528\u51fd\u6570\uff08\u5305\u62ec <code>completion.sh</code> Tab \u8865\u5168\uff09 - <code>src/</code>\uff1a\u4ea4\u4e92\u6a21\u5f0f\u83dc\u5355\u51fd\u6570\u7684 Shell \u811a\u672c   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>skills/</code>\uff1aAI agent \u6280\u80fd\u5b9a\u4e49\uff08\u7528\u4e8e opencode/Claude Code \u96c6\u6210\u7684 SKILL.md \u6587\u4ef6\uff09 - <code>docs/</code>\uff1a\u6587\u6863\u6587\u4ef6   - <code>tutorials/en/</code> \u548c <code>tutorials/zh/</code>\uff1a\u53cc\u8bed\u6559\u7a0b\u9875\u9762   - <code>mkdocs.yml</code>\uff1a\u6784\u5efa\u6559\u7a0b HTML \u7684 MkDocs \u914d\u7f6e   - <code>command_reference.tsv</code>\uff1a\u673a\u5668\u53ef\u8bfb\u7684\u547d\u4ee4\u53c2\u8003   - <code>htmls/</code>\uff1aMkDocs \u751f\u6210\u7684 HTML \u8f93\u51fa</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_12","title":"\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e","text":"<p>\u8981\u6dfb\u52a0\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u8bbf\u95ee\u7684\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u5728\u76f8\u5e94\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a</li> </ol> <pre><code># \u793a\u4f8b\uff1a\u6dfb\u52a0\u65b0\u7684\u683c\u5f0f\u8f6c\u6362\u811a\u672c\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u9075\u5faa\u6a21\u5757\u5316\u51c6\u5219\uff08\u63a5\u53d7\u53c2\u6570\uff0c\u907f\u514d\u786c\u7f16\u7801\uff09\u3002</p> </li> <li> <p>\u5728\u76f8\u5e94\u7684 <code>src/</code> \u6587\u4ef6\u4e2d\u6dfb\u52a0\u5305\u88c5\u51fd\u6570\uff1a    <pre><code># \u793a\u4f8b\uff1a\u7f16\u8f91 src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>\u6dfb\u52a0\u65b0\u51fd\u6570\uff1a    <pre><code>function f111_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input &lt;required_param1&gt; &lt;required_param2&gt;\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -r -a converter_args\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py \"${converter_args[@]}\"\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u66f4\u65b0\u83dc\u5355\u663e\u793a\uff1a    <pre><code># \u627e\u5230 menu() \u51fd\u6570\u5e76\u6309\u9700\u66f4\u65b0\n# \u627e\u5230 array_choice \u6570\u7ec4\u5e76\u6dfb\u52a0\u4f60\u7684\u65b0\u9009\u62e9\u7f16\u53f7\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\" \"107\" \"108\" \"109\" \"110\" \"111\"  # \u6dfb\u52a0 \"111\"\n    # ... \u5176\u4f59\u9009\u62e9\n)\n</code></pre></p> </li> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0 case \u8bed\u53e5\uff1a    <pre><code># \u5728 main() \u51fd\u6570\u4e2d\u627e\u5230\u76f8\u5e94\u7684 case \u8bed\u53e5\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n            \"101\") f101_out2xyz ;;\n            # ... \u73b0\u6709 case ...\n            \"111\") f111_new_converter ;;  # \u6dfb\u52a0\u4f60\u7684 case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_13","title":"\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e","text":"<p>\u8981\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c\u6807\u5fd7\u6216\u5b50\u547d\u4ee4\uff1a</p> <ol> <li> <p>\u5728\u76f8\u5e94\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a    <pre><code># \u793a\u4f8b\uff1a\u6dfb\u52a0\u65b0\u7684\u5206\u6790\u5668\u811a\u672c\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u660e\u786e\u53c2\u6570\u8981\u6c42\uff1a    <pre><code># \u793a\u4f8b\uff1aScripts/analyzer/analyze_bonds.py\nimport sys\n\nif len(sys.argv) != 3:\n    print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n    print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n    sys.exit(1)\n\ninput_file = sys.argv[1]\ncutoff = float(sys.argv[2])\n\n# \u4f60\u7684\u5b9e\u73b0\n</code></pre></p> </li> </ol> <p>\u6ce8\u610f\uff1aGPUMDkit Python \u811a\u672c\u8bbe\u8ba1\u4e3a\u76f4\u63a5\u8fd0\u884c\uff08\u4e0d\u4f5c\u4e3a\u6a21\u5757\u5bfc\u5165\uff09\u3002 \u5982\u679c\u4f60\u613f\u610f\uff0c\u53ef\u4ee5\u4f7f\u7528 <code>main()</code> \u51fd\u6570\u914d\u5408 <code>if __name__ == \"__main__\":</code> \u4fdd\u62a4\uff0c \u4f46\u8fd9\u4e0d\u662f\u5fc5\u9700\u7684\u3002\u5927\u591a\u6570\u73b0\u6709\u811a\u672c\u5728\u6a21\u5757\u7ea7\u522b\u6267\u884c\u3002</p> <ol> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0\u547d\u4ee4\u884c\u6807\u5fd7\u5904\u7406\uff1a    <pre><code># \u627e\u5230\u547d\u4ee4\u884c\u89e3\u6790\u90e8\u5206\uff08\u5927\u7684 \"case $1 in\" \u5757\uff09\n# \u5728\u9002\u5f53\u4f4d\u7f6e\u6dfb\u52a0\u4f60\u7684\u65b0\u6807\u5fd7\n\ncase $1 in\n    # ... \u73b0\u6709 case ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ \"$2\" != \"-h\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py $2 $3\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n        fi ;;\n    # ... \u5176\u4f59 case ...\nesac\n</code></pre></p> </li> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u66f4\u65b0\u5e2e\u52a9\u4fe1\u606f\uff1a    <pre><code># \u627e\u5230 help_info_table() \u51fd\u6570\u5e76\u6dfb\u52a0\u4f60\u7684\u547d\u4ee4\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... \u5176\u4f59\u5e2e\u52a9\u8868 ...\n}\n</code></pre></p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#tab","title":"\u66f4\u65b0 Tab \u8865\u5168","text":"<p>\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c\u6807\u5fd7\u65f6\uff0c\u66f4\u65b0 Tab \u8865\u5168\u811a\u672c\uff1a</p> <pre><code># \u7f16\u8f91 Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>\u5c06\u4f60\u7684\u65b0\u6807\u5fd7\u6dfb\u52a0\u5230 <code>opts</code> \u53d8\u91cf\uff1a <pre><code># \u627e\u5230 local opts=... \u884c\nlocal opts=\"-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...\"\n#                                                        \u5728\u6b64\u6dfb\u52a0\u4f60\u7684\u6807\u5fd7\n</code></pre></p> <p>\u5982\u679c\u4f60\u7684\u6807\u5fd7\u9700\u8981\u6587\u4ef6\u53c2\u6570\uff0c\u5c06\u5176\u6dfb\u52a0\u5230\u73b0\u6709\u7684\u6587\u4ef6\u8865\u5168 case \u4e2d\uff1a <pre><code># \u627e\u5230\u9700\u8981\u6587\u4ef6\u53c2\u6570\u7684 case \u5e76\u7528 | \u6dfb\u52a0\u4f60\u7684\u6807\u5fd7\n-out2xyz|-out2exyz|-...|-your_new_flag)\n    COMPREPLY=($(compgen -f -- \"$cur\")) ;;\n</code></pre></p> <p>\u5982\u679c\u4f60\u7684\u6807\u5fd7\u63a5\u53d7\u4e8c\u7ea7\u9009\u9879\uff08\u5982 <code>-plt</code> \u6216 <code>-calc</code>\uff09\uff0c\u6dfb\u52a0\u65b0 case\uff1a <pre><code>case \"$prev\" in\n    # ... \u73b0\u6709 case ...\n    -your_new_flag)\n        COMPREPLY=($(compgen -W \"option1 option2 option3\" -- \"$cur\")) ;;\n    # ... \u5176\u4f59 case ...\nesac\n</code></pre></p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_14","title":"\u4ee3\u7801\u98ce\u683c\u4e0e\u6700\u4f73\u5b9e\u8df5","text":"<ul> <li>Shell \u811a\u672c\uff1a</li> <li>\u4f7f\u7528 <code>${variable}</code> \u8fdb\u884c\u53d8\u91cf\u5c55\u5f00</li> <li>\u4f7f\u7528 <code>[ ! -z \"$var\" ]</code> \u8fdb\u884c\u975e\u7a7a\u68c0\u67e5\uff08\u9879\u76ee\u7ea6\u5b9a\uff09</li> <li>\u4ea4\u4e92\u51fd\u6570\u5e94\u9075\u5faa banner \u683c\u5f0f\uff1a     <pre><code>echo \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/&lt;category&gt;        |\"\necho \" | Script: &lt;script_name&gt;.py                        |\"\necho \" | Developer: &lt;Name&gt; (&lt;email&gt;)                     |\"\necho \" &gt;-------------------------------------------------&lt;\"\n</code></pre></li> <li>\u4f7f\u7528 <code>read -r -a varname</code> \u8bfb\u53d6\u591a\u8bcd\u8f93\u5165\uff0c\u7136\u540e\u7528 <code>\"${varname[@]}\"</code> \u4f20\u9012</li> <li> <p><code>src/</code> \u4e2d\u7684 Shell \u811a\u672c\u5e94\u4ee5\u6587\u4ef6\u5934\u6ce8\u91ca\u5757\u5f00\u59cb\uff1a     <pre><code># ============================================================\n# GPUMDkit &lt;module name&gt; module\n# Repository: https://github.com/zhyan0603/GPUMDkit\n# Author: &lt;Name&gt; (&lt;email&gt;)\n# ============================================================\n</code></pre></p> </li> <li> <p>Python \u811a\u672c\uff1a</p> </li> <li>\u7f16\u5199\u6e05\u6670\u3001\u53ef\u7ef4\u62a4\u7684\u4ee3\u7801</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u540d</li> <li>\u4f7f\u7528 <code>sys.argv</code> \u8fdb\u884c\u53c2\u6570\u89e3\u6790\uff08\u4e0e\u5927\u591a\u6570\u73b0\u6709\u811a\u672c\u4e00\u81f4\uff09</li> <li>\u63d0\u4f9b\u6e05\u6670\u7684\u4f7f\u7528\u4fe1\u606f\uff1a<code>print(\"Usage: ...\")</code> \u548c <code>print(\"Example: ...\")</code></li> <li>\u5982\u679c\u4f60\u7684\u811a\u672c\u4f7f\u7528\u91cd\u578b/\u7279\u6b8a\u5305\uff08<code>NepTrain</code>\u3001<code>calorine</code>\u3001<code>dpdata</code>\uff09\uff0c\u8bf7\u6dfb\u52a0     <code>print_dependency_notice()</code> \u51fd\u6570\u4ee5\u901a\u77e5\u7528\u6237\u5f15\u7528\u5efa\u8bae</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_15","title":"\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539","text":"<p>\u63d0\u4ea4\u8d21\u732e\u524d\uff0c\u8fd0\u884c\u76f8\u5173\u9a8c\u8bc1\u547d\u4ee4\uff1a</p> <pre><code># Shell \u8bed\u6cd5\u68c0\u67e5\uff08\u59cb\u7ec8\u8fd0\u884c\uff09\nbash -n gpumdkit.sh\nfind src Scripts -name '*.sh' -exec bash -n {} +\n\n# Python \u8bed\u6cd5\u68c0\u67e5\uff08\u9488\u5bf9\u4fee\u6539\u7684 Python \u6587\u4ef6\uff09\npython3 -m py_compile path/to/modified_script.py\n\n# MkDocs \u6784\u5efa\uff08\u5982\u679c\u4fee\u6539\u4e86\u6587\u6863\uff09\nmkdocs build -f docs/mkdocs.yml\n\n# \u68c0\u67e5\u5c3e\u968f\u7a7a\u683c\u95ee\u9898\ngit diff --check\n</code></pre> <p>\u7136\u540e\u6d4b\u8bd5\u529f\u80fd\uff1a</p> <ol> <li> <p>\u6d4b\u8bd5\u4ea4\u4e92\u6a21\u5f0f\uff08\u5982\u9002\u7528\uff09\uff1a    <pre><code>gpumdkit.sh\n# \u5bfc\u822a\u5230\u4f60\u7684\u65b0\u529f\u80fd\u5e76\u5145\u5206\u6d4b\u8bd5\n</code></pre></p> </li> <li> <p>\u6d4b\u8bd5\u547d\u4ee4\u884c\u6a21\u5f0f\uff08\u5982\u9002\u7528\uff09\uff1a    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # \u6d4b\u8bd5\u5e2e\u52a9\u4fe1\u606f\n</code></pre></p> </li> <li> <p>\u6d4b\u8bd5 Tab \u8865\u5168\uff08\u5982\u679c\u4f60\u4fee\u6539\u4e86 <code>completion.sh</code>\uff09\uff1a    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # \u5e94\u663e\u793a\u4f60\u7684\u65b0\u6807\u5fd7\n</code></pre></p> </li> <li> <p>\u7528\u5404\u79cd\u8f93\u5165\u6d4b\u8bd5\uff1a</p> </li> <li>\u7528\u5178\u578b\u8f93\u5165\u6d4b\u8bd5</li> <li>\u7528\u8fb9\u7f18\u60c5\u51b5\u6d4b\u8bd5\uff08\u7a7a\u6587\u4ef6\u3001\u5927\u6587\u4ef6\u7b49\uff09</li> <li> <p>\u6d4b\u8bd5\u9519\u8bef\u5904\u7406\uff08\u7f3a\u5c11\u6587\u4ef6\u3001\u65e0\u6548\u53c2\u6570\uff09</p> </li> <li> <p>\u9a8c\u8bc1\u65e0\u56de\u5f52\uff1a\u786e\u4fdd\u73b0\u6709\u529f\u80fd\u4ecd\u7136\u6b63\u5e38\u5de5\u4f5c\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_16","title":"\u63d0\u4ea4\u4fe1\u606f","text":"<p>\u7f16\u5199\u6e05\u6670\u3001\u63cf\u8ff0\u6027\u7684\u63d0\u4ea4\u4fe1\u606f\u6765\u89e3\u91ca\u4f60\u505a\u4e86\u4ec0\u4e48\u66f4\u6539\u3002\u6ca1\u6709\u4e25\u683c\u7684\u683c\u5f0f\u8981\u6c42\u2014\u2014\u53ea\u8981\u786e\u4fdd\u4f60\u7684\u4fe1\u606f\u662f\u53ef\u7406\u89e3\u7684\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#pull-request","title":"\u63a8\u9001\u5e76\u521b\u5efa Pull Request","text":"<ol> <li> <p>\u63d0\u4ea4\u4f60\u7684\u4fee\u6539\uff1a    <pre><code>git add .\ngit commit -m \"\u4f60\u7684\u63cf\u8ff0\u6027\u4fe1\u606f\"\n</code></pre></p> </li> <li> <p>\u4fdd\u6301\u4f60\u7684\u5206\u652f\u4e0e\u6700\u65b0\u7684 <code>dev</code> \u5206\u652f\u540c\u6b65\uff1a    <pre><code>git fetch origin\ngit rebase origin/dev\n</code></pre></p> </li> <li> <p>\u63a8\u9001\u4f60\u7684\u5206\u652f\u5230\u4f60\u7684 fork\uff1a    <pre><code>git push origin your-branch-name\n</code></pre></p> </li> <li> <p>\u521b\u5efa Pull Request\uff1a</p> </li> <li>\u524d\u5f80 GPUMDkit \u4ed3\u5e93</li> <li>\u70b9\u51fb \"Pull Requests\" \u2192 \"New Pull Request\"</li> <li>\u8bbe\u7f6e\u76ee\u6807\u5206\u652f\u4e3a <code>dev</code> \u8fdb\u884c\u4ee3\u7801\u5ba1\u67e5</li> <li>\u8bbe\u7f6e\u6bd4\u8f83\u5206\u652f\u4e3a\u4f60\u7684\u529f\u80fd\u5206\u652f</li> <li> <p>\u586b\u5199 PR \u63cf\u8ff0\uff1a</p> <ul> <li>\u6807\u9898\uff1a\u7b80\u8981\u63cf\u8ff0\u66f4\u6539</li> <li>\u63cf\u8ff0\uff1a\u8be6\u7ec6\u89e3\u91ca\u66f4\u6539\u5185\u5bb9\u548c\u539f\u56e0</li> <li>\u6d4b\u8bd5\uff1a\u63cf\u8ff0\u4f60\u5982\u4f55\u6d4b\u8bd5\u8fd9\u4e9b\u66f4\u6539</li> </ul> </li> <li> <p>\u56de\u5e94\u5ba1\u67e5\u53cd\u9988\uff1a</p> </li> <li>\u5bf9\u5efa\u8bae\u548c\u5efa\u8bbe\u6027\u6279\u8bc4\u4fdd\u6301\u5f00\u653e</li> <li>\u53ca\u65f6\u8fdb\u884c\u8bf7\u6c42\u7684\u4fee\u6539</li> <li> <p>\u63a8\u9001\u989d\u5916\u63d0\u4ea4\u5230\u4f60\u7684\u5206\u652f\uff08\u5b83\u4eec\u4f1a\u81ea\u52a8\u51fa\u73b0\u5728 PR \u4e2d\uff09</p> </li> <li> <p>\u6279\u51c6\u540e\uff1a\u7ef4\u62a4\u8005\u5c06\u5408\u5e76\u4f60\u7684 PR\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_17","title":"\u6709\u95ee\u9898\u6216\u9700\u8981\u5e2e\u52a9\uff1f","text":"<p>\u5982\u679c\u4f60\u5bf9\u8d21\u732e\u6709\u7591\u95ee\u6216\u9700\u8981\u5e2e\u52a9\uff1a</p> <ul> <li>\u53d1\u8d77\u8ba8\u8bba\uff1a\u4f7f\u7528 GitHub Discussions \u63d0\u51fa\u4e00\u822c\u6027\u95ee\u9898</li> <li>\u5728 issue \u4e2d\u63d0\u95ee\uff1a\u5728\u76f8\u5173 issue \u4e2d\u8bc4\u8bba\u4ee5\u83b7\u53d6\u5177\u4f53\u95ee\u9898\u7684\u5e2e\u52a9</li> <li>\u8054\u7cfb\u7ef4\u62a4\u8005\uff1a\u8054\u7cfb README \u4e2d\u5217\u51fa\u7684\u6838\u5fc3\u5f00\u53d1\u8005</li> </ul> <p>\u518d\u6b21\u611f\u8c22\u4f60\u4e3a <code>GPUMDkit</code> \u505a\u51fa\u8d21\u732e\uff01\u4f60\u7684\u52aa\u529b\u5e2e\u52a9\u8fd9\u4e2a\u5de5\u5177\u5305\u4e3a\u6574\u4e2a GPUMD \u548c NEP \u793e\u533a\u53d8\u5f97\u66f4\u597d\u3002</p>"}]}
\ No newline at end of file
+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"],"fields":{"title":{"boost":1000.0},"text":{"boost":1.0},"tags":{"boost":1000000.0}}},"docs":[{"location":"index.html","title":"Home","text":"\ud83d\udcda GPUMDkit Documentation <p>A practical bilingual tutorial for GPUMDkit, covering installation, command-line tools, interactive workflows, plotting, and analysis utilities.</p>"},{"location":"index.html#language","title":"Language","text":"Language Start Here Command Reference English GPUMDkit Tutorials Command Reference \u7b80\u4f53\u4e2d\u6587 GPUMDkit \u6559\u7a0b \u547d\u4ee4\u53c2\u8003"},{"location":"index.html#what-you-can-learn-here","title":"What You Can Learn Here","text":"<p>This documentation is organized as a practical tutorial rather than only a command list. New users are encouraged to start from the overview and quick start pages, then move to the topic that matches their task.</p> Topic What it Covers Quick Start Installation, environment setup, interactive mode, direct command mode Format Conversion VASP, LAMMPS, CP2K, ABACUS, CIF, extxyz, group labels, weights Sampling Uniform/random sampling, NepTrain FPS, perturbation, force-deviation selection Calculators MSD, ionic conductivity, NEP prediction, descriptors, DOAS, NEB, polarization tools Analyzers Composition checks, distance checks, filters, property range analysis Visualization NEP training plots, MD plots, transport plots, thermal transport plots, example figures Workflows Batch DFT/MD processing and active-learning style workflows <p>For complex operations, use the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>For common operations with fixed arguments, use direct command-line mode:</p> <pre><code>gpumdkit.sh -h\ngpumdkit.sh -plt -h\ngpumdkit.sh -calc -h\n</code></pre>"},{"location":"en/index.html","title":"GPUMDkit Tutorials","text":"\ud83d\udcda GPUMDkit Tutorials <p>Welcome to GPUMDkit, a command-line toolkit for GPUMD and NEP.</p>"},{"location":"en/index.html#what-it-does","title":"What it does","text":"<p>GPUMDkit helps you perform common tasks in computational materials science without writing custom scripts. It supports format conversion, structure analysis, property calculation, visualization, and batch workflows \u2014 all from one command-line tool.</p>"},{"location":"en/index.html#common-tasks","title":"Common Tasks","text":"I want to... Tutorial Install GPUMDkit and run my first command Quick Start Convert VASP, LAMMPS, CP2K, or CIF files to extxyz Format Conversion Check structure distances, filter datasets, or find outliers Analyzer Scripts Calculate MSD, ionic conductivity, or descriptors Calculator Scripts Analyze polar materials, ferroelectrics, or ABO3 systems Polar Material Analysis Plot NEP training results or thermodynamic data Plot Scripts Run batch DFT or MD simulations Workflow Scripts Select representative structures from a dataset Structure Sampling Add my own shortcuts to GPUMDkit Custom Commands"},{"location":"en/index.html#before-you-start","title":"Before you start","text":""},{"location":"en/index.html#installation","title":"Installation","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"en/index.html#dependencies","title":"Dependencies","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"en/index.html#interactive-mode","title":"Interactive mode","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>This opens a menu where you can select modules by number.</p>"},{"location":"en/index.html#cli-mode","title":"CLI mode","text":"<pre><code>gpumdkit.sh -&lt;option&gt; [args...]\n</code></pre> <p>For example:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>Use <code>gpumdkit.sh -h</code> to see all available options.</p>"},{"location":"en/index.html#module-overview","title":"Module Overview","text":"Module Menu CLI Description Format Conversion 1 <code>-out2xyz</code>, <code>-pos2exyz</code> File conversion Sample Structures 2 interactive menu, <code>-frame_range</code>, <code>-pynep</code> (deprecated) Structure sampling Workflow 3 - Batch processing Calculators 4 <code>-calc &lt;type&gt;</code> Property calculations Analyzer 5 <code>-range</code>, <code>-min_dist</code> Structure analysis Visualization 6 <code>-plt &lt;type&gt;</code> Plotting tools Utilities 7 <code>-time</code>, <code>-clean</code> Utility functions"},{"location":"en/index.html#all-tutorials","title":"All Tutorials","text":"Tutorial Description Quick Start Installation and first steps Command Reference One-page CLI and menu reference Format Conversion Convert between file formats Calculator Scripts Compute material properties Analyzer Scripts Structure analysis and validation Plot Scripts Plotting and visualization Workflow Scripts Batch processing and automation Structure Sampling Structure selection methods Custom Commands User-defined GPUMDkit shortcuts Active Learning Workflow Batch active-learning workflow notes Polar Material Analysis Ferroelectric and polarization tools Contributing to GPUMDkit Development notes"},{"location":"en/index.html#links","title":"Links","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>Documentation: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"en/active_learning_workflow.html","title":"Active Learning Workflow","text":"\ud83d\udd01 Active Learning Workflow <p>This tutorial explains the steps and considerations involved in the <code>workflow_active_learning_dev.sh</code> script. The workflow is used to generate, select, and analyze molecular structures, followed by simulations and data collection.</p> <p>Script Location: <code>Scripts/workflow/</code></p>"},{"location":"en/active_learning_workflow.html#overview","title":"Overview","text":"<p>This script automates one iteration of NEP active learning. The typical workflow includes:</p> Step Action Purpose 1 Run MD simulations Generate candidate structures with current NEP model 2 Filter structures Remove unphysical configurations (short distances, large boxes) 3 Sample structures Select diverse or uncertain structures for DFT 4 Run SCF calculations Compute DFT reference energies/forces 5 NEP prediction Check model accuracy on new structures <p>Unlike menu-driven modules, this workflow is a shell script that you customize and run directly:</p> <pre><code>bash Scripts/workflow/workflow_active_learning_dev.sh\n</code></pre> <p>The sections below explain the main blocks in the script and what each part does.</p>"},{"location":"en/active_learning_workflow.html#1-slurm-directives","title":"1. SLURM Directives","text":"<pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>The SLURM directives are used to define how the job will be submitted to the cluster:</p> <ul> <li><code>#SBATCH -p</code> defines the partition, in this case, it's <code>intel-sc3</code> and <code>intel-sc3-32c</code>.</li> <li><code>#SBATCH -q</code> specifies the queue, in this case, <code>huge</code>.</li> <li><code>#SBATCH -N</code> allocates 1 node for the job.</li> <li><code>#SBATCH -J</code> names the job <code>workflow</code>.</li> <li><code>#SBATCH -o</code> defines the output log file as <code>workflow.log</code>.</li> <li><code>--ntasks-per-node=1</code> specifies that only one task should run per node.</li> </ul> <p>NOTE: If your machine does not have the SLURM environment, you can also run the script directly from the command line. For example:</p> <pre><code>nohup bash workflow_active_learning_dev.sh &amp;&gt;workflow.log &amp;\n</code></pre>"},{"location":"en/active_learning_workflow.html#2-basic-setup","title":"2. Basic Setup","text":"<pre><code>cd $SLURM_SUBMIT_DIR \n</code></pre> <p>Ensure the working directory is correct, and that all necessary files are present for the job.</p> <pre><code>source ${GPUMDkit_path}/Scripts/workflow/submit_template.sh  # Load the submit template\npython_pynep=python  # Python executable for the deprecated pynep branch if needed\n</code></pre> <ul> <li><code>GPUMDkit_path</code> is the environment variable that stores the path for the <code>GPUMDkit</code> .</li> <li><code>python_pynep</code> points to the Python environment used for the deprecated <code>pynep</code>-related branch if needed.</li> </ul>"},{"location":"en/active_learning_workflow.html#3-variable-definitions","title":"3. Variable Definitions","text":"<pre><code>work_dir=${PWD}  # Set the working directory\nprefix_name=LiF_iter01  # Prefix for calculations\nmin_dist=1.4  # Minimum atom distance\nbox_limit=13  # Simulation box limit\nmax_fp_num=50  # Maximum number of single point calculations\nsample_method=pynep  # Sampling method (options: uniform, random, pynep)\npynep_sample_dist=0.01  # Sampling distance for pynep\n</code></pre> <p>You can customize:</p> <ul> <li><code>prefix_name</code> to reflect the name of your current work.</li> <li><code>min_dist</code>, <code>box_limit</code>, and <code>max_fp_num</code> based on your own system.</li> <li><code>sample_method</code> (choose between <code>uniform</code>, <code>random</code>, or <code>pynep</code>).</li> <li><code>pynep_sample_dist</code> is the sampling distance for <code>pynep</code>.</li> </ul>"},{"location":"en/active_learning_workflow.html#4-check-required-files","title":"4. Check Required Files","text":"<pre><code>if [ -f nep.txt ] &amp;&amp; [ -f nep.in ] &amp;&amp; [ -f train.xyz ] &amp;&amp; [ \"$(find . -maxdepth 1 -name 'run_*.in' | wc -l)\" -ge 1 ] &amp;&amp; [ -f INCAR ] &amp;&amp; [ -f POTCAR ] ; then\n    # Check for the required files before proceeding.\nelse\n    echo \"Please put nep.in nep.txt train.xyz run_*.in (eg. run_1.in, run_2.in, ...) INCAR POTCAR [KPOINTS] and the sample_struct.xyz in the current directory.\"\n    exit 1\nfi\n</code></pre> <p>Make sure the necessary files (<code>nep.txt</code>, <code>nep.in</code>, <code>train.xyz</code>, <code>run_*.in</code> (e.g., <code>run_1.in</code>, <code>run_2.in</code>, ...), <code>INCAR</code>, <code>POTCAR</code>, <code>KPOINTS</code>) are available in the working directory. If any of these are missing, the script will terminate. <code>train.xyz</code> and <code>nep.txt</code> are always required as prerequisites for NEP model operation, and <code>run_*.in</code> files define the simulation parameters of MD in the current iteration.</p>"},{"location":"en/active_learning_workflow.html#5-file-organization","title":"5. File Organization","text":"<pre><code>mkdir 00.md common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run_*.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.md\n</code></pre> <p>The script organizes the working files into two folders:</p> <ul> <li><code>00.md</code>: For molecular dynamics simulation.</li> <li><code>common</code>: For shared resources such as <code>nep.txt</code>, <code>run_*.in</code> files, and the structure files, etc.</li> </ul>"},{"location":"en/active_learning_workflow.html#6-molecular-dynamics-simulation-submission","title":"6. Molecular Dynamics Simulation Submission","text":"<pre><code>submit_gpumd_array md ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>After preparing the input files, the script submits an array of molecular dynamics (MD) tasks using <code>submit_gpumd_array</code>.</p>"},{"location":"en/active_learning_workflow.html#7-monitoring-task-completion","title":"7. Monitoring Task Completion","text":"<pre><code>while true; do\n    logs=$(find \"${work_dir}/00.md/\" -type f -name log -path \"*/sample_*/log\")\n    finished_tasks_md=$(grep \"Finished running GPUMD.\" $logs | wc -l)\n    error_tasks_md=$(grep \"Error\" $logs | wc -l)\n\n    if [ \"$error_tasks_md\" -ne 0 ]; then\n        echo \"Error: MD simulation encountered an error.\"\n        exit 1\n    fi\n    if [ $finished_tasks_md -eq $sample_struct_num ]; then\n        break\n    fi\n    sleep 30\ndone\n</code></pre> <p>The script continuously checks whether all MD tasks have finished by searching for a <code>Finished running GPUMD.</code> message in the logs. If an error is encountered, the script terminates.</p>"},{"location":"en/active_learning_workflow.html#8-analysis-and-filtering","title":"8. Analysis and Filtering","text":"<pre><code>mkdir ${work_dir}/01.select\n...\n</code></pre> <p>In the <code>01.select</code> folder, all structures in the trajectory file <code>dump.xyz</code> during the MD process will be analyzed and filtered to avoid the generation of non-physical structures as much as possible. Specifically, the <code>get_min_dist.py</code>, <code>filter_structures_by_distance.py</code> and <code>filter_exyz_by_box.py</code> scripts will be employed to check whether there are situations where the distance between atoms is too close or the simulated box exceeds the limit value, and such structures will be filtered out.</p>"},{"location":"en/active_learning_workflow.html#9-sampling-methods","title":"9. Sampling Methods","text":"<pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <p>The script supports three sampling methods: <code>uniform</code>, <code>random</code>, and <code>pynep</code>. It selects structures according to the chosen method and checks if the number exceeds <code>max_fp_num</code>, ensuring the final structure count is within limits.</p>"},{"location":"en/active_learning_workflow.html#10-scf-calculations","title":"10. SCF Calculations","text":"<pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>After sampling, SCF calculations are submitted using <code>submit_vasp_array</code>. The process is similar to the MD submission, but for SCF calculations.</p>"},{"location":"en/active_learning_workflow.html#11-prediction-step","title":"11. Prediction Step","text":"<pre><code>submit_nep_prediction\n</code></pre> <p>The final step involves submitting the NEP prediction task to check the accuracy of the NEP model. </p> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/analyzer_scripts.html","title":"Analyzer Scripts","text":"\ud83d\udd0d Analyzer Scripts <p>Analyzer scripts provide structure statistics, distance checks, filters, composition analysis, outlier detection, and time estimation for extxyz datasets.</p>"},{"location":"en/analyzer_scripts.html#what-it-does","title":"What it does","text":"<p>This module helps you inspect, filter, and validate structure datasets. You can check composition, analyze property ranges, detect short contacts, filter structures by various criteria, find outliers in NEP training data, and estimate remaining simulation time.</p>"},{"location":"en/analyzer_scripts.html#before-you-start","title":"Before you start","text":"<p>Script location: <code>Scripts/analyzer/</code></p> <p>Make sure GPUMDkit is installed. See Quick Start for installation instructions.</p>"},{"location":"en/analyzer_scripts.html#overview","title":"Overview","text":"Task Command Purpose Composition <code>gpumdkit.sh -analyze_comp train.xyz</code> Group structures by chemical composition Chemical species <code>gpumdkit.sh -chem_species train.xyz</code> List species in a file Property range <code>gpumdkit.sh -range train.xyz force</code> Inspect energy/force/virial range Minimum distance <code>gpumdkit.sh -min_dist dump.xyz</code> Fast distance check without PBC Minimum distance with PBC <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> Accurate distance check with PBC Charge balance <code>gpumdkit.sh -cbc train.xyz</code> Oxidation-state balance check Distance filter <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> Remove structures with short contacts Box filter <code>gpumdkit.sh -filter_box dump.xyz 13</code> Remove structures with too-large box edges Property filter <code>gpumdkit.sh -filter_value train.xyz force 20</code> Filter by energy/force/virial threshold Pair-distance range <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> Extract structures by pair distance Outlier detection Menu 502 Find high-RMSE structures in training set Probability density <code>gpumdkit.sh -pda &lt;ref&gt; &lt;traj&gt; &lt;element&gt; &lt;interval&gt;</code> 3D probability density for diffusion channels GPUMD time <code>gpumdkit.sh -time gpumd</code> Estimate remaining GPUMD run time NEP time <code>gpumdkit.sh -time nep</code> Estimate remaining NEP training time"},{"location":"en/analyzer_scripts.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit and choose <code>5) Analyzer</code>:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>The analyzer menu is:</p> <pre><code>+------------------------------------------------------+\n|                    ANALYZER TOOLS                    |\n+------------------------------------------------------+\n| 501) Analyze composition of extxyz                   |\n| 502) Find outliers of extxyz                         |\n| 503) Analyze chemical species of extxyz              |\n| 504) Check charge balance of extxyz                  |\n| 505) Analyze energy/force/virial range               |\n| 506) Filter structures by minimum distance           |\n| 507) Get minimum interatomic distance                |\n| 508) Probability density analysis                    |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Most analyzer functions also have direct CLI shortcuts, which are listed in the overview table and in the sections below.</p>"},{"location":"en/analyzer_scripts.html#composition-analysis","title":"Composition Analysis","text":"<p><code>analyze_composition.py</code> analyzes the composition of your extxyz file and lets you export subsets.</p> <p>What it does: Groups structures by chemical composition and shows how many structures belong to each composition. You can export subsets by composition.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>Interactive mode: Choose <code>501</code> from the analyzer menu.</p> <p>Output example:</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>This is useful when <code>train.xyz</code> contains structures from different systems or different cell sizes. You can export a subset by composition from the interactive prompt.</p>"},{"location":"en/analyzer_scripts.html#chemical-species","title":"Chemical Species","text":"<p><code>analyze_chem_species.py</code> lists all unique chemical species in an extxyz file.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -chem_species train.xyz\n</code></pre>"},{"location":"en/analyzer_scripts.html#property-range-analysis","title":"Property Range Analysis","text":"<p><code>energy_force_virial_analyzer.py</code> calculates and visualizes the range of properties from an extxyz file.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <p>Supported properties: <code>energy</code>, <code>force</code>, <code>virial</code></p> <pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist    # Show histogram\n</code></pre> <p>Output example:</p> <pre><code>Force range: 0.03210566767721861 to 9.230115912468435\n</code></pre> <p>With <code>hist</code> option:</p>"},{"location":"en/analyzer_scripts.html#minimum-distance-checks","title":"Minimum Distance Checks","text":""},{"location":"en/analyzer_scripts.html#without-pbc-fast","title":"Without PBC (Fast)","text":"<p><code>get_min_dist.py</code> calculates minimum interatomic distances without considering periodic boundary conditions. Fast but may be inaccurate for periodic systems.</p> <p>What it does: Reports the minimum distance between each pair of elements in every frame, ignoring periodic boundary conditions.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>Interactive mode: Choose <code>507</code> from the analyzer menu.</p> <p>Output example:</p> <pre><code>+---------------------------+\n|   PBC ignored for speed   |\n| use -min_dist_pbc for PBC |\n+---------------------------+\nMinimum interatomic distances:\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.480     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre> <p>Notes: Use this for a quick check. For periodic systems, prefer <code>-min_dist_pbc</code> for accurate results.</p>"},{"location":"en/analyzer_scripts.html#with-pbc-accurate","title":"With PBC (Accurate)","text":"<p><code>get_min_dist_pbc.py</code> calculates minimum interatomic distances considering periodic boundary conditions.</p> <p>What it does: Reports the minimum distance between each pair of elements, accounting for periodic boundary conditions.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>Interactive mode: Choose <code>507</code> from the analyzer menu and answer <code>y</code> when asked whether to consider PBC.</p> <p>Output example:</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre>"},{"location":"en/analyzer_scripts.html#filtering-structures","title":"Filtering Structures","text":""},{"location":"en/analyzer_scripts.html#filter-by-minimum-distance","title":"Filter by Minimum Distance","text":"<p><code>filter_structures_by_distance_pbc.py</code> removes structures with any interatomic distance below a threshold.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>This removes structures with any interatomic distance below <code>1.0 \u00c5</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-box-size","title":"Filter by Box Size","text":"<p><code>filter_exyz_by_box.py</code> filters structures by box-edge length.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>This keeps structures where all box edges are below <code>13 \u00c5</code>.</p>"},{"location":"en/analyzer_scripts.html#filter-by-property-value","title":"Filter by Property Value","text":"<p><code>filter_exyz_by_value.py</code> filters structures by energy, force, or virial threshold.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <p>Supported properties: <code>energy</code>, <code>force</code>, <code>virial</code></p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre> <p>This filters out structures with force components exceeding <code>20 eV/\u00c5</code> (or energy exceeding <code>5 eV/atom</code>).</p>"},{"location":"en/analyzer_scripts.html#filter-by-pair-distance-range","title":"Filter by Pair-Distance Range","text":"<p><code>filter_dist_range.py</code> extracts structures where a specific element-pair distance falls within a given range.</p> <p>Input file: <code>dump.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>This extracts structures where the Li-Li minimum distance is between <code>1.8 \u00c5</code> and <code>2.0 \u00c5</code>. Output: <code>filtered_Li_Li_1.8_2.0.xyz</code>.</p>"},{"location":"en/analyzer_scripts.html#charge-balance-check","title":"Charge Balance Check","text":"<p><code>charge_balance_check.py</code> checks the oxidation-state balance of structures.</p> <p>Input file: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>Output files:</p> <ul> <li><code>balanced.xyz</code> \u2014 structures with balanced charges</li> <li><code>unbalanced.xyz</code> \u2014 structures with unbalanced charges</li> <li><code>indices.txt</code> \u2014 indices of balanced structures</li> </ul> <p>This is intended for systems where common oxidation states are meaningful.</p>"},{"location":"en/analyzer_scripts.html#outlier-detection","title":"Outlier Detection","text":"<p><code>find_outliers.py</code> finds outlier structures in NEP training data based on RMSE thresholds for energy, force, and stress.</p> <p>Input files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>stress_train.out</code>, <code>train.xyz</code></p> <p>These files are generated during NEP training. The script compares DFT vs NEP predictions and identifies structures with large errors.</p> <pre><code># Interactive mode\ngpumdkit.sh    # Select: 5) Analyzer \u2192 502) Find outliers of extxyz\n</code></pre> <p>Interactive prompts:</p> <pre><code>Enter energy RMSE threshold (meV/atom): 1\nEnter force RMSE threshold (meV/\u00c5): 60\nEnter stress RMSE threshold (GPa): 0.03\n</code></pre> <p>Output files:</p> <ul> <li><code>selected.xyz</code> \u2014 structures exceeding the RMSE thresholds (outliers)</li> <li><code>remained.xyz</code> \u2014 structures within the thresholds</li> <li><code>selected_remained.png</code> \u2014 comparison plot</li> </ul> <p>Use case: After NEP training, use this to identify problematic structures that contribute most to the error. Remove or improve these structures to enhance the training set.</p>"},{"location":"en/analyzer_scripts.html#time-estimation","title":"Time Estimation","text":""},{"location":"en/analyzer_scripts.html#gpumd-remaining-time","title":"GPUMD Remaining Time","text":"<p><code>time_consuming_gpumd.sh</code> estimates the remaining time for a GPUMD simulation.</p> <p>Input files: <code>run.in</code>, <code>thermo.out</code> (in the current GPUMD working directory)</p> <pre><code>gpumdkit.sh -time gpumd\n</code></pre> <p>Output example:</p> <pre><code>----------------- System Information ----------------\ntotal frames: 1050000\n-----------------------------------------------------\nCurrent Frame  Speed (steps/s)   Total Time       Time Left       Estimated End\n-------------   -------------   -------------   -------------   -----------------\n    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04\n    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56\n</code></pre>"},{"location":"en/analyzer_scripts.html#nep-remaining-time","title":"NEP Remaining Time","text":"<p><code>time_consuming_nep.sh</code> estimates the remaining time for NEP training.</p> <p>Input files: <code>loss.out</code> (in the current NEP working directory)</p> <pre><code>gpumdkit.sh -time nep\n</code></pre> <p>Output example:</p> <pre><code>+-----------------+-----------+-----------------+---------------------+\n|       Step      | Time Diff |    Time Left    |    Finish Time      |\n+-----------------+-----------+-----------------+---------------------+\n| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |\n| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |\n| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |\n+-----------------+-----------+-----------------+---------------------+\n</code></pre>"},{"location":"en/analyzer_scripts.html#probability-density-analysis","title":"Probability Density Analysis","text":"<p><code>probability_density_analysis.py</code> calculates 3D probability density of mobile ions for diffusion channel analysis.</p> <p>Input files: Reference structure (POSCAR), trajectory file (extxyz)</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n</code></pre> <p>Arguments:</p> Argument Meaning <code>LLZO.vasp</code> Reference structure (POSCAR format) <code>dump.xyz</code> Trajectory file (extxyz format) <code>Li</code> Target mobile species <code>0.25</code> Grid interval for the probability density (\u00c5) <p>Output: <code>probability_density_0.25.vasp</code> \u2014 probability density grid in VASP format for visualization with VESTA or similar tools.</p> <p>Visualization suggestions:</p> <ol> <li>Open <code>probability_density_0.25.vasp</code> in VESTA</li> <li>Use \"Edit \u2192 Data \u2192 Volumetric Data\" to adjust isosurface levels</li> <li>Color the probability density by value to highlight preferred diffusion pathways</li> <li>Overlay with the crystal structure for context</li> </ol>"},{"location":"en/analyzer_scripts.html#example-workflows","title":"Example Workflows","text":""},{"location":"en/analyzer_scripts.html#structure-quality-check","title":"Structure Quality Check","text":"<pre><code># 1. Check composition\ngpumdkit.sh -analyze_comp train.xyz\n\n# 2. Check energy/force range\ngpumdkit.sh -range train.xyz force hist\n\n# 3. Check minimum distances\ngpumdkit.sh -min_dist_pbc train.xyz\n\n# 4. Find outliers (after NEP training)\n# Interactive: 5) Analyzer \u2192 502\n</code></pre>"},{"location":"en/analyzer_scripts.html#structure-filtering-pipeline","title":"Structure Filtering Pipeline","text":"<pre><code># 1. Filter by minimum distance\ngpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n\n# 2. Filter by box size\ngpumdkit.sh -filter_box filtered_dist_pbc.xyz 13\n\n# 3. Filter by force threshold\ngpumdkit.sh -filter_value filtered_box.xyz force 20\n</code></pre>"},{"location":"en/analyzer_scripts.html#diffusion-channel-analysis","title":"Diffusion Channel Analysis","text":"<pre><code># 1. Calculate probability density\ngpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n\n# 2. Visualize with VESTA\n# Open probability_density_0.25.vasp\n</code></pre>"},{"location":"en/calculator_scripts.html","title":"Calculator Scripts","text":"\ud83e\uddee Calculator Scripts <p>The calculator module contains scripts for computing properties from MD trajectories, NEP models, and structure files.</p> <p>Script Location: <code>Scripts/calculators/</code></p>"},{"location":"en/calculator_scripts.html#overview","title":"Overview","text":"<p>The calculator module can be read as three groups:</p> <ul> <li>Trajectory properties: compute time-dependent quantities such as MSD and ionic conductivity from GPUMD or extxyz trajectories;</li> <li>NEP-assisted calculations: use a NEP model to predict energies/forces/stresses, extract descriptors, calculate DOAS, run NEB, or minimize structures;</li> <li>Polar-material analysis: build neighbor lists and calculate local displacement, averaged structures, octahedral tilt, and local polarization for perovskite or polar systems.</li> </ul> <p>If you are not sure about the required arguments, start from the interactive menu to see the prompt. If the arguments are already clear, use <code>gpumdkit.sh -calc ...</code> directly.</p> Task Command Main Input Ionic conductivity <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>, <code>thermo.out</code>, <code>model.xyz</code> MSD from trajectory <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz trajectory NEP prediction <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP model NEP descriptors <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP model DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP model NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> initial/final structures Minimization <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> structure + NEP model Neighbor list <code>gpumdkit.sh -calc nlist ...</code> see Polar Material Analysis Displacement <code>gpumdkit.sh -calc disp ...</code> see Polar Material Analysis Average structure <code>gpumdkit.sh -calc avg-struct ...</code> see Polar Material Analysis Octahedral tilt <code>gpumdkit.sh -calc oct-tilt ...</code> see Polar Material Analysis ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 ...</code> see Polar Material Analysis <p>For a full command list:</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>The command-line help table looks like:</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>In interactive mode, choose <code>4) Calculators</code>. The menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"en/calculator_scripts.html#ionic-conductivity","title":"Ionic Conductivity","text":"<p><code>calc_ion_conductivity.py</code> calculates ionic diffusivity and conductivity from <code>msd.out</code>.</p>"},{"location":"en/calculator_scripts.html#required-and-optional-files","title":"Required and Optional Files","text":"File Role <code>msd.out</code> Required MSD data <code>thermo.out</code> Optional, used for automatic temperature detection <code>model.xyz</code> Optional, used for volume and ion-count detection <code>run.in</code> Optional, used to detect replication"},{"location":"en/calculator_scripts.html#usage","title":"Usage","text":"<pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>From interactive mode, choose <code>401</code>. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>If automatic files are missing, the script will ask for temperature, volume, and ion count interactively.</p> <p>Interactive prompts in manual mode look like:</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre>"},{"location":"en/calculator_scripts.html#example-output","title":"Example Output","text":"<pre><code>Diffusivity (D):\n  D_x: 4.153e-07 cm^2/s\n  D_y: 4.174e-07 cm^2/s\n  D_z: 2.610e-07 cm^2/s\n  D_total: 3.646e-07 cm^2/s\n------------------------------\nIonic Conductivity:\n  Sigma_x: 2.576e-02 mS/cm\n  Sigma_y: 2.589e-02 mS/cm\n  Sigma_z: 1.619e-02 mS/cm\n  Sigma_total: 2.261e-02 mS/cm\n</code></pre>"},{"location":"en/calculator_scripts.html#mean-square-displacement","title":"Mean Square Displacement","text":"<p><code>calc_msd.py</code> computes MSD directly from an extxyz trajectory.</p> <pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>From interactive mode, choose <code>412</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>Li</code> target mobile species <code>10</code> time interval between frames, in fs <code>5000</code> optional maximum correlation steps <p>Output:</p> <ul> <li><code>msd.out</code></li> </ul> <p>The beginning of <code>msd.out</code> is a text table with time and MSD columns. After generating it, use the plot commands below.</p> <p>You can then plot:</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-property-prediction","title":"NEP Property Prediction","text":"<p><code>calc_properties_with_nep.py</code> calculates energy, force, and stress for structures using a NEP model.</p> <p>Dependency: <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>Use this function to run predictions with a trained NEP model. For best results, validate model quality on your target structures before relying on the output.</p> <p>Tip: Before prediction, you may want to clean the extxyz metadata:</p> <pre><code>gpumdkit.sh -clean_xyz train.xyz clean_train.xyz\n</code></pre>"},{"location":"en/calculator_scripts.html#nep-descriptors","title":"NEP Descriptors","text":"<p><code>calc_descriptors.py</code> extracts NEP descriptors for a selected element.</p> <pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>Use cases:</p> <ul> <li>visualize chemical environments with PCA/UMAP;</li> <li>compare training and candidate structures;</li> <li>inspect whether new data expands descriptor space.</li> </ul> <p>Plot descriptors with:</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/calculator_scripts.html#density-of-atomistic-states","title":"Density of Atomistic States","text":"<p><code>calc_doas.py</code> calculates density of atomistic states (DOAS), following the idea proposed by Wang et al..</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>The script:</p> <ol> <li>reads all structures;</li> <li>relaxes each structure with a NEP calculator;</li> <li>extracts per-atom energies;</li> <li>groups atomic energies by element;</li> <li>writes the grouped values to the output file.</li> </ol> <p>For very large systems, running minimization and atomistic-energy extraction directly in GPUMD can be more efficient.</p>"},{"location":"en/calculator_scripts.html#neb-with-a-nep-model","title":"NEB with a NEP Model","text":"<pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>This runs a NEB calculation with <code>9</code> intermediate images. During execution, the script asks how atoms should be fixed:</p> <ul> <li><code>none</code>: no atoms fixed;</li> <li><code>index</code>: fix atoms by index;</li> <li><code>element</code>: fix all atoms of one element;</li> <li><code>position</code>: fix atoms inside a coordinate range.</li> </ul>"},{"location":"en/calculator_scripts.html#structure-minimization","title":"Structure Minimization","text":"<p><code>calc_minimize.py</code> minimizes a structure using a NEP model through <code>calorine</code>.</p> <p>Dependency: <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input structure, POSCAR/CONTCAR or extxyz <code>nep.txt</code> NEP model <code>0.01</code> optional force convergence threshold in eV/Ang <code>1000</code> optional maximum optimization steps <p>Output:</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"en/calculator_scripts.html#rdf-calculation-with-ovito","title":"RDF Calculation with OVITO","text":"<p><code>rdf_calculator_ovito.py</code> calculates radial distribution function using OVITO's analysis tools.</p> <p>Dependency: OVITO</p> <pre><code>pip install ovito\n</code></pre> <p>Input file: Structure file (single frame or trajectory)</p> <pre><code>python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400\n</code></pre> <p>Parameters:</p> Argument Meaning <code>trajectory.xyz</code> Input structure file <code>6.0</code> Maximum distance for RDF calculation (\u00c5) <code>400</code> Number of histogram bins <p>Visualization:</p> <pre><code>gpumdkit.sh -plt rdf\n</code></pre> <p>Note: It is recommended to use the <code>compute_rdf</code> command directly in GPUMD when possible.</p>"},{"location":"en/calculator_scripts.html#ferroelectric-and-polar-material-tools","title":"Ferroelectric and Polar Material Tools","text":"<p>Options <code>406\u2013410</code> are for perovskite and polar-material analysis. They are commonly used to extract local structural information from MD trajectories before analyzing phase transitions, domain patterns, or polarization textures.</p> <p>This page only gives a quick index for these scripts because they are usually used together. For full workflows and argument details, see Polar Material Analysis.</p> Menu CLI subcommand Purpose Details <code>406</code> <code>gpumdkit.sh -calc nlist ...</code> Build neighbor lists between selected center and neighbor atoms Polar Material Analysis <code>407</code> <code>gpumdkit.sh -calc disp ...</code> Calculate local displacement from a trajectory and neighbor list Polar Material Analysis <code>408</code> <code>gpumdkit.sh -calc avg-struct ...</code> Calculate an averaged structure from a trajectory Polar Material Analysis <code>409</code> <code>gpumdkit.sh -calc oct-tilt ...</code> Calculate octahedral tilt angles Polar Material Analysis <code>410</code> <code>gpumdkit.sh -calc pol-abo3 ...</code> Estimate local ABO3 polarization from Born effective charges Polar Material Analysis <p>Some scripts require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>A typical sequence is to build neighbor lists with <code>nlist</code>, then reuse those lists for displacement, tilt, or polarization calculations. For averaged structures, you can start directly from the trajectory and use the length tolerance to control which frames are included.</p>"},{"location":"en/command_reference.html","title":"Command Reference","text":"\ud83d\udccb Command Reference <p>This page lists the stable GPUMDkit command-line shortcuts. Interactive mode is available for workflows with many choices.</p> <p>The source table is maintained in <code>docs/command_reference.tsv</code>.</p>"},{"location":"en/command_reference.html#gpumdkitsh-h-output","title":"<code>gpumdkit.sh -h</code> Output","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |\n| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/command_reference.html#main","title":"Main","text":"Command Syntax Description <code>-h</code> <code>gpumdkit.sh -h</code> Show general help <code>-update</code> <code>gpumdkit.sh -update</code> Update GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> Clean extra files in the current directory"},{"location":"en/command_reference.html#format-conversion","title":"Format Conversion","text":"Command Syntax Description <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR to extxyz, shell version <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR to extxyz, Python version <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K output to xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR to extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF to POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF to extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR to extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz frames to POSCAR files <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR to LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump to extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory to extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> Replicate by cell factors <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> Replicate toward a target atom count <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> Add GPUMD group labels <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> Add structure weights <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> Extract one frame <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> Remove extra extxyz properties <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> Extract frames by fractional range"},{"location":"en/command_reference.html#calculators","title":"Calculators","text":"Command Syntax Description <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> Ionic conductivity <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP property prediction <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP descriptors <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> Density of atomistic states <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> NEB with a NEP model <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> Structure minimization <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> MSD from trajectory <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> Neighbor lists <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> Displacements <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> Averaged structure <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> Octahedral tilt <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 local polarization"},{"location":"en/command_reference.html#analyzers","title":"Analyzers","text":"Command Syntax Description <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> Property range analysis <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> Composition analysis <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> Chemical species list <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> Charge-balance check <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> Minimum distance without PBC <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> Minimum distance with PBC <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> Distance filtering <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> PBC-aware distance filtering <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> Box-edge filtering <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> Property threshold filtering <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> Element-pair distance range filtering <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> Probability density analysis"},{"location":"en/command_reference.html#visualization","title":"Visualization","text":"<p>Use:</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>Common types include <code>train</code>, <code>prediction</code> (alias: <code>test</code>), <code>thermo</code>, <code>msd</code>, <code>sdc</code>, <code>rdf</code>, <code>emd</code>, <code>nemd</code>, <code>hnemd</code>, <code>pdos</code>, and <code>plane-grid</code>.</p>"},{"location":"en/command_reference.html#utilities","title":"Utilities","text":"Command Syntax Description <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> Monitor GPUMD or NEP progress <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> Modify NEP models interactively <code>-pynep</code> <code>gpumdkit.sh -pynep</code> Deprecated PyNEP FPS sampling"},{"location":"en/contributing_to_gpumdkit.html","title":"Contributing to GPUMDkit","text":"\ud83e\udd1d Contributing to GPUMDkit <p>Thank you for your interest in contributing to GPUMDkit! We appreciate your time and effort in helping improve this toolkit.</p> <p> English   \u00a0\u00b7\u00a0   \u7b80\u4f53\u4e2d\u6587 </p> <p><code>GPUMDkit</code> is an open-source package, and we welcome contributions from the community, whether you're fixing bugs, adding new features, improving documentation, or suggesting enhancements.</p> <p>Note: The authoritative version of this document is <code>CONTRIBUTING.md</code> in the repository root. This tutorial page mirrors its content.</p>"},{"location":"en/contributing_to_gpumdkit.html#table-of-contents","title":"Table of Contents","text":"<ul> <li>Development Restrictions and Guidelines</li> <li>Reporting Bugs</li> <li>Suggesting Features</li> <li>Contributing Code</li> <li>Fork and Clone the Repository</li> <li>Create a Feature Branch</li> <li>Making Changes<ul> <li>Interactive Mode Contributions</li> <li>Command-Line Mode Contributions</li> <li>Updating Tab Completion</li> </ul> </li> <li>Code Style and Best Practices</li> <li>Testing Your Changes</li> <li>Commit Messages</li> <li>Push and Open a Pull Request</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#development-restrictions-and-guidelines","title":"Development Restrictions and Guidelines","text":"<p>To maintain code quality and consistency across the project, please adhere to these guidelines:</p>"},{"location":"en/contributing_to_gpumdkit.html#language-requirements","title":"Language Requirements","text":"<ul> <li>All code should be written in English: This includes variable names, function names, comments, docstrings, commit messages, and documentation.</li> <li>While we understand that contributors come from diverse backgrounds, using English ensures that the codebase is accessible to the widest possible audience.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#modularity-and-reusability","title":"Modularity and Reusability","text":"<ul> <li>Write modular and reusable code: Functions and scripts should be designed with flexibility in mind.</li> <li>Prefer passing parameters over hardcoding values: Use function arguments, command-line parameters, or configuration files instead of hardcoded values. However, some filenames are required to be fixed by GPUMD and NEP programs (e.g., <code>train.xyz</code>, <code>thermo.out</code>), and these can be hardcoded as needed.</li> <li>Example:    <pre><code># Good: accepts parameters\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # processing logic\n}\n\n# Avoid: hardcoded values (unless required by GPUMD/NEP)\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # processing logic\n}\n</code></pre></li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#code-style","title":"Code Style","text":"<ul> <li>Write code that is clear and easy for others to maintain and modify.</li> <li>Use meaningful variable and function names.</li> <li>Add comments where necessary to explain complex logic.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#documentation","title":"Documentation","text":"<ul> <li>Ensure that help messages (e.g., <code>-h</code> flags) are clear and accurate.</li> <li>Tutorial documentation lives in <code>docs/tutorials/en/</code> (English) and <code>docs/tutorials/zh/</code> (Chinese).   If you add a new feature, consider updating the relevant tutorial page.</li> <li>After editing tutorial markdown files, rebuild the HTML with <code>mkdocs build -f docs/mkdocs.yml</code>.</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#reporting-bugs","title":"Reporting Bugs","text":"<p>If you encounter a bug, please help us fix it by reporting it through GitHub Issues:</p> <ol> <li>Search existing issues to see if the bug has already been reported.</li> <li>Open a new issue if it hasn't been reported yet: Create an Issue</li> <li>Describe the problem in detail and provide test files if possible.</li> </ol> <p>You can also reach out to us through: - QQ Group: 825696376 - Email: yanzihan@westlake.edu.cn - Script Developer: Contact the developer listed in the script header</p>"},{"location":"en/contributing_to_gpumdkit.html#suggesting-features","title":"Suggesting Features","text":"<p>We welcome feature suggestions! To propose a new feature:</p> <ol> <li>Search existing issues to see if someone has already suggested it.</li> <li>Open a new feature request: Create a Feature Request and mention @zhyan0603</li> <li>Describe what you need clearly and explain how it would be useful.</li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#contributing-code","title":"Contributing Code","text":""},{"location":"en/contributing_to_gpumdkit.html#fork-and-clone-the-repository","title":"Fork and Clone the Repository","text":"<ol> <li> <p>Fork the repository on GitHub by clicking the \"Fork\" button at the top right of the repository page.</p> </li> <li> <p>Clone your fork to your local machine:</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>Set up the upstream remote to keep your fork in sync:    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#create-a-feature-branch","title":"Create a Feature Branch","text":"<p>Create a new branch for your changes:</p> <pre><code># Create and checkout a new branch from main\ngit checkout -b your-branch-name\n</code></pre> <p>Name your branch as you prefer.</p>"},{"location":"en/contributing_to_gpumdkit.html#making-changes","title":"Making Changes","text":"<p>The structure of <code>GPUMDkit</code> consists of: - <code>gpumdkit.sh</code>: Main entry point (Bash script) handling both interactive menu mode and command-line mode - <code>install.sh</code>: Installation script that sets up environment variables and shell configuration - <code>Scripts/</code>: Python and Bash implementation scripts organized by functionality   - <code>plt_scripts/</code>: Plotting scripts   - <code>calculators/</code>: Calculation utilities   - <code>format_conversion/</code>: Format conversion tools   - <code>workflow/</code>: Workflow automation   - <code>sample_structures/</code>: Structure sampling utilities   - <code>analyzer/</code>: Analysis tools   - <code>utils/</code>: Utility functions (including <code>completion.sh</code> for tab completion) - <code>src/</code>: Shell scripts containing menu functions for interactive mode   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>skills/</code>: AI agent skill definitions (SKILL.md files for opencode/Claude Code integration) - <code>docs/</code>: Documentation files   - <code>tutorials/en/</code> and <code>tutorials/zh/</code>: Bilingual tutorial pages   - <code>mkdocs.yml</code>: MkDocs configuration for building tutorial HTML   - <code>command_reference.tsv</code>: Machine-readable command reference   - <code>htmls/</code>: Generated HTML output from MkDocs</p>"},{"location":"en/contributing_to_gpumdkit.html#interactive-mode-contributions","title":"Interactive Mode Contributions","text":"<p>To add a new feature accessible through the interactive menu:</p> <ol> <li>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:</li> </ol> <pre><code># Example: Add a new format conversion script\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>Implement your functionality following the modularity guidelines (accept parameters, avoid hardcoding).</p> </li> <li> <p>Add a wrapper function in the corresponding <code>src/</code> file:    <pre><code># Example: Edit src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>Add a new function:    <pre><code>function f111_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input &lt;required_param1&gt; &lt;required_param2&gt;\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -r -a converter_args\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py \"${converter_args[@]}\"\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>Update the menu display in <code>gpumdkit.sh</code>:    <pre><code># Find the menu() function and update it if needed\n# Find the array_choice array and add your new choice number\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\" \"107\" \"108\" \"109\" \"110\" \"111\"  # Added \"111\"\n    # ... rest of choices\n)\n</code></pre></p> </li> <li> <p>Add the case statement in <code>gpumdkit.sh</code>:    <pre><code># In the main() function, find the appropriate case statement\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n             \"101\") f101_out2xyz ;;\n             # ... existing cases ...\n             \"111\") f111_new_converter ;;  # Add your case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#command-line-mode-contributions","title":"Command-Line Mode Contributions","text":"<p>To add a new command-line flag or subcommand:</p> <ol> <li> <p>Create your implementation script in the appropriate <code>Scripts/</code> subdirectory:    <pre><code># Example: Add a new analyzer script\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>Implement your functionality with clear parameter requirements:    <pre><code># Example: Scripts/analyzer/analyze_bonds.py\nimport sys\n\nif len(sys.argv) != 3:\n    print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n    print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n    sys.exit(1)\n\ninput_file = sys.argv[1]\ncutoff = float(sys.argv[2])\n\n# Your implementation here\n</code></pre></p> </li> </ol> <p>Note: GPUMDkit Python scripts are designed to run directly (not imported as modules). You may use a <code>main()</code> function with <code>if __name__ == \"__main__\":</code> guard if you prefer, but it is not required. Most existing scripts execute at module level.</p> <ol> <li> <p>Add the command-line flag handler in <code>gpumdkit.sh</code>:    <pre><code># Find the command-line parsing section (the large \"case $1 in\" block)\n# Add your new flag in the appropriate location\n\ncase $1 in\n    # ... existing cases ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ \"$2\" != \"-h\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py $2 $3\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n        fi ;;\n    # ... rest of cases ...\nesac\n</code></pre></p> </li> <li> <p>Update the help information in <code>gpumdkit.sh</code>:    <pre><code># Find the help_info_table() function and add your command\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... rest of help table ...\n}\n</code></pre></p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#updating-tab-completion","title":"Updating Tab Completion","text":"<p>When adding new command-line flags, update the tab completion script:</p> <pre><code># Edit Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>Add your new flag to the <code>opts</code> variable: <pre><code># Find the line with local opts=...\nlocal opts=\"-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...\"\n#                                                        Add your flag here\n</code></pre></p> <p>If your flag requires file arguments, add it to the existing file-completion case: <pre><code># Find the case for file-requiring flags and add yours with |\n-out2xyz|-out2exyz|-...|-your_new_flag)\n    COMPREPLY=($(compgen -f -- \"$cur\")) ;;\n</code></pre></p> <p>If your flag accepts secondary options (like <code>-plt</code> or <code>-calc</code>), add a new case: <pre><code>case \"$prev\" in\n    # ... existing cases ...\n    -your_new_flag)\n        COMPREPLY=($(compgen -W \"option1 option2 option3\" -- \"$cur\")) ;;\n    # ... rest of cases ...\nesac\n</code></pre></p>"},{"location":"en/contributing_to_gpumdkit.html#code-style-and-best-practices","title":"Code Style and Best Practices","text":"<ul> <li>Shell Scripts:</li> <li>Use <code>${variable}</code> for variable expansion</li> <li>Use <code>[ ! -z \"$var\" ]</code> for non-empty checks (project convention)</li> <li>Interactive functions should follow the banner format:     <pre><code>echo \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/&lt;category&gt;        |\"\necho \" | Script: &lt;script_name&gt;.py                        |\"\necho \" | Developer: &lt;Name&gt; (&lt;email&gt;)                     |\"\necho \" &gt;-------------------------------------------------&lt;\"\n</code></pre></li> <li>Use <code>read -r -a varname</code> for multi-word input, then pass with <code>\"${varname[@]}\"</code></li> <li> <p>Shell scripts in <code>src/</code> should start with a file header block:     <pre><code># ============================================================\n# GPUMDkit &lt;module name&gt; module\n# Repository: https://github.com/zhyan0603/GPUMDkit\n# Author: &lt;Name&gt; (&lt;email&gt;)\n# ============================================================\n</code></pre></p> </li> <li> <p>Python Scripts:</p> </li> <li>Write clear, maintainable code</li> <li>Use meaningful variable names</li> <li>Use <code>sys.argv</code> for argument parsing (consistent with most existing scripts)</li> <li>Provide clear usage messages with <code>print(\"Usage: ...\")</code> and <code>print(\"Example: ...\")</code></li> <li>If your script uses heavy/special packages (<code>NepTrain</code>, <code>calorine</code>, <code>dpdata</code>), add a     <code>print_dependency_notice()</code> function to inform users about citation recommendations</li> </ul>"},{"location":"en/contributing_to_gpumdkit.html#testing-your-changes","title":"Testing Your Changes","text":"<p>Before submitting your contribution, run the relevant validation commands:</p> <pre><code># Shell syntax checks (always run these)\nbash -n gpumdkit.sh\nfind src Scripts -name '*.sh' -exec bash -n {} +\n\n# Python syntax checks (for modified Python files)\npython3 -m py_compile path/to/modified_script.py\n\n# MkDocs build (if you modified documentation)\nmkdocs build -f docs/mkdocs.yml\n\n# Check for trailing whitespace issues\ngit diff --check\n</code></pre> <p>Then test functionality:</p> <ol> <li> <p>Test interactive mode (if applicable):    <pre><code>gpumdkit.sh\n# Navigate to your new feature and test it thoroughly\n</code></pre></p> </li> <li> <p>Test command-line mode (if applicable):    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # Test help message\n</code></pre></p> </li> <li> <p>Test tab completion (if you modified <code>completion.sh</code>):    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # Should show your new flag\n</code></pre></p> </li> <li> <p>Test with various inputs:</p> </li> <li>Test with typical inputs</li> <li>Test with edge cases (empty files, large files, etc.)</li> <li> <p>Test error handling (missing files, invalid parameters)</p> </li> <li> <p>Verify no regressions: Ensure existing functionality still works correctly.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#commit-messages","title":"Commit Messages","text":"<p>Write clear, descriptive commit messages that explain what you changed. There are no strict format requirements - just make sure your message is understandable.</p>"},{"location":"en/contributing_to_gpumdkit.html#push-and-open-a-pull-request","title":"Push and Open a Pull Request","text":"<ol> <li> <p>Commit your changes:    <pre><code>git add .\ngit commit -m \"your descriptive message\"\n</code></pre></p> </li> <li> <p>Keep your branch updated with the latest <code>dev</code> branch:    <pre><code>git fetch origin\ngit rebase origin/dev\n</code></pre></p> </li> <li> <p>Push your branch to your fork:    <pre><code>git push origin your-branch-name\n</code></pre></p> </li> <li> <p>Open a Pull Request:</p> </li> <li>Go to the GPUMDkit repository</li> <li>Click \"Pull Requests\" \u2192 \"New Pull Request\"</li> <li>Set the base branch to <code>dev</code> for code review</li> <li>Set the compare branch to your feature branch</li> <li> <p>Fill in the PR description with:</p> <ul> <li>Title: Brief description of changes</li> <li>Description: Detailed explanation of what changed and why</li> <li>Testing: Describe how you tested the changes</li> </ul> </li> <li> <p>Respond to review feedback:</p> </li> <li>Be open to suggestions and constructive criticism</li> <li>Make requested changes promptly</li> <li> <p>Push additional commits to your branch (they'll automatically appear in the PR)</p> </li> <li> <p>After approval: A maintainer will merge your PR.</p> </li> </ol>"},{"location":"en/contributing_to_gpumdkit.html#questions-or-need-help","title":"Questions or Need Help?","text":"<p>If you have questions about contributing or need help with your contribution:</p> <ul> <li>Open a discussion: Use GitHub Discussions for general questions</li> <li>Ask in an issue: Comment on related issues for specific questions</li> <li>Contact maintainers: Reach out to the core developers listed in the README</li> </ul> <p>Thank you again for contributing to <code>GPUMDkit</code>! Your efforts help make this toolkit better for the entire GPUMD and NEP community.</p>"},{"location":"en/custom_commands.html","title":"Custom Commands","text":"\ud83d\udd27 Custom Commands <p>GPUMDkit allows users to extend the command-line interface with custom commands. Define shortcuts for frequently used scripts in your ~/.gpumdkit.in file.</p>"},{"location":"en/custom_commands.html#setup","title":"Setup","text":"<p>Create or edit <code>~/.gpumdkit.in</code>: <pre><code>vi ~/.gpumdkit.in\n</code></pre></p> <p>Define custom functions with the <code>custom_</code> prefix.</p>"},{"location":"en/custom_commands.html#examples","title":"Examples","text":""},{"location":"en/custom_commands.html#simple-greeting","title":"Simple Greeting","text":"<p>Write the following code in your <code>~/.gpumdkit.in</code> </p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>and run <code>gpumdkit.sh -hello</code>, you will see:</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"en/custom_commands.html#command-with-required-arguments","title":"Command with Required Arguments","text":"<p>For the following function:</p> <pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>and you can add an argument, for example: <code>gpumdkit.sh -greet Zihan</code>, then you will see:</p> <pre><code>Hello, Zihan!\n</code></pre> <p>Passing arguments: Use <code>\"$@\"</code> to forward all arguments safely. Use <code>${@:1}</code> when you need to refer to arguments starting from the first one. </p>"},{"location":"en/custom_commands.html#calling-an-external-script","title":"Calling an External Script","text":"<p>If you want to call an external script like <code>gpumdkit.sh</code>.</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>and run <code>gpumdkit.sh -nepanalyse</code></p>"},{"location":"en/custom_commands.html#advanced-examples","title":"Advanced Examples","text":""},{"location":"en/custom_commands.html#batch-processing","title":"Batch Processing","text":"<p>Process multiple files: <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -batch_plot dir1 dir2 dir3</code></p>"},{"location":"en/custom_commands.html#analysis-pipeline","title":"Analysis Pipeline","text":"<p>Combine multiple operations: <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -analyze_training train.xyz</code></p>"},{"location":"en/custom_commands.html#custom-workflow","title":"Custom Workflow","text":"<p>Automate common workflow: <pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    # Convert VASP outputs\n    gpumdkit.sh -out2xyz ./\n\n    # Filter outliers\n    gpumdkit.sh -filter_value train.xyz force 30\n\n    # Check quality\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre></p> <p>Usage: <code>gpumdkit.sh -prep_training</code></p>"},{"location":"en/custom_commands.html#tips","title":"Tips","text":"<ul> <li>Use descriptive names: <code>custom_analyze_nep_training</code> is clearer than <code>custom_ant</code></li> <li>Add help messages: Echo usage info when no arguments provided</li> <li>Error handling: Check if required files exist before processing</li> <li>Forward arguments safely: Use <code>\"$@\"</code> to preserve spaces and special characters</li> </ul> <p>Thank you for using <code>GPUMDkit</code>! If you have any questions or need further assistance, feel free to open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).</p>"},{"location":"en/format_conversion.html","title":"Format Conversion","text":"\ud83d\udd04 Format Conversion <p>GPUMDkit contains utilities for converting common atomistic simulation formats, with extra handling for metadata such as group labels, weights, and frame extraction.</p>"},{"location":"en/format_conversion.html#what-it-does","title":"What it does","text":"<p>This module converts structure and trajectory files between common formats used in computational materials science. It supports VASP, LAMMPS, CP2K, ABACUS, CIF, ASE trajectories, and extxyz. It also provides tools for adding group labels, weights, extracting frames, and replicating structures.</p>"},{"location":"en/format_conversion.html#before-you-start","title":"Before you start","text":"<p>Script location: <code>Scripts/format_conversion/</code></p> <p>Make sure GPUMDkit is installed. See Quick Start for installation instructions.</p>"},{"location":"en/format_conversion.html#supported-formats","title":"Supported formats","text":"<p>The format conversion module covers:</p> <ul> <li>VASP: <code>POSCAR</code>, <code>CONTCAR</code>, <code>OUTCAR</code>, <code>XDATCAR</code></li> <li>LAMMPS: data files and dump trajectories</li> <li>CP2K: output logs, position, force, and cell files</li> <li>ABACUS: SCF/MD logs</li> <li>CIF: crystallographic structure files</li> <li>ASE trajectory: <code>.traj</code></li> <li>extxyz: a common structure format for GPUMD and NEP</li> </ul>"},{"location":"en/format_conversion.html#interactive-mode","title":"Interactive Mode","text":"<p>Open GPUMDkit:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>1) Format Conversion\n</code></pre> <p>The format conversion menu is:</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"en/format_conversion.html#what-each-entry-does","title":"What Each Entry Does","text":"Entry Called script Function When to Use <code>101</code> <code>out2xyz.sh</code> VASP OUTCAR to extxyz, shell version convert VASP calculation directories <code>102</code> <code>mtp2xyz.py</code> MTP cfg to extxyz convert MTP training data <code>103</code> <code>cp2k_log2xyz.py</code> / <code>cp2k2xyz.py</code> CP2K to extxyz choose CP2K log/inp route or pos/frc/cell route <code>104</code> <code>abacus2xyz_scf.sh</code> / <code>abacus2xyz_md.sh</code> ABACUS to extxyz convert ABACUS SCF or MD output <code>105</code> <code>exyz2pos.py</code> extxyz to POSCAR write each extxyz frame as a POSCAR-style file <code>106</code> <code>add_groups.py</code> add group labels add atom group labels for GPUMD-related workflows <code>107</code> <code>add_weight.py</code> add weights assign training weights in extxyz <code>108</code> <code>get_frame.py</code> extract frame export one frame from an extxyz trajectory <code>109</code> <code>clean_xyz.py</code> clean XYZ info remove extra extxyz properties <code>110</code> <code>replicate.py</code> replicate structure build supercells by factors or target atom count <code>out2exyz</code> <code>out2exyz.py</code> OUTCAR to extxyz, Python version alternative VASP OUTCAR converter <code>pos2exyz</code> <code>pos2exyz.py</code> POSCAR to extxyz convert a single structure <code>cif2pos</code> <code>cif2pos.py</code> CIF to POSCAR prepare VASP input from CIF <code>cif2exyz</code> <code>cif2exyz.py</code> CIF to extxyz prepare GPUMDkit input from CIF <code>xdat2exyz</code> <code>xdatcar2exyz.py</code> XDATCAR to extxyz convert VASP MD trajectory <code>pos2lmp</code> <code>pos2lmp.py</code> POSCAR to LAMMPS data prepare LAMMPS input <code>lmp2exyz</code> <code>lmp2exyz.py</code> LAMMPS dump to extxyz convert LAMMPS trajectory <code>traj2exyz</code> <code>traj2exyz.py</code> ASE traj to extxyz convert ASE trajectory"},{"location":"en/format_conversion.html#quick-command-reference","title":"Quick Command Reference","text":"Source Target Command OUTCAR directory extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR directory extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> extxyz POSCAR files <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"en/format_conversion.html#common-examples","title":"Common Examples","text":""},{"location":"en/format_conversion.html#convert-vasp-calculations-to-extxyz","title":"Convert VASP calculations to extxyz","text":"<p>What it does: Searches a directory for VASP OUTCAR files and converts them into a single extxyz file for NEP training or analysis.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>The shell version searches the target directory and converts VASP results into an extxyz file. If you prefer the Python implementation:</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>Interactive mode: Choose <code>101</code> from the format conversion menu. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre> <p>Output: An extxyz file containing the converted structures, suitable for NEP training or further analysis.</p>"},{"location":"en/format_conversion.html#add-group-labels","title":"Add group labels","text":"<p>What it does: Adds atom group labels to a structure file. Group labels are required by some GPUMD-related workflows, such as species-specific MSD or diffusion calculations.</p> <p>CLI mode:</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>This command reads the input structure and writes an extxyz file with group information.</p> <p>Interactive mode: Choose <code>106</code> from the format conversion menu. You will see:</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre> <p>Output: An extxyz file with group labels added.</p>"},{"location":"en/format_conversion.html#script-details","title":"Script Details","text":""},{"location":"en/format_conversion.html#poscar-to-extxyz","title":"POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>Use this when you have a single VASP structure and want an extxyz output.</p> <p>Interactive keyword: <code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#extxyz-to-poscar","title":"extxyz to POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>This converts all frames in an extxyz file into <code>POSCAR_*.vasp</code> files. Frame indices are 0-based in most GPUMDkit scripts, but output filenames are meant for direct inspection and batch calculations.</p> <p>Interactive entry: <code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#lammps-dump-to-extxyz","title":"LAMMPS dump to extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>The element symbols must match the LAMMPS atom type IDs. For example, if type <code>1</code> is Li, type <code>2</code> is Y, and type <code>3</code> is Cl, the order should be <code>Li Y Cl</code>.</p> <p>Interactive keyword: <code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#cif-conversion","title":"CIF conversion","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>Use <code>-cif2pos</code> if you want a VASP-style structure, and <code>-cif2exyz</code> if the next step is GPUMDkit analysis.</p>"},{"location":"en/format_conversion.html#add-weights","title":"Add weights","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>This is useful when you want some structures to have a different training weight in a NEP dataset.</p>"},{"location":"en/format_conversion.html#replicate-structures","title":"Replicate structures","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>The first form uses explicit replication factors. The second form tries to build a supercell close to a target atom count.</p>"},{"location":"en/format_conversion.html#extract-one-frame","title":"Extract one frame","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>This extracts frame index <code>1000</code> from an extxyz trajectory.</p>"},{"location":"en/format_conversion.html#split-multi-frame-extxyz","title":"Split multi-frame extxyz","text":"<p><code>split_single_xyz.py</code> splits an extxyz file into individual frames, each written to a separate file.</p> <pre><code>python Scripts/format_conversion/split_single_xyz.py dump.xyz\n</code></pre> <p>This creates <code>model_0.xyz</code>, <code>model_1.xyz</code>, ... for each frame in the trajectory.</p>"},{"location":"en/format_conversion.html#mtp-conversion","title":"MTP conversion","text":"<p>Convert MTP <code>.cfg</code> format to extxyz:</p> <pre><code>gpumdkit.sh    # Select: 1) Format Conversion \u2192 102\n</code></pre> <p>Interactive prompt:</p> <pre><code>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;\nExample: train.cfg Pd Ag\n------------&gt;&gt;\n</code></pre>"},{"location":"en/format_conversion.html#abacus-conversion","title":"ABACUS conversion","text":"<p>Convert ABACUS output to extxyz:</p> <pre><code>gpumdkit.sh    # Select: 1) Format Conversion \u2192 104\n</code></pre> <p>The menu offers two options:</p> <ol> <li>SCF output (<code>running_scf.log</code>)</li> <li>MD output (<code>running_md.log</code>)</li> </ol>"},{"location":"en/format_conversion.html#common-mistakes","title":"Common Mistakes","text":"Problem What to Check LAMMPS elements are wrong Check the element order passed after the dump file A trajectory has strange metadata Try <code>-clean_xyz input.xyz clean.xyz</code> A converted structure looks shifted Inspect PBC/cell information in the source file Frame extraction gives the wrong structure Remember that frame indices are 0-based"},{"location":"en/format_conversion.html#notes","title":"Notes","text":"<p>If a Python package required by a specific converter is missing, Python will report it when that converter is used.</p>"},{"location":"en/plot_scripts.html","title":"Plot Scripts","text":"\ud83d\udcca Plot Scripts <p>The plotting module contains Python scripts for visualizing data generated by GPUMD, NEP, and GPUMDkit calculators. All plots can be displayed interactively or saved as high-resolution PNG files.</p> <p>Script Location: <code>Scripts/plt_scripts/</code></p>"},{"location":"en/plot_scripts.html#quick-access","title":"Quick Access","text":"<pre><code>gpumdkit.sh -plt              # Show all plotting options\ngpumdkit.sh -plt &lt;type&gt;       # Generate a plot\ngpumdkit.sh -plt &lt;type&gt; save  # Save plot as PNG\ngpumdkit.sh -plt &lt;type&gt; -h    # Show help for a specific plot type\n</code></pre> <p>Running <code>gpumdkit.sh -plt</code> prints the plotting command menu:</p> <pre><code>+-----------------------------------------------------------------------------------------------+\n|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |\n+-----------------------------------------------------------------------------------------------+\n|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |\n+-----------------------------------------------------------------------------------------------+\n|                                    NEP Training &amp; Evaluation                                  |\n+-----------------------------------------------------------------------------------------------+\n|  train          - NEP training results           prediction     - NEP prediction results      |\n|  train_test     - NEP train and test results     parity_density - Parity density plot         |\n|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |\n|  charge         - Charge distribution            born_charge    - Born effective charges      |\n|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |\n|  des            - Descriptors                    lr             - Learning rate for gnep      |\n+-----------------------------------------------------------------------------------------------+\n|                                     Diffusion &amp; Transport                                     |\n+-----------------------------------------------------------------------------------------------+\n|  msd            - Mean square displacement       msd_conv       - MSD convergence             |\n|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |\n|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|\n|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |\n|  D_xyz          - Directional Arrhenius D                                                     |\n|  doas           - Density of atomistic states                                                 |\n+-----------------------------------------------------------------------------------------------+\n|                                    MD &amp; Structural Analysis                                   |\n+-----------------------------------------------------------------------------------------------+\n|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |\n|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |\n|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |\n|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |\n+-----------------------------------------------------------------------------------------------+\n|                                        Heat Transport                                         |\n+-----------------------------------------------------------------------------------------------+\n|  emd            - EMD results                    nemd           - NEMD results                |\n|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |\n+-----------------------------------------------------------------------------------------------+\n|                                          Phonons                                              |\n+-----------------------------------------------------------------------------------------------+\n|  pdos           - VAC and PDOS                                                                |\n+-----------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"en/plot_scripts.html#nep-training-and-prediction","title":"NEP Training and Prediction","text":""},{"location":"en/plot_scripts.html#plt_trainpy","title":"plt_train.py","text":"<p>Visualizes NEP training progress including loss curves, RMSE evolution, and parity plots comparing DFT vs NEP predictions for energy, forces, and stresses.</p> <p>Input Files: <code>loss.out</code>, <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/plot_scripts.html#plt_predictionpy","title":"plt_prediction.py","text":"<p>Visualizes NEP prediction results on the test set.</p> <p>Input Files: <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test         # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#plt_train_testpy","title":"plt_train_test.py","text":"<p>Creates combined parity plots for both training and testing datasets.</p> <p>Input Files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code>, <code>energy_test.out</code>, <code>force_test.out</code>, <code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"en/plot_scripts.html#plt_parity_densitypy","title":"plt_parity_density.py","text":"<p>Generates density-based parity plots for energies, forces, and stresses. Useful for large datasets where scatter plots become unreadable.</p> <p>Input Files: <code>energy_train.out</code>, <code>force_train.out</code>, <code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"en/plot_scripts.html#plt_force_errorspy","title":"plt_force_errors.py","text":"<p>Plots force error evaluation metrics as proposed by Liu et al..</p> <p>Input File: <code>force_train.out</code></p> <p>Metrics Displayed: - Force magnitude errors (delta_F) - Force angle errors (delta_theta) - Distribution of errors</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"en/plot_scripts.html#plt_learning_ratepy","title":"plt_learning_rate.py","text":"<p>Visualizes learning rate during <code>gnep</code> training.</p> <p>Input File: <code>loss.out</code></p> <p>Note: Only for the <code>gnep</code> training process.</p> <pre><code>gpumdkit.sh -plt lr\n</code></pre>"},{"location":"en/plot_scripts.html#plt_nep_restartpy","title":"plt_nep_restart.py","text":"<p>Visualizes parameters stored in the <code>nep.restart</code> file.</p> <p>Input File: <code>nep.restart</code></p> <pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"en/plot_scripts.html#plt_chargepy","title":"plt_charge.py","text":"<p>Plots charge distribution from <code>qNEP</code> model.</p> <p>Input File: <code>charge_train.out</code></p> <p>Important: Ensure consistency between training set and charge output atom ordering. Use full batch training or run prediction step first.</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre>"},{"location":"en/plot_scripts.html#plt_born_chargepy","title":"plt_born_charge.py","text":"<p>Creates parity plots for Born effective charges (BEC) on training and testing datasets. Structures with all-zero reference BEC are filtered out.</p> <p>Input Files: <code>bec_train.out</code>, <code>bec_test.out</code></p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec          # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#thermodynamic-properties","title":"Thermodynamic Properties","text":""},{"location":"en/plot_scripts.html#plt_thermopy","title":"plt_thermo.py","text":"<p>Primary script for comprehensive thermodynamic property visualization.</p> <p>Input File: <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/plot_scripts.html#plt_thermo2py-plt_thermo3py","title":"plt_thermo2.py &amp; plt_thermo3.py","text":"<p>Alternative thermodynamic visualization with different styles.</p> <p>Input File: <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"en/plot_scripts.html#diffusion-and-ionic-transport","title":"Diffusion and Ionic Transport","text":""},{"location":"en/plot_scripts.html#plt_msdpy","title":"plt_msd.py","text":"<p>Plots mean square displacement (MSD) for all directions.</p> <p>Input File: <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"en/plot_scripts.html#plt_msd_allpy","title":"plt_msd_all.py","text":"<p>Plots MSD for all atomic species separately when using <code>all_groups</code> in GPUMD.</p> <p>Input File: <code>msd.out</code> (computed with <code>all_groups</code> option)</p> <p>Requirements: Must use <code>all_groups</code> in the <code>compute_msd</code> command in <code>run.in</code>.</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"en/plot_scripts.html#plt_msd_convergence_checkpy","title":"plt_msd_convergence_check.py","text":"<p>Checks convergence of MSD calculations across different time windows.</p> <p>Input File: <code>msd_step*.out</code> (computed with <code>save_every</code> option)</p> <p>Requirements: Use <code>save_every</code> in the <code>compute_msd</code> command.</p> <p>Purpose: Verify MSD has converged sufficiently for accurate diffusion coefficient calculation.</p> <pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"en/plot_scripts.html#plt_sdcpy","title":"plt_sdc.py","text":"<p>Plots self-diffusion coefficient (SDC) vs time.</p> <p>Input File: <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/plot_scripts.html#plt_arrhenius_dpy","title":"plt_arrhenius_d.py","text":"<p>Creates Arrhenius plot for diffusivity (log10 D vs 1000/T).</p> <p>Input Files: <code>*K/msd.out</code> files (each temperature subdirectory should contain an <code>msd.out</code>)</p> <pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D             # Alternative command\n</code></pre> <p>Output example:</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"en/plot_scripts.html#plt_arrhenius_sigmapy","title":"plt_arrhenius_sigma.py","text":"<p>Creates Arrhenius plot for ionic conductivity (ln(\u03c3\u00b7T) vs 1000/T).</p> <p>Input Files: <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> (each temperature subdirectory)</p> <pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma         # Alternative command\n</code></pre>"},{"location":"en/plot_scripts.html#heat-transport","title":"Heat Transport","text":""},{"location":"en/plot_scripts.html#plt_emdpy","title":"plt_emd.py","text":"<p>Analyzes and plots thermal conductivity from equilibrium molecular dynamics (EMD).</p> <p>Input Files: EMD output files from GPUMD</p> <pre><code>gpumdkit.sh -plt emd x        # for x direction\n</code></pre>"},{"location":"en/plot_scripts.html#plt_nemdpy","title":"plt_nemd.py","text":"<p>Visualizes non-equilibrium molecular dynamics (NEMD) thermal transport properties.</p> <p>Input Files: NEMD output files from GPUMD</p> <p>Parameters:</p> Parameter Description <code>real_length</code> Real length of heat transfer zone in nm (set to <code>Auto</code> for auto-calculation) <code>scale_eff_size</code> Scale factor for effective cross-sectional area (default: 1). For 3D bulk: use 1. For low-dimensional systems with vacuum: S_box / S_eff <code>cutoff_freq</code> Cutoff frequency for SHC calculation in THz (default: 60) <code>save</code> Optional, save the plot as <code>nemd.png</code> <p>Note: If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p> <pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#plt_hnemdpy","title":"plt_hnemd.py","text":"<p>Plots homogeneous non-equilibrium molecular dynamics (HNEMD) results.</p> <p>Input Files: HNEMD output files from GPUMD</p> <p>Parameters:</p> Parameter Description <code>scale_eff_size</code> Scale factor for effective cross-sectional area (default: 1) <code>cutoff_freq</code> Cutoff frequency for SHC calculation in THz (default: 60) <code>save</code> Optional, save the plot as <code>hnemd.png</code> <p>Note: If no SHC data, set <code>scale_eff_size</code> and <code>cutoff_freq</code> to any number as placeholders when using <code>save</code>.</p> <pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"en/plot_scripts.html#structural-analysis","title":"Structural Analysis","text":""},{"location":"en/plot_scripts.html#plt_rdfpy","title":"plt_rdf.py","text":"<p>Plots radial distribution function (RDF) showing pair correlations.</p> <p>Input File: <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf               # Plot all RDF pairs\ngpumdkit.sh -plt rdf &lt;column&gt;      # Plot specific pair\n</code></pre> <p>Full RDF output:</p> <p>Single pair RDF:</p>"},{"location":"en/plot_scripts.html#plt_rdf_pmfpy","title":"plt_rdf_pmf.py","text":"<p>Plots RDF combined with potential of mean force (PMF).</p> <p>Input File: <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf_pmf\n</code></pre>"},{"location":"en/plot_scripts.html#plt_vacpy","title":"plt_vac.py","text":"<p>Plots velocity autocorrelation function (VAC). Useful for analyzing phonon properties and atomic dynamics.</p> <p>Input File: <code>sdc.out</code> (the VAC columns are read from this file by the plotting script)</p> <p>Output: Interactive plot or <code>vac.png</code> (with <code>save</code> option)</p> <pre><code>gpumdkit.sh -plt vac\n</code></pre>"},{"location":"en/plot_scripts.html#plt_cohesivepy","title":"plt_cohesive.py","text":"<p>Plots cohesive energy curve from <code>cohesive.out</code>. Useful for analyzing lattice stability and equilibrium lattice constants.</p> <p>Input File: <code>cohesive.out</code> (isotropic scaling factor vs cohesive energy)</p> <p>Output: Interactive plot or <code>cohesive.png</code> (with <code>save</code> option)</p> <pre><code>gpumdkit.sh -plt cohesive\n</code></pre>"},{"location":"en/plot_scripts.html#plt_net_forcepy","title":"plt_net_force.py","text":"<p>Plots distribution of net forces on structures, useful for identifying problematic configurations.</p> <p>Input File: <code>train.xyz</code> (extxyz format)</p> <pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>Reference: arXiv:2510.19774</p>"},{"location":"en/plot_scripts.html#phonons","title":"Phonons","text":""},{"location":"en/plot_scripts.html#plt_pdospy","title":"plt_pdos.py","text":"<p>Calculates and plots normalized VAC, PDOS, and Heat Capacity (Cv).</p> <p>Input Files: <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code></p> <pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>Heat capacity output:</p>"},{"location":"en/plot_scripts.html#descriptor-dimer-and-extra-analysis","title":"Descriptor, Dimer, and Extra Analysis","text":""},{"location":"en/plot_scripts.html#plt_descriptorspy","title":"plt_descriptors.py","text":"<p>Visualizes high-dimensional NEP descriptors using dimensionality reduction (PCA or UMAP).</p> <p>Input File: <code>descriptors.npy</code> (generated by <code>gpumdkit.sh -calc des</code>)</p> <p>Methods: - <code>pca</code> \u2014 Principal Component Analysis - <code>umap</code> \u2014 Uniform Manifold Approximation and Projection</p> <pre><code># First generate descriptors\ngpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n\n# Then visualize\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"en/plot_scripts.html#plt_dimerpy","title":"plt_dimer.py","text":"<p>Plots dimer interaction curves. Two atoms are placed in a cubic box (30 \u00c5) and the potential energy and force are calculated as a function of dimer distance using a NEP model.</p> <p>Input File: <code>nep.txt</code></p> <pre><code>gpumdkit.sh -plt dimer &lt;element1&gt; &lt;element2&gt; &lt;nep_model&gt;\ngpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>Reference: J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"en/plot_scripts.html#plt_doaspy","title":"plt_doas.py","text":"<p>Plots density of atomistic states (DOAS) proposed by Wang et al..</p> <p>Input File: <code>doas.out</code> (calculated by <code>gpumdkit.sh -calc doas</code>)</p> <pre><code>gpumdkit.sh -plt doas &lt;doas.out&gt; &lt;species&gt;\ngpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"en/plot_scripts.html#plane-grid-plot-for-polar-materials","title":"Plane-Grid Plot for Polar Materials","text":"<p>This workflow maps displacement or polarization data onto a grid and plots selected plane profiles. For detailed usage and real-world examples, see Polar Material Analysis.</p> <p>Dependency:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>Typical upstream steps:</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>Usage:</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre>"},{"location":"en/plot_scripts.html#quick-reference-table","title":"Quick Reference Table","text":"Command Input File(s) Description <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP training plots <code>prediction</code> / <code>test</code> <code>*_test.out</code> NEP prediction plots <code>train_test</code> <code>*_train.out</code>, <code>*_test.out</code> Combined parity plots <code>parity_density</code> <code>*_train.out</code> Density-based parity plots <code>force_errors</code> <code>force_train.out</code> Force error metrics <code>lr</code> <code>loss.out</code> (gnep) Learning rate <code>restart</code> <code>nep.restart</code> Restart file parameters <code>charge</code> <code>charge_train.out</code> Charge distribution <code>born_charge</code> / <code>bec</code> <code>bec_train.out</code>, <code>bec_test.out</code> Born effective charges <code>thermo</code> <code>thermo.out</code> Thermodynamic properties <code>msd</code> <code>msd.out</code> Mean square displacement <code>msd_all</code> <code>msd.out</code> (all_groups) MSD for all species <code>msd_conv</code> <code>msd_step*.out</code> MSD convergence check <code>sdc</code> <code>msd.out</code> Self-diffusion coefficient <code>arrhenius_d</code> / <code>D</code> <code>*K/msd.out</code> Arrhenius diffusivity <code>arrhenius_sigma</code> / <code>sigma</code> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> Arrhenius ionic conductivity <code>rdf</code> <code>rdf.out</code> Radial distribution function <code>rdf_pmf</code> <code>rdf.out</code> RDF + potential of mean force <code>vac</code> <code>sdc.out</code> Velocity autocorrelation <code>cohesive</code> <code>cohesive.out</code> Cohesive energy curve <code>net_force</code> <code>train.xyz</code> Net force distribution <code>doas</code> <code>doas.out</code> Density of atomistic states <code>des</code> <code>descriptors.npy</code> Descriptor PCA/UMAP <code>dimer</code> <code>nep.txt</code> Dimer energy/force curve <code>pdos</code> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code> VAC and PDOS <code>emd</code> EMD outputs EMD thermal conductivity <code>nemd</code> NEMD outputs NEMD thermal transport <code>hnemd</code> HNEMD outputs HNEMD thermal transport <code>viscosity</code> Viscosity outputs Viscosity"},{"location":"en/polar_material_analysis.html","title":"Polar Material Analysis","text":"\ud83e\uddf2 Polar Material Analysis <p>This tutorial covers GPUMDkit calculator options <code>406-410</code> and the <code>plane-grid</code> plotting workflow.</p> <p>Script Location: <code>Scripts/calculators/</code> and <code>Scripts/plt_scripts/</code></p> <p>This tutorial includes both general and system-specific tools:</p> <ul> <li><code>nlist</code>, <code>disp</code>, and <code>avg-struct</code> are broadly useful for structure/trajectory analysis.</li> <li><code>oct-tilt</code> is for octahedral environments (requires 6 neighbors around each center).</li> <li><code>pol-abo3</code> is specific to <code>ABO3</code> polarization analysis.</li> </ul>"},{"location":"en/polar_material_analysis.html#overview","title":"Overview","text":"Step CLI Command Main Input Output Build neighbor list <code>gpumdkit.sh -calc nlist ...</code> <code>model.xyz</code> <code>nl-*.dat</code> Calculate displacement <code>gpumdkit.sh -calc disp ...</code> trajectory + <code>nl-*.dat</code> <code>displacements.dat</code> Average trajectory <code>gpumdkit.sh -calc avg-struct ...</code> trajectory averaged extxyz Octahedral tilt <code>gpumdkit.sh -calc oct-tilt ...</code> trajectory + B-O neighbor list tilt-angle table ABO3 polarization <code>gpumdkit.sh -calc pol-abo3 ...</code> trajectory + neighbor lists polarization table Plane-grid plot <code>gpumdkit.sh -plt plane-grid ...</code> structure + displacement data plane profile plot"},{"location":"en/polar_material_analysis.html#dependency","title":"Dependency","text":"<p>These scripts require <code>ferrodispcalc</code>:</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"en/polar_material_analysis.html#interactive-mode-entry","title":"Interactive mode entry","text":"<p>Options <code>406-410</code> are the core functions for this tutorial. The sections below explain when to use each one and how to run it.</p> <pre><code>gpumdkit.sh\n# choose 4) Calculators\n</code></pre> <p>The calculator menu is:</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre> <p>For full argument details, use:</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"en/polar_material_analysis.html#406-build-neighbor-list-calc_neighbor_listpy","title":"406) Build neighbor list (<code>calc_neighbor_list.py</code>)","text":"<p>Build neighbor lists for selected center and neighbor elements.</p> <p>When to use it: This is usually the first step before <code>disp</code>, <code>oct-tilt</code>, and <code>pol-abo3</code>, because those scripts read <code>nl-*.dat</code> neighbor files.</p>"},{"location":"en/polar_material_analysis.html#usage","title":"Usage","text":"<pre><code># Example 1: Ti-O nearest 6 neighbors for octahedral analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# Example 2: Pb/Sr-O nearest 12 neighbors for A-site centered analysis\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input structure file. Default: <code>model.xyz</code>.</li> <li><code>-x, --index</code>:   Frame index to read from input. Default: <code>0</code>.</li> <li><code>-c, --cutoff</code> (required):   Neighbor search cutoff (Angstrom).</li> <li><code>-n, --neighbor-num</code> (required):   Number of neighbors per center.</li> <li><code>-d, --defect</code>:   Defect mode. If enabled and neighbors are insufficient, missing slots are filled with the center index.</li> <li><code>-C, --center-elements</code> (required):   Center species list.</li> <li><code>-E, --neighbor-elements</code> (required):   Neighbor species list.</li> <li><code>-o, --output</code>:   Output file path. Default: <code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file","title":"Output file","text":"<ul> <li>Main output: neighbor list text file (for example <code>nl-Ti-O.dat</code>).</li> <li>The file is a 2D integer array with shape <code>(n_center, neighbor_num + 1)</code>. Each row corresponds to one center atom: the first column is the center index, and the remaining columns are its neighbor indices (all 1-based).</li> </ul>"},{"location":"en/polar_material_analysis.html#407-calc-displacement-from-trajectory-calc_displacementpy","title":"407) Calc displacement from trajectory (<code>calc_displacement.py</code>)","text":"<p>Compute local displacement vectors from a trajectory/model and a neighbor list.</p>"},{"location":"en/polar_material_analysis.html#usage_1","title":"Usage","text":"<pre><code># Example 1: single-frame displacement from model.xyz\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# Example 2: use the last 20% frames in movie.xyz\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_1","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   Neighbor list file from <code>nlist</code>.</li> <li><code>-o, --output</code>:   Output file. Default: <code>displacements.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames.   Integer: last <code>N</code> frames.   <code>0 &lt; value &lt; 1</code>: last ratio of frames.</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_1","title":"Output file","text":"<ul> <li>Main output: <code>displacements.dat</code> (or your custom output name).</li> <li>The saved text file is a 2D array: for a single-frame input, its shape is <code>(n_center, 3)</code>; for a multi-frame input, it is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The three columns are <code>dx</code>, <code>dy</code>, and <code>dz</code> displacement components in Angstrom.</li> </ul>"},{"location":"en/polar_material_analysis.html#408-calc-averaged-structure-calc_averaged_structurepy","title":"408) Calc averaged structure (<code>calc_averaged_structure.py</code>)","text":"<p>Generate one averaged structure from selected trajectory frames. Use this after equilibration. For a solid near equilibrium, average a frame window at the target temperature and analyze that representative structure instead of processing every snapshot.</p>"},{"location":"en/polar_material_analysis.html#usage_2","title":"Usage","text":"<pre><code># Example 1: average all frames\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# Example 2: average selected frames (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_2","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input trajectory file. Default: <code>movie.xyz</code>.</li> <li><code>-o, --output</code>:   Output structure file. Default: <code>averaged_structure.xyz</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_2","title":"Output file","text":"<ul> <li>Main output: averaged single-frame extxyz file.</li> <li>Position averaging applies MIC/PBC correction relative to the first selected frame.</li> </ul>"},{"location":"en/polar_material_analysis.html#409-calc-octahedral-tilt-calc_oct_tiltpy","title":"409) Calc octahedral tilt (<code>calc_oct_tilt.py</code>)","text":"<p>Calculate octahedral tilt angles from a B-O neighbor list. This is commonly used to analyze octahedral rotation patterns in <code>ABO3</code> systems, such as <code>SrTiO3</code> and <code>PbZrO3</code>.</p>"},{"location":"en/polar_material_analysis.html#usage_3","title":"Usage","text":"<pre><code># Example 1: octahedral tilt of the TiO6 octahedra from a single frame\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# Example 2: octahedral tilt of the TiO6 octahedra from the last 20% trajectory frames\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_3","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>-n, --neighbor-list</code> (required):   B-O neighbor list file.</li> <li><code>-o, --output</code>:   Output file. Default: <code>octahedral_tilt.dat</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_3","title":"Output file","text":"<ul> <li>Main output: <code>octahedral_tilt.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>theta_x</code>, <code>theta_y</code>, <code>theta_z</code>, in degree): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#410-calc-polarization-for-abo3-calc_polarization_abo3py","title":"410) Calc polarization for ABO3 (<code>calc_polarization_abo3.py</code>)","text":"<p>Calculate local polarization vectors for <code>ABO3</code> systems.</p>"},{"location":"en/polar_material_analysis.html#usage_4","title":"Usage","text":"<pre><code># Example 1: single-frame ABO3 polarization\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# Example 2: trajectory polarization on a selected frame window\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#arguments-complete_4","title":"Arguments (complete)","text":"<ul> <li><code>-i, --input</code>:   Input xyz file. Default: <code>model.xyz</code>.</li> <li><code>--nl-ba</code> (required):   B-A neighbor list.</li> <li><code>--nl-bo</code> (required):   B-O neighbor list.</li> <li><code>-o, --output</code>:   Output file. Default: <code>polarization.dat</code>.</li> <li><code>--bec</code> (required):   Born effective charge terms in <code>Element=value</code> format.   Example: <code>Pb=2.5 Ti=4.0 O=-2.0</code>.</li> <li><code>-s, --start</code>:   Slice start index. Default: <code>0</code>.</li> <li><code>-t, --stop</code>:   Slice stop index. Default: end.</li> <li><code>-p, --step</code>:   Slice step. Default: <code>1</code>.</li> <li><code>-l, --last</code>:   Select trailing frames (<code>last N</code> or <code>last ratio</code>).</li> <li><code>-l/--last</code> is mutually exclusive with <code>-s/-t/-p</code>.</li> </ul> <p>Important checks:</p> <ul> <li><code>--bec</code> must include all element species in the input structure.</li> <li>Center atom indices in <code>--nl-ba</code> and <code>--nl-bo</code> must match.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-file_4","title":"Output file","text":"<ul> <li>Main output: <code>polarization.dat</code> (or custom name).</li> <li>The saved text file is a 2D array with three columns (<code>Px</code>, <code>Py</code>, <code>Pz</code>, in <code>C/m^2</code>): for a single-frame input, shape is <code>(n_center, 3)</code>; for a multi-frame input, shape is <code>(n_selected_frame * n_center, 3)</code> in frame-major order. The script prints a warning if the total Born charge is not balanced.</li> </ul>"},{"location":"en/polar_material_analysis.html#plane-grid-visualization-plt_plane_gridpy","title":"Plane-grid visualization (<code>plt_plane_grid.py</code>)","text":"<p>You can visualize either <code>displacements.dat</code> or <code>polarization.dat</code>:</p> <pre><code># Example 1: displacement map on Ti sites, first XY layer\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# Example 2: polarization map on Pb sites, XZ and YZ layers\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>Arguments (complete):</p> <ul> <li><code>-i, --input</code>:   Input xyz file for atomic layout and layering. Default: <code>model.xyz</code>.</li> <li><code>-d, --disp</code>:   Vector-field data file. Default: <code>displacements.dat</code>.</li> <li><code>-e, --elements</code> (required):   Center element symbols used to map vectors to lattice layers.</li> <li><code>-m, --tol</code>:   Layer tolerance for grid mapping. Default: <code>1.0</code>.</li> <li><code>-g, --target-size</code>:   Expected grid size as <code>nx ny nz</code>.</li> <li><code>-o, --save-dir</code>:   Figure output directory. Default: <code>plot</code>.</li> <li><code>-f, --frame</code>:   Frame index to visualize when vector data has multiple frames. Default: <code>0</code>.</li> <li><code>--select-xy</code>:   Selected XY layer indices.</li> <li><code>--select-xz</code>:   Selected XZ layer indices.</li> <li><code>--select-yz</code>:   Selected YZ layer indices.</li> </ul> <p>Output:</p> <ul> <li>Creates output directory if needed.</li> <li>Saves figures as <code>XY_*.png</code>, <code>XZ_*.png</code>, <code>YZ_*.png</code>.</li> </ul>"},{"location":"en/polar_material_analysis.html#output-files-at-a-glance","title":"Output files at a glance","text":"Script Main output What it stores <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based center index + neighbor indices <code>calc_displacement.py</code> <code>*.dat</code> Local displacement vectors (<code>dx dy dz</code>, Angstrom) <code>calc_averaged_structure.py</code> <code>*.xyz</code> One averaged structure <code>calc_oct_tilt.py</code> <code>*.dat</code> Octahedral tilt angles (<code>theta_x theta_y theta_z</code>, degree) <code>calc_polarization_abo3.py</code> <code>*.dat</code> Local polarization vectors (<code>Px Py Pz</code>, <code>C/m^2</code>) <code>plt_plane_grid.py</code> <code>plot/*.png</code> XY/XZ/YZ plane maps from vector-field data"},{"location":"en/polar_material_analysis.html#real-examples","title":"Real Examples","text":""},{"location":"en/polar_material_analysis.html#temperature-driven-ferroelectric-to-paraelectric-phase-transition-for-pbtio3","title":"Temperature-driven Ferroelectric-to-paraelectric phase transition for PbTiO3","text":"<p>Assume all files are in the current directory <code>./</code>:</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> is the initial structure used to run MD simulations. Each <code>TEMP K.xyz</code> is a trajectory at that temperature.</p>"},{"location":"en/polar_material_analysis.html#step-1-get-averaged-structures-from-the-last-half-of-each-trajectory","title":"Step 1: get averaged structures from the last half of each trajectory","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>This writes <code>300K-avg.xyz</code>, <code>350K-avg.xyz</code>, ..., <code>800K-avg.xyz</code>.</p>"},{"location":"en/polar_material_analysis.html#step-2-build-neighbor-lists-from-modelxyz","title":"Step 2: build neighbor lists from <code>model.xyz</code>","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-compute-displacement-and-polarization-for-each-temperature","title":"Step 3: compute displacement and polarization for each temperature","text":"<p>Use Born effective charges (BEC), not nominal ionic charges. For PbTiO3 in this example:</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>You can obtain BEC from your own DFPT calculation or from literature values. Thus use following commands to compute local displacement and polarization:</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-4-plot-displacement-and-polarization-maps-in-real-space","title":"Step 4: plot displacement and polarization maps in real space","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-5-build-a-temperature-order-parameter-curve","title":"Step 5: build a temperature-order-parameter curve","text":"<p>By analyzing the lattice of each temperature-averaged structure together with its polarization (<code>XX-pol.dat</code>), we can obtain the following figure:</p> <p>The trend shows a clear phase transition around <code>600 K</code>, where the polarization vanishes.</p>"},{"location":"en/polar_material_analysis.html#topological-structure-in-pbtio3srtio3-superlattice","title":"Topological structure in PbTiO3/SrTiO3 superlattice","text":"<p>Assume <code>movie.xyz</code> is the trajectory of the PbTiO3/SrTiO3 superlattice in the current directory.</p>"},{"location":"en/polar_material_analysis.html#step-1-build-an-averaged-structure-from-the-last-25-frames","title":"Step 1: build an averaged structure from the last 25% frames","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-2-build-the-ti-neighbor-list","title":"Step 2: build the Ti neighbor list","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"en/polar_material_analysis.html#step-3-plot-the-plane-grid-map","title":"Step 3: plot the plane-grid map","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>This gives a map similar to the one shown earlier. In the PTO region, a vortex-like polarization pattern is visible, while polarization in the STO region is close to zero.</p> <p>Note: the example figure uses a custom colormap. The default GPUMDkit output uses a different style, which can be adjusted by editing the plotting script.</p>"},{"location":"en/polar_material_analysis.html#other-systems","title":"Other Systems","text":""},{"location":"en/polar_material_analysis.html#organic-inorganic-hybrid-ferroelectrics","title":"Organic-inorganic hybrid ferroelectrics","text":"<p>In many organic-inorganic ferroelectrics, polarization is strongly tied to anisotropic molecular units. A practical way to track molecular orientation is to use bond vectors.</p> <p>For TMCM-CdCl3, you can use the C-Cl bond direction of the TMCM molecule as an orientation proxy, then use it to estimate the polarization state:</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p><code>ccl_vectors.dat</code> can then be analyzed as an orientation order parameter. More details could be found at: Phys. Rev. Lett. 136, 016801</p>"},{"location":"en/polar_material_analysis.html#other-ferroelectric-families","title":"Other ferroelectric families","text":"<p>Beyond <code>ABO3</code>, <code>ferrodispcalc</code> can be adapted to many ferroelectric systems, including nitrides, hafnia-based compounds, organic-inorganic hybrids, and some 2D ferroelectrics.</p>"},{"location":"en/quick_start.html","title":"Quick Start","text":"\ud83d\ude80 Quick Start <p>This page helps you install GPUMDkit and run your first commands. You can use GPUMDkit through an interactive menu or direct command-line options.</p>"},{"location":"en/quick_start.html#what-it-does","title":"What it does","text":"<p>GPUMDkit provides a single entry point for common tasks in computational materials science \u2014 format conversion, structure analysis, property calculation, and visualization \u2014 without writing custom scripts.</p>"},{"location":"en/quick_start.html#before-you-start","title":"Before you start","text":""},{"location":"en/quick_start.html#1-prepare-a-python-environment","title":"1. Prepare a Python environment","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>Some optional functions require additional packages:</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>Other Python dependencies are loaded by the corresponding scripts. If a package is missing, Python will report it when that function is used.</p>"},{"location":"en/quick_start.html#2-install-gpumdkit","title":"2. Install GPUMDkit","text":"<p>Clone the repository and run the installer:</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre> <p>The installer writes <code>GPUMDkit_path</code> and <code>PATH</code> settings to your shell configuration and loads them for the current shell. It writes to <code>~/.bashrc</code> by default; if the current shell is zsh, it writes to <code>~/.zshrc</code>. If an existing GPUMDkit path is found, the installer prints the old path and asks whether to replace it. Before changing the rc file, it creates a backup.</p> <p>Typical installation output:</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>If GPUMDkit was installed before, you may see:</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre>"},{"location":"en/quick_start.html#3-verify-the-installation","title":"3. Verify the installation","text":"<pre><code>gpumdkit.sh -h\n</code></pre> <p>This prints a help table listing all available options.</p>"},{"location":"en/quick_start.html#interactive-mode","title":"Interactive mode","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>This opens the main menu:</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Help                \n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre> <p>Select a module by number. Each module provides sub-menus with specific functions.</p>"},{"location":"en/quick_start.html#cli-mode","title":"CLI mode","text":"<p>Direct commands use fixed positional arguments:</p> <pre><code>gpumdkit.sh -&lt;option&gt; [args...]\n</code></pre> <p>Examples:</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>The first example reads <code>POSCAR</code> and writes <code>model.xyz</code>.</p>"},{"location":"en/quick_start.html#hello-world-example","title":"Hello World Example","text":"<p>A minimal end-to-end check that your install works \u2014 create a tiny silicon POSCAR, convert it to extxyz, and inspect the output:</p> <pre><code>cat &gt; POSCAR &lt;&lt; 'EOF'\nSi\n1.0\n0 2.715 2.715\n2.715 0 2.715\n2.715 2.715 0\nSi\n1\ndirect\n0 0 0\nEOF\ngpumdkit.sh -pos2exyz POSCAR model.xyz\nhead model.xyz\n</code></pre> <p>If <code>model.xyz</code> shows a single Si atom with lattice info, your install works.</p> <p>What is extxyz? extxyz is the extended XYZ format: line 1 is the atom count, line 2 contains the lattice and per-structure properties (energy/forces/virial as needed), and lines 3+ list each atom with its per-atom properties. It is the native training-data format for NEP.</p>"},{"location":"en/quick_start.html#common-examples","title":"Common examples","text":""},{"location":"en/quick_start.html#convert-a-poscar-to-extxyz","title":"Convert a POSCAR to extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"en/quick_start.html#add-gpumd-group-labels","title":"Add GPUMD group labels","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>Group labels are used by some GPUMD-related workflows that need atom grouping, such as species-specific MSD or diffusion calculations.</p>"},{"location":"en/quick_start.html#plot-nep-training-results","title":"Plot NEP training results","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"en/quick_start.html#plot-nep-test-results","title":"Plot NEP test results","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"en/quick_start.html#plot-thermodynamic-data","title":"Plot thermodynamic data","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"en/quick_start.html#plot-msd-and-self-diffusion-coefficient","title":"Plot MSD and self-diffusion coefficient","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"en/quick_start.html#notes","title":"Notes","text":"<ul> <li>Use <code>gpumdkit.sh -h</code> to see all available options.</li> <li>Use <code>gpumdkit.sh -&lt;option&gt; -h</code> to get help for a specific option (e.g., <code>gpumdkit.sh -plt train -h</code>).</li> <li>For detailed usage of each module, see the corresponding tutorial pages linked in the index.</li> </ul>"},{"location":"en/structure_sampling.html","title":"Structure Sampling","text":"\ud83d\udce6 Structure Sampling <p>Structure sampling is used to select, generate, or filter candidate configurations for NEP training and molecular dynamics workflows.</p> <p>Script Location: <code>Scripts/sample_structures/</code></p>"},{"location":"en/structure_sampling.html#interactive-mode","title":"Interactive Mode","text":"<p>Sampling tasks are usually easier to run from the interactive menu:</p> <pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>2) Sample Structures\n</code></pre> <p>The menu is:</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Method Use Case 201 Uniform/random sampling quick frame selection from a trajectory 202 PyNEP notice prints a notice; use <code>gpumdkit.sh -pynep</code> to run PyNEP 203 NepTrain FPS descriptor-based FPS with NepTrain 204 Perturb structure generate perturbed structures from POSCAR/CONTCAR 205 Force-deviation selection select structures with high model deviation"},{"location":"en/structure_sampling.html#uniform-and-random-sampling","title":"Uniform and Random Sampling","text":"<p>From interactive mode, choose <code>201</code>. You will see:</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>Example input:</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>or:</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>Arguments:</p> Argument Meaning <code>dump.xyz</code> input trajectory <code>uniform</code> / <code>random</code> sampling method <code>50</code> / <code>100</code> number of selected structures <code>500</code> optional number of initial frames to skip <p>Output:</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#farthest-point-sampling-with-neptrain","title":"Farthest Point Sampling with NepTrain","text":"<p>This entry uses NepTrain descriptors for FPS. Choose <code>203</code> in interactive mode, or run the script directly:</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>From interactive mode, choose <code>203</code>. You will see:</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>Inputs:</p> File Meaning <code>dump.xyz</code> candidate structures <code>train.xyz</code> existing training set <code>nep.txt</code> current NEP model used to compute descriptors <p>Outputs:</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>During execution, choose one of two selection modes:</p> <ol> <li>select until the descriptor distance is below a threshold;</li> <li>select a specified number of structures.</li> </ol> <p>The script then prints a selection prompt:</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>This function requires the <code>NepTrain</code> package. If you use this function, we recommend citing the NepTrain paper printed by the script.</p>"},{"location":"en/structure_sampling.html#deprecated-pynep-fps","title":"Deprecated PyNEP FPS","text":"<p>PyNEP FPS is kept for compatibility, but it is only exposed through the direct <code>-pynep</code> entry.</p> <p>If you choose <code>202</code> from the interactive menu, it prints:</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre>"},{"location":"en/structure_sampling.html#serial-pynep","title":"Serial PyNEP","text":"<pre><code>python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"en/structure_sampling.html#parallel-pynep","title":"Parallel PyNEP","text":"<pre><code>python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8\n</code></pre> <p>The last argument is the number of CPU threads.</p>"},{"location":"en/structure_sampling.html#gpumdkit-entry","title":"GPUMDkit Entry","text":"<pre><code>gpumdkit.sh -pynep\n</code></pre> <p>Then input:</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>This entry requires <code>pynep</code> and is kept for compatibility.</p>"},{"location":"en/structure_sampling.html#structure-perturbation","title":"Structure Perturbation","text":"<p>Use perturbation when you want to generate initial structures around a known configuration. Choose <code>204</code> in interactive mode, or run the script directly:</p> <pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>From interactive mode, choose <code>204</code>. You will see:</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>POSCAR</code> input VASP structure <code>20</code> number of perturbed structures <code>0.03</code> cell perturbation fraction <code>0.2</code> atom perturbation distance in Angstrom <code>uniform</code> perturbation style: <code>normal</code>, <code>uniform</code>, or <code>const</code> <p>Output:</p> <ul> <li><code>POSCAR_01.vasp</code>, <code>POSCAR_02.vasp</code>, ...</li> </ul> <p>This function requires <code>dpdata</code>. If you use this function, we recommend citing the dpdata package.</p>"},{"location":"en/structure_sampling.html#force-deviation-selection","title":"Force-Deviation Selection","text":"<p>Use this together with the GPUMD <code>active</code> command. The <code>active</code> command uses a committee model approach: multiple potentials predict forces for the same structure, and GPUMD records the maximum force deviation. <code>select_max_modev.py</code> selects structures with large force deviations from <code>active.out</code> and <code>active.xyz</code>, then writes them to <code>selected.xyz</code>.</p> <p>Choose <code>205</code> in interactive mode, or run the script directly:</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>From interactive mode, choose <code>205</code>. You will see:</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>Arguments:</p> Argument Meaning <code>200</code> maximum number of structures to keep <code>0.15</code> minimum force deviation threshold <p>Required files:</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>Output:</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"en/structure_sampling.html#frame-range-extraction","title":"Frame Range Extraction","text":"<p><code>frame_range.py</code> is an independent CLI tool and is not part of the interactive sampling menu <code>201\u2013205</code>. Use it when you want to keep only a fraction of a trajectory before sampling, for example after equilibration.</p> <pre><code>gpumdkit.sh -frame_range dump.xyz 0 0.8\npython Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>This writes frames from 0% to 80% of the trajectory. The range arguments are trajectory fractions from <code>0</code> to <code>1</code>.</p>"},{"location":"en/structure_sampling.html#example-commands","title":"Example Commands","text":"<p>An example preprocessing-and-sampling sequence is shown below. The first two commands are analyzer tools; the final step is structure sampling.</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>The final step can also be run from interactive mode by choosing <code>2) Sample Structures -&gt; 203</code>.</p>"},{"location":"en/structure_sampling.html#common-mistakes","title":"Common Mistakes","text":"Problem Recommendation FPS selects too many similar structures increase the distance threshold or select fewer structures Perturbed structures are unphysical reduce <code>cell_pert</code> and <code>atom_pert</code>, then check minimum distances <code>active.out</code> and <code>active.xyz</code> do not match regenerate both from the same GPUMD active run PCA plot looks strange check whether <code>nep.txt</code> matches the chemical species in both datasets"},{"location":"en/workflow_scripts.html","title":"Workflow Scripts","text":"\ud83d\udd27 Workflow Scripts <p>Workflow scripts automate repetitive preparation steps for DFT, MD, and NEP development.</p> <p>Script Location: <code>Scripts/workflow/</code></p>"},{"location":"en/workflow_scripts.html#interactive-entry","title":"Interactive Entry","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>Choose:</p> <pre><code>3) Workflow\n</code></pre> <p>The workflow menu looks like:</p> <pre><code>+---------------------------------------------------------+\n|                      WORKFLOW TOOLS                     |\n+---------------------------------------------------------+\n| 301) SCF batch pretreatment                             |\n| 302) MD sample batch pretreatment (gpumd)               |\n| 303) MD sample batch pretreatment (lmp)                 |\n+---------------------------------------------------------+\n| 000) Return to the main menu                            |\n+---------------------------------------------------------+\nInput the function number:\n</code></pre> <p>Available entries:</p> Menu Workflow Purpose 301 SCF batch pretreatment Prepare single-point DFT calculations 302 MD sample batch pretreatment (GPUMD) Prepare GPUMD sampling calculations 303 MD sample batch pretreatment (LAMMPS) Prepare LAMMPS sampling calculations"},{"location":"en/workflow_scripts.html#scf-batch-pretreatment","title":"SCF Batch Pretreatment","text":"<p>Use this when you have many structures and want to prepare single-point DFT calculations.</p>"},{"location":"en/workflow_scripts.html#vasp","title":"VASP","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>Before running, put structure files in the current directory. The script checks files in this order:</p> <ol> <li>if one or more <code>.vasp</code> files exist, it processes <code>.vasp</code> files;</li> <li>if both <code>.vasp</code> and <code>.xyz</code> files exist, it prints a notice and only processes <code>.vasp</code> files;</li> <li>if no <code>.vasp</code> file exists and one <code>.xyz</code> file exists, it converts that extxyz file to POSCAR files;</li> <li>if no <code>.vasp</code> file exists and multiple <code>.xyz</code> files exist, it asks you to choose one.</li> </ol> <p>Typical input directory before running:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>INCAR</code>, <code>POTCAR</code>, and <code>KPOINTS</code> in the generated <code>fp/</code> directory after the script creates it. The calculation folders link to files in <code>fp/</code>.</p> <p>The <code>prefix</code> you input during the workflow becomes the calculation folder prefix. When <code>out2xyz</code> is later used to extract results, the folder name is stored as <code>config_type</code> in the extxyz file, which makes it easier to trace where each structure came from.</p>"},{"location":"en/workflow_scripts.html#cp2k","title":"CP2K","text":"<p>CP2K SCF batch pretreatment is available from the workflow menu and can also be called directly:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>The interactive wrapper asks for:</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>Example:</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>The template should be configured to read coordinates from <code>pos.xyz</code>. A reference template is available at:</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>The script creates <code>&lt;prefix&gt;_&lt;index&gt;/</code> directories, writes <code>input.inp</code>, and writes <code>pos.xyz</code> for each structure.</p>"},{"location":"en/workflow_scripts.html#md-sampling-pretreatment","title":"MD Sampling Pretreatment","text":""},{"location":"en/workflow_scripts.html#gpumd","title":"GPUMD","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 302\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. The detection order is the same as the VASP SCF workflow: <code>.vasp</code> files are preferred; if multiple <code>.xyz</code> files are found without <code>.vasp</code>, the script asks you to choose one.</p> <p>Typical input directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>or:</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>After running, the script creates:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>nep.txt</code> and <code>run_*.in</code> files in the generated <code>md/</code> directory. The script links <code>run_1.in</code> to <code>sample_1/run.in</code>, <code>run_2.in</code> to <code>sample_2/run.in</code>, and so on.</p>"},{"location":"en/workflow_scripts.html#lammps","title":"LAMMPS","text":"<p>Interactive mode:</p> <pre><code>gpumdkit.sh\n# choose 3 -&gt; 303\n</code></pre> <p>Typical preparation: Before running, put <code>.vasp</code> files or one extxyz file in the current directory. <code>.vasp</code> files are preferred when both formats exist.</p> <p>After running, the script creates LAMMPS data files in <code>struct_md/</code>, sample folders, and an <code>md/</code> directory:</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>You must place <code>lmprun.in</code> and <code>nep.txt</code> in the generated <code>md/</code> directory.</p>"},{"location":"en/workflow_scripts.html#active-learning-style-workflow","title":"Active-Learning Style Workflow","text":"<p>A common NEP improvement loop is:</p> <ol> <li>run MD with the current <code>nep.txt</code>;</li> <li>collect <code>dump.xyz</code> or <code>active.xyz</code>;</li> <li>remove unphysical structures;</li> <li>select diverse or uncertain structures;</li> <li>run DFT single-point calculations;</li> <li>convert DFT results to extxyz;</li> <li>append new structures to <code>train.xyz</code>;</li> <li>retrain the NEP model.</li> </ol> <p>For the development active-learning script, see Active Learning.</p>"},{"location":"en/workflow_scripts.html#template-based-temperature-series","title":"Template-Based Temperature Series","text":"<p>For a simple temperature series, a shell loop is often enough:</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>Then submit the generated folders according to your local cluster system.</p>"},{"location":"en/workflow_scripts.html#practical-notes","title":"Practical Notes","text":"<ul> <li>Workflow scripts are cluster- and template-dependent. Always test with a small number of structures first.</li> <li>Keep template files (<code>INCAR</code>, <code>KPOINTS</code>, <code>POTCAR</code>, <code>run.in</code>, CP2K inputs) under version control if possible.</li> <li>Check generated folders before submitting a large batch.</li> <li>Use analyzers and sampling scripts before expensive DFT calculations.</li> </ul>"},{"location":"zh/index.html","title":"GPUMDkit \u6559\u7a0b","text":"\ud83d\udcda GPUMDkit \u6559\u7a0b <p>\u6b22\u8fce\u4f7f\u7528 GPUMDkit\uff0c\u8fd9\u662f\u4e00\u4e2a\u9762\u5411 GPUMD \u548c NEP \u7684\u547d\u4ee4\u884c\u5de5\u5177\u5305\u3002</p>"},{"location":"zh/index.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>GPUMDkit \u5e2e\u52a9\u4f60\u5728\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u7814\u7a76\u4e2d\u5b8c\u6210\u5e38\u89c1\u4efb\u52a1\uff0c\u65e0\u9700\u7f16\u5199\u81ea\u5b9a\u4e49\u811a\u672c\u3002\u5b83\u652f\u6301\u683c\u5f0f\u8f6c\u6362\u3001\u7ed3\u6784\u5206\u6790\u3001\u6027\u8d28\u8ba1\u7b97\u3001\u53ef\u89c6\u5316\u548c\u6279\u91cf\u5de5\u4f5c\u6d41\u2014\u2014\u5168\u90e8\u901a\u8fc7\u4e00\u4e2a\u547d\u4ee4\u884c\u5de5\u5177\u5b8c\u6210\u3002</p>"},{"location":"zh/index.html#_2","title":"\u5e38\u89c1\u4efb\u52a1","text":"\u6211\u60f3\u8981... \u6559\u7a0b \u5b89\u88c5 GPUMDkit \u5e76\u8fd0\u884c\u7b2c\u4e00\u4e2a\u547d\u4ee4 \u5feb\u901f\u5165\u95e8 \u5c06 VASP\u3001LAMMPS\u3001CP2K \u6216 CIF \u6587\u4ef6\u8f6c\u6362\u4e3a extxyz \u683c\u5f0f\u8f6c\u6362 \u68c0\u67e5\u7ed3\u6784\u8ddd\u79bb\u3001\u8fc7\u6ee4\u6570\u636e\u96c6\u6216\u67e5\u627e\u5f02\u5e38\u503c \u5206\u6790\u5de5\u5177 \u8ba1\u7b97 MSD\u3001\u79bb\u5b50\u7535\u5bfc\u7387\u6216\u63cf\u8ff0\u7b26 \u8ba1\u7b97\u5668\u811a\u672c \u5206\u6790\u6781\u6027\u6750\u6599\u3001\u94c1\u7535\u4f53\u6216 ABO3 \u4f53\u7cfb \u6781\u6027\u6750\u6599\u5206\u6790 \u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c\u6216\u70ed\u529b\u5b66\u6570\u636e \u7ed8\u56fe\u811a\u672c \u8fd0\u884c\u6279\u91cf DFT \u6216 MD \u6a21\u62df \u5de5\u4f5c\u6d41\u811a\u672c \u4ece\u6570\u636e\u96c6\u4e2d\u9009\u62e9\u4ee3\u8868\u6027\u7ed3\u6784 \u7ed3\u6784\u91c7\u6837 \u6dfb\u52a0\u81ea\u5df1\u7684 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u81ea\u5b9a\u4e49\u547d\u4ee4"},{"location":"zh/index.html#_3","title":"\u51c6\u5907\u5de5\u4f5c","text":""},{"location":"zh/index.html#_4","title":"\u5b89\u88c5","text":"<pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre>"},{"location":"zh/index.html#_5","title":"\u4f9d\u8d56","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\npip install neptrain dpdata calorine\n</code></pre>"},{"location":"zh/index.html#_6","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u6253\u5f00\u83dc\u5355\u540e\uff0c\u6309\u6570\u5b57\u9009\u62e9\u6a21\u5757\u3002</p>"},{"location":"zh/index.html#_7","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n</code></pre> <p>\u4f8b\u5982\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>\u4f7f\u7528 <code>gpumdkit.sh -h</code> \u67e5\u770b\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</p>"},{"location":"zh/index.html#_8","title":"\u6a21\u5757\u6982\u89c8","text":"\u6a21\u5757 \u83dc\u5355 CLI \u63cf\u8ff0 \u683c\u5f0f\u8f6c\u6362 1 <code>-out2xyz</code>, <code>-pos2exyz</code> \u6587\u4ef6\u8f6c\u6362 \u7ed3\u6784\u91c7\u6837 2 \u4ea4\u4e92\u83dc\u5355\u3001<code>-frame_range</code>\u3001<code>-pynep</code>\uff08\u5df2\u5f03\u7528\uff09 \u7ed3\u6784\u91c7\u6837 \u5de5\u4f5c\u6d41 3 - \u6279\u5904\u7406 \u8ba1\u7b97\u5668 4 <code>-calc &lt;\u7c7b\u578b&gt;</code> \u5c5e\u6027\u8ba1\u7b97 \u5206\u6790\u5de5\u5177 5 <code>-range</code>, <code>-min_dist</code> \u7ed3\u6784\u5206\u6790 \u53ef\u89c6\u5316 6 <code>-plt &lt;\u7c7b\u578b&gt;</code> \u7ed8\u56fe\u5de5\u5177 \u5b9e\u7528\u5de5\u5177 7 <code>-time</code>, <code>-clean</code> \u5b9e\u7528\u529f\u80fd"},{"location":"zh/index.html#_9","title":"\u5168\u90e8\u6559\u7a0b","text":"\u6559\u7a0b \u63cf\u8ff0 \u5feb\u901f\u5165\u95e8 \u5b89\u88c5\u548c\u7b2c\u4e00\u6b65 \u547d\u4ee4\u53c2\u8003 \u5e38\u7528 CLI \u548c\u83dc\u5355\u5165\u53e3\u901f\u67e5 \u683c\u5f0f\u8f6c\u6362 \u5728\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362 \u8ba1\u7b97\u5668\u811a\u672c \u8ba1\u7b97\u6750\u6599\u5c5e\u6027 \u5206\u6790\u5de5\u5177 \u7ed3\u6784\u5206\u6790\u548c\u9a8c\u8bc1 \u7ed8\u56fe\u811a\u672c \u7ed8\u56fe\u548c\u53ef\u89c6\u5316 \u5de5\u4f5c\u6d41\u811a\u672c \u6279\u5904\u7406\u548c\u81ea\u52a8\u5316 \u7ed3\u6784\u91c7\u6837 \u7ed3\u6784\u9009\u62e9\u65b9\u6cd5 \u81ea\u5b9a\u4e49\u547d\u4ee4 \u7528\u6237\u81ea\u5b9a\u4e49 GPUMDkit \u5feb\u6377\u547d\u4ee4 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 \u6279\u91cf\u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\u8bf4\u660e \u6781\u6027\u6750\u6599\u5206\u6790 \u94c1\u7535\u548c\u6781\u5316\u76f8\u5173\u5de5\u5177 \u8d21\u732e\u6307\u5357 \u5f00\u53d1\u548c\u8d21\u732e\u8bf4\u660e"},{"location":"zh/index.html#_10","title":"\u94fe\u63a5","text":"<ul> <li>GitHub: https://github.com/zhyan0603/GPUMDkit</li> <li>\u6587\u6863: https://zhyan0603.github.io/GPUMDkit/</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html","title":"\u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41","text":"\ud83d\udd01 \u4e3b\u52a8\u5b66\u4e60\u5de5\u4f5c\u6d41 <p><code>workflow_active_learning_dev.sh</code> \u7528\u4e8e\u7ec4\u7ec7\u4e00\u8f6e NEP \u4e3b\u52a8\u5b66\u4e60\u6d41\u7a0b\uff1a\u8fd0\u884c GPUMD \u5206\u5b50\u52a8\u529b\u5b66\u3001\u7b5b\u9009\u7ed3\u6784\u3001\u62bd\u6837\u3001\u63d0\u4ea4\u7b2c\u4e00\u6027\u539f\u7406\u8ba1\u7b97\uff0c\u5e76\u8fdb\u884c NEP \u9884\u6d4b\u68c0\u67e5\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#_1","title":"\u6982\u89c8","text":"<p>\u8be5\u811a\u672c\u81ea\u52a8\u5316\u4e86 NEP \u4e3b\u52a8\u5b66\u4e60\u7684\u4e00\u8f6e\u8fed\u4ee3\u3002\u5178\u578b\u6d41\u7a0b\u5305\u62ec\uff1a</p> \u6b65\u9aa4 \u64cd\u4f5c \u76ee\u7684 1 \u8fd0\u884c MD \u6a21\u62df \u4f7f\u7528\u5f53\u524d NEP \u6a21\u578b\u751f\u6210\u5019\u9009\u7ed3\u6784 2 \u8fc7\u6ee4\u7ed3\u6784 \u79fb\u9664\u4e0d\u5408\u7406\u7684\u6784\u578b\uff08\u77ed\u8ddd\u79bb\u3001\u5927\u76d2\u5b50\uff09 3 \u91c7\u6837\u7ed3\u6784 \u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\u8fdb\u884c DFT \u8ba1\u7b97 4 \u8fd0\u884c SCF \u8ba1\u7b97 \u8ba1\u7b97 DFT \u53c2\u8003\u80fd\u91cf/\u529b 5 NEP \u9884\u6d4b \u68c0\u67e5\u6a21\u578b\u5728\u65b0\u7ed3\u6784\u4e0a\u7684\u7cbe\u5ea6 <p>\u4e0e\u83dc\u5355\u9a71\u52a8\u7684\u6a21\u5757\u4e0d\u540c\uff0c\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u662f\u4e00\u4e2a\u9700\u8981\u6309\u4f53\u7cfb\u4fee\u6539\u540e\u76f4\u63a5\u8fd0\u884c\u7684 shell \u811a\u672c\uff1a</p> <pre><code>bash Scripts/workflow/workflow_active_learning_dev.sh\n</code></pre> <p>\u4e0b\u9762\u6309\u811a\u672c\u4e2d\u7684\u4e3b\u8981\u4ee3\u7801\u5757\u8bf4\u660e\u6bcf\u4e00\u6b65\u7684\u4f5c\u7528\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#1-slurm","title":"1. SLURM \u8bbe\u7f6e","text":"<p>\u811a\u672c\u5f00\u5934\u5305\u542b\u96c6\u7fa4\u63d0\u4ea4\u53c2\u6570\uff0c\u4f8b\u5982\uff1a</p> <pre><code>#!/bin/bash -l\n#SBATCH -p intel-sc3,intel-sc3-32c\n#SBATCH -q huge\n#SBATCH -N 1\n#SBATCH -J workflow\n#SBATCH -o workflow.log\n#SBATCH --ntasks-per-node=1\n</code></pre> <p>\u8fd9\u4e9b\u53c2\u6570\u9700\u8981\u6839\u636e\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u4fee\u6539\u3002\u5982\u679c\u6ca1\u6709 SLURM \u73af\u5883\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u540e\u53f0\u8fd0\u884c\uff1a</p> <pre><code>nohup bash workflow_active_learning_dev.sh &gt; workflow.log 2&gt;&amp;1 &amp;\n</code></pre>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#2","title":"2. \u57fa\u672c\u8bbe\u7f6e","text":"<p>\u811a\u672c\u4f1a\u8fdb\u5165\u63d0\u4ea4\u76ee\u5f55\uff0c\u5e76\u52a0\u8f7d\u63d0\u4ea4\u6a21\u677f\uff1a</p> <pre><code>cd $SLURM_SUBMIT_DIR\nsource ${GPUMDkit_path}/Scripts/workflow/submit_template.sh\npython_pynep=python\n</code></pre> <ul> <li><code>GPUMDkit_path</code> \u662f\u5b89\u88c5\u811a\u672c\u5199\u5165\u7684 GPUMDkit \u8def\u5f84\u3002</li> <li><code>python_pynep</code> \u4ec5\u7528\u4e8e\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#3","title":"3. \u4e3b\u8981\u53d8\u91cf","text":"<p>\u8fd9\u4e2a\u5de5\u4f5c\u6d41\u9002\u5408\u5df2\u7ecf\u6709\u521d\u59cb <code>nep.txt</code>\u3001<code>nep.in</code>\u3001<code>train.xyz</code> \u548c GPUMD/DFT \u8f93\u5165\u6587\u4ef6\uff0c\u5e76\u5e0c\u671b\u5728\u96c6\u7fa4\u4e0a\u81ea\u52a8\u6269\u5c55\u8bad\u7ec3\u96c6\u7684\u60c5\u51b5\u3002</p> <p>\u811a\u672c\u5f00\u5934\u901a\u5e38\u9700\u8981\u6839\u636e\u4f53\u7cfb\u4fee\u6539\uff1a</p> <pre><code>work_dir=${PWD}\nprefix_name=LiF_iter01\nmin_dist=1.4\nbox_limit=13\nmax_fp_num=50\nsample_method=pynep\npynep_sample_dist=0.01\n</code></pre> <ul> <li><code>prefix_name</code> \u7528\u4e8e\u547d\u540d\u672c\u8f6e\u8ba1\u7b97\u3002</li> <li><code>min_dist</code> \u548c <code>box_limit</code> \u7528\u4e8e\u8fc7\u6ee4\u660e\u663e\u4e0d\u5408\u7406\u7684\u7ed3\u6784\u3002</li> <li><code>max_fp_num</code> \u63a7\u5236\u6700\u591a\u63d0\u4ea4\u591a\u5c11\u4e2a\u5355\u70b9\u8ba1\u7b97\u3002</li> <li><code>sample_method</code> \u53ef\u9009 <code>uniform</code>\u3001<code>random</code> \u6216 <code>pynep</code>\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#4","title":"4. \u68c0\u67e5\u8f93\u5165\u6587\u4ef6","text":"<p>\u5e38\u89c1\u8f93\u5165\u5305\u62ec\uff1a</p> <ul> <li><code>nep.txt</code></li> <li><code>nep.in</code></li> <li><code>train.xyz</code></li> <li><code>run_*.in</code>\uff08\u5982 <code>run_1.in</code>\u3001<code>run_2.in</code> \u7b49\uff09</li> <li><code>INCAR</code></li> <li><code>POTCAR</code></li> <li><code>KPOINTS</code></li> <li>\u521d\u59cb\u91c7\u6837\u7ed3\u6784\u6587\u4ef6\uff0c\u4f8b\u5982 <code>sample_struct.xyz</code></li> </ul> <p>\u811a\u672c\u4f1a\u628a\u516c\u5171\u8f93\u5165\u79fb\u52a8\u5230 <code>common/</code>\uff0c\u5e76\u521b\u5efa <code>00.md/</code>\u3001<code>01.select/</code> \u7b49\u5de5\u4f5c\u76ee\u5f55\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#5","title":"5. \u6587\u4ef6\u7ec4\u7ec7","text":"<p>\u811a\u672c\u4f1a\u521b\u5efa\u516c\u5171\u8f93\u5165\u76ee\u5f55\u548c MD \u76ee\u5f55\uff1a</p> <pre><code>mkdir 00.md common\nmv ${work_dir}/{nep.txt,nep.in,*.xyz,run_*.in,INCAR,KPOINTS,POTCAR} ./common\ncp ${work_dir}/common/$sample_xyz_file ${work_dir}/00.md\n</code></pre> <ul> <li><code>00.md</code>\uff1a\u7528\u4e8e\u8fd0\u884c GPUMD MD \u91c7\u6837\u3002</li> <li><code>common</code>\uff1a\u4fdd\u5b58 <code>nep.txt</code>\u3001<code>run_*.in</code> \u6587\u4ef6\u3001\u7ed3\u6784\u6587\u4ef6\u548c DFT \u8f93\u5165\u6587\u4ef6\u7b49\u516c\u5171\u8d44\u6e90\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#6-md","title":"6. \u63d0\u4ea4 MD \u4efb\u52a1","text":"<pre><code>submit_gpumd_array md ${sample_struct_num}\nsbatch submit.slurm\n</code></pre> <p>\u811a\u672c\u4f1a\u901a\u8fc7\u63d0\u4ea4\u6a21\u677f\u521b\u5efa\u6570\u7ec4\u4efb\u52a1\u3002\u4e0d\u540c\u96c6\u7fa4\u4e0a\u7684\u63d0\u4ea4\u547d\u4ee4\u548c\u6a21\u677f\u53ef\u80fd\u9700\u8981\u81ea\u5df1\u4fee\u6539\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#7","title":"7. \u68c0\u67e5\u4efb\u52a1\u5b8c\u6210","text":"<p>\u811a\u672c\u4f1a\u6301\u7eed\u68c0\u67e5 <code>00.md/</code> \u4e0b\u5404\u4e2a <code>sample_*/log</code> \u6587\u4ef6\uff0c\u786e\u8ba4\u662f\u5426\u51fa\u73b0\uff1a</p> <pre><code>Finished running GPUMD.\n</code></pre> <p>\u5982\u679c\u53d1\u73b0 <code>Error</code>\uff0c\u811a\u672c\u4f1a\u505c\u6b62\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#8","title":"8. \u5206\u6790\u548c\u8fc7\u6ee4\u7ed3\u6784","text":"<p>MD \u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u8fdb\u5165 <code>01.select</code>\uff0c\u5bf9 <code>dump.xyz</code> \u4e2d\u7684\u7ed3\u6784\u8fdb\u884c\u7b5b\u9009\u3002\u5e38\u89c1\u68c0\u67e5\u5305\u62ec\uff1a</p> <ul> <li>\u6700\u5c0f\u539f\u5b50\u8ddd\u79bb\uff1b</li> <li>\u6a21\u62df\u76d2\u5b50\u8fb9\u957f\uff1b</li> <li>\u7ed3\u6784\u6570\u91cf\u662f\u5426\u8d85\u8fc7 <code>max_fp_num</code>\u3002</li> </ul> <p>\u8fd9\u4e9b\u6b65\u9aa4\u4f1a\u8c03\u7528 analyzer \u548c sample_structures \u4e2d\u7684\u811a\u672c\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#9","title":"9. \u62bd\u6837\u65b9\u6cd5","text":"<p>\u811a\u672c\u6839\u636e <code>sample_method</code> \u9009\u62e9\u62bd\u6837\u65b9\u5f0f\uff1a</p> <pre><code>case $sample_method in\n    \"uniform\")\n    \"random\")\n    \"pynep\")\n</code></pre> <ul> <li><code>uniform</code>\uff1a\u5747\u5300\u62bd\u5e27\uff1b</li> <li><code>random</code>\uff1a\u968f\u673a\u62bd\u5e27\uff1b</li> <li><code>pynep</code>\uff1a\u65e7\u7684 PyNEP \u517c\u5bb9\u5206\u652f\u3002</li> </ul>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#10-scf","title":"10. \u63d0\u4ea4 SCF \u8ba1\u7b97","text":"<p>\u62bd\u6837\u5b8c\u6210\u540e\uff0c\u811a\u672c\u4f1a\u63d0\u4ea4 VASP \u5355\u70b9\u8ba1\u7b97\uff1a</p> <pre><code>submit_vasp_array scf ${selected_struct_num} ${prefix_name}\n</code></pre> <p>\u8fd9\u91cc\u7684 <code>prefix_name</code> \u4f1a\u7528\u4e8e\u8ba1\u7b97\u76ee\u5f55\u547d\u540d\uff0c\u4e5f\u65b9\u4fbf\u540e\u7eed\u8ffd\u8e2a\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html#11-prediction","title":"11. Prediction \u6b65\u9aa4","text":"<p>\u6700\u540e\u811a\u672c\u4f1a\u63d0\u4ea4 NEP prediction\uff0c\u7528\u4e8e\u68c0\u67e5\u5f53\u524d\u6a21\u578b\u5728\u65b0\u589e\u7ed3\u6784\u4e0a\u7684\u8bef\u5dee\u3002</p> <p>\u8fd9\u4e2a\u811a\u672c\u548c\u8ba1\u7b97\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u4f7f\u7528\u524d\u5efa\u8bae\u5148\u7528\u5c0f\u4f53\u7cfb\u6216\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u4e00\u8f6e\uff0c\u5e76\u68c0\u67e5\u63d0\u4ea4\u6a21\u677f\u3001\u8def\u5f84\u548c\u8f93\u5165\u6587\u4ef6\u662f\u5426\u7b26\u5408\u81ea\u5df1\u7684\u96c6\u7fa4\u73af\u5883\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html","title":"\u5206\u6790\u5de5\u5177","text":"\ud83d\udd0d \u5206\u6790\u5de5\u5177 <p>\u5206\u6790\u811a\u672c\u4e3a extxyz \u6570\u636e\u96c6\u63d0\u4f9b\u7ed3\u6784\u7edf\u8ba1\u3001\u8ddd\u79bb\u68c0\u67e5\u3001\u8fc7\u6ee4\u3001\u6210\u5206\u5206\u6790\u3001\u5f02\u5e38\u68c0\u6d4b\u548c\u65f6\u95f4\u4f30\u7b97\u529f\u80fd\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>\u672c\u6a21\u5757\u5e2e\u52a9\u4f60\u68c0\u67e5\u3001\u8fc7\u6ee4\u548c\u9a8c\u8bc1\u7ed3\u6784\u6570\u636e\u96c6\u3002\u53ef\u4ee5\u68c0\u67e5\u6210\u5206\u3001\u5206\u6790\u6027\u8d28\u8303\u56f4\u3001\u68c0\u6d4b\u77ed\u8ddd\u79bb\u63a5\u89e6\u3001\u6309\u5404\u79cd\u6761\u4ef6\u8fc7\u6ee4\u7ed3\u6784\u3001\u67e5\u627e NEP \u8bad\u7ec3\u6570\u636e\u4e2d\u7684\u5f02\u5e38\u503c\uff0c\u4ee5\u53ca\u4f30\u7b97\u5269\u4f59\u6a21\u62df\u65f6\u95f4\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":"<p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/analyzer/</code></p> <p>\u786e\u4fdd\u5df2\u5b89\u88c5 GPUMDkit\u3002\u5b89\u88c5\u8bf4\u660e\u8bf7\u53c2\u89c1\u5feb\u901f\u5165\u95e8\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_3","title":"\u6982\u89c8","text":"\u4efb\u52a1 \u547d\u4ee4 \u7528\u9014 \u6210\u5206\u5206\u6790 <code>gpumdkit.sh -analyze_comp train.xyz</code> \u6309\u5316\u5b66\u6210\u5206\u5206\u7ec4 \u5316\u5b66\u7269\u79cd <code>gpumdkit.sh -chem_species train.xyz</code> \u5217\u51fa\u6587\u4ef6\u4e2d\u7684\u5143\u7d20 \u6027\u8d28\u8303\u56f4 <code>gpumdkit.sh -range train.xyz force</code> \u68c0\u67e5\u80fd\u91cf/\u529b/virial \u8303\u56f4 \u6700\u77ed\u8ddd\u79bb <code>gpumdkit.sh -min_dist dump.xyz</code> \u5feb\u901f\u8ddd\u79bb\u68c0\u67e5\uff08\u65e0 PBC\uff09 \u6700\u77ed\u8ddd\u79bb\uff08PBC\uff09 <code>gpumdkit.sh -min_dist_pbc dump.xyz</code> \u51c6\u786e\u8ddd\u79bb\u68c0\u67e5\uff08\u542b PBC\uff09 \u7535\u8377\u5e73\u8861 <code>gpumdkit.sh -cbc train.xyz</code> \u6c27\u5316\u6001\u5e73\u8861\u68c0\u67e5 \u8ddd\u79bb\u8fc7\u6ee4 <code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0</code> \u79fb\u9664\u77ed\u8ddd\u79bb\u63a5\u89e6\u7684\u7ed3\u6784 \u76d2\u5b50\u8fc7\u6ee4 <code>gpumdkit.sh -filter_box dump.xyz 13</code> \u79fb\u9664\u76d2\u5b50\u8fc7\u5927\u7684\u7ed3\u6784 \u6027\u8d28\u8fc7\u6ee4 <code>gpumdkit.sh -filter_value train.xyz force 20</code> \u6309\u80fd\u91cf/\u529b/virial \u9608\u503c\u8fc7\u6ee4 \u5bf9\u8ddd\u79bb\u8303\u56f4 <code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0</code> \u6309\u5bf9\u8ddd\u79bb\u63d0\u53d6\u7ed3\u6784 \u5f02\u5e38\u68c0\u6d4b \u83dc\u5355 502 \u67e5\u627e\u8bad\u7ec3\u96c6\u4e2d\u9ad8 RMSE \u7684\u7ed3\u6784 \u6982\u7387\u5bc6\u5ea6 <code>gpumdkit.sh -pda &lt;\u53c2\u8003\u7ed3\u6784&gt; &lt;\u8f68\u8ff9&gt; &lt;\u5143\u7d20&gt; &lt;\u7f51\u683c\u95f4\u8ddd&gt;</code> 3D \u6982\u7387\u5bc6\u5ea6\u5206\u6790\u6269\u6563\u901a\u9053 GPUMD \u65f6\u95f4 <code>gpumdkit.sh -time gpumd</code> \u4f30\u7b97 GPUMD \u5269\u4f59\u8fd0\u884c\u65f6\u95f4 NEP \u65f6\u95f4 <code>gpumdkit.sh -time nep</code> \u4f30\u7b97 NEP \u5269\u4f59\u8bad\u7ec3\u65f6\u95f4"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_4","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit \u5e76\u9009\u62e9 <code>5) Analyzer</code>\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u5206\u6790\u5de5\u5177\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                    ANALYZER TOOLS                    |\n+------------------------------------------------------+\n| 501) Analyze composition of extxyz                   |\n| 502) Find outliers of extxyz                         |\n| 503) Analyze chemical species of extxyz              |\n| 504) Check charge balance of extxyz                  |\n| 505) Analyze energy/force/virial range               |\n| 506) Filter structures by minimum distance           |\n| 507) Get minimum interatomic distance                |\n| 508) Probability density analysis                    |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5927\u591a\u6570\u5206\u6790\u529f\u80fd\u4e5f\u63d0\u4f9b\u76f4\u63a5 CLI \u8c03\u7528\u65b9\u5f0f\uff0c\u6982\u89c8\u8868\u548c\u540e\u7eed\u5c0f\u8282\u4e2d\u5217\u51fa\u4e86\u5e38\u7528\u547d\u4ee4\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_5","title":"\u6210\u5206\u5206\u6790","text":"<p><code>analyze_composition.py</code> \u5206\u6790 extxyz \u6587\u4ef6\u7684\u6210\u5206\uff0c\u5e76\u5141\u8bb8\u5bfc\u51fa\u5b50\u96c6\u3002</p> <p>\u529f\u80fd\uff1a \u6309\u5316\u5b66\u6210\u5206\u5bf9\u7ed3\u6784\u5206\u7ec4\uff0c\u5e76\u663e\u793a\u6bcf\u79cd\u6210\u5206\u7684\u7ed3\u6784\u6570\u91cf\u3002\u53ef\u4ee5\u6309\u6210\u5206\u5bfc\u51fa\u5b50\u96c6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -analyze_comp train.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>501</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Index    Compositions           N atoms      Count\n---------------------------------------------------\n1        Li56O96Zr16La24        192          51\n---------------------------------------------------\nEnter index to export (e.g., '1,2', '2-3', 'all'), or press Enter to skip:\n</code></pre> <p>\u5f53 <code>train.xyz</code> \u5305\u542b\u4e0d\u540c\u4f53\u7cfb\u6216\u4e0d\u540c\u5c3a\u5bf8\u7684\u7ed3\u6784\u65f6\u5f88\u6709\u7528\u3002\u53ef\u4ee5\u4ece\u4ea4\u4e92\u63d0\u793a\u4e2d\u6309\u6210\u5206\u5bfc\u51fa\u5b50\u96c6\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_6","title":"\u5316\u5b66\u7269\u79cd","text":"<p><code>analyze_chem_species.py</code> \u5217\u51fa extxyz \u6587\u4ef6\u4e2d\u6240\u6709\u552f\u4e00\u7684\u5316\u5b66\u7269\u79cd\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -chem_species train.xyz\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_7","title":"\u6027\u8d28\u8303\u56f4\u5206\u6790","text":"<p><code>energy_force_virial_analyzer.py</code> \u8ba1\u7b97\u5e76\u53ef\u89c6\u5316 extxyz \u6587\u4ef6\u4e2d\u6027\u8d28\u7684\u8303\u56f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <p>\u652f\u6301\u7684\u6027\u8d28\uff1a <code>energy</code>\u3001<code>force</code>\u3001<code>virial</code></p> <pre><code>gpumdkit.sh -range train.xyz force\ngpumdkit.sh -range train.xyz energy\ngpumdkit.sh -range train.xyz virial\ngpumdkit.sh -range train.xyz force hist    # \u663e\u793a\u76f4\u65b9\u56fe\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Force range: 0.03210566767721861 to 9.230115912468435\n</code></pre> <p>\u4f7f\u7528 <code>hist</code> \u9009\u9879\uff1a</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_8","title":"\u6700\u77ed\u8ddd\u79bb\u68c0\u67e5","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#pbc","title":"\u65e0 PBC\uff08\u5feb\u901f\uff09","text":"<p><code>get_min_dist.py</code> \u8ba1\u7b97\u4e0d\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u7684\u6700\u77ed\u539f\u5b50\u95f4\u8ddd\u3002\u901f\u5ea6\u5feb\uff0c\u4f46\u5bf9\u5468\u671f\u6027\u4f53\u7cfb\u53ef\u80fd\u4e0d\u51c6\u786e\u3002</p> <p>\u529f\u80fd\uff1a \u62a5\u544a\u6bcf\u5e27\u4e2d\u6bcf\u5bf9\u5143\u7d20\u4e4b\u95f4\u7684\u6700\u77ed\u8ddd\u79bb\uff0c\u5ffd\u7565\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -min_dist dump.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>507</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>+---------------------------+\n|   PBC ignored for speed   |\n| use -min_dist_pbc for PBC |\n+---------------------------+\nMinimum interatomic distances:\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.480     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre> <p>\u8bf4\u660e\uff1a \u7528\u4e8e\u5feb\u901f\u68c0\u67e5\u3002\u5bf9\u4e8e\u5468\u671f\u6027\u4f53\u7cfb\uff0c\u5efa\u8bae\u4f7f\u7528 <code>-min_dist_pbc</code> \u83b7\u5f97\u51c6\u786e\u7ed3\u679c\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#pbc_1","title":"\u542b PBC\uff08\u51c6\u786e\uff09","text":"<p><code>get_min_dist_pbc.py</code> \u8ba1\u7b97\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u7684\u6700\u77ed\u539f\u5b50\u95f4\u8ddd\u3002</p> <p>\u529f\u80fd\uff1a \u62a5\u544a\u6bcf\u5bf9\u5143\u7d20\u4e4b\u95f4\u7684\u6700\u77ed\u8ddd\u79bb\uff0c\u8003\u8651\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u5206\u6790\u5de5\u5177\u83dc\u5355\u4e2d\u9009\u62e9 <code>507</code>\uff0c\u5f53\u63d0\u793a\u662f\u5426\u8003\u8651 PBC \u65f6\u8f93\u5165 <code>y</code>\u3002</p> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Minimum interatomic distances (with PBC):\n+---------------------------+\n| Atom Pair |  Distance (\u00c5) |\n+---------------------------+\n|   Li-Li   |     1.696     |\n|   Li-O    |     1.587     |\n|   O-O     |     2.355     |\n+---------------------------+\nOverall min_distance: 1.587 \u00c5\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_9","title":"\u7ed3\u6784\u8fc7\u6ee4","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_10","title":"\u6309\u6700\u77ed\u8ddd\u79bb\u8fc7\u6ee4","text":"<p><code>filter_structures_by_distance_pbc.py</code> \u79fb\u9664\u4efb\u4f55\u539f\u5b50\u95f4\u8ddd\u4f4e\u4e8e\u9608\u503c\u7684\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n</code></pre> <p>\u79fb\u9664\u4efb\u4f55\u539f\u5b50\u95f4\u8ddd\u4f4e\u4e8e <code>1.0 \u00c5</code> \u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_11","title":"\u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4","text":"<p><code>filter_exyz_by_box.py</code> \u6309\u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_box dump.xyz 13\n</code></pre> <p>\u4fdd\u7559\u6240\u6709\u76d2\u5b50\u8fb9\u957f\u4f4e\u4e8e <code>13 \u00c5</code> \u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_12","title":"\u6309\u6027\u8d28\u503c\u8fc7\u6ee4","text":"<p><code>filter_exyz_by_value.py</code> \u6309\u80fd\u91cf\u3001\u529b\u6216 virial \u9608\u503c\u8fc7\u6ee4\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <p>\u652f\u6301\u7684\u6027\u8d28\uff1a <code>energy</code>\u3001<code>force</code>\u3001<code>virial</code></p> <pre><code>gpumdkit.sh -filter_value train.xyz force 20\ngpumdkit.sh -filter_value train.xyz energy 5\n</code></pre> <p>\u8fc7\u6ee4\u6389\u529b\u5206\u91cf\u8d85\u8fc7 <code>20 eV/\u00c5</code>\uff08\u6216\u80fd\u91cf\u8d85\u8fc7 <code>5 eV/atom</code>\uff09\u7684\u7ed3\u6784\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_13","title":"\u6309\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4","text":"<p><code>filter_dist_range.py</code> \u63d0\u53d6\u7279\u5b9a\u5143\u7d20\u5bf9\u8ddd\u79bb\u5728\u7ed9\u5b9a\u8303\u56f4\u5185\u7684\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>dump.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -filter_range dump.xyz Li Li 1.8 2.0\n</code></pre> <p>\u63d0\u53d6 Li-Li \u6700\u77ed\u8ddd\u79bb\u5728 <code>1.8 \u00c5</code> \u5230 <code>2.0 \u00c5</code> \u4e4b\u95f4\u7684\u7ed3\u6784\u3002\u8f93\u51fa\uff1a<code>filtered_Li_Li_1.8_2.0.xyz</code>\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_14","title":"\u7535\u8377\u5e73\u8861\u68c0\u67e5","text":"<p><code>charge_balance_check.py</code> \u68c0\u67e5\u7ed3\u6784\u7684\u6c27\u5316\u6001\u5e73\u8861\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -cbc train.xyz\n</code></pre> <p>\u8f93\u51fa\u6587\u4ef6\uff1a</p> <ul> <li><code>balanced.xyz</code> \u2014 \u7535\u8377\u5e73\u8861\u7684\u7ed3\u6784</li> <li><code>unbalanced.xyz</code> \u2014 \u7535\u8377\u4e0d\u5e73\u8861\u7684\u7ed3\u6784</li> <li><code>indices.txt</code> \u2014 \u5e73\u8861\u7ed3\u6784\u7684\u7d22\u5f15</li> </ul> <p>\u9002\u7528\u4e8e\u5177\u6709\u660e\u786e\u6c27\u5316\u6001\u7684\u4f53\u7cfb\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_15","title":"\u5f02\u5e38\u68c0\u6d4b","text":"<p><code>find_outliers.py</code> \u57fa\u4e8e\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u7684 RMSE \u9608\u503c\u67e5\u627e NEP \u8bad\u7ec3\u6570\u636e\u4e2d\u7684\u5f02\u5e38\u7ed3\u6784\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>stress_train.out</code>\u3001<code>train.xyz</code></p> <p>\u8fd9\u4e9b\u6587\u4ef6\u5728 NEP \u8bad\u7ec3\u8fc7\u7a0b\u4e2d\u751f\u6210\u3002\u811a\u672c\u6bd4\u8f83 DFT \u4e0e NEP \u7684\u9884\u6d4b\uff0c\u8bc6\u522b\u8bef\u5dee\u8f83\u5927\u7684\u7ed3\u6784\u3002</p> <pre><code># \u4ea4\u4e92\u6a21\u5f0f\ngpumdkit.sh    # \u9009\u62e9\uff1a5) \u5206\u6790\u5de5\u5177 \u2192 502) \u67e5\u627e\u5f02\u5e38\u7ed3\u6784\n</code></pre> <p>\u4ea4\u4e92\u63d0\u793a\uff1a</p> <pre><code>Enter energy RMSE threshold (meV/atom): 1\nEnter force RMSE threshold (meV/\u00c5): 60\nEnter stress RMSE threshold (GPa): 0.03\n</code></pre> <p>\u8f93\u51fa\u6587\u4ef6\uff1a</p> <ul> <li><code>selected.xyz</code> \u2014 \u8d85\u8fc7 RMSE \u9608\u503c\u7684\u7ed3\u6784\uff08\u5f02\u5e38\u503c\uff09</li> <li><code>remained.xyz</code> \u2014 \u5728\u9608\u503c\u5185\u7684\u7ed3\u6784</li> <li><code>selected_remained.png</code> \u2014 \u5bf9\u6bd4\u56fe</li> </ul> <p>\u7528\u9014\uff1a NEP \u8bad\u7ec3\u540e\uff0c\u7528\u6b64\u5de5\u5177\u8bc6\u522b\u5bf9\u8bef\u5dee\u8d21\u732e\u6700\u5927\u7684\u95ee\u9898\u7ed3\u6784\u3002\u79fb\u9664\u6216\u6539\u8fdb\u8fd9\u4e9b\u7ed3\u6784\u4ee5\u63d0\u5347\u8bad\u7ec3\u96c6\u8d28\u91cf\u3002</p>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_16","title":"\u65f6\u95f4\u4f30\u7b97","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#gpumd","title":"GPUMD \u5269\u4f59\u65f6\u95f4","text":"<p><code>time_consuming_gpumd.sh</code> \u4f30\u7b97 GPUMD \u6a21\u62df\u7684\u5269\u4f59\u65f6\u95f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>run.in</code>\u3001<code>thermo.out</code>\uff08\u5728\u5f53\u524d GPUMD \u5de5\u4f5c\u76ee\u5f55\u4e2d\uff09</p> <pre><code>gpumdkit.sh -time gpumd\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>----------------- System Information ----------------\ntotal frames: 1050000\n-----------------------------------------------------\nCurrent Frame  Speed (steps/s)   Total Time       Time Left       Estimated End\n-------------   -------------   -------------   -------------   -----------------\n    13000          499.86         0h 35m 0s      0h 34m 34s    2025-12-27 18:12:04\n    14000          199.93        1h 27m 31s      1h 26m 21s    2025-12-27 19:03:56\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#nep","title":"NEP \u5269\u4f59\u65f6\u95f4","text":"<p><code>time_consuming_nep.sh</code> \u4f30\u7b97 NEP \u8bad\u7ec3\u7684\u5269\u4f59\u65f6\u95f4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code>\uff08\u5728\u5f53\u524d NEP \u5de5\u4f5c\u76ee\u5f55\u4e2d\uff09</p> <pre><code>gpumdkit.sh -time nep\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>+-----------------+-----------+-----------------+---------------------+\n|       Step      | Time Diff |    Time Left    |    Finish Time      |\n+-----------------+-----------+-----------------+---------------------+\n| 6700            | 1 s       | 0 h 15 m 33 s   | 2025-10-23 15:34:11 |\n| 6800            | 2 s       | 0 h 31 m 4 s    | 2025-10-23 15:49:44 |\n| 6900            | 2 s       | 0 h 31 m 2 s    | 2025-10-23 15:49:44 |\n+-----------------+-----------+-----------------+---------------------+\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_17","title":"\u6982\u7387\u5bc6\u5ea6\u5206\u6790","text":"<p><code>probability_density_analysis.py</code> \u8ba1\u7b97\u79fb\u52a8\u79bb\u5b50\u7684 3D \u6982\u7387\u5bc6\u5ea6\uff0c\u7528\u4e8e\u6269\u6563\u901a\u9053\u5206\u6790\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a \u53c2\u8003\u7ed3\u6784\uff08POSCAR\uff09\u3001\u8f68\u8ff9\u6587\u4ef6\uff08extxyz\uff09</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n</code></pre> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>LLZO.vasp</code> \u53c2\u8003\u7ed3\u6784\uff08POSCAR \u683c\u5f0f\uff09 <code>dump.xyz</code> \u8f68\u8ff9\u6587\u4ef6\uff08extxyz \u683c\u5f0f\uff09 <code>Li</code> \u76ee\u6807\u79fb\u52a8\u79bb\u5b50 <code>0.25</code> \u6982\u7387\u5bc6\u5ea6\u7f51\u683c\u95f4\u8ddd\uff08\u00c5\uff09 <p>\u8f93\u51fa\uff1a <code>probability_density_0.25.vasp</code> \u2014 VASP \u683c\u5f0f\u7684\u6982\u7387\u5bc6\u5ea6\u7f51\u683c\uff0c\u53ef\u7528 VESTA \u7b49\u5de5\u5177\u53ef\u89c6\u5316\u3002</p> <p>\u53ef\u89c6\u5316\u5efa\u8bae\uff1a</p> <ol> <li>\u5728 VESTA \u4e2d\u6253\u5f00 <code>probability_density_0.25.vasp</code></li> <li>\u4f7f\u7528 \"Edit \u2192 Data \u2192 Volumetric Data\" \u8c03\u6574\u7b49\u503c\u9762\u7ea7\u522b</li> <li>\u6309\u6570\u503c\u5bf9\u6982\u7387\u5bc6\u5ea6\u7740\u8272\uff0c\u4ee5\u7a81\u51fa\u4f18\u9009\u6269\u6563\u8def\u5f84</li> <li>\u53e0\u52a0\u6676\u4f53\u7ed3\u6784\u4f5c\u4e3a\u53c2\u8003</li> </ol>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_18","title":"\u793a\u4f8b\u5de5\u4f5c\u6d41","text":""},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_19","title":"\u7ed3\u6784\u8d28\u91cf\u68c0\u67e5","text":"<pre><code># 1. \u68c0\u67e5\u6210\u5206\ngpumdkit.sh -analyze_comp train.xyz\n\n# 2. \u68c0\u67e5\u80fd\u91cf/\u529b\u8303\u56f4\ngpumdkit.sh -range train.xyz force hist\n\n# 3. \u68c0\u67e5\u6700\u77ed\u8ddd\u79bb\ngpumdkit.sh -min_dist_pbc train.xyz\n\n# 4. \u67e5\u627e\u5f02\u5e38\u503c\uff08NEP \u8bad\u7ec3\u540e\uff09\n# \u4ea4\u4e92\uff1a5) \u5206\u6790\u5de5\u5177 \u2192 502\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_20","title":"\u7ed3\u6784\u8fc7\u6ee4\u6d41\u6c34\u7ebf","text":"<pre><code># 1. \u6309\u6700\u77ed\u8ddd\u79bb\u8fc7\u6ee4\ngpumdkit.sh -filter_dist_pbc dump.xyz 1.0\n\n# 2. \u6309\u76d2\u5b50\u5927\u5c0f\u8fc7\u6ee4\ngpumdkit.sh -filter_box filtered_dist_pbc.xyz 13\n\n# 3. \u6309\u529b\u9608\u503c\u8fc7\u6ee4\ngpumdkit.sh -filter_value filtered_box.xyz force 20\n</code></pre>"},{"location":"zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html#_21","title":"\u6269\u6563\u901a\u9053\u5206\u6790","text":"<pre><code># 1. \u8ba1\u7b97\u6982\u7387\u5bc6\u5ea6\ngpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25\n\n# 2. \u7528 VESTA \u53ef\u89c6\u5316\n# \u6253\u5f00 probability_density_0.25.vasp\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html","title":"\u547d\u4ee4\u53c2\u8003","text":"\ud83d\udccb \u547d\u4ee4\u53c2\u8003 <p>\u672c\u9875\u5217\u51fa GPUMDkit \u7a33\u5b9a\u7684\u547d\u4ee4\u884c\u5feb\u6377\u5165\u53e3\u3002\u5bf9\u4e8e\u53c2\u6570\u8f83\u591a\u3001\u9700\u8981\u9009\u62e9\u7684\u4efb\u52a1\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528\u4ea4\u4e92\u6a21\u5f0f\u3002</p> <p>\u6e90\u8868\u7ef4\u62a4\u5728 <code>docs/command_reference.tsv</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#gpumdkitsh-h","title":"<code>gpumdkit.sh -h</code> \u8f93\u51fa","text":"<pre><code>+-------------------------------------------------------------------------------------------------------+\n|                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |\n+-------------------------------------------------------------------------------------------------------+\n|                                          MAIN FUNCTIONS                                               |\n+-------------------------------------------------------------------------------------------------------+\n| -h            Show this help table            | -plt &lt;type&gt;        Plot and visualization tools       |\n| -calc &lt;type&gt;  Calculator tools                | -time &lt;gpumd|nep&gt;  Time-consuming analyzer            |\n| -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |\n+-------------------------------------------------------------------------------------------------------+\n|                                         FORMAT CONVERSION                                             |\n+-------------------------------------------------------------------------------------------------------+\n| -out2xyz      OUTCAR -&gt; extxyz (shell)        | -out2exyz          OUTCAR -&gt; extxyz (python)          |\n| -cp2k2xyz     CP2K log -&gt; xyz                 | -xdat2exyz         XDATCAR -&gt; extxyz                  |\n| -cif2pos      cif -&gt; POSCAR                   | -cif2exyz          cif -&gt; extxyz                      |\n| -pos2exyz     POSCAR -&gt; extxyz                | -exyz2pos          extxyz -&gt; POSCAR                   |\n| -pos2lmp      POSCAR -&gt; LAMMPS data           | -lmp2exyz          LAMMPS dump -&gt; extxyz              |\n| -traj2exyz    ASE traj -&gt; extxyz              | -replicate         Replicate structure                |\n| -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |\n| -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |\n| -frame_range  Extract frames by range         |                                                       |\n+-------------------------------------------------------------------------------------------------------+\n|                                            ANALYSIS                                                   |\n+-------------------------------------------------------------------------------------------------------+\n| -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |\n| -chem_species Analyze chemical species        | -cbc               Charge balance check               |\n| -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |\n| -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |\n| -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |\n| -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |\n+-------------------------------------------------------------------------------------------------------+\n| Detailed usage: gpumdkit.sh -&lt;option&gt; -h    Plot details: gpumdkit.sh -plt &lt;type&gt; -h                  |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_1","title":"\u4e3b\u547d\u4ee4","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-h</code> <code>gpumdkit.sh -h</code> \u663e\u793a\u901a\u7528\u5e2e\u52a9 <code>-update</code> <code>gpumdkit.sh -update</code> \u66f4\u65b0 GPUMDkit <code>-clean</code> <code>gpumdkit.sh -clean</code> \u6e05\u7406\u5f53\u524d\u76ee\u5f55\u4e2d\u7684\u5197\u4f59\u6587\u4ef6"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_2","title":"\u683c\u5f0f\u8f6c\u6362","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-out2xyz</code> <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c <code>-out2exyz</code> <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c <code>-cp2k2xyz</code> <code>gpumdkit.sh -cp2k2xyz</code> CP2K \u8f93\u51fa\u8f6c xyz/extxyz <code>-xdat2exyz</code> <code>gpumdkit.sh -xdat2exyz &lt;XDATCAR&gt; &lt;output.xyz&gt;</code> XDATCAR \u8f6c extxyz <code>-cif2pos</code> <code>gpumdkit.sh -cif2pos &lt;input.cif&gt; &lt;output.vasp&gt;</code> CIF \u8f6c POSCAR/VASP <code>-cif2exyz</code> <code>gpumdkit.sh -cif2exyz &lt;input.cif&gt; &lt;output.xyz&gt;</code> CIF \u8f6c extxyz <code>-pos2exyz</code> <code>gpumdkit.sh -pos2exyz &lt;POSCAR&gt; &lt;output.xyz&gt;</code> POSCAR \u8f6c extxyz <code>-exyz2pos</code> <code>gpumdkit.sh -exyz2pos &lt;input.xyz&gt;</code> extxyz \u591a\u5e27\u8f6c POSCAR \u6587\u4ef6 <code>-pos2lmp</code> <code>gpumdkit.sh -pos2lmp &lt;POSCAR&gt; &lt;output.data&gt;</code> POSCAR \u8f6c LAMMPS data <code>-lmp2exyz</code> <code>gpumdkit.sh -lmp2exyz &lt;dump&gt; &lt;element...&gt;</code> LAMMPS dump \u8f6c extxyz <code>-traj2exyz</code> <code>gpumdkit.sh -traj2exyz &lt;input.traj&gt; &lt;output.xyz&gt;</code> ASE trajectory \u8f6c extxyz <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; a b c</code> \u6309\u6676\u80de\u500d\u6570\u6269\u80de <code>-replicate</code> <code>gpumdkit.sh -replicate &lt;input&gt; &lt;output&gt; &lt;target_num&gt;</code> \u6309\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>-addgroup</code> <code>gpumdkit.sh -addgroup &lt;POSCAR&gt; &lt;element...&gt;</code> \u6dfb\u52a0 GPUMD group \u6807\u7b7e <code>-addweight</code> <code>gpumdkit.sh -addweight &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;weight&gt;</code> \u6dfb\u52a0\u7ed3\u6784\u6743\u91cd <code>-get_frame</code> <code>gpumdkit.sh -get_frame &lt;input.xyz&gt; &lt;frame_index&gt;</code> \u63d0\u53d6\u5355\u5e27 <code>-clean_xyz</code> <code>gpumdkit.sh -clean_xyz &lt;input.xyz&gt; &lt;output.xyz&gt;</code> \u6e05\u7406 extxyz \u5197\u4f59\u5c5e\u6027 <code>-frame_range</code> <code>gpumdkit.sh -frame_range &lt;input.xyz&gt; &lt;start_frac&gt; &lt;end_frac&gt;</code> \u6309\u6bd4\u4f8b\u8303\u56f4\u63d0\u53d6\u5e27"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_3","title":"\u8ba1\u7b97\u5668","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-calc ionic-cond</code> <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> \u79bb\u5b50\u7535\u5bfc\u7387 <code>-calc nep</code> <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> NEP \u6027\u8d28\u9884\u6d4b <code>-calc des</code> <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> NEP \u63cf\u8ff0\u7b26 <code>-calc doas</code> <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>-calc neb</code> <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u57fa\u4e8e NEP \u7684 NEB <code>-calc minimize</code> <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784\u4f18\u5316 <code>-calc msd</code> <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [max_corr_steps]</code> \u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD <code>-calc nlist</code> <code>gpumdkit.sh -calc nlist [args...]</code> \u90bb\u5c45\u5217\u8868 <code>-calc disp</code> <code>gpumdkit.sh -calc disp [args...]</code> \u4f4d\u79fb <code>-calc avg-struct</code> <code>gpumdkit.sh -calc avg-struct [args...]</code> \u5e73\u5747\u7ed3\u6784 <code>-calc oct-tilt</code> <code>gpumdkit.sh -calc oct-tilt [args...]</code> \u516b\u9762\u4f53\u503e\u659c <code>-calc pol-abo3</code> <code>gpumdkit.sh -calc pol-abo3 [args...]</code> ABO3 \u5c40\u57df\u6781\u5316"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_4","title":"\u5206\u6790\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-range</code> <code>gpumdkit.sh -range &lt;input.xyz&gt; &lt;energy\\|force\\|virial&gt; [hist]</code> \u6027\u8d28\u8303\u56f4\u5206\u6790 <code>-analyze_comp</code> <code>gpumdkit.sh -analyze_comp &lt;input.xyz&gt;</code> \u6210\u5206\u5206\u6790 <code>-chem_species</code> <code>gpumdkit.sh -chem_species &lt;input.xyz&gt;</code> \u5143\u7d20\u5217\u8868 <code>-cbc</code> <code>gpumdkit.sh -cbc &lt;input.xyz&gt;</code> \u7535\u8377\u5e73\u8861\u68c0\u67e5 <code>-min_dist</code> <code>gpumdkit.sh -min_dist &lt;input.xyz&gt;</code> \u65e0 PBC \u6700\u5c0f\u8ddd\u79bb <code>-min_dist_pbc</code> <code>gpumdkit.sh -min_dist_pbc &lt;input.xyz&gt;</code> \u5e26 PBC \u6700\u5c0f\u8ddd\u79bb <code>-filter_dist</code> <code>gpumdkit.sh -filter_dist &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_dist_pbc</code> <code>gpumdkit.sh -filter_dist_pbc &lt;input.xyz&gt; &lt;min_dist&gt;</code> \u5e26 PBC \u8ddd\u79bb\u8fc7\u6ee4 <code>-filter_box</code> <code>gpumdkit.sh -filter_box &lt;input.xyz&gt; &lt;edge_limit&gt;</code> \u76d2\u5b50\u8fb9\u957f\u8fc7\u6ee4 <code>-filter_value</code> <code>gpumdkit.sh -filter_value &lt;input.xyz&gt; &lt;property&gt; &lt;threshold&gt;</code> \u6027\u8d28\u9608\u503c\u8fc7\u6ee4 <code>-filter_range</code> <code>gpumdkit.sh -filter_range &lt;input.xyz&gt; &lt;element1&gt; &lt;element2&gt; &lt;min_dist&gt; &lt;max_dist&gt;</code> \u5143\u7d20\u5bf9\u8ddd\u79bb\u8303\u56f4\u8fc7\u6ee4 <code>-pda</code> <code>gpumdkit.sh -pda &lt;ref_struct&gt; &lt;trajectory.xyz&gt; &lt;species&gt; &lt;interval&gt;</code> \u6982\u7387\u5bc6\u5ea6\u5206\u6790"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_5","title":"\u53ef\u89c6\u5316","text":"<p>\u4f7f\u7528\uff1a</p> <pre><code>gpumdkit.sh -plt &lt;type&gt; [options]\ngpumdkit.sh -plt -h\n</code></pre> <p>\u5e38\u7528\u7c7b\u578b\u5305\u62ec <code>train</code>\u3001<code>prediction</code>\uff08\u522b\u540d\uff1a<code>test</code>\uff09\u3001<code>thermo</code>\u3001<code>msd</code>\u3001<code>sdc</code>\u3001<code>rdf</code>\u3001<code>emd</code>\u3001<code>nemd</code>\u3001<code>hnemd</code>\u3001<code>pdos</code> \u548c <code>plane-grid</code>\u3002</p>"},{"location":"zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html#_6","title":"\u5de5\u5177","text":"\u547d\u4ee4 \u8bed\u6cd5 \u8bf4\u660e <code>-time</code> <code>gpumdkit.sh -time &lt;gpumd\\|nep&gt;</code> \u76d1\u63a7 GPUMD \u6216 NEP \u8fdb\u5ea6 <code>-nep_modifier</code> <code>gpumdkit.sh -nep_modifier</code> \u4ea4\u4e92\u5f0f\u4fee\u6539 NEP \u6a21\u578b <code>-pynep</code> <code>gpumdkit.sh -pynep</code> \u5df2\u5f03\u7528\u7684 PyNEP FPS \u91c7\u6837"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html","title":"\u5de5\u4f5c\u6d41\u811a\u672c","text":"\ud83d\udd27 \u5de5\u4f5c\u6d41\u811a\u672c <p>\u5de5\u4f5c\u6d41\u811a\u672c\u7528\u4e8e\u81ea\u52a8\u5316\u91cd\u590d\u6027\u7684 DFT\u3001MD \u548c NEP \u6570\u636e\u51c6\u5907\u6b65\u9aa4\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/workflow/</code></p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_1","title":"\u4ea4\u4e92\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>3) Workflow\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+---------------------------------------------------------+\n|                      WORKFLOW TOOLS                     |\n+---------------------------------------------------------+\n| 301) SCF batch pretreatment                             |\n| 302) MD sample batch pretreatment (gpumd)               |\n| 303) MD sample batch pretreatment (lmp)                 |\n+---------------------------------------------------------+\n| 000) Return to the main menu                            |\n+---------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u5de5\u4f5c\u6d41 \u7528\u9014 301 SCF batch pretreatment \u51c6\u5907 DFT \u5355\u70b9\u8ba1\u7b97 302 MD sample batch pretreatment (GPUMD) \u51c6\u5907 GPUMD \u91c7\u6837\u8ba1\u7b97 303 MD sample batch pretreatment (LAMMPS) \u51c6\u5907 LAMMPS \u91c7\u6837\u8ba1\u7b97"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#scf","title":"SCF \u6279\u5904\u7406\u9884\u5904\u7406","text":"<p>\u9002\u7528\u4e8e\u5df2\u6709\u591a\u4e2a\u7ed3\u6784\uff0c\u9700\u8981\u51c6\u5907\u7b2c\u4e00\u6027\u539f\u7406\u5355\u70b9\u8ba1\u7b97\u7684\u60c5\u51b5\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#vasp","title":"VASP","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; VASP\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a\u7ed3\u6784\u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u811a\u672c\u6309\u4ee5\u4e0b\u987a\u5e8f\u68c0\u6d4b\uff1a</p> <ol> <li>\u5982\u679c\u5b58\u5728\u4e00\u4e2a\u6216\u591a\u4e2a <code>.vasp</code> \u6587\u4ef6\uff0c\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c <code>.vasp</code> \u548c <code>.xyz</code> \u540c\u65f6\u5b58\u5728\uff0c\u4f1a\u6253\u5370\u63d0\u793a\uff0c\u5e76\u53ea\u5904\u7406 <code>.vasp</code>\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u53ea\u6709\u4e00\u4e2a <code>.xyz</code>\uff0c\u4f1a\u628a\u8fd9\u4e2a extxyz \u8f6c\u4e3a POSCAR \u6587\u4ef6\uff1b</li> <li>\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</li> </ol> <p>\u8fd0\u884c\u524d\u7684\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u251c\u2500\u2500 POSCAR_2.vasp\n\u2514\u2500\u2500 POSCAR_3.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 sampled.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_fp/\n\u2502   \u251c\u2500\u2500 POSCAR_1.vasp\n\u2502   \u251c\u2500\u2500 POSCAR_2.vasp\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 fp/\n\u251c\u2500\u2500 &lt;prefix&gt;_1/\n\u251c\u2500\u2500 &lt;prefix&gt;_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>fp/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u7528\u6237\u628a <code>INCAR</code>\u3001<code>POTCAR</code>\u3001<code>KPOINTS</code> \u653e\u5230 <code>fp/</code> \u4e2d\uff0c\u8ba1\u7b97\u76ee\u5f55\u4f1a\u94fe\u63a5\u8fd9\u91cc\u7684\u6587\u4ef6\u3002</p> <p>\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u8f93\u5165\u7684 <code>prefix</code> \u4f1a\u4f5c\u4e3a\u8ba1\u7b97\u6587\u4ef6\u5939\u540d\u524d\u7f00\u3002\u540e\u7eed\u4f7f\u7528 <code>out2xyz</code> \u63d0\u53d6\u7ed3\u679c\u65f6\uff0c\u6587\u4ef6\u5939\u540d\u4f1a\u4f5c\u4e3a <code>config_type</code> \u5199\u5165 extxyz\uff0c\u4fbf\u4e8e\u4e4b\u540e\u68c0\u67e5\u7ed3\u6784\u6765\u6e90\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#cp2k","title":"CP2K","text":"<p>CP2K \u53ef\u4ee5\u4ece\u4ea4\u4e92\u83dc\u5355\u8fdb\u5165\uff0c\u4e5f\u53ef\u4ee5\u76f4\u63a5\u547d\u4ee4\u884c\u8c03\u7528\uff1a</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 301 -&gt; CP2K\n</code></pre> <pre><code>python Scripts/workflow/scf_batch_pretreatment_cp2k.py train.xyz template.inp calc\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4f1a\u8981\u6c42\u8f93\u5165\uff1a</p> <pre><code>&lt;extxyz_file&gt; &lt;template.inp&gt; &lt;prefix_name&gt;\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>dump.xyz template.inp H2O\n</code></pre> <p>CP2K \u6a21\u677f\u5e94\u8bbe\u7f6e\u4e3a\u4ece <code>pos.xyz</code> \u8bfb\u53d6\u5750\u6807\u3002\u53c2\u8003\u6a21\u677f\u5728\uff1a</p> <pre><code>Scripts/workflow/cp2k_template.inp\n</code></pre> <p>\u811a\u672c\u4f1a\u4e3a\u6bcf\u4e2a\u7ed3\u6784\u751f\u6210 <code>&lt;prefix&gt;_&lt;index&gt;/</code> \u76ee\u5f55\uff0c\u5e76\u5199\u5165 <code>input.inp</code> \u548c <code>pos.xyz</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#md","title":"MD \u91c7\u6837\u9884\u5904\u7406","text":""},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#gpumd","title":"GPUMD","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 302\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\u3002\u68c0\u6d4b\u987a\u5e8f\u4e0e VASP SCF \u9884\u5904\u7406\u4e00\u81f4\uff1a\u4f18\u5148\u5904\u7406 <code>.vasp</code>\uff1b\u5982\u679c\u6ca1\u6709 <code>.vasp</code> \u4e14\u5b58\u5728\u591a\u4e2a <code>.xyz</code>\uff0c\u4f1a\u8ba9\u7528\u6237\u9009\u62e9\u4e00\u4e2a\u3002</p> <p>\u8fd0\u884c\u524d\u5178\u578b\u76ee\u5f55\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 POSCAR_1.vasp\n\u2514\u2500\u2500 POSCAR_2.vasp\n</code></pre> <p>\u6216\uff1a</p> <pre><code>current directory/\n\u2514\u2500\u2500 dump.xyz\n</code></pre> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 model_1.xyz\n\u2502   \u251c\u2500\u2500 model_2.xyz\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p><code>md/</code> \u662f\u811a\u672c\u81ea\u52a8\u521b\u5efa\u7684\u3002\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>nep.txt</code> \u548c <code>run_*.in</code> \u653e\u5165 <code>md/</code>\u3002\u4f8b\u5982 <code>run_1.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_1/run.in</code>\uff0c<code>run_2.in</code> \u4f1a\u94fe\u63a5\u5230 <code>sample_2/run.in</code>\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#lammps","title":"LAMMPS","text":"<pre><code>gpumdkit.sh\n# \u9009\u62e9 3 -&gt; 303\n</code></pre> <p>\u8fd0\u884c\u524d\uff0c\u628a <code>.vasp</code> \u6587\u4ef6\u6216\u4e00\u4e2a extxyz \u6587\u4ef6\u653e\u5728\u5f53\u524d\u76ee\u5f55\uff1b\u4e24\u79cd\u683c\u5f0f\u540c\u65f6\u5b58\u5728\u65f6\u4f18\u5148\u5904\u7406 <code>.vasp</code>\u3002</p> <p>\u8fd0\u884c\u540e\u811a\u672c\u4f1a\u521b\u5efa\uff1a</p> <pre><code>current directory/\n\u251c\u2500\u2500 struct_md/\n\u2502   \u251c\u2500\u2500 lammps_1.data\n\u2502   \u251c\u2500\u2500 lammps_2.data\n\u2502   \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 md/\n\u251c\u2500\u2500 sample_1/\n\u251c\u2500\u2500 sample_2/\n\u2514\u2500\u2500 presub.sh\n</code></pre> <p>\u811a\u672c\u7ed3\u675f\u540e\uff0c\u9700\u8981\u628a <code>lmprun.in</code> \u548c <code>nep.txt</code> \u653e\u5230 <code>md/</code> \u4e2d\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_2","title":"\u4e3b\u52a8\u5b66\u4e60\u5f0f\u6d41\u7a0b","text":"<p>\u5e38\u89c1 NEP \u6570\u636e\u8fed\u4ee3\u6d41\u7a0b\uff1a</p> <ol> <li>\u4f7f\u7528\u5f53\u524d <code>nep.txt</code> \u8fd0\u884c MD\uff1b</li> <li>\u6536\u96c6 <code>dump.xyz</code> \u6216 <code>active.xyz</code>\uff1b</li> <li>\u5220\u9664\u660e\u663e\u4e0d\u5408\u7406\u7ed3\u6784\uff1b</li> <li>\u9009\u62e9\u591a\u6837\u6027\u9ad8\u6216\u504f\u5dee\u5927\u7684\u7ed3\u6784\uff1b</li> <li>\u8fd0\u884c DFT \u5355\u70b9\uff1b</li> <li>\u5c06 DFT \u7ed3\u679c\u8f6c\u6362\u4e3a extxyz\uff1b</li> <li>\u8ffd\u52a0\u5230 <code>train.xyz</code>\uff1b</li> <li>\u91cd\u65b0\u8bad\u7ec3 NEP\u3002</li> </ol> <p>\u66f4\u5b8c\u6574\u7684\u5f00\u53d1\u7248\u4e3b\u52a8\u5b66\u4e60\u811a\u672c\u8bf4\u660e\u89c1 \u4e3b\u52a8\u5b66\u4e60\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_3","title":"\u57fa\u4e8e\u6a21\u677f\u7684\u6e29\u5ea6\u7cfb\u5217","text":"<p>\u5bf9\u4e8e\u7b80\u5355\u7684\u6e29\u5ea6\u7cfb\u5217\u6a21\u62df\uff0c\u4f7f\u7528 shell \u5faa\u73af\u5373\u53ef\uff1a</p> <pre><code>for temp in 300 500 700 900; do\n    mkdir -p \"${temp}K\"\n    cp model.xyz \"${temp}K/\"\n    cp nep.txt \"${temp}K/\"\n    sed \"s/TEMPERATURE/$temp/g\" run_template.in &gt; \"${temp}K/run.in\"\ndone\n</code></pre> <p>\u7136\u540e\u6839\u636e\u4f60\u7684\u96c6\u7fa4\u7cfb\u7edf\u63d0\u4ea4\u751f\u6210\u7684\u6587\u4ef6\u5939\u3002</p>"},{"location":"zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html#_4","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u5de5\u4f5c\u6d41\u811a\u672c\u548c\u96c6\u7fa4\u73af\u5883\u5f3a\u76f8\u5173\uff0c\u6b63\u5f0f\u6279\u91cf\u63d0\u4ea4\u524d\u5148\u7528\u5c11\u91cf\u7ed3\u6784\u6d4b\u8bd5\u3002</li> <li>\u6a21\u677f\u6587\u4ef6\u5982 <code>INCAR</code>\u3001<code>KPOINTS</code>\u3001<code>POTCAR</code>\u3001<code>run.in</code> \u5e94\u4ed4\u7ec6\u68c0\u67e5\u3002</li> <li>\u6279\u91cf DFT \u524d\u5148\u7528\u5206\u6790\u548c\u91c7\u6837\u811a\u672c\u6e05\u7406\u5019\u9009\u7ed3\u6784\u3002</li> </ul>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html","title":"\u5feb\u901f\u5165\u95e8","text":"\ud83d\ude80 \u5feb\u901f\u5165\u95e8 <p>\u672c\u9875\u5e2e\u52a9\u4f60\u5b89\u88c5 GPUMDkit \u5e76\u8fd0\u884c\u7b2c\u4e00\u4e2a\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u6216\u76f4\u63a5\u4f7f\u7528\u547d\u4ee4\u884c\u9009\u9879\u6765\u4f7f\u7528 GPUMDkit\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>GPUMDkit \u4e3a\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u7684\u5e38\u89c1\u4efb\u52a1\u63d0\u4f9b\u7edf\u4e00\u5165\u53e3\u2014\u2014\u683c\u5f0f\u8f6c\u6362\u3001\u7ed3\u6784\u5206\u6790\u3001\u6027\u8d28\u8ba1\u7b97\u548c\u53ef\u89c6\u5316\u2014\u2014\u65e0\u9700\u7f16\u5199\u81ea\u5b9a\u4e49\u811a\u672c\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#1-python","title":"1. \u51c6\u5907 Python \u73af\u5883","text":"<pre><code>conda create -n gpumdkit python=3.12\nconda activate gpumdkit\n</code></pre> <p>\u90e8\u5206\u53ef\u9009\u529f\u80fd\u9700\u8981\u989d\u5916\u4f9d\u8d56\uff1a</p> <pre><code>pip install neptrain dpdata calorine\n</code></pre> <p>\u5176\u4ed6 Python \u4f9d\u8d56\u7531\u5bf9\u5e94\u811a\u672c\u5728\u8fd0\u884c\u65f6\u5bfc\u5165\u3002\u5982\u679c\u7f3a\u5c11\u67d0\u4e2a\u5305\uff0c\u4f7f\u7528\u5bf9\u5e94\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u63d0\u793a\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#2-gpumdkit","title":"2. \u5b89\u88c5 GPUMDkit","text":"<p>\u514b\u9686\u4ed3\u5e93\u5e76\u8fd0\u884c\u5b89\u88c5\u811a\u672c\uff1a</p> <pre><code>git clone https://github.com/zhyan0603/GPUMDkit.git\ncd GPUMDkit\nsource ./install.sh\n</code></pre> <p>\u5b89\u88c5\u811a\u672c\u4f1a\u5199\u5165 <code>GPUMDkit_path</code> \u548c <code>PATH</code> \u8bbe\u7f6e\uff0c\u5e76\u5728\u5f53\u524d shell \u4e2d\u52a0\u8f7d\u3002\u9ed8\u8ba4\u5199\u5165 <code>~/.bashrc</code>\uff1b\u5982\u679c\u5f53\u524d shell \u662f zsh\uff0c\u5219\u5199\u5165 <code>~/.zshrc</code>\u3002\u5982\u679c\u68c0\u6d4b\u5230\u5df2\u6709 GPUMDkit \u8def\u5f84\uff0c\u5b89\u88c5\u811a\u672c\u4f1a\u6253\u5370\u65e7\u8def\u5f84\u5e76\u8be2\u95ee\u662f\u5426\u66ff\u6362\uff1b\u4fee\u6539 rc \u6587\u4ef6\u524d\u4f1a\u5148\u521b\u5efa\u5907\u4efd\u3002</p> <p>\u5178\u578b\u5b89\u88c5\u8f93\u51fa\uff1a</p> <pre><code>======================================================\n  GPUMDkit Installation\n======================================================\n [1/4] Detecting GPUMDkit directory...\n       /path/to/GPUMDkit\n [2/4] Detecting shell configuration...\n       Target: /Users/you/.bashrc\n       Adding environment variables to /Users/you/.bashrc\n       Success: Environment variables added.\n [3/4] Setting executable permissions...\n       Added executable permission to gpumdkit.sh\n [4/4] Loading environment...\n\n======================================================\n  Installation Complete!  GPUMDkit is ready to use.\n======================================================\n</code></pre> <p>\u5982\u679c\u4e4b\u524d\u5df2\u7ecf\u5b89\u88c5\u8fc7 GPUMDkit\uff0c\u53ef\u80fd\u4f1a\u770b\u5230\uff1a</p> <pre><code>Existing GPUMDkit configuration found.\nExisting path(s):\n  - /old/path/to/GPUMDkit\nNew path:\n  - /new/path/to/GPUMDkit\n\nReplace the existing GPUMDkit configuration with the new path? [y/N]:\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#3","title":"3. \u9a8c\u8bc1\u5b89\u88c5","text":"<pre><code>gpumdkit.sh -h\n</code></pre> <p>\u6b64\u547d\u4ee4\u4f1a\u6253\u5370\u5e2e\u52a9\u8868\uff0c\u5217\u51fa\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_3","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u6253\u5f00\u4e3b\u83dc\u5355\uff1a</p> <pre><code>           ____ ____  _   _ __  __ ____  _    _ _\n          / ___|  _ \\| | | |  \\/  |  _ \\| | _(_) |_\n         | |  _| |_) | | | | |\\/| | | | | |/ / | __|\n         | |_| |  __/| |_| | |  | | |_| |   &lt;| | |_\n          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__|\n\n          GPUMDkit Version 1.5.6 (dev) (2026-06-17)\n    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn)\n Main Contributors: Denan LI, Xin WU, Zhoulin LIU &amp; Chen HUA\n\n ---------------------- GPUMD ------------------------\n 1) Format Conversion          2) Sample Structures\n 3) Workflow                   4) Calculators\n 5) Analyzer                   6) Visualization\n 7) Utilities                  8) Help                \n 0) Exit\n ------------&gt;&gt;\n Input the function number:\n</code></pre> <p>\u6309\u6570\u5b57\u9009\u62e9\u6a21\u5757\u3002\u6bcf\u4e2a\u6a21\u5757\u63d0\u4f9b\u5305\u542b\u5177\u4f53\u529f\u80fd\u7684\u5b50\u83dc\u5355\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_4","title":"\u547d\u4ee4\u884c\u6a21\u5f0f","text":"<p>\u76f4\u63a5\u547d\u4ee4\u4f7f\u7528\u56fa\u5b9a\u7684\u4f4d\u7f6e\u53c2\u6570\uff1a</p> <pre><code>gpumdkit.sh -&lt;\u9009\u9879&gt; [\u53c2\u6570...]\n</code></pre> <p>\u793a\u4f8b\uff1a</p> <pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\ngpumdkit.sh -plt train\ngpumdkit.sh -calc msd trajectory.xyz Li 10\n</code></pre> <p>\u7b2c\u4e00\u4e2a\u793a\u4f8b\u8bfb\u53d6 <code>POSCAR</code>\uff0c\u5199\u51fa <code>model.xyz</code>\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#hello-world","title":"Hello World \u793a\u4f8b","text":"<p>\u4e00\u4e2a\u6700\u5c0f\u5316\u7684\u7aef\u5230\u7aef\u68c0\u67e5\uff0c\u786e\u8ba4\u5b89\u88c5\u662f\u5426\u6b63\u5e38\u2014\u2014\u521b\u5efa\u4e00\u4e2a\u6781\u5c0f\u7684\u7845 POSCAR\uff0c\u8f6c\u6362\u4e3a extxyz\uff0c\u5e76\u67e5\u770b\u8f93\u51fa\uff1a</p> <pre><code>cat &gt; POSCAR &lt;&lt; 'EOF'\nSi\n1.0\n0 2.715 2.715\n2.715 0 2.715\n2.715 2.715 0\nSi\n1\ndirect\n0 0 0\nEOF\ngpumdkit.sh -pos2exyz POSCAR model.xyz\nhead model.xyz\n</code></pre> <p>\u5982\u679c <code>model.xyz</code> \u663e\u793a\u4e00\u4e2a Si \u539f\u5b50\u53ca\u6676\u683c\u4fe1\u606f\uff0c\u8bf4\u660e\u5b89\u88c5\u6210\u529f\u3002</p> <p>\u4ec0\u4e48\u662f extxyz\uff1f extxyz \u662f\u6269\u5c55 XYZ \u683c\u5f0f\uff1a\u7b2c 1 \u884c\u662f\u539f\u5b50\u6570\uff0c\u7b2c 2 \u884c\u5305\u542b\u6676\u683c\u53ca\u7ed3\u6784\u7ea7\u5c5e\u6027\uff08\u6309\u9700\u5305\u542b\u80fd\u91cf/\u529b/\u7ef4\u91cc\uff09\uff0c\u7b2c 3 \u884c\u53ca\u4ee5\u540e\u662f\u6bcf\u4e2a\u539f\u5b50\u53ca\u5176\u539f\u5b50\u7ea7\u5c5e\u6027\u3002\u5b83\u662f NEP \u7684\u539f\u751f\u8bad\u7ec3\u6570\u636e\u683c\u5f0f\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_5","title":"\u5e38\u89c1\u793a\u4f8b","text":""},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#gpumd-group","title":"\u6dfb\u52a0 GPUMD group \u6807\u7b7e","text":"<pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>group \u6807\u7b7e\u7528\u4e8e\u4e00\u4e9b\u9700\u8981\u539f\u5b50\u5206\u7ec4\u7684 GPUMD \u76f8\u5173\u6d41\u7a0b\u548c\u5206\u6790\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep","title":"\u7ed8\u5236 NEP \u8bad\u7ec3\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#nep_1","title":"\u7ed8\u5236 NEP \u6d4b\u8bd5\u96c6\u7ed3\u679c","text":"<pre><code>gpumdkit.sh -plt test\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_6","title":"\u7ed8\u5236\u70ed\u529b\u5b66\u91cf","text":"<pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#msd","title":"\u7ed8\u5236 MSD \u548c\u81ea\u6269\u6563\u7cfb\u6570","text":"<pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html#_7","title":"\u8bf4\u660e","text":"<ul> <li>\u4f7f\u7528 <code>gpumdkit.sh -h</code> \u67e5\u770b\u6240\u6709\u53ef\u7528\u9009\u9879\u3002</li> <li>\u4f7f\u7528 <code>gpumdkit.sh -&lt;\u9009\u9879&gt; -h</code> \u83b7\u53d6\u7279\u5b9a\u9009\u9879\u7684\u5e2e\u52a9\uff08\u4f8b\u5982 <code>gpumdkit.sh -plt train -h</code>\uff09\u3002</li> <li>\u5404\u6a21\u5757\u7684\u8be6\u7ec6\u7528\u6cd5\u8bf7\u53c2\u89c1\u9996\u9875\u4e2d\u94fe\u63a5\u7684\u5bf9\u5e94\u6559\u7a0b\u9875\u9762\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html","title":"\u6781\u6027\u6750\u6599\u5206\u6790","text":"\ud83e\uddf2 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u672c\u6559\u7a0b\u4ecb\u7ecd GPUMDkit \u4e2d\u8ba1\u7b97\u5668\u9009\u9879 <code>406-410</code>\uff0c\u4ee5\u53ca <code>plane-grid</code> \u7ed8\u56fe\u6d41\u7a0b\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code> \u548c <code>Scripts/plt_scripts/</code></p> <p>\u672c\u6559\u7a0b\u5305\u542b\u901a\u7528\u5de5\u5177\u548c\u4f53\u7cfb\u76f8\u5173\u5de5\u5177\uff1a</p> <ul> <li><code>nlist</code>\u3001<code>disp</code> \u548c <code>avg-struct</code> \u53ef\u5e7f\u6cdb\u7528\u4e8e\u7ed3\u6784\u548c\u8f68\u8ff9\u5206\u6790\u3002</li> <li><code>oct-tilt</code> \u7528\u4e8e\u516b\u9762\u4f53\u73af\u5883\u5206\u6790\uff0c\u9700\u8981\u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u5468\u56f4\u6709 6 \u4e2a\u8fd1\u90bb\u3002</li> <li><code>pol-abo3</code> \u4e13\u7528\u4e8e <code>ABO3</code> \u4f53\u7cfb\u7684\u6781\u5316\u5206\u6790\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_1","title":"\u6982\u89c8","text":"\u6b65\u9aa4 CLI \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u8f93\u51fa \u6784\u5efa\u8fd1\u90bb\u5217\u8868 <code>gpumdkit.sh -calc nlist ...</code> <code>model.xyz</code> <code>nl-*.dat</code> \u8ba1\u7b97\u4f4d\u79fb <code>gpumdkit.sh -calc disp ...</code> \u8f68\u8ff9 + <code>nl-*.dat</code> <code>displacements.dat</code> \u5e73\u5747\u8f68\u8ff9\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct ...</code> \u8f68\u8ff9 \u5e73\u5747\u7ed3\u6784 extxyz \u516b\u9762\u4f53\u503e\u659c <code>gpumdkit.sh -calc oct-tilt ...</code> \u8f68\u8ff9 + B-O \u8fd1\u90bb\u5217\u8868 \u503e\u659c\u89d2\u6570\u636e\u8868 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 ...</code> \u8f68\u8ff9 + \u8fd1\u90bb\u5217\u8868 \u6781\u5316\u6570\u636e\u8868 plane-grid \u7ed8\u56fe <code>gpumdkit.sh -plt plane-grid ...</code> \u7ed3\u6784 + \u4f4d\u79fb\u6570\u636e \u5e73\u9762\u5256\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_2","title":"\u4f9d\u8d56","text":"<p>\u8fd9\u4e9b\u811a\u672c\u9700\u8981 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_3","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<p>\u9009\u9879 <code>406-410</code> \u662f\u672c\u6559\u7a0b\u4e2d\u7684\u6838\u5fc3\u529f\u80fd\u3002\u4e0b\u9762\u5404\u8282\u4f1a\u8bf4\u660e\u6bcf\u4e2a\u529f\u80fd\u7684\u7528\u9014\u548c\u8fd0\u884c\u65b9\u5f0f\u3002</p> <pre><code>gpumdkit.sh\n# \u9009\u62e9 4) Calculators\n</code></pre> <p>\u8ba1\u7b97\u5668\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5b8c\u6574\u53c2\u6570\u8bf4\u660e\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u547d\u4ee4\u67e5\u770b\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -h\ngpumdkit.sh -calc disp -h\ngpumdkit.sh -calc avg-struct -h\ngpumdkit.sh -calc oct-tilt -h\ngpumdkit.sh -calc pol-abo3 -h\ngpumdkit.sh -plt plane-grid -h\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#406-calc_neighbor_listpy","title":"406) \u6784\u5efa\u8fd1\u90bb\u5217\u8868 (<code>calc_neighbor_list.py</code>)","text":"<p>\u4e3a\u6307\u5b9a\u4e2d\u5fc3\u5143\u7d20\u548c\u8fd1\u90bb\u5143\u7d20\u6784\u5efa\u8fd1\u90bb\u5217\u8868\u3002</p> <p>\u4f7f\u7528\u573a\u666f\uff1a \u8fd9\u901a\u5e38\u662f\u8fd0\u884c <code>disp</code>\u3001<code>oct-tilt</code> \u548c <code>pol-abo3</code> \u4e4b\u524d\u7684\u7b2c\u4e00\u6b65\uff0c\u56e0\u4e3a\u8fd9\u4e9b\u811a\u672c\u4f1a\u8bfb\u53d6 <code>nl-*.dat</code> \u8fd1\u90bb\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_4","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4e3a\u516b\u9762\u4f53\u5206\u6790\u6784\u5efa Ti-O \u6700\u8fd1 6 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# \u793a\u4f8b 2\uff1a\u4e3a A \u4f4d\u4e2d\u5fc3\u5206\u6790\u6784\u5efa Pb/Sr-O \u6700\u8fd1 12 \u4e2a\u8fd1\u90bb\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb Sr -E O\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_5","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-x, --index</code>\uff1a   \u4ece\u8f93\u5165\u6587\u4ef6\u4e2d\u8bfb\u53d6\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-c, --cutoff</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u641c\u7d22\u622a\u65ad\u8ddd\u79bb\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> <li><code>-n, --neighbor-num</code>\uff08\u5fc5\u9700\uff09\uff1a   \u6bcf\u4e2a\u4e2d\u5fc3\u539f\u5b50\u7684\u8fd1\u90bb\u6570\u91cf\u3002</li> <li><code>-d, --defect</code>\uff1a   \u7f3a\u9677\u6a21\u5f0f\u3002\u542f\u7528\u540e\uff0c\u5982\u679c\u8fd1\u90bb\u6570\u91cf\u4e0d\u8db3\uff0c\u7f3a\u5931\u4f4d\u7f6e\u4f1a\u7528\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u586b\u5145\u3002</li> <li><code>-C, --center-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u4e2d\u5fc3\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-E, --neighbor-elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u8fd1\u90bb\u5143\u7d20\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u8def\u5f84\u3002\u9ed8\u8ba4\u503c\uff1a<code>nl-&lt;center&gt;-&lt;neighbor&gt;.dat</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_6","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u8fd1\u90bb\u5217\u8868\u6587\u672c\u6587\u4ef6\uff0c\u4f8b\u5982 <code>nl-Ti-O.dat</code>\u3002</li> <li>\u6587\u4ef6\u662f\u4e00\u4e2a\u4e8c\u7ef4\u6574\u6570\u6570\u7ec4\uff0c\u5f62\u72b6\u4e3a <code>(n_center, neighbor_num + 1)</code>\u3002\u6bcf\u4e00\u884c\u5bf9\u5e94\u4e00\u4e2a\u4e2d\u5fc3\u539f\u5b50\uff1a\u7b2c\u4e00\u5217\u662f\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\uff0c\u540e\u7eed\u5217\u662f\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7\uff0c\u6240\u6709\u7f16\u53f7\u5747\u4e3a 1-based\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#407-calc_displacementpy","title":"407) \u4ece\u8f68\u8ff9\u8ba1\u7b97\u4f4d\u79fb (<code>calc_displacement.py</code>)","text":"<p>\u6839\u636e\u8f68\u8ff9\u6216\u6a21\u578b\u7ed3\u6784\u4ee5\u53ca\u8fd1\u90bb\u5217\u8868\uff0c\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_7","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece model.xyz \u8ba1\u7b97\u5355\u5e27\u4f4d\u79fb\ngpumdkit.sh -calc disp -i model.xyz -n nl-Ti-O.dat -o disp_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4f7f\u7528 movie.xyz \u7684\u6700\u540e 20% \u5e27\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o displacements.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_8","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7531 <code>nlist</code> \u751f\u6210\u7684\u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u90e8\u5206\u5e27\u3002   \u6574\u6570\u8868\u793a\u6700\u540e <code>N</code> \u5e27\uff1b   <code>0 &lt; value &lt; 1</code> \u8868\u793a\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_9","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>displacements.dat</code>\uff0c\u6216\u4f60\u6307\u5b9a\u7684\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e8c\u7ef4\u6570\u7ec4\uff1a\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u4e09\u5217\u5206\u522b\u4e3a <code>dx</code>\u3001<code>dy</code> \u548c <code>dz</code> \u4f4d\u79fb\u5206\u91cf\uff0c\u5355\u4f4d\u4e3a Angstrom\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#408-calc_averaged_structurepy","title":"408) \u8ba1\u7b97\u5e73\u5747\u7ed3\u6784 (<code>calc_averaged_structure.py</code>)","text":"<p>\u4ece\u9009\u5b9a\u8f68\u8ff9\u5e27\u751f\u6210\u4e00\u4e2a\u5e73\u5747\u7ed3\u6784\u3002 \u901a\u5e38\u53ef\u5728\u4f53\u7cfb\u5e73\u8861\u540e\u4f7f\u7528\uff1a\u5bf9\u4e8e\u63a5\u8fd1\u5e73\u8861\u7684\u56fa\u4f53\uff0c\u53ef\u4ee5\u5bf9\u76ee\u6807\u6e29\u5ea6\u4e0b\u7684\u4e00\u6bb5\u8f68\u8ff9\u53d6\u5e73\u5747\uff0c\u5e76\u5206\u6790\u8be5\u4ee3\u8868\u6027\u7ed3\u6784\uff0c\u800c\u4e0d\u662f\u9010\u5e27\u5904\u7406\u6bcf\u4e2a snapshot\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_10","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5e73\u5747\u6240\u6709\u5e27\ngpumdkit.sh -calc avg-struct -i movie.xyz -o averaged_structure.xyz\n\n# \u793a\u4f8b 2\uff1a\u5e73\u5747\u9009\u5b9a\u5e27\u8303\u56f4 (100:500:2)\ngpumdkit.sh -calc avg-struct -i movie.xyz -s 100 -t 500 -p 2 -o avg_slice.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_11","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165\u8f68\u8ff9\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>movie.xyz</code>\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u7ed3\u6784\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>averaged_structure.xyz</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_12","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a\u5355\u5e27\u5e73\u5747\u7ed3\u6784 extxyz \u6587\u4ef6\u3002</li> <li>\u4f4d\u7f6e\u5e73\u5747\u4f1a\u76f8\u5bf9\u4e8e\u6240\u9009\u7b2c\u4e00\u5e27\u8fdb\u884c MIC/PBC \u4fee\u6b63\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#409-calc_oct_tiltpy","title":"409) \u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c (<code>calc_oct_tilt.py</code>)","text":"<p>\u6839\u636e B-O \u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c\u89d2\u3002 \u8be5\u529f\u80fd\u5e38\u7528\u4e8e\u5206\u6790 <code>ABO3</code> \u4f53\u7cfb\u4e2d\u7684\u516b\u9762\u4f53\u8f6c\u52a8\u6a21\u5f0f\uff0c\u4f8b\u5982 <code>SrTiO3</code> \u548c <code>PbZrO3</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_13","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u4ece\u5355\u5e27\u7ed3\u6784\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i model.xyz -n nl-Ti-O.dat -o oct_tilt_model.dat\n\n# \u793a\u4f8b 2\uff1a\u4ece\u8f68\u8ff9\u6700\u540e 20% \u5e27\u8ba1\u7b97 TiO6 \u516b\u9762\u4f53\u503e\u8f6c\ngpumdkit.sh -calc oct-tilt -i movie.xyz -n nl-Ti-O.dat -l 0.2 -o octahedral_tilt.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_14","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-n, --neighbor-list</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u6587\u4ef6\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>octahedral_tilt.dat</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_15","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>octahedral_tilt.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>theta_x</code>\u3001<code>theta_y</code>\u3001<code>theta_z</code>\uff0c\u5355\u4f4d\u4e3a degree\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#410-abo3-calc_polarization_abo3py","title":"410) \u8ba1\u7b97 ABO3 \u4f53\u7cfb\u6781\u5316 (<code>calc_polarization_abo3.py</code>)","text":"<p>\u8ba1\u7b97 <code>ABO3</code> \u4f53\u7cfb\u7684\u5c40\u57df\u6781\u5316\u77e2\u91cf\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_16","title":"\u7528\u6cd5","text":"<pre><code># \u793a\u4f8b 1\uff1a\u5355\u5e27 ABO3 \u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i model.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Sr=2 Ti=4.0 O=-2.0 -o polarization_model.dat\n\n# \u793a\u4f8b 2\uff1a\u9009\u5b9a\u8f68\u8ff9\u5e27\u8303\u56f4\u4e0a\u7684\u6781\u5316\ngpumdkit.sh -calc pol-abo3 -i movie.xyz --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n  --bec Pb=2 Ti=4.0 O=-2.0 -s 200 -t 600 -p 5 -o polarization_slice.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_17","title":"\u53c2\u6570\uff08\u5b8c\u6574\uff09","text":"<ul> <li><code>-i, --input</code>\uff1a   \u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>--nl-ba</code>\uff08\u5fc5\u9700\uff09\uff1a   B-A \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>--nl-bo</code>\uff08\u5fc5\u9700\uff09\uff1a   B-O \u8fd1\u90bb\u5217\u8868\u3002</li> <li><code>-o, --output</code>\uff1a   \u8f93\u51fa\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>polarization.dat</code>\u3002</li> <li><code>--bec</code>\uff08\u5fc5\u9700\uff09\uff1a   Born \u6709\u6548\u7535\u8377\u9879\uff0c\u683c\u5f0f\u4e3a <code>Element=value</code>\u3002   \u793a\u4f8b\uff1a<code>Pb=2.5 Ti=4.0 O=-2.0</code>\u3002</li> <li><code>-s, --start</code>\uff1a   \u5207\u7247\u8d77\u59cb\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>-t, --stop</code>\uff1a   \u5207\u7247\u7ec8\u6b62\u5e27\u3002\u9ed8\u8ba4\u503c\uff1a\u5230\u672b\u5c3e\u3002</li> <li><code>-p, --step</code>\uff1a   \u5207\u7247\u6b65\u957f\u3002\u9ed8\u8ba4\u503c\uff1a<code>1</code>\u3002</li> <li><code>-l, --last</code>\uff1a   \u9009\u62e9\u672b\u5c3e\u5e27\uff0c\u53ef\u4ee5\u662f\u6700\u540e <code>N</code> \u5e27\u6216\u6700\u540e\u4e00\u90e8\u5206\u6bd4\u4f8b\u7684\u5e27\u3002</li> <li><code>-l/--last</code> \u4e0e <code>-s/-t/-p</code> \u4e92\u65a5\u3002</li> </ul> <p>\u91cd\u8981\u68c0\u67e5\uff1a</p> <ul> <li><code>--bec</code> \u5fc5\u987b\u5305\u542b\u8f93\u5165\u7ed3\u6784\u4e2d\u7684\u6240\u6709\u5143\u7d20\u79cd\u7c7b\u3002</li> <li><code>--nl-ba</code> \u548c <code>--nl-bo</code> \u4e2d\u7684\u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u5fc5\u987b\u5339\u914d\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_18","title":"\u8f93\u51fa\u6587\u4ef6","text":"<ul> <li>\u4e3b\u8981\u8f93\u51fa\uff1a<code>polarization.dat</code>\uff0c\u6216\u81ea\u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d\u3002</li> <li>\u4fdd\u5b58\u7684\u6587\u672c\u6587\u4ef6\u662f\u4e09\u5217\u4e8c\u7ef4\u6570\u7ec4\uff0c\u5206\u522b\u4e3a <code>Px</code>\u3001<code>Py</code>\u3001<code>Pz</code>\uff0c\u5355\u4f4d\u4e3a <code>C/m^2</code>\u3002\u5bf9\u4e8e\u5355\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_center, 3)</code>\uff1b\u5bf9\u4e8e\u591a\u5e27\u8f93\u5165\uff0c\u5f62\u72b6\u4e3a <code>(n_selected_frame * n_center, 3)</code>\uff0c\u6309\u5e27\u4f18\u5148\u987a\u5e8f\u6392\u5217\u3002\u5982\u679c\u603b Born \u7535\u8377\u4e0d\u5e73\u8861\uff0c\u811a\u672c\u4f1a\u6253\u5370 warning\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#plane-grid-plt_plane_gridpy","title":"Plane-grid \u53ef\u89c6\u5316 (<code>plt_plane_grid.py</code>)","text":"<p>\u4f60\u53ef\u4ee5\u53ef\u89c6\u5316 <code>displacements.dat</code> \u6216 <code>polarization.dat</code>\uff1a</p> <pre><code># \u793a\u4f8b 1\uff1aTi \u4f4d\u70b9\u4e0a\u7684\u4f4d\u79fb\u56fe\uff0c\u9009\u62e9\u7b2c\u4e00\u4e2a XY \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d displacements.dat -e Ti --select-xy 0\n\n# \u793a\u4f8b 2\uff1aPb \u4f4d\u70b9\u4e0a\u7684\u6781\u5316\u56fe\uff0c\u9009\u62e9 XZ \u548c YZ \u5c42\ngpumdkit.sh -plt plane-grid -i model.xyz -d polarization.dat -e Pb --select-xz 0 1 2 --select-yz 3 4\n</code></pre> <p>\u53c2\u6570\uff08\u5b8c\u6574\uff09\uff1a</p> <ul> <li><code>-i, --input</code>\uff1a   \u7528\u4e8e\u539f\u5b50\u5e03\u5c40\u548c\u5206\u5c42\u7684\u8f93\u5165 xyz \u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>model.xyz</code>\u3002</li> <li><code>-d, --disp</code>\uff1a   \u77e2\u91cf\u573a\u6570\u636e\u6587\u4ef6\u3002\u9ed8\u8ba4\u503c\uff1a<code>displacements.dat</code>\u3002</li> <li><code>-e, --elements</code>\uff08\u5fc5\u9700\uff09\uff1a   \u7528\u4e8e\u5c06\u77e2\u91cf\u6620\u5c04\u5230\u6676\u683c\u5c42\u4e0a\u7684\u4e2d\u5fc3\u5143\u7d20\u7b26\u53f7\u3002</li> <li><code>-m, --tol</code>\uff1a   \u7f51\u683c\u6620\u5c04\u7684\u5c42\u5bb9\u5dee\u3002\u9ed8\u8ba4\u503c\uff1a<code>1.0</code>\u3002</li> <li><code>-g, --target-size</code>\uff1a   \u671f\u671b\u7f51\u683c\u5927\u5c0f\uff0c\u683c\u5f0f\u4e3a <code>nx ny nz</code>\u3002</li> <li><code>-o, --save-dir</code>\uff1a   \u56fe\u7247\u8f93\u51fa\u76ee\u5f55\u3002\u9ed8\u8ba4\u503c\uff1a<code>plot</code>\u3002</li> <li><code>-f, --frame</code>\uff1a   \u5f53\u77e2\u91cf\u6570\u636e\u5305\u542b\u591a\u5e27\u65f6\uff0c\u8981\u53ef\u89c6\u5316\u7684\u5e27\u7f16\u53f7\u3002\u9ed8\u8ba4\u503c\uff1a<code>0</code>\u3002</li> <li><code>--select-xy</code>\uff1a   \u9009\u5b9a\u7684 XY \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-xz</code>\uff1a   \u9009\u5b9a\u7684 XZ \u5c42\u7f16\u53f7\u3002</li> <li><code>--select-yz</code>\uff1a   \u9009\u5b9a\u7684 YZ \u5c42\u7f16\u53f7\u3002</li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li>\u5982\u679c\u9700\u8981\uff0c\u4f1a\u521b\u5efa\u8f93\u51fa\u76ee\u5f55\u3002</li> <li>\u56fe\u7247\u4fdd\u5b58\u4e3a <code>XY_*.png</code>\u3001<code>XZ_*.png</code>\u3001<code>YZ_*.png</code>\u3002</li> </ul>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_19","title":"\u8f93\u51fa\u6587\u4ef6\u4e00\u89c8","text":"\u811a\u672c \u4e3b\u8981\u8f93\u51fa \u4fdd\u5b58\u5185\u5bb9 <code>calc_neighbor_list.py</code> <code>nl-*.dat</code> 1-based \u4e2d\u5fc3\u539f\u5b50\u7f16\u53f7\u548c\u8fd1\u90bb\u539f\u5b50\u7f16\u53f7 <code>calc_displacement.py</code> <code>*.dat</code> \u5c40\u57df\u4f4d\u79fb\u77e2\u91cf\uff08<code>dx dy dz</code>\uff0cAngstrom\uff09 <code>calc_averaged_structure.py</code> <code>*.xyz</code> \u4e00\u4e2a\u5e73\u5747\u7ed3\u6784 <code>calc_oct_tilt.py</code> <code>*.dat</code> \u516b\u9762\u4f53\u503e\u8f6c\u89d2\uff08<code>theta_x theta_y theta_z</code>\uff0cdegree\uff09 <code>calc_polarization_abo3.py</code> <code>*.dat</code> \u5c40\u57df\u6781\u5316\u77e2\u91cf\uff08<code>Px Py Pz</code>\uff0c<code>C/m^2</code>\uff09 <code>plt_plane_grid.py</code> <code>plot/*.png</code> \u6839\u636e\u77e2\u91cf\u573a\u6570\u636e\u7ed8\u5236\u7684 XY/XZ/YZ \u5e73\u9762\u56fe"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_20","title":"\u771f\u5b9e\u6848\u4f8b","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3-","title":"PbTiO3 \u7684\u6e29\u5ea6\u9a71\u52a8\u94c1\u7535-\u987a\u7535\u76f8\u53d8","text":"<p>\u5047\u8bbe\u6240\u6709\u6587\u4ef6\u90fd\u4f4d\u4e8e\u5f53\u524d\u76ee\u5f55 <code>./</code>\uff1a</p> <pre><code>./\n\u251c\u2500\u2500 model.xyz\n\u251c\u2500\u2500 300K.xyz\n\u251c\u2500\u2500 350K.xyz\n\u251c\u2500\u2500 400K.xyz\n\u251c\u2500\u2500 ...\n\u2514\u2500\u2500 800K.xyz\n</code></pre> <p><code>model.xyz</code> \u662f\u7528\u4e8e\u8fdb\u884c MD \u6a21\u62df\u7684\u521d\u59cb\u7ed3\u6784\u3002\u6bcf\u4e2a <code>TEMP K.xyz</code> \u662f\u5bf9\u5e94\u6e29\u5ea6\u4e0b\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1","title":"\u7b2c 1 \u6b65\uff1a\u4ece\u6bcf\u6761\u8f68\u8ff9\u7684\u540e\u534a\u6bb5\u5f97\u5230\u5e73\u5747\u7ed3\u6784","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc avg-struct -i \"$f\" -l 0.5 -o \"${tag}-avg.xyz\"\ndone\n</code></pre> <p>\u8fd9\u4f1a\u5199\u51fa <code>300K-avg.xyz</code>\u3001<code>350K-avg.xyz</code>\u3001...\u3001<code>800K-avg.xyz</code>\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-modelxyz","title":"\u7b2c 2 \u6b65\uff1a\u57fa\u4e8e <code>model.xyz</code> \u6784\u5efa\u8fd1\u90bb\u5217\u8868","text":"<pre><code># B-O list: for each Ti, find the nearest 6 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n\n# A-O list: for each Pb, find the nearest 12 O atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 4.0 -n 12 -C Pb -E O -o nl-Pb-O.dat\n\n# B-A list required by pol-abo3: for each Ti, find the nearest 8 Pb atoms\ngpumdkit.sh -calc nlist -i model.xyz -c 5.0 -n 8 -C Ti -E Pb -o nl-Ti-Pb.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3","title":"\u7b2c 3 \u6b65\uff1a\u4e3a\u6bcf\u4e2a\u6e29\u5ea6\u8ba1\u7b97\u4f4d\u79fb\u548c\u6781\u5316","text":"<p>\u8fd9\u91cc\u4f7f\u7528 Born \u6709\u6548\u7535\u8377\uff08BEC\uff09\uff0c\u4e0d\u662f\u540d\u4e49\u79bb\u5b50\u7535\u8377\u3002\u5bf9\u4e8e\u672c\u4f8b\u4e2d\u7684 PbTiO3\uff1a</p> <pre><code>PTO = {\n    'Pb': 3.44,\n    'Ti': 5.18,\n    'O': -(3.44 + 5.18) / 3\n}\n</code></pre> <p>\u4f60\u53ef\u4ee5\u4ece\u81ea\u5df1\u7684 DFPT \u8ba1\u7b97\u6216\u6587\u732e\u4e2d\u83b7\u5f97 BEC\u3002\u56e0\u6b64\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u548c\u6781\u5316\uff1a</p> <pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -calc disp -i \"$f\" -n nl-Ti-O.dat -l 0.5 -o \"${tag}-disp.dat\"\n  gpumdkit.sh -calc pol-abo3 -i \"$f\" --nl-ba nl-Ti-Pb.dat --nl-bo nl-Ti-O.dat \\\n    --bec Pb=3.44 Ti=5.18 O=-2.8733333333 -l 0.5 -o \"${tag}-pol.dat\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#4","title":"\u7b2c 4 \u6b65\uff1a\u7ed8\u5236\u5b9e\u7a7a\u95f4\u4f4d\u79fb\u548c\u6781\u5316\u56fe","text":"<pre><code>for f in *K.xyz; do\n  tag=\"${f%.xyz}\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-disp.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-disp\"\n  gpumdkit.sh -plt plane-grid -i \"${tag}-avg.xyz\" -d \"${tag}-pol.dat\" -e Ti --select-xz 1 -o \"plot-${tag}-pol\"\ndone\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#5-","title":"\u7b2c 5 \u6b65\uff1a\u6784\u5efa\u6e29\u5ea6-\u5e8f\u53c2\u91cf\u66f2\u7ebf","text":"<p>\u7ed3\u5408\u6bcf\u4e2a\u6e29\u5ea6\u5e73\u5747\u7ed3\u6784\u7684\u6676\u683c\u4fe1\u606f\u548c\u6781\u5316\u6587\u4ef6\uff08<code>XX-pol.dat</code>\uff09\u8fdb\u884c\u5206\u6790\uff0c\u53ef\u4ee5\u5f97\u5230\u5982\u4e0b\u56fe\uff1a</p> <p>\u8be5\u8d8b\u52bf\u663e\u793a\u5728\u7ea6 <code>600 K</code> \u9644\u8fd1\u53d1\u751f\u660e\u663e\u76f8\u53d8\uff0c\u6b64\u65f6\u6781\u5316\u6d88\u5931\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#pbtio3srtio3","title":"PbTiO3/SrTiO3 \u8d85\u6676\u683c\u4e2d\u7684\u62d3\u6251\u7ed3\u6784","text":"<p>\u5047\u8bbe <code>movie.xyz</code> \u662f\u5f53\u524d\u76ee\u5f55\u4e0b PbTiO3/SrTiO3 \u8d85\u6676\u683c\u7684\u8f68\u8ff9\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#1-25","title":"\u7b2c 1 \u6b65\uff1a\u4f7f\u7528\u6700\u540e 25% \u5e27\u6784\u5efa\u5e73\u5747\u7ed3\u6784","text":"<pre><code>gpumdkit.sh -calc avg-struct -i movie.xyz -l 0.25 -o model-avg.xyz\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#2-ti","title":"\u7b2c 2 \u6b65\uff1a\u6784\u5efa Ti \u8fd1\u90bb\u5217\u8868","text":"<pre><code>gpumdkit.sh -calc nlist -i model-avg.xyz -c 4.0 -n 6 -C Ti -E O -o nl-Ti-O.dat\n</code></pre>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#3-plane-grid","title":"\u7b2c 3 \u6b65\uff1a\u7ed8\u5236 plane-grid \u56fe","text":"<pre><code>gpumdkit.sh -calc disp -i movie.xyz -n nl-Ti-O.dat -l 0.25 -o disp-last25.dat\ngpumdkit.sh -plt plane-grid -i model-avg.xyz -d disp-last25.dat -e Ti --select-xy 0 -o plot-topology\n</code></pre> <p>\u8fd9\u4f1a\u5f97\u5230\u4e0e\u524d\u9762\u5c55\u793a\u76f8\u4f3c\u7684\u56fe\u3002\u5728 PTO \u533a\u57df\u53ef\u4ee5\u770b\u5230\u7c7b\u4f3c\u6da1\u65cb\u7684\u6781\u5316\u56fe\u6837\uff0c\u800c STO \u533a\u57df\u7684\u6781\u5316\u63a5\u8fd1\u4e8e\u96f6\u3002</p> <p>\u6ce8\u610f\uff1a\u793a\u4f8b\u56fe\u4f7f\u7528\u4e86\u81ea\u5b9a\u4e49 colormap\u3002GPUMDkit \u9ed8\u8ba4\u8f93\u51fa\u4f7f\u7528\u4e0d\u540c\u98ce\u683c\uff0c\u53ef\u901a\u8fc7\u4fee\u6539\u7ed8\u56fe\u811a\u672c\u8fdb\u884c\u8c03\u6574\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_21","title":"\u5176\u4ed6\u4f53\u7cfb","text":""},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#-","title":"\u6709\u673a-\u65e0\u673a\u6742\u5316\u94c1\u7535\u4f53","text":"<p>\u5728\u8bb8\u591a\u6709\u673a-\u65e0\u673a\u94c1\u7535\u4f53\u4e2d\uff0c\u6781\u5316\u4e0e\u5404\u5411\u5f02\u6027\u7684\u5206\u5b50\u5355\u5143\u5bc6\u5207\u76f8\u5173\u3002\u8ddf\u8e2a\u5206\u5b50\u53d6\u5411\u7684\u4e00\u79cd\u5b9e\u7528\u65b9\u6cd5\u662f\u4f7f\u7528\u952e\u77e2\u91cf\u3002</p> <p>\u5bf9\u4e8e TMCM-CdCl3\uff0c\u53ef\u4ee5\u4f7f\u7528 TMCM \u5206\u5b50\u4e2d\u7684 C-Cl \u952e\u65b9\u5411\u4f5c\u4e3a\u53d6\u5411\u4ee3\u7406\uff0c\u5e76\u636e\u6b64\u4f30\u8ba1\u6781\u5316\u6001\uff1a</p> <pre><code># Find the nearest Cl around each C (tune cutoff if needed)\ngpumdkit.sh -calc nlist -i model.xyz -c 3 -n 1 -C C -E Cl -o nl-C-Cl.dat\n\n# Compute C-Cl bond vectors from the trajectory\ngpumdkit.sh -calc disp -i movie.xyz -n nl-C-Cl.dat -o ccl_vectors.dat\n</code></pre> <p>\u968f\u540e\u53ef\u4ee5\u628a <code>ccl_vectors.dat</code> \u4f5c\u4e3a\u53d6\u5411\u5e8f\u53c2\u91cf\u8fdb\u884c\u5206\u6790\u3002\u66f4\u591a\u7ec6\u8282\u53ef\u53c2\u8003\uff1aPhys. Rev. Lett. 136, 016801\u3002</p>"},{"location":"zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html#_22","title":"\u5176\u4ed6\u94c1\u7535\u6750\u6599\u5bb6\u65cf","text":"<p>\u9664 <code>ABO3</code> \u5916\uff0c<code>ferrodispcalc</code> \u4e5f\u53ef\u4ee5\u9002\u914d\u8bb8\u591a\u94c1\u7535\u4f53\u7cfb\uff0c\u5305\u62ec\u6c2e\u5316\u7269\u3001\u6c27\u5316\u94ea\u57fa\u5316\u5408\u7269\u3001\u6709\u673a-\u65e0\u673a\u6742\u5316\u4f53\u7cfb\u4ee5\u53ca\u90e8\u5206\u4e8c\u7ef4\u94c1\u7535\u6750\u6599\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html","title":"\u683c\u5f0f\u8f6c\u6362","text":"\ud83d\udd04 \u683c\u5f0f\u8f6c\u6362 <p>\u683c\u5f0f\u8f6c\u6362\u6a21\u5757\u7528\u4e8e\u5728\u5e38\u89c1\u539f\u5b50\u6a21\u62df\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8f6c\u6362\uff0c\u540c\u65f6\u63d0\u4f9b group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u5e27\u63d0\u53d6\u7b49\u5143\u6570\u636e\u5904\u7406\u529f\u80fd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_1","title":"\u529f\u80fd\u7b80\u4ecb","text":"<p>\u672c\u6a21\u5757\u5728\u8ba1\u7b97\u6750\u6599\u79d1\u5b66\u4e2d\u5e38\u7528\u7684\u7ed3\u6784\u548c\u8f68\u8ff9\u6587\u4ef6\u683c\u5f0f\u4e4b\u95f4\u8fdb\u884c\u8f6c\u6362\u3002\u652f\u6301 VASP\u3001LAMMPS\u3001CP2K\u3001ABACUS\u3001CIF\u3001ASE \u8f68\u8ff9\u548c extxyz \u683c\u5f0f\u3002\u8fd8\u63d0\u4f9b\u6dfb\u52a0 group \u6807\u7b7e\u3001\u6743\u91cd\u3001\u63d0\u53d6\u5e27\u548c\u6269\u80de\u7b49\u5de5\u5177\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_2","title":"\u51c6\u5907\u5de5\u4f5c","text":"<p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/format_conversion/</code></p> <p>\u786e\u4fdd\u5df2\u5b89\u88c5 GPUMDkit\u3002\u5b89\u88c5\u8bf4\u660e\u8bf7\u53c2\u89c1\u5feb\u901f\u5165\u95e8\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_3","title":"\u652f\u6301\u7684\u683c\u5f0f","text":"<ul> <li>VASP\uff1a<code>POSCAR</code>\u3001<code>CONTCAR</code>\u3001<code>OUTCAR</code>\u3001<code>XDATCAR</code></li> <li>LAMMPS\uff1adata \u6587\u4ef6\u548c dump \u8f68\u8ff9</li> <li>CP2K\uff1a\u8f93\u51fa log\u3001\u5750\u6807\u3001\u529b\u548c\u6676\u80de\u6587\u4ef6</li> <li>ABACUS\uff1aSCF/MD \u8f93\u51fa</li> <li>CIF\uff1a\u6676\u4f53\u7ed3\u6784\u6587\u4ef6</li> <li>ASE trajectory\uff1a<code>.traj</code></li> <li>extxyz\uff1aGPUMD \u548c NEP \u5e38\u7528\u7684\u7ed3\u6784\u683c\u5f0f</li> </ul>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_4","title":"\u4ea4\u4e92\u6a21\u5f0f","text":"<p>\u6253\u5f00 GPUMDkit\uff1a</p> <pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>1) Format Conversion\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+-------------------------------------------------------------+\n|                   FORMAT CONVERSION TOOLS                   |\n+-------------------------------------------------------------+\n| 101) VASP to extxyz            106) Add group labels        |\n| 102) MTP to extxyz             107) Add weight to extxyz    |\n| 103) CP2K to extxyz            108) Extract frame extxyz    |\n| 104) ABACUS to extxyz          109) Clean XYZ info          |\n| 105) extxyz to POSCAR          110) Replicate structure     |\n+-------------------------------------------------------------+\n| out2exyz) OUTCAR to extxyz     xdat2exyz) XDATCAR to extxyz |\n| pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |\n| cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |\n| cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|\n+-------------------------------------------------------------+\n| 000) Return to main menu                                    |\n+-------------------------------------------------------------+\nInput the function number or converter keyword:\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_5","title":"\u6bcf\u4e2a\u5165\u53e3\u7684\u4f5c\u7528","text":"\u5165\u53e3 \u8c03\u7528\u811a\u672c \u529f\u80fd \u9002\u7528\u573a\u666f <code>101</code> <code>out2xyz.sh</code> VASP OUTCAR \u8f6c extxyz\uff0cshell \u7248\u672c \u6279\u91cf\u8f6c\u6362 VASP \u8ba1\u7b97\u76ee\u5f55 <code>102</code> <code>mtp2xyz.py</code> MTP cfg \u8f6c extxyz \u8f6c\u6362 MTP \u6570\u636e <code>103</code> <code>cp2k_log2xyz.py</code> / <code>cp2k2xyz.py</code> CP2K \u8f6c extxyz \u53ef\u9009\u62e9 log/inp \u8def\u7ebf\u6216 pos/frc/cell \u8def\u7ebf <code>104</code> <code>abacus2xyz_scf.sh</code> / <code>abacus2xyz_md.sh</code> ABACUS \u8f6c extxyz \u8f6c\u6362 ABACUS SCF \u6216 MD \u8f93\u51fa <code>105</code> <code>exyz2pos.py</code> extxyz \u8f6c POSCAR \u5c06 extxyz \u6bcf\u4e00\u5e27\u5199\u6210 POSCAR <code>106</code> <code>add_groups.py</code> \u6dfb\u52a0 group \u6807\u7b7e \u4e3a GPUMD \u76f8\u5173\u6d41\u7a0b\u6dfb\u52a0\u539f\u5b50\u5206\u7ec4\u6807\u7b7e <code>107</code> <code>add_weight.py</code> \u6dfb\u52a0\u6743\u91cd \u4fee\u6539\u8bad\u7ec3\u96c6\u7ed3\u6784\u6743\u91cd <code>108</code> <code>get_frame.py</code> \u63d0\u53d6\u5355\u5e27 \u4ece extxyz \u8f68\u8ff9\u5bfc\u51fa\u67d0\u4e00\u5e27 <code>109</code> <code>clean_xyz.py</code> \u6e05\u7406 XYZ \u4fe1\u606f \u5220\u9664\u591a\u4f59 extxyz \u5c5e\u6027 <code>110</code> <code>replicate.py</code> \u6269\u80de \u6309\u500d\u6570\u6216\u76ee\u6807\u539f\u5b50\u6570\u6269\u80de <code>out2exyz</code> <code>out2exyz.py</code> OUTCAR \u8f6c extxyz\uff0cPython \u7248\u672c VASP OUTCAR \u8f6c\u6362\u7684\u53e6\u4e00\u4e2a\u5165\u53e3 <code>pos2exyz</code> <code>pos2exyz.py</code> POSCAR \u8f6c extxyz \u8f6c\u6362\u5355\u4e2a\u7ed3\u6784 <code>cif2pos</code> <code>cif2pos.py</code> CIF \u8f6c POSCAR \u4ece CIF \u51c6\u5907 VASP \u8f93\u5165 <code>cif2exyz</code> <code>cif2exyz.py</code> CIF \u8f6c extxyz \u4ece CIF \u51c6\u5907 GPUMDkit \u8f93\u5165 <code>xdat2exyz</code> <code>xdatcar2exyz.py</code> XDATCAR \u8f6c extxyz \u8f6c\u6362 VASP MD \u8f68\u8ff9 <code>pos2lmp</code> <code>pos2lmp.py</code> POSCAR \u8f6c LAMMPS data \u51c6\u5907 LAMMPS \u8f93\u5165 <code>lmp2exyz</code> <code>lmp2exyz.py</code> LAMMPS dump \u8f6c extxyz \u8f6c\u6362 LAMMPS \u8f68\u8ff9 <code>traj2exyz</code> <code>traj2exyz.py</code> ASE traj \u8f6c extxyz \u8f6c\u6362 ASE \u8f68\u8ff9"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_6","title":"\u5feb\u901f\u547d\u4ee4\u8868","text":"\u6765\u6e90 \u76ee\u6807 \u547d\u4ee4 OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2xyz &lt;dir&gt;</code> OUTCAR \u76ee\u5f55 extxyz <code>gpumdkit.sh -out2exyz &lt;dir&gt;</code> POSCAR extxyz <code>gpumdkit.sh -pos2exyz POSCAR model.xyz</code> extxyz POSCAR \u6587\u4ef6 <code>gpumdkit.sh -exyz2pos train.xyz</code> XDATCAR extxyz <code>gpumdkit.sh -xdat2exyz XDATCAR dump.xyz</code> POSCAR LAMMPS data <code>gpumdkit.sh -pos2lmp POSCAR lammps.data</code> LAMMPS dump extxyz <code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl</code> CIF POSCAR <code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp</code> CIF extxyz <code>gpumdkit.sh -cif2exyz input.cif model.xyz</code> ASE traj extxyz <code>gpumdkit.sh -traj2exyz input.traj output.xyz</code> extxyz clean extxyz <code>gpumdkit.sh -clean_xyz input.xyz clean.xyz</code>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_7","title":"\u5e38\u89c1\u4f8b\u5b50","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#vasp","title":"\u8f6c\u6362 VASP \u7ed3\u679c","text":"<p>\u529f\u80fd\uff1a \u5728\u76ee\u5f55\u4e2d\u641c\u7d22 VASP OUTCAR \u6587\u4ef6\uff0c\u5e76\u5c06\u5b83\u4eec\u8f6c\u6362\u4e3a\u5355\u4e2a extxyz \u6587\u4ef6\uff0c\u7528\u4e8e NEP \u8bad\u7ec3\u6216\u5206\u6790\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -out2xyz ./vasp_results/\n</code></pre> <p>\u4e5f\u53ef\u4ee5\u4f7f\u7528 Python \u7248\u672c\uff1a</p> <pre><code>gpumdkit.sh -out2exyz ./vasp_results/\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u683c\u5f0f\u8f6c\u6362\u83dc\u5355\u4e2d\u9009\u62e9 <code>101</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: out2xyz.sh                              |\n| Developer: Yanzhou WANG (yanzhowang@gmail.com)  |\n&gt;-------------------------------------------------&lt;\nInput the directory containing OUTCARs\nExample: ./\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u51fa\uff1a \u5305\u542b\u8f6c\u6362\u540e\u7ed3\u6784\u7684 extxyz \u6587\u4ef6\uff0c\u53ef\u7528\u4e8e NEP \u8bad\u7ec3\u6216\u8fdb\u4e00\u6b65\u5206\u6790\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#group","title":"\u6dfb\u52a0 group \u6807\u7b7e","text":"<p>\u529f\u80fd\uff1a \u4e3a\u7ed3\u6784\u6587\u4ef6\u6dfb\u52a0\u539f\u5b50 group \u6807\u7b7e\u3002\u4e00\u4e9b GPUMD \u76f8\u5173\u6d41\u7a0b\u9700\u8981 group \u6807\u7b7e\uff0c\u4f8b\u5982\u7279\u5b9a\u5143\u7d20\u7684 MSD \u6216\u6269\u6563\u6027\u8d28\u8ba1\u7b97\u3002</p> <p>\u547d\u4ee4\u884c\u6a21\u5f0f\uff1a</p> <pre><code>gpumdkit.sh -addgroup POSCAR Li Y Cl\n</code></pre> <p>\u8be5\u547d\u4ee4\u8bfb\u53d6\u8f93\u5165\u7ed3\u6784\uff0c\u5e76\u5199\u51fa\u5e26 group \u4fe1\u606f\u7684 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\uff1a \u5728\u683c\u5f0f\u8f6c\u6362\u83dc\u5355\u4e2d\u9009\u62e9 <code>106</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| Calling the script in Scripts/format_conversion |\n| Script: add_groups.py                           |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;POSCAR&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: POSCAR Li Y Cl\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u51fa\uff1a \u6dfb\u52a0\u4e86 group \u6807\u7b7e\u7684 extxyz \u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_8","title":"\u5e38\u7528\u811a\u672c\u8bf4\u660e","text":""},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#poscar-extxyz","title":"POSCAR \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -pos2exyz POSCAR model.xyz\n</code></pre> <p>\u9002\u5408\u628a\u5355\u4e2a VASP \u7ed3\u6784\u8f6c\u6210 extxyz \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>pos2exyz</code></p> <pre><code>Input &lt;POSCAR&gt; &lt;output.xyz&gt;\nExample: POSCAR model.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz-poscar","title":"extxyz \u8f6c POSCAR","text":"<pre><code>gpumdkit.sh -exyz2pos structures.xyz\n</code></pre> <p>\u4f1a\u5c06 extxyz \u4e2d\u6240\u6709\u5e27\u8f6c\u6362\u6210 <code>POSCAR_*.vasp</code> \u6587\u4ef6\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3\uff1a<code>105</code></p> <pre><code>Input the name of extxyz\nExample: ./train.xyz\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#lammps-dump-extxyz","title":"LAMMPS dump \u8f6c extxyz","text":"<pre><code>gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl\n</code></pre> <p>\u5143\u7d20\u987a\u5e8f\u5fc5\u987b\u5bf9\u5e94 LAMMPS \u4e2d\u7684 atom type ID\u3002\u4f8b\u5982 type 1 \u662f Li\u3001type 2 \u662f Y\u3001type 3 \u662f Cl\uff0c\u5219\u8f93\u5165 <code>Li Y Cl</code>\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u5173\u952e\u8bcd\uff1a<code>lmp2exyz</code></p> <pre><code>Input &lt;dump_file&gt; &lt;element1&gt; &lt;element2&gt; ...\nExample: dump.lammpstrj Li O\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#cif","title":"CIF \u8f6c\u6362","text":"<pre><code>gpumdkit.sh -cif2pos input.cif POSCAR.vasp\ngpumdkit.sh -cif2exyz input.cif model.xyz\n</code></pre> <p>\u5982\u679c\u540e\u7eed\u9700\u8981 VASP \u8ba1\u7b97\uff0c\u4f7f\u7528 <code>-cif2pos</code>\uff1b\u5982\u679c\u540e\u7eed\u8981\u8fdb\u5165 GPUMDkit \u5206\u6790\uff0c\u4f7f\u7528 <code>-cif2exyz</code>\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_9","title":"\u6dfb\u52a0\u6743\u91cd","text":"<pre><code>gpumdkit.sh -addweight train.xyz train_weighted.xyz 5\n</code></pre> <p>\u7528\u4e8e\u7ed9\u8bad\u7ec3\u96c6\u7ed3\u6784\u6dfb\u52a0\u6216\u4fee\u6539\u6743\u91cd\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_10","title":"\u6269\u80de","text":"<pre><code>gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2\ngpumdkit.sh -replicate POSCAR supercell.vasp 256\n</code></pre> <p>\u7b2c\u4e00\u79cd\u6309\u6676\u80de\u500d\u6570\u6269\u80de\uff0c\u7b2c\u4e8c\u79cd\u6309\u76ee\u6807\u539f\u5b50\u6570\u81ea\u52a8\u9009\u62e9\u6269\u80de\u65b9\u5f0f\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_11","title":"\u63d0\u53d6\u5355\u5e27","text":"<pre><code>gpumdkit.sh -get_frame dump.xyz 1000\n</code></pre> <p>\u4ece extxyz \u8f68\u8ff9\u4e2d\u63d0\u53d6\u7b2c <code>1000</code> \u5e27\uff08\u7d22\u5f15\u4ece 0 \u5f00\u59cb\uff09\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#extxyz","title":"\u62c6\u5206\u591a\u5e27 extxyz","text":"<p><code>split_single_xyz.py</code> \u5c06\u591a\u5e27 extxyz \u6587\u4ef6\u62c6\u5206\u4e3a\u5355\u5e27\u6587\u4ef6\u3002</p> <pre><code>python Scripts/format_conversion/split_single_xyz.py dump.xyz\n</code></pre> <p>\u751f\u6210 <code>model_0.xyz</code>\u3001<code>model_1.xyz</code>\u3001... \u7b49\u5355\u5e27\u6587\u4ef6\u3002</p>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#mtp","title":"MTP \u8f6c\u6362","text":"<p>\u5c06 MTP <code>.cfg</code> \u683c\u5f0f\u8f6c\u6362\u4e3a extxyz\uff1a</p> <pre><code>gpumdkit.sh    # \u9009\u62e9\uff1a1) \u683c\u5f0f\u8f6c\u6362 \u2192 102\n</code></pre> <p>\u4ea4\u4e92\u63d0\u793a\uff1a</p> <pre><code>Input &lt;filename.cfg&gt; &lt;Symbol1 Symbol2 Symbol3 ...&gt;\nExample: train.cfg Pd Ag\n------------&gt;&gt;\n</code></pre>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#abacus","title":"ABACUS \u8f6c\u6362","text":"<p>\u5c06 ABACUS \u8f93\u51fa\u8f6c\u6362\u4e3a extxyz\uff1a</p> <pre><code>gpumdkit.sh    # \u9009\u62e9\uff1a1) \u683c\u5f0f\u8f6c\u6362 \u2192 104\n</code></pre> <p>\u83dc\u5355\u63d0\u4f9b\u4e24\u4e2a\u9009\u9879\uff1a</p> <ol> <li>SCF \u8f93\u51fa\uff08<code>running_scf.log</code>\uff09</li> <li>MD \u8f93\u51fa\uff08<code>running_md.log</code>\uff09</li> </ol>"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_12","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae LAMMPS \u8f6c\u6362\u540e\u5143\u7d20\u4e0d\u5bf9 \u68c0\u67e5 dump \u6587\u4ef6\u540e\u7684\u5143\u7d20\u987a\u5e8f extxyz \u5143\u6570\u636e\u592a\u591a \u4f7f\u7528 <code>-clean_xyz input.xyz clean.xyz</code> \u8f6c\u6362\u540e\u7684\u7ed3\u6784\u770b\u8d77\u6765\u504f\u79fb \u68c0\u67e5\u6e90\u6587\u4ef6\u4e2d\u7684\u5468\u671f\u6027\u8fb9\u754c\u6761\u4ef6/\u6676\u80de\u4fe1\u606f \u63d0\u53d6\u5e27\u4e0d\u5bf9 \u6ce8\u610f\u5e27\u7d22\u5f15\u901a\u5e38\u4ece 0 \u5f00\u59cb"},{"location":"zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html#_13","title":"\u8bf4\u660e","text":"<p>\u5982\u679c\u67d0\u4e2a\u8f6c\u6362\u811a\u672c\u7f3a\u5c11\u6240\u9700 Python \u5305\uff0c\u8fd0\u884c\u8be5\u529f\u80fd\u65f6 Python \u4f1a\u7ed9\u51fa\u76f8\u5e94\u63d0\u793a\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html","title":"\u7ed3\u6784\u91c7\u6837","text":"\ud83d\udce6 \u7ed3\u6784\u91c7\u6837 <p>\u7ed3\u6784\u91c7\u6837\u7528\u4e8e\u4ece\u8f68\u8ff9\u4e2d\u9009\u62e9\u5019\u9009\u7ed3\u6784\u3001\u751f\u6210\u6270\u52a8\u7ed3\u6784\uff0c\u6216\u6839\u636e\u6a21\u578b\u504f\u5dee\u6311\u9009\u503c\u5f97\u8fdb\u4e00\u6b65\u8ba1\u7b97\u7684\u7ed3\u6784\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/sample_structures/</code></p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_1","title":"\u4ea4\u4e92\u6a21\u5f0f\u5165\u53e3","text":"<pre><code>gpumdkit.sh\n</code></pre> <p>\u9009\u62e9\uff1a</p> <pre><code>2) Sample Structures\n</code></pre> <p>\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+------------------------------------------------------+\n|                 SAMPLE STRUCTURE TOOLS               |\n+------------------------------------------------------+\n| 201) Sample structures from extxyz                   |\n| 202) PyNEP sampling [deprecated]                    |\n| 203) FPS sampling by NepTrain [preferred]            |\n| 204) Perturb structure                               |\n| 205) Select max force deviation structs              |\n+------------------------------------------------------+\n| 000) Return to the main menu                         |\n+------------------------------------------------------+\nInput the function number:\n</code></pre> <p>\u5e38\u7528\u529f\u80fd\uff1a</p> \u83dc\u5355 \u65b9\u6cd5 \u7528\u9014 201 uniform/random \u4ece\u8f68\u8ff9\u4e2d\u5747\u5300\u6216\u968f\u673a\u62bd\u5e27 202 PyNEP notice \u53ea\u6253\u5370\u63d0\u793a\uff1b\u771f\u6b63\u8fd0\u884c PyNEP \u8bf7\u7528 <code>gpumdkit.sh -pynep</code> 203 NepTrain FPS \u4f7f\u7528 NepTrain \u63cf\u8ff0\u7b26\u7684 FPS \u91c7\u6837 204 perturb \u4ece POSCAR/CONTCAR \u751f\u6210\u6270\u52a8\u7ed3\u6784 205 force deviation \u4ece active learning \u8f93\u51fa\u4e2d\u9009\u62e9\u9ad8\u504f\u5dee\u7ed3\u6784"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_2","title":"\u5747\u5300/\u968f\u673a\u91c7\u6837","text":"<p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>201</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;sampling_method&gt; &lt;num_samples&gt; [skip_num]\n[skip_num]: number of initial frames to skip, default value is 0\nSampling_method: 'uniform' or 'random'\nExample: train.xyz uniform 50\n------------&gt;&gt;\n</code></pre> <p>\u4f8b\u5982\u8f93\u5165\uff1a</p> <pre><code>dump.xyz uniform 50\n</code></pre> <p>\u6216\uff1a</p> <pre><code>dump.xyz random 100 500\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>uniform</code> / <code>random</code> \u91c7\u6837\u65b9\u6cd5 <code>50</code> / <code>100</code> \u91c7\u6837\u7ed3\u6784\u6570 <code>500</code> \u53ef\u9009\uff0c\u8df3\u8fc7\u524d 500 \u5e27 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>sampled_structures.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#neptrain-fps","title":"NepTrain FPS","text":"<p>NepTrain \u7248\u672c\u7684 FPS\u3002\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>203</code>\uff1b\u4e5f\u53ef\u4ee5\u76f4\u63a5\u8fd0\u884c\u811a\u672c\uff1a</p> <pre><code>python Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>203</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;sample.xyz&gt; &lt;train.xyz&gt; &lt;nep_model&gt;\nExample: dump.xyz train.xyz nep.txt\n------------&gt;&gt;\n</code></pre> <p>\u8f93\u5165\uff1a</p> \u6587\u4ef6 \u542b\u4e49 <code>dump.xyz</code> \u5019\u9009\u7ed3\u6784 <code>train.xyz</code> \u5f53\u524d\u8bad\u7ec3\u96c6 <code>nep.txt</code> \u7528\u4e8e\u8ba1\u7b97\u63cf\u8ff0\u7b26\u7684 NEP \u6a21\u578b <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> <li><code>select.png</code></li> <li><code>pca_sample.txt</code></li> <li><code>pca_train.txt</code></li> <li><code>pca_selected.txt</code></li> </ul> <p>\u8fd0\u884c\u65f6\u53ef\u4ee5\u9009\u62e9\u6309\u6700\u5c0f\u8ddd\u79bb\u9608\u503c\u91c7\u6837\uff0c\u6216\u6307\u5b9a\u91c7\u6837\u7ed3\u6784\u6570\u3002\u811a\u672c\u968f\u540e\u4f1a\u6253\u5370\uff1a</p> <pre><code>Choose selection method:\n1) Select structures based on minimum distance\n2) Select structures based on number of structures\n------------&gt;&gt;\n</code></pre> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>NepTrain</code>\uff0c\u8fd0\u884c\u65f6\u4f1a\u63d0\u793a\u76f8\u5173\u5f15\u7528\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep","title":"PyNEP \u65e7\u5165\u53e3","text":"<p>PyNEP FPS \u4ecd\u7136\u4fdd\u7559\u517c\u5bb9\uff0c\u4f46\u53ea\u901a\u8fc7 <code>-pynep</code> \u5165\u53e3\u8c03\u7528\u3002</p> <p>\u5982\u679c\u5728\u4ea4\u4e92\u83dc\u5355\u4e2d\u9009\u62e9 <code>202</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+-------------------------------------------------+\n| Function 202 is no longer supported here.       |\n| PyNEP package is no longer actively maintained. |\n| Please use 203) NepTrain sampling instead.      |\n| If you still need PyNEP compatibility, run:     |\n|                 gpumdkit.sh -pynep              |\n+-------------------------------------------------+\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep_1","title":"\u4e32\u884c PyNEP","text":"<pre><code>python Scripts/sample_structures/pynep_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#pynep_2","title":"\u5e76\u884c PyNEP","text":"<pre><code>python Scripts/sample_structures/parallel_pynep_select_structs.py dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u6700\u540e\u4e00\u4e2a\u53c2\u6570\u662f CPU \u7ebf\u7a0b\u6570\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#gpumdkit","title":"GPUMDkit \u5165\u53e3","text":"<pre><code>gpumdkit.sh -pynep\n</code></pre> <p>\u968f\u540e\u8f93\u5165\uff1a</p> <pre><code>dump.xyz train.xyz nep.txt 8\n</code></pre> <p>\u8fd9\u4e2a\u5165\u53e3\u9700\u8981 <code>pynep</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_3","title":"\u7ed3\u6784\u6270\u52a8","text":"<p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>204</code>\uff1b\u4e5f\u53ef\u4ee5\u76f4\u63a5\u8fd0\u884c\u811a\u672c\uff1a</p> <pre><code>python Scripts/sample_structures/perturb_structure.py POSCAR 20 0.03 0.2 uniform\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>204</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;input.vasp&gt; &lt;pert_num&gt; &lt;cell_pert_fraction&gt; &lt;atom_pert_distance&gt; &lt;atom_pert_style&gt;\nThe default parameters for perturb are 20 0.03 0.2 uniform\nExample: POSCAR 20 0.03 0.2 uniform\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>POSCAR</code> \u8f93\u5165\u7ed3\u6784 <code>20</code> \u751f\u6210\u7ed3\u6784\u6570 <code>0.03</code> \u6676\u80de\u6270\u52a8\u6bd4\u4f8b <code>0.2</code> \u539f\u5b50\u6270\u52a8\u8ddd\u79bb\uff0c\u5355\u4f4d Angstrom <code>uniform</code> \u6270\u52a8\u65b9\u5f0f\uff0c\u53ef\u9009 <code>normal</code>\u3001<code>uniform</code>\u3001<code>const</code> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>POSCAR_01.vasp</code>\u3001<code>POSCAR_02.vasp</code> \u7b49</li> </ul> <p>\u8be5\u529f\u80fd\u9700\u8981 <code>dpdata</code>\u3002\u4f7f\u7528\u6b64\u529f\u80fd\u65f6\u5efa\u8bae\u5f15\u7528 dpdata \u5305\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_4","title":"\u6700\u5927\u529b\u504f\u5dee\u7ed3\u6784\u9009\u62e9","text":"<p>\u8be5\u529f\u80fd\u9700\u8981\u914d\u5408 GPUMD \u7684 <code>active</code> \u547d\u4ee4\u4f7f\u7528\u3002<code>active</code> \u901a\u8fc7\u59d4\u5458\u4f1a\u8bc4\u5ba1\u673a\u5236\uff0c\u8ba9\u591a\u6761\u52bf\u51fd\u6570\u5bf9\u540c\u4e00\u7ed3\u6784\u8fdb\u884c\u9884\u6d4b\uff0c\u5e76\u8bb0\u5f55\u6bcf\u4e2a\u7ed3\u6784\u7684\u6700\u5927\u529b\u504f\u5dee\u3002<code>select_max_modev.py</code> \u4f1a\u4ece <code>active.out</code> \u548c <code>active.xyz</code> \u4e2d\u9009\u62e9\u529b\u504f\u5dee\u8f83\u5927\u7684\u7ed3\u6784\uff0c\u5199\u5165 <code>selected.xyz</code>\u3002</p> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>205</code>\uff1b\u4e5f\u53ef\u4ee5\u76f4\u63a5\u8fd0\u884c\u811a\u672c\uff1a</p> <pre><code>python Scripts/sample_structures/select_max_modev.py 200 0.15\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>205</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>+----------------------------------------------------+\n| Select max force deviation structs from active.xyz |\n|     generated by the active command in gpumd.      |\n+----------------------------------------------------+\nInput &lt;structs_num&gt; &lt;threshold&gt; (eg. 200 0.15)\n------------&gt;&gt;\n</code></pre> <p>\u9700\u8981\u5f53\u524d\u76ee\u5f55\u4e0b\u6709\uff1a</p> <ul> <li><code>active.out</code></li> <li><code>active.xyz</code></li> </ul> <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>selected.xyz</code></li> </ul>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_5","title":"\u5e27\u8303\u56f4\u63d0\u53d6","text":"<p><code>frame_range.py</code> \u662f\u4e00\u4e2a\u72ec\u7acb\u7684 CLI \u5de5\u5177\uff0c\u4e0d\u5728\u7ed3\u6784\u91c7\u6837\u4ea4\u4e92\u83dc\u5355 <code>201\u2013205</code> \u4e2d\u3002\u5b83\u9002\u5408\u5728\u91c7\u6837\u524d\u5148\u622a\u53d6\u8f68\u8ff9\u7684\u4e00\u6bb5\uff0c\u4f8b\u5982\u53ea\u4fdd\u7559\u5e73\u8861\u540e\u7684\u540e\u534a\u6bb5\u8f68\u8ff9\u3002</p> <pre><code>gpumdkit.sh -frame_range dump.xyz 0 0.8\npython Scripts/sample_structures/frame_range.py dump.xyz 0 0.8\n</code></pre> <p>\u8fd9\u4f1a\u5199\u5165\u8f68\u8ff9 0% \u5230 80% \u7684\u5e27\u3002\u53c2\u6570\u4f7f\u7528\u8f68\u8ff9\u6bd4\u4f8b\uff0c\u8303\u56f4\u4e3a <code>0</code> \u5230 <code>1</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_6","title":"\u793a\u4f8b\u547d\u4ee4","text":"<p>\u4e0b\u9762\u662f\u4e00\u4e2a\u5e38\u89c1\u7684\u91c7\u6837\u524d\u5904\u7406\u987a\u5e8f\uff1a\u5148\u7528\u5206\u6790\u5de5\u5177\u68c0\u67e5\u548c\u8fc7\u6ee4\u5019\u9009\u8f68\u8ff9\uff0c\u518d\u8fdb\u884c FPS \u91c7\u6837\u3002\u524d\u4e24\u4e2a\u547d\u4ee4\u5c5e\u4e8e\u5206\u6790\u5de5\u5177\uff0c\u6700\u540e\u4e00\u6b65\u5c5e\u4e8e\u672c\u9875\u7684\u7ed3\u6784\u91c7\u6837\u3002</p> <pre><code>gpumdkit.sh -min_dist_pbc dump.xyz\ngpumdkit.sh -filter_box dump.xyz 13\npython Scripts/sample_structures/neptrain_select_structs.py dump.xyz train.xyz nep.txt\n</code></pre> <p>\u6700\u540e\u4e00\u6b65\u4e5f\u53ef\u4ee5\u5728\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>2) \u7ed3\u6784\u91c7\u6837 \u2192 203</code>\u3002</p>"},{"location":"zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html#_7","title":"\u5e38\u89c1\u95ee\u9898","text":"\u95ee\u9898 \u5efa\u8bae FPS \u9009\u51fa\u592a\u591a\u76f8\u4f3c\u7ed3\u6784 \u8c03\u5927\u8ddd\u79bb\u9608\u503c\u6216\u9650\u5236\u6700\u5927\u9009\u62e9\u6570 \u6270\u52a8\u7ed3\u6784\u4e0d\u5408\u7406 \u51cf\u5c0f <code>cell_pert</code> \u548c <code>atom_pert</code> <code>active.out</code> \u548c <code>active.xyz</code> \u4e0d\u5339\u914d \u786e\u4fdd\u6765\u81ea\u540c\u4e00\u6b21 GPUMD active \u8fd0\u884c PCA \u56fe\u5f02\u5e38 \u68c0\u67e5 <code>nep.txt</code> \u662f\u5426\u548c\u4e24\u4e2a\u6570\u636e\u96c6\u5143\u7d20\u4e00\u81f4"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html","title":"\u7ed8\u56fe\u811a\u672c","text":"\ud83d\udcca \u7ed8\u56fe\u811a\u672c <p>\u7ed8\u56fe\u6a21\u5757\u5305\u542b\u4e00\u7cfb\u5217 Python \u811a\u672c\uff0c\u7528\u4e8e\u53ef\u89c6\u5316 GPUMD\u3001NEP \u548c GPUMDkit \u8ba1\u7b97\u5668\u4ea7\u751f\u7684\u6570\u636e\u3002\u6240\u6709\u56fe\u8868\u5747\u53ef\u4ea4\u4e92\u663e\u793a\u6216\u4fdd\u5b58\u4e3a\u9ad8\u5206\u8fa8\u7387 PNG \u6587\u4ef6\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/plt_scripts/</code></p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_1","title":"\u5feb\u901f\u5165\u53e3","text":"<pre><code>gpumdkit.sh -plt              # \u663e\u793a\u6240\u6709\u7ed8\u56fe\u9009\u9879\ngpumdkit.sh -plt &lt;type&gt;       # \u751f\u6210\u6307\u5b9a\u56fe\u8868\ngpumdkit.sh -plt &lt;type&gt; save  # \u4fdd\u5b58\u4e3a PNG\ngpumdkit.sh -plt &lt;type&gt; -h    # \u663e\u793a\u7279\u5b9a\u56fe\u8868\u7684\u5e2e\u52a9\n</code></pre> <p>\u8fd0\u884c <code>gpumdkit.sh -plt</code> \u4f1a\u663e\u793a\u7ed8\u56fe\u547d\u4ee4\u83dc\u5355\uff1a</p> <pre><code>+-----------------------------------------------------------------------------------------------+\n|                     GPUMDkit &lt;version&gt; PLOT &amp; VISUALIZATION TOOLS              |\n+-----------------------------------------------------------------------------------------------+\n|  Usage: gpumdkit.sh -plt &lt;type&gt;                        Help: gpumdkit.sh -plt &lt;type&gt; -h       |\n+-----------------------------------------------------------------------------------------------+\n|                                    NEP Training &amp; Evaluation                                  |\n+-----------------------------------------------------------------------------------------------+\n|  train          - NEP training results           prediction     - NEP prediction results      |\n|  train_test     - NEP train and test results     parity_density - Parity density plot         |\n|  train_density  - Training results density plot  restart        - Parameters in nep.restart   |\n|  charge         - Charge distribution            born_charge    - Born effective charges      |\n|  dimer          - Dimer energy/force curve       force_errors   - Force errors                |\n|  des            - Descriptors                    lr             - Learning rate for gnep      |\n+-----------------------------------------------------------------------------------------------+\n|                                     Diffusion &amp; Transport                                     |\n+-----------------------------------------------------------------------------------------------+\n|  msd            - Mean square displacement       msd_conv       - MSD convergence             |\n|  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |\n|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|\n|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |\n|  D_xyz          - Directional Arrhenius D                                                     |\n|  doas           - Density of atomistic states                                                 |\n+-----------------------------------------------------------------------------------------------+\n|                                    MD &amp; Structural Analysis                                   |\n+-----------------------------------------------------------------------------------------------+\n|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |\n|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |\n|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |\n|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |\n+-----------------------------------------------------------------------------------------------+\n|                                        Heat Transport                                         |\n+-----------------------------------------------------------------------------------------------+\n|  emd            - EMD results                    nemd           - NEMD results                |\n|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |\n+-----------------------------------------------------------------------------------------------+\n|                                          Phonons                                              |\n+-----------------------------------------------------------------------------------------------+\n|  pdos           - VAC and PDOS                                                                |\n+-----------------------------------------------------------------------------------------------+\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u8bad\u7ec3\u4e0e\u9884\u6d4b","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_trainpy","title":"plt_train.py","text":"<p>\u53ef\u89c6\u5316 NEP \u8bad\u7ec3\u8fc7\u7a0b\uff0c\u5305\u62ec loss \u66f2\u7ebf\u3001RMSE \u6f14\u5316\uff0c\u4ee5\u53ca\u80fd\u91cf/\u529b/virial \u7684 DFT vs NEP parity plot\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code>\u3001<code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt train\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_predictionpy","title":"plt_prediction.py","text":"<p>\u53ef\u89c6\u5316\u6d4b\u8bd5\u96c6\u4e0a\u7684 NEP \u9884\u6d4b\u7ed3\u679c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_test.out</code>\u3001<code>force_test.out</code>\u3001<code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt prediction\ngpumdkit.sh -plt test         # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_train_testpy","title":"plt_train_test.py","text":"<p>\u5c06\u8bad\u7ec3\u96c6\u548c\u6d4b\u8bd5\u96c6\u7684 parity plot \u5408\u5e76\u663e\u793a\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code>\u3001<code>energy_test.out</code>\u3001<code>force_test.out</code>\u3001<code>virial_test.out</code></p> <pre><code>gpumdkit.sh -plt train_test\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_parity_densitypy","title":"plt_parity_density.py","text":"<p>\u751f\u6210\u57fa\u4e8e\u5bc6\u5ea6\u7684 parity plot\uff0c\u9002\u7528\u4e8e\u5927\u6570\u636e\u96c6\uff08\u6563\u70b9\u56fe\u8fc7\u4e8e\u5bc6\u96c6\u65f6\u66f4\u6613\u9605\u8bfb\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>energy_train.out</code>\u3001<code>force_train.out</code>\u3001<code>virial_train.out</code></p> <pre><code>gpumdkit.sh -plt parity_density\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_force_errorspy","title":"plt_force_errors.py","text":"<p>\u53c2\u8003 Liu et al. \u7684\u65b9\u6cd5\u7ed8\u5236\u529b\u8bef\u5dee\u8bc4\u4f30\u6307\u6807\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>force_train.out</code></p> <p>\u663e\u793a\u6307\u6807\uff1a - \u529b\u5927\u5c0f\u8bef\u5dee (delta_F) - \u529b\u89d2\u5ea6\u8bef\u5dee (delta_theta) - \u8bef\u5dee\u5206\u5e03</p> <pre><code>gpumdkit.sh -plt force_errors\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_learning_ratepy","title":"plt_learning_rate.py","text":"<p>\u53ef\u89c6\u5316 <code>gnep</code> \u8bad\u7ec3\u8fc7\u7a0b\u4e2d\u7684\u5b66\u4e60\u7387\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>loss.out</code></p> <p>\u6ce8\u610f\uff1a \u4ec5\u9002\u7528\u4e8e <code>gnep</code> \u8bad\u7ec3\u8fc7\u7a0b\u3002</p> <pre><code>gpumdkit.sh -plt lr\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_nep_restartpy","title":"plt_nep_restart.py","text":"<p>\u53ef\u89c6\u5316 <code>nep.restart</code> \u6587\u4ef6\u4e2d\u5b58\u50a8\u7684\u53c2\u6570\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>nep.restart</code></p> <pre><code>gpumdkit.sh -plt restart\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_chargepy","title":"plt_charge.py","text":"<p>\u7ed8\u5236 <code>qNEP</code> \u6a21\u578b\u7684\u7535\u8377\u5206\u5e03\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>charge_train.out</code></p> <p>\u91cd\u8981\u63d0\u793a\uff1a \u786e\u4fdd\u8bad\u7ec3\u96c6\u548c\u7535\u8377\u8f93\u51fa\u7684\u539f\u5b50\u6392\u5e8f\u4e00\u81f4\u3002\u5efa\u8bae\u4f7f\u7528\u5168 batch \u8bad\u7ec3\u6216\u5148\u8fd0\u884c\u9884\u6d4b\u6b65\u9aa4\u3002</p> <pre><code>gpumdkit.sh -plt charge\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_born_chargepy","title":"plt_born_charge.py","text":"<p>\u4e3a\u8bad\u7ec3\u96c6\u548c\u6d4b\u8bd5\u96c6\u521b\u5efa Born \u6709\u6548\u7535\u8377 (BEC) \u7684 parity plot\u3002\u5168\u96f6\u53c2\u8003 BEC \u7684\u7ed3\u6784\u4f1a\u88ab\u8fc7\u6ee4\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>bec_train.out</code>\u3001<code>bec_test.out</code></p> <pre><code>gpumdkit.sh -plt born_charge\ngpumdkit.sh -plt bec          # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_2","title":"\u70ed\u529b\u5b66\u91cf","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_thermopy","title":"plt_thermo.py","text":"<p>\u7efc\u5408\u53ef\u89c6\u5316\u70ed\u529b\u5b66\u6027\u8d28\u7684\u4e3b\u811a\u672c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_thermo2py-plt_thermo3py","title":"plt_thermo2.py &amp; plt_thermo3.py","text":"<p>\u4e0d\u540c\u98ce\u683c\u7684\u70ed\u529b\u5b66\u91cf\u53ef\u89c6\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>thermo.out</code></p> <pre><code>gpumdkit.sh -plt thermo2\ngpumdkit.sh -plt thermo3\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_3","title":"\u6269\u6563\u548c\u79bb\u5b50\u8f93\u8fd0","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msdpy","title":"plt_msd.py","text":"<p>\u7ed8\u5236\u5404\u65b9\u5411\u7684\u5747\u65b9\u4f4d\u79fb (MSD)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt msd\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msd_allpy","title":"plt_msd_all.py","text":"<p>\u5f53 GPUMD \u4e2d\u4f7f\u7528 <code>all_groups</code> \u65f6\uff0c\u5206\u522b\u7ed8\u5236\u6bcf\u79cd\u539f\u5b50\u7684 MSD\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code>\uff08\u9700\u8981\u4f7f\u7528 <code>all_groups</code> \u9009\u9879\u8ba1\u7b97\uff09</p> <p>\u8981\u6c42\uff1a <code>run.in</code> \u4e2d\u7684 <code>compute_msd</code> \u547d\u4ee4\u5fc5\u987b\u4f7f\u7528 <code>all_groups</code>\u3002</p> <pre><code>gpumdkit.sh -plt msd_all msd.out Li P S\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_msd_convergence_checkpy","title":"plt_msd_convergence_check.py","text":"<p>\u68c0\u67e5\u4e0d\u540c\u65f6\u95f4\u7a97\u53e3\u4e0b MSD \u8ba1\u7b97\u7684\u6536\u655b\u6027\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd_step*.out</code>\uff08\u9700\u8981\u5728 <code>compute_msd</code> \u4e2d\u4f7f\u7528 <code>save_every</code> \u9009\u9879\uff09</p> <p>\u8981\u6c42\uff1a \u5728 <code>compute_msd</code> \u547d\u4ee4\u4e2d\u4f7f\u7528 <code>save_every</code>\u3002</p> <p>\u7528\u9014\uff1a \u9a8c\u8bc1 MSD \u662f\u5426\u5df2\u5145\u5206\u6536\u655b\u4ee5\u51c6\u786e\u8ba1\u7b97\u6269\u6563\u7cfb\u6570\u3002</p> <pre><code>gpumdkit.sh -plt msd_conv\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_sdcpy","title":"plt_sdc.py","text":"<p>\u7ed8\u5236\u81ea\u6269\u6563\u7cfb\u6570 (SDC) \u968f\u65f6\u95f4\u7684\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>msd.out</code></p> <pre><code>gpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_arrhenius_dpy","title":"plt_arrhenius_d.py","text":"<p>\u521b\u5efa Arrhenius \u6269\u6563\u7cfb\u6570\u56fe\uff08log10 D vs 1000/T\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>*K/msd.out</code>\uff08\u6bcf\u4e2a\u6e29\u5ea6\u5b50\u76ee\u5f55\u4e0b\u7684 <code>msd.out</code>\uff09</p> <pre><code>gpumdkit.sh -plt arrhenius_d\ngpumdkit.sh -plt D             # \u66ff\u4ee3\u547d\u4ee4\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>T: 300K, D_total: 1.001e-07 cm2/s\nT: 350K, D_total: 4.184e-07 cm2/s\nT: 400K, D_total: 1.027e-06 cm2/s\nEa: 0.230 eV\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_arrhenius_sigmapy","title":"plt_arrhenius_sigma.py","text":"<p>\u521b\u5efa Arrhenius \u79bb\u5b50\u7535\u5bfc\u7387\u56fe\uff08ln(\u03c3\u00b7T) vs 1000/T\uff09\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code>\uff08\u6bcf\u4e2a\u6e29\u5ea6\u5b50\u76ee\u5f55\uff09</p> <pre><code>gpumdkit.sh -plt arrhenius_sigma\ngpumdkit.sh -plt sigma         # \u66ff\u4ee3\u547d\u4ee4\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_4","title":"\u70ed\u8f93\u8fd0","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_emdpy","title":"plt_emd.py","text":"<p>\u5206\u6790\u5e76\u7ed8\u5236\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (EMD) \u70ed\u5bfc\u7387\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 EMD \u8f93\u51fa\u6587\u4ef6</p> <pre><code>gpumdkit.sh -plt emd x        # x \u65b9\u5411\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_nemdpy","title":"plt_nemd.py","text":"<p>\u53ef\u89c6\u5316\u975e\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (NEMD) \u70ed\u8f93\u8fd0\u6027\u8d28\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 NEMD \u8f93\u51fa\u6587\u4ef6</p> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u8bf4\u660e <code>real_length</code> \u4f20\u70ed\u533a\u5b9e\u9645\u957f\u5ea6\uff08nm\uff09\uff0c\u8bbe\u4e3a <code>Auto</code> \u53ef\u81ea\u52a8\u8ba1\u7b97 <code>scale_eff_size</code> \u6709\u6548\u622a\u9762\u79ef\u7f29\u653e\u56e0\u5b50\uff08\u9ed8\u8ba4\uff1a1\uff09\u3002\u4e09\u7ef4\u4f53\u76f8\u7528 1\uff1b\u542b\u771f\u7a7a\u5c42\u7684\u4f4e\u7ef4\u4f53\u7cfb\u7528 S_box / S_eff <code>cutoff_freq</code> SHC \u8ba1\u7b97\u7684\u622a\u6b62\u9891\u7387\uff08THz\uff0c\u9ed8\u8ba4\uff1a60\uff09 <code>save</code> \u53ef\u9009\uff0c\u4fdd\u5b58\u56fe\u7247\u4e3a <code>nemd.png</code> <p>\u6ce8\u610f\uff1a \u5982\u679c\u6ca1\u6709 SHC \u6570\u636e\uff0c\u4f7f\u7528 <code>save</code> \u65f6\u8bf7\u5c06 <code>scale_eff_size</code> \u548c <code>cutoff_freq</code> \u8bbe\u4e3a\u4efb\u610f\u5360\u4f4d\u6570\u5b57\u3002</p> <pre><code>gpumdkit.sh -plt nemd [real_length] [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_hnemdpy","title":"plt_hnemd.py","text":"<p>\u7ed8\u5236\u5747\u5300\u975e\u5e73\u8861\u5206\u5b50\u52a8\u529b\u5b66 (HNEMD) \u7ed3\u679c\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a GPUMD \u7684 HNEMD \u8f93\u51fa\u6587\u4ef6</p> <p>\u53c2\u6570\u8bf4\u660e\uff1a</p> \u53c2\u6570 \u8bf4\u660e <code>scale_eff_size</code> \u6709\u6548\u622a\u9762\u79ef\u7f29\u653e\u56e0\u5b50\uff08\u9ed8\u8ba4\uff1a1\uff09 <code>cutoff_freq</code> SHC \u8ba1\u7b97\u7684\u622a\u6b62\u9891\u7387\uff08THz\uff0c\u9ed8\u8ba4\uff1a60\uff09 <code>save</code> \u53ef\u9009\uff0c\u4fdd\u5b58\u56fe\u7247\u4e3a <code>hnemd.png</code> <p>\u6ce8\u610f\uff1a \u5982\u679c\u6ca1\u6709 SHC \u6570\u636e\uff0c\u4f7f\u7528 <code>save</code> \u65f6\u8bf7\u5c06 <code>scale_eff_size</code> \u548c <code>cutoff_freq</code> \u8bbe\u4e3a\u4efb\u610f\u5360\u4f4d\u6570\u5b57\u3002</p> <pre><code>gpumdkit.sh -plt hnemd [scale_eff_size] [cutoff_freq] [save]\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_5","title":"\u7ed3\u6784\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_rdfpy","title":"plt_rdf.py","text":"<p>\u7ed8\u5236\u5f84\u5411\u5206\u5e03\u51fd\u6570 (RDF)\uff0c\u5c55\u793a\u539f\u5b50\u5bf9\u5173\u8054\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf               # \u663e\u793a\u6240\u6709 RDF \u5bf9\ngpumdkit.sh -plt rdf &lt;column&gt;      # \u663e\u793a\u7279\u5b9a\u5bf9\n</code></pre> <p>\u5b8c\u6574 RDF \u8f93\u51fa\uff1a</p> <p>\u5355\u5bf9 RDF\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_rdf_pmfpy","title":"plt_rdf_pmf.py","text":"<p>\u7ed8\u5236 RDF \u4e0e\u5e73\u5747\u529b\u52bf (PMF) \u7684\u7ec4\u5408\u56fe\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>rdf.out</code></p> <pre><code>gpumdkit.sh -plt rdf_pmf\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_vacpy","title":"plt_vac.py","text":"<p>\u7ed8\u5236\u901f\u5ea6\u81ea\u76f8\u5173\u51fd\u6570 (VAC)\u3002\u53ef\u7528\u4e8e\u5206\u6790\u58f0\u5b50\u6027\u8d28\u548c\u539f\u5b50\u52a8\u529b\u5b66\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>sdc.out</code>\uff08\u7ed8\u56fe\u811a\u672c\u4f1a\u4ece\u8be5\u6587\u4ef6\u4e2d\u8bfb\u53d6 VAC \u76f8\u5173\u5217\uff09</p> <p>\u8f93\u51fa\uff1a \u4ea4\u4e92\u5f0f\u56fe\u8868\u6216 <code>vac.png</code>\uff08\u4f7f\u7528 <code>save</code> \u9009\u9879\u65f6\uff09</p> <pre><code>gpumdkit.sh -plt vac\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_cohesivepy","title":"plt_cohesive.py","text":"<p>\u4ece <code>cohesive.out</code> \u7ed8\u5236\u5185\u805a\u80fd\u66f2\u7ebf\u3002\u53ef\u7528\u4e8e\u5206\u6790\u6676\u683c\u7a33\u5b9a\u6027\u548c\u5e73\u8861\u6676\u683c\u5e38\u6570\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>cohesive.out</code>\uff08\u5404\u5411\u540c\u6027\u7f29\u653e\u56e0\u5b50 vs \u5185\u805a\u80fd\uff09</p> <p>\u8f93\u51fa\uff1a \u4ea4\u4e92\u5f0f\u56fe\u8868\u6216 <code>cohesive.png</code>\uff08\u4f7f\u7528 <code>save</code> \u9009\u9879\u65f6\uff09</p> <pre><code>gpumdkit.sh -plt cohesive\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_net_forcepy","title":"plt_net_force.py","text":"<p>\u7ed8\u5236\u7ed3\u6784\u4e0a\u7684\u51c0\u529b\u5206\u5e03\uff0c\u53ef\u7528\u4e8e\u8bc6\u522b\u95ee\u9898\u6784\u578b\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>train.xyz</code>\uff08extxyz \u683c\u5f0f\uff09</p> <pre><code>gpumdkit.sh -plt net_force train.xyz\n</code></pre> <p>\u53c2\u8003\u6587\u732e\uff1a arXiv:2510.19774</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_6","title":"\u58f0\u5b50","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_pdospy","title":"plt_pdos.py","text":"<p>\u8ba1\u7b97\u5e76\u7ed8\u5236\u5f52\u4e00\u5316\u7684\u901f\u5ea6\u81ea\u76f8\u5173\u51fd\u6570 (VAC)\u3001\u58f0\u5b50\u6001\u5bc6\u5ea6 (PDOS) \u548c\u70ed\u5bb9 (Cv)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>model.xyz</code>\u3001<code>run.in</code>\u3001<code>dos.out</code>\u3001<code>mvac.out</code></p> <pre><code>gpumdkit.sh -plt pdos\ngpumdkit.sh -plt pdos save\n</code></pre> <p>\u70ed\u5bb9\u8f93\u51fa\uff1a</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#dimer","title":"\u63cf\u8ff0\u7b26\u3001Dimer \u548c\u5176\u4ed6\u5206\u6790","text":""},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_descriptorspy","title":"plt_descriptors.py","text":"<p>\u4f7f\u7528\u964d\u7ef4\u65b9\u6cd5\uff08PCA \u6216 UMAP\uff09\u53ef\u89c6\u5316\u9ad8\u7ef4 NEP \u63cf\u8ff0\u7b26\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>descriptors.npy</code>\uff08\u7531 <code>gpumdkit.sh -calc des</code> \u751f\u6210\uff09</p> <p>\u65b9\u6cd5\uff1a - <code>pca</code> \u2014 \u4e3b\u6210\u5206\u5206\u6790 - <code>umap</code> \u2014 \u7edf\u4e00\u6d41\u5f62\u903c\u8fd1\u4e0e\u6295\u5f71</p> <pre><code># \u5148\u8ba1\u7b97\u63cf\u8ff0\u7b26\ngpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n\n# \u518d\u53ef\u89c6\u5316\ngpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_dimerpy","title":"plt_dimer.py","text":"<p>\u7ed8\u5236\u4e8c\u805a\u4f53\u76f8\u4e92\u4f5c\u7528\u66f2\u7ebf\u3002\u5c06\u4e24\u4e2a\u539f\u5b50\u653e\u5165\u7acb\u65b9\u76d2\u5b50\uff0830 \u00c5\uff09\uff0c\u4f7f\u7528 NEP \u6a21\u578b\u8ba1\u7b97\u52bf\u80fd\u548c\u529b\u968f\u8ddd\u79bb\u7684\u53d8\u5316\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>nep.txt</code></p> <pre><code>gpumdkit.sh -plt dimer &lt;element1&gt; &lt;element2&gt; &lt;nep_model&gt;\ngpumdkit.sh -plt dimer Li Li nep.txt\n</code></pre> <p>\u53c2\u8003\u6587\u732e\uff1a J. Chem. Inf. Model. 2026, 66, 3, 1406-1413</p>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plt_doaspy","title":"plt_doas.py","text":"<p>\u7ed8\u5236 Wang et al. \u63d0\u51fa\u7684\u539f\u5b50\u6001\u5bc6\u5ea6 (DOAS)\u3002</p> <p>\u8f93\u5165\u6587\u4ef6\uff1a <code>doas.out</code>\uff08\u7531 <code>gpumdkit.sh -calc doas</code> \u8ba1\u7b97\uff09</p> <pre><code>gpumdkit.sh -plt doas &lt;doas.out&gt; &lt;species&gt;\ngpumdkit.sh -plt doas doas.out Li\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#plane-grid","title":"\u6781\u6027\u6750\u6599\u7684 Plane-Grid \u7ed8\u56fe","text":"<p>\u6b64\u5de5\u4f5c\u6d41\u5c06\u4f4d\u79fb\u6216\u6781\u5316\u6570\u636e\u6620\u5c04\u5230\u7f51\u683c\u4e0a\uff0c\u5e76\u7ed8\u5236\u9009\u5b9a\u5e73\u9762\u7684\u8f6e\u5ed3\u3002\u8be6\u7ec6\u7528\u6cd5\u548c\u5b9e\u9645\u6848\u4f8b\u8bf7\u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790\u3002</p> <p>\u4f9d\u8d56\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>\u5178\u578b\u524d\u7f6e\u6b65\u9aa4\uff1a</p> <pre><code>gpumdkit.sh -calc nlist -i model.xyz -c 4 -n 12 -C Pb Sr -E O\ngpumdkit.sh -calc disp -i movie.xyz -n nl-Pb_Sr-O.dat -o displacements.dat\ngpumdkit.sh -calc avg-struct -i movie.xyz -l 0.2 -o averaged_structure.xyz\n</code></pre> <p>\u4f7f\u7528\u65b9\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr\ngpumdkit.sh -plt plane-grid -i averaged_structure.xyz -d displacements.dat -e Pb Sr --select-xy 0 1\n</code></pre>"},{"location":"zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html#_7","title":"\u5feb\u901f\u53c2\u8003\u8868","text":"\u547d\u4ee4 \u8f93\u5165\u6587\u4ef6 \u7528\u9014 <code>train</code> <code>loss.out</code>, <code>*_train.out</code> NEP \u8bad\u7ec3\u7ed3\u679c <code>prediction</code> / <code>test</code> <code>*_test.out</code> NEP \u9884\u6d4b\u7ed3\u679c <code>train_test</code> <code>*_train.out</code>, <code>*_test.out</code> \u5408\u5e76 parity plot <code>parity_density</code> <code>*_train.out</code> \u5bc6\u5ea6 parity plot <code>force_errors</code> <code>force_train.out</code> \u529b\u8bef\u5dee\u6307\u6807 <code>lr</code> <code>loss.out</code> (gnep) \u5b66\u4e60\u7387 <code>restart</code> <code>nep.restart</code> \u91cd\u542f\u6587\u4ef6\u53c2\u6570 <code>charge</code> <code>charge_train.out</code> \u7535\u8377\u5206\u5e03 <code>born_charge</code> / <code>bec</code> <code>bec_train.out</code>, <code>bec_test.out</code> Born \u6709\u6548\u7535\u8377 <code>thermo</code> <code>thermo.out</code> \u70ed\u529b\u5b66\u91cf <code>msd</code> <code>msd.out</code> \u5747\u65b9\u4f4d\u79fb <code>msd_all</code> <code>msd.out</code> (all_groups) \u5168\u7ec4\u5206 MSD <code>msd_conv</code> <code>msd_step*.out</code> MSD \u6536\u655b\u6027\u68c0\u67e5 <code>sdc</code> <code>msd.out</code> \u81ea\u6269\u6563\u7cfb\u6570 <code>arrhenius_d</code> / <code>D</code> <code>*K/msd.out</code> Arrhenius \u6269\u6563\u7cfb\u6570 <code>arrhenius_sigma</code> / <code>sigma</code> <code>*K/{model.xyz, run.in, thermo.out, msd.out}</code> Arrhenius \u79bb\u5b50\u7535\u5bfc\u7387 <code>rdf</code> <code>rdf.out</code> \u5f84\u5411\u5206\u5e03\u51fd\u6570 <code>rdf_pmf</code> <code>rdf.out</code> RDF + \u5e73\u5747\u529b\u52bf <code>vac</code> <code>sdc.out</code> \u901f\u5ea6\u81ea\u76f8\u5173 <code>cohesive</code> <code>cohesive.out</code> \u5185\u805a\u80fd\u66f2\u7ebf <code>net_force</code> <code>train.xyz</code> \u51c0\u529b\u5206\u5e03 <code>doas</code> <code>doas.out</code> \u539f\u5b50\u6001\u5bc6\u5ea6 <code>des</code> <code>descriptors.npy</code> \u63cf\u8ff0\u7b26 PCA/UMAP <code>dimer</code> <code>nep.txt</code> \u4e8c\u805a\u4f53\u80fd\u91cf/\u529b\u66f2\u7ebf <code>pdos</code> <code>model.xyz</code>, <code>run.in</code>, <code>dos.out</code>, <code>mvac.out</code> VAC \u548c PDOS <code>emd</code> EMD \u8f93\u51fa EMD \u70ed\u5bfc\u7387 <code>nemd</code> NEMD \u8f93\u51fa NEMD \u70ed\u8f93\u8fd0 <code>hnemd</code> HNEMD \u8f93\u51fa HNEMD \u70ed\u8f93\u8fd0 <code>viscosity</code> \u7c98\u5ea6\u8f93\u51fa \u7c98\u5ea6"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html","title":"\u81ea\u5b9a\u4e49\u547d\u4ee4","text":"\ud83d\udd27 \u81ea\u5b9a\u4e49\u547d\u4ee4 <p>GPUMDkit \u652f\u6301\u4ece ~/.gpumdkit.in \u52a0\u8f7d\u81ea\u5b9a\u4e49\u547d\u4ee4\u3002\u4f60\u53ef\u4ee5\u628a\u5e38\u7528\u811a\u672c\u6216\u5de5\u4f5c\u6d41\u5c01\u88c5\u6210 <code>custom_</code> \u5f00\u5934\u7684 Bash \u51fd\u6570\uff0c\u7136\u540e\u901a\u8fc7 <code>gpumdkit.sh -\u547d\u4ee4\u540d</code> \u8c03\u7528\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_1","title":"\u8bbe\u7f6e","text":"<p>\u7f16\u8f91\u914d\u7f6e\u6587\u4ef6\uff1a</p> <pre><code>vi ~/.gpumdkit.in\n</code></pre> <p>\u81ea\u5b9a\u4e49\u51fd\u6570\u9700\u8981\u4f7f\u7528 <code>custom_</code> \u524d\u7f00\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_2","title":"\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_3","title":"\u7b80\u5355\u95ee\u5019","text":"<p>\u5728 <code>~/.gpumdkit.in</code> \u4e2d\u5199\u5165\uff1a</p> <pre><code>custom_hello() {\n    echo \"Hello, GPUMDkit user! This is a custom command.\"\n    echo \"Current GPUMDkit path: ${GPUMDkit_path}\"\n}\n</code></pre> <p>\u7136\u540e\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -hello\n</code></pre> <p>\u4f60\u4f1a\u770b\u5230\u7c7b\u4f3c\u8f93\u51fa\uff1a</p> <pre><code>Hello, GPUMDkit user! This is a custom command.\nCurrent GPUMDkit path: /home/yanzihan/software/GPUMDkit\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_4","title":"\u5e26\u5fc5\u9700\u53c2\u6570\u7684\u547d\u4ee4","text":"<pre><code>custom_greet() {\n    name=$1\n    echo \"Hello, ${name}!\"\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -greet Zihan\n</code></pre> <p>\u8f93\u51fa\uff1a</p> <pre><code>Hello, Zihan!\n</code></pre> <p>\u4f20\u9012\u53c2\u6570\u65f6\uff0c\u53ef\u4ee5\u7528 <code>\"$@\"</code> \u5b89\u5168\u5730\u8f6c\u53d1\u6240\u6709\u53c2\u6570\uff1b\u5982\u679c\u9700\u8981\u4ece\u7b2c\u4e00\u4e2a\u53c2\u6570\u5f00\u59cb\u5f15\u7528\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528 <code>${@:1}</code>\u3002</p>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_5","title":"\u8c03\u7528\u5916\u90e8\u811a\u672c","text":"<p>\u5982\u679c\u5e0c\u671b\u50cf\u8c03\u7528 GPUMDkit \u5185\u7f6e\u547d\u4ee4\u4e00\u6837\u8c03\u7528\u81ea\u5df1\u7684\u811a\u672c\uff1a</p> <pre><code>custom_nepanalyse() {\n    python ~/my_gpumd_tools/analyse_nep.py\n}\n</code></pre> <p>\u8fd0\u884c\uff1a</p> <pre><code>gpumdkit.sh -nepanalyse\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_6","title":"\u8fdb\u9636\u793a\u4f8b","text":""},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_7","title":"\u6279\u5904\u7406\u7ed8\u56fe","text":"<p>\u5bf9\u591a\u4e2a\u76ee\u5f55\u6279\u91cf\u7ed8\u56fe\uff1a</p> <pre><code>custom_batch_plot() {\n    for dir in \"$@\"; do\n        cd \"$dir\"\n        gpumdkit.sh -plt thermo save\n        gpumdkit.sh -plt msd save\n        cd ..\n    done\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -batch_plot dir1 dir2 dir3\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_8","title":"\u8bad\u7ec3\u96c6\u5206\u6790\u6d41\u7a0b","text":"<p>\u628a\u591a\u4e2a\u5206\u6790\u547d\u4ee4\u7ec4\u5408\u6210\u4e00\u4e2a\u5165\u53e3\uff1a</p> <pre><code>custom_analyze_training() {\n    xyz_file=$1\n    echo \"Analyzing $xyz_file...\"\n\n    gpumdkit.sh -range \"$xyz_file\" force\n    gpumdkit.sh -min_dist_pbc \"$xyz_file\"\n    gpumdkit.sh -analyze_comp \"$xyz_file\"\n\n    echo \"Analysis complete!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -analyze_training train.xyz\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_9","title":"\u81ea\u5b9a\u4e49\u6570\u636e\u51c6\u5907\u6d41\u7a0b","text":"<pre><code>custom_prep_training() {\n    echo \"Preparing training data...\"\n\n    gpumdkit.sh -out2xyz ./\n    gpumdkit.sh -filter_value train.xyz force 30\n    gpumdkit.sh -range filtered_force.xyz energy\n\n    echo \"Training data ready!\"\n}\n</code></pre> <p>\u7528\u6cd5\uff1a</p> <pre><code>gpumdkit.sh -prep_training\n</code></pre>"},{"location":"zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html#_10","title":"\u4f7f\u7528\u5efa\u8bae","text":"<ul> <li>\u547d\u4ee4\u540d\u5c3d\u91cf\u6e05\u695a\uff0c\u4f8b\u5982 <code>custom_analyze_training</code> \u6bd4 <code>custom_at</code> \u66f4\u5bb9\u6613\u7ef4\u62a4\u3002</li> <li>\u5bf9\u9700\u8981\u53c2\u6570\u7684\u547d\u4ee4\uff0c\u5efa\u8bae\u5728\u53c2\u6570\u4e3a\u7a7a\u65f6\u6253\u5370\u7528\u6cd5\u63d0\u793a\u3002</li> <li>\u8c03\u7528\u5916\u90e8\u811a\u672c\u65f6\uff0c\u5c3d\u91cf\u7528 <code>\"$@\"</code> \u4fdd\u7559\u53c2\u6570\u4e2d\u7684\u7a7a\u683c\u548c\u7279\u6b8a\u5b57\u7b26\u3002</li> <li>\u6279\u5904\u7406\u76ee\u5f55\u65f6\uff0c\u6ce8\u610f\u4f7f\u7528 <code>cd \"$dir\"</code>\uff0c\u907f\u514d\u8def\u5f84\u4e2d\u6709\u7a7a\u683c\u65f6\u51fa\u9519\u3002</li> </ul> <p>\u611f\u8c22\u4f60\u4f7f\u7528 <code>GPUMDkit</code>\uff01\u5982\u6709\u4efb\u4f55\u95ee\u9898\u6216\u9700\u8981\u8fdb\u4e00\u6b65\u5e2e\u52a9\uff0c\u6b22\u8fce\u5728\u6211\u4eec\u7684 GitHub \u4ed3\u5e93\u63d0 issue \u6216\u8054\u7cfb Zihan YAN (yanzihan@westlake.edu.cn)\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html","title":"\u8ba1\u7b97\u5668\u811a\u672c","text":"\ud83e\uddee \u8ba1\u7b97\u5668\u811a\u672c <p>\u8ba1\u7b97\u5668\u6a21\u5757\u7528\u4e8e\u4ece MD \u8f68\u8ff9\u3001NEP \u6a21\u578b\u548c\u7ed3\u6784\u6587\u4ef6\u4e2d\u8ba1\u7b97\u6750\u6599\u6027\u8d28\u3002</p> <p>\u811a\u672c\u4f4d\u7f6e\uff1a <code>Scripts/calculators/</code></p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_1","title":"\u529f\u80fd\u6982\u89c8","text":"<p>\u8ba1\u7b97\u5668\u6a21\u5757\u5927\u81f4\u53ef\u4ee5\u5206\u4e3a\u4e09\u7c7b\uff1a</p> <ul> <li>\u8f68\u8ff9\u6027\u8d28\uff1a \u4ece GPUMD \u6216 extxyz \u8f68\u8ff9\u8ba1\u7b97 MSD\u3001\u79bb\u5b50\u7535\u5bfc\u7387\u7b49\u65f6\u95f4\u76f8\u5173\u6027\u8d28\uff1b</li> <li>NEP \u8f85\u52a9\u8ba1\u7b97\uff1a \u4f7f\u7528 NEP \u6a21\u578b\u9884\u6d4b\u80fd\u91cf/\u529b/\u5e94\u529b\u3001\u63d0\u53d6\u63cf\u8ff0\u7b26\u3001\u8ba1\u7b97 DOAS\u3001\u8fdb\u884c NEB \u6216\u7ed3\u6784\u4f18\u5316\uff1b</li> <li>\u6781\u6027\u6750\u6599\u5206\u6790\uff1a \u4e3a\u9499\u949b\u77ff\u548c\u6781\u6027\u6750\u6599\u6784\u5efa\u8fd1\u90bb\u5217\u8868\u3001\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb\u3001\u5e73\u5747\u7ed3\u6784\u3001\u516b\u9762\u4f53\u503e\u8f6c\u548c\u5c40\u57df\u6781\u5316\u3002</li> </ul> <p>\u5982\u679c\u4f60\u8fd8\u4e0d\u719f\u6089\u67d0\u4e2a\u811a\u672c\uff0c\u5efa\u8bae\u5148\u7528\u4ea4\u4e92\u6a21\u5f0f\u67e5\u770b\u8f93\u5165\u63d0\u793a\uff1b\u5982\u679c\u5df2\u7ecf\u77e5\u9053\u53c2\u6570\uff0c\u5219\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528 <code>gpumdkit.sh -calc ...</code> \u8c03\u7528\u3002</p> \u4efb\u52a1 \u547d\u4ee4 \u4e3b\u8981\u8f93\u5165 \u79bb\u5b50\u7535\u5bfc\u7387 <code>gpumdkit.sh -calc ionic-cond &lt;element&gt; &lt;charge&gt;</code> <code>msd.out</code>\u3001<code>thermo.out</code>\u3001<code>model.xyz</code> MSD <code>gpumdkit.sh -calc msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt;</code> extxyz \u8f68\u8ff9 NEP \u9884\u6d4b <code>gpumdkit.sh -calc nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep.txt&gt;</code> extxyz + NEP \u6a21\u578b NEP \u63cf\u8ff0\u7b26 <code>gpumdkit.sh -calc des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep.txt&gt; &lt;element&gt;</code> extxyz + NEP \u6a21\u578b DOAS <code>gpumdkit.sh -calc doas &lt;input.xyz&gt; &lt;nep.txt&gt; &lt;output.txt&gt;</code> extxyz + NEP \u6a21\u578b NEB <code>gpumdkit.sh -calc neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep.txt&gt;</code> \u521d\u672b\u6001\u7ed3\u6784 \u7ed3\u6784\u4f18\u5316 <code>gpumdkit.sh -calc minimize &lt;structure&gt; &lt;nep.txt&gt; [fmax] [max_steps]</code> \u7ed3\u6784 + NEP \u6a21\u578b \u90bb\u5c45\u5217\u8868 <code>gpumdkit.sh -calc nlist ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u4f4d\u79fb <code>gpumdkit.sh -calc disp ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u5e73\u5747\u7ed3\u6784 <code>gpumdkit.sh -calc avg-struct ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 \u516b\u9762\u4f53\u503e\u8f6c <code>gpumdkit.sh -calc oct-tilt ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 ABO3 \u6781\u5316 <code>gpumdkit.sh -calc pol-abo3 ...</code> \u53c2\u89c1 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u67e5\u770b\u5b8c\u6574\u5e2e\u52a9\uff1a</p> <pre><code>gpumdkit.sh -calc -h\n</code></pre> <p>\u547d\u4ee4\u884c\u5e2e\u52a9\u8868\u7c7b\u4f3c\uff1a</p> <pre><code>+-------------------------------------------------------------------------------------------------------+\n|                                      CALCULATOR TOOLS                                                 |\n+-------------------------------------------------------------------------------------------------------+\n| Usage: gpumdkit.sh -calc &lt;type&gt; [args...]                                                             |\n+-------------------------------------------------------------------------------------------------------+\n| ionic-cond &lt;element&gt; &lt;charge&gt;                 Calculate ionic conductivity from MSD data              |\n| nep &lt;input.xyz&gt; &lt;output.xyz&gt; &lt;nep_model&gt;      Calculate energy/force/virial with a NEP model          |\n| des &lt;input.xyz&gt; &lt;output.npy&gt; &lt;nep_model&gt; &lt;el&gt; Calculate NEP descriptors for one element               |\n| doas &lt;input.xyz&gt; &lt;nep_model&gt; &lt;output.txt&gt;     Calculate density of atomistic states                   |\n| neb &lt;initial.xyz&gt; &lt;final.xyz&gt; &lt;n_images&gt; &lt;nep&gt; Run NEB calculation with a NEP model                   |\n| minimize &lt;structure&gt; &lt;nep_model&gt; [fmax] [n]   Minimize a structure with a NEP model                   |\n| msd &lt;trajectory.xyz&gt; &lt;element&gt; &lt;dt_fs&gt; [n]    Calculate MSD from an extxyz trajectory                 |\n| nlist [script args...]                        Build neighbor lists                                    |\n| disp [script args...]                         Calculate displacement from trajectory                  |\n| avg-struct [script args...]                   Calculate averaged structure                            |\n| oct-tilt [script args...]                     Calculate octahedral tilt                               |\n| pol-abo3 [script args...]                     Calculate local polarization for ABO3                   |\n+-------------------------------------------------------------------------------------------------------+\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u4e2d\u9009\u62e9 <code>4) Calculators</code>\uff0c\u83dc\u5355\u5982\u4e0b\uff1a</p> <pre><code>+----------------------------------------------------------+\n|                     CALCULATOR TOOLS                     |\n+----------------------------------------------------------+\n| 401) Calc ionic conductivity                             |\n| 402) Calc properties by nep                              |\n| 403) Calc descriptors of specific elements               |\n| 404) Calc density of atomistic states (DOAS)             |\n| 405) Calc nudged elastic band (NEB) by nep               |\n| 406) Build neighbor list                                 |\n| 407) Calc displacement from trajectory                   |\n| 408) Calc averaged structure                             |\n| 409) Calc octahedral tilt                                |\n| 410) Calc polarization for ABO3                          |\n| 411) Minimize structure by nep                           |\n| 412) Calc mean square displacement (MSD) from trajectory |\n+----------------------------------------------------------+\n| 000) Return to the main menu                             |\n+----------------------------------------------------------+\nInput the function number:\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_2","title":"\u79bb\u5b50\u7535\u5bfc\u7387","text":"<p><code>calc_ion_conductivity.py</code> \u4ece <code>msd.out</code> \u8ba1\u7b97\u79bb\u5b50\u6269\u6563\u7cfb\u6570\u548c\u79bb\u5b50\u7535\u5bfc\u7387\u3002</p> <pre><code>gpumdkit.sh -calc ionic-cond Li 1\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>401</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>&gt;-------------------------------------------------&lt;\n| This function calls the script in calculators   |\n| Script: calc_ion_conductivity.py                |\n| Developer: Zihan YAN (yanzihan@westlake.edu.cn) |\n&gt;-------------------------------------------------&lt;\nInput &lt;element&gt; &lt;charge&gt; (eg. Li 1)\n------------&gt;&gt;\n</code></pre> <p>\u5e38\u7528\u8f93\u5165\u6587\u4ef6\uff1a</p> \u6587\u4ef6 \u4f5c\u7528 <code>msd.out</code> \u5fc5\u9700\uff0cMSD \u6570\u636e <code>thermo.out</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u6e29\u5ea6 <code>model.xyz</code> \u53ef\u9009\uff0c\u81ea\u52a8\u8bfb\u53d6\u4f53\u79ef\u548c\u79bb\u5b50\u6570 <code>run.in</code> \u53ef\u9009\uff0c\u8bc6\u522b\u6269\u80de\u4fe1\u606f <p>\u5982\u679c\u7f3a\u5c11\u81ea\u52a8\u8bc6\u522b\u6240\u9700\u6587\u4ef6\uff0c\u811a\u672c\u4f1a\u4ea4\u4e92\u5f0f\u8be2\u95ee\u6e29\u5ea6\u3001\u4f53\u79ef\u548c\u79bb\u5b50\u6570\u3002</p> <p>\u624b\u52a8\u6a21\u5f0f\u7684\u63d0\u793a\u7c7b\u4f3c\uff1a</p> <pre><code>Files 'thermo.out' and 'model.xyz' are not found.\nPlease provide the following values:\n---------------------------&gt;\nEnter average temperature (in K):\nEnter system volume (in A^3):\nEnter number of ions:\n</code></pre> <p>\u8f93\u51fa\u793a\u4f8b\uff1a</p> <pre><code>Diffusivity (D):\n  D_x: 4.153e-07 cm^2/s\n  D_y: 4.174e-07 cm^2/s\n  D_z: 2.610e-07 cm^2/s\n  D_total: 3.646e-07 cm^2/s\n------------------------------\nIonic Conductivity:\n  Sigma_x: 2.576e-02 mS/cm\n  Sigma_y: 2.589e-02 mS/cm\n  Sigma_z: 1.619e-02 mS/cm\n  Sigma_total: 2.261e-02 mS/cm\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#msd","title":"\u4ece\u8f68\u8ff9\u8ba1\u7b97 MSD","text":"<p><code>calc_msd.py</code> \u53ef\u4ee5\u76f4\u63a5\u4ece extxyz \u8f68\u8ff9\u4e2d\u8ba1\u7b97\u6307\u5b9a\u5143\u7d20\u7684 MSD\u3002</p> <pre><code>gpumdkit.sh -calc msd dump.xyz Li 10\ngpumdkit.sh -calc msd dump.xyz Li 10 5000\n</code></pre> <p>\u4ea4\u4e92\u6a21\u5f0f\u9009\u62e9 <code>412</code>\uff0c\u4f1a\u770b\u5230\uff1a</p> <pre><code>Input &lt;extxyz_file&gt; &lt;element_symbol&gt; &lt;dt_fs&gt; [max_corr_steps]\n  Optional argument: max_corr_steps (default: frame number)\nExample: dump.xyz Li 10\n------------&gt;&gt;\n</code></pre> <p>\u53c2\u6570\u542b\u4e49\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>dump.xyz</code> \u8f93\u5165\u8f68\u8ff9 <code>Li</code> \u76ee\u6807\u6269\u6563\u5143\u7d20 <code>10</code> \u5e27\u95f4\u9694\uff0c\u5355\u4f4d fs <code>5000</code> \u53ef\u9009\uff0c\u6700\u5927\u76f8\u5173\u6b65\u6570 <p>\u8f93\u51fa\uff1a</p> <ul> <li><code>msd.out</code></li> </ul> <p><code>msd.out</code> \u7684\u5f00\u5934\u662f\u6587\u672c\u8868\u683c\uff0c\u5305\u542b\u65f6\u95f4\u548c\u4e0d\u540c\u65b9\u5411\u7684 MSD \u5217\u3002\u751f\u6210\u540e\u53ef\u4ee5\u7ee7\u7eed\u4f7f\u7528\u7ed8\u56fe\u547d\u4ee4\u68c0\u67e5\u6269\u6563\u533a\u95f4\u548c\u81ea\u6269\u6563\u7cfb\u6570\u3002</p> <p>\u968f\u540e\u53ef\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt msd\ngpumdkit.sh -plt sdc\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep","title":"NEP \u9884\u6d4b\u6027\u8d28","text":"<p><code>calc_properties_with_nep.py</code> \u4f7f\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8ba1\u7b97\u80fd\u91cf\u3001\u529b\u548c\u5e94\u529b\u3002</p> <p>\u4f9d\u8d56\uff1a <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc nep structures.xyz predictions.xyz nep.txt\n</code></pre> <p>\u4f7f\u7528\u6b64\u529f\u80fd\u53ef\u4ee5\u7528\u8bad\u7ec3\u597d\u7684 NEP \u6a21\u578b\u8fdb\u884c\u9884\u6d4b\u3002\u5efa\u8bae\u5728\u4f7f\u7528\u524d\u5148\u9a8c\u8bc1\u6a21\u578b\u5728\u76ee\u6807\u7ed3\u6784\u4e0a\u7684\u9884\u6d4b\u8d28\u91cf\uff0c\u518d\u5c06\u8f93\u51fa\u4f5c\u4e3a\u540e\u7eed\u5206\u6790\u6216\u7b5b\u9009\u4f9d\u636e\u3002</p> <p>\u63d0\u793a\uff1a \u9884\u6d4b\u524d\u53ef\u4ee5\u6e05\u7406 extxyz \u5143\u6570\u636e\uff1a</p> <pre><code>gpumdkit.sh -clean_xyz train.xyz clean_train.xyz\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#nep_1","title":"NEP \u63cf\u8ff0\u7b26","text":"<pre><code>gpumdkit.sh -calc des train.xyz descriptors.npy nep.txt Li\n</code></pre> <p>\u7528\u9014\u5305\u62ec\uff1a</p> <ul> <li>\u7528 PCA/UMAP \u53ef\u89c6\u5316\u5c40\u57df\u73af\u5883\uff1b</li> <li>\u6bd4\u8f83\u8bad\u7ec3\u96c6\u548c\u5019\u9009\u7ed3\u6784\uff1b</li> <li>\u5224\u65ad\u65b0\u6570\u636e\u662f\u5426\u6269\u5c55\u4e86\u63cf\u8ff0\u7b26\u7a7a\u95f4\u3002</li> </ul> <p>\u7ed8\u56fe\uff1a</p> <pre><code>gpumdkit.sh -plt des pca\ngpumdkit.sh -plt des umap\n</code></pre>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#doas","title":"DOAS","text":"<p><code>calc_doas.py</code> \u7528\u4e8e\u8ba1\u7b97 Wang et al. \u63d0\u51fa\u7684 density of atomistic states\u3002</p> <pre><code>gpumdkit.sh -calc doas structures.xyz nep.txt doas.out\ngpumdkit.sh -plt doas doas.out Li\n</code></pre> <p>\u811a\u672c\u4f1a\uff1a</p> <ol> <li>\u8bfb\u53d6\u6240\u6709\u7ed3\u6784\uff1b</li> <li>\u4f7f\u7528 NEP \u8fdb\u884c\u7ed3\u6784\u4f18\u5316\uff1b</li> <li>\u63d0\u53d6\u6bcf\u4e2a\u539f\u5b50\u7684\u80fd\u91cf\uff1b</li> <li>\u6309\u5143\u7d20\u5206\u7ec4\u8f93\u51fa\uff1b</li> <li>\u7528\u7ed8\u56fe\u811a\u672c\u53ef\u89c6\u5316\u5206\u5e03\u3002</li> </ol> <p>\u5bf9\u4e8e\u5f88\u5927\u7684\u4f53\u7cfb\uff0c\u5982\u679c\u4e3b\u8981\u76ee\u7684\u662f\u83b7\u5f97\u4f18\u5316\u540e\u7684\u7ed3\u6784\u548c\u539f\u5b50\u80fd\u91cf\u5206\u5e03\uff0c\u76f4\u63a5\u5728 GPUMD \u4e2d\u5b8c\u6210\u6700\u5c0f\u5316\u548c\u539f\u5b50\u80fd\u91cf\u8f93\u51fa\u901a\u5e38\u4f1a\u66f4\u9ad8\u6548\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#neb","title":"NEB \u548c\u7ed3\u6784\u4f18\u5316","text":"<p>NEB\uff1a</p> <pre><code>gpumdkit.sh -calc neb initial.xyz final.xyz 9 nep.txt\n</code></pre> <p>\u8fd9\u4f1a\u4f7f\u7528 NEP \u6a21\u578b\u8fd0\u884c\u542b <code>9</code> \u4e2a\u4e2d\u95f4\u50cf\u7684 NEB \u8ba1\u7b97\u3002\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u811a\u672c\u4f1a\u8be2\u95ee\u539f\u5b50\u56fa\u5b9a\u65b9\u5f0f\uff1a</p> <ul> <li><code>none</code>\uff1a\u4e0d\u56fa\u5b9a\u539f\u5b50\uff1b</li> <li><code>index</code>\uff1a\u6309\u539f\u5b50\u5e8f\u53f7\u56fa\u5b9a\uff1b</li> <li><code>element</code>\uff1a\u56fa\u5b9a\u67d0\u4e00\u79cd\u5143\u7d20\u7684\u6240\u6709\u539f\u5b50\uff1b</li> <li><code>position</code>\uff1a\u56fa\u5b9a\u5750\u6807\u8303\u56f4\u5185\u7684\u539f\u5b50\u3002</li> </ul> <p>\u7ed3\u6784\u4f18\u5316\uff08\u901a\u8fc7 <code>calorine</code>\uff09\uff1a</p> <p>\u4f9d\u8d56\uff1a <code>calorine</code></p> <pre><code>pip install calorine\n</code></pre> <pre><code>gpumdkit.sh -calc minimize POSCAR nep.txt 0.01 1000\n</code></pre> <p>\u8f93\u51fa\u5305\u62ec\uff1a</p> <ul> <li><code>minimize.xyz</code></li> <li><code>minimize.log</code></li> </ul>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#ovito-rdf","title":"\u4f7f\u7528 OVITO \u8ba1\u7b97 RDF","text":"<p><code>rdf_calculator_ovito.py</code> \u4f7f\u7528 OVITO \u7684\u5206\u6790\u5de5\u5177\u8ba1\u7b97\u5f84\u5411\u5206\u5e03\u51fd\u6570\u3002</p> <p>\u4f9d\u8d56\uff1a OVITO</p> <pre><code>pip install ovito\n</code></pre> <p>\u8f93\u5165\u6587\u4ef6\uff1a \u7ed3\u6784\u6587\u4ef6\uff08\u5355\u5e27\u6216\u8f68\u8ff9\uff09</p> <pre><code>python Scripts/calculators/rdf_calculator_ovito.py trajectory.xyz 6.0 400\n</code></pre> <p>\u53c2\u6570\uff1a</p> \u53c2\u6570 \u542b\u4e49 <code>trajectory.xyz</code> \u8f93\u5165\u7ed3\u6784\u6587\u4ef6 <code>6.0</code> RDF \u8ba1\u7b97\u7684\u6700\u5927\u8ddd\u79bb\uff08\u00c5\uff09 <code>400</code> \u76f4\u65b9\u56fe\u7684\u5206\u7bb1\u6570 <p>\u53ef\u89c6\u5316\uff1a</p> <pre><code>gpumdkit.sh -plt rdf\n</code></pre> <p>\u6ce8\u610f\uff1a \u5efa\u8bae\u4f18\u5148\u4f7f\u7528 GPUMD \u4e2d\u7684 <code>compute_rdf</code> \u547d\u4ee4\u3002</p>"},{"location":"zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html#_3","title":"\u94c1\u7535\u548c\u6781\u6027\u6750\u6599\u5de5\u5177","text":"<p>\u9009\u9879 <code>406\u2013410</code> \u9762\u5411\u9499\u949b\u77ff\u548c\u6781\u6027\u6750\u6599\u5206\u6790\uff0c\u5e38\u7528\u4e8e\u4ece MD \u8f68\u8ff9\u4e2d\u63d0\u53d6\u5c40\u57df\u7ed3\u6784\u4fe1\u606f\uff0c\u7136\u540e\u8fdb\u4e00\u6b65\u5206\u6790\u76f8\u53d8\u3001\u7574\u7ed3\u6784\u6216\u6781\u5316\u7eb9\u7406\u3002</p> <p>\u8fd9\u4e9b\u811a\u672c\u5728\u672c\u9875\u53ea\u505a\u5feb\u901f\u7d22\u5f15\uff0c\u56e0\u4e3a\u5b83\u4eec\u901a\u5e38\u9700\u8981\u7ec4\u5408\u4f7f\u7528\u3002\u63a8\u8350\u9605\u8bfb\u4e13\u9898\u6559\u7a0b\u4e2d\u7684\u5b8c\u6574\u5de5\u4f5c\u6d41\u548c\u53c2\u6570\u8bf4\u660e\uff1a\u6781\u6027\u6750\u6599\u5206\u6790\u3002</p> \u83dc\u5355 CLI \u5b50\u547d\u4ee4 \u4f5c\u7528 \u8be6\u7ec6\u8bf4\u660e <code>406</code> <code>gpumdkit.sh -calc nlist ...</code> \u6784\u5efa\u6307\u5b9a\u4e2d\u5fc3\u539f\u5b50\u548c\u8fd1\u90bb\u539f\u5b50\u4e4b\u95f4\u7684\u8fd1\u90bb\u5217\u8868 \u6781\u6027\u6750\u6599\u5206\u6790 <code>407</code> <code>gpumdkit.sh -calc disp ...</code> \u6839\u636e\u8f68\u8ff9\u548c\u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u5c40\u57df\u4f4d\u79fb \u6781\u6027\u6750\u6599\u5206\u6790 <code>408</code> <code>gpumdkit.sh -calc avg-struct ...</code> \u4ece\u8f68\u8ff9\u4e2d\u8ba1\u7b97\u5e73\u5747\u7ed3\u6784 \u6781\u6027\u6750\u6599\u5206\u6790 <code>409</code> <code>gpumdkit.sh -calc oct-tilt ...</code> \u8ba1\u7b97\u516b\u9762\u4f53\u503e\u8f6c\u89d2 \u6781\u6027\u6750\u6599\u5206\u6790 <code>410</code> <code>gpumdkit.sh -calc pol-abo3 ...</code> \u6839\u636e Born \u6709\u6548\u7535\u8377\u4f30\u7b97 ABO3 \u5c40\u57df\u6781\u5316 \u6781\u6027\u6750\u6599\u5206\u6790 <p>\u90e8\u5206\u811a\u672c\u9700\u8981\u5b89\u88c5 <code>ferrodispcalc</code>\uff1a</p> <pre><code>pip3 install git+https://github.com/MoseyQAQ/ferrodispcalc.git\n</code></pre> <p>\u4e00\u4e2a\u5178\u578b\u987a\u5e8f\u662f\u5148\u7528 <code>nlist</code> \u5efa\u7acb\u8fd1\u90bb\u5217\u8868\uff0c\u518d\u7528\u8be5\u8fd1\u90bb\u5217\u8868\u8ba1\u7b97\u4f4d\u79fb\u3001\u503e\u8f6c\u6216\u6781\u5316\u3002\u5bf9\u4e8e\u5e73\u5747\u7ed3\u6784\uff0c\u53ef\u4ee5\u76f4\u63a5\u4ece\u8f68\u8ff9\u51fa\u53d1\uff0c\u7528\u957f\u5ea6\u5bb9\u5dee\u63a7\u5236\u54ea\u4e9b\u5e27\u53c2\u4e0e\u5e73\u5747\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html","title":"\u8d21\u732e\u6307\u5357","text":"\ud83e\udd1d \u4e3a GPUMDkit \u8d21\u732e\u4ee3\u7801 <p>\u611f\u8c22\u4f60\u6709\u5174\u8da3\u4e3a GPUMDkit \u505a\u51fa\u8d21\u732e\uff01\u6211\u4eec\u611f\u8c22\u4f60\u4e3a\u6539\u5584\u8fd9\u4e2a\u5de5\u5177\u5305\u6240\u4ed8\u51fa\u7684\u65f6\u95f4\u548c\u52aa\u529b\u3002</p> <p> English   \u00a0\u00b7\u00a0   \u7b80\u4f53\u4e2d\u6587 </p> <p><code>GPUMDkit</code> \u662f\u4e00\u4e2a\u5f00\u6e90\u9879\u76ee\uff0c\u6211\u4eec\u6b22\u8fce\u793e\u533a\u7684\u5404\u79cd\u8d21\u732e\uff0c\u65e0\u8bba\u662f\u4fee\u590d bug\u3001\u6dfb\u52a0\u65b0\u529f\u80fd\u3001\u6539\u8fdb\u6587\u6863\u8fd8\u662f\u63d0\u51fa\u5efa\u8bae\u3002</p> <p>\u6ce8\u610f\uff1a\u672c\u6587\u6863\u7684\u6743\u5a01\u7248\u672c\u4f4d\u4e8e\u4ed3\u5e93\u6839\u76ee\u5f55\u7684 <code>CONTRIBUTING.md</code>\u3002\u672c\u6559\u7a0b\u9875\u9762\u540c\u6b65\u5176\u5185\u5bb9\u3002\u4e2d\u6587\u7248\u8bf7\u53c2\u89c1 <code>docs/CONTRIBUTING_zh-CN.md</code>\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_1","title":"\u76ee\u5f55","text":"<ul> <li>\u5f00\u53d1\u89c4\u8303\u4e0e\u51c6\u5219</li> <li>\u62a5\u544a\u95ee\u9898</li> <li>\u529f\u80fd\u5efa\u8bae</li> <li>\u8d21\u732e\u4ee3\u7801</li> <li>Fork \u5e76\u514b\u9686\u4ed3\u5e93</li> <li>\u521b\u5efa\u529f\u80fd\u5206\u652f</li> <li>\u8fdb\u884c\u4fee\u6539<ul> <li>\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e</li> <li>\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e</li> <li>\u66f4\u65b0 Tab \u8865\u5168</li> </ul> </li> <li>\u4ee3\u7801\u98ce\u683c\u4e0e\u6700\u4f73\u5b9e\u8df5</li> <li>\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539</li> <li>\u63d0\u4ea4\u4fe1\u606f</li> <li>\u63a8\u9001\u5e76\u521b\u5efa Pull Request</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u5f00\u53d1\u89c4\u8303\u4e0e\u51c6\u5219","title":"\u5f00\u53d1\u89c4\u8303\u4e0e\u51c6\u5219","text":"<p>\u4e3a\u4fdd\u6301\u4ee3\u7801\u8d28\u91cf\u548c\u9879\u76ee\u4e00\u81f4\u6027\uff0c\u8bf7\u9075\u5faa\u4ee5\u4e0b\u51c6\u5219\uff1a</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_2","title":"\u8bed\u8a00\u8981\u6c42","text":"<ul> <li>\u6240\u6709\u4ee3\u7801\u5e94\u4f7f\u7528\u82f1\u6587\u7f16\u5199\uff1a\u5305\u62ec\u53d8\u91cf\u540d\u3001\u51fd\u6570\u540d\u3001\u6ce8\u91ca\u3001\u6587\u6863\u5b57\u7b26\u4e32\u3001\u63d0\u4ea4\u4fe1\u606f\u548c\u6587\u6863\u3002</li> <li>\u867d\u7136\u6211\u4eec\u7406\u89e3\u8d21\u732e\u8005\u6765\u81ea\u4e0d\u540c\u80cc\u666f\uff0c\u4f46\u4f7f\u7528\u82f1\u6587\u80fd\u786e\u4fdd\u4ee3\u7801\u5e93\u5bf9\u6700\u5e7f\u6cdb\u7684\u7528\u6237\u7fa4\u4f53\u53ef\u8bbf\u95ee\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_3","title":"\u6a21\u5757\u5316\u4e0e\u53ef\u590d\u7528\u6027","text":"<ul> <li>\u7f16\u5199\u6a21\u5757\u5316\u548c\u53ef\u590d\u7528\u7684\u4ee3\u7801\uff1a\u51fd\u6570\u548c\u811a\u672c\u7684\u8bbe\u8ba1\u5e94\u5177\u6709\u7075\u6d3b\u6027\u3002</li> <li>\u4f18\u5148\u4f20\u9012\u53c2\u6570\u800c\u975e\u786c\u7f16\u7801\u503c\uff1a\u4f7f\u7528\u51fd\u6570\u53c2\u6570\u3001\u547d\u4ee4\u884c\u53c2\u6570\u6216\u914d\u7f6e\u6587\u4ef6\u6765\u66ff\u4ee3\u786c\u7f16\u7801\u503c\u3002\u4f46\u67d0\u4e9b\u6587\u4ef6\u540d\u7531 GPUMD \u548c NEP \u7a0b\u5e8f\u56fa\u5b9a\u8981\u6c42\uff08\u5982 <code>train.xyz</code>\u3001<code>thermo.out</code>\uff09\uff0c\u8fd9\u4e9b\u53ef\u4ee5\u6309\u9700\u786c\u7f16\u7801\u3002</li> <li>\u793a\u4f8b\uff1a   <pre><code># \u597d\u7684\u505a\u6cd5\uff1a\u63a5\u53d7\u53c2\u6570\nfunction convert_file() {\n    local input_file=$1\n    local output_file=$2\n    # \u5904\u7406\u903b\u8f91\n}\n\n# \u907f\u514d\uff1a\u786c\u7f16\u7801\u503c\uff08\u9664\u975e GPUMD/NEP \u8981\u6c42\uff09\nfunction convert_file() {\n    local input_file=\"hardcoded_input.xyz\"\n    # \u5904\u7406\u903b\u8f91\n}\n</code></pre></li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_4","title":"\u4ee3\u7801\u98ce\u683c","text":"<ul> <li>\u7f16\u5199\u6e05\u6670\u3001\u6613\u4e8e\u4ed6\u4eba\u7ef4\u62a4\u548c\u4fee\u6539\u7684\u4ee3\u7801\u3002</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u548c\u51fd\u6570\u540d\u3002</li> <li>\u5728\u5fc5\u8981\u5904\u6dfb\u52a0\u6ce8\u91ca\u4ee5\u89e3\u91ca\u590d\u6742\u903b\u8f91\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_5","title":"\u6587\u6863","text":"<ul> <li>\u786e\u4fdd\u5e2e\u52a9\u4fe1\u606f\uff08\u5982 <code>-h</code> \u6807\u5fd7\uff09\u6e05\u6670\u51c6\u786e\u3002</li> <li>\u6559\u7a0b\u6587\u6863\u4f4d\u4e8e <code>docs/tutorials/en/</code>\uff08\u82f1\u6587\uff09\u548c <code>docs/tutorials/zh/</code>\uff08\u4e2d\u6587\uff09\u3002\u5982\u679c\u4f60\u6dfb\u52a0\u4e86\u65b0\u529f\u80fd\uff0c\u8bf7\u8003\u8651\u66f4\u65b0\u76f8\u5173\u6559\u7a0b\u9875\u9762\u3002</li> <li>\u7f16\u8f91\u6559\u7a0b Markdown \u6587\u4ef6\u540e\uff0c\u4f7f\u7528 <code>mkdocs build -f docs/mkdocs.yml</code> \u91cd\u65b0\u6784\u5efa HTML\u3002</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u62a5\u544a\u95ee\u9898","title":"\u62a5\u544a\u95ee\u9898","text":"<p>\u5982\u679c\u4f60\u9047\u5230 bug\uff0c\u8bf7\u901a\u8fc7 GitHub Issues \u5e2e\u52a9\u6211\u4eec\u4fee\u590d\uff1a</p> <ol> <li>\u641c\u7d22\u73b0\u6709 issues \u67e5\u770b\u8be5 bug \u662f\u5426\u5df2\u88ab\u62a5\u544a\u3002</li> <li>\u521b\u5efa\u65b0 issue\uff08\u5982\u679c\u5c1a\u672a\u88ab\u62a5\u544a\uff09\uff1a\u521b\u5efa Issue</li> <li>\u8be6\u7ec6\u63cf\u8ff0\u95ee\u9898\uff0c\u5982\u679c\u53ef\u80fd\u8bf7\u63d0\u4f9b\u6d4b\u8bd5\u6587\u4ef6\u3002</li> </ol> <p>\u4f60\u4e5f\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u65b9\u5f0f\u8054\u7cfb\u6211\u4eec\uff1a - QQ \u7fa4\uff1a825696376 - \u90ae\u7bb1\uff1ayanzihan@westlake.edu.cn - \u811a\u672c\u5f00\u53d1\u8005\uff1a\u8054\u7cfb\u811a\u672c\u5934\u90e8\u5217\u51fa\u7684\u5f00\u53d1\u8005</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u529f\u80fd\u5efa\u8bae","title":"\u529f\u80fd\u5efa\u8bae","text":"<p>\u6211\u4eec\u6b22\u8fce\u529f\u80fd\u5efa\u8bae\uff01\u63d0\u51fa\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u641c\u7d22\u73b0\u6709 issues \u67e5\u770b\u662f\u5426\u5df2\u6709\u4eba\u63d0\u51fa\u3002</li> <li>\u521b\u5efa\u65b0\u529f\u80fd\u8bf7\u6c42\uff1a\u521b\u5efa\u529f\u80fd\u8bf7\u6c42 \u5e76 mention @zhyan0603</li> <li>\u6e05\u695a\u63cf\u8ff0\u4f60\u7684\u9700\u6c42 \u5e76\u89e3\u91ca\u5176\u7528\u9014\u3002</li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u8d21\u732e\u4ee3\u7801","title":"\u8d21\u732e\u4ee3\u7801","text":""},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#fork-\u5e76\u514b\u9686\u4ed3\u5e93","title":"Fork \u5e76\u514b\u9686\u4ed3\u5e93","text":"<ol> <li> <p>\u5728 GitHub \u4e0a Fork \u4ed3\u5e93\uff0c\u70b9\u51fb \u4ed3\u5e93\u9875\u9762 \u53f3\u4e0a\u89d2\u7684 \"Fork\" \u6309\u94ae\u3002</p> </li> <li> <p>\u514b\u9686\u4f60\u7684 fork \u5230\u672c\u5730\uff1a</p> </li> </ol> <pre><code>git clone https://github.com/YOUR_USERNAME/GPUMDkit.git\ncd GPUMDkit\n</code></pre> <ol> <li>\u8bbe\u7f6e upstream remote \u4ee5\u4fdd\u6301 fork \u540c\u6b65\uff1a    <pre><code>git remote add upstream https://github.com/zhyan0603/GPUMDkit.git\n</code></pre></li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u521b\u5efa\u529f\u80fd\u5206\u652f","title":"\u521b\u5efa\u529f\u80fd\u5206\u652f","text":"<p>\u4e3a\u4f60\u7684\u4fee\u6539\u521b\u5efa\u65b0\u5206\u652f\uff1a</p> <pre><code># \u4ece main \u521b\u5efa\u5e76\u5207\u6362\u5230\u65b0\u5206\u652f\ngit checkout -b your-branch-name\n</code></pre> <p>\u5206\u652f\u540d\u79f0\u968f\u610f\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u8fdb\u884c\u4fee\u6539","title":"\u8fdb\u884c\u4fee\u6539","text":"<p><code>GPUMDkit</code> \u7684\u7ed3\u6784\u5305\u62ec\uff1a - <code>gpumdkit.sh</code>\uff1a\u4e3b\u5165\u53e3\uff08Bash \u811a\u672c\uff09\uff0c\u5904\u7406\u4ea4\u4e92\u83dc\u5355\u6a21\u5f0f\u548c\u547d\u4ee4\u884c\u6a21\u5f0f - <code>install.sh</code>\uff1a\u5b89\u88c5\u811a\u672c\uff0c\u8bbe\u7f6e\u73af\u5883\u53d8\u91cf\u548c shell \u914d\u7f6e - <code>Scripts/</code>\uff1a\u6309\u529f\u80fd\u7ec4\u7ec7\u7684 Python \u548c Bash \u5b9e\u73b0\u811a\u672c   - <code>plt_scripts/</code>\uff1a\u7ed8\u56fe\u811a\u672c   - <code>calculators/</code>\uff1a\u8ba1\u7b97\u5de5\u5177   - <code>format_conversion/</code>\uff1a\u683c\u5f0f\u8f6c\u6362\u5de5\u5177   - <code>workflow/</code>\uff1a\u5de5\u4f5c\u6d41\u81ea\u52a8\u5316   - <code>sample_structures/</code>\uff1a\u7ed3\u6784\u91c7\u6837\u5de5\u5177   - <code>analyzer/</code>\uff1a\u5206\u6790\u5de5\u5177   - <code>utils/</code>\uff1a\u5b9e\u7528\u51fd\u6570\uff08\u5305\u62ec <code>completion.sh</code> Tab \u8865\u5168\uff09 - <code>src/</code>\uff1a\u4ea4\u4e92\u6a21\u5f0f\u83dc\u5355\u51fd\u6570\u7684 Shell \u811a\u672c   - <code>f1_format_conversions.sh</code>   - <code>f2_sample_structures.sh</code>   - <code>f3_workflows.sh</code>   - <code>f4_calculators.sh</code>   - <code>f5_analyzers.sh</code>   - <code>f6_plots.sh</code>   - <code>f7_utilities.sh</code> - <code>skills/</code>\uff1aAI agent \u6280\u80fd\u5b9a\u4e49\uff08\u7528\u4e8e opencode/Claude Code \u96c6\u6210\u7684 SKILL.md \u6587\u4ef6\uff09 - <code>docs/</code>\uff1a\u6587\u6863\u6587\u4ef6   - <code>tutorials/en/</code> \u548c <code>tutorials/zh/</code>\uff1a\u53cc\u8bed\u6559\u7a0b\u9875\u9762   - <code>mkdocs.yml</code>\uff1a\u6784\u5efa\u6559\u7a0b HTML \u7684 MkDocs \u914d\u7f6e   - <code>command_reference.tsv</code>\uff1a\u673a\u5668\u53ef\u8bfb\u7684\u547d\u4ee4\u53c2\u8003   - <code>htmls/</code>\uff1aMkDocs \u751f\u6210\u7684 HTML \u8f93\u51fa</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e","title":"\u4ea4\u4e92\u6a21\u5f0f\u8d21\u732e","text":"<p>\u8981\u6dfb\u52a0\u901a\u8fc7\u4ea4\u4e92\u83dc\u5355\u8bbf\u95ee\u7684\u65b0\u529f\u80fd\uff1a</p> <ol> <li>\u5728\u76f8\u5e94\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a</li> </ol> <pre><code># \u793a\u4f8b\uff1a\u6dfb\u52a0\u65b0\u7684\u683c\u5f0f\u8f6c\u6362\u811a\u672c\ntouch Scripts/format_conversion/new_converter.py\n</code></pre> <ol> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u9075\u5faa\u6a21\u5757\u5316\u51c6\u5219\uff08\u63a5\u53d7\u53c2\u6570\uff0c\u907f\u514d\u786c\u7f16\u7801\uff09\u3002</p> </li> <li> <p>\u5728\u76f8\u5e94\u7684 <code>src/</code> \u6587\u4ef6\u4e2d\u6dfb\u52a0\u5305\u88c5\u51fd\u6570\uff1a    <pre><code># \u793a\u4f8b\uff1a\u7f16\u8f91 src/f1_format_conversions.sh\nvim src/f1_format_conversions.sh\n</code></pre></p> </li> </ol> <p>\u6dfb\u52a0\u65b0\u51fd\u6570\uff1a    <pre><code>function f111_new_converter(){\necho \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/format_conversion |\"\necho \" | Script: new_converter.py                        |\"\necho \" | Developer: Your Name (your@email.com)           |\"\necho \" &gt;-------------------------------------------------&lt;\"\necho \" Input &lt;required_param1&gt; &lt;required_param2&gt;\"\necho \" Example: input.xyz output.lmp\"\necho \" ------------&gt;&gt;\"\nread -r -a converter_args\necho \" ---------------------------------------------------\"\npython ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py \"${converter_args[@]}\"\necho \" Code path: ${GPUMDkit_path}/Scripts/format_conversion/new_converter.py\"\necho \" ---------------------------------------------------\"\n}\n</code></pre></p> <ol> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u66f4\u65b0\u83dc\u5355\u663e\u793a\uff1a    <pre><code># \u627e\u5230 menu() \u51fd\u6570\u5e76\u6309\u9700\u66f4\u65b0\n# \u627e\u5230 array_choice \u6570\u7ec4\u5e76\u6dfb\u52a0\u4f60\u7684\u65b0\u9009\u62e9\u7f16\u53f7\narray_choice=(\n    \"0\" \"1\" \"101\" \"102\" \"103\" \"104\" \"105\" \"106\" \"107\" \"108\" \"109\" \"110\" \"111\"  # \u6dfb\u52a0 \"111\"\n    # ... \u5176\u4f59\u9009\u62e9\n)\n</code></pre></p> </li> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0 case \u8bed\u53e5\uff1a    <pre><code># \u5728 main() \u51fd\u6570\u4e2d\u627e\u5230\u76f8\u5e94\u7684 case \u8bed\u53e5\ncase \"${choice:0:1}\" in\n    # ...\n    \"1\")\n        source ${GPUMDkit_path}/src/f1_format_conversions.sh\n        case $choice in\n            \"1\") f1_format_conversion ;;\n            \"101\") f101_out2xyz ;;\n            # ... \u73b0\u6709 case ...\n            \"111\") f111_new_converter ;;  # \u6dfb\u52a0\u4f60\u7684 case\n        esac ;;\n    # ...\nesac\n</code></pre></p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e","title":"\u547d\u4ee4\u884c\u6a21\u5f0f\u8d21\u732e","text":"<p>\u8981\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c\u6807\u5fd7\u6216\u5b50\u547d\u4ee4\uff1a</p> <ol> <li> <p>\u5728\u76f8\u5e94\u7684 <code>Scripts/</code> \u5b50\u76ee\u5f55\u4e2d\u521b\u5efa\u5b9e\u73b0\u811a\u672c\uff1a    <pre><code># \u793a\u4f8b\uff1a\u6dfb\u52a0\u65b0\u7684\u5206\u6790\u5668\u811a\u672c\ntouch Scripts/analyzer/analyze_bonds.py\n</code></pre></p> </li> <li> <p>\u5b9e\u73b0\u4f60\u7684\u529f\u80fd\uff0c\u660e\u786e\u53c2\u6570\u8981\u6c42\uff1a    <pre><code># \u793a\u4f8b\uff1aScripts/analyzer/analyze_bonds.py\nimport sys\n\nif len(sys.argv) != 3:\n    print(\"Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\")\n    print(\"Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\")\n    sys.exit(1)\n\ninput_file = sys.argv[1]\ncutoff = float(sys.argv[2])\n\n# \u4f60\u7684\u5b9e\u73b0\n</code></pre></p> </li> </ol> <p>\u6ce8\u610f\uff1aGPUMDkit Python \u811a\u672c\u8bbe\u8ba1\u4e3a\u76f4\u63a5\u8fd0\u884c\uff08\u4e0d\u4f5c\u4e3a\u6a21\u5757\u5bfc\u5165\uff09\u3002 \u5982\u679c\u4f60\u613f\u610f\uff0c\u53ef\u4ee5\u4f7f\u7528 <code>main()</code> \u51fd\u6570\u914d\u5408 <code>if __name__ == \"__main__\":</code> \u4fdd\u62a4\uff0c \u4f46\u8fd9\u4e0d\u662f\u5fc5\u9700\u7684\u3002\u5927\u591a\u6570\u73b0\u6709\u811a\u672c\u5728\u6a21\u5757\u7ea7\u522b\u6267\u884c\u3002</p> <ol> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u6dfb\u52a0\u547d\u4ee4\u884c\u6807\u5fd7\u5904\u7406\uff1a    <pre><code># \u627e\u5230\u547d\u4ee4\u884c\u89e3\u6790\u90e8\u5206\uff08\u5927\u7684 \"case $1 in\" \u5757\uff09\n# \u5728\u9002\u5f53\u4f4d\u7f6e\u6dfb\u52a0\u4f60\u7684\u65b0\u6807\u5fd7\n\ncase $1 in\n    # ... \u73b0\u6709 case ...\n    -analyze_bonds)\n        if [ ! -z \"$2\" ] &amp;&amp; [ \"$2\" != \"-h\" ] &amp;&amp; [ ! -z \"$3\" ]; then\n            python ${analyzer_path}/analyze_bonds.py $2 $3\n        else\n            echo \" Usage: gpumdkit.sh -analyze_bonds &lt;input.xyz&gt; &lt;cutoff_distance&gt;\"\n            echo \" Example: gpumdkit.sh -analyze_bonds structure.xyz 3.0\"\n            echo \" Code path: ${analyzer_path}/analyze_bonds.py\"\n        fi ;;\n    # ... \u5176\u4f59 case ...\nesac\n</code></pre></p> </li> <li> <p>\u5728 <code>gpumdkit.sh</code> \u4e2d\u66f4\u65b0\u5e2e\u52a9\u4fe1\u606f\uff1a    <pre><code># \u627e\u5230 help_info_table() \u51fd\u6570\u5e76\u6dfb\u52a0\u4f60\u7684\u547d\u4ee4\nfunction help_info_table(){\n    echo \"+====================================== Analysis ===============================================+\"\n    echo \"| -analyze_bonds Analyze bond lengths in struct | -analyze_comp Analyze composition of extxyz      |\"\n    # ... \u5176\u4f59\u5e2e\u52a9\u8868 ...\n}\n</code></pre></p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u66f4\u65b0-tab-\u8865\u5168","title":"\u66f4\u65b0 Tab \u8865\u5168","text":"<p>\u6dfb\u52a0\u65b0\u7684\u547d\u4ee4\u884c\u6807\u5fd7\u65f6\uff0c\u66f4\u65b0 Tab \u8865\u5168\u811a\u672c\uff1a</p> <pre><code># \u7f16\u8f91 Scripts/utils/completion.sh\nvim Scripts/utils/completion.sh\n</code></pre> <p>\u5c06\u4f60\u7684\u65b0\u6807\u5fd7\u6dfb\u52a0\u5230 <code>opts</code> \u53d8\u91cf\uff1a <pre><code># \u627e\u5230 local opts=... \u884c\nlocal opts=\"-h -help -update -U -clean -time -plt -calc ... -your_new_flag ...\"\n#                                                        \u5728\u6b64\u6dfb\u52a0\u4f60\u7684\u6807\u5fd7\n</code></pre></p> <p>\u5982\u679c\u4f60\u7684\u6807\u5fd7\u9700\u8981\u6587\u4ef6\u53c2\u6570\uff0c\u5c06\u5176\u6dfb\u52a0\u5230\u73b0\u6709\u7684\u6587\u4ef6\u8865\u5168 case \u4e2d\uff1a <pre><code># \u627e\u5230\u9700\u8981\u6587\u4ef6\u53c2\u6570\u7684 case \u5e76\u7528 | \u6dfb\u52a0\u4f60\u7684\u6807\u5fd7\n-out2xyz|-out2exyz|-...|-your_new_flag)\n    COMPREPLY=($(compgen -f -- \"$cur\")) ;;\n</code></pre></p> <p>\u5982\u679c\u4f60\u7684\u6807\u5fd7\u63a5\u53d7\u4e8c\u7ea7\u9009\u9879\uff08\u5982 <code>-plt</code> \u6216 <code>-calc</code>\uff09\uff0c\u6dfb\u52a0\u65b0 case\uff1a <pre><code>case \"$prev\" in\n    # ... \u73b0\u6709 case ...\n    -your_new_flag)\n        COMPREPLY=($(compgen -W \"option1 option2 option3\" -- \"$cur\")) ;;\n    # ... \u5176\u4f59 case ...\nesac\n</code></pre></p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u4ee3\u7801\u98ce\u683c\u4e0e\u6700\u4f73\u5b9e\u8df5","title":"\u4ee3\u7801\u98ce\u683c\u4e0e\u6700\u4f73\u5b9e\u8df5","text":"<ul> <li>Shell \u811a\u672c\uff1a</li> <li>\u4f7f\u7528 <code>${variable}</code> \u8fdb\u884c\u53d8\u91cf\u5c55\u5f00</li> <li>\u4f7f\u7528 <code>[ ! -z \"$var\" ]</code> \u8fdb\u884c\u975e\u7a7a\u68c0\u67e5\uff08\u9879\u76ee\u7ea6\u5b9a\uff09</li> <li>\u4ea4\u4e92\u51fd\u6570\u5e94\u9075\u5faa banner \u683c\u5f0f\uff1a     <pre><code>echo \" &gt;-------------------------------------------------&lt;\"\necho \" | Calling the script in Scripts/&lt;category&gt;        |\"\necho \" | Script: &lt;script_name&gt;.py                        |\"\necho \" | Developer: &lt;Name&gt; (&lt;email&gt;)                     |\"\necho \" &gt;-------------------------------------------------&lt;\"\n</code></pre></li> <li>\u4f7f\u7528 <code>read -r -a varname</code> \u8bfb\u53d6\u591a\u8bcd\u8f93\u5165\uff0c\u7136\u540e\u7528 <code>\"${varname[@]}\"</code> \u4f20\u9012</li> <li> <p><code>src/</code> \u4e2d\u7684 Shell \u811a\u672c\u5e94\u4ee5\u6587\u4ef6\u5934\u6ce8\u91ca\u5757\u5f00\u59cb\uff1a     <pre><code># ============================================================\n# GPUMDkit &lt;module name&gt; module\n# Repository: https://github.com/zhyan0603/GPUMDkit\n# Author: &lt;Name&gt; (&lt;email&gt;)\n# ============================================================\n</code></pre></p> </li> <li> <p>Python \u811a\u672c\uff1a</p> </li> <li>\u7f16\u5199\u6e05\u6670\u3001\u53ef\u7ef4\u62a4\u7684\u4ee3\u7801</li> <li>\u4f7f\u7528\u6709\u610f\u4e49\u7684\u53d8\u91cf\u540d</li> <li>\u4f7f\u7528 <code>sys.argv</code> \u8fdb\u884c\u53c2\u6570\u89e3\u6790\uff08\u4e0e\u5927\u591a\u6570\u73b0\u6709\u811a\u672c\u4e00\u81f4\uff09</li> <li>\u63d0\u4f9b\u6e05\u6670\u7684\u4f7f\u7528\u4fe1\u606f\uff1a<code>print(\"Usage: ...\")</code> \u548c <code>print(\"Example: ...\")</code></li> <li>\u5982\u679c\u4f60\u7684\u811a\u672c\u4f7f\u7528\u91cd\u578b/\u7279\u6b8a\u5305\uff08<code>NepTrain</code>\u3001<code>calorine</code>\u3001<code>dpdata</code>\uff09\uff0c\u8bf7\u6dfb\u52a0     <code>print_dependency_notice()</code> \u51fd\u6570\u4ee5\u901a\u77e5\u7528\u6237\u5f15\u7528\u5efa\u8bae</li> </ul>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539","title":"\u6d4b\u8bd5\u4f60\u7684\u4fee\u6539","text":"<p>\u63d0\u4ea4\u8d21\u732e\u524d\uff0c\u8fd0\u884c\u76f8\u5173\u9a8c\u8bc1\u547d\u4ee4\uff1a</p> <pre><code># Shell \u8bed\u6cd5\u68c0\u67e5\uff08\u59cb\u7ec8\u8fd0\u884c\uff09\nbash -n gpumdkit.sh\nfind src Scripts -name '*.sh' -exec bash -n {} +\n\n# Python \u8bed\u6cd5\u68c0\u67e5\uff08\u9488\u5bf9\u4fee\u6539\u7684 Python \u6587\u4ef6\uff09\npython3 -m py_compile path/to/modified_script.py\n\n# MkDocs \u6784\u5efa\uff08\u5982\u679c\u4fee\u6539\u4e86\u6587\u6863\uff09\nmkdocs build -f docs/mkdocs.yml\n\n# \u68c0\u67e5\u5c3e\u968f\u7a7a\u683c\u95ee\u9898\ngit diff --check\n</code></pre> <p>\u7136\u540e\u6d4b\u8bd5\u529f\u80fd\uff1a</p> <ol> <li> <p>\u6d4b\u8bd5\u4ea4\u4e92\u6a21\u5f0f\uff08\u5982\u9002\u7528\uff09\uff1a    <pre><code>gpumdkit.sh\n# \u5bfc\u822a\u5230\u4f60\u7684\u65b0\u529f\u80fd\u5e76\u5145\u5206\u6d4b\u8bd5\n</code></pre></p> </li> <li> <p>\u6d4b\u8bd5\u547d\u4ee4\u884c\u6a21\u5f0f\uff08\u5982\u9002\u7528\uff09\uff1a    <pre><code>gpumdkit.sh -your_new_flag [arguments]\ngpumdkit.sh -your_new_flag -h  # \u6d4b\u8bd5\u5e2e\u52a9\u4fe1\u606f\n</code></pre></p> </li> <li> <p>\u6d4b\u8bd5 Tab \u8865\u5168\uff08\u5982\u679c\u4f60\u4fee\u6539\u4e86 <code>completion.sh</code>\uff09\uff1a    <pre><code>source Scripts/utils/completion.sh\ngpumdkit.sh -&lt;TAB&gt;  # \u5e94\u663e\u793a\u4f60\u7684\u65b0\u6807\u5fd7\n</code></pre></p> </li> <li> <p>\u7528\u5404\u79cd\u8f93\u5165\u6d4b\u8bd5\uff1a</p> </li> <li>\u7528\u5178\u578b\u8f93\u5165\u6d4b\u8bd5</li> <li>\u7528\u8fb9\u7f18\u60c5\u51b5\u6d4b\u8bd5\uff08\u7a7a\u6587\u4ef6\u3001\u5927\u6587\u4ef6\u7b49\uff09</li> <li> <p>\u6d4b\u8bd5\u9519\u8bef\u5904\u7406\uff08\u7f3a\u5c11\u6587\u4ef6\u3001\u65e0\u6548\u53c2\u6570\uff09</p> </li> <li> <p>\u9a8c\u8bc1\u65e0\u56de\u5f52\uff1a\u786e\u4fdd\u73b0\u6709\u529f\u80fd\u4ecd\u7136\u6b63\u5e38\u5de5\u4f5c\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u63d0\u4ea4\u4fe1\u606f","title":"\u63d0\u4ea4\u4fe1\u606f","text":"<p>\u7f16\u5199\u6e05\u6670\u3001\u63cf\u8ff0\u6027\u7684\u63d0\u4ea4\u4fe1\u606f\u6765\u89e3\u91ca\u4f60\u505a\u4e86\u4ec0\u4e48\u66f4\u6539\u3002\u6ca1\u6709\u4e25\u683c\u7684\u683c\u5f0f\u8981\u6c42\u2014\u2014\u53ea\u8981\u786e\u4fdd\u4f60\u7684\u4fe1\u606f\u662f\u53ef\u7406\u89e3\u7684\u3002</p>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#\u63a8\u9001\u5e76\u521b\u5efa-pull-request","title":"\u63a8\u9001\u5e76\u521b\u5efa Pull Request","text":"<ol> <li> <p>\u63d0\u4ea4\u4f60\u7684\u4fee\u6539\uff1a    <pre><code>git add .\ngit commit -m \"\u4f60\u7684\u63cf\u8ff0\u6027\u4fe1\u606f\"\n</code></pre></p> </li> <li> <p>\u4fdd\u6301\u4f60\u7684\u5206\u652f\u4e0e\u6700\u65b0\u7684 <code>dev</code> \u5206\u652f\u540c\u6b65\uff1a    <pre><code>git fetch origin\ngit rebase origin/dev\n</code></pre></p> </li> <li> <p>\u63a8\u9001\u4f60\u7684\u5206\u652f\u5230\u4f60\u7684 fork\uff1a    <pre><code>git push origin your-branch-name\n</code></pre></p> </li> <li> <p>\u521b\u5efa Pull Request\uff1a</p> </li> <li>\u524d\u5f80 GPUMDkit \u4ed3\u5e93</li> <li>\u70b9\u51fb \"Pull Requests\" \u2192 \"New Pull Request\"</li> <li>\u8bbe\u7f6e\u76ee\u6807\u5206\u652f\u4e3a <code>dev</code> \u8fdb\u884c\u4ee3\u7801\u5ba1\u67e5</li> <li>\u8bbe\u7f6e\u6bd4\u8f83\u5206\u652f\u4e3a\u4f60\u7684\u529f\u80fd\u5206\u652f</li> <li> <p>\u586b\u5199 PR \u63cf\u8ff0\uff1a</p> <ul> <li>\u6807\u9898\uff1a\u7b80\u8981\u63cf\u8ff0\u66f4\u6539</li> <li>\u63cf\u8ff0\uff1a\u8be6\u7ec6\u89e3\u91ca\u66f4\u6539\u5185\u5bb9\u548c\u539f\u56e0</li> <li>\u6d4b\u8bd5\uff1a\u63cf\u8ff0\u4f60\u5982\u4f55\u6d4b\u8bd5\u8fd9\u4e9b\u66f4\u6539</li> </ul> </li> <li> <p>\u56de\u5e94\u5ba1\u67e5\u53cd\u9988\uff1a</p> </li> <li>\u5bf9\u5efa\u8bae\u548c\u5efa\u8bbe\u6027\u6279\u8bc4\u4fdd\u6301\u5f00\u653e</li> <li>\u53ca\u65f6\u8fdb\u884c\u8bf7\u6c42\u7684\u4fee\u6539</li> <li> <p>\u63a8\u9001\u989d\u5916\u63d0\u4ea4\u5230\u4f60\u7684\u5206\u652f\uff08\u5b83\u4eec\u4f1a\u81ea\u52a8\u51fa\u73b0\u5728 PR \u4e2d\uff09</p> </li> <li> <p>\u6279\u51c6\u540e\uff1a\u7ef4\u62a4\u8005\u5c06\u5408\u5e76\u4f60\u7684 PR\u3002</p> </li> </ol>"},{"location":"zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html#_6","title":"\u6709\u95ee\u9898\u6216\u9700\u8981\u5e2e\u52a9\uff1f","text":"<p>\u5982\u679c\u4f60\u5bf9\u8d21\u732e\u6709\u7591\u95ee\u6216\u9700\u8981\u5e2e\u52a9\uff1a</p> <ul> <li>\u53d1\u8d77\u8ba8\u8bba\uff1a\u4f7f\u7528 GitHub Discussions \u63d0\u51fa\u4e00\u822c\u6027\u95ee\u9898</li> <li>\u5728 issue \u4e2d\u63d0\u95ee\uff1a\u5728\u76f8\u5173 issue \u4e2d\u8bc4\u8bba\u4ee5\u83b7\u53d6\u5177\u4f53\u95ee\u9898\u7684\u5e2e\u52a9</li> <li>\u8054\u7cfb\u7ef4\u62a4\u8005\uff1a\u8054\u7cfb README \u4e2d\u5217\u51fa\u7684\u6838\u5fc3\u5f00\u53d1\u8005</li> </ul> <p>\u518d\u6b21\u611f\u8c22\u4f60\u4e3a <code>GPUMDkit</code> \u505a\u51fa\u8d21\u732e\uff01\u4f60\u7684\u52aa\u529b\u5e2e\u52a9\u8fd9\u4e2a\u5de5\u5177\u5305\u4e3a\u6574\u4e2a GPUMD \u548c NEP \u793e\u533a\u53d8\u5f97\u66f4\u597d\u3002</p>"}]}
\ No newline at end of file
diff --git "a/docs/htmls/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.html" "b/docs/htmls/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.html"
index 49b05be..b42efb7 100644
--- "a/docs/htmls/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.html"
+++ "b/docs/htmls/zh/\344\270\273\345\212\250\345\255\246\344\271\240\345\267\245\344\275\234\346\265\201.html"
@@ -1604,30 +1604,30 @@ <h2 id="4">4. 检查输入文件</h2>
 <li><code>nep.txt</code></li>
 <li><code>nep.in</code></li>
 <li><code>train.xyz</code></li>
-<li><code>run.in</code></li>
+<li><code>run_*.in</code>（如 <code>run_1.in</code>、<code>run_2.in</code> 等）</li>
 <li><code>INCAR</code></li>
 <li><code>POTCAR</code></li>
 <li><code>KPOINTS</code></li>
 <li>初始采样结构文件，例如 <code>sample_struct.xyz</code></li>
 </ul>
-<p>脚本会把公共输入移动到 <code>common/</code>，并创建 <code>00.modev/</code>、<code>01.select/</code> 等工作目录。</p>
+<p>脚本会把公共输入移动到 <code>common/</code>，并创建 <code>00.md/</code>、<code>01.select/</code> 等工作目录。</p>
 <h2 id="5">5. 文件组织</h2>
 <p>脚本会创建公共输入目录和 MD 目录：</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>mkdir<span class="w"> </span><span class="m">00</span>.modev<span class="w"> </span>common
-<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>mv<span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/<span class="o">{</span>nep.txt,nep.in,*.xyz,run.in,INCAR,KPOINTS,POTCAR<span class="o">}</span><span class="w"> </span>./common
-<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>cp<span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/common/<span class="nv">$sample_xyz_file</span><span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/00.modev
+<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>mkdir<span class="w"> </span><span class="m">00</span>.md<span class="w"> </span>common
+<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>mv<span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/<span class="o">{</span>nep.txt,nep.in,*.xyz,run_*.in,INCAR,KPOINTS,POTCAR<span class="o">}</span><span class="w"> </span>./common
+<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>cp<span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/common/<span class="nv">$sample_xyz_file</span><span class="w"> </span><span class="si">${</span><span class="nv">work_dir</span><span class="si">}</span>/00.md
 </code></pre></div>
 <ul>
-<li><code>00.modev</code>：用于运行 GPUMD MD 采样。</li>
-<li><code>common</code>：保存 <code>nep.txt</code>、<code>run.in</code>、结构文件和 DFT 输入文件等公共资源。</li>
+<li><code>00.md</code>：用于运行 GPUMD MD 采样。</li>
+<li><code>common</code>：保存 <code>nep.txt</code>、<code>run_*.in</code> 文件、结构文件和 DFT 输入文件等公共资源。</li>
 </ul>
 <h2 id="6-md">6. 提交 MD 任务</h2>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>submit_gpumd_array<span class="w"> </span>modev<span class="w"> </span><span class="si">${</span><span class="nv">sample_struct_num</span><span class="si">}</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>submit_gpumd_array<span class="w"> </span>md<span class="w"> </span><span class="si">${</span><span class="nv">sample_struct_num</span><span class="si">}</span>
 <a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>sbatch<span class="w"> </span>submit.slurm
 </code></pre></div>
 <p>脚本会通过提交模板创建数组任务。不同集群上的提交命令和模板可能需要自己修改。</p>
 <h2 id="7">7. 检查任务完成</h2>
-<p>脚本会持续检查 <code>00.modev/</code> 下各个 <code>sample_*/log</code> 文件，确认是否出现：</p>
+<p>脚本会持续检查 <code>00.md/</code> 下各个 <code>sample_*/log</code> 文件，确认是否出现：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>Finished<span class="w"> </span>running<span class="w"> </span>GPUMD.
 </code></pre></div>
 <p>如果发现 <code>Error</code>，脚本会停止。</p>
diff --git "a/docs/htmls/zh/\345\221\275\344\273\244\345\217\202\350\200\203.html" "b/docs/htmls/zh/\345\221\275\344\273\244\345\217\202\350\200\203.html"
index 69657a5..59b391a 100644
--- "a/docs/htmls/zh/\345\221\275\344\273\244\345\217\202\350\200\203.html"
+++ "b/docs/htmls/zh/\345\221\275\344\273\244\345\217\202\350\200\203.html"
@@ -1718,7 +1718,7 @@ <h2 id="_5">可视化</h2>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>&lt;type&gt;<span class="w"> </span><span class="o">[</span>options<span class="o">]</span>
 <a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>-h
 </code></pre></div>
-<p>常用类型包括 <code>train</code>、<code>prediction</code>、<code>thermo</code>、<code>msd</code>、<code>sdc</code>、<code>rdf</code>、<code>emd</code>、<code>nemd</code>、<code>hnemd</code>、<code>pdos</code> 和 <code>plane-grid</code>。</p>
+<p>常用类型包括 <code>train</code>、<code>prediction</code>（别名：<code>test</code>）、<code>thermo</code>、<code>msd</code>、<code>sdc</code>、<code>rdf</code>、<code>emd</code>、<code>nemd</code>、<code>hnemd</code>、<code>pdos</code> 和 <code>plane-grid</code>。</p>
 <h2 id="_6">工具</h2>
 <table>
 <thead>
diff --git "a/docs/htmls/zh/\345\277\253\351\200\237\345\205\245\351\227\250.html" "b/docs/htmls/zh/\345\277\253\351\200\237\345\205\245\351\227\250.html"
index 2bacb2e..0faa4e8 100644
--- "a/docs/htmls/zh/\345\277\253\351\200\237\345\205\245\351\227\250.html"
+++ "b/docs/htmls/zh/\345\277\253\351\200\237\345\205\245\351\227\250.html"
@@ -959,6 +959,17 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#hello-world" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Hello World 示例
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1484,6 +1495,17 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#hello-world" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Hello World 示例
+      
+    </span>
+  </a>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1672,7 +1694,7 @@ <h2 id="_3">交互模式</h2>
 <a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a> 1) Format Conversion          2) Sample Structures
 <a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a> 3) Workflow                   4) Calculators
 <a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a> 5) Analyzer                   6) Visualization
-<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a> 7) Utilities                  8) Developing...
+<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a> 7) Utilities                  8) Help                
 <a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a> 0) Exit
 <a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a> ------------&gt;&gt;
 <a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a> Input the function number:
@@ -1688,38 +1710,58 @@ <h2 id="_4">命令行模式</h2>
 <a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>msd<span class="w"> </span>trajectory.xyz<span class="w"> </span>Li<span class="w"> </span><span class="m">10</span>
 </code></pre></div>
 <p>第一个示例读取 <code>POSCAR</code>，写出 <code>model.xyz</code>。</p>
+<h2 id="hello-world">Hello World 示例</h2>
+<p>一个最小化的端到端检查，确认安装是否正常——创建一个极小的硅 POSCAR，转换为 extxyz，并查看输出：</p>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>cat<span class="w"> </span>&gt;<span class="w"> </span>POSCAR<span class="w"> </span><span class="s">&lt;&lt; &#39;EOF&#39;</span>
+<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a><span class="s">Si</span>
+<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a><span class="s">1.0</span>
+<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="s">0 2.715 2.715</span>
+<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a><span class="s">2.715 0 2.715</span>
+<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a><span class="s">2.715 2.715 0</span>
+<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a><span class="s">Si</span>
+<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a><span class="s">1</span>
+<a id="__codelineno-10-9" name="__codelineno-10-9" href="#__codelineno-10-9"></a><span class="s">direct</span>
+<a id="__codelineno-10-10" name="__codelineno-10-10" href="#__codelineno-10-10"></a><span class="s">0 0 0</span>
+<a id="__codelineno-10-11" name="__codelineno-10-11" href="#__codelineno-10-11"></a><span class="s">EOF</span>
+<a id="__codelineno-10-12" name="__codelineno-10-12" href="#__codelineno-10-12"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<a id="__codelineno-10-13" name="__codelineno-10-13" href="#__codelineno-10-13"></a>head<span class="w"> </span>model.xyz
+</code></pre></div>
+<p>如果 <code>model.xyz</code> 显示一个 Si 原子及晶格信息，说明安装成功。</p>
+<blockquote>
+<p><strong>什么是 extxyz？</strong> extxyz 是扩展 XYZ 格式：第 1 行是原子数，第 2 行包含晶格及结构级属性（按需包含能量/力/维里），第 3 行及以后是每个原子及其原子级属性。它是 NEP 的原生训练数据格式。</p>
+</blockquote>
 <h2 id="_5">常见示例</h2>
 <h3 id="poscar-extxyz">POSCAR 转 extxyz</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-pos2exyz<span class="w"> </span>POSCAR<span class="w"> </span>model.xyz
 </code></pre></div>
 <h3 id="gpumd-group">添加 GPUMD group 标签</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
+<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-addgroup<span class="w"> </span>POSCAR<span class="w"> </span>Li<span class="w"> </span>Y<span class="w"> </span>Cl
 </code></pre></div>
 <p>group 标签用于一些需要原子分组的 GPUMD 相关流程和分析，例如特定元素的 MSD 或扩散性质计算。</p>
 <h3 id="nep">绘制 NEP 训练结果</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
+<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>train
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/train.png" alt="NEP training results" width="72%" />
 </div>
 
 <h3 id="nep_1">绘制 NEP 测试集结果</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span><span class="nb">test</span>
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/prediction.png" alt="NEP test results" width="72%" />
 </div>
 
 <h3 id="_6">绘制热力学量</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
+<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>thermo
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/thermo.png" alt="Thermo plot" width="72%" />
 </div>
 
 <h3 id="msd">绘制 MSD 和自扩散系数</h3>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
-<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
+<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>msd
+<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>sdc
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/msd.png" alt="MSD plot" width="45%" />
diff --git "a/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html" "b/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html"
index 02e073d..46d93fb 100644
--- "a/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html"
+++ "b/docs/htmls/zh/\346\240\274\345\274\217\350\275\254\346\215\242.html"
@@ -2124,6 +2124,10 @@ <h2 id="_12">常见问题</h2>
 <td>使用 <code>-clean_xyz input.xyz clean.xyz</code></td>
 </tr>
 <tr>
+<td>转换后的结构看起来偏移</td>
+<td>检查源文件中的周期性边界条件/晶胞信息</td>
+</tr>
+<tr>
 <td>提取帧不对</td>
 <td>注意帧索引通常从 0 开始</td>
 </tr>
diff --git "a/docs/htmls/zh/\347\273\230\345\233\276\350\204\232\346\234\254.html" "b/docs/htmls/zh/\347\273\230\345\233\276\350\204\232\346\234\254.html"
index 12209da..1708b0b 100644
--- "a/docs/htmls/zh/\347\273\230\345\233\276\350\204\232\346\234\254.html"
+++ "b/docs/htmls/zh/\347\273\230\345\233\276\350\204\232\346\234\254.html"
@@ -1494,17 +1494,6 @@
     </span>
   </a>
   
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#plt_descriptors_comparepy" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        plt_descriptors_compare.py
-      
-    </span>
-  </a>
-  
 </li>
         
           <li class="md-nav__item">
@@ -2128,17 +2117,6 @@
     </span>
   </a>
   
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#plt_descriptors_comparepy" class="md-nav__link">
-    <span class="md-ellipsis">
-      
-        plt_descriptors_compare.py
-      
-    </span>
-  </a>
-  
 </li>
         
           <li class="md-nav__item">
@@ -2244,20 +2222,24 @@ <h2 id="_1">快速入口</h2>
 <a id="__codelineno-1-19" name="__codelineno-1-19" href="#__codelineno-1-19"></a>|  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|
 <a id="__codelineno-1-20" name="__codelineno-1-20" href="#__codelineno-1-20"></a>|  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |
 <a id="__codelineno-1-21" name="__codelineno-1-21" href="#__codelineno-1-21"></a>|  D_xyz          - Directional Arrhenius D                                                     |
-<a id="__codelineno-1-22" name="__codelineno-1-22" href="#__codelineno-1-22"></a>+-----------------------------------------------------------------------------------------------+
-<a id="__codelineno-1-23" name="__codelineno-1-23" href="#__codelineno-1-23"></a>|                                    MD &amp; Structural Analysis                                   |
-<a id="__codelineno-1-24" name="__codelineno-1-24" href="#__codelineno-1-24"></a>+-----------------------------------------------------------------------------------------------+
-<a id="__codelineno-1-25" name="__codelineno-1-25" href="#__codelineno-1-25"></a>|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |
-<a id="__codelineno-1-26" name="__codelineno-1-26" href="#__codelineno-1-26"></a>|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
-<a id="__codelineno-1-27" name="__codelineno-1-27" href="#__codelineno-1-27"></a>|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
-<a id="__codelineno-1-28" name="__codelineno-1-28" href="#__codelineno-1-28"></a>|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
-<a id="__codelineno-1-29" name="__codelineno-1-29" href="#__codelineno-1-29"></a>|  doas           - Density of atomistic states                                                 |
+<a id="__codelineno-1-22" name="__codelineno-1-22" href="#__codelineno-1-22"></a>|  doas           - Density of atomistic states                                                 |
+<a id="__codelineno-1-23" name="__codelineno-1-23" href="#__codelineno-1-23"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-24" name="__codelineno-1-24" href="#__codelineno-1-24"></a>|                                    MD &amp; Structural Analysis                                   |
+<a id="__codelineno-1-25" name="__codelineno-1-25" href="#__codelineno-1-25"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-26" name="__codelineno-1-26" href="#__codelineno-1-26"></a>|  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |
+<a id="__codelineno-1-27" name="__codelineno-1-27" href="#__codelineno-1-27"></a>|  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
+<a id="__codelineno-1-28" name="__codelineno-1-28" href="#__codelineno-1-28"></a>|  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
+<a id="__codelineno-1-29" name="__codelineno-1-29" href="#__codelineno-1-29"></a>|  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
 <a id="__codelineno-1-30" name="__codelineno-1-30" href="#__codelineno-1-30"></a>+-----------------------------------------------------------------------------------------------+
 <a id="__codelineno-1-31" name="__codelineno-1-31" href="#__codelineno-1-31"></a>|                                        Heat Transport                                         |
 <a id="__codelineno-1-32" name="__codelineno-1-32" href="#__codelineno-1-32"></a>+-----------------------------------------------------------------------------------------------+
 <a id="__codelineno-1-33" name="__codelineno-1-33" href="#__codelineno-1-33"></a>|  emd            - EMD results                    nemd           - NEMD results                |
 <a id="__codelineno-1-34" name="__codelineno-1-34" href="#__codelineno-1-34"></a>|  hnemd          - HNEMD results                  viscosity      - Viscosity                   |
 <a id="__codelineno-1-35" name="__codelineno-1-35" href="#__codelineno-1-35"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-36" name="__codelineno-1-36" href="#__codelineno-1-36"></a>|                                          Phonons                                              |
+<a id="__codelineno-1-37" name="__codelineno-1-37" href="#__codelineno-1-37"></a>+-----------------------------------------------------------------------------------------------+
+<a id="__codelineno-1-38" name="__codelineno-1-38" href="#__codelineno-1-38"></a>|  pdos           - VAC and PDOS                                                                |
+<a id="__codelineno-1-39" name="__codelineno-1-39" href="#__codelineno-1-39"></a>+-----------------------------------------------------------------------------------------------+
 </code></pre></div>
 <hr />
 <h2 id="nep">NEP 训练与预测</h2>
@@ -2495,7 +2477,7 @@ <h3 id="plt_nemdpy">plt_nemd.py</h3>
 
 <hr />
 <h3 id="plt_hnemdpy">plt_hnemd.py</h3>
-<p>绘制非均匀非平衡分子动力学 (HNEMD) 结果。</p>
+<p>绘制均匀非平衡分子动力学 (HNEMD) 结果。</p>
 <p><strong>输入文件：</strong> GPUMD 的 HNEMD 输出文件</p>
 <p><strong>参数说明：</strong></p>
 <table>
@@ -2612,17 +2594,12 @@ <h3 id="plt_descriptorspy">plt_descriptors.py</h3>
   <img src="../../Gallery/des_umap.png" alt="UMAP descriptor visualization" width="52%" />
 </div>
 
-<hr />
-<h3 id="plt_descriptors_comparepy">plt_descriptors_compare.py</h3>
-<p>比较多个训练集或模型的描述符。</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-30-1" name="__codelineno-30-1" href="#__codelineno-30-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>des_compare
-</code></pre></div>
 <hr />
 <h3 id="plt_dimerpy">plt_dimer.py</h3>
 <p>绘制二聚体相互作用曲线。将两个原子放入立方盒子（30 Å），使用 NEP 模型计算势能和力随距离的变化。</p>
 <p><strong>输入文件：</strong> <code>nep.txt</code></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-31-1" name="__codelineno-31-1" href="#__codelineno-31-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>&lt;element1&gt;<span class="w"> </span>&lt;element2&gt;<span class="w"> </span>&lt;nep_model&gt;
-<a id="__codelineno-31-2" name="__codelineno-31-2" href="#__codelineno-31-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span>nep.txt
+<div class="highlight"><pre><span></span><code><a id="__codelineno-30-1" name="__codelineno-30-1" href="#__codelineno-30-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>&lt;element1&gt;<span class="w"> </span>&lt;element2&gt;<span class="w"> </span>&lt;nep_model&gt;
+<a id="__codelineno-30-2" name="__codelineno-30-2" href="#__codelineno-30-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>dimer<span class="w"> </span>Li<span class="w"> </span>Li<span class="w"> </span>nep.txt
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/dimer_nep.png" alt="Dimer NEP curve" width="45%" />
@@ -2634,8 +2611,8 @@ <h3 id="plt_dimerpy">plt_dimer.py</h3>
 <h3 id="plt_doaspy">plt_doas.py</h3>
 <p>绘制 <a href="https://doi.org/10.1002/anie.202215544">Wang et al.</a> 提出的原子态密度 (DOAS)。</p>
 <p><strong>输入文件：</strong> <code>doas.out</code>（由 <code>gpumdkit.sh -calc doas</code> 计算）</p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-32-1" name="__codelineno-32-1" href="#__codelineno-32-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>&lt;doas.out&gt;<span class="w"> </span>&lt;species&gt;
-<a id="__codelineno-32-2" name="__codelineno-32-2" href="#__codelineno-32-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
+<div class="highlight"><pre><span></span><code><a id="__codelineno-31-1" name="__codelineno-31-1" href="#__codelineno-31-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>&lt;doas.out&gt;<span class="w"> </span>&lt;species&gt;
+<a id="__codelineno-31-2" name="__codelineno-31-2" href="#__codelineno-31-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>doas<span class="w"> </span>doas.out<span class="w"> </span>Li
 </code></pre></div>
 <div align="center">
   <img src="../../Gallery/doas.png" alt="Density of atomistic states" width="52%" />
@@ -2645,16 +2622,16 @@ <h3 id="plt_doaspy">plt_doas.py</h3>
 <h2 id="plane-grid">极性材料的 Plane-Grid 绘图</h2>
 <p>此工作流将位移或极化数据映射到网格上，并绘制选定平面的轮廓。详细用法和实际案例请参见 <strong><a href="%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html">极性材料分析</a></strong>。</p>
 <p><strong>依赖：</strong></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-33-1" name="__codelineno-33-1" href="#__codelineno-33-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
+<div class="highlight"><pre><span></span><code><a id="__codelineno-32-1" name="__codelineno-32-1" href="#__codelineno-32-1"></a>pip3<span class="w"> </span>install<span class="w"> </span>git+https://github.com/MoseyQAQ/ferrodispcalc.git
 </code></pre></div>
 <p><strong>典型前置步骤：</strong></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-34-1" name="__codelineno-34-1" href="#__codelineno-34-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span><span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
-<a id="__codelineno-34-2" name="__codelineno-34-2" href="#__codelineno-34-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Pb_Sr-O.dat<span class="w"> </span>-o<span class="w"> </span>displacements.dat
-<a id="__codelineno-34-3" name="__codelineno-34-3" href="#__codelineno-34-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
+<div class="highlight"><pre><span></span><code><a id="__codelineno-33-1" name="__codelineno-33-1" href="#__codelineno-33-1"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>nlist<span class="w"> </span>-i<span class="w"> </span>model.xyz<span class="w"> </span>-c<span class="w"> </span><span class="m">4</span><span class="w"> </span>-n<span class="w"> </span><span class="m">12</span><span class="w"> </span>-C<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>-E<span class="w"> </span>O
+<a id="__codelineno-33-2" name="__codelineno-33-2" href="#__codelineno-33-2"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>disp<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-n<span class="w"> </span>nl-Pb_Sr-O.dat<span class="w"> </span>-o<span class="w"> </span>displacements.dat
+<a id="__codelineno-33-3" name="__codelineno-33-3" href="#__codelineno-33-3"></a>gpumdkit.sh<span class="w"> </span>-calc<span class="w"> </span>avg-struct<span class="w"> </span>-i<span class="w"> </span>movie.xyz<span class="w"> </span>-l<span class="w"> </span><span class="m">0</span>.2<span class="w"> </span>-o<span class="w"> </span>averaged_structure.xyz
 </code></pre></div>
 <p><strong>使用方法：</strong></p>
-<div class="highlight"><pre><span></span><code><a id="__codelineno-35-1" name="__codelineno-35-1" href="#__codelineno-35-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr
-<a id="__codelineno-35-2" name="__codelineno-35-2" href="#__codelineno-35-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span>
+<div class="highlight"><pre><span></span><code><a id="__codelineno-34-1" name="__codelineno-34-1" href="#__codelineno-34-1"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr
+<a id="__codelineno-34-2" name="__codelineno-34-2" href="#__codelineno-34-2"></a>gpumdkit.sh<span class="w"> </span>-plt<span class="w"> </span>plane-grid<span class="w"> </span>-i<span class="w"> </span>averaged_structure.xyz<span class="w"> </span>-d<span class="w"> </span>displacements.dat<span class="w"> </span>-e<span class="w"> </span>Pb<span class="w"> </span>Sr<span class="w"> </span>--select-xy<span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">1</span>
 </code></pre></div>
 <hr />
 <h2 id="_7">快速参考表</h2>
diff --git "a/docs/htmls/zh/\350\207\252\345\256\232\344\271\211\345\221\275\344\273\244.html" "b/docs/htmls/zh/\350\207\252\345\256\232\344\271\211\345\221\275\344\273\244.html"
index 2b615cc..44e4764 100644
--- "a/docs/htmls/zh/\350\207\252\345\256\232\344\271\211\345\221\275\344\273\244.html"
+++ "b/docs/htmls/zh/\350\207\252\345\256\232\344\271\211\345\221\275\344\273\244.html"
@@ -1589,6 +1589,8 @@ <h2 id="_10">使用建议</h2>
 <li>调用外部脚本时，尽量用 <code>"$@"</code> 保留参数中的空格和特殊字符。</li>
 <li>批处理目录时，注意使用 <code>cd "$dir"</code>，避免路径中有空格时出错。</li>
 </ul>
+<hr />
+<p>感谢你使用 <code>GPUMDkit</code>！如有任何问题或需要进一步帮助，欢迎在我们的 GitHub 仓库提 issue 或联系 Zihan YAN (yanzihan@westlake.edu.cn)。</p>
 
 
 
diff --git "a/docs/htmls/zh/\350\264\241\347\214\256\346\214\207\345\215\227.html" "b/docs/htmls/zh/\350\264\241\347\214\256\346\214\207\345\215\227.html"
index 44bf15f..f9c6e3c 100644
--- "a/docs/htmls/zh/\350\264\241\347\214\256\346\214\207\345\215\227.html"
+++ "b/docs/htmls/zh/\350\264\241\347\214\256\346\214\207\345\215\227.html"
@@ -1196,7 +1196,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_2" class="md-nav__link">
+  <a href="#开发规范与准则" class="md-nav__link">
     <span class="md-ellipsis">
       
         开发规范与准则
@@ -1208,7 +1208,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
+  <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
         语言要求
@@ -1219,7 +1219,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
+  <a href="#_3" class="md-nav__link">
     <span class="md-ellipsis">
       
         模块化与可复用性
@@ -1230,7 +1230,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
+  <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
         代码风格
@@ -1241,7 +1241,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
+  <a href="#_5" class="md-nav__link">
     <span class="md-ellipsis">
       
         文档
@@ -1257,7 +1257,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
+  <a href="#报告问题" class="md-nav__link">
     <span class="md-ellipsis">
       
         报告问题
@@ -1268,7 +1268,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_8" class="md-nav__link">
+  <a href="#功能建议" class="md-nav__link">
     <span class="md-ellipsis">
       
         功能建议
@@ -1279,7 +1279,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_9" class="md-nav__link">
+  <a href="#贡献代码" class="md-nav__link">
     <span class="md-ellipsis">
       
         贡献代码
@@ -1291,7 +1291,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#fork" class="md-nav__link">
+  <a href="#fork-并克隆仓库" class="md-nav__link">
     <span class="md-ellipsis">
       
         Fork 并克隆仓库
@@ -1302,7 +1302,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_10" class="md-nav__link">
+  <a href="#创建功能分支" class="md-nav__link">
     <span class="md-ellipsis">
       
         创建功能分支
@@ -1313,7 +1313,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_11" class="md-nav__link">
+  <a href="#进行修改" class="md-nav__link">
     <span class="md-ellipsis">
       
         进行修改
@@ -1325,7 +1325,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_12" class="md-nav__link">
+  <a href="#交互模式贡献" class="md-nav__link">
     <span class="md-ellipsis">
       
         交互模式贡献
@@ -1336,7 +1336,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_13" class="md-nav__link">
+  <a href="#命令行模式贡献" class="md-nav__link">
     <span class="md-ellipsis">
       
         命令行模式贡献
@@ -1347,7 +1347,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#tab" class="md-nav__link">
+  <a href="#更新-tab-补全" class="md-nav__link">
     <span class="md-ellipsis">
       
         更新 Tab 补全
@@ -1363,7 +1363,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_14" class="md-nav__link">
+  <a href="#代码风格与最佳实践" class="md-nav__link">
     <span class="md-ellipsis">
       
         代码风格与最佳实践
@@ -1374,7 +1374,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_15" class="md-nav__link">
+  <a href="#测试你的修改" class="md-nav__link">
     <span class="md-ellipsis">
       
         测试你的修改
@@ -1385,7 +1385,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_16" class="md-nav__link">
+  <a href="#提交信息" class="md-nav__link">
     <span class="md-ellipsis">
       
         提交信息
@@ -1396,7 +1396,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#pull-request" class="md-nav__link">
+  <a href="#推送并创建-pull-request" class="md-nav__link">
     <span class="md-ellipsis">
       
         推送并创建 Pull Request
@@ -1412,7 +1412,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_17" class="md-nav__link">
+  <a href="#_6" class="md-nav__link">
     <span class="md-ellipsis">
       
         有问题或需要帮助？
@@ -1474,7 +1474,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_2" class="md-nav__link">
+  <a href="#开发规范与准则" class="md-nav__link">
     <span class="md-ellipsis">
       
         开发规范与准则
@@ -1486,7 +1486,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#_3" class="md-nav__link">
+  <a href="#_2" class="md-nav__link">
     <span class="md-ellipsis">
       
         语言要求
@@ -1497,7 +1497,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_4" class="md-nav__link">
+  <a href="#_3" class="md-nav__link">
     <span class="md-ellipsis">
       
         模块化与可复用性
@@ -1508,7 +1508,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_5" class="md-nav__link">
+  <a href="#_4" class="md-nav__link">
     <span class="md-ellipsis">
       
         代码风格
@@ -1519,7 +1519,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_6" class="md-nav__link">
+  <a href="#_5" class="md-nav__link">
     <span class="md-ellipsis">
       
         文档
@@ -1535,7 +1535,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_7" class="md-nav__link">
+  <a href="#报告问题" class="md-nav__link">
     <span class="md-ellipsis">
       
         报告问题
@@ -1546,7 +1546,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_8" class="md-nav__link">
+  <a href="#功能建议" class="md-nav__link">
     <span class="md-ellipsis">
       
         功能建议
@@ -1557,7 +1557,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_9" class="md-nav__link">
+  <a href="#贡献代码" class="md-nav__link">
     <span class="md-ellipsis">
       
         贡献代码
@@ -1569,7 +1569,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#fork" class="md-nav__link">
+  <a href="#fork-并克隆仓库" class="md-nav__link">
     <span class="md-ellipsis">
       
         Fork 并克隆仓库
@@ -1580,7 +1580,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_10" class="md-nav__link">
+  <a href="#创建功能分支" class="md-nav__link">
     <span class="md-ellipsis">
       
         创建功能分支
@@ -1591,7 +1591,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_11" class="md-nav__link">
+  <a href="#进行修改" class="md-nav__link">
     <span class="md-ellipsis">
       
         进行修改
@@ -1603,7 +1603,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
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+  <a href="#交互模式贡献" class="md-nav__link">
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         交互模式贡献
@@ -1614,7 +1614,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_13" class="md-nav__link">
+  <a href="#命令行模式贡献" class="md-nav__link">
     <span class="md-ellipsis">
       
         命令行模式贡献
@@ -1625,7 +1625,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#tab" class="md-nav__link">
+  <a href="#更新-tab-补全" class="md-nav__link">
     <span class="md-ellipsis">
       
         更新 Tab 补全
@@ -1641,7 +1641,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_14" class="md-nav__link">
+  <a href="#代码风格与最佳实践" class="md-nav__link">
     <span class="md-ellipsis">
       
         代码风格与最佳实践
@@ -1652,7 +1652,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_15" class="md-nav__link">
+  <a href="#测试你的修改" class="md-nav__link">
     <span class="md-ellipsis">
       
         测试你的修改
@@ -1663,7 +1663,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#_16" class="md-nav__link">
+  <a href="#提交信息" class="md-nav__link">
     <span class="md-ellipsis">
       
         提交信息
@@ -1674,7 +1674,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#pull-request" class="md-nav__link">
+  <a href="#推送并创建-pull-request" class="md-nav__link">
     <span class="md-ellipsis">
       
         推送并创建 Pull Request
@@ -1690,7 +1690,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#_17" class="md-nav__link">
+  <a href="#_6" class="md-nav__link">
     <span class="md-ellipsis">
       
         有问题或需要帮助？
@@ -1756,14 +1756,14 @@ <h2 id="_1">目录</h2>
 <li><a href="#推送并创建-pull-request">推送并创建 Pull Request</a></li>
 </ul>
 <hr />
-<h2 id="_2">开发规范与准则</h2>
+<h2 id="开发规范与准则">开发规范与准则</h2>
 <p>为保持代码质量和项目一致性，请遵循以下准则：</p>
-<h3 id="_3">语言要求</h3>
+<h3 id="_2">语言要求</h3>
 <ul>
 <li><strong>所有代码应使用英文编写</strong>：包括变量名、函数名、注释、文档字符串、提交信息和文档。</li>
 <li>虽然我们理解贡献者来自不同背景，但使用英文能确保代码库对最广泛的用户群体可访问。</li>
 </ul>
-<h3 id="_4">模块化与可复用性</h3>
+<h3 id="_3">模块化与可复用性</h3>
 <ul>
 <li><strong>编写模块化和可复用的代码</strong>：函数和脚本的设计应具有灵活性。</li>
 <li><strong>优先传递参数而非硬编码值</strong>：使用函数参数、命令行参数或配置文件来替代硬编码值。但某些文件名由 GPUMD 和 NEP 程序固定要求（如 <code>train.xyz</code>、<code>thermo.out</code>），这些可以按需硬编码。</li>
@@ -1782,20 +1782,20 @@ <h3 id="_4">模块化与可复用性</h3>
 <a id="__codelineno-0-12" name="__codelineno-0-12" href="#__codelineno-0-12"></a><span class="o">}</span>
 </code></pre></div></li>
 </ul>
-<h3 id="_5">代码风格</h3>
+<h3 id="_4">代码风格</h3>
 <ul>
 <li>编写清晰、易于他人维护和修改的代码。</li>
 <li>使用有意义的变量和函数名。</li>
 <li>在必要处添加注释以解释复杂逻辑。</li>
 </ul>
-<h3 id="_6">文档</h3>
+<h3 id="_5">文档</h3>
 <ul>
 <li>确保帮助信息（如 <code>-h</code> 标志）清晰准确。</li>
 <li>教程文档位于 <code>docs/tutorials/en/</code>（英文）和 <code>docs/tutorials/zh/</code>（中文）。如果你添加了新功能，请考虑更新相关教程页面。</li>
 <li>编辑教程 Markdown 文件后，使用 <code>mkdocs build -f docs/mkdocs.yml</code> 重新构建 HTML。</li>
 </ul>
 <hr />
-<h2 id="_7">报告问题</h2>
+<h2 id="报告问题">报告问题</h2>
 <p>如果你遇到 bug，请通过 GitHub Issues 帮助我们修复：</p>
 <ol>
 <li><strong>搜索现有 issues</strong> 查看该 bug 是否已被报告。</li>
@@ -1807,7 +1807,7 @@ <h2 id="_7">报告问题</h2>
 - <strong>邮箱</strong>：yanzihan@westlake.edu.cn
 - <strong>脚本开发者</strong>：联系脚本头部列出的开发者</p>
 <hr />
-<h2 id="_8">功能建议</h2>
+<h2 id="功能建议">功能建议</h2>
 <p>我们欢迎功能建议！提出新功能：</p>
 <ol>
 <li><strong>搜索现有 issues</strong> 查看是否已有人提出。</li>
@@ -1815,8 +1815,8 @@ <h2 id="_8">功能建议</h2>
 <li><strong>清楚描述你的需求</strong> 并解释其用途。</li>
 </ol>
 <hr />
-<h2 id="_9">贡献代码</h2>
-<h3 id="fork">Fork 并克隆仓库</h3>
+<h2 id="贡献代码">贡献代码</h2>
+<h3 id="fork-并克隆仓库">Fork 并克隆仓库</h3>
 <ol>
 <li>
 <p>在 GitHub 上 <strong>Fork 仓库</strong>，点击 <a href="https://github.com/zhyan0603/GPUMDkit">仓库页面</a> 右上角的 "Fork" 按钮。</p>
@@ -1833,13 +1833,13 @@ <h3 id="fork">Fork 并克隆仓库</h3>
    <div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>git<span class="w"> </span>remote<span class="w"> </span>add<span class="w"> </span>upstream<span class="w"> </span>https://github.com/zhyan0603/GPUMDkit.git
 </code></pre></div></li>
 </ol>
-<h3 id="_10">创建功能分支</h3>
+<h3 id="创建功能分支">创建功能分支</h3>
 <p>为你的修改创建新分支：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># 从 main 创建并切换到新分支</span>
 <a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>git<span class="w"> </span>checkout<span class="w"> </span>-b<span class="w"> </span>your-branch-name
 </code></pre></div>
 <p>分支名称随意。</p>
-<h3 id="_11">进行修改</h3>
+<h3 id="进行修改">进行修改</h3>
 <p><code>GPUMDkit</code> 的结构包括：
 - <strong><code>gpumdkit.sh</code></strong>：主入口（Bash 脚本），处理交互菜单模式和命令行模式
 - <strong><code>install.sh</code></strong>：安装脚本，设置环境变量和 shell 配置
@@ -1865,7 +1865,7 @@ <h3 id="_11">进行修改</h3>
   - <code>mkdocs.yml</code>：构建教程 HTML 的 MkDocs 配置
   - <code>command_reference.tsv</code>：机器可读的命令参考
   - <code>htmls/</code>：MkDocs 生成的 HTML 输出</p>
-<h4 id="_12">交互模式贡献</h4>
+<h4 id="交互模式贡献">交互模式贡献</h4>
 <p>要添加通过交互菜单访问的新功能：</p>
 <ol>
 <li><strong>在相应的 <code>Scripts/</code> 子目录中创建实现脚本</strong>：</li>
@@ -1930,7 +1930,7 @@ <h4 id="_12">交互模式贡献</h4>
 </code></pre></div></p>
 </li>
 </ol>
-<h4 id="_13">命令行模式贡献</h4>
+<h4 id="命令行模式贡献">命令行模式贡献</h4>
 <p>要添加新的命令行标志或子命令：</p>
 <ol>
 <li>
@@ -1992,7 +1992,7 @@ <h4 id="_13">命令行模式贡献</h4>
 </code></pre></div></p>
 </li>
 </ol>
-<h4 id="tab">更新 Tab 补全</h4>
+<h4 id="更新-tab-补全">更新 Tab 补全</h4>
 <p>添加新的命令行标志时，更新 Tab 补全脚本：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="c1"># 编辑 Scripts/utils/completion.sh</span>
 <a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>vim<span class="w"> </span>Scripts/utils/completion.sh
@@ -2015,7 +2015,7 @@ <h4 id="tab">更新 Tab 补全</h4>
 <a id="__codelineno-16-5" name="__codelineno-16-5" href="#__codelineno-16-5"></a><span class="w">    </span><span class="c1"># ... 其余 case ...</span>
 <a id="__codelineno-16-6" name="__codelineno-16-6" href="#__codelineno-16-6"></a><span class="k">esac</span>
 </code></pre></div></p>
-<h3 id="_14">代码风格与最佳实践</h3>
+<h3 id="代码风格与最佳实践">代码风格与最佳实践</h3>
 <ul>
 <li><strong>Shell 脚本</strong>：</li>
 <li>使用 <code>${variable}</code> 进行变量展开</li>
@@ -2047,7 +2047,7 @@ <h3 id="_14">代码风格与最佳实践</h3>
 <li>如果你的脚本使用重型/特殊包（<code>NepTrain</code>、<code>calorine</code>、<code>dpdata</code>），请添加
     <code>print_dependency_notice()</code> 函数以通知用户引用建议</li>
 </ul>
-<h3 id="_15">测试你的修改</h3>
+<h3 id="测试你的修改">测试你的修改</h3>
 <p>提交贡献前，运行相关验证命令：</p>
 <div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a><span class="c1"># Shell 语法检查（始终运行）</span>
 <a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a>bash<span class="w"> </span>-n<span class="w"> </span>gpumdkit.sh
@@ -2094,9 +2094,9 @@ <h3 id="_15">测试你的修改</h3>
 <p><strong>验证无回归</strong>：确保现有功能仍然正常工作。</p>
 </li>
 </ol>
-<h3 id="_16">提交信息</h3>
+<h3 id="提交信息">提交信息</h3>
 <p>编写清晰、描述性的提交信息来解释你做了什么更改。没有严格的格式要求——只要确保你的信息是可理解的。</p>
-<h3 id="pull-request">推送并创建 Pull Request</h3>
+<h3 id="推送并创建-pull-request">推送并创建 Pull Request</h3>
 <ol>
 <li>
 <p><strong>提交你的修改</strong>：
@@ -2143,7 +2143,7 @@ <h3 id="pull-request">推送并创建 Pull Request</h3>
 </li>
 </ol>
 <hr />
-<h2 id="_17">有问题或需要帮助？</h2>
+<h2 id="_6">有问题或需要帮助？</h2>
 <p>如果你对贡献有疑问或需要帮助：</p>
 <ul>
 <li><strong>发起讨论</strong>：使用 <a href="https://github.com/zhyan0603/GPUMDkit/discussions">GitHub Discussions</a> 提出一般性问题</li>
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
index 78f7ac1..7865e33 100644
--- a/docs/mkdocs.yml
+++ b/docs/mkdocs.yml
@@ -40,6 +40,7 @@ use_directory_urls: false
 
 markdown_extensions:
   - admonition
+  - attr_list
   - pymdownx.details
   - pymdownx.highlight:  # Code highlighting
       anchor_linenums: true
diff --git a/docs/tutorials/en/index.md b/docs/tutorials/en/index.md
index 18207b1..d729439 100644
--- a/docs/tutorials/en/index.md
+++ b/docs/tutorials/en/index.md
@@ -91,7 +91,6 @@ Use `gpumdkit.sh -h` to see all available options.
 | [Active Learning Workflow](active_learning_workflow.md) | Batch active-learning workflow notes |
 | [Polar Material Analysis](polar_material_analysis.md) | Ferroelectric and polarization tools |
 | [Contributing to GPUMDkit](contributing_to_gpumdkit.md) | Development notes |
-| [Troubleshooting](troubleshooting.md) | Common issues, diagnostics, and fixes |
 
 ## Links
 
diff --git a/docs/tutorials/en/troubleshooting.md b/docs/tutorials/en/troubleshooting.md
deleted file mode 100644
index fc352d0..0000000
--- a/docs/tutorials/en/troubleshooting.md
+++ /dev/null
@@ -1,128 +0,0 @@
-<div align="center">
-  <h1>🛠️ Troubleshooting</h1>
-  <p style="text-align: justify;">This page collects the most common problems users hit when installing or running GPUMDkit, with a quick diagnostic command and fix for each. If your issue is not listed here, see <a href="#getting-more-help">Getting More Help</a> at the bottom.</p>
-</div>
-
-## Common Issues
-
-### 1. After install, `gpumdkit.sh: command not found` in a new terminal
-
-**Symptom:** Opening a fresh terminal and typing `gpumdkit.sh` gives `command not found`, even though installation appeared to succeed.
-
-**Diagnostic:**
-
-```bash
-echo $GPUMDkit_path
-```
-
-This should print the install directory. If it is empty or wrong, your shell did not load the environment variables.
-
-**Fix:**
-
-```bash
-source ~/.bashrc        # on Linux / bash
-source ~/.zshrc         # on macOS / zsh
-```
-
-If the variable is still empty after sourcing, run the installer again from the GPUMDkit directory:
-
-```bash
-cd /path/to/GPUMDkit
-bash install.sh
-```
-
----
-
-### 2. Plot crashes with `FileNotFoundError: loss.out` (or `thermo.out`, `msd.out`, etc.)
-
-**Symptom:** Running `gpumdkit.sh -plt <type>` fails with a `FileNotFoundError` for an `.out` file.
-
-**Diagnostic:**
-
-```bash
-ls *.out
-```
-
-If nothing is listed, you are not in the directory that holds the GPUMD/NEP output files.
-
-**Fix:**
-
-```bash
-cd /path/to/your/simulation/run
-gpumdkit.sh -plt <type>
-```
-
-Always run `-plt` from the directory containing the output files, or pass the correct path.
-
----
-
-### 3. `No module named 'calorine'` (or `'neptrain'`, `'dpdata'`) when running certain calculators
-
-**Symptom:** A calculator or converter aborts with `ModuleNotFoundError: No module named 'calorine'` (or `neptrain`, `dpdata`).
-
-**Diagnostic:**
-
-```bash
-pip list | grep -iE 'calorine|neptrain|dpdata'
-```
-
-If the package is missing, install it.
-
-**Fix:**
-
-```bash
-pip install calorine neptrain dpdata
-```
-
-Or, if you use conda, run the equivalent `conda install` / `pip install` inside your activated `gpumdkit` environment. Make sure the environment is activated before running GPUMDkit.
-
----
-
-### 4. MSD plot oscillates wildly instead of showing linear diffusion
-
-**Symptom:** The MSD curve is noisy or oscillates instead of growing roughly linearly with time, giving an unreliable diffusion coefficient.
-
-**Diagnostic:**
-
-Check the actual frame interval used in the simulation:
-
-```bash
-head thermo.out
-```
-
-Compare the sampling interval there with the `dt_fs` value you passed to `-calc msd`.
-
-**Fix:**
-
-- Ensure `dt_fs` passed to `gpumdkit.sh -calc msd` equals the real MD timestep multiplied by the sample (output) interval — not just the MD timestep alone.
-- Confirm the trajectory is long enough for the diffusion timescale of your system.
-- Note that solids at low temperature may genuinely not show a linear MSD regime (the atoms are localized); this is physical, not a bug.
-
----
-
-### 5. `-out2xyz` or `-pos2exyz` says "No files found"
-
-**Symptom:** A format-conversion command reports that no input files were found, even though you expected them to be there.
-
-**Diagnostic:**
-
-```bash
-ls *.vasp *.xyz *.OUTCAR
-```
-
-If nothing matches, you are either in the wrong directory or the file extensions do not match what the command expects.
-
-**Fix:**
-
-- `cd` into the directory that actually contains your structure files before running the conversion.
-- Verify the file extensions match the expected ones (e.g., `POSCAR`, `*.vasp`, `OUTCAR`, `*.xyz`).
-
----
-
-## Getting More Help
-
-If none of the above solves your problem:
-
-- **Issue tracker:** Open an issue at <https://github.com/zhyan0603/GPUMDkit/issues> (please include the full command you ran and the error message).
-- **Email:** Zihan YAN — <yanzihan@westlake.edu.cn>
-- **QQ group:** 825696376 — for community discussion and quick help.
diff --git a/docs/tutorials/zh/index.md b/docs/tutorials/zh/index.md
index 5b1069a..7ba7749 100644
--- a/docs/tutorials/zh/index.md
+++ b/docs/tutorials/zh/index.md
@@ -91,7 +91,6 @@ gpumdkit.sh -calc msd trajectory.xyz Li 10
 | [主动学习工作流](主动学习工作流.md) | 批量主动学习流程说明 |
 | [极性材料分析](极性材料分析.md) | 铁电和极化相关工具 |
 | [贡献指南](贡献指南.md) | 开发和贡献说明 |
-| [故障排除](故障排除.md) | 常见问题、诊断和修复方法 |
 
 ## 链接
 
diff --git "a/docs/tutorials/zh/\346\225\205\351\232\234\346\216\222\351\231\244.md" "b/docs/tutorials/zh/\346\225\205\351\232\234\346\216\222\351\231\244.md"
deleted file mode 100644
index 775ebf4..0000000
--- "a/docs/tutorials/zh/\346\225\205\351\232\234\346\216\222\351\231\244.md"
+++ /dev/null
@@ -1,128 +0,0 @@
-<div align="center">
-  <h1>🛠️ 故障排除</h1>
-  <p style="text-align: justify;">本页收集了用户在安装或运行 GPUMDkit 时最常遇到的问题，每个问题都给出了快速诊断命令和修复方法。如果此处未列出你的问题，请参见页面底部的<a href="#获取更多帮助">获取更多帮助</a>。</p>
-</div>
-
-## 常见问题
-
-### 1. 安装后在新终端中提示 `gpumdkit.sh: command not found`
-
-**症状：** 打开新终端输入 `gpumdkit.sh` 时提示 `command not found`，尽管安装过程看似成功。
-
-**诊断：**
-
-```bash
-echo $GPUMDkit_path
-```
-
-应打印出安装目录。如果为空或不正确，说明 shell 未加载环境变量。
-
-**修复：**
-
-```bash
-source ~/.bashrc        # Linux / bash
-source ~/.zshrc         # macOS / zsh
-```
-
-如果 source 后变量仍为空，请在 GPUMDkit 目录下重新运行安装脚本：
-
-```bash
-cd /path/to/GPUMDkit
-bash install.sh
-```
-
----
-
-### 2. 绘图时报错 `FileNotFoundError: loss.out`（或 `thermo.out`、`msd.out` 等）
-
-**症状：** 运行 `gpumdkit.sh -plt <type>` 时因找不到某个 `.out` 文件而报 `FileNotFoundError`。
-
-**诊断：**
-
-```bash
-ls *.out
-```
-
-如果没有输出，说明当前目录不包含 GPUMD/NEP 的输出文件。
-
-**修复：**
-
-```bash
-cd /path/to/your/simulation/run
-gpumdkit.sh -plt <type>
-```
-
-务必在包含输出文件的目录中运行 `-plt`，或传入正确的路径。
-
----
-
-### 3. 运行某些计算器时报 `No module named 'calorine'`（或 `'neptrain'`、`'dpdata'`）
-
-**症状：** 计算器或转换器中止并报 `ModuleNotFoundError: No module named 'calorine'`（或 `neptrain`、`dpdata`）。
-
-**诊断：**
-
-```bash
-pip list | grep -iE 'calorine|neptrain|dpdata'
-```
-
-如果缺少该包，请安装。
-
-**修复：**
-
-```bash
-pip install calorine neptrain dpdata
-```
-
-如果使用 conda，请在已激活的 `gpumdkit` 环境中运行对应的 `conda install` 或 `pip install`。运行 GPUMDkit 前请确保环境已激活。
-
----
-
-### 4. MSD 曲线剧烈震荡而非线性扩散
-
-**症状：** MSD 曲线噪声很大或来回震荡，没有随时间近似线性增长，导致扩散系数不可靠。
-
-**诊断：**
-
-检查模拟中实际使用的帧间隔：
-
-```bash
-head thermo.out
-```
-
-将那里的采样间隔与你传给 `-calc msd` 的 `dt_fs` 进行对比。
-
-**修复：**
-
-- 确保传给 `gpumdkit.sh -calc msd` 的 `dt_fs` 等于真实 MD 时间步长乘以采样（输出）间隔，而不仅仅是 MD 时间步长。
-- 确认轨迹长度足以覆盖你体系的扩散时间尺度。
-- 注意：低温下固体可能确实不会出现线性 MSD 区域（原子被局域化），这是物理现象，不是 bug。
-
----
-
-### 5. `-out2xyz` 或 `-pos2exyz` 提示 "No files found"
-
-**症状：** 格式转换命令报告找不到输入文件，尽管你预期文件就在那里。
-
-**诊断：**
-
-```bash
-ls *.vasp *.xyz *.OUTCAR
-```
-
-如果没有匹配项，说明你所在目录不对，或文件扩展名与命令预期的不一致。
-
-**修复：**
-
-- 运行转换前先 `cd` 到实际包含结构文件的目录。
-- 确认文件扩展名与预期一致（例如 `POSCAR`、`*.vasp`、`OUTCAR`、`*.xyz`）。
-
----
-
-## 获取更多帮助
-
-如果以上方法均未解决问题：
-
-- **Issue 跟踪器：** 在 <https://github.com/zhyan0603/GPUMDkit/issues> 提交 issue（请附上你运行的完整命令和错误信息）。
-- **邮件：** Zihan YAN — <yanzihan@westlake.edu.cn>
-- **QQ 群：** 825696376 — 用于社区交流和快速帮助。
diff --git "a/docs/tutorials/zh/\350\264\241\347\214\256\346\214\207\345\215\227.md" "b/docs/tutorials/zh/\350\264\241\347\214\256\346\214\207\345\215\227.md"
index 043f6ff..ad2a146 100644
--- "a/docs/tutorials/zh/\350\264\241\347\214\256\346\214\207\345\215\227.md"
+++ "b/docs/tutorials/zh/\350\264\241\347\214\256\346\214\207\345\215\227.md"
@@ -34,7 +34,7 @@
 
 ---
 
-## 开发规范与准则
+## 开发规范与准则 {#开发规范与准则}
 
 为保持代码质量和项目一致性，请遵循以下准则：
 
@@ -77,7 +77,7 @@
 
 ---
 
-## 报告问题
+## 报告问题 {#报告问题}
 
 如果你遇到 bug，请通过 GitHub Issues 帮助我们修复：
 
@@ -92,7 +92,7 @@
 
 ---
 
-## 功能建议
+## 功能建议 {#功能建议}
 
 我们欢迎功能建议！提出新功能：
 
@@ -102,9 +102,9 @@
 
 ---
 
-## 贡献代码
+## 贡献代码 {#贡献代码}
 
-### Fork 并克隆仓库
+### Fork 并克隆仓库 {#fork-并克隆仓库}
 
 1. 在 GitHub 上 **Fork 仓库**，点击 [仓库页面](https://github.com/zhyan0603/GPUMDkit) 右上角的 "Fork" 按钮。
 
@@ -120,7 +120,7 @@
    git remote add upstream https://github.com/zhyan0603/GPUMDkit.git
    ```
 
-### 创建功能分支
+### 创建功能分支 {#创建功能分支}
 
 为你的修改创建新分支：
 
@@ -131,7 +131,7 @@ git checkout -b your-branch-name
 
 分支名称随意。
 
-### 进行修改
+### 进行修改 {#进行修改}
 
 `GPUMDkit` 的结构包括：
 - **`gpumdkit.sh`**：主入口（Bash 脚本），处理交互菜单模式和命令行模式
@@ -159,7 +159,7 @@ git checkout -b your-branch-name
   - `command_reference.tsv`：机器可读的命令参考
   - `htmls/`：MkDocs 生成的 HTML 输出
 
-#### 交互模式贡献
+#### 交互模式贡献 {#交互模式贡献}
 
 要添加通过交互菜单访问的新功能：
 
@@ -224,7 +224,7 @@ git checkout -b your-branch-name
    esac
    ```
 
-#### 命令行模式贡献
+#### 命令行模式贡献 {#命令行模式贡献}
 
 要添加新的命令行标志或子命令：
 
@@ -283,7 +283,7 @@ git checkout -b your-branch-name
    }
    ```
 
-#### 更新 Tab 补全
+#### 更新 Tab 补全 {#更新-tab-补全}
 
 添加新的命令行标志时，更新 Tab 补全脚本：
 
@@ -316,7 +316,7 @@ case "$prev" in
 esac
 ```
 
-### 代码风格与最佳实践
+### 代码风格与最佳实践 {#代码风格与最佳实践}
 
 - **Shell 脚本**：
   - 使用 `${variable}` 进行变量展开
@@ -347,7 +347,7 @@ esac
   - 如果你的脚本使用重型/特殊包（`NepTrain`、`calorine`、`dpdata`），请添加
     `print_dependency_notice()` 函数以通知用户引用建议
 
-### 测试你的修改
+### 测试你的修改 {#测试你的修改}
 
 提交贡献前，运行相关验证命令：
 
@@ -393,11 +393,11 @@ git diff --check
 
 5. **验证无回归**：确保现有功能仍然正常工作。
 
-### 提交信息
+### 提交信息 {#提交信息}
 
 编写清晰、描述性的提交信息来解释你做了什么更改。没有严格的格式要求——只要确保你的信息是可理解的。
 
-### 推送并创建 Pull Request
+### 推送并创建 Pull Request {#推送并创建-pull-request}
 
 1. **提交你的修改**：
    ```bash

From 23c6236c2094f107aec3e9a2921a26e875f794f4 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Wed, 1 Jul 2026 19:00:01 +0800
Subject: [PATCH 17/24] update

---
 Scripts/format_conversion/dp2xyz.py   |  96 +++++++++++++++++++
 Scripts/utils/completion.sh           |   4 +-
 gpumdkit.sh                           |   5 +-
 skills/AGENTS.md                      |   3 +
 skills/gpumdkit-contributing/SKILL.md | 130 ++++++++++++++++++++------
 src/f1_format_conversions.sh          |  21 ++++-
 6 files changed, 224 insertions(+), 35 deletions(-)
 create mode 100644 Scripts/format_conversion/dp2xyz.py

diff --git a/Scripts/format_conversion/dp2xyz.py b/Scripts/format_conversion/dp2xyz.py
new file mode 100644
index 0000000..7f434e4
--- /dev/null
+++ b/Scripts/format_conversion/dp2xyz.py
@@ -0,0 +1,96 @@
+"""
+=============================================================================
+GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
+Repository: https://github.com/zhyan0603/GPUMDkit
+Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
+=============================================================================
+Script:     dp2xyz.py
+Category:   Format Conversion Scripts
+Purpose:    Convert DeepMD npy datasets under a directory to extended XYZ
+            format using dpdata. Recursively finds type.raw + set.000
+            directories and converts all frames into a single extxyz file.
+Usage:      gpumdkit.sh -dp2xyz <input_dir/> [output.xyz]
+            python3 dp2xyz.py <input_dir/> [output.xyz]
+Arguments:
+  input_dir/    Directory to scan recursively for DeepMD npy datasets
+  output.xyz    Output extxyz file (default: train.xyz)
+Output:
+  <output.xyz>  (converted structures in extxyz format)
+Author:     Denan LI (lidenan@westlake.edu.cn)
+Last-modified: 2026-07-01
+=============================================================================
+"""
+
+import os
+import sys
+
+args = sys.argv[1:]
+if len(args) < 1 or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -dp2xyz <input_dir/> [output.xyz]")
+    print("    or: python3 dp2xyz.py <input_dir/> [output.xyz]")
+    print("")
+    print(" Arguments:")
+    print("   input_dir/    Directory to scan recursively for DeepMD npy datasets")
+    print("   output.xyz    Output extxyz file (default: train.xyz)")
+    print("")
+    print(" Example: gpumdkit.sh -dp2xyz database train.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+import dpdata
+from ase.io import write
+
+
+def is_deepmd_npy_dataset(path):
+    return (
+        os.path.isfile(os.path.join(path, "type.raw"))
+        and os.path.isfile(os.path.join(path, "type_map.raw"))
+        and os.path.isdir(os.path.join(path, "set.000"))
+    )
+
+
+def find_deepmd_npy_datasets(input_dir):
+    dataset_dirs = []
+    for root, dirs, _ in os.walk(input_dir):
+        dirs.sort()
+        if is_deepmd_npy_dataset(root):
+            dataset_dirs.append(root)
+    return dataset_dirs
+
+
+if __name__ == "__main__":
+    input_dir = args[0]
+    output_file = args[1] if len(args) == 2 else "train.xyz"
+
+    if not os.path.isdir(input_dir):
+        print(f" Error: input directory '{input_dir}' does not exist.")
+        sys.exit(1)
+
+    dataset_dirs = find_deepmd_npy_datasets(input_dir)
+    if not dataset_dirs:
+        print(f" Error: no DeepMD npy datasets found under {input_dir}")
+        sys.exit(1)
+
+    all_frames = []
+    print(f" Found {len(dataset_dirs)} DeepMD npy dataset(s) under {input_dir}")
+
+    for dataset_dir in dataset_dirs:
+        try:
+            system = dpdata.LabeledSystem(dataset_dir, fmt="deepmd/npy")
+        except Exception as e:
+            print(f" Error: failed to load {dataset_dir}: {e}")
+            sys.exit(1)
+
+        frames = system.to_ase_structure()
+        all_frames.extend(frames)
+        print(f" Loaded {len(frames)} frames from {dataset_dir}")
+
+    try:
+        write(output_file, all_frames, format="extxyz", append=False)
+    except Exception as e:
+        print(f" Error: failed to write {output_file}: {e}")
+        sys.exit(1)
+
+    print(f" Converted {len(all_frames)} frames from {len(dataset_dirs)} dataset(s)")
+    print(f" Saved extxyz file to {output_file}")
diff --git a/Scripts/utils/completion.sh b/Scripts/utils/completion.sh
index 5a2a440..63bf70d 100644
--- a/Scripts/utils/completion.sh
+++ b/Scripts/utils/completion.sh
@@ -13,7 +13,7 @@ _gpumdkit_completions() {
     prev="${COMP_WORDS[COMP_CWORD-1]}" # Previous word
 
     # List of primary options (extracted from gpumdkit.sh)
-    local opts="-h -help -update -U -clean -time -plt -calc -cbc -range -out2xyz -out2exyz -cp2k2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -xdat2exyz -pos2lmp -lmp2exyz -traj2exyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -filter_range -get_frame -clean_xyz -analyze_comp -chem_species -replicate -pda -pynep -frame_range -nep_modifier"
+    local opts="-h -help -update -U -clean -time -plt -calc -cbc -range -out2xyz -out2exyz -cp2k2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -xdat2exyz -pos2lmp -lmp2exyz -traj2exyz -dp2xyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -filter_range -get_frame -clean_xyz -analyze_comp -chem_species -replicate -pda -pynep -frame_range -nep_modifier"
 
     # Calculator subcommands
     local calc_subcmds="ionic-cond nep des doas neb minimize msd nlist disp avg-struct oct-tilt pol-abo3"
@@ -35,7 +35,7 @@ _gpumdkit_completions() {
             COMPREPLY=($(compgen -W "thermo thermo2 thermo3 train train_density prediction test train_test parity_density born_charge bec msd msd_all msd_conv msd_sdc sdc rdf rdf_pmf vac restart dimer force_errors des doas charge lr arrhenius_d arrhenius_sigma sigma D sigma_xyz D_xyz net_force emd nemd hnemd pdos plane-grid cohesive viscosity" -- "$cur")) ;;
 
         # Options requiring files or directories, complete with filenames
-        -out2xyz|-out2exyz|-cp2k2xyz|-exyz2pos|-min_dist|-min_dist_pbc|-filter_dist|-filter_dist_pbc|-filter_box|-filter_value|-filter_range|-get_frame|-clean_xyz|-pos2exyz|-cif2exyz|-cif2pos|-pos2lmp|-lmp2exyz|-traj2exyz|-addgroup|-addlabel|-addweight|-analyze_comp|-replicate|-pda|-cbc|-frame_range|-chem_species|-xdat2exyz)
+        -out2xyz|-out2exyz|-cp2k2xyz|-exyz2pos|-min_dist|-min_dist_pbc|-filter_dist|-filter_dist_pbc|-filter_box|-filter_value|-filter_range|-get_frame|-clean_xyz|-pos2exyz|-cif2exyz|-cif2pos|-pos2lmp|-lmp2exyz|-traj2exyz|-dp2xyz|-addgroup|-addlabel|-addweight|-analyze_comp|-replicate|-pda|-cbc|-frame_range|-chem_species|-xdat2exyz)
             COMPREPLY=($(compgen -f -- "$cur")) ;;
 
         # Default case: complete primary options
diff --git a/gpumdkit.sh b/gpumdkit.sh
index 6887329..8090a0b 100755
--- a/gpumdkit.sh
+++ b/gpumdkit.sh
@@ -204,7 +204,7 @@ function help_info_table(){
     echo " | -traj2exyz    ASE traj -> extxyz              | -replicate         Replicate structure                |"
     echo " | -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |"
     echo " | -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |"
-    echo " | -frame_range  Extract frames by range         |                                                       |"
+    echo " | -frame_range  Extract frames by range         | -dp2xyz            DeepMD npy -> extxyz               |"
     echo " +-------------------------------------------------------------------------------------------------------+"
     echo " |                                            ANALYSIS                                                   |"
     echo " +-------------------------------------------------------------------------------------------------------+"
@@ -431,6 +431,9 @@ if [ ! -z "$1" ]; then
         -traj2exyz)
             run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/traj2exyz.py" "${@:2}" ;;
 
+        -dp2xyz)
+            run_python_script "Denan LI (lidenan@westlake.edu.cn)" "${format_conv_path}/dp2xyz.py" "${@:2}" ;;
+
         -addgroup|-addlabel)
             run_python_script "Zihan YAN (yanzihan@westlake.edu.cn)" "${format_conv_path}/add_groups.py" "${@:2}" ;;
 
diff --git a/skills/AGENTS.md b/skills/AGENTS.md
index 82df07b..c80ac31 100644
--- a/skills/AGENTS.md
+++ b/skills/AGENTS.md
@@ -246,6 +246,9 @@ find src Scripts -name '*.sh' -exec bash -n {} +
 # Python syntax
 python3 -m py_compile <modified_file>
 
+# 🧹 CLEANUP — always run after debugging / py_compile
+find . -type d -name "__pycache__" -not -path './.git/*' -exec rm -rf {} +
+
 # Interactive menu paths
 echo "0" | bash gpumdkit.sh                         # Exit
 printf '8\n0\n' | bash gpumdkit.sh                   # About/Help → Exit
diff --git a/skills/gpumdkit-contributing/SKILL.md b/skills/gpumdkit-contributing/SKILL.md
index c81a058..70aead3 100644
--- a/skills/gpumdkit-contributing/SKILL.md
+++ b/skills/gpumdkit-contributing/SKILL.md
@@ -159,52 +159,128 @@ Edit `Scripts/utils/completion.sh`:
 
 ## Python Script Conventions
 
-### File header
+### File header (complete docstring)
+
+Every script over 50 lines must have a module-level docstring with all sections:
 
 ```python
 """
-Script:     new_script.py
-Category:   Calculator Scripts
-Purpose:    Brief description of what this script does.
-Usage:      python new_script.py <param1> <param2>
+=============================================================================
+GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP
+Repository: https://github.com/zhyan0603/GPUMDkit
+Citation: Z. Yan et al., GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP,
+          MGE Advances, 2026, 4, e70074 (https://doi.org/10.1002/mgea.70074)
+=============================================================================
+Script:     script_name.py
+Category:   Category Name
+Purpose:    One-line description of what this script does.
+            Multi-line elaboration if needed.
+Usage:      gpumdkit.sh -flag <param1> <param2> [optional]
+            python3 script_name.py <param1> <param2> [optional]
 Arguments:
   param1    Description of param1
   param2    Description of param2
-Author:     Your Name (your@email.com)
+  optional  Description of optional (default: value)
+Output:
+  <file>     (description of output)
+Author:     Name (email)
+Last-modified: YYYY-MM-DD
+=============================================================================
 """
 ```
 
-### Argument parsing
+### Argument parsing — the standard pattern
 
-Use `sys.argv` for simple scripts (most common pattern):
+Use `sys.argv` positional for simple scripts. Use this EXACT pattern (mirrors `traj2exyz.py`, `dp2xyz.py`, `pos2exyz.py`, etc.):
 
 ```python
 import sys
 
-if len(sys.argv) != 3:
-    print("Usage: python new_script.py <param1> <param2>")
-    print("Example: python new_script.py input.xyz nep.txt")
+args = sys.argv[1:]
+if len(args) < N or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -flag <param1> <param2>")
+    print("    or: python3 script_name.py <param1> <param2>")
+    print("")
+    print(" Arguments:")
+    print("   param1    Description")
+    print("   param2    Description")
+    print("")
+    print(" Example: gpumdkit.sh -flag input.xyz output.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+```
+
+Key points about this pattern:
+- `sys.exit(0 ...)` for `-h`/`--help` (success exit), `sys.exit(1)` for missing args (error exit)
+- Uses `args = sys.argv[1:]` slice pattern, then `args[0]`, `args[1]` instead of `sys.argv[1]`, `sys.argv[2]`
+- The `Usage:` line shows BOTH gpumdkit.sh invocation AND direct python invocation
+- **Critically: put this block BEFORE any heavy/optional imports** (like `import dpdata`, `import calorine`, `import ovito`). Ordinary imports (`os`, `sys`, `numpy`) go first, then the help check, then optional imports. This ensures `-h` works even when optional packages are not installed.
+- After the check, read positional args: `input_file = args[0]`, `output_file = args[1] if len(args) >= 2 else "default"`
+
+Use `argparse` only if the script has many optional flags with complex defaults (e.g., `calc_neighbor_list.py`, `calc_displacement.py`).
+
+### Main guard
+
+`if __name__ == "__main__":` is optional for GPUMDkit scripts (they run standalone). However, **new scripts are encouraged to use it** for clean module-level readability. Existing scripts without it should not be retrofitted (explicitly rejected by maintainer).
+
+### Error handling
+
+Python scripts use `print()` with `sys.exit(1)`, never raw exceptions:
+
+```python
+# ✓ Correct — leading space, f-string for clarity, sys.exit after
+if not os.path.isfile(input_file):
+    print(f" Error: file '{input_file}' does not exist.")
     sys.exit(1)
 
-param1 = sys.argv[1]
-param2 = sys.argv[2]
+# ✓ Correct — f-string with leading space
+print(f" Error: failed to load {dataset_dir}: {e}")
+
+# ✗ Wrong — missing leading space
+print(f"Error: file '{input_file}' does not exist.")
+
+# ✗ Wrong — raise Exception instead of print + exit
+raise FileNotFoundError(input_file)
+```
+
+For try/except blocks that catch expected failures:
+
+```python
+try:
+    result = do_something()
+except Exception as e:
+    print(f" Error: operation failed: {e}")
+    sys.exit(1)
 ```
 
-Use `argparse` only if the script has many optional flags with complex defaults.
+### Input validation
+
+Always validate file/directory existence before reading:
+
+```python
+if not os.path.isdir(input_dir):
+    print(f" Error: input directory '{input_dir}' does not exist.")
+    sys.exit(1)
+
+if not os.path.isfile(input_file):
+    print(f" Error: file '{input_file}' does not exist.")
+    sys.exit(1)
+```
 
-### Main guard (optional)
+### Output file naming
 
-GPUMDkit scripts run directly — a `main()` function with `if __name__ == "__main__":` guard is optional. Most existing scripts execute at module level. Use whichever style you prefer, but do not wrap the entire script in a `main()` function just for the sake of it.
+- Output filenames should include enough context to avoid collisions (e.g., `filtered_Li_Li_1.8_2.0.xyz`, not just `filtered.xyz`)
+- Overwriting existing files without warning is accepted (project convention — this is a CLI toolkit, not interactive software)
 
 ### Dependency notices
 
-If your script requires a heavy/special package (`NepTrain`, `calorine`, `dpdata`), add a notice:
+If your script requires a heavy/special package (`NepTrain`, `calorine`, `dpdata`, `ovito`), add a notice:
 
 ```python
 def print_dependency_notice():
-    print("This function requires the 'calorine' package.")
-    print("If you use this function, please cite:")
-    print("  Bochkov et al., npj Comput Mater 6, 170 (2020)")
+    print(" This function requires the 'calorine' package.")
+    print(" If you use this function, please cite:")
+    print("   Bochkov et al., npj Comput Mater 6, 170 (2020)")
 
 # Call it early in the script
 print_dependency_notice()
@@ -212,17 +288,6 @@ print_dependency_notice()
 
 Do NOT add notices for common packages like `ase`, `numpy`, `pymatgen`.
 
-### Error messages
-
-```python
-# Good (leading space, clear message, sys.exit)
-print(" Error: File 'input.xyz' not found.")
-sys.exit(1)
-
-# Avoid
-raise FileNotFoundError("input.xyz")
-```
-
 ## Shell Script Conventions
 
 ### File header (in `src/`)
@@ -391,6 +456,9 @@ python3 -m py_compile Scripts/path/to/your_script.py
 # Clean up __pycache__ after py_compile
 find . -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null
 
+# Clean up __pycache__ after py_compile
+find . -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null
+
 # MkDocs build (if docs changed)
 mkdocs build -f docs/mkdocs.yml
 
diff --git a/src/f1_format_conversions.sh b/src/f1_format_conversions.sh
index bf07a8b..6ddb1f9 100644
--- a/src/f1_format_conversions.sh
+++ b/src/f1_format_conversions.sh
@@ -368,6 +368,23 @@ echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/traj2exyz.py"
 echo " ---------------------------------------------------"
 }
 
+# Convert DeepMD npy to extxyz
+function dp2extxyz(){
+echo " >-------------------------------------------------<"
+echo " | Calling the script in Scripts/format_conversion |"
+echo " | Script: dp2xyz.py                               |"
+echo " | Developer: GPUMDkit Contributors                |"
+echo " >-------------------------------------------------<"
+echo " Input <input_dir> [output.xyz]"
+echo " Example: ./database train.xyz"
+echo " ------------>>"
+read_menu_array dp2extxyz_args || return 1
+echo " ---------------------------------------------------"
+python3 ${GPUMDkit_path}/Scripts/format_conversion/dp2xyz.py "${dp2extxyz_args[@]}"
+echo " Code path: ${GPUMDkit_path}/Scripts/format_conversion/dp2xyz.py"
+echo " ---------------------------------------------------"
+}
+
 #--------------------- function 1 ----------------------
 function f1_format_conversion(){
     echo " +-------------------------------------------------------------+"
@@ -383,6 +400,7 @@ function f1_format_conversion(){
     echo " | pos2exyz) POSCAR to extxyz     pos2lmp)   POSCAR to LAMMPS  |"
     echo " | cif2pos)  CIF to POSCAR        lmp2exyz)  LAMMPS to extxyz  |"
     echo " | cif2exyz) CIF to extxyz        traj2exyz) ASE traj to extxyz|"
+    echo " | dp2xyz)   DeepMD to extxyz                                  |"
     echo " +-------------------------------------------------------------+"
     echo " | 000) Return to main menu                                    |"
     echo " +-------------------------------------------------------------+"
@@ -390,7 +408,7 @@ function f1_format_conversion(){
 
 valid_menu_choices=(
     "000" "101" "102" "103" "104" "105" "106" "107" "108" "109" "110" \
-    "out2exyz" "pos2exyz" "cif2pos" "cif2exyz" "xdat2exyz" "pos2lmp" "lmp2exyz" "traj2exyz"
+    "out2exyz" "pos2exyz" "cif2pos" "cif2exyz" "xdat2exyz" "pos2lmp" "lmp2exyz" "traj2exyz" "dp2xyz"
 ) 
 read_menu_choice num_choice || return 1
 while ! echo "${valid_menu_choices[@]}" | grep -wq "$num_choice" 
@@ -419,6 +437,7 @@ case $num_choice in
     "pos2lmp") poscar2lammps ;;
     "lmp2exyz") lammps2extxyz ;;
     "traj2exyz") traj2extxyz ;;
+    "dp2xyz") dp2extxyz ;;
     "000") menu; main ;;
 esac
 }

From c785674290d2f7a2327fb858a6f2422091ead1db Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Wed, 1 Jul 2026 20:52:51 +0800
Subject: [PATCH 18/24] update skill

---
 AGENTS.md                                  |  38 +++
 skills/AGENTS.md                           | 277 ---------------------
 skills/gpumdkit-contributing/SKILL.md      |  59 ++++-
 skills/gpumdkit-format-conversion/SKILL.md |  12 +
 4 files changed, 108 insertions(+), 278 deletions(-)
 create mode 100644 AGENTS.md
 delete mode 100644 skills/AGENTS.md

diff --git a/AGENTS.md b/AGENTS.md
new file mode 100644
index 0000000..a04d147
--- /dev/null
+++ b/AGENTS.md
@@ -0,0 +1,38 @@
+# GPUMDkit
+
+GPUMDkit is a Bash + Python command-line toolkit for [GPUMD](https://gpumd.org/) and [NEP](https://gitlab.com/brucefan1983/nep) — molecular dynamics and neuroevolution potential programs. It provides format conversion, structure sampling, workflows, property calculation, plotting, and analysis utilities.
+
+**Entry point**: `gpumdkit.sh` — dual-mode (interactive menu + CLI flags):
+
+```bash
+gpumdkit.sh                                # Interactive mode
+gpumdkit.sh -h                             # Show all CLI flags
+gpumdkit.sh -plt train                     # Plot NEP training
+gpumdkit.sh -calc msd dump.xyz Li 10       # Calculate MSD
+gpumdkit.sh -dp2xyz database train.xyz     # DeepMD npy → extxyz
+```
+
+**Documentation**: https://zhyan0603.github.io/GPUMDkit/
+
+## Agent Skills
+
+When the user asks about GPUMDkit features, use the skills in `.opencode/skills/`:
+
+| Skill | Use When |
+|-------|----------|
+| `gpumdkit-main` | General usage, navigation, entry point |
+| `gpumdkit-format-conversion` | Converting structure files between formats |
+| `gpumdkit-calculators` | Computing material properties |
+| `gpumdkit-analyzers` | Analyzing structures and datasets |
+| `gpumdkit-visualization` | Plotting simulation data |
+| `gpumdkit-workflows` | Batch processing and automation |
+| `gpumdkit-sampling` | Sampling and selecting structures |
+
+## If You Need to Modify Code
+
+**Read [skills/gpumdkit-contributing/SKILL.md](skills/gpumdkit-contributing/SKILL.md) first.** It contains all coding conventions, function templates, shell/Python patterns, and explicit rejections (things NOT to propose). The project follows a strict minimum-invasion principle — do not touch working code unless fixing a confirmed bug.
+
+Key facts:
+- Tutorials are bilingual (`docs/tutorials/en/` + `zh/`). Feature changes must update both languages.
+- After Python edits: `python3 -m py_compile <file>` then clean `__pycache__`.
+- After doc edits: `mkdocs build -f docs/mkdocs.yml`.
diff --git a/skills/AGENTS.md b/skills/AGENTS.md
deleted file mode 100644
index c80ac31..0000000
--- a/skills/AGENTS.md
+++ /dev/null
@@ -1,277 +0,0 @@
-# GPUMDkit — AI Agent Knowledge File
-
-> This document records architecture, conventions, preferences, and known pitfalls of the GPUMDkit project for future AI agents. Last updated: 2026-07-01 (project VERSION="1.5.6 (dev)").
-
-## Project Overview
-
-GPUMDkit is a Bash + Python command-line toolkit for GPUMD and NEP. It provides format conversion, structure sampling, workflows, property calculation, plotting, and analysis utilities. The entry point is `gpumdkit.sh` (dual-mode: interactive menu + CLI).
-
-**Repository**: https://github.com/zhyan0603/GPUMDkit
-**Primary Author**: Zihan YAN (yanzihan@westlake.edu.cn)
-**Citation**: MGE Advances, 2026, 4, e70074
-
-## Architecture
-
-```
-gpumdkit.sh          ← Main entry point: menu rendering + CLI dispatch
-  │
-  ├── src/f1_format_conversions.sh  ← Interactive menu wrappers (f101-f110 + keyword converters)
-  ├── src/f2_sample_structures.sh   ← f201-f205
-  ├── src/f3_workflows.sh           ← f301-f303
-  ├── src/f4_calculators.sh         ← f401-f412
-  ├── src/f5_analyzers.sh           ← f501-f508
-  ├── src/f6_plots.sh               ← f6_plots_one_column / f6_plots_two_column (dynamic layout)
-  │     └── Layout is selected based on terminal width
-  ├── src/f7_utilities.sh           ← f701
-  │
-  └── Scripts/                      ← Implementation scripts
-        ├── format_conversion/      ← Python/Bash converters
-        ├── sample_structures/      ← Sampling utilities
-        ├── calculators/            ← Calculators (MSD, ionic conductivity, NEB, descriptors, ...)
-        ├── analyzer/               ← Analyzers (composition, distance, filter, ...)
-        ├── plt_scripts/            ← Plotting (35 scripts)
-        ├── workflow/               ← Workflows (SCF pretreatment, active learning)
-        └── utils/                  ← Update, clean, completion, NEP modifier
-```
-
-## Key Files
-
-| File | Purpose |
-|------|---------|
-| `gpumdkit.sh` | Main entry: defines `GPUMDkit_path`, `menu()`, `main()`, `help_info_table()`, `calculator_help_table()`, `citation()`, CLI `case`, `read_menu_choice()`, `read_menu_array()`, `run_python_script()` |
-| `src/fN_*.sh` | Interactive menu modules. Each defines `fN_category()` display functions and leaf `fNXX_*` wrapper functions with `valid_menu_choices` validation loops. |
-| `Scripts/utils/completion.sh` | Bash TAB completion |
-| `Scripts/utils/update_gpumdkit.sh` | Update command |
-| `Scripts/utils/clean_extra_files.sh` | Clean command |
-| `install.sh` | Installation (writes `GPUMDkit_path` to bashrc/zshrc) |
-| `docs/tutorials/en/*.md` + `zh/*.md` | Bilingual tutorials (13 pairs + index + troubleshooting) |
-| `skills/*/SKILL.md` | AI agent skill definitions |
-| `~/.gpumdkit.in` | User custom commands |
-
-## Variable Reference
-
-```bash
-GPUMDkit_path          # Set by user; points to GPUMDkit root directory
-VERSION                # "1.5.6 (dev) (2026-06-17)" (only in gpumdkit.sh)
-plt_path               # ${GPUMDkit_path}/Scripts/plt_scripts
-analyzer_path          # ${GPUMDkit_path}/Scripts/analyzer
-calc_path              # ${GPUMDkit_path}/Scripts/calculators
-workflow_path          # ${GPUMDkit_path}/Scripts/workflow
-format_conv_path       # ${GPUMDkit_path}/Scripts/format_conversion
-utils_path             # ${GPUMDkit_path}/Scripts/utils
-sample_path            # ${GPUMDkit_path}/Scripts/sample_structures
-```
-
-## Shell Script Conventions
-
-### Entry Point / Dispatch
-
-**Interactive**: `gpumdkit.sh` (no args) → `menu()` → `main()` reads choice → first character of choice selects module → nested `case` calls `fNXX_*` functions → after function returns, `citation()` runs → script exits (no loop back to menu).
-
-**CLI**: `gpumdkit.sh -flag [args]` → dispatched via `case $1 in`.
-
-### Read Conventions (EOF Safety)
-
-**Always use the EOF-safe helpers defined in `gpumdkit.sh`:**
-
-- `read_menu_choice var || return 1` — reads a single line into a variable
-- `read_menu_array arr || return 1` — reads whitespace-separated tokens into an array
-
-**Never use bare `read -p " "` or `read -r -a`.** On closed stdin (pipe, redirect, /dev/null), bare read silently hangs or returns empty values without detection. The helpers print `" Input closed. Exiting."` and return 1.
-
-### Menu Conventions
-
-- Validation array: always named `valid_menu_choices`
-- Validation loop: `while ! echo "${valid_menu_choices[@]}" | grep -wq "$num_choice"; do ...; done`
-- Return to main menu: `case ... "000") menu; main ;;` (recursive)
-
-### Box Drawing Styles
-
-- **Menu boxes**: `+---+` style, constructed with sequential `echo` lines.
-- **Script banners**: `>----<` style, inner width 49 dashes (53 chars total including `>` and `<`). Content uses ` | ... |` wrapper.
-- **Input prompt marker**: `echo " ------------>>"` before any `read_menu_choice` or `read_menu_array`.
-
-### Error Message Style
-
-**Every user-facing `echo` must start with a space character:**
-
-```bash
-echo " Error: GPUMDkit_path is not set."        # ✓ Correct
-echo " Error: Unable to determine current branch."  # ✓ Correct
-echo "Error: ..."   # ✗ Wrong — missing leading space
-
-# Normal informational messages also use leading space:
-echo " Deleting the files..."   # ✓
-echo " Operation canceled."     # ✓
-```
-
-### ASCII Only Box Drawing
-
-All border characters must be pure ASCII: `|`, `+`, `-`, `/`, `\`, `>`, `<`. **Never use** Unicode box-drawing characters like `│` (U+2502) — they render as mojibake on non-UTF-8 terminals.
-
-### Function Naming
-
-- Interactive entry functions: `f<Module><Number>_<descriptive_name>` (e.g., `f101_out2xyz`, `f302_md_sample_batch_pretreatment_gpumd`)
-- Menu display functions: `f<Module>_<module_name>` (e.g., `f1_format_conversion`, `f4_calculators`)
-- Utility functions: lowercase snake_case (e.g., `clean_extra_files`, `update_gpumdkit`)
-- `run_python_script` (helper in gpumdkit.sh): prints author + path banner, then calls `python "$@"`
-
-### Other Shell Conventions
-
-- Non-empty check: `[ ! -z "$var" ]` (project convention)
-- CLI help flag check: `[ "$2" != "-h" ]`
-- `"${@:2}"` / `"${@:3}"` patterns for argument forwarding
-- `run_python_script "Author" /path/to/script.py "${@:2}"` used in CLI branches
-- Functions are `source`d into the current shell; `type -t` can verify definition
-
-## Python Script Conventions
-
-- **Scripts are designed to run standalone, not to be imported.** Module-level `sys.exit(1)`, `input()`, `plt.show()` etc. are all acceptable.
-- **Arguments**: prefer `sys.argv` positional (88% of scripts), `argparse` only for complex flag-heavy scripts (12%).
-- **`np.loadtxt()` default `comments='#'`** handles GPUMD's newer output files that have `#` header lines automatically. No extra handling needed.
-- **`np.savetxt(header=...)`** auto-prefixes the header string with `# `. Writers and readers are pair-compatible.
-- **File header docstring**: all scripts over 50 lines should have a module-level docstring (Script / Author / Purpose / Usage).
-- **Error exits**: `print(" Error: ..."); sys.exit(1)` — do not raise raw exceptions.
-- `ase.io.read` provides reasonably clear errors when files are missing; this can serve as a minimal defense.
-
-## Documentation Conventions
-
-- **Tutorials**: `docs/tutorials/en/` + `zh/` bilingual. Any feature change should update the corresponding tutorial page in both languages.
-- **SKILL.md**: `skills/<category>/SKILL.md` with YAML frontmatter (the `name` field must match the directory name exactly).
-- **Help tables**: `help_info_table()` and `calculator_help_table()` in `gpumdkit.sh` — CLI flag tables must be kept in sync manually.
-
-## Contributor Rules
-
-### Must Do
-
-1. All CLI help text and tutorial `echo`/`print` messages start with a **space** character.
-2. All box-drawing characters must be **pure ASCII** (no `│` or other Unicode).
-3. All interactive input reads must go through `read_menu_choice` or `read_menu_array` (**never** bare `read`).
-4. Menu validation arrays must be named `valid_menu_choices`.
-5. Script banners must name the **exact** filename (no abbreviations or wrong suffixes).
-6. Changes must not break existing functionality — **minimum-invasion principle**.
-7. After any change, validate with `bash -n` and `python3 -m py_compile`.
-
-### Do NOT Do (explicitly rejected by maintainer)
-
-| Rejected | Rationale |
-|---|---|
-| Force `if __name__ == "__main__":` on Python scripts | Scripts are standalone; main guards are unnecessary churn |
-| Replace `from pylab import *` with explicit imports | Keep as-is |
-| Unify `-plt` "save" argument position | Different scripts have different arg counts; inflexible |
-| Unify DPI (e.g., 150 → 300) across plotting scripts | Keep per-script DPI |
-| Change `exit` → `return` in workflow sourced scripts | Keep as-is |
-| Make interactive mode loop back to menu after one function | Intentionally single-shot |
-| Add `-filter_value` / `-filter_range` / `-get_volume` / `-re_atoms` to help table | Intentionally undocumented |
-| Add color / ANSI escape codes | User rejected; keep monochrome |
-| Add debug examples to every tutorial page | Keep tutorials lean |
-| Change MSD fitting range without maintainer approval | 40%-80% is the settled range; changing it is a scientific decision |
-| Add `des_compare` to CLI | Script exists but not exposed |
-| Add extra troubleshooting FAQ items | Keep the 5-item set |
-
-### macOS / Cross-Platform Notes
-
-- macOS ships **bash 3.2** (no `local -n` nameref). Use `read -a "$varname"` for array reads.
-- macOS **sed is BSD**, not GNU. For cross-platform sed, use `perl -i -pe` instead.
-- **zsh does not support `read -a`** (bash-only). All scripts run under bash.
-- `timeout` command is unavailable on macOS. Rely on EOF-safe `read_menu_choice` / `read_menu_array` to avoid hangs.
-
-## Key Data Flows
-
-### Interactive Mode
-
-```
-User runs: gpumdkit.sh
-         → menu() prints menu
-         → main() reads choice
-         → ${choice:0:1} selects module (1-7)
-         → source src/fN_*.sh
-         → nested case calls fNXX_* function
-         → Function: echo banner → read_menu_choice/read_menu_array for args → python/bash runs script
-         → Return to main → citation() → script exits
-```
-
-### CLI Mode
-
-```
-User runs: gpumdkit.sh -flag args
-         → case $1 in
-         → source / python / bash dispatches to script
-         → ${@:2} or ${@:3} forwards arguments
-         → exit
-```
-
-### Custom Commands (~/.gpumdkit.in)
-
-```
-gpumdkit.sh -mycommand args
-         → alias_key="${1#-}"        → "mycommand"
-         → func_name="custom_${alias_key}" → "custom_mycommand"
-         → source ~/.gpumdkit.in
-         → custom_mycommand "$@"
-```
-
-## GPUMD/NEP Output File Behavior
-
-- **`#` comment lines**: GPUMD now prints `#`-prefixed comment lines at the start of `.out` files (e.g., msd.out). `np.loadtxt()` default `comments='#'` handles these automatically — all 35+ reading scripts are SAFE.
-- **`np.savetxt(header=...)`**: auto-prefixes the header with `# `. Writers (like `calc_msd.py`) and readers (like `plt_msd.py`) are pair-compatible.
-- **`.out` column counts vary by compute command**: msd.out may have 4 or 7 columns depending on whether `compute_sdc` was enabled. Scripts with hardcoded column assumptions (`plt_sdc.py`, `plt_msd_sdc.py` assume 7) will crash on 4-column files. See "Known Pitfalls" below.
-
-## Known Pitfalls
-
-1. **`plt_sdc.py` / `plt_msd_sdc.py`**: hardcode 7-column msd.out. Crashes with `IndexError` when only `compute_msd` (4 columns) was used. These are the most common script crashes for GPUMD users.
-2. **`plt_arrhenius_sigma.py` / `_xyz.py`**: hardcode `z = 1` (species charge). Produces **wrong conductivity values** (off by z²) for multivalent ions (Mg²⁺, Ca²⁺, Al³⁺, etc.).
-3. **`plt_emd.py` / `plt_nemd.py` / `plt_hnemd.py` / `plt_pdos.py`**: call `plt.show()` without Agg backend detection. Crash with `TclError` on headless servers/SSH. The other 34 plotting scripts all have proper Agg detection.
-4. **`plt_rdf_pmf.py`**: calls `input()` when run without arguments — hangs in non-interactive mode. `gpumdkit.sh -plt rdf_pmf` (no extra args) triggers this.
-5. **~30 plotting scripts** use `np.loadtxt()` / `open()` without file-existence checks. Users running from the wrong directory get cryptic tracebacks instead of friendly "file not found" messages.
-6. **macOS bash 3.2**: no `local -n` nameref. Use alternative patterns (read -a "$varname", eval, or herestring redirection).
-
-## Design Decisions (recent fixes — do not revert)
-
-- **`calc_ion_conductivity.py` lines 107-108**: MSD fitting range is now 40%-80% (was 10%-40%). The Arrhenius plotting scripts also use 40%-80%. This is a settled scientific choice.
-- **`select_max_modev.py` line 111**: The index mapping `atoms_list[filtered_indices[i]]` was recently fixed from a bug (`atoms_list[i]`). The old version silently selected the wrong structures.
-- **`charge_balance_check.py` lines 118-131**: Now uses a manual loop instead of `dict()` to handle 3-tuple error returns from `check_oxidation_state()`. The `dict()` constructor crashes on 3-tuples.
-- **`clean_extra_files.sh`**: Uses whole-word matching for the keep-exclusion logic, not substring removal. Substring removal (`${var/pattern/}`) corrupts filenames that share substrings with the keep input.
-- **`clean_extra_files.sh`**: `read user_input` changed to EOF-safe read with `|| return 1`. On EOF (closed stdin), the old code would proceed to `rm -f` the entire deletion list.
-- **`src/f6_plots.sh`**: `doas` is now in the "Diffusion & Transport" section of `f6_plots_two_column` (previously was in "MD & Structural Analysis"). Both one-column and two-column layouts are now consistent.
-- **All workflow ATTENTION blocks**: standardized to uniform width (57 dashes inner), with consistent `|` bar edges.
-
-## Verification Checklist
-
-```bash
-# Shell syntax
-bash -n gpumdkit.sh
-find src Scripts -name '*.sh' -exec bash -n {} +
-
-# Python syntax
-python3 -m py_compile <modified_file>
-
-# 🧹 CLEANUP — always run after debugging / py_compile
-find . -type d -name "__pycache__" -not -path './.git/*' -exec rm -rf {} +
-
-# Interactive menu paths
-echo "0" | bash gpumdkit.sh                         # Exit
-printf '8\n0\n' | bash gpumdkit.sh                   # About/Help → Exit
-
-# CLI paths
-bash gpumdkit.sh -h >/dev/null                       # Help table
-bash gpumdkit.sh -plt badtype 2>&1                    # Should print "Unknown plot type"
-bash gpumdkit.sh -plt -h >/dev/null                   # Plot list
-
-# Documentation build
-mkdocs build -f docs/mkdocs.yml
-```
-
-## Quick Reference: Skill Files
-
-| Skill | Directory | Purpose |
-|-------|-----------|---------|
-| Main | `skills/gpumdkit-main/SKILL.md` | Entry point and project overview |
-| Format Conversion | `skills/gpumdkit-format-conversion/SKILL.md` | Structure file conversion |
-| Calculators | `skills/gpumdkit-calculators/SKILL.md` | Material property calculations |
-| Analyzers | `skills/gpumdkit-analyzers/SKILL.md` | Structure analysis and validation |
-| Visualization | `skills/gpumdkit-visualization/SKILL.md` | Plotting and visualization |
-| Workflows | `skills/gpumdkit-workflows/SKILL.md` | Batch processing and automation |
-| Sampling | `skills/gpumdkit-sampling/SKILL.md` | Structure sampling and selection |
-| Contributing | `skills/gpumdkit-contributing/SKILL.md` | Conventions and adding new features |
-| Agents | `skills/AGENTS.md` | This file — AI agent project knowledge |
diff --git a/skills/gpumdkit-contributing/SKILL.md b/skills/gpumdkit-contributing/SKILL.md
index 70aead3..29bf166 100644
--- a/skills/gpumdkit-contributing/SKILL.md
+++ b/skills/gpumdkit-contributing/SKILL.md
@@ -10,6 +10,8 @@ description: >
 allowed-tools: Bash(gpumdkit *) Bash(python3 *) Bash(python *) Bash(ls *) Bash(mkdir *)
 ---
 
+> **Covers**: coding conventions, file structure, shell/Python templates, adding new features, and what NOT to propose.
+
 # GPUMDkit Contributing Guide
 
 ## Project Structure
@@ -137,6 +139,8 @@ Key conventions:
 - No `exit 1` in the else branch (just print usage and fall through)
 - Place alphabetically among existing flags for readability
 
+> When the script needs an interactive menu entry as well, also add a keyword converter wrapper function in `src/f1_format_conversions.sh` following the same banner pattern. Reference the existing `dp2extxyz` function as a template.
+
 ### Step 3: Add to help table
 
 Update `help_info_table()` or `calculator_help_table()` in `gpumdkit.sh`:
@@ -334,6 +338,48 @@ echo " ---------------------------------------------------"
 }
 ```
 
+### File structure for a new Python script
+
+Use `dp2xyz.py` or `traj2exyz.py` as reference. The import order pattern is:
+
+```python
+import os
+import sys
+# heavy/optional imports come AFTER the help check
+
+args = sys.argv[1:]
+if len(args) < N or args[0] in ("-h", "--help"):
+    print(" Usage: gpumdkit.sh -flag <param1> <param2>")
+    print("    or: python3 script_name.py <param1> <param2>")
+    print("")
+    print(" Arguments:")
+    print("   param1    Description")
+    print("   param2    Description")
+    print("")
+    print(" Example: gpumdkit.sh -flag input.xyz output.xyz")
+    print("")
+    sys.exit(0 if args and args[0] in ("-h", "--help") else 1)
+
+import heavy_dependency  # only after help check
+from ase.io import write  # only after help check
+
+def helper_functions():
+    """Docstrings for all helper functions."""
+    ...
+
+if __name__ == "__main__":
+    input_file = args[0]
+    output_file = args[1] if len(args) == 2 else "default.xyz"
+    ...
+```
+
+Key rules:
+- Ordinary imports (`os`, `sys`, `numpy`) go before the help check
+- Heavy/optional imports (`dpdata`, `calorine`, `ovito`, `ase`) go **after** the help check so `-h` works even when optional packages are missing
+- All helper functions have docstrings
+- The `if __name__ == "__main__":` guard is encouraged for new scripts
+- Use `args = sys.argv[1:]` pattern, then access `args[0]`, `args[1]`, etc.
+
 ## Project Conventions & Personal Preferences
 
 These are the maintainer's conventions. Follow them strictly.
@@ -422,7 +468,9 @@ These changes have been **explicitly rejected** by the project maintainer. Do no
 | Add color/ANSI escape codes | User explicitly rejected; keep monochrome |
 | Add debug examples to every tutorial page | Unnecessary; keep tutorials lean |
 | Change MSD fitting range arbitrarily | Scientific choice; ask maintainer first |
-| Add `des_compare` to CLI | Script exists but user chose not to expose it |
+| Remove troubleshooting pages | Removed by maintainer's explicit request; do not re-add |
+| Add `des_compare` to CLI | Script exists but maintainer chose not to wire it |
+| Keep `__pycache__` after debugging | Must always `find . -type d -name __pycache__ -exec rm -rf {} +` |
 
 ### macOS / Cross-Platform Notes
 
@@ -431,6 +479,15 @@ These changes have been **explicitly rejected** by the project maintainer. Do no
 - **zsh does not support `read -a`** (bash-only). All scripts run under bash.
 - `timeout` command is not available on macOS. Use background jobs or rely on EOF-safe read.
 
+### Testing new scripts
+
+For ANY new script, run BOTH of these before committing:
+
+```bash
+python3 Scripts/path/to/script.py -h    # help must work without dependencies
+python3 Scripts/path/to/script.py        # missing args must print usage + exit 1
+```
+
 ### Specific Design Decisions
 
 - **calc_ion_conductivity.py**: MSD fitting range is 40%-80% of data (lines 107-108). The Arrhenius plotting scripts use the same range. Do not change without maintainer approval.
diff --git a/skills/gpumdkit-format-conversion/SKILL.md b/skills/gpumdkit-format-conversion/SKILL.md
index 6e3397e..6b99b30 100644
--- a/skills/gpumdkit-format-conversion/SKILL.md
+++ b/skills/gpumdkit-format-conversion/SKILL.md
@@ -72,6 +72,17 @@ gpumdkit.sh -cif2exyz input.cif model.xyz
 gpumdkit.sh -traj2exyz input.traj output.xyz
 ```
 
+### dp2xyz
+
+Converts DeepMD npy datasets to extxyz format. Recursively scans a directory for datasets containing `type.raw`, `type_map.raw`, and `set.000/`.
+
+**Usage:**
+```
+gpumdkit.sh -dp2xyz database train.xyz
+```
+Dependencies: `dpdata`, `ase`. Requires `conda activate gpumd` environment.
+Author: Denan LI (lidenan@westlake.edu.cn)
+
 ### Structure Manipulation
 
 ```bash
@@ -108,6 +119,7 @@ gpumdkit.sh -clean_xyz input.xyz clean.xyz
 | `-cif2exyz` | CIF -> extxyz | `gpumdkit.sh -cif2exyz <cif> <output>` |
 | `-xdat2exyz` | XDATCAR -> extxyz | `gpumdkit.sh -xdat2exyz XDATCAR dump.xyz` |
 | `-traj2exyz` | ASE traj -> extxyz | `gpumdkit.sh -traj2exyz <traj> <xyz>` |
+| `-dp2xyz` | DeepMD npy → extxyz (via dpdata) | `gpumdkit.sh -dp2xyz <input_dir/> [output.xyz]` |
 | `-addgroup` | Add group labels | `gpumdkit.sh -addgroup <poscar> <elem...>` |
 | `-addweight` | Add weight | `gpumdkit.sh -addweight <in> <out> <weight>` |
 | `-replicate` | Replicate structure | `gpumdkit.sh -replicate <in> <out> a b c` |

From a2e3c13051038fbb5ee0856f4272426efe1b2154 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Wed, 1 Jul 2026 22:42:49 +0800
Subject: [PATCH 19/24] refactor

---
 README.md                                              | 4 ++++
 Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh | 2 +-
 Scripts/workflow/md_sample_batch_pretreatment_lmp.sh   | 2 +-
 Scripts/workflow/scf_batch_pretreatment_vasp.sh        | 2 +-
 docs/README_zh-CN.md                                   | 4 ++++
 gpumdkit.sh                                            | 6 +++---
 skills/gpumdkit-contributing/SKILL.md                  | 2 ++
 7 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 692cc5b..a61e5c8 100644
--- a/README.md
+++ b/README.md
@@ -298,3 +298,7 @@ Also, welcome to join our QQ group ([825696376](https://qun.qq.com/universal-sha
 **GPUMDkit** is an open-source tool freely available for everyone. If you find it helpful in your research or workflow, please ⭐ [star us on GitHub](https://github.com/zhyan0603/GPUMDkit). Additionally, if GPUMDkit contributes to your published work, please cite our paper:
 
 > Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, 4, e70074](https://doi.org/10.1002/mgea.70074).
+
+In your manuscript you may write something like:
+
+> Data processing and figure generation were performed using GPUMDkit [x].
diff --git a/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh b/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
index ae69f11..47df30a 100644
--- a/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
+++ b/Scripts/workflow/md_sample_batch_pretreatment_gpumd.sh
@@ -73,7 +73,7 @@ function f302_md_sample_batch_pretreatment_gpumd(){
 	        # Perform additional operations if needed after moving .vasp files
 	    else
 	        echo " No .vasp files or .xyz files found."
-	        exit 1
+	        return 1
 	    fi
 	fi
 
diff --git a/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh b/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
index 3cc7c8a..c319640 100644
--- a/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
+++ b/Scripts/workflow/md_sample_batch_pretreatment_lmp.sh
@@ -86,7 +86,7 @@ function f303_md_sample_batch_pretreatment_lmp(){
 	        # Perform additional operations if needed after moving .vasp files
 	    else
 	        echo " No .vasp files or .xyz files found."
-	        exit 1
+	        return 1
 	    fi
 	fi
 
diff --git a/Scripts/workflow/scf_batch_pretreatment_vasp.sh b/Scripts/workflow/scf_batch_pretreatment_vasp.sh
index 0c92556..aeb1297 100644
--- a/Scripts/workflow/scf_batch_pretreatment_vasp.sh
+++ b/Scripts/workflow/scf_batch_pretreatment_vasp.sh
@@ -65,7 +65,7 @@ function vasp_scf_batch_pretreatment(){
 	        # Perform additional operations if needed after moving .vasp files
 	    else
 	        echo " No .vasp files or .xyz files found."
-	        exit 1
+	        return 1
 	    fi
 	fi
 
diff --git a/docs/README_zh-CN.md b/docs/README_zh-CN.md
index 7f5c4b2..447d5fe 100644
--- a/docs/README_zh-CN.md
+++ b/docs/README_zh-CN.md
@@ -297,3 +297,7 @@ gpumdkit.sh -plt thermo save
 **GPUMDkit** 是一款面向所有人的开源工具。如果在你的研究或工作中它有所帮助，欢迎 ⭐ [在 GitHub 上给我们点亮 Star](https://github.com/zhyan0603/GPUMDkit)。此外，如果 GPUMDkit 对你的发表工作有贡献，请引用我们的论文：
 
 > Z. Yan\*, D. Li, X. Wu, Z. Liu, C. Hua, B. Situ, H. Yang, S. Tang, B. Tang, Z. Wang, S. Yi, H. Wang, D. Huang, K. Li, Q. Guo, Z. Chen, K. Xu, Y. Wang, Z. Wang, G. Tang, S. Liu, Z. Fan, and Y. Zhu\*. **GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP**. [MGE Advances, 2026, 4, e70074](https://doi.org/10.1002/mgea.70074).
+
+在论文中可以参考类似表述：
+
+> Data processing and figure generation were performed using GPUMDkit [x].
diff --git a/gpumdkit.sh b/gpumdkit.sh
index 8090a0b..bec8378 100755
--- a/gpumdkit.sh
+++ b/gpumdkit.sh
@@ -61,7 +61,7 @@ function read_menu_array(){
 function main(){
     echo " ------------>>"
     echo ' Input the function number:'
-    array_choice=(
+    valid_menu_choices=(
         "0" "1" "101" "102" "103" "104" "105" "106" "107" "108" "109" "110"
         "2" "201" "202" "203" "204" "205" 
         "3" "301" "302" "303" 
@@ -72,7 +72,7 @@ function main(){
         "8"
     ) 
     read_menu_choice choice || return 1
-    while ! echo "${array_choice[@]}" | grep -wq "$choice" 
+    while ! echo "${valid_menu_choices[@]}" | grep -wq "$choice" 
     do
       echo " ------------>>"
       echo " Please reinput function number:"
@@ -177,7 +177,6 @@ function main(){
             ;;
 
     esac
-    citation
 }
 
 #--------------------- help info ----------------------
@@ -531,3 +530,4 @@ echo -e "\
       "
 menu
 main
+citation
diff --git a/skills/gpumdkit-contributing/SKILL.md b/skills/gpumdkit-contributing/SKILL.md
index 29bf166..5a4c950 100644
--- a/skills/gpumdkit-contributing/SKILL.md
+++ b/skills/gpumdkit-contributing/SKILL.md
@@ -471,6 +471,8 @@ These changes have been **explicitly rejected** by the project maintainer. Do no
 | Remove troubleshooting pages | Removed by maintainer's explicit request; do not re-add |
 | Add `des_compare` to CLI | Script exists but maintainer chose not to wire it |
 | Keep `__pycache__` after debugging | Must always `find . -type d -name __pycache__ -exec rm -rf {} +` |
+| Add `-get_volume` / `-re_atoms` to completion.sh | Intentionally excluded from completion and help table |
+| Modify logic in plt_scripts | Unless explicitly requested, only cosmetic/formatting changes to plotting scripts |
 
 ### macOS / Cross-Platform Notes
 

From ffba028a6e304661b90796041ab3d1b2f20354a4 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Thu, 2 Jul 2026 16:59:49 +0800
Subject: [PATCH 20/24] support torchnep

---
 Scripts/plt_scripts/plt_train.py | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/Scripts/plt_scripts/plt_train.py b/Scripts/plt_scripts/plt_train.py
index e3c9869..bed9b94 100644
--- a/Scripts/plt_scripts/plt_train.py
+++ b/Scripts/plt_scripts/plt_train.py
@@ -34,7 +34,7 @@
 # plt.rcParams['axes.prop_cycle'] = cycler(color=custom_colors)
 
 # Load data
-loss = np.loadtxt('loss.out')
+loss = np.loadtxt('loss.out', comments='#')
 energy_data = np.loadtxt('energy_train.out')
 force_data = np.loadtxt('force_train.out')
 stress_data = np.loadtxt('stress_train.out')
@@ -67,16 +67,24 @@ def calculate_limits(train_data, padding=0.08):
 # Create a subplot with 2 rows and 2 columns
 fig, axs = plt.subplots(2, 2, figsize=(9, 7), dpi=100)
 
-if loss[0, 0] == 100:
-    xlabel = 'Generation/100'
-    plot_cols = slice(1, 7) # loss[:, 1:7]
-    legend_labels = ['Total', 'L1-Reg', 'L2-Reg', 'Energy-train', 'Force-train', 'Virial-train']
-elif loss[0, 0] == 1:
+if loss.shape[1] == 6:  # torchnep
     xlabel = 'Epoch'
-    plot_cols = slice(1, 5) # loss[:, 1:5]
-    legend_labels = ['Total', 'Energy-train', 'Force-train', 'Virial-train']
+    plot_cols = slice(1, 5)
+    legend_labels = ['Loss', 'Energy-train', 'Force-train', 'Virial-train']
+elif loss.shape[1] >= 9:  # nep/gnep
+    step = loss[1, 0] - loss[0, 0]  
+    if step == 100: 
+        xlabel = 'Generation/100'
+        plot_cols = slice(1, 7)
+        legend_labels = ['Total', 'L1-Reg', 'L2-Reg', 'Energy-train', 'Force-train', 'Virial-train']
+    elif step == 1: 
+        xlabel = 'Epoch'
+        plot_cols = slice(1, 5)
+        legend_labels = ['Total', 'Energy-train', 'Force-train', 'Virial-train']
+    else:
+        raise ValueError(f"Unsupported step size: {step}")
 else:
-    raise ValueError("Unexpected loss data format.")
+    raise ValueError(f"Unsupported loss format with {loss.shape[1]} columns")
 
 # Plotting the loss figure
 axs[0, 0].loglog(loss[:, plot_cols], '-', linewidth=2)

From 97eb08387e3a57ac4fdc7519161c10052029d19f Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Fri, 3 Jul 2026 14:58:31 +0800
Subject: [PATCH 21/24] update htmls

---
 docs/css/home.css        |   2 +-
 docs/index.html          |  38 ++--
 docs/index_zh.html       | 402 +++++++++++++++++++++++++++++++++++++++
 docs/js/home-terminal.js | 138 ++++++++------
 4 files changed, 514 insertions(+), 66 deletions(-)
 create mode 100644 docs/index_zh.html

diff --git a/docs/css/home.css b/docs/css/home.css
index ec50fda..f6ea275 100644
--- a/docs/css/home.css
+++ b/docs/css/home.css
@@ -171,7 +171,7 @@ body {
     box-shadow: 0 20px 50px rgba(0,0,0,0.1);
     border: 1px solid rgba(0,0,0,0.05);
     overflow: hidden;
-    height: 650px;
+    height: 520px;
     display: flex;
     flex-direction: column;
     position: relative;
diff --git a/docs/index.html b/docs/index.html
index 07e8e14..9bbf217 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,6 +6,24 @@
     <meta name="msvalidate.01" content="C54B40775F728A768032AB60C92F3A42" />
     <meta name="google-site-verification" content="sDBlfmdKvrOL-RYHTskPd2kfi_VtOqHSp9Joa9ZRPj4" />
     <title>GPUMDkit - A User-friendly Toolkit for GPUMD and NEP</title>
+    <meta name="description" content="GPUMDkit is a user-friendly toolkit for GPUMD and NEP, providing format conversion, structure sampling, workflow automation, calculators, analyzers, and visualization tools for molecular dynamics and neuroevolution potential simulations.">
+    <meta property="og:title" content="GPUMDkit - A User-friendly Toolkit for GPUMD and NEP">
+    <meta property="og:description" content="GPUMDkit is a user-friendly toolkit for GPUMD and NEP, providing format conversion, structure sampling, workflow automation, calculators, analyzers, and visualization tools.">
+    <meta property="og:image" content="https://zhyan0603.github.io/GPUMDkit/Gallery/gpumdkit_logo_lateral.png">
+    <meta property="og:url" content="https://zhyan0603.github.io/GPUMDkit/">
+    <meta property="og:type" content="website">
+    <meta name="twitter:card" content="summary_large_image">
+    <link rel="canonical" href="https://zhyan0603.github.io/GPUMDkit/">
+    <script>
+        (function() {
+            var lang = (navigator.language || navigator.userLanguage || '').toLowerCase();
+            var saved = localStorage.getItem('gpumdkit-lang');
+            if (saved === 'en') return;
+            if (saved === 'zh' || lang.startsWith('zh')) {
+                window.location.href = 'index_zh.html';
+            }
+        })();
+    </script>
     <link rel="stylesheet" href="css/home.css">
     <link rel="stylesheet" href="css/mobile.css">
     <link rel="preconnect" href="https://fonts.googleapis.com">
@@ -33,6 +51,7 @@
             <a href="publications.html" class="nav-item">Publications</a>            
             <!-- <a href="https://github.com/zhyan0603/GPUMDkit" class="nav-item">Join Us</a> -->
             <a href="https://github.com/zhyan0603/GPUMDkit/archive/refs/heads/main.zip" class="nav-item">Download</a>
+            <a href="index_zh.html" class="nav-item lang-switch" onclick="localStorage.setItem('gpumdkit-lang','zh')">中文</a>
         </nav>
     </header>
 
@@ -41,7 +60,7 @@
         <section class="hero-section animate-on-scroll">
             <h1 class="hero-title"><span class="gpumd">GPUMD</span><span class="kit">kit</span></h1>
             <h2 class="hero-subtitle">A Toolkit for GPUMD and NEP</h2>
-            <p class="hero-desc">
+            <p class="hero-desc" style="text-align: justify;">
                 GPUMDkit is a user-friendly toolkit for the GPUMD (Graphics Processing Units Molecular Dynamics) and NEP (Neuroevolution Potential) program. It provides a set of tools to streamline the use of common scripts in GPUMD and NEP, simplifying workflows and enhancing efficiency.
             </p>
             <div class="cta-group">
@@ -92,10 +111,7 @@ <h2 class="section-header">Quick Start</h2>
                         <span class="code-line"><span class="cmd">cd</span> <span class="arg">GPUMDkit</span></span>
                         <span class="code-line"><span class="cmd">source</span> <span class="arg"> ./install.sh</span></span>
                         <br>
-                        <span class="code-line"><span class="comment"># 3. Reload shell configuration</span></span>
-                        <span class="code-line"><span class="cmd">source</span> <span class="path">~/.bashrc</span></span>
-                        <br>
-                        <span class="code-line"><span class="comment"># 4. Ready to go!</span></span>
+                        <span class="code-line"><span class="comment"># 3. Ready to go!</span></span>
                         <span class="code-line"><span class="cmd">gpumdkit.sh</span></span>
                     </div>
                 </div>
@@ -143,37 +159,37 @@ <h2 class="section-header">Preview</h2>
         <section id="documentation" class="animate-on-scroll">
             <h2 class="section-header">Documentation</h2>
             <div class="doc-grid">
-                <a href="htmls/format_conversion.html" class="doc-card">
+                <a href="htmls/en/format_conversion.html" class="doc-card">
                     <div class="doc-icon">🔄</div>
                     <h3>Format Conversion</h3>
                     <p>Convert seamlessly between POSCAR, XYZ, CIF, and other formats.</p>
                     <div class="doc-arrow">Read more</div>
                 </a>
-                <a href="htmls/sample_structures.html" class="doc-card">
+                <a href="htmls/en/structure_sampling.html" class="doc-card">
                     <div class="doc-icon">🧪</div>
                     <h3>Sample Structures</h3>
                     <p>Generate and sample structures for NEP training.</p>
                     <div class="doc-arrow">Read more</div>
                 </a>
-                <a href="htmls/workflow.html" class="doc-card">
+                <a href="htmls/en/workflow_scripts.html" class="doc-card">
                     <div class="doc-icon">🚀</div>
                     <h3>Workflow</h3>
                     <p>Guides on setting up efficient active learning loops.</p>
                     <div class="doc-arrow">Read more</div>
                 </a>
-                <a href="htmls/calculators.html" class="doc-card">
+                <a href="htmls/en/calculator_scripts.html" class="doc-card">
                     <div class="doc-icon">🧮</div>
                     <h3>Calculators</h3>
                     <p>Compute various properties and metrics directly.</p>
                     <div class="doc-arrow">Read more</div>
                 </a>
-                <a href="htmls/analyzer.html" class="doc-card">
+                <a href="htmls/en/analyzer_scripts.html" class="doc-card">
                     <div class="doc-icon">📊</div>
                     <h3>Analyzer</h3>
                     <p>Trajectory analysis and property extraction.</p>
                     <div class="doc-arrow">Read more</div>
                 </a>
-                <a href="htmls/plot_scripts.html" class="doc-card">
+                <a href="htmls/en/plot_scripts.html" class="doc-card">
                     <div class="doc-icon">📈</div>
                     <h3>Visualization</h3>
                     <p>Plotting tools for MSD, RDF, PDOS, and other data.</p>
diff --git a/docs/index_zh.html b/docs/index_zh.html
new file mode 100644
index 0000000..d481a24
--- /dev/null
+++ b/docs/index_zh.html
@@ -0,0 +1,402 @@
+<!DOCTYPE html>
+<html lang="zh-CN">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta name="msvalidate.01" content="C54B40775F728A768032AB60C92F3A42" />
+    <meta name="google-site-verification" content="sDBlfmdKvrOL-RYHTskPd2kfi_VtOqHSp9Joa9ZRPj4" />
+    <title>GPUMDkit - GPUMD 与 NEP 用户友好工具包</title>
+    <meta name="description" content="GPUMDkit 是一款面向 GPUMD 和 NEP 的用户友好工具包，提供格式转换、结构采样、工作流自动化、计算器、分析与可视化等功能，支持交互模式和命令行模式。">
+    <meta property="og:title" content="GPUMDkit - GPUMD 与 NEP 用户友好工具包">
+    <meta property="og:description" content="GPUMDkit 是一款面向 GPUMD 和 NEP 的用户友好工具包，提供格式转换、结构采样、工作流自动化、计算器、分析与可视化等功能。">
+    <meta property="og:image" content="https://zhyan0603.github.io/GPUMDkit/Gallery/gpumdkit_logo_lateral.png">
+    <meta property="og:url" content="https://zhyan0603.github.io/GPUMDkit/index_zh.html">
+    <meta property="og:type" content="website">
+    <meta name="twitter:card" content="summary_large_image">
+    <link rel="canonical" href="https://zhyan0603.github.io/GPUMDkit/index_zh.html">
+    <script>
+        (function() {
+            var lang = (navigator.language || navigator.userLanguage || '').toLowerCase();
+            var saved = localStorage.getItem('gpumdkit-lang');
+            if (saved === 'zh') return;
+            if (saved === 'en' || !lang.startsWith('zh')) {
+                window.location.href = 'index.html';
+            }
+        })();
+    </script>
+    <link rel="stylesheet" href="css/home.css">
+    <link rel="stylesheet" href="css/mobile.css">
+    <link rel="preconnect" href="https://fonts.googleapis.com">
+    <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
+    <link href="https://fonts.googleapis.com/css2?family=Fira+Code:wght@400;500&family=Inter:wght@400;500;600;700;800&display=swap" rel="stylesheet">
+</head>
+<body>
+
+    <div class="background-decorations">
+        <div class="blob blob-1"></div>
+        <div class="blob blob-2"></div>
+        <div class="blob blob-3"></div>
+    </div>
+
+    <!-- Main Header -->
+    <header class="main-header animate-on-scroll">
+        <div class="logo-container">
+            <img src="Gallery/gpumdkit_logo_lateral.png" alt="GPUMDkit Logo" class="logo">
+        </div>
+        <button class="mobile-menu-btn" style="display: none;">☰</button>
+        <nav class="nav-links">
+            <a href="index_zh.html" class="nav-item">首页</a>
+            <a href="htmls/zh/index.html" class="nav-item">文档</a>
+            <a href="gallery.html" class="nav-item">图库</a>
+            <a href="publications.html" class="nav-item">出版物</a>
+            <a href="https://github.com/zhyan0603/GPUMDkit/archive/refs/heads/main.zip" class="nav-item">下载</a>
+            <a href="index.html" class="nav-item lang-switch" onclick="localStorage.setItem('gpumdkit-lang','en')">English</a>
+        </nav>
+    </header>
+
+    <div class="home-container">
+        <!-- Hero Section -->
+        <section class="hero-section animate-on-scroll">
+            <h1 class="hero-title"><span class="gpumd">GPUMD</span><span class="kit">kit</span></h1>
+            <h2 class="hero-subtitle">GPUMD 与 NEP 工具包</h2>
+            <p class="hero-desc" style="text-align: left;">
+                GPUMDkit 是一款面向 GPUMD（Graphics Processing Units Molecular Dynamics）和 NEP（Neuroevolution Potential）程序的用户友好工具包。它提供用户友好的命令行界面，涵盖脚本调用、格式转换、结构采样、NEP 构建流程以及各类分析与可视化功能，并提供交互模式和命令行模式两种使用方式，极大简化了工作流程，旨在提升用户工作效率。
+            </p>
+            <div class="cta-group">
+                <a href="#quick-start" class="cta-btn cta-primary">快速开始</a>
+            </div>
+        </section>
+
+        <!-- Features Section -->
+        <section id="features" class="animate-on-scroll">
+            <h2 class="section-header">核心功能</h2>
+            <div class="features-grid">
+                <div class="feature-item">
+                    <div class="feature-icon">🔄</div>
+                    <div class="feature-title">格式转换</div>
+                    <p class="feature-desc">在 POSCAR、XYZ、CIF 等多种原子结构格式之间无缝转换。</p>
+                </div>
+                <div class="feature-item">
+                    <div class="feature-icon">📦</div>
+                    <div class="feature-title">结构采样</div>
+                    <p class="feature-desc">为 NEP 训练生成和采样结构。</p>
+                </div>
+                <div class="feature-item">
+                    <div class="feature-icon">📊</div>
+                    <div class="feature-title">数据分析</div>
+                    <p class="feature-desc">内置轨迹分析、性质计算和模拟结果可视化工具。</p>
+                </div>
+            </div>
+        </section>
+
+        <!-- Quick Start Section -->
+        <section id="quick-start" class="animate-on-scroll">
+            <h2 class="section-header">快速开始</h2>
+            <div class="quick-start-container">
+                <div class="qs-header">
+                    <div class="qs-title">安装</div>
+                    <div class="qs-actions">
+                        <a href="https://github.com/zhyan0603/GPUMDkit" target="_blank">在 GitHub 上查看 &rarr;</a>
+                    </div>
+                </div>
+                <div class="qs-body">
+                    <div class="code-block">
+                        <span class="code-line"><span class="comment"># 1. 克隆仓库</span></span>
+                        <span class="code-line"><span class="cmd">git clone</span> <span class="arg">https://github.com/zhyan0603/GPUMDkit.git</span></span>
+                        <br>
+                        <span class="code-line"><span class="comment"># 2. 进入目录并运行安装脚本</span></span>
+                        <span class="code-line"><span class="cmd">cd</span> <span class="arg">GPUMDkit</span></span>
+                        <span class="code-line"><span class="cmd">source</span> <span class="arg"> ./install.sh</span></span>
+                        <br>
+                        <span class="code-line"><span class="comment"># 3. 开始使用！</span></span>
+                        <span class="code-line"><span class="cmd">gpumdkit.sh</span></span>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- Terminal Showcase Section -->
+        <section id="terminal-showcase" class="animate-on-scroll">
+            <h2 class="section-header">预览</h2>
+            <div class="showcase-container">
+                <div class="showcase-tabs">
+                    <div class="showcase-tab active" data-target="panel-main">主菜单</div>
+                    <div class="showcase-tab" data-target="panel-logs">命令行演示</div>
+                    <div class="showcase-tab" data-target="panel-plot">绘图</div>
+                    <div class="showcase-tab" data-target="panel-help">帮助</div>
+                </div>
+                <div class="showcase-window">
+                    <div class="showcase-header">
+                        <div class="showcase-buttons">
+                            <span class="btn btn-close"></span>
+                            <span class="btn btn-minimize"></span>
+                            <span class="btn btn-maximize"></span>
+                        </div>
+                        <div class="showcase-title">终端</div>
+                    </div>
+                    <div class="showcase-body">
+                        <div class="showcase-panel active" id="panel-main">
+                            <div class="terminal-content" id="showcase-content-main"></div>
+                        </div>
+                        <div class="showcase-panel" id="panel-logs">
+                            <div class="terminal-content" id="showcase-content-logs"></div>
+                        </div>
+                        <div class="showcase-panel" id="panel-plot">
+                            <div class="terminal-content" id="showcase-content-plot"></div>
+                        </div>
+                        <div class="showcase-panel" id="panel-help">
+                            <div class="terminal-content" id="showcase-content-help"></div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- Documentation Section -->
+        <section id="documentation" class="animate-on-scroll">
+            <h2 class="section-header">文档</h2>
+            <div class="doc-grid">
+                <a href="htmls/zh/格式转换.html" class="doc-card">
+                    <div class="doc-icon">🔄</div>
+                    <h3>格式转换</h3>
+                    <p>在 POSCAR、XYZ、CIF 等多种格式间无缝转换。</p>
+                    <div class="doc-arrow">了解更多</div>
+                </a>
+                <a href="htmls/zh/结构采样.html" class="doc-card">
+                    <div class="doc-icon">🧪</div>
+                    <h3>结构采样</h3>
+                    <p>为 NEP 训练生成和采样结构。</p>
+                    <div class="doc-arrow">了解更多</div>
+                </a>
+                <a href="htmls/zh/工作流脚本.html" class="doc-card">
+                    <div class="doc-icon">🚀</div>
+                    <h3>工作流</h3>
+                    <p>高效主动学习循环的搭建指南。</p>
+                    <div class="doc-arrow">了解更多</div>
+                </a>
+                <a href="htmls/zh/计算器脚本.html" class="doc-card">
+                    <div class="doc-icon">🧮</div>
+                    <h3>计算器</h3>
+                    <p>直接计算各种性质和指标。</p>
+                    <div class="doc-arrow">了解更多</div>
+                </a>
+                <a href="htmls/zh/分析工具.html" class="doc-card">
+                    <div class="doc-icon">📊</div>
+                    <h3>分析器</h3>
+                    <p>轨迹分析与性质提取。</p>
+                    <div class="doc-arrow">了解更多</div>
+                </a>
+                <a href="htmls/zh/绘图脚本.html" class="doc-card">
+                    <div class="doc-icon">📈</div>
+                    <h3>可视化</h3>
+                    <p>用于 MSD、RDF、PDOS 等数据的绘图工具。</p>
+                    <div class="doc-arrow">了解更多</div>
+                </a>
+            </div>
+        </section>
+
+        <!-- Gallery Section -->
+        <section id="gallery" class="animate-on-scroll">
+            <h2 class="section-header">图库</h2>
+            <div class="gallery-grid">
+                <div class="gallery-card">
+                    <img src="Gallery/train.png" alt="训练图" class="gallery-img">
+                    <div class="gallery-caption">训练图</div>
+                </div>
+                <div class="gallery-card">
+                    <img src="Gallery/thermo.png" alt="热力学分析" class="gallery-img">
+                    <div class="gallery-caption">热力学分析</div>
+                </div>
+                <div class="gallery-card">
+                    <img src="Gallery/prediction.png" alt="Parity 图" class="gallery-img">
+                    <div class="gallery-caption">Parity 图</div>
+                </div>
+                <div class="gallery-card">
+                    <img src="Gallery/emd.png" alt="EMD" class="gallery-img">
+                    <div class="gallery-caption">EMD</div>
+                </div>
+                <div class="gallery-card">
+                    <img src="Gallery/nemd.png" alt="NEMD" class="gallery-img">
+                    <div class="gallery-caption">NEMD</div>
+                </div>
+                <div class="gallery-card">
+                    <img src="Gallery/hnemd.png" alt="HNEMD" class="gallery-img">
+                    <div class="gallery-caption">HNEMD</div>
+                </div>
+            </div>
+            <div class="view-all-container">
+                <a href="gallery.html" class="view-all-btn">查看全部图库</a>
+            </div>
+        </section>
+
+        <!-- Publications Section -->
+        <section id="publications" class="animate-on-scroll">
+            <h2 class="section-header">使用 GPUMDkit 的出版物</h2>
+            <div id="pub-count-container" style="text-align: center; margin-bottom: 30px; font-weight: 500; color: var(--text-secondary);">
+                总出版物数：<span id="pub-count">...</span>
+            </div>
+            <div class="pub-list" id="recent-publications">
+                <!-- Dynamic Content -->
+            </div>
+            <div class="view-all-container">
+                <a href="publications.html" class="view-all-btn">查看全部出版物</a>
+            </div>
+        </section>
+
+        <!-- Community & Citation Section -->
+        <section id="community" class="animate-on-scroll">
+            <h2 class="section-header">加入我们 &amp; 引用</h2>
+            <div class="community-citation-wrapper">
+                
+                <!-- Community Column 1: Contribute & Star -->
+                <div class="col-actions">
+                    <div class="cc-card action-card">
+                        <div class="cc-bg-decor-1"></div>
+                        <div class="card-content">
+                            <div class="card-header">
+                                <div class="icon-box-modern">
+                                    <svg width="20" height="20" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
+                                        <path d="M15 22v-4a4.8 4.8 0 0 0-1-3.5c3 0 6-2 6-5.5.08-1.25-.27-2.48-1-3.5.28-1.15.28-2.35 0-3.5 0 0-1 0-3 1.5-2.64-.5-5.36-.5-8 0C6 2 5 2 5 2c-.3 1.15-.3 2.35 0 3.5A5.403 5.403 0 0 0 4 9c0 3.5 3 5.5 6 5.5-.39.49-.68 1.05-.85 1.65-.17.6-.22 1.23-.15 1.85v4"/>
+                                        <path d="M9 18c-4.51 2-5-2-7-2"/>
+                                    </svg>
+                                </div>
+                                <h3>贡献</h3>
+                            </div>
+                            <p class="card-desc">通过贡献代码帮助改进 GPUMDkit。</p>
+                            <a href="https://github.com/zhyan0603/GPUMDkit" target="_blank" class="modern-btn outline">
+                                Fork 并提交 PR
+                            </a>
+                        </div>
+                    </div>
+
+                    <div class="cc-card action-card">
+                        <div class="cc-bg-decor-2"></div>
+                        <div class="card-content">
+                            <div class="card-header">
+                                <div class="icon-box-modern">
+                                    <svg width="20" height="20" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
+                                        <polygon points="12 2 15.09 8.26 22 9.27 17 14.14 18.18 21.02 12 17.77 5.82 21.02 7 14.14 2 9.27 8.91 8.26 12 2"/>
+                                    </svg>
+                                </div>
+                                <h3>点亮 Star</h3>
+                            </div>
+                            <p class="card-desc">在 GitHub 上为我们点亮 Star，支持项目发展。</p>
+                            <a href="https://github.com/zhyan0603/GPUMDkit" target="_blank" class="modern-btn outline">
+                                <svg height="16" width="16" viewBox="0 0 16 16" fill="currentColor" style="margin-right: 6px;">
+                                    <path d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0016 8c0-4.42-3.58-8-8-8z"></path>
+                                </svg>
+                                Star
+                            </a>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Community Column 2: QQ Group -->
+                <div class="col-qq">
+                    <div class="cc-card qq-card">
+                        <div class="cc-bg-decor-3"></div>
+                        <div class="card-content-center">
+                            <div class="card-header-center">
+                                <div class="icon-box-modern">
+                                    <svg width="20" height="20" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
+                                        <path d="M21 15a2 2 0 0 1-2 2H7l-4 4V5a2 2 0 0 1 2-2h14a2 2 0 0 1 2 2z"/>
+                                    </svg>
+                                </div>
+                                <h3>加入 QQ 群</h3>
+                            </div>
+                            <div class="qr-container-modern">
+                                <img src="Gallery/gpumdkit_qqgroup.jpg" alt="QQ 群二维码" class="qr-img-modern">
+                                <span class="qr-caption-modern">扫码加入</span>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Community Column 3: Citation -->
+                <div class="col-citation">
+                    <div class="cc-card citation-card-modern">
+                        <div class="cc-bg-decor-4"></div>
+                        <div class="card-content citation-layout">
+                            <div class="citation-header">
+                                <div style="display: flex; align-items: center; gap: 12px;">
+                                    <div class="icon-box-modern">
+                                        <svg width="20" height="20" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
+                                            <path d="M4 19.5A2.5 2.5 0 0 1 6.5 17H20"/>
+                                            <path d="M6.5 2H20v20H6.5A2.5 2.5 0 0 1 4 19.5v-15A2.5 2.5 0 0 1 6.5 2z"/>
+                                        </svg>
+                                    </div>
+                                    <h3>引用</h3>
+                                </div>
+                                <a href="https://doi.org/10.1002/mgea.70074" class="modern-btn outline" target="_blank">
+                                    在 Wiley 上查看
+                                </a>
+                            </div>
+                            <div class="citation-body-modern">
+                                <h4 class="paper-title-modern">GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP</h4>
+                                <div class="paper-meta-modern">
+                                    <span class="meta-text">MGE Advances, 2026, 4, e70074</span>
+                                </div>
+                                <div class="paper-authors-modern">
+                                    Zihan Yan, Denan Li, Xin Wu, Zhoulin Liu, Chen Hua, Boyi Situ, Hao Yang, Shengjie Tang, Benrui Tang, Ziyang Wang, Shangzhao Yi, Huan Wang, Dian Huang, Ke Li, Qilin Guo, Zherui Chen, Ke Xu, Yanzhou Wang, Ziliang Wang, Gang Tang, Shi Liu, Zheyong Fan, Yizhou Zhu
+                                </div>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+            </div>
+        </section>
+
+    </div>
+    <footer class="footer">
+            <div class="footer-content">
+                <div class="footer-column">
+                    <h4>快速链接</h4>
+                    <ul>
+                        <li><a href="htmls/zh/index.html">文档</a></li>
+                        <li><a href="gallery.html">图库</a></li>
+                        <li><a href="publications.html">出版物</a></li>
+                        <li><a href="https://github.com/zhyan0603/GPUMDkit/archive/refs/heads/main.zip">下载</a></li>
+                    </ul>
+                </div>
+                <div class="footer-column">
+                    <h4>GPUMD 项目</h4>
+                    <ul>
+                        <li><a href="https://github.com/brucefan1983/GPUMD" target="_blank">GPUMD 仓库</a></li>
+                        <li><a href="https://gpumd.org/" target="_blank">GPUMD 文档</a></li>
+                        <li><a href="https://github.com/brucefan1983/GPUMD-Tutorials" target="_blank">GPUMD-Tutorials</a></li>
+                        <li><a href="https://github.com/brucefan1983/GPUMD/tree/master/tools" target="_blank">GPUMD-Tools</a></li>
+                    </ul>
+                </div>
+                <div class="footer-column">
+                    <h4>GPUMD 生态</h4>
+                    <ul class="ecosystem-list">
+                        <li><a href="https://gitlab.com/brucefan1983/nep-data" target="_blank">nep-data</a></li>
+                        <li><a href="https://gitlab.com/materials-modeling/calorine" target="_blank">calorine</a></li>
+                        <li><a href="https://github.com/aboys-cb/NepTrainKit" target="_blank">NepTrainKit</a></li>
+                        <li><a href="https://github.com/Jonsnow-willow/GPUMD-Wizard" target="_blank">GPUMD-Wizard</a></li>
+                    </ul>
+                </div>
+            </div>
+            <div class="footer-bottom">
+                <div class="footer-info-row">
+                    <span class="copyright">&copy; 2026 GPUMDkit 团队，保留所有权利。</span>
+                    <span class="beian-info">
+                        <a href="https://beian.miit.gov.cn/" target="_blank">苏ICP备2026013707-1号</a>
+                        <span class="separator">|</span>
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+    <script async src="//busuanzi.ibruce.info/busuanzi/2.3/busuanzi.pure.mini.js"></script>
+    <script src="js/home-terminal.js"></script>
+    <script src="js/publications.js"></script>
+    <script src="js/ui-interactions.js"></script>
+</body>
+</html>
diff --git a/docs/js/home-terminal.js b/docs/js/home-terminal.js
index a2021e0..dc01436 100644
--- a/docs/js/home-terminal.js
+++ b/docs/js/home-terminal.js
@@ -7,17 +7,19 @@ const mainContentText = `
         | |  _| |_) | | | | |\\/| | | | | |/ / | __| 
         | |_| |  __/| |_| | |  | | |_| |   <| | |_ 
          \\____|_|    \\___/|_|  |_|____/|_|\\_\\_|\\__| 
- 
-         GPUMDkit Version 1.5.2 (dev) (2025-03-10) 
+
+         GPUMDkit Version 1.5.6 (dev) (2026-06-17) 
    Core Developer: Zihan YAN (yanzihan@westlake.edu.cn) 
- 
-  ----------------------- GPUMD ----------------------- 
+
+ ----------------------- GPUMD ----------------------- 
   1) Format Conversion          2) Sample Structures 
   3) Workflow                   4) Calculators 
-  5) Analyzer                   6) Developing ... 
-  0) Quit! 
-  ------------>> 
-  Input the function number: `;
+  5) Analyzer                   6) Visualization 
+  7) Utilities                  8) Help 
+  0) Exit 
+
+ ------------>> 
+ Input the function number: `;
 
 const logsCommand1 = `
    Calling script by Yanzhou WANG et al. 
@@ -38,52 +40,80 @@ const logsCommand2 = `
    Code path: Scripts/format_conversion/replicate.py
 `;
 
-const helpContentText = ` +==================================================================================================+ 
- |                              GPUMDkit 1.5.2 (dev) (2025-03-10) Usage                             | 
- +======================================== Conversions =============================================+ 
- | -out2xyz       Convert OUTCAR to extxyz       | -pos2exyz     Convert POSCAR to extxyz           | 
- | -cif2pos       Convert cif to POSCAR          | -pos2lmp      Convert POSCAR to LAMMPS           | 
- | -cif2exyz      Convert cif to extxyz          | -lmp2exyz     Convert LAMMPS-dump to extxyz      | 
- | -addgroup      Add group label                | -addweight    Add weight to the struct in extxyz | 
- | -cp2k2xyz      Convert CP2K file to extxyz    | -traj2exyz    Convert ASE traj to extxyz         | 
- | -xdat2exyz     Convert XDATCAR to extxyz      | Developing...                                    | 
- +========================================= Analysis ===============================================+ 
- | -range         Print range of energy etc.     | -max_rmse     Get max RMSE from extxyz           | 
- | -min_dist      Get min_dist between atoms     | -min_dist_pbc Get min_dist considering PBC       | 
- | -filter_box    Filter struct by box limits    | -filter_value Filter struct by value (efs)       | 
- | -filter_dist   Filter struct by min_dist      | -analyze_comp Analyze composition of extxyz      | 
- | -pynep         Sample struct by pynep         | Developing...                                    | 
- +====================================== Misc Utilities ============================================+ 
- | -plt           Plot scripts                   | -get_frame     Extract the specified frame       | 
- | -calc          Calculators                    | -frame_range   Extract frames by fraction range  | 
- | -clean         Clear files for work_dir       | -clean_xyz     Clean extra info in XYZ file      | 
- | -time          Time consuming Analyzer        | -update        Update GPUMDkit                   | 
- +==================================================================================================+ 
- | For detailed usage and examples, use: gpumdkit.sh -<option> -h                                   | 
- +==================================================================================================+`;
-
-const plotContentText = ` +=====================================================================================================+ 
- |                              GPUMDkit 1.5.2 (dev) (2025-03-10) Plotting Usage                       | 
- +=============================================== Plot Types ==========================================+ 
- | thermo          Plot thermo info                   | train          Plot NEP train results          | 
- | prediction      Plot NEP prediction results        | train_test     Plot NEP train and test results | 
- | msd             Plot mean square displacement      | msd_conv       Plot the convergence of MSD     | 
- | msd_all         Plot MSD of all species            | sdc            Plot self diffusion coefficient | 
- | rdf             Plot radial distribution function  | vac            Plot velocity autocorrelation   | 
- | restart         Plot parameters in nep.restart     | dimer          Plot dimer plot                 | 
- | force_errors    Plot force errors                  | des            Plot descriptors                | 
- | charge          Plot charge distribution           | lr             Plot learning rate              | 
- | doas            Plot density of atomistic states   | net_force      Plot net force distribution     | 
- | sigma           Plot Arrhenius sigma               | D              Plot Arrhenius diffusivity      | 
- | sigma_xyz       Plot directional Arrhenius sigma   | D_xyz          Plot directional Arrhenius D    | 
- | emd             Plot EMD results                   | nemd           Plot NEMD results               | 
- | hnemd           Plot HNEMD results                 | pdos           Plot VAC and PDOS               | 
- | plane-grid      Plot displacement plane grid       | parity_density Plot parity plot density        | 
- +=====================================================================================================+ 
- | For detailed usage and examples, use: gpumdkit.sh -plt <plot_type> -h                               | 
- +=====================================================================================================+ 
-  See the codes in plt_scripts for more details 
-  Code path: /d/Westlake/GPUMD/Gpumdkit/Scripts/plt_scripts`;
+const helpContentText = ` +-------------------------------------------------------------------------------------------------------+
+ |                          GPUMDkit 1.5.6 (dev) (2026-06-17) Command Help                               |
+ +-------------------------------------------------------------------------------------------------------+
+ |                                          MAIN FUNCTIONS                                               |
+ +-------------------------------------------------------------------------------------------------------+
+ | -h            Show this help table            | -plt <type>        Plot and visualization tools       |
+ | -calc <type>  Calculator tools                | -time <gpumd|nep>  Time-consuming analyzer            |
+ | -update       Update GPUMDkit                 | -clean             Clean extra files in current dir   |
+ +-------------------------------------------------------------------------------------------------------+
+ |                                         FORMAT CONVERSION                                             |
+ +-------------------------------------------------------------------------------------------------------+
+ | -out2xyz      OUTCAR -> extxyz (shell)        | -out2exyz          OUTCAR -> extxyz (python)          |
+ | -cp2k2xyz     CP2K log -> xyz                 | -xdat2exyz         XDATCAR -> extxyz                  |
+ | -cif2pos      cif -> POSCAR                   | -cif2exyz          cif -> extxyz                      |
+ | -pos2exyz     POSCAR -> extxyz                | -exyz2pos          extxyz -> POSCAR                   |
+ | -pos2lmp      POSCAR -> LAMMPS data           | -lmp2exyz          LAMMPS dump -> extxyz              |
+ | -traj2exyz    ASE traj -> extxyz              | -replicate         Replicate structure                |
+ | -addgroup     Add group labels                | -addweight         Add structure weight in extxyz     |
+ | -clean_xyz    Clean extra info in extxyz      | -get_frame         Extract specific frame             |
+ | -frame_range  Extract frames by range         | -dp2xyz            DeepMD npy -> extxyz               |
+ +-------------------------------------------------------------------------------------------------------+
+ |                                            ANALYSIS                                                   |
+ +-------------------------------------------------------------------------------------------------------+
+ | -range        Energy/force/virial statistics  | -analyze_comp      Analyze composition                |
+ | -chem_species Analyze chemical species        | -cbc               Charge balance check               |
+ | -min_dist     Min distance (no PBC)           | -min_dist_pbc      Min distance with PBC              |
+ | -filter_dist  Filter by min_dist (no PBC)     | -filter_dist_pbc   Filter by min_dist (PBC)           |
+ | -pda          Probability density analysis    | -filter_box        Filter by box-edge length          |
+ | -pynep        Deprecated PyNEP sampling       | -nep_modifier      Modify NEP model interactively     |
+ +-------------------------------------------------------------------------------------------------------+
+ | Detailed usage: gpumdkit.sh -<option> -h    Plot details: gpumdkit.sh -plt <type> -h                  |
+ +-------------------------------------------------------------------------------------------------------+`;
+
+const plotContentText = ` +-----------------------------------------------------------------------------------------------+
+ |                     GPUMDkit 1.5.6 (dev) (2026-06-17) PLOT & VISUALIZATION TOOLS              |
+ +-----------------------------------------------------------------------------------------------+
+ |  Usage: gpumdkit.sh -plt <type>                        Help: gpumdkit.sh -plt <type> -h       |
+ +-----------------------------------------------------------------------------------------------+
+ |                                    NEP Training & Evaluation                                  |
+ +-----------------------------------------------------------------------------------------------+
+ |  train          - NEP training results           prediction     - NEP prediction results      |
+ |  train_test     - NEP train and test results     parity_density - Parity density plot         |
+ |  train_density  - Training results density plot  restart        - Parameters in nep.restart   |
+ |  charge         - Charge distribution            born_charge    - Born effective charges      |
+ |  dimer          - Dimer energy/force curve       force_errors   - Force errors                |
+ |  des            - Descriptors                    lr             - Learning rate for gnep      |
+ +-----------------------------------------------------------------------------------------------+
+ |                                     Diffusion & Transport                                     |
+ +-----------------------------------------------------------------------------------------------+
+ |  msd            - Mean square displacement       msd_conv       - MSD convergence             |
+ |  msd_all        - MSD for all species            sdc            - Self diffusion coefficient  |
+ |  msd_sdc        - MSD and SDC together           sigma          - Arrhenius ionic conductivity|
+ |  D              - Arrhenius diffusivity          sigma_xyz      - Directional Arrhenius sigma |
+ |  D_xyz          - Directional Arrhenius D                                                     |
+ |  doas           - Density of atomistic states                                                 |
+ +-----------------------------------------------------------------------------------------------+
+ |                                    MD & Structural Analysis                                   |
+ +-----------------------------------------------------------------------------------------------+
+ |  thermo         - thermo info in thermo.out      thermo2/3      - Thermo in different styles  |
+ |  rdf            - Radial distribution function   rdf_pmf        - Potential of mean force     |
+ |  vac            - Velocity autocorrelation       cohesive       - Cohesive energy curve       |
+ |  net_force      - Net force distribution         plane-grid     - Displacement plane grid     |
+ +-----------------------------------------------------------------------------------------------+
+ |                                        Heat Transport                                         |
+ +-----------------------------------------------------------------------------------------------+
+ |  emd            - EMD results                    nemd           - NEMD results                |
+ |  hnemd          - HNEMD results                  viscosity      - Viscosity                   |
+ +-----------------------------------------------------------------------------------------------+
+ |                                          Phonons                                              |
+ +-----------------------------------------------------------------------------------------------+
+ |  pdos           - VAC and PDOS                                                                |
+ +-----------------------------------------------------------------------------------------------+
+   See the codes in plt_scripts for more details 
+   Code path: Scripts/plt_scripts`;
 
 document.addEventListener('DOMContentLoaded', () => {
     // Render Main Content immediately

From ba5917394b236be212f4980240f768cedb14e89c Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Fri, 3 Jul 2026 15:57:34 +0800
Subject: [PATCH 22/24] update

---
 docs/htmls/sitemap.xml    |  54 +++++++++++++++++++-------------------
 docs/htmls/sitemap.xml.gz | Bin 614 -> 614 bytes
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/docs/htmls/sitemap.xml b/docs/htmls/sitemap.xml
index bd1616c..885ea58 100644
--- a/docs/htmls/sitemap.xml
+++ b/docs/htmls/sitemap.xml
@@ -2,110 +2,110 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/index.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/index.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/active_learning_workflow.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/analyzer_scripts.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/calculator_scripts.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/command_reference.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/contributing_to_gpumdkit.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/custom_commands.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/format_conversion.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/plot_scripts.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/polar_material_analysis.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/quick_start.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/structure_sampling.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/en/workflow_scripts.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/index.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E4%B8%BB%E5%8A%A8%E5%AD%A6%E4%B9%A0%E5%B7%A5%E4%BD%9C%E6%B5%81.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%88%86%E6%9E%90%E5%B7%A5%E5%85%B7.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%91%BD%E4%BB%A4%E5%8F%82%E8%80%83.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%B7%A5%E4%BD%9C%E6%B5%81%E8%84%9A%E6%9C%AC.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E5%BF%AB%E9%80%9F%E5%85%A5%E9%97%A8.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E6%9E%81%E6%80%A7%E6%9D%90%E6%96%99%E5%88%86%E6%9E%90.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E6%A0%BC%E5%BC%8F%E8%BD%AC%E6%8D%A2.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E7%BB%93%E6%9E%84%E9%87%87%E6%A0%B7.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%AC.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E8%87%AA%E5%AE%9A%E4%B9%89%E5%91%BD%E4%BB%A4.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E8%AE%A1%E7%AE%97%E5%99%A8%E8%84%9A%E6%9C%AC.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
     <url>
          <loc>https://zhyan0603.github.io/GPUMDkit/zh/%E8%B4%A1%E7%8C%AE%E6%8C%87%E5%8D%97.html</loc>
-         <lastmod>2026-07-01</lastmod>
+         <lastmod>2026-07-03</lastmod>
     </url>
 </urlset>
\ No newline at end of file
diff --git a/docs/htmls/sitemap.xml.gz b/docs/htmls/sitemap.xml.gz
index 1cdbc89fd0109640ce64f23e458a943cdae7c612..7549638680ea2246ea87e55e10f979e1a019cc13 100644
GIT binary patch
delta 31
ncmaFH@{EODzMF%i;kVmF_KQrLS~lKlVdU6XQq<HZz`y_i!@&#G

delta 31
ncmaFH@{EODzMF%iA;M)M`$Z<B_Kmk%7&(50bBFf{FfafBthfq4


From 225581afdaf352e43a430dcc5f2808419726c656 Mon Sep 17 00:00:00 2001
From: Zihan Yan <119929382+zhyan0603@users.noreply.github.com>
Date: Fri, 3 Jul 2026 16:21:34 +0800
Subject: [PATCH 23/24] Create CNAME

---
 docs/CNAME | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 docs/CNAME

diff --git a/docs/CNAME b/docs/CNAME
new file mode 100644
index 0000000..f19c0a6
--- /dev/null
+++ b/docs/CNAME
@@ -0,0 +1 @@
+gpumdkit.cn
\ No newline at end of file

From f603745e91a203da32a679ded501ae468e738cb7 Mon Sep 17 00:00:00 2001
From: ZihanYAN <yanzihan@westlake.edu.cn>
Date: Fri, 3 Jul 2026 18:32:56 +0800
Subject: [PATCH 24/24] update

---
 docs/CNAME         | 1 +
 docs/index_zh.html | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)
 create mode 100644 docs/CNAME

diff --git a/docs/CNAME b/docs/CNAME
new file mode 100644
index 0000000..306eef6
--- /dev/null
+++ b/docs/CNAME
@@ -0,0 +1 @@
+gpumdkit.cn
diff --git a/docs/index_zh.html b/docs/index_zh.html
index d481a24..641f5b0 100644
--- a/docs/index_zh.html
+++ b/docs/index_zh.html
@@ -59,7 +59,7 @@
         <section class="hero-section animate-on-scroll">
             <h1 class="hero-title"><span class="gpumd">GPUMD</span><span class="kit">kit</span></h1>
             <h2 class="hero-subtitle">GPUMD 与 NEP 工具包</h2>
-            <p class="hero-desc" style="text-align: left;">
+            <p class="hero-desc" style="text-align: justify;">
                 GPUMDkit 是一款面向 GPUMD（Graphics Processing Units Molecular Dynamics）和 NEP（Neuroevolution Potential）程序的用户友好工具包。它提供用户友好的命令行界面，涵盖脚本调用、格式转换、结构采样、NEP 构建流程以及各类分析与可视化功能，并提供交互模式和命令行模式两种使用方式，极大简化了工作流程，旨在提升用户工作效率。
             </p>
             <div class="cta-group">